bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering Designer Transcription Activator‐‐Like Effector Nucleases (TALENs) by REAL or REAL‐Fast Assembly
Authors: Reyon Deepak , Khayter Cyd , Regan Maureen R. , Joung J. Keith , Sander Jeffry D. 
Published: October 2012

AbstractEngineered transcription activator–like effector nucleases (TALENs) are broadly useful tools for performing targeted genome editing in a wide variety of organisms and cell types including plants, zebrafish, C. elegans, rat, human somatic cells, and human pluripotent stem cells. Here we describe detailed protocols for the serial, hierarchical assembly of TALENs that require neither PCR nor specialized multi‐fragment ligations and that can be implemented by any laboratory. These restriction enzyme and ligation (REAL)–based protocols can be practiced using plasmid libraries and user‐friendly, Web‐based software that both identifies target sites in sequences of interest and generates printable graphical guides that facilitate assembly of TALENs. With the described platform of reagents, protocols, and software, researchers can easily engineer multiple TALENs within 2 weeks using standard cloning techniques. Curr. Protoc. Mol. Biol. 100:12.15.1‐12.15.14. © 2012 by John Wiley & Sons, Inc.
Using Cell‐ID 1.4 with R for Microscope‐Based Cytometry
Authors: Bush Alan , Chernomoretz Ariel , Yu Richard , Gordon Andrew , Colman‐Lerner Alejandro 
Published: October 2012

AbstractThis unit describes a method for quantifying various cellular features (e.g., volume, total and subcellular fluorescence localization) from sets of microscope images of individual cells. It includes procedures for tracking cells over time. One purposely defocused transmission image (sometimes referred to as bright‐field or BF) is acquired to segment the image and locate each cell. Fluorescence images (one for each of the color channels to be analyzed) are then acquired by conventional wide‐field epifluorescence or confocal microscopy. This method uses the image‐processing capabilities of Cell‐ID and data analysis by the statistical programming framework R, which is supplemented with a package of routines for analyzing Cell‐ID output. Both Cell‐ID and the analysis package are open‐source. Curr. Protoc. Mol. Biol. 100:14.18.1‐14.18.26. © 2012 by John Wiley & Sons, Inc.
ChIP‐exo Method for Identifying Genomic Location of DNA‐Binding Proteins with Near‐Single‐Nucleotide Accuracy
Authors: Rhee Ho Sung , Pugh B. Franklin 
Published: October 2012

AbstractThis unit describes the ChIP‐exo methodology, which combines chromatin immunoprecipitation (ChIP) with lambda exonuclease digestion followed by high‐throughput sequencing. ChIP‐exo allows identification of a nearly complete set of the binding locations of DNA‐binding proteins at near‐single‐nucleotide resolution with almost no background. The process is initiated by cross‐linking DNA and associated proteins. Chromatin is then isolated from nuclei and subjected to sonication. Subsequently, an antibody against the desired protein is used to immunoprecipitate specific DNA‐protein complexes. ChIP DNA is purified, sequencing adaptors are ligated, and the adaptor‐ligated DNA is then digested by lambda exonuclease, generating 25‐ to 50‐nucleotide fragments for high‐throughput sequencing. The sequences of the fragments are mapped back to the reference genome to determine the binding locations. The 5′ ends of DNA fragments on the forward and reverse strands indicate the left and right boundaries of the DNA‐protein binding regions, respectively. Curr. Protoc. Mol. Biol. 100:21.24.1‐21.24.14. © 2012 by John Wiley & Sons, Inc.
Interaction of Carbon Coating on LiFePO4: A Local Visualization Study of the Influence of Impurity Phases
Authors: Wang Jiajun , Yang Jinli , Zhang Yong , Li Yongliang , Tang Yongji , Banis Mohammad Norouzi , Li Xifei , Liang Guoxian , Li Ruying , Sun Xueliang 
Published: October 2012

