From 362e39df1c0368e2717c2c1b8f4d8cbfd363bbd3 Mon Sep 17 00:00:00 2001 From: Ling Wang Date: Wed, 7 May 2014 20:06:29 -0700 Subject: [PATCH 1/4] fix the right-click menu `move-to-group` and the scrollbar of GroupAddRemoveDialog; Add expandAll and collapseAll buttons. --- .gitignore | 1 + .../java/net/sf/jabref/RightClickMenu.java | 7 +- .../sf/jabref/gui/GroupAddRemoveDialog.java | 70 ++++++++++++++++++- 3 files changed, 74 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 2a86cd5384d..61330a076dd 100644 --- a/.gitignore +++ b/.gitignore @@ -17,3 +17,4 @@ buildant/ .settings/ .classpath .project +jabref.xml \ No newline at end of file diff --git a/src/main/java/net/sf/jabref/RightClickMenu.java b/src/main/java/net/sf/jabref/RightClickMenu.java index 59a29a56f10..27431d8c3fc 100644 --- a/src/main/java/net/sf/jabref/RightClickMenu.java +++ b/src/main/java/net/sf/jabref/RightClickMenu.java @@ -46,7 +46,7 @@ public class RightClickMenu extends JPopupMenu rankingMenu = new JMenu(), priorityMenu = new JMenu(), typeMenu = new JMenu(Globals.lang("Change entry type")); - JMenuItem groupAdd, groupRemove; + JMenuItem groupAdd, groupRemove, groupMoveTo; JCheckBoxMenuItem floatMarked = new JCheckBoxMenuItem(Globals.lang("Float marked entries"), Globals.prefs.getBoolean("floatMarkedEntries")); @@ -323,16 +323,17 @@ public void actionPerformed(ActionEvent e) { }); add(groupRemove); - add(new AbstractAction(Globals.lang("Remove from group")) + groupMoveTo=add(new AbstractAction(Globals.lang("move to group")) { public void actionPerformed(ActionEvent e) { try { - panel.runCommand("removeFromGroup"); + panel.runCommand("moveToGroup"); } catch (Throwable ex) { logger.warning(ex.getMessage()); } } }); + add(groupMoveTo); floatMarked.addActionListener(new ActionListener() { diff --git a/src/main/java/net/sf/jabref/gui/GroupAddRemoveDialog.java b/src/main/java/net/sf/jabref/gui/GroupAddRemoveDialog.java index fd71a9d1818..43a7132685e 100644 --- a/src/main/java/net/sf/jabref/gui/GroupAddRemoveDialog.java +++ b/src/main/java/net/sf/jabref/gui/GroupAddRemoveDialog.java @@ -10,10 +10,14 @@ import javax.swing.*; import javax.swing.event.TreeSelectionEvent; import javax.swing.event.TreeSelectionListener; +import javax.swing.tree.DefaultTreeModel; +import javax.swing.tree.TreeNode; +import javax.swing.tree.TreePath; import javax.swing.tree.TreeSelectionModel; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.util.Enumeration; /** * Created with IntelliJ IDEA. @@ -53,14 +57,43 @@ public void action() throws Throwable { tree = new JTree(groups); tree.setCellRenderer(new AddRemoveGroupTreeCellRenderer()); tree.setVisibleRowCount(22); - tree.setPreferredSize(new Dimension(200, tree.getPreferredSize().height)); + +// tree.setPreferredSize(new Dimension(200, tree.getPreferredSize().height)); +// The scrollbar appears when the preferred size of a component is greater than the size of the viewport. If one hard coded the preferred size, it will never change according to the expansion/collapse. Thus the scrollbar cannot appear accordingly. //tree.setSelectionModel(new VetoableTreeSelectionModel()); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION); tree.addTreeSelectionListener(new SelectionListener()); + + + + //STA add expand and collapse all buttons + JButton jbExpandAll = new JButton("Expand All"); + + jbExpandAll.addActionListener(new ActionListener() { + + + public void actionPerformed(ActionEvent e) { + expandAll(tree, true); + } + + }); + + JButton jbCollapseAll = new JButton("Collapse All"); + jbCollapseAll.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { + expandAll(tree, false); + } + }); + //END add expand and collapse all buttons + ButtonBarBuilder bb = new ButtonBarBuilder(); bb.addGlue(); bb.addButton(ok); bb.addButton(cancel); + + bb.addButton(jbExpandAll); + bb.addButton(jbCollapseAll); + bb.addGlue(); bb.getPanel().setBorder(BorderFactory.createEmptyBorder(5,5,5,5)); @@ -76,6 +109,7 @@ public void actionPerformed(ActionEvent actionEvent) { } }); ok.setEnabled(false); + JScrollPane sp = new JScrollPane(tree); @@ -90,6 +124,11 @@ public void actionPerformed(ActionEvent e) { }); diag.getContentPane().add(sp, BorderLayout.CENTER); + + + + + diag.getContentPane().add(bb.getPanel(), BorderLayout.SOUTH); diag.pack(); diag.setLocationRelativeTo(panel.frame()); @@ -97,6 +136,35 @@ public void actionPerformed(ActionEvent e) { } + // If "expand" is true, all nodes in the tree area expanded + // otherwise all nodes in the tree are collapsed: + public void expandAll(final JTree tree, final boolean expand) { + SwingUtilities.invokeLater(new Runnable() { + public void run() { + TreeNode root = ((TreeNode) tree.getModel().getRoot()); + // walk through the tree, beginning at the root: + expandAll(tree, new TreePath(((DefaultTreeModel) tree.getModel()).getPathToRoot(root)), expand); + tree.requestFocusInWindow(); + } + }); + } + private void expandAll(final JTree tree, final TreePath parent, final boolean expand) { + // walk through the children: + TreeNode node = (TreeNode) parent.getLastPathComponent(); + if (node.getChildCount() >= 0) { + for (Enumeration e = node.children(); e.hasMoreElements();) { + TreeNode n = (TreeNode) e.nextElement(); + TreePath path = parent.pathByAddingChild(n); + expandAll(tree, path, expand); + } + } + // "expand" / "collapse" occurs from bottom to top: + if (expand) { + tree.expandPath(parent); + } else { + tree.collapsePath(parent); + } + } class SelectionListener implements TreeSelectionListener { public void valueChanged(TreeSelectionEvent e) { From 898d9728bca6ba940d1ab09b880a0d501d7beaf0 Mon Sep 17 00:00:00 2001 From: Ling Wang Date: Mon, 19 May 2014 15:16:16 -0700 Subject: [PATCH 2/4] Add feature "allowing user to control the order of fields in saved database". --- src/main/java/net/sf/jabref/BibtexEntry.java | 127 ++++++++++++++++++ src/main/java/net/sf/jabref/FileTab.java | 114 ++++++++++++++++ .../java/net/sf/jabref/JabRefPreferences.java | 11 +- .../resources/resource/JabRef_en.properties | 4 + 4 files changed, 255 insertions(+), 1 deletion(-) diff --git a/src/main/java/net/sf/jabref/BibtexEntry.java b/src/main/java/net/sf/jabref/BibtexEntry.java index dc74a915140..2c064d39791 100644 --- a/src/main/java/net/sf/jabref/BibtexEntry.java +++ b/src/main/java/net/sf/jabref/BibtexEntry.java @@ -158,6 +158,12 @@ public String[] getRequiredFields() { return _type.getRequiredFields(); } + + public String[] getUserDefinedFields() + { + + return Globals.prefs.getStringArray(JabRefPreferences.WRITEFIELD_USERDEFINEDORDER); + } /** * Returns an set containing the names of all fields that are @@ -409,6 +415,127 @@ public void removePropertyChangeListener(VetoableChangeListener listener) * isDisplayableField(String). */ public void write(Writer out, FieldFormatter ff, boolean write) throws IOException { + switch (Globals.prefs.getInt(JabRefPreferences.WRITEFIELD_SORTSTYLE)) { + case 0: + writeSorted(out, ff, write); + break; + case 1: + writeUnsorted(out, ff, write); + case 2: + writeUserOrder(out,ff,write); + } + + + } + + + /** old style ver<=2.9.2, write fields in the order of requiredFields, optionalFields and other fields, but does not sort the fields. + * @param out + * @param ff A formatter to filter field contents before writing + * @param write True if this is a write, false if it is a display. The write will not include non-writeable fields if it is a write, otherwise non-displayable fields will be ignored. Refer to GUIGlobals for isWriteableField(String) and isDisplayableField(String). + * @throws IOException + */ + private void writeUserOrder(Writer out, FieldFormatter ff, boolean write) throws IOException { + // Write header with type and bibtex-key. + out.write("@"+_type.getName()+"{"); + + String str = Util.shaveString(getField(BibtexFields.KEY_FIELD)); + out.write(((str == null) ? "" : str)+","+Globals.NEWLINE); + HashMap written = new HashMap(); + written.put(BibtexFields.KEY_FIELD, null); + boolean hasWritten = false; + + // Write user defined fields first. + String[] s = getUserDefinedFields(); + if (s != null) { + //do not sort, write as it is. + for (String value : s) { + if (!written.containsKey(value)) { // If field appears both in req. and opt. don't repeat. + hasWritten = hasWritten | writeField(value, out, ff, hasWritten, false); + written.put(value, null); + } + } + } + + // Then write remaining fields in alphabetic order. + boolean first = true, previous = true; + previous = false; + //STA get remaining fields + TreeSet remainingFields = new TreeSet(); + for (String key : _fields.keySet()){ + //iterate through all fields + boolean writeIt = (write ? BibtexFields.isWriteableField(key) : + BibtexFields.isDisplayableField(key)); + //find the ones has not been written. + if (!written.containsKey(key) && writeIt) + remainingFields.add(key); + } + //END get remaining fields + + first = previous; + for (String field: remainingFields) { + hasWritten = hasWritten | writeField(field, out, ff, hasWritten, hasWritten && first); + first = false; + } + + // Finally, end the entry. + out.write((hasWritten ? Globals.NEWLINE : "")+"}"+Globals.NEWLINE); + + } + + /** old style ver<=2.9.2, write fields in the order of requiredFields, optionalFields and other fields, but does not sort the fields. + * @param out + * @param ff A formatter to filter field contents before writing + * @param write True if this is a write, false if it is a display. The write will not include non-writeable fields if it is a write, otherwise non-displayable fields will be ignored. Refer to GUIGlobals for isWriteableField(String) and isDisplayableField(String). + * @throws IOException + */ + private void writeUnsorted(Writer out, FieldFormatter ff, boolean write) throws IOException { + // Write header with type and bibtex-key. + out.write("@"+_type.getName().toUpperCase(Locale.US)+"{"); + + String str = Util.shaveString(getField(BibtexFields.KEY_FIELD)); + out.write(((str == null) ? "" : str)+","+Globals.NEWLINE); + HashMap written = new HashMap(); + written.put(BibtexFields.KEY_FIELD, null); + boolean hasWritten = false; + // Write required fields first. + String[] s = getRequiredFields(); + if (s != null) for (int i=0; i remainingFields = new TreeSet(); + for (String key : _fields.keySet()){ + boolean writeIt = (write ? BibtexFields.isWriteableField(key) : + BibtexFields.isDisplayableField(key)); + if (!written.containsKey(key) && writeIt) + remainingFields.add(key); + } + for (String field: remainingFields) + hasWritten = hasWritten | writeField(field, out, ff, hasWritten,false); + + // Finally, end the entry. + out.write((hasWritten ? Globals.NEWLINE : "")+"}"+Globals.NEWLINE); + } + + /** + * new style ver>=2.10, sort the field for requiredFields, optionalFields and other fields separately + * @param out + * @param ff A formatter to filter field contents before writing + * @param write True if this is a write, false if it is a display. The write will not include non-writeable fields if it is a write, otherwise non-displayable fields will be ignored. Refer to GUIGlobals for isWriteableField(String) and isDisplayableField(String). + * @throws IOException + */ + private void writeSorted(Writer out, FieldFormatter ff, boolean write) throws IOException { // Write header with type and bibtex-key. out.write("@"+_type.getName()+"{"); diff --git a/src/main/java/net/sf/jabref/FileTab.java b/src/main/java/net/sf/jabref/FileTab.java index 8391862397f..86bc0b8768c 100644 --- a/src/main/java/net/sf/jabref/FileTab.java +++ b/src/main/java/net/sf/jabref/FileTab.java @@ -16,6 +16,11 @@ package net.sf.jabref; import java.awt.*; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.Iterator; import javax.swing.*; import javax.swing.event.ChangeListener; @@ -44,6 +49,13 @@ public class FileTab extends JPanel implements PrefsTab { doNotResolveStringsFor; private JSpinner autoSaveInterval; private boolean origAutoSaveSetting = false; + + //for LWang_AdjustableFieldOrder +// private JRadioButton sortFieldInAlphabetaOrder,unSortFieldStyle,orderAsUserDefined; + private ButtonGroup bgFieldOrderStyle; +// int fieldOrderStyle; + private JTextField userDefinedFieldOrder; + public FileTab(JabRefFrame frame, JabRefPreferences prefs) { _prefs = prefs; @@ -68,6 +80,18 @@ public FileTab(JabRefFrame frame, JabRefPreferences prefs) { bg.add(resolveStringsAll); bg.add(resolveStringsStandard); + //for LWang_AdjustableFieldOrder +// ButtonGroup bgFieldOrderStyle=new ButtonGroup(); +// sortFieldInAlphabetaOrder = new JRadioButton(Globals.lang("Sort fields in alphabeta order (as ver >= 2.10)")); +// unSortFieldStyle = new JRadioButton(Globals.lang("Do not sort fields (as ver<=2.9.2)")); +// orderAsUserDefined= new JRadioButton(Globals.lang("Save fields as user defined order")); +// bgFieldOrderStyle.add(sortFieldInAlphabetaOrder); +// bgFieldOrderStyle.add(unSortFieldStyle); +// bgFieldOrderStyle.add(orderAsUserDefined); + + userDefinedFieldOrder=new JTextField(_prefs.get(JabRefPreferences.WRITEFIELD_USERDEFINEDORDER)); //need to use JcomboBox in the future + + // This is sort of a quick hack newlineSeparator = new JComboBox(new String[] {"CR", "CR/LF", "LF"}); @@ -149,12 +173,89 @@ public void stateChanged(ChangeEvent changeEvent) { builder.append(includeEmptyFields); builder.append(new JPanel()); builder.nextLine(); + + //for LWang_AdjustableFieldOrder + String [] _rbs0={"Sort fields in alphabeta order (as ver 2.10)", "Sort fields in old fasion (as ver 2.9.2)","Save fields as user defined order"}; + ArrayList _rbs = new ArrayList(); + for (String _rb:_rbs0){ + _rbs.add(Globals.lang(_rb)); + } + bgFieldOrderStyle=createRadioBg(_rbs); + userDefinedFieldOrder=new JTextField(_prefs.get(JabRefPreferences.WRITEFIELD_USERDEFINEDORDER)); //need to use JcomboBox in the future + createAdFieldOrderBg(builder, bgFieldOrderStyle, userDefinedFieldOrder); +// builder.append(sortFieldInAlphabetaOrder); +// builder.nextLine(); +// builder.append(unSortFieldStyle); +// builder.nextLine(); +// builder.append(orderAsUserDefined); +// builder.append(userDefinedFieldOrder); +// builder.nextLine(); + JPanel pan = builder.getPanel(); pan.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5)); setLayout(new BorderLayout()); add(pan, BorderLayout.CENTER); } + + private ButtonGroup createRadioBg(Iterable radioButtonLabels){ + ButtonGroup _bg=new ButtonGroup(); + for (String _s: radioButtonLabels){ + JRadioButton _rb=new JRadioButton(_s); + _bg.add(_rb); + + } + return _bg; + } + + private int getBgValue(ButtonGroup bg){ + int _i=0; + for (Enumeration _it = bg.getElements(); _it.hasMoreElements();){ + if (_it.nextElement().isSelected()){ + return _i; + } + _i++; + + } + return 0; + + } + private void setBgSelected(ButtonGroup bg,int x){ + int _i=0; + + for (Enumeration _it = bg.getElements(); _it.hasMoreElements();){ + if (_i==x){ + _it.nextElement().setSelected(true); + + } else { + _it.nextElement().setSelected(false); + + } + _i++; + + } + + } + + +// private void setValueFieldOrderStyle(){ +// fieldOrderStyle=getBgValue(bgFieldOrderStyle); +// } + + private void createAdFieldOrderBg(DefaultFormBuilder builder, ButtonGroup bg, JTextField jtf){ + //for LWang_AdjustableFieldOrder + + + + for (Enumeration _it = bg.getElements(); _it.hasMoreElements();){ + builder.append(_it.nextElement()); + builder.nextLine(); + } + builder.append(jtf); + builder.nextLine(); + } + + public void setValues() { openLast.setSelected(_prefs.getBoolean("openLastEdited")); @@ -186,6 +287,11 @@ public void setValues() { includeEmptyFields.setSelected(_prefs.getBoolean("includeEmptyFields")); camelCase.setSelected(_prefs.getBoolean(JabRefPreferences.WRITEFIELD_CAMELCASENAME)); sameColumn.setSelected(_prefs.getBoolean(JabRefPreferences.WRITEFIELD_ADDSPACES)); + + //for LWang_AdjustableFieldOrder + setBgSelected(bgFieldOrderStyle, _prefs.getInt(JabRefPreferences.WRITEFIELD_SORTSTYLE)); + userDefinedFieldOrder.setText(_prefs.get(JabRefPreferences.WRITEFIELD_USERDEFINEDORDER)); + } public void storeSettings() { @@ -218,6 +324,12 @@ public void storeSettings() { _prefs.putBoolean(JabRefPreferences.WRITEFIELD_CAMELCASENAME, camelCase.isSelected()); _prefs.putBoolean(JabRefPreferences.WRITEFIELD_ADDSPACES, sameColumn.isSelected()); doNotResolveStringsFor.setText(_prefs.get("doNotResolveStringsFor")); + + //for LWang_AdjustableFieldOrder + _prefs.putInt(JabRefPreferences.WRITEFIELD_SORTSTYLE,getBgValue(bgFieldOrderStyle)); + _prefs.put(JabRefPreferences.WRITEFIELD_USERDEFINEDORDER,userDefinedFieldOrder.getText().trim()); + + boolean updateSpecialFields = false; if (!bracesAroundCapitalsFields.getText().trim().equals(_prefs.get("putBracesAroundCapitals"))) { _prefs.put("putBracesAroundCapitals", bracesAroundCapitalsFields.getText()); @@ -248,4 +360,6 @@ public boolean readyToClose() { public String getTabName() { return Globals.lang("File"); } + + } diff --git a/src/main/java/net/sf/jabref/JabRefPreferences.java b/src/main/java/net/sf/jabref/JabRefPreferences.java index 98edb294556..d5f8d9631a2 100644 --- a/src/main/java/net/sf/jabref/JabRefPreferences.java +++ b/src/main/java/net/sf/jabref/JabRefPreferences.java @@ -92,7 +92,10 @@ public class JabRefPreferences { EXPORT_SECONDARY_SORT_FIELD = "exportSecSort", EXPORT_SECONDARY_SORT_DESCENDING = "exportSecDescending", EXPORT_TERTIARY_SORT_FIELD = "exportTerSort", - EXPORT_TERTIARY_SORT_DESCENDING = "exportTerDescending"; + EXPORT_TERTIARY_SORT_DESCENDING = "exportTerDescending", + WRITEFIELD_SORTSTYLE = "writefieldSortStyle", + WRITEFIELD_USERDEFINEDORDER = "writefieldUserdefinedOrder"; + // This String is used in the encoded list in prefs of external file type // modifications, in order to indicate a removed default file type: @@ -515,6 +518,12 @@ private JabRefPreferences() { // behavior of JabRef before 2.10: both: false defaults.put(WRITEFIELD_ADDSPACES, Boolean.TRUE); defaults.put(WRITEFIELD_CAMELCASENAME, Boolean.TRUE); + + //behavior of JabRef before LWang_AdjustableFieldOrder 1 + //0 sorted order (2.10 default), 1 unsorted order (2.9.2 default), 2 user defined + defaults.put(WRITEFIELD_SORTSTYLE, 0); + defaults.put(WRITEFIELD_USERDEFINEDORDER, "author;title;journal;year;volume;number;pages;month;note;volume;pages;part;eid"); + defaults.put("useRemoteServer", Boolean.FALSE); defaults.put("remoteServerPort", 6050); diff --git a/src/main/resources/resource/JabRef_en.properties b/src/main/resources/resource/JabRef_en.properties index 0f0b2d5392c..8bd3fa44ca9 100644 --- a/src/main/resources/resource/JabRef_en.properties +++ b/src/main/resources/resource/JabRef_en.properties @@ -1513,6 +1513,10 @@ Sorted_all_subgroups_recursively.=Sorted_all_subgroups_recursively. Sorted_immediate_subgroups.=Sorted_immediate_subgroups. +Sort_fields_in_alphabeta_order_(as_ver_2.10)=Sort_fields_in_alphabeta_order_(as_ver_2.10) +Sort_fields_in_old_fasion_(as_ver_2.9.2)=Sort_fields_in_old_fasion_(as_ver_2.9.2) +Save_fields_as_user_defined_order=Save_fields_as_user_defined_order + source_edit=source_edit Special_Name_Formatters=Special_Name_Formatters From f45976eef29b5b48da1d602149891e08853016c4 Mon Sep 17 00:00:00 2001 From: Ling Wang Date: Mon, 19 May 2014 18:02:21 -0700 Subject: [PATCH 3/4] add option to wrap the fields as 2.9.2 --- src/main/java/net/sf/jabref/BibtexEntry.java | 6 +++-- src/main/java/net/sf/jabref/FileTab.java | 7 ++++++ .../java/net/sf/jabref/JabRefPreferences.java | 5 ++-- .../sf/jabref/export/LatexFieldFormatter.java | 25 ++++++++++--------- 4 files changed, 27 insertions(+), 16 deletions(-) diff --git a/src/main/java/net/sf/jabref/BibtexEntry.java b/src/main/java/net/sf/jabref/BibtexEntry.java index 2c064d39791..c1c46a191af 100644 --- a/src/main/java/net/sf/jabref/BibtexEntry.java +++ b/src/main/java/net/sf/jabref/BibtexEntry.java @@ -429,7 +429,8 @@ public void write(Writer out, FieldFormatter ff, boolean write) throws IOExcepti } - /** old style ver<=2.9.2, write fields in the order of requiredFields, optionalFields and other fields, but does not sort the fields. + /** + * user defined order * @param out * @param ff A formatter to filter field contents before writing * @param write True if this is a write, false if it is a display. The write will not include non-writeable fields if it is a