bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network-based inference from complex proteomic mixtures using SNIPE
Authors: Nusinow David P. , Kiezun Adam , O’Connell Daniel J. , Chick Joel M. , Yue Yingzi , Maas Richard L. , Gygi Steven P. , Sunyaev Shamil R. 
Published: October 2012

Abstract
Motivation: Proteomics presents the opportunity to provide novel insights about the global biochemical state of a tissue. However, a significant problem with current methods is that shotgun proteomics has limited success at detecting many low abundance proteins, such as transcription factors from complex mixtures of cells and tissues. The ability to assay for these proteins in the context of the entire proteome would be useful in many areas of experimental biology.
Results: We used network-based inference in an approach named SNIPE (Software for Network Inference of Proteomics Experiments) that selectively highlights proteins that are more likely to be active but are otherwise undetectable in a shotgun proteomic sample. SNIPE integrates spectral counts from paired case–control samples over a network neighbourhood and assesses the statistical likelihood of enrichment by a permutation test. As an initial application, SNIPE was able to select several proteins required for early murine tooth development. Multiple lines of additional experimental evidence confirm that SNIPE can uncover previously unreported transcription factors in this system. We conclude that SNIPE can enhance the utility of shotgun proteomics data to facilitate the study of poorly detected proteins in complex mixtures.
Availability and Implementation: An implementation for the R statistical computing environment named snipeR has been made freely available at http://genetics.bwh.harvard.edu/snipe/.
Contact: ssunyaev@rics.bwh.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments
Authors: Slater Alex W. , Castellanos Javier I. , Sippl Manfred J. , Melo Francisco 
Published: October 2012

Abstract
Motivation: Pairwise alignment of protein structures is a fundamental task in structural bioinformatics. There are numerous computer programs in the public domain that produce alignments for a given pair of protein structures, but the results obtained by the various programs generally differ substantially. Hence, in the application of such programs the question arises which of the alignment programs are the most trustworthy in the sense of overall performance, and which programs provide the best result for a given pair of proteins. The major problem in comparing, evaluating and judging alignment results is that there is no clear notion of the optimality of an alignment. As a consequence, the numeric criteria and scores reported by the individual structure alignment programs are largely incomparable.
Results: Here we report on the development and application of a new approach for the evaluation of structure alignment results. The method uses the translation vector and rotation matrix to generate the superposition of two structures but discards the alignment reported by the individual programs. The optimal alignment is then generated in standardized form based on a suitably implemented dynamic programming algorithm where the length of the alignment is the single most informative parameter. We demonstrate that some of the most popular programs in protein structure research differ considerably in their overall performance. In particular, each of the programs investigated here produced in at least in one case the best and the worst alignment compared with all others. Hence, at the current state of development of structure comparison techniques, it is advisable to use several programs in parallel and to choose the optimal alignment in the way reported here.
Availability and implementation: The computer software that implement the method described here is freely available at http://melolab.org/stovca.
Contact: fmelo@bio.puc.cl
TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis
Authors: Lin Yu , Rajan Vaibhav , Moret Bernard M. E. 
Published: October 2012

AbstractSummary: TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, through rearrangement operations, is modelled by the uniform Double-Cut-and-Join model. Using a true distance estimate under this model and simple distance-based methods, TIBA reconstructs a phylogeny of the input genomes. Unlike any previous tool for inferring phylogenies from rearrangement data, TIBA uses novel methods of robustness estimation to provide support values for the edges in the inferred tree.Availability: http://lcbb.epfl.ch/softwares/tiba.html.Contact: vaibhav.rajan@epfl.ch
A high-performance computing toolset for relatedness and principal component analysis of SNP data
Authors: Zheng Xiuwen , Levine David , Shen Jess , Gogarten Stephanie M. , Laurie Cathy , Weir Bruce S. 
Published: October 2012