AbstractCarbon coating is a proven successful approach for improving the conductivity of LiFePO4 used in rechargeable Li‐ion batteries. Different impurity phases can be formed during LiFePO4 synthesis. Here, a direct visualization of the impact of impurity phases in LiFePO4 on a carbon coating is presented; they are investigated on a model material using various surface‐characterization techniques. By using polished ingot model materials, impurity phases can be clearly observed, identified, and located on the surface of the sample by scanning electron microscopy (SEM), focused‐ion‐beam lithography (FIB), high‐resolution transmission electron microscopy (HR‐TEM), and Raman spectroscopy. During the carbon‐coating process, the phosphorus‐rich phase is found to have an inhibiting effect (or no positive catalytic effect) on carbon formation, while iron‐rich phases (mainly iron phosphides) promote carbon growth by contributing to more carbon deposition and a higher graphitic carbon content. This finding, and the methodological evaluation here, will help us to understand and reveal the influencing factors of impurity phases on the basic carbon‐deposition process to obtain high‐performance LiFePO4 material for future energy‐storage devices.
Doping‐Induced Screening of the Built‐in‐Field in Organic Solar Cells: Effect on Charge Transport and Recombination
Authors: Armin Ardalan , Juska Gytis , Philippa Bronson W. , Burn Paul L. , Meredith Paul , White Ronald D. , Pivrikas Almantas 
Published: October 2012

AbstractWe report on the effects of screening of the electric field by doping‐induced mobile charges on photocurrent collection in operational organic solar cells. Charge transport and recombination were studied using double injection (DI) and charge extraction by linearly increasing voltage (CELIV) transient techniques in bulk‐heterojunction solar cells made from acceptor‐donor blends of poly(3‐n‐hexylthiophene):phenyl‐C61‐butyric acid methyl ester (P3HT:PC60BM). It is shown that the screening of the built‐in field in operational solar cells can be controlled by an external voltage while the influence on charge transport and recombination is measured. An analytical theory to extract the bimolecular recombination coefficient as a function of electric field from the injection current is also reported. The results demonstrate that the suppressed (non‐Langevin) bimolecular recombination rate and charge collection are not strongly affected by native doping levels in this materials combination. Hence, it is not necessary to reduce the level of doping further to improve the device performance of P3HT‐based solar cells.
Processing aids for biodegradable polymers
Authors: Jazrawi Bashar , Noroozi Nazbanoo , Ansari Mahmoud , Hatzikiriakos Savvas G. 
Published: October 2012

AbstractThe melt fracture behavior of several commercial polylactides (PLAs) and poly(ε‐caprolactone) (PCL) is investigated. PLAs and PCL with molecular weights greater than a certain value were found to exhibit melt fracture phenomena in capillary extrusion, which manifests itself as distortions on their surface once the extrusion rate exceeds a critical value. It was found that the addition of a small amount of PCL (typically 0.5 wt %) into the PLA and vice versa is effective in eliminating and delaying the onset of melt fracture to higher shear rates in the capillary extrusion of PLA and PCL, respectively. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Synthesis and characterization of organic/inorganic epoxy nanocomposites from poly(aminopropyl/phenyl)silsesquioxanes
Authors: Samthong Chavakorn , Laine Richard M. , Somwangthanaroj Anongnat 
Published: October 2012

AbstractOrganic/inorganic epoxy nanocomposites containing diglycidyl ether of bisphenol A (DGEBA), 4‐methylhexahydrophthalic anhydride (MHHPA) and poly(aminopropyl/phenyl) silsesquioxanes (PAPPS) were prepared and characterized. PAPPS were synthesized via fluoride‐catalyzed cage formation from random‐structured poly(phenyl)silsesquioxane (PPS) and 3‐aminopropyltriethoxysilane (APTES) in tetrahydrofuran (THF) using tetrabutylammonium fluoride (TBAF) catalyst containing substantial water. The PPS/APTES stoichiometric ratios were varied. The FTIR, 1H, solid‐state 29Si‐NMR studies show that PAPPS probably consists of cages, partial cages, and some linear structures containing phenyl and aminopropyl functional groups. The amine content was determined by back titration and elemental analysis. In comparison with neat epoxy, incorporation of these materials can improve the resultant thermal stabilities, raise glass transition temperatures (Tgs), and reduce coefficients of thermal expansion (CTEs) of epoxy nanocomposites as confirmed by TG/DTA, DMA and TMA tests, respectively. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Surgical stress after robot-assisted distal gastrectomy and its economic implications
Authors: Park J Y , Jo M J , Nam B-H , Kim Y , Eom B W , Yoon H M , Ryu K W , Kim Y-W , Lee J H 
Published: October 2012

Abstract

Background
There is a lack of reports evaluating the outcomes of robotic gastrectomy and conventional laparoscopic surgery. The aim of this study was to compare the surgical stress response and costs of robot-assisted distal gastrectomy (RADG) with those of laparoscopy-assisted distal gastrectomy (LADG).