write, otherwise non-displayable fields will be ignored. Refer to GUIGlobals for isWriteableField(String) and isDisplayableField(String). @@ -483,7 +484,8 @@ private void writeUserOrder(Writer out, FieldFormatter ff, boolean write) throws } - /** old style ver<=2.9.2, write fields in the order of requiredFields, optionalFields and other fields, but does not sort the fields. + /** + * old style ver<=2.9.2, write fields in the order of requiredFields, optionalFields and other fields, but does not sort the fields. * @param out * @param ff A formatter to filter field contents before writing * @param write True if this is a write, false if it is a display. The write will not include non-writeable fields if it is a write, otherwise non-displayable fields will be ignored. Refer to GUIGlobals for isWriteableField(String) and isDisplayableField(String). diff --git a/src/main/java/net/sf/jabref/FileTab.java b/src/main/java/net/sf/jabref/FileTab.java index 86bc0b8768c..a14512162bd 100644 --- a/src/main/java/net/sf/jabref/FileTab.java +++ b/src/main/java/net/sf/jabref/FileTab.java @@ -56,6 +56,7 @@ public class FileTab extends JPanel implements PrefsTab { // int fieldOrderStyle; private JTextField userDefinedFieldOrder; + private JCheckBox wrapFieldLine; public FileTab(JabRefFrame frame, JabRefPreferences prefs) { _prefs = prefs; @@ -174,6 +175,10 @@ public void stateChanged(ChangeEvent changeEvent) { builder.append(new JPanel()); builder.nextLine(); + + wrapFieldLine = new JCheckBox(Globals.lang("Wrap fields as ver 2.9.2")); + builder.append(wrapFieldLine); + builder.nextLine(); //for LWang_AdjustableFieldOrder String [] _rbs0={"Sort fields in alphabeta order (as ver 2.10)", "Sort fields in old fasion (as ver 2.9.2)","Save fields as user defined order"}; ArrayList _rbs = new ArrayList(); @@ -272,6 +277,7 @@ public void setValues() { } //preserveFormatting.setSelected(_prefs.getBoolean("preserveFieldFormatting")); + wrapFieldLine.setSelected(_prefs.getBoolean(JabRefPreferences.WRITEFIELD_WRAPFIELD)); autoDoubleBraces.setSelected(_prefs.getBoolean("autoDoubleBraces")); resolveStringsAll.setSelected(_prefs.getBoolean("resolveStringsAllFields")); resolveStringsStandard.setSelected(!resolveStringsAll.isSelected()); @@ -328,6 +334,7 @@ public void storeSettings() { //for LWang_AdjustableFieldOrder _prefs.putInt(JabRefPreferences.WRITEFIELD_SORTSTYLE,getBgValue(bgFieldOrderStyle)); _prefs.put(JabRefPreferences.WRITEFIELD_USERDEFINEDORDER,userDefinedFieldOrder.getText().trim()); + _prefs.putBoolean(JabRefPreferences.WRITEFIELD_WRAPFIELD,wrapFieldLine.isSelected()); boolean updateSpecialFields = false; diff --git a/src/main/java/net/sf/jabref/JabRefPreferences.java b/src/main/java/net/sf/jabref/JabRefPreferences.java index d5f8d9631a2..1361563acdc 100644 --- a/src/main/java/net/sf/jabref/JabRefPreferences.java +++ b/src/main/java/net/sf/jabref/JabRefPreferences.java @@ -94,7 +94,8 @@ public class JabRefPreferences { EXPORT_TERTIARY_SORT_FIELD = "exportTerSort", EXPORT_TERTIARY_SORT_DESCENDING = "exportTerDescending", WRITEFIELD_SORTSTYLE = "writefieldSortStyle", - WRITEFIELD_USERDEFINEDORDER = "writefieldUserdefinedOrder"; + WRITEFIELD_USERDEFINEDORDER = "writefieldUserdefinedOrder", + WRITEFIELD_WRAPFIELD="wrapFieldLine"; // This String is used in the encoded list in prefs of external file type @@ -523,7 +524,7 @@ private JabRefPreferences() { //0 sorted order (2.10 default), 1 unsorted order (2.9.2 default), 2 user defined defaults.put(WRITEFIELD_SORTSTYLE, 0); defaults.put(WRITEFIELD_USERDEFINEDORDER, "author;title;journal;year;volume;number;pages;month;note;volume;pages;part;eid"); - + defaults.put(WRITEFIELD_WRAPFIELD, Boolean.FALSE); defaults.put("useRemoteServer", Boolean.FALSE); defaults.put("remoteServerPort", 6050); diff --git a/src/main/java/net/sf/jabref/export/LatexFieldFormatter.java b/src/main/java/net/sf/jabref/export/LatexFieldFormatter.java index eea74cabec7..0fb9cceb57b 100644 --- a/src/main/java/net/sf/jabref/export/LatexFieldFormatter.java +++ b/src/main/java/net/sf/jabref/export/LatexFieldFormatter.java @@ -20,6 +20,7 @@ import net.sf.jabref.BibtexFields; import net.sf.jabref.GUIGlobals; import net.sf.jabref.Globals; +import net.sf.jabref.JabRefPreferences; import net.sf.jabref.Util; public class LatexFieldFormatter implements FieldFormatter { @@ -87,13 +88,13 @@ public String format(String text, String fieldName) sb = new StringBuffer( Globals.prefs.getValueDelimiters(0) + ""); // No formatting at all for these fields, to allow custom formatting? - //if (Globals.prefs.getBoolean("preserveFieldFormatting")) - // sb.append(text); - //else - // currently, we do not do any more wrapping - //if (!Globals.prefs.isNonWrappableField(fieldName)) - // sb.append(Util.wrap2(text, GUIGlobals.LINE_LENGTH)); - //else +// if (Globals.prefs.getBoolean("preserveFieldFormatting")) +// sb.append(text); +// else +// currently, we do not do any more wrapping + if (Globals.prefs.getBoolean(JabRefPreferences.WRITEFIELD_WRAPFIELD)&&!Globals.prefs.isNonWrappableField(fieldName)) + sb.append(Util.wrap2(text, GUIGlobals.LINE_LENGTH)); + else sb.append(text); sb.append(Globals.prefs.getValueDelimiters(1)); @@ -155,11 +156,11 @@ public String format(String text, String fieldName) } // currently, we do not add newlines and new formatting - //if (!Globals.prefs.isNonWrappableField(fieldName)) { - // introduce a line break to be read at the parser - // the old code called Util.wrap2(sb.toString(), GUIGlobals.LINE_LENGTH), but that lead to ugly .tex - // alternative: return sb.toString().replaceAll(Globals.NEWLINE, Globals.NEWLINE + Globals.NEWLINE); - //} else + if (Globals.prefs.getBoolean(JabRefPreferences.WRITEFIELD_WRAPFIELD)&&!Globals.prefs.isNonWrappableField(fieldName)) { +// introduce a line break to be read at the parser + return Util.wrap2(sb.toString(), GUIGlobals.LINE_LENGTH);//, but that lead to ugly .tex + + } else return sb.toString(); From b6a89a81a983332d35420534a766d8dfabb6b81e Mon Sep 17 00:00:00 2001 From: Ling Wang Date: Mon, 19 May 2014 19:56:41 -0700 Subject: [PATCH 4/4] fix bug causing double entries. --- src/main/java/net/sf/jabref/BibtexEntry.java | 2 + .../java/net/sf/jabref/BibtexEntryType.java | 2 +- testbib/testjabref.bib | 313 ++++++++++++ testbib/testjabref_210as292.bib | 482 ++++++++++++++++++ testbib/testjabref_292.bib | 301 +++++++++++ 5 files changed, 1099 insertions(+), 1 deletion(-) create mode 100644 testbib/testjabref.bib create mode 100644 testbib/testjabref_210as292.bib create mode 100644 testbib/testjabref_292.bib diff --git a/src/main/java/net/sf/jabref/BibtexEntry.java b/src/main/java/net/sf/jabref/BibtexEntry.java index c1c46a191af..b7bc8d83193 100644 --- a/src/main/java/net/sf/jabref/BibtexEntry.java +++ b/src/main/java/net/sf/jabref/BibtexEntry.java @@ -421,8 +421,10 @@ public void write(Writer out, FieldFormatter ff, boolean write) throws IOExcepti break; case 1: writeUnsorted(out, ff, write); + break; case 2: writeUserOrder(out,ff,write); + break; } diff --git a/src/main/java/net/sf/jabref/BibtexEntryType.java b/src/main/java/net/sf/jabref/BibtexEntryType.java index 14df3a3eaec..05e946fe21d 100644 --- a/src/main/java/net/sf/jabref/BibtexEntryType.java +++ b/src/main/java/net/sf/jabref/BibtexEntryType.java @@ -84,7 +84,7 @@ public String[] getOptionalFields() { return new String[] { - "volume", "number", "pages", "month", "note", //- "volume", "pages", "part", "eid" + "volume", "pages", "number", "month", "note", //- "volume", "pages", "part", "eid" }; } diff --git a/testbib/testjabref.bib b/testbib/testjabref.bib new file mode 100644 index 00000000000..a5fc0fec81b --- /dev/null +++ b/testbib/testjabref.bib @@ -0,0 +1,313 @@ +% This file was created with JabRef devel - 1st edition family. +% Encoding: UTF8 + + +@Article{Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS, + Title = {256-Channel Neural Recording and Delta Compression Microsystem With + 3D Electrodes}, + Author = {Aziz, Joseph N. Y. and Abdelhalim, Karim and Shulyzki, Ruslana and + Genov, Roman and Bardakjian, Berj L. and Derchansky, Miron and Serletis, + Demitre and Carlen, Peter L.}, + Journal = {IEEE JOURNAL OF SOLID-STATE CIRCUITS}, + Year = {2009}, + + Month = {MAR}, + Number = {3}, + Pages = {995-1005}, + Volume = {44}, + + Abstract = {A 3D microsystem for multi-site penetrating extracellular neural recording + from the brain is presented. A 16 x 16-channel neural recording interface + integrated prototype fabricated in 0.35 mu m CMOS occupies 3.5 mm + x 4.5 mm area. Each recording channel dissipates 15 mu W of power + with input-referred noise of 7 mu V-rms over 5 kHz bandwidth. A switched-capacitor + delta read-out data compression circuit trades recording accuracy + for the output data rate. An array of 1.5 mm platinum-coated microelectrodes + is bonded directly onto the die. Results of in vitro experimental + recordings from intact mouse hippocampus validate the circuit design + and the on-chip electrode bonding technology.}, + Address = {445 HOES LANE, PISCATAWAY, NJ 08855 USA}, + Affiliation = {Aziz, JNY (Reprint Author), Broadcom, Irvine, CA 92617 USA. {[}Aziz, + Joseph N. Y.; Abdelhalim, Karim; Shulyzki, Ruslana; Genov, Roman] + Univ Toronto, Dept Elect \& Comp Engn, Toronto, ON M5S 3G4, Canada. + {[}Bardakjian, Berj L.] Univ Toronto, Inst Biomat \& Biomed Engn, + Edward S Rogers Sr Dept Elect \& Comp Engn, Toronto, ON M5S 1A4, + Canada. {[}Derchansky, Miron; Serletis, Demitre; Carlen, Peter L.] + Univ Toronto, Toronto Western Res Inst, Toronto, ON M5S 1A4, Canada. + {[}Derchansky, Miron; Serletis, Demitre; Carlen, Peter L.] Univ Toronto, + Dept Physiol, Toronto, ON M5S 1A4, Canada.