Abstract
Summary: Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed gdsfmt and SNPRelate (R packages for multi-core symmetric multiprocessing computer architectures) to accelerate two key computations on SNP data: principal component analysis (PCA) and relatedness analysis using identity-by-descent measures. The kernels of our algorithms are written in C/C++ and highly optimized. Benchmarks show the uniprocessor implementations of PCA and identity-by-descent are ∼8–50 times faster than the implementations provided in the popular EIGENSTRAT (v3.0) and PLINK (v1.07) programs, respectively, and can be sped up to 30–300-fold by using eight cores. SNPRelate can analyse tens of thousands of samples with millions of SNPs. For example, our package was used to perform PCA on 55 324 subjects from the ‘Gene-Environment Association Studies’ consortium studies.
Availability and implementation: gdsfmt and SNPRelate are available from R CRAN (http://cran.r-project.org), including a vignette. A tutorial can be found at https://www.genevastudy.org/Accomplishments/software.
Contact: zhengx@u.washington.edu
GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies
Authors: Gogarten Stephanie M. , Bhangale Tushar , Conomos Matthew P. , Laurie Cecelia A. , McHugh Caitlin P. , Painter Ian , Zheng Xiuwen , Crosslin David R. , Levine David , Lumley Thomas , Nelson Sarah C. , Rice Kenneth , Shen Jess , Swarnkar Rohit , Weir Bruce S. , Laurie Cathy C. 
Published: October 2012

Abstract
Summary: GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R’s memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation.
Availability and implementation: GWASTools is implemented in R and is available from Bioconductor (http://www.bioconductor.org). An extensive vignette detailing a recommended work flow is included.
Contact: sdmorris@uw.edu
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
Authors: Sato Kengo , Kato Yuki , Akutsu Tatsuya , Asai Kiyoshi , Sakakibara Yasubumi 
Published: October 2012

Abstract
Motivation: It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a comparative approach that predicts a common secondary structure from aligned sequences is a better choice if homologous sequences with reliable alignments are available. However, correct secondary structure information is needed to produce reliable alignments of RNA sequences. To tackle this dilemma, we require a fast and accurate aligner that takes structural information into consideration to yield reliable structural alignments, which are suitable for common secondary structure prediction.
Results: We develop DAFS, a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment. DAFS decomposes the pairwise structural alignment problem into two independent secondary structure prediction problems and one pairwise (non-structural) alignment problem by the dual decomposition technique, and maintains the consistency of a pairwise structural alignment by imposing penalties on inconsistent base pairs and alignment columns that are iteratively updated. Furthermore, we extend DAFS to consider pseudoknots in RNA structural alignments by integrating IPknot for predicting a pseudoknotted structure. The experiments on publicly available datasets showed that DAFS can produce reliable structural alignments from unaligned sequences in terms of accuracy of common secondary structure prediction.
Availability: The program of DAFS and the datasets are available at http://www.ncrna.org/software/dafs/.
Contact: satoken@bio.keio.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Clinical comparison of the pneumatic and the combined lithotripters in percutaneous nephrolithotomy
Authors: Koc Gokhan , Akbay Kaan Esat , Tarhan Huseyin , Cakmak Ozgur , Yilmaz Yuksel 
Published: October 2012

AimTo compare the effectiveness of the pneumatic lithotripter and the combined lithotripter (pneumatic + ultrasonic) in percutaneous nephrolithotomy (PNL).Patients and MethodsA total of 150 patients who underwent PNL between March 2009 and January 2011 were included in the study. In the first 49 cases, only the pneumatic lithotripter (group 1) was used, while in the next 101 patients, combined lithotripter (group 2) was used. Differences with regard to total clearance time, fluoroscopic screening time (FST), duration of hospital stay, duration of nephrostomy removal, haematocrit loss, blood transfusion rate and successful treatment rate were investigated between the two groups.ResultsThe general characteristics of the patients were similar between the two groups. However, the mean stone size was statistically significantly higher in group 2. No statistically‐significant difference was detected between the two groups in terms of hospital stay, nephrostomy removal days, successful treatment rate and blood transfusion rate, but compared to group 1 patients, total clearance time, FST and haematocrit loss were significantly less in group 2.ConclusionAlthough pneumatic and ultrasonic lithotripters are both sufficiently effective when used separately, the combined device was observed to positively influence total clearance time, FST and haematocrit loss significantly.
Assessment of block height for satisfactory spinal anaesthesia for caesarean section
Authors: Ousley R. , Egan C. , Dowling K. , Cyna A. M. 
Published: October 2012