Methods
This prospective study compared a cohort of patients who had RADG with a cohort that underwent conventional LADG for early gastric cancer between March 2010 and May 2011. The surgical outcomes including Eastern Cooperative Oncology Group performance status and complications, surgical stress response and overall costs were compared between the two groups.

Results
Thirty patients were enrolled in the RADG group and 120 in the LADG group. There were no conversions. Median duration of operation was longer in the RADG group (218 (interquartile range 200–254) versus 140 (118–175) min; P &lt; 0·001). Postoperative abdominal drain production was less (P = 0·001) and postoperative performance status was worse (P &lt; 0·001) in the RADG group. C-reactive protein (CRP) levels on postoperative days 1 and 3, and interleukin (IL) 6 level on the third postoperative day, were lower in the LADG compared with the RADG group (CRP: P = 0·002 and P = 0·014 respectively; IL-6: P &lt; 0·001). Costs for robotic surgery were much higher than for laparoscopic surgery (difference €3189).

Conclusion
RADG did not reduce surgical stress compared with LADG. The substantial RADG costs due to robotic system expenses may not be justified.
Surgical strategies for non-functioning pancreatic neuroendocrine tumours
Authors: Kim M J , Choi D W , Choi S H , Heo J S , Park H J , Choi K K , Jang K-T , Sung J-Y 
Published: October 2012

Abstract

Background
The purpose of this study was to identify management strategies for non-functioning pancreatic neuroendocrine tumours (NF-PNETs) by analysis of surgical outcomes at a single institution.

Methods
Archived records of patients with NF-PNETs who underwent surgery between 1994 and 2010 were reviewed.

Results
Among 125 patients, the median tumour size was 2·5 (range 0·15–20·5) cm. Of the 51 NF-PNETs with a diameter of no more than 2 cm, 12 (24 per cent) were diagnosed as carcinoma. Overall 20 patients (16·0 per cent) had metastases to the lymph nodes. The minimum size of the tumour with lymph node metastasis was 1·2 cm. Having a NF-PNET of 2 cm or larger significantly increased the probability of a poorly differentiated carcinoma (P = 0·006), and having a NF-PNET of at least 2·5 cm significantly increased the probability of lymph node metastasis (P = 0·048). The 5-year cumulative survival rate after curative resection was 89·7 per cent. During a median follow-up of 31·5 months, there were 27 recurrences (23·1 per cent) and 13 disease-specific deaths (11·1 per cent) among the 117 patients who had an R0 resection. All patients who underwent repeat operations were alive without additional recurrence after a mean(s.d.) follow-up of 27·1(18·0) months.

Conclusion
Curative surgery should be performed for control of primary NF-PNETs. Lymph node dissection for NF-PNETs of 2·5 cm or larger and at least node sampling for tumours with a diameter of 1 cm or more are recommended. Debulking surgery should be considered for advanced tumours.
External biliary drainage and liver regeneration after major hepatectomy
Authors: Otao R , Beppu T , Isiko T , Mima K , Okabe H , Hayashi H , Masuda T , Chikamoto A , Takamori H , Baba H 
Published: October 2012

Abstract

Background
Bile acid signalling and farnesoid X receptor activation are assumed to be essential for liver regeneration. This study was designed to investigate the association between serum bile acid levels and extent of liver regeneration after major hepatectomy.

Methods
Patients who underwent left- or right-sided hemihepatectomy between 2006 and 2009 at the authors' institution were eligible for inclusion. Patients were divided into two groups: those undergoing hemihepatectomy with external bile drainage by cystic duct tube (group 1) and those having hemihepatectomy without drainage (group 2). Serum bile acid levels were measured before and after hepatectomy. Computed tomography was used to calculate liver volume before hepatectomy and remnant liver volume on day 7 after surgery.

Results
A total of 46 patients were enrolled. Mean(s.d.) serum bile acid levels on day 3 after hemihepatectomy were significantly higher in group 2 than in group 1 (11·6(13·5) versus 2·7(2·1) µmol/l; P = 0·003). Regenerated liver volumes on day 7 after hepatectomy were significantly greater in group 2 138·1(135·9) ml versus 40·0(158·8) ml in group 1; P = 0·038). Liver regeneration volumes and rates on day 7 after hemihepatectomy were positively associated with serum bile acid levels on day 3 after hemihepatectomy (P = 0·006 and P &lt; 0·001 respectively). The incidence of bile leakage was similar in the two groups.