}, + Author-email = {roman@eecg.utoronto.ca}, + Cited-references = {ATLURI S, 2006, P IEEE INT S CIRC SY, P1131. AZIZ J, 2006, P IEEE + INT S CIRC SY. AZIZ J, 2007, IEEE INT SOL STAT CI, P160. AZIZ JNY, + 2006, P IEEE INT S CIRC SY, P5075. AZIZ JNY, 2007, IEEE T BIOMED + CIRCUI, V1. AZIZ JNY, 2007, P IEEE INT S CIRC SY. CHAIMANONART N, + 2005, P ANN INT IEEE EMBS, P5194. DELBRUCK T, 1994, P IEEE INT S + CIRC SY, V4, P339. ENZ CC, 1996, P IEEE, V84, P1584. EVERSMANN B, + 2003, IEEE J SOLID-ST CIRC, V38, P2306, DOI 10.1109/JSSC.2003.819174. + HARRISON R, 2006, IEEE INT SOL STAT C, P2258. HARRISON RR, 2003, + IEEE J SOLID-ST CIRC, V38, P958, DOI 10.1009/JSSC.2003.811979. HARRISON + RR, 2007, IEEE CUST INTEGR CIR, P115. HEER F, 2006, IEEE J SOLID-ST + CIRC, V41, P1620, DOI 10.1109/JSSC.2006.873677. KIM S, 2006, P 2006 + INT C IEEE EN, P2986. MALLIK U, 2005, IEEE ISSCC, P362. MOHSENI P, + 2004, IEEE T BIO-MED ENG, V51, P832, DOI 10.1109/TBME.2004.824126. + MOTCHENBACHER CD, 1993, LOW NOISE ELECT SYST. OLSSON RH, 2005, IEEE + J SOLID-ST CIRC, V40, P2796. PATTERSON WR, 2004, IEEE T BIO-MED ENG, + V51, P1845, DOI 10.1109/TBME.2004.831521. RILEY G, 1987, SURFACE + MOUNT INT, P535. STEYAERT MSJ, 1987, IEEE J SOLID-ST CIRC, V22, P1163. + TSIVIDIS Y, 2003, OPERATION MODELING M. WATTANAPANITCH W, 2007, IEEE + T BIOMED CIRC S, V1, P136, DOI 10.1109/TBCAS.2007.907868. WISE KD, + 2005, IEEE ENG MED BIOL, V24, P22.}, + Doc-delivery-number = {415FE}, + Doi = {10.1109/JSSC.2008.2010997}, + File = {Draft:JabRef\\Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS_draft.pdf:PDF;Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS.pdf:JabRef\\Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS.pdf:PDF}, + ISSN = {0018-9200}, + Journal-iso = {IEEE J. Solid-State Circuit}, + Keywords = {Multi-channel recording; microelectrodes; extracellular recording; + electrode array; implantable; brain; hippocampus; delta compression; + neural amplifier}, + Keywords-plus = {AMPLIFIER; STABILIZATION; CIRCUIT; ARRAY}, + Language = {English}, + Number-of-cited-references = {25}, + Publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC}, + Subject-category = {Engineering, Electrical \& Electronic}, + Times-cited = {2}, + Timestamp = {10.04.15.11.41}, + Type = {Article}, + Unique-id = {ISI:000263918900029} +} + +@Article{BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering, + Title = {Patterning PDMS using a combination of wet and dry etching}, + Author = {B Balakrisnan , S Patil and E Smela}, + Journal = {Journal of Micromechanics and Microengineering}, + Year = {2009}, + Number = {4}, + Pages = {047002}, + Volume = {19}, + + Abstract = {PDMS films of 10 �m thickness can be patterned within 30 min by combining + dry etching to achieve substantially vertical sidewalls with wet + etching to achieve high etch rates and to protect the underlying + substrate from attack. Dry etching alone would have taken 5 h, and + wet etching alone would produce severe undercutting. In addition, + using either technique alone produces undesirable surface morphologies. + The mask used during etching is critical to a successful patterning + outcome. E-beam evaporated Al was found to work well, adhering strongly + to oxygen-plasma-treated PDMS and holding up well during both dry + and wet etching. To prevent wrinkling of the PDMS, a fast deposition + rate should be used.}, + File = {BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering.pdf:JabRef\\BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering.pdf:PDF}, + Timestamp = {09.06.17.13.03}, + Url = {http://stacks.iop.org/0960-1317/19/i=4/a=047002} +} + +@Article{Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA, + Title = {Synaptic facilitation by reflected action potentials: enhancement + of transmission when nerve impulses reverse direction at axon branch + points.}, + Author = {S. A. Baccus}, + Journal = {Proc Natl Acad Sci U S A}, + Year = {1998}, + + Month = {Jul}, + Number = {14}, + Pages = {8345--8350}, + Volume = {95}, + + Abstract = {A rapid, reversible enhancement of synaptic transmission from a sensory + neuron is reported and explained by impulses that reverse direction, + or reflect, at axon branch points. In leech mechanosensory neurons, + where one can detect reflection because it is possible simultaneously + to study electrical activity in separate branches, action potentials + reflected from branch points within the central nervous system under + physiological conditions. Synapses adjacent to these branch points + were activated twice in rapid succession, first by an impulse arriving + from the periphery and then by its reflection. This fast double-firing + facilitated synaptic transmission, increasing it to more than twice + its normal level. Reflection occurred within a range of resting membrane + potentials, and electrical activity produced by mechanical stimulation + changed membrane potential so as to produce and cease reflection. + A compartmental model was used to investigate how branch-point morphology + and electrical activity contribute to produce reflection. The model + shows that mechanisms that hyperpolarize the membrane so as to impair + action potential propagation can increase the range of structures + that can produce reflection. This suggests that reflection is more + likely to occur in other structures where impulses fail, such as + in axons and dendrites in the mammalian brain. In leech sensory neurons, + reflection increased transmission from central synapses only in those + axon branches that innervate the edges of the receptive field in + the skin, thereby sharpening spatial contrast. Reflection thus allows + a neuron to amplify synaptic transmission from a selected group of + its branches in a way that can be regulated by electrical activity.}, + File = {Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA.pdf:JabRef\\Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA.pdf:PDF}, + Institution = {Neuroscience Program, University of Miami, Miami, FL 33136, USA. + sbaccus@mednet.med.miami.edu}, + Keywords = {Action Potentials, physiology; Animals; Axons, physiology; Electrophysiology; + Ganglia, Invertebrate, physiology; Ganglia, Sensory, physiology; + Leeches; Neurons, physiology; Synapses, physiology; Synaptic Transmission, + physiology}, + Language = {eng}, + Medline-pst = {ppublish}, + Pmid = {9653189}, + Timestamp = {11.05.01.13.02} +} + +@Article{Brewer1995Serum-freeB27/neurobasalmediumsupportsdifferentiatedgrowthofneuronsfromthestriatumsubstantianigraseptumcerebralcortexcerebellumanddentategyrus.JNeurosciRes, + Title = {Serum-free B27/neurobasal medium supports differentiated growth of + neurons from the striatum, substantia nigra, septum, cerebral cortex, + cerebellum, and dentate gyrus.}, + Author = {G. J. Brewer}, + Journal = {J Neurosci Res}, + Year = {1995}, + + Month = {Dec}, + Number = {5}, + Pages = {674--683}, + Volume = {42}, + + Abstract = {Two fundamental questions about neuron cell culture were addressed. + Can one serum-free medium that was developed for optimum growth of + hippocampal neurons support the growth of neurons from other regions + of the brain? Is the region specific state of differentiation maintained + in culture? To answer these questions, we isolated neurons from six + other rat brain regions, placed them in culture in B27/Neurobasal + defined medium, and analyzed their morphology and growth dependence + on cell density after 4 days in culture. Neuronal identity was confirmed + by immunostaining with antibodies to neurofilament 200. Neurons from + each brain region maintained distinctive morphologies in culture + in the virtual absence of glia. Cells isolated from embryonic day + 18 cerebral cortex by digestion with papain showed the same high + survival as hippocampal neurons, e.g., 70\% survival for cells plated + at 160/mm2. At this age and density, neurons from the septum showed + slightly lower survival, 45\%. Survival of dentate granule neurons + from postnatal day four brains was 30-40\%, significantly lower, + and relatively independent of plating density. This suggests an absence + of dependence on trophic factors or contact for dentate granule neurons. + Growth of cerebellar granule neurons isolated from postnatal day + 7, 8, or 9 brains in B27/Neurobasal was compared to growth in BME/10\% + serum. Viability in serum-free medium at 4 days was much better than + that in serum, did not require KCl elevated to 25 mM, and occurred + without substantial growth of glia. Cerebellar granule neurons plated + at 1,280 cells/mm2 were maintained in culture for three weeks with + 17\% of the original cell density surviving. Survival of cells isolated + from embryonic day 18 substantia nigra was 50\% at 160 cells/mm2 + after 4 days, similar to that of striatum, but slightly less than + hippocampal neuron survival. The dopaminergic phenotype of the substantia + nigral neurons was maintained over 2 weeks in culture as judged by + immunoreactivity with antibodies to tyrosine hydroxylase. During + this time, immunoreactivity was found in the processes as they grew + out from the soma. Together, these studies suggest that B27/Neurobasal + will be a useful medium for maintaining the differentiated growth + of neurons from many brain regions. Potential applications of a common + growth medium for different neurons are discussed.}, + Doi = {10.1002/jnr.490420510}, + Institution = {Southern Illinois University School of Medicine, Springfield 62794-1220, + USA.}, + Keywords = {Animals; Brain, anatomy /&/ histology/cytology/enzymology; Cell Culture + Techniques; Cell Survival; Cells, Cultured; Cerebellum, cytology/embryology; + Cerebral Cortex, cytology/embryology; Corpus Striatum, cytology/embryology; + Culture Media, Serum-Free; Dentate Gyrus, cytology/embryology; Electrophysiology; + Hippocampus, cytology/embryology; Neurofilament Proteins, metabolism; + Neurons, cytology/enzymology; Rats; Rats, Sprague-Dawley; Septum + Pellucidum, embryology; Substantia Nigra, cytology/embryology; Tyrosine + 3-Monooxygenase, metabolism}, + Pmid = {8600300}, + Timestamp = {2008.12.12}, + Url = {http://dx.doi.org/10.1002/jnr.490420510} +} + +@Article{Brewer1997Isolationandcultureofadultrathippocampalneurons.JNeurosciMethods, + Title = {Isolation and culture of adult rat hippocampal neurons.