SummaryWe investigated block heights that anaesthetists considered adequate for caesarean section to proceed under spinal anaesthesia. During 3 months, 15 obstetric anaesthetists recorded block height to touch, pinprick or cold when spinal anaesthesia was considered satisfactory for caesarean section to proceed. Median (IQR [range]) block height for touch, pinprick, first cold and icy were: T10 (T7–T12 [T3–L1]); T5 (T4–T6 [C7–L1]); T5 (T4–T6 [C7–L1]); and T3 (T2–T4 [C7–L1]), respectively. Modalities were significantly correlated for: touch and cold, p = 0.0001; touch and icy, p = 0.0007; touch and pinprick, p = 0.0018; cold and icy, p < 0.0001; cold and pinprick, p = 0.0001; icy and pinprick, p < 0.0001. Pairwise comparisons showed differences between all modalities (p < 0.001) apart from pinprick and first cold (p = 0.94). All women had satisfactory anaesthesia despite 76 (81%) having a block to touch below T6. Single modality assessment of block height, particularly using touch, may erroneously indicate inadequate anaesthesia for caesarean section.
Modified patient‐controlled remifentanil bolus delivery regimen for labour pain*
Authors: Jost A. , Ban B. , Kamenik M. 
Published: October 2012

SummaryTo improve the analgesic efficiency and to simplify the administration of remifentanil for systemic analgesia in labour, we contrived a modified delivery regimen with a specific infusion profile and variable dosing and conducted a single‐blind randomised crossover study to compare it with the previous ‘classical’ regimen. Parturients received both regimens in interchangeable sets, each with five contractions. We compared pain and satisfaction scores, maternal and fetal vital parameters, side‐effects and other events. Twenty‐three parturients completed the study. No differences in observed parameters were noticed except for slightly lower blood pressure with the modified regimen. Pain estimates were lower in women starting with the modified regimen (p = 0.005), and there were fewer requests for analgesia within the lockout period (31 vs 69, p = 0.041) and bolus adjustments (0 vs 25, p < 0.001) with the modified regimen.
Thromboelastography to monitor the intra‐operative effects of low‐molecular weight heparin following bridging anticoagulation in a child with normal renal function*
Authors: Casey M. E. , Hodges O. , Dunn R. , Thomas J. 
Published: October 2012

SummaryPaediatric patients who require anticoagulation with therapeutic doses of low‐molecular weight heparin are at risk of having a residual anticoagulant effect at the time of surgery, even if managed according to current peri‐operative guidelines. Testing for residual effect is not currently recommended in such circumstances. A 15‐year‐old child with a mechanical aortic valve replacement requiring long‐term warfarin treatment, as well as underlying coagulation defects, was administered low‐molecular weight heparin for bridging anticoagulation before kyphoscoliosis surgery. Thromboelastography was used intra‐operatively to diagnose residual heparinisation, which was demonstrated by a prolonged reaction (R) time of 16.0 min in the plain cup, compared with 9.2 min in the heparinase cup. Subsequently, thromboelastography was also used to monitor haemostatic therapy, which consisted of protamine 2 mg.kg−1 and 500 IU cryoprecipitate. Thromboelastography was used intra‐operatively to allow rapid testing of coagulation status and guide therapy, thereby minimising use of blood products and reducing complications.
The effect of warm ischemia at uterus transplantation in a rat model
Authors: DÍAZ‐GARCÍA CÉSAR , AKHI SHAMIMA N. , MARTÍNEZ‐VAREA ALICIA , BRÄNNSTRÖM MATS 
Published: October 2012