Conclusion
Initial liver regeneration after major hepatectomy was less after biliary drainage and was associated with serum bile acid levels. External biliary drainage should be used judiciously after liver resection.
KRAS status and outcome of liver resection after neoadjuvant chemotherapy including bevacizumab
Authors: Stremitzer S , Stift J , Gruenberger B , Tamandl D , Aschacher T , Wolf B , Wrba F , Gruenberger T 
Published: October 2012

Abstract

Background
The prognostic value of KRAS mutation in patients with colorectal cancer liver metastases (CLM) receiving neoadjuvant chemotherapy including bevacizumab before liver resection is unclear.

Methods
The KRAS and BRAF status of resected CLM was assessed in prospectively studied patients. Mutations were correlated with recurrence-free and overall survival. Only patients with remaining vital tumour cells in the resected specimen and those without disease progression were analysed; those with progressive disease did not undergo resection.

Results
A total of 60 patients were enrolled. Fifteen (25 per cent) had a KRAS mutation, but none of the 60 patients had a BRAF mutation. The radiological response to neoadjuvant chemotherapy including bevacizumab, assessed according to the Response Evaluation Criteria In Solid Tumours, was partial in 52 patients (87 per cent) and the remaining eight had stable disease. The partial response rate was similar in patients with a KRAS mutation and those with the wild-type gene (12 of 15 versus 40 of 45 patients; P = 0·400). KRAS mutation had a negative prognostic effect on recurrence-free survival (hazard ratio (HR) 2·48, 95 per cent confidence interval 1·26 to 4·89; P = 0·009) and overall survival (HR 3·51, 1·30 to 9·45; P = 0·013).

Conclusion
This study provided further evidence for the prognostic importance of KRAS status in terms of recurrence-free and overall survival. Neoadjuvant chemotherapy including bevacizumab elicited a response, irrespective of KRAS status, in this selected group of patients with CLM.
Effects of hybrid minimally invasive oesophagectomy on major postoperative pulmonary complications8
Authors: Briez N , Piessen G , Torres F , Lebuffe G , Triboulet J-P , Mariette C 
Published: October 2012

Abstract

Background
Morbidity after oesophageal cancer surgery remains high, mainly due to major postoperative pulmonary complications (MPPCs). The aim of this study was to test the hypothesis that hybrid minimally invasive oesophagectomy (HMIO) decreases the 30-day MPPC rate without compromising oncological outcomes.

Methods
Consecutive patients undergoing curative oesophagectomy for cancer by laparoscopic gastric mobilization and open thoracotomy (HMIO) between January 2004 and December 2009 were matched to randomly selected patients undergoing a totally open approach during the same study interval. Matching variables were age, sex, cancer stage, location of the primary tumour, histological subtype, American Society of Anesthesiologists grade, malnutrition, neoadjuvant chemoradiation and epidural analgesia.

Results
MPPCs at 30 days were significantly less frequent after HMIO compared with open surgery (15·7 versus 42·9 per cent; P &lt; 0·001). Postoperative in-hospital mortality and overall morbidity rates were 4·3 and 47·5 per cent respectively, again significantly lower in the HMIO group: 1·4 versus 7·1 per cent (P = 0·018) and 35·7 versus 59·3 per cent (P &lt; 0·001). In multivariable analysis, HMIO, adenocarcinoma subtype, epidural analgesia and surgery after 2006 were independent protective factors against MPPCs, and HMIO was independently protective against acute respiratory distress syndrome (ARDS). Lymph node yields and survival were similar in the two groups.

Conclusion
HMIO for oesophageal cancer, using laparoscopic gastric mobilization and open right thoracotomy, offered a substantial and independent protective effect against MPPCs, including ARDS, without compromising oncological outcomes.
Liquid chromatography and mass spectrometry of haem biosynthetic intermediates: a review
Authors: Benton Christopher M. , Lim Chang Kee 
Published: October 2012

ABSTRACTThis article discusses the separation, analysis and characterisation of intermediates and oxidative by‐products of the haem biosynthetic pathway by liquid chromatography and mass spectrometry. Techniques reviewed include high‐performance liquid chromatography, ultra‐high‐performance liquid chromatography, capillary electrophoresis, ion mobility spectrometry, mass spectrometry and tandem mass spectrometry. The emphasis was on the analysis of biological and clinical samples. Copyright © 2012 John Wiley & Sons, Ltd.
Two critical periods in early visual cortex during figure–ground segregation
Authors: Wokke Martijn E. , Sligte Ilja G. , Steven Scholte H. , Lamme Victor A. F. 
Published: October 2012