}, + Author = {G. J. Brewer}, + Journal = {J Neurosci Methods}, + Year = {1997}, + + Month = {Feb}, + Number = {2}, + Pages = {143--155}, + Volume = {71}, + + Abstract = {Inability to culture adult central neurons and the failure of injured + neurons to regenerate in the brain could be due to genetic controls + or environmental inhibitors. We tested the environmental inhibitor + hypothesis by attempting to regenerate adult rat neurons in B27/Neurobasal + culture medium, a medium optimized for survival of embryonic neurons. + To isolate neurons from their numerous connections, papain was the + best of six different proteases screened on slices of hippocampus + for survival of isolated cells after 4 days of culture. Use of a + density gradient enabled separation of oligodendroglia and some enrichment + of neurons and microglia from considerable debris which was inhibitory + to sprouting and viability. With these techniques, about 900000 viable + neurons were isolated from each hippocampus of any age rat from birth + to 24-36 months, near the median mortality. FGF2 was found to enhance + viability at least 3-fold to 40-80\%, independent of age, without + affecting the length of the processes. Neurons were cultured for + more than 3 weeks. These methods demonstrate that hippocampal neurons + can regenerate axons and dendrites if provided with adequate nutrition + and if inhibitors are removed. They also will enable aging studies. + Therefore, the concept of environmental growth restriction may be + more appropriate for neurons in the brain than the concept of a genetic + block that precludes regeneration of processes.}, + Institution = {Department of Medical Microbiology and Immunology, Southern Illinois + University School of Medicine, Springfield 62794-1220, USA. gbrewer@siumed.edu}, + Keywords = {Age Factors; Animals; Cell Adhesion, physiology; Cell Culture Techniques, + methods; Cell Separation, methods; Cell Survival, physiology; Cells, + Cultured; Cerebral Cortex, cytology; Dose-Response Relationship, + Drug; Fibroblast Growth Factor 2, physiology; Glutamic Acid, pharmacology; + Hippocampus, cytology; Male; Neurons, cytology/drug effects; Osmolar + Concentration; Oxygen, pharmacology; Papain; Rats; Rats, Inbred F344; + Rats, Sprague-Dawley}, + Pii = {S0165-0270(96)00136-7}, + Pmid = {9128149}, + Timestamp = {09.02.26.19.31} +} + +@Article{Brewer2008NbActiv4mediumimprovementtoNeurobasal/B27increasesneuronsynapsedensitiesandnetworkspikeratesonmultielectrodearrays.JNeurosciMethods, + Title = {NbActiv4 medium improvement to Neurobasal/B27 increases neuron synapse + densities and network spike rates on multielectrode arrays.}, + Author = {Gregory J Brewer and Michael D Boehler and Torrie T Jones and Bruce + C Wheeler}, + Journal = {J Neurosci Methods}, + Year = {2008}, + + Month = {May}, + Number = {2}, + Pages = {181--187}, + Volume = {170}, + + Abstract = {The most interesting property of neurons is their long-distance propagation + of signals as spiking action potentials. Since 1993, Neurobasal/B27 + has been used as a serum-free medium optimized for hippocampal neuron + survival. Neurons on microelectrode arrays (MEA) were used as an + assay system to increase spontaneous spike rates in media of different + compositions. We find spike rates of 0.5 s(-1) (Hz) for rat embryonic + hippocampal neurons cultured in Neurobasal/B27, lower than cultures + in serum-based media and offering an opportunity for improvement. + NbActiv4 was formulated by addition of creatine, cholesterol and + estrogen to Neurobasal/B27 that synergistically produced an eightfold + increase in spontaneous spike activity. The increased activity with + NbActiv4 correlated with a twofold increase in immunoreactive synaptophysin + bright puncta and GluR1 total puncta. Characteristic of synaptic + scaling, immunoreactive GABAAbeta puncta also increased 1.5-fold + and NMDA-R1 puncta increased 1.8-fold. Neuron survival in NbActiv4 + equaled that in Neurobasal/B27, but with slightly higher astroglia. + Resting respiratory demand was decreased and demand capacity was + increased in NbActiv4, indicating less stress and higher efficiency. + These results show that NbActiv4 is an improvement to Neurobasal/B27 + for cultured networks with an increased density of synapses and transmitter + receptors which produces higher spontaneous spike rates in neuron + networks.}, + Doi = {10.1016/j.jneumeth.2008.01.009}, + Institution = {Southern Illinois University School of Medicine, Springfield, IL + 62794-9626, USA. gbrewer@siumed.edu}, + Keywords = {Cell Survival; Cells, Cultured; Culture Media; Electrophysiology; + Hippocampus, cytology; Humans; Image Processing, Computer-Assisted; + Immunohistochemistry; Kinetics; Microelectrodes; Nerve Net, physiology; + Neurons, physiology; Oxygen Consumption, physiology; Oxygen, analysis; + Synapses, physiology}, + Pii = {S0165-0270(08)00039-3}, + Pmid = {18308400}, + Timestamp = {09.02.26.19.31}, + Url = {http://dx.doi.org/10.1016/j.jneumeth.2008.01.009} +} + diff --git a/testbib/testjabref_210as292.bib b/testbib/testjabref_210as292.bib new file mode 100644 index 00000000000..0ed1bb90666 --- /dev/null +++ b/testbib/testjabref_210as292.bib @@ -0,0 +1,482 @@ +% This file was created with JabRef devel - 1st edition family. +% Encoding: UTF8 + + +@ARTICLE{Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS, + author = {Aziz, Joseph N. Y. and Abdelhalim, Karim and Shulyzki, Ruslana and + + Genov, Roman and Bardakjian, Berj L. and Derchansky, Miron and Serletis, + + Demitre and Carlen, Peter L.}, + title = {256-Channel Neural Recording and Delta Compression Microsystem With + + 3D Electrodes}, + journal = {IEEE JOURNAL OF SOLID-STATE CIRCUITS}, + year = {2009}, + volume = {44}, + pages = {995-1005}, + number = {3}, + month = {MAR}, + abstract = {A 3D microsystem for multi-site penetrating extracellular neural recording + + from the brain is presented. A 16 x 16-channel neural recording interface + + integrated prototype fabricated in 0.35 mu m CMOS occupies 3.5 mm + + x 4.5 mm area. Each recording channel dissipates 15 mu W of power + + with input-referred noise of 7 mu V-rms over 5 kHz bandwidth. A switched-capacitor + + delta read-out data compression circuit trades recording accuracy + + for the output data rate. An array of 1.5 mm platinum-coated microelectrodes + + is bonded directly onto the die. Results of in vitro experimental + + recordings from intact mouse hippocampus validate the circuit design + + and the on-chip electrode bonding technology.}, + address = {445 HOES LANE, PISCATAWAY, NJ 08855 USA}, + affiliation = {Aziz, JNY (Reprint Author), Broadcom, Irvine, CA 92617 USA. {[}Aziz, + + Joseph N. Y.; Abdelhalim, Karim; Shulyzki, Ruslana; Genov, Roman] + + Univ Toronto, Dept Elect \& Comp Engn, Toronto, ON M5S 3G4, Canada. + + {[}Bardakjian, Berj L.] Univ Toronto, Inst Biomat \& Biomed Engn, + + Edward S Rogers Sr Dept Elect \& Comp Engn, Toronto, ON M5S 1A4, + + Canada. {[}Derchansky, Miron; Serletis, Demitre; Carlen, Peter L.] + + Univ Toronto, Toronto Western Res Inst, Toronto, ON M5S 1A4, Canada. + + {[}Derchansky, Miron; Serletis, Demitre; Carlen, Peter L.] Univ Toronto, + + Dept Physiol, Toronto, ON M5S 1A4, Canada.}, + author-email = {roman@eecg.utoronto.ca}, + cited-references = {ATLURI S, 2006, P IEEE INT S CIRC SY, P1131. AZIZ J, 2006, P IEEE + + INT S CIRC SY. AZIZ J, 2007, IEEE INT SOL STAT CI, P160. AZIZ JNY, + + 2006, P IEEE INT S CIRC SY, P5075. AZIZ JNY, 2007, IEEE T BIOMED + + CIRCUI, V1. AZIZ JNY, 2007, P IEEE INT S CIRC SY. CHAIMANONART N, + + 2005, P ANN INT IEEE EMBS, P5194. DELBRUCK T, 1994, P IEEE INT S + + CIRC SY, V4, P339. ENZ CC, 1996, P IEEE, V84, P1584. EVERSMANN B, + + 2003, IEEE J SOLID-ST CIRC, V38, P2306, DOI 10.1109/JSSC.2003.819174. + + HARRISON R, 2006, IEEE INT SOL STAT C, P2258. HARRISON RR, 2003, + + IEEE J SOLID-ST CIRC, V38, P958, DOI 10.1009/JSSC.2003.811979. HARRISON + + RR, 2007, IEEE CUST INTEGR CIR, P115. HEER F, 2006, IEEE J SOLID-ST + + CIRC, V41, P1620, DOI 10.1109/JSSC.2006.873677. KIM S, 2006, P 2006 + + INT C IEEE EN, P2986. MALLIK U, 2005, IEEE ISSCC, P362. MOHSENI P, + + 2004, IEEE T BIO-MED ENG, V51, P832, DOI 10.1109/TBME.2004.824126. + + MOTCHENBACHER CD, 1993, LOW NOISE ELECT SYST. OLSSON RH, 2005, IEEE + + J SOLID-ST CIRC, V40, P2796. PATTERSON WR, 2004, IEEE T BIO-MED ENG, + + V51, P1845, DOI 10.1109/TBME.2004.831521. RILEY G, 1987, SURFACE + + MOUNT INT, P535. STEYAERT MSJ, 1987, IEEE J SOLID-ST CIRC, V22, P1163. + + TSIVIDIS Y, 2003, OPERATION MODELING M. WATTANAPANITCH W, 2007, IEEE + + T BIOMED CIRC S, V1, P136, DOI 10.1109/TBCAS.2007.907868. WISE KD, + + 2005, IEEE ENG MED BIOL, V24, P22.}, + doc-delivery-number = {415FE}, + doi = {10.1109/JSSC.2008.2010997}, + file = {Draft:JabRef\\Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS_draft.pdf:PDF;Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS.pdf:JabRef\\Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS.pdf:PDF}, + issn = {0018-9200}, + journal-iso = {IEEE J. Solid-State Circuit}, + keywords = {Multi-channel recording; microelectrodes; extracellular recording; + + electrode array; implantable; brain; hippocampus; delta compression; + + neural amplifier}, + keywords-plus = {AMPLIFIER; STABILIZATION; CIRCUIT; ARRAY}, + language = {English}, + number-of-cited-references = {25}, + publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC}, + subject-category = {Engineering, Electrical \& Electronic}, + times-cited = {2}, + timestamp = {10.04.15.11.41}, + type = {Article}, + unique-id = {ISI:000263918900029} +} + +@ARTICLE{BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering, + author = {B Balakrisnan , S Patil and E Smela}, + title = {Patterning PDMS using a combination of wet and dry etching}, + journal = {Journal of Micromechanics and Microengineering}, + year = {2009}, + volume = {19}, + pages = {047002}, + number = {4}, + abstract = {PDMS films of 10 �m thickness can be patterned within 30 min by combining + + dry etching to achieve substantially vertical sidewalls with wet + + etching to achieve high etch rates and to protect the underlying + + substrate from attack. Dry etching alone would have taken 5 h, and + + wet etching alone would produce severe undercutting. In addition, + + using either technique alone produces undesirable surface morphologies. + + The mask used during etching is critical to a successful patterning + + outcome. E-beam evaporated Al was found to work well, adhering strongly + + to oxygen-plasma-treated PDMS and holding up well during both dry + + and wet etching. To prevent wrinkling of the PDMS, a fast deposition + + rate should be used.}, + file = {BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering.pdf:JabRef\\BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering.pdf:PDF}, + timestamp = {09.06.17.13.03}, + url = {http://stacks.iop.org/0960-1317/19/i=4/a=047002} +} + +@ARTICLE{Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA, + author = {S. A. Baccus}, + title = {Synaptic facilitation by reflected action potentials: enhancement + + of transmission when nerve impulses reverse direction at axon branch + + points.}, + journal = {Proc Natl Acad Sci U S A}, + year = {1998}, + volume = {95}, + pages = {8345--8350}, + number = {14}, + month = {Jul}, + abstract = {A rapid, reversible enhancement of synaptic transmission from a sensory + + neuron is reported and explained by impulses that reverse direction, + + or reflect, at axon branch points. In leech mechanosensory neurons, + + where one can detect reflection because it is possible simultaneously + + to study electrical activity in separate branches, action potentials + + reflected from branch points within the central nervous system under + + physiological conditions. Synapses adjacent to these branch points + + were activated twice in rapid succession, first by an impulse arriving + + from the periphery and then by its reflection. This fast double-firing + + facilitated synaptic transmission, increasing it to more than twice + + its normal level. Reflection occurred within a range of resting membrane + + potentials, and electrical activity produced by mechanical stimulation + + changed membrane potential so as to produce and cease reflection. + + A compartmental model was used to investigate how branch-point morphology + + and electrical activity contribute to produce reflection. The model + + shows that mechanisms that hyperpolarize the membrane so as to impair + + action potential propagation can increase the range of structures + + that can produce reflection. This suggests that reflection is more + + likely to occur in other structures where impulses fail, such as + + in axons and dendrites in the mammalian brain. In leech sensory neurons, + + reflection increased transmission from central synapses only in those + + axon branches that innervate the edges of the receptive field in + + the skin, thereby sharpening spatial contrast. Reflection thus allows + + a neuron to amplify synaptic transmission from a selected group of + + its branches in a way that can be regulated by electrical activity.}, + file = {Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA.pdf:JabRef\\Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA.pdf:PDF}, + institution = {Neuroscience Program, University of Miami, Miami, FL 33136, USA. + + sbaccus@mednet.med.miami.edu}, + keywords = {Action Potentials, physiology; Animals; Axons, physiology; Electrophysiology; + + Ganglia, Invertebrate, physiology; Ganglia, Sensory, physiology; + + Leeches; Neurons, physiology; Synapses, physiology; Synaptic Transmission, + + physiology}, + language = {eng}, + medline-pst = {ppublish}, + pmid = {9653189}, + timestamp = {11.05.01.13.02} +} + +@ARTICLE{Brewer1995Serum-freeB27/neurobasalmediumsupportsdifferentiatedgrowthofneuronsfromthestriatumsubstantianigraseptumcerebralcortexcerebellumanddentategyrus.JNeurosciRes, + author = {G. J. Brewer}, + title = {Serum-free B27/neurobasal medium supports differentiated growth of + + neurons from the striatum, substantia nigra, septum, cerebral cortex, + + cerebellum, and dentate gyrus.}, + journal = {J Neurosci Res}, + year = {1995}, + volume = {42}, + pages = {674--683}, + number = {5}, + month = {Dec}, + abstract = {Two fundamental questions about neuron cell culture were addressed. + + Can one serum-free medium that was developed for optimum growth of + + hippocampal neurons support the growth of neurons from other regions + + of the brain? Is the region specific state of differentiation maintained + + in culture? To answer these questions, we isolated neurons from six + + other rat brain regions, placed them in culture in B27/Neurobasal + + defined medium, and analyzed their morphology and growth dependence + + on cell density after 4 days in culture. Neuronal identity was confirmed + + by immunostaining with antibodies to neurofilament 200. Neurons from + + each brain region maintained distinctive morphologies in culture + + in the virtual absence of glia. Cells isolated from embryonic day + + 18 cerebral cortex by digestion with papain showed the same high + + survival as hippocampal neurons, e.g., 70\% survival for cells plated + + at 160/mm2. At this age and density, neurons from the septum showed + + slightly lower survival, 45\%. Survival of dentate granule neurons + + from postnatal day four brains was 30-40\%, significantly lower, + + and relatively independent of plating density. This suggests an absence + + of dependence on trophic factors or contact for dentate granule neurons. + + Growth of cerebellar granule neurons isolated from postnatal day + + 7, 8, or 9 brains in B27/Neurobasal was compared to growth in BME/10\% + + serum. Viability in serum-free medium at 4 days was much better than + + that in serum, did not require KCl elevated to 25 mM, and occurred + + without substantial growth of glia. Cerebellar granule neurons plated + + at 1,280 cells/mm2 were maintained in culture for three weeks with + + 17\% of the original cell density surviving. Survival of cells isolated + + from embryonic day 18 substantia nigra was 50\% at 160 cells/mm2 + + after 4 days, similar to that of striatum, but slightly less than + + hippocampal neuron survival. The dopaminergic phenotype of the substantia + + nigral neurons was maintained over 2 weeks in culture as judged by + + immunoreactivity with antibodies to tyrosine hydroxylase. During + + this time, immunoreactivity was found in the processes as they grew + + out from the soma. Together, these studies suggest that B27/Neurobasal + + will be a useful medium for maintaining the differentiated growth + + of neurons from many brain regions. Potential applications of a common + + growth medium for different neurons are discussed.}, + doi = {10.1002/jnr.490420510}, + institution = {Southern Illinois University School of Medicine, Springfield 62794-1220, + + USA.}, + keywords = {Animals; Brain, anatomy /&/ histology/cytology/enzymology; Cell Culture + + Techniques; Cell Survival; Cells, Cultured; Cerebellum, cytology/embryology; + + Cerebral Cortex, cytology/embryology; Corpus Striatum, cytology/embryology; + + Culture Media, Serum-Free; Dentate Gyrus, cytology/embryology; Electrophysiology; + + Hippocampus, cytology/embryology; Neurofilament Proteins, metabolism; + + Neurons, cytology/enzymology; Rats; Rats, Sprague-Dawley; Septum + + Pellucidum, embryology; Substantia Nigra, cytology/embryology; Tyrosine + + 3-Monooxygenase, metabolism}, + pmid = {8600300}, + timestamp = {2008.12.12}, + url = {http://dx.doi.org/10.1002/jnr.490420510} +} + +@ARTICLE{Brewer1997Isolationandcultureofadultrathippocampalneurons.JNeurosciMethods, + author = {G. J. Brewer}, + title = {Isolation and culture of adult rat hippocampal neurons.}, + journal = {J Neurosci Methods}, + year = {1997}, + volume = {71}, + pages = {143--155}, + number = {2}, + month = {Feb}, + abstract = {Inability to culture adult central neurons and the failure of injured + + neurons to regenerate in the brain could be due to genetic controls + + or environmental inhibitors. We tested the environmental inhibitor + + hypothesis by attempting to regenerate adult rat neurons in B27/Neurobasal + + culture medium, a medium optimized for survival of embryonic neurons. + + To isolate neurons from their numerous connections, papain was the + + best of six different proteases screened on slices of hippocampus + + for survival of isolated cells after 4 days of culture. Use of a + + density gradient enabled separation of oligodendroglia and some enrichment + + of neurons and microglia from considerable debris which was inhibitory + + to sprouting and viability. With these techniques, about 900000 viable + + neurons were isolated from each hippocampus of any age rat from birth + + to 24-36 months, near the median mortality. FGF2 was found to enhance + + viability at least 3-fold to 40-80\%, independent of age, without + + affecting the length of the processes. Neurons were cultured for + + more than 3 weeks. These methods demonstrate that hippocampal neurons + + can regenerate axons and dendrites if provided with adequate nutrition + + and if inhibitors are removed. They also will enable aging studies. + + Therefore, the concept of environmental growth restriction may be + + more appropriate for neurons in the brain than the concept of a genetic + + block that precludes regeneration of processes.}, + institution = {Department of Medical Microbiology and Immunology, Southern Illinois + + University School of Medicine, Springfield 62794-1220, USA. gbrewer@siumed.edu}, + keywords = {Age Factors; Animals; Cell Adhesion, physiology; Cell Culture Techniques, + + methods; Cell Separation, methods; Cell Survival, physiology; Cells, + + Cultured; Cerebral Cortex, cytology; Dose-Response Relationship, + + Drug; Fibroblast Growth Factor 2, physiology; Glutamic Acid, pharmacology; + + Hippocampus, cytology; Male; Neurons, cytology/drug effects; Osmolar + + Concentration; Oxygen, pharmacology; Papain; Rats; Rats, Inbred F344; + + Rats, Sprague-Dawley}, + pii = {S0165-0270(96)00136-7}, + pmid = {9128149}, + timestamp = {09.02.26.19.31} +} + +@ARTICLE{Brewer2008NbActiv4mediumimprovementtoNeurobasal/B27increasesneuronsynapsedensitiesandnetworkspikeratesonmultielectrodearrays.JNeurosciMethods, + author = {Gregory J Brewer and Michael D Boehler and Torrie T Jones and Bruce + + C Wheeler}, + title = {NbActiv4 medium improvement to Neurobasal/B27 increases neuron synapse + + densities and network spike rates on multielectrode arrays.