AbstractThe ability to distinguish a figure from its background is crucial for visual perception. To date, it remains unresolved where and how in the visual system different stages of figure–ground segregation emerge. Neural correlates of figure border detection have consistently been found in early visual cortex (V1/V2). However, areas V1/V2 have also been frequently associated with later stages of figure–ground segregation (such as border ownership or surface segregation). To causally link activity in early visual cortex to different stages of figure–ground segregation, we briefly disrupted activity in areas V1/V2 at various moments in time using transcranial magnetic stimulation (TMS). Prior to stimulation we presented stimuli that made it possible to differentiate between figure border detection and surface segregation. We concurrently recorded electroencephalographic (EEG) signals to examine how neural correlates of figure–ground segregation were affected by TMS. Results show that disruption of V1/V2 in an early time window (96–119 msec) affected detection of figure stimuli and affected neural correlates of figure border detection, border ownership, and surface segregation. TMS applied in a relatively late time window (236–259 msec) selectively deteriorated performance associated with surface segregation. We conclude that areas V1/V2 are not only essential in an early stage of figure–ground segregation when figure borders are detected, but subsequently causally contribute to more sophisticated stages of figure–ground segregation such as surface segregation.
Targeted proteomic dissection of Toxoplasma cytoskeleton sub‐compartments using MORN1
Authors: Lorestani Alexander , Ivey F. Douglas , Thirugnanam Sivasakthivel , Busby Michele A. , Marth Gabor T. , Cheeseman Iain M. , Gubbels Marc‐Jan 
Published: October 2012

AbstractThe basal complex in Toxoplasma functions as the contractile ring in the cell division process. Basal complex contraction tapers the daughter cytoskeleton toward the basal end and is required for daughter segregation. We have previously shown that the protein MORN1 is essential for basal complex assembly and likely acts as a scaffolding protein. To further our understanding of the basal complex, we combined subcellular fractionation with an affinity purification of the MORN1 complex and identified its protein composition. We identified two new components of the basal complex, one of which uniquely associated with the basal complex in mature parasites, the first of its kind. In addition, we identified several other novel cytoskeleton proteins with different spatiotemporal dynamics throughout cell division. Since many of these proteins are unique to Apicomplexa this study significantly contributes to the annotation of their unique cytoskeleton. Furthermore, we show that G‐actin binding protein TgCAP is localized at the apical cap region in intracellular parasites, but quickly redistributes to a cytoplasmic localization pattern upon egress. © 2012 Wiley Periodicals, Inc.
Polar expansion during cytokinesis
Authors: Gudejko Heather F.M. , Alford Lea M. , Burgess David R. 
Published: October 2012

AbstractVesicle trafficking and new membrane addition at the cleavage furrow have been extensively documented. However, less clear is the old idea that expansion at the cell poles occurs during cytokinesis. We find that new membrane is added to the cell poles during anaphase, causing the plasma membrane to expand coincident with the constriction of the contractile ring and may provide a pushing force for membrane ingression at the furrow. This membrane addition occurs earlier during mitosis than membrane addition at the furrow and is dependent on actin and astral microtubules. The membrane that is added at the polar regions is compositionally distinct from the original cell membrane in that it is devoid of GM1, a component of lipid rafts. These findings suggest that the growth of the plasma membrane at the cell poles during cell division is not due to stretching as previously thought, but due to the addition of compositionally unique new membrane. © 2012 Wiley Periodicals, Inc
Quantification of MAP and molecular motor activities on geometrically controlled microtubule networks
Authors: Portran Didier , Gaillard Jeremie , Vantard Marylin , Thery Manuel 
Published: October 2012

AbstractThe spatial organization of the microtubule (MT) network directs cell polarity and mitosis. It is finely regulated by hundreds of different types of microtubule‐associated proteins and molecular motors whose specific functions are difficult to investigate directly in cells. Here, we have investigated their functions using geometrically controlled MT networks in vitro in cell‐free assay. This was achieved by developing a new method to spatially define MT nucleation using MT microseeds adsorbed on a micropatterned glass substrate. This method could be used to control MT growth and the induction of complex MT networks. We selected the interaction of two radial arrays of dynamic and polarized MTs to analyze the formation of the central antiparallel MT bundle. We investigated the effects of the MT cross‐linker anaphase spindle elongation 1 (Ase1) and the kinesin motor Klp2, which are known to regulate MT organization in the spindle midzone. We thus identified the respective roles of each protein and revealed their synergy on the establishment of stable antiparallel MT bundles by quantifying MT interactions over hundreds of comparable MT networks. © 2012 Wiley Periodicals, Inc