}, + journal = {J Neurosci Methods}, + year = {2008}, + volume = {170}, + pages = {181--187}, + number = {2}, + month = {May}, + abstract = {The most interesting property of neurons is their long-distance propagation + + of signals as spiking action potentials. Since 1993, Neurobasal/B27 + + has been used as a serum-free medium optimized for hippocampal neuron + + survival. Neurons on microelectrode arrays (MEA) were used as an + + assay system to increase spontaneous spike rates in media of different + + compositions. We find spike rates of 0.5 s(-1) (Hz) for rat embryonic + + hippocampal neurons cultured in Neurobasal/B27, lower than cultures + + in serum-based media and offering an opportunity for improvement. + + NbActiv4 was formulated by addition of creatine, cholesterol and + + estrogen to Neurobasal/B27 that synergistically produced an eightfold + + increase in spontaneous spike activity. The increased activity with + + NbActiv4 correlated with a twofold increase in immunoreactive synaptophysin + + bright puncta and GluR1 total puncta. Characteristic of synaptic + + scaling, immunoreactive GABAAbeta puncta also increased 1.5-fold + + and NMDA-R1 puncta increased 1.8-fold. Neuron survival in NbActiv4 + + equaled that in Neurobasal/B27, but with slightly higher astroglia. + + Resting respiratory demand was decreased and demand capacity was + + increased in NbActiv4, indicating less stress and higher efficiency. + + These results show that NbActiv4 is an improvement to Neurobasal/B27 + + for cultured networks with an increased density of synapses and transmitter + + receptors which produces higher spontaneous spike rates in neuron + + networks.}, + doi = {10.1016/j.jneumeth.2008.01.009}, + institution = {Southern Illinois University School of Medicine, Springfield, IL + + 62794-9626, USA. gbrewer@siumed.edu}, + keywords = {Cell Survival; Cells, Cultured; Culture Media; Electrophysiology; + + Hippocampus, cytology; Humans; Image Processing, Computer-Assisted; + + Immunohistochemistry; Kinetics; Microelectrodes; Nerve Net, physiology; + + Neurons, physiology; Oxygen Consumption, physiology; Oxygen, analysis; + + Synapses, physiology}, + pii = {S0165-0270(08)00039-3}, + pmid = {18308400}, + timestamp = {09.02.26.19.31}, + url = {http://dx.doi.org/10.1016/j.jneumeth.2008.01.009} +} + diff --git a/testbib/testjabref_292.bib b/testbib/testjabref_292.bib new file mode 100644 index 00000000000..17979575c2d --- /dev/null +++ b/testbib/testjabref_292.bib @@ -0,0 +1,301 @@ +% This file was created with JabRef 2.9.2. +% Encoding: UTF8 + +@ARTICLE{Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS, + author = {Aziz, Joseph N. Y. and Abdelhalim, Karim and Shulyzki, Ruslana and + Genov, Roman and Bardakjian, Berj L. and Derchansky, Miron and Serletis, + Demitre and Carlen, Peter L.}, + title = {256-Channel Neural Recording and Delta Compression Microsystem With + 3D Electrodes}, + journal = {IEEE JOURNAL OF SOLID-STATE CIRCUITS}, + year = {2009}, + volume = {44}, + pages = {995-1005}, + number = {3}, + month = {MAR}, + abstract = {A 3D microsystem for multi-site penetrating extracellular neural recording + from the brain is presented. A 16 x 16-channel neural recording interface + integrated prototype fabricated in 0.35 mu m CMOS occupies 3.5 mm + x 4.5 mm area. Each recording channel dissipates 15 mu W of power + with input-referred noise of 7 mu V-rms over 5 kHz bandwidth. A switched-capacitor + delta read-out data compression circuit trades recording accuracy + for the output data rate. An array of 1.5 mm platinum-coated microelectrodes + is bonded directly onto the die. Results of in vitro experimental + recordings from intact mouse hippocampus validate the circuit design + and the on-chip electrode bonding technology.}, + address = {445 HOES LANE, PISCATAWAY, NJ 08855 USA}, + affiliation = {Aziz, JNY (Reprint Author), Broadcom, Irvine, CA 92617 USA. {[}Aziz, + Joseph N. Y.; Abdelhalim, Karim; Shulyzki, Ruslana; Genov, Roman] + Univ Toronto, Dept Elect \& Comp Engn, Toronto, ON M5S 3G4, Canada. + {[}Bardakjian, Berj L.] Univ Toronto, Inst Biomat \& Biomed Engn, + Edward S Rogers Sr Dept Elect \& Comp Engn, Toronto, ON M5S 1A4, + Canada. {[}Derchansky, Miron; Serletis, Demitre; Carlen, Peter L.] + Univ Toronto, Toronto Western Res Inst, Toronto, ON M5S 1A4, Canada. + {[}Derchansky, Miron; Serletis, Demitre; Carlen, Peter L.] Univ Toronto, + Dept Physiol, Toronto, ON M5S 1A4, Canada.}, + author-email = {roman@eecg.utoronto.ca}, + cited-references = {ATLURI S, 2006, P IEEE INT S CIRC SY, P1131. AZIZ J, 2006, P IEEE + INT S CIRC SY. AZIZ J, 2007, IEEE INT SOL STAT CI, P160. AZIZ JNY, + 2006, P IEEE INT S CIRC SY, P5075. AZIZ JNY, 2007, IEEE T BIOMED + CIRCUI, V1. AZIZ JNY, 2007, P IEEE INT S CIRC SY. CHAIMANONART N, + 2005, P ANN INT IEEE EMBS, P5194. DELBRUCK T, 1994, P IEEE INT S + CIRC SY, V4, P339. ENZ CC, 1996, P IEEE, V84, P1584. EVERSMANN B, + 2003, IEEE J SOLID-ST CIRC, V38, P2306, DOI 10.1109/JSSC.2003.819174. + HARRISON R, 2006, IEEE INT SOL STAT C, P2258. HARRISON RR, 2003, + IEEE J SOLID-ST CIRC, V38, P958, DOI 10.1009/JSSC.2003.811979. HARRISON + RR, 2007, IEEE CUST INTEGR CIR, P115. HEER F, 2006, IEEE J SOLID-ST + CIRC, V41, P1620, DOI 10.1109/JSSC.2006.873677. KIM S, 2006, P 2006 + INT C IEEE EN, P2986. MALLIK U, 2005, IEEE ISSCC, P362. MOHSENI P, + 2004, IEEE T BIO-MED ENG, V51, P832, DOI 10.1109/TBME.2004.824126. + MOTCHENBACHER CD, 1993, LOW NOISE ELECT SYST. OLSSON RH, 2005, IEEE + J SOLID-ST CIRC, V40, P2796. PATTERSON WR, 2004, IEEE T BIO-MED ENG, + V51, P1845, DOI 10.1109/TBME.2004.831521. RILEY G, 1987, SURFACE + MOUNT INT, P535. STEYAERT MSJ, 1987, IEEE J SOLID-ST CIRC, V22, P1163. + TSIVIDIS Y, 2003, OPERATION MODELING M. WATTANAPANITCH W, 2007, IEEE + T BIOMED CIRC S, V1, P136, DOI 10.1109/TBCAS.2007.907868. WISE KD, + 2005, IEEE ENG MED BIOL, V24, P22.}, + doc-delivery-number = {415FE}, + doi = {10.1109/JSSC.2008.2010997}, + file = {Draft:JabRef\\Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS_draft.pdf:PDF;Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS.pdf:JabRef\\Aziz2009256-ChannelNeuralRecordingandDeltaCompressionMicrosystemWith3DElectrodesIEEEJOURNALOFSOLID-STATECIRCUITS.pdf:PDF}, + issn = {0018-9200}, + journal-iso = {IEEE J. Solid-State Circuit}, + keywords = {Multi-channel recording; microelectrodes; extracellular recording; + electrode array; implantable; brain; hippocampus; delta compression; + neural amplifier}, + keywords-plus = {AMPLIFIER; STABILIZATION; CIRCUIT; ARRAY}, + language = {English}, + number-of-cited-references = {25}, + publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC}, + subject-category = {Engineering, Electrical \& Electronic}, + times-cited = {2}, + timestamp = {10.04.15.11.41}, + type = {Article}, + unique-id = {ISI:000263918900029} +} + +@ARTICLE{Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA, + author = {S. A. Baccus}, + title = {Synaptic facilitation by reflected action potentials: enhancement + of transmission when nerve impulses reverse direction at axon branch + points.}, + journal = {Proc Natl Acad Sci U S A}, + year = {1998}, + volume = {95}, + pages = {8345--8350}, + number = {14}, + month = {Jul}, + abstract = {A rapid, reversible enhancement of synaptic transmission from a sensory + neuron is reported and explained by impulses that reverse direction, + or reflect, at axon branch points. In leech mechanosensory neurons, + where one can detect reflection because it is possible simultaneously + to study electrical activity in separate branches, action potentials + reflected from branch points within the central nervous system under + physiological conditions. Synapses adjacent to these branch points + were activated twice in rapid succession, first by an impulse arriving + from the periphery and then by its reflection. This fast double-firing + facilitated synaptic transmission, increasing it to more than twice + its normal level. Reflection occurred within a range of resting membrane + potentials, and electrical activity produced by mechanical stimulation + changed membrane potential so as to produce and cease reflection. + A compartmental model was used to investigate how branch-point morphology + and electrical activity contribute to produce reflection. The model + shows that mechanisms that hyperpolarize the membrane so as to impair + action potential propagation can increase the range of structures + that can produce reflection. This suggests that reflection is more + likely to occur in other structures where impulses fail, such as + in axons and dendrites in the mammalian brain. In leech sensory neurons, + reflection increased transmission from central synapses only in those + axon branches that innervate the edges of the receptive field in + the skin, thereby sharpening spatial contrast. Reflection thus allows + a neuron to amplify synaptic transmission from a selected group of + its branches in a way that can be regulated by electrical activity.}, + file = {Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA.pdf:JabRef\\Baccus1998Synapticfacilitationbyreflectedactionpotentials--enhancementoftransmissionwhennerveimpulsesreversedirectionataxonbranchpoints.ProcNatlAcadSciUSA.pdf:PDF}, + institution = {Neuroscience Program, University of Miami, Miami, FL 33136, USA. + sbaccus@mednet.med.miami.edu}, + keywords = {Action Potentials, physiology; Animals; Axons, physiology; Electrophysiology; + Ganglia, Invertebrate, physiology; Ganglia, Sensory, physiology; + Leeches; Neurons, physiology; Synapses, physiology; Synaptic Transmission, + physiology}, + language = {eng}, + medline-pst = {ppublish}, + pmid = {9653189}, + timestamp = {11.05.01.13.02} +} + +@ARTICLE{BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering, + author = {B Balakrisnan , S Patil and E Smela}, + title = {Patterning PDMS using a combination of wet and dry etching}, + journal = {Journal of Micromechanics and Microengineering}, + year = {2009}, + volume = {19}, + pages = {047002}, + number = {4}, + abstract = {PDMS films of 10 �m thickness can be patterned within 30 min by combining + dry etching to achieve substantially vertical sidewalls with wet + etching to achieve high etch rates and to protect the underlying + substrate from attack. Dry etching alone would have taken 5 h, and + wet etching alone would produce severe undercutting. In addition, + using either technique alone produces undesirable surface morphologies. + The mask used during etching is critical to a successful patterning + outcome. E-beam evaporated Al was found to work well, adhering strongly + to oxygen-plasma-treated PDMS and holding up well during both dry + and wet etching. To prevent wrinkling of the PDMS, a fast deposition + rate should be used.}, + file = {BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering.pdf:JabRef\\BBalakrisnan2009PatterningPDMSusingacombinationofwetanddryetchingJournalofMicromechanicsandMicroengineering.pdf:PDF}, + timestamp = {09.06.17.13.03}, + url = {http://stacks.iop.org/0960-1317/19/i=4/a=047002} +} + +@ARTICLE{Brewer1997Isolationandcultureofadultrathippocampalneurons.JNeurosciMethods, + author = {G. J. Brewer}, + title = {Isolation and culture of adult rat hippocampal neurons.}, + journal = {J Neurosci Methods}, + year = {1997}, + volume = {71}, + pages = {143--155}, + number = {2}, + month = {Feb}, + abstract = {Inability to culture adult central neurons and the failure of injured + neurons to regenerate in the brain could be due to genetic controls + or environmental inhibitors. We tested the environmental inhibitor + hypothesis by attempting to regenerate adult rat neurons in B27/Neurobasal + culture medium, a medium optimized for survival of embryonic neurons. + To isolate neurons from their numerous connections, papain was the + best of six different proteases screened on slices of hippocampus + for survival of isolated cells after 4 days of culture. Use of a + density gradient enabled separation of oligodendroglia and some enrichment + of neurons and microglia from considerable debris which was inhibitory + to sprouting and viability. With these techniques, about 900000 viable + neurons were isolated from each hippocampus of any age rat from birth + to 24-36 months, near the median mortality. FGF2 was found to enhance + viability at least 3-fold to 40-80\%, independent of age, without + affecting the length of the processes. Neurons were cultured for + more than 3 weeks. These methods demonstrate that hippocampal neurons + can regenerate axons and dendrites if provided with adequate nutrition + and if inhibitors are removed. They also will enable aging studies. + Therefore, the concept of environmental growth restriction may be + more appropriate for neurons in the brain than the concept of a genetic + block that precludes regeneration of processes.}, + institution = {Department of Medical Microbiology and Immunology, Southern Illinois + University School of Medicine, Springfield 62794-1220, USA. gbrewer@siumed.edu}, + keywords = {Age Factors; Animals; Cell Adhesion, physiology; Cell Culture Techniques, + methods; Cell Separation, methods; Cell Survival, physiology; Cells, + Cultured; Cerebral Cortex, cytology; Dose-Response Relationship, + Drug; Fibroblast Growth Factor 2, physiology; Glutamic Acid, pharmacology; + Hippocampus, cytology; Male; Neurons, cytology/drug effects; Osmolar + Concentration; Oxygen, pharmacology; Papain; Rats; Rats, Inbred F344; + Rats, Sprague-Dawley}, + pii = {S0165-0270(96)00136-7}, + pmid = {9128149}, + timestamp = {09.02.26.19.31} +} + +@ARTICLE{Brewer1995Serum-freeB27/neurobasalmediumsupportsdifferentiatedgrowthofneuronsfromthestriatumsubstantianigraseptumcerebralcortexcerebellumanddentategyrus.JNeurosciRes, + author = {G. J. Brewer}, + title = {Serum-free B27/neurobasal medium supports differentiated growth of + neurons from the striatum, substantia nigra, septum, cerebral cortex, + cerebellum, and dentate gyrus.}, + journal = {J Neurosci Res}, + year = {1995}, + volume = {42}, + pages = {674--683}, + number = {5}, + month = {Dec}, + abstract = {Two fundamental questions about neuron cell culture were addressed. + Can one serum-free medium that was developed for optimum growth of + hippocampal neurons support the growth of neurons from other regions + of the brain? Is the region specific state of differentiation maintained + in culture? To answer these questions, we isolated neurons from six + other rat brain regions, placed them in culture in B27/Neurobasal + defined medium, and analyzed their morphology and growth dependence + on cell density after 4 days in culture. Neuronal identity was confirmed + by immunostaining with antibodies to neurofilament 200. Neurons from + each brain region maintained distinctive morphologies in culture + in the virtual absence of glia. Cells isolated from embryonic day + 18 cerebral cortex by digestion with papain showed the same high + survival as hippocampal neurons, e.g., 70\% survival for cells plated + at 160/mm2. At this age and density, neurons from the septum showed + slightly lower survival, 45\%. Survival of dentate granule neurons + from postnatal day four brains was 30-40\%, significantly lower, + and relatively independent of plating density. This suggests an absence + of dependence on trophic factors or contact for dentate granule neurons. + Growth of cerebellar granule neurons isolated from postnatal day + 7, 8, or 9 brains in B27/Neurobasal was compared to growth in BME/10\% + serum. Viability in serum-free medium at 4 days was much better than + that in serum, did not require KCl elevated to 25 mM, and occurred + without substantial growth of glia. Cerebellar granule neurons plated + at 1,280 cells/mm2 were maintained in culture for three weeks with + 17\% of the original cell density surviving. Survival of cells isolated + from embryonic day 18 substantia nigra was 50\% at 160 cells/mm2 + after 4 days, similar to that of striatum, but slightly less than + hippocampal neuron survival. The dopaminergic phenotype of the substantia + nigral neurons was maintained over 2 weeks in culture as judged by + immunoreactivity with antibodies to tyrosine hydroxylase. During + this time, immunoreactivity was found in the processes as they grew + out from the soma. Together, these studies suggest that B27/Neurobasal + will be a useful medium for maintaining the differentiated growth + of neurons from many brain regions. Potential applications of a common + growth medium for different neurons are discussed.}, + doi = {10.1002/jnr.490420510}, + institution = {Southern Illinois University School of Medicine, Springfield 62794-1220, + USA.}, + keywords = {Animals; Brain, anatomy /&/ histology/cytology/enzymology; Cell Culture + Techniques; Cell Survival; Cells, Cultured; Cerebellum, cytology/embryology; + Cerebral Cortex, cytology/embryology; Corpus Striatum, cytology/embryology; + Culture Media, Serum-Free; Dentate Gyrus, cytology/embryology; Electrophysiology; + Hippocampus, cytology/embryology; Neurofilament Proteins, metabolism; + Neurons, cytology/enzymology; Rats; Rats, Sprague-Dawley; Septum + Pellucidum, embryology; Substantia Nigra, cytology/embryology; Tyrosine + 3-Monooxygenase, metabolism}, + pmid = {8600300}, + timestamp = {2008.12.12}, + url = {http://dx.doi.org/10.1002/jnr.490420510} +} + +@ARTICLE{Brewer2008NbActiv4mediumimprovementtoNeurobasal/B27increasesneuronsynapsedensitiesandnetworkspikeratesonmultielectrodearrays.JNeurosciMethods, + author = {Gregory J Brewer and Michael D Boehler and Torrie T Jones and Bruce + C Wheeler}, + title = {NbActiv4 medium improvement to Neurobasal/B27 increases neuron synapse + densities and network spike rates on multielectrode arrays.}, + journal = {J Neurosci Methods}, + year = {2008}, + volume = {170}, + pages = {181--187}, + number = {2}, + month = {May}, + abstract = {The most interesting property of neurons is their long-distance propagation + of signals as spiking action potentials. Since 1993, Neurobasal/B27 + has been used as a serum-free medium optimized for hippocampal neuron + survival. Neurons on microelectrode arrays (MEA) were used as an + assay system to increase spontaneous spike rates in media of different + compositions. We find spike rates of 0.5 s(-1) (Hz) for rat embryonic + hippocampal neurons cultured in Neurobasal/B27, lower than cultures + in serum-based media and offering an opportunity for improvement. + NbActiv4 was formulated by addition of creatine, cholesterol and + estrogen to Neurobasal/B27 that synergistically produced an eightfold + increase in spontaneous spike activity. The increased activity with + NbActiv4 correlated with a twofold increase in immunoreactive synaptophysin + bright puncta and GluR1 total puncta. Characteristic of synaptic + scaling, immunoreactive GABAAbeta puncta also increased 1.5-fold + and NMDA-R1 puncta increased 1.8-fold. Neuron survival in NbActiv4 + equaled that in Neurobasal/B27, but with slightly higher astroglia. + Resting respiratory demand was decreased and demand capacity was + increased in NbActiv4, indicating less stress and higher efficiency. + These results show that NbActiv4 is an improvement to Neurobasal/B27 + for cultured networks with an increased density of synapses and transmitter + receptors which produces higher spontaneous spike rates in neuron + networks.}, + doi = {10.1016/j.jneumeth.2008.01.009}, + institution = {Southern Illinois University School of Medicine, Springfield, IL + 62794-9626, USA. gbrewer@siumed.edu}, + keywords = {Cell Survival; Cells, Cultured; Culture Media; Electrophysiology; + Hippocampus, cytology; Humans; Image Processing, Computer-Assisted; + Immunohistochemistry; Kinetics; Microelectrodes; Nerve Net, physiology; + Neurons, physiology; Oxygen Consumption, physiology; Oxygen, analysis; + Synapses, physiology}, + pii = {S0165-0270(08)00039-3}, + pmid = {18308400}, + timestamp = {09.02.26.19.31}, + url = {http://dx.doi.org/10.1016/j.jneumeth.2008.01.009} +} +