AbstractObjective. Uterus transplantation (UTx) has been proposed as a method to treat women with absolute uterine factor infertility. The aim of this study was to evaluate the viability of the transplanted rat uterus after exposure to long warm ischemic times, in order to mimic a time frame likely to occur in a human situation during complicated pelvic vascular anastomosis surgery. Design. Experimental study. Setting. Obstetrics and Gynecology Department. Population. Female Lewis rats. Methods. Pseudopregnant rats were randomly allocated into two intervention groups, a standardized syngeneic UTx procedure (control; n = 10) and a modified UTx protocol with a four hour extended period of warm ischemia (n = 10). Main outcome measures. Scoring systems of gross morphology and histology at three and six days after transplantation. Results. Evident signs of necrosis were seen in five of 10 animals in the warm ischemia group compared with only one of 10 in the control group. Overall, uterine grafts from the warm ischemia group obtained poorer gross morphology scores. Histological findings correlated with the surgical findings at inspections three and six days after surgery. Conclusions. An extended warm ischemic time has detrimental effects on the survival of the uterus after transplantation.
Maternal inflammatory response to microbial invasion of the amniotic cavity: analyses of multiple proteins in the maternal serum
Authors: COBO TERESA , TSIARTAS PANAGIOTIS , KACEROVSKY MARIAN , HOLST ROSE‐MARIE , HOUGAARD DAVID M. , SKOGSTRAND KRISTIN , WENNERHOLM ULLA‐BRITT , HAGBERG HENRIK , JACOBSSON BO 
Published: October 2012

AbstractObjective. To evaluate the maternal inflammatory response to microbial invasion of the amniotic cavity (MIAC) in women with preterm labor and preterm prelabor rupture of membranes using selected proteins in the maternal serum. Design. A prospective cohort study. Setting. Labor ward from Salgrenska University Hospital. The evaluation of the maternal inflammatory response in the presence of MIAC in preterm labor and preterm prelabor rupture of membranes. Population. One hundred and sixteen women with preterm labor and 73 women with preterm prelabor rupture of membranes between the gestational ages of 22+0 and 33+6 weeks. Methods. Twenty‐seven maternal serum proteins were assayed by a multiple immunoassay. Main outcome measures. The maternal serum inflammatory response was evaluated according to the presence of MIAC. Data were stratified by gestational age. Results. There were few differences in the maternal serum protein levels when MIAC was present in both preterm labor and preterm prelabor rupture of membranes. In preterm prelabor rupture of membranes, higher levels of interleukin‐18 (median 654 vs. 361 pg/mL, p= 0.003) and lower levels of interleukin‐1β (9.5 vs. 19.9 pg/mL, p= 0.008) and monocyte chemotactic protein‐1 (139.1 vs. 212.6 pg/mL, p= 0.039) were observed in women with MIAC. Interleukin‐6 (20.8 vs. 13.9 pg/mL, p= 0.019) was the only biomarker that increased significantly in preterm labor complicated with MIAC. All of the differences between preterm labor and preterm prelabor rupture of membranes were observed at less than 32+0 weeks of gestation. Conclusions. A weak maternal inflammatory response in the serum was observed in women with MIAC.
Expressed breast milk for procedural pain in preterm neonates: a randomized, double‐blind, placebo‐controlled trial
Authors: Ou‐Yang Mei‐Chen , Chen I‐Lun , Chen Chih‐Cheng , Chung Mei‐Yung , Chen Feng‐Shun , Huang Hsin‐Chun 
Published: October 2012

AbstractAimTo determine whether expressed breast milk (milk) reduces procedural pain associated with heel lancing in preterm neonates.MethodsIn this placebo‐controlled trial, preterm neonates received 5 mL of distilled water as placebo (water, n = 44), 25% glucose water (glucose, n = 39) or milk (n = 40). Heel lancing was performed 2 min later. The primary outcome was the duration of first cry after lancing.ResultsParticipants had similar baseline demographic and clinical characteristics. There was a significant difference in the median duration of first cry among the groups: water = 70.5 sec [interquartile range (IQR) = 5.5–104.5]; glucose = 2.0 sec (IQR = 0.0–45.0); milk = 29.5 sec (IQR = 0.0–65.0). Specifically, the duration of first cry was significantly shorter in the glucose group compared with the water group (Bonferroni adjustment, p = 0.011). Pain scores were significantly lower in the glucose and milk groups compared with the water group 1, 2 and 3 min after heel lancing (p < 0.05).ConclusionsAlthough milk did not significantly reduce crying time, our finding that pain scores were significantly lower in the milk group suggests that milk may reduce pain associated with heel lancing in preterm neonates.
Sustained unemployment in psychiatric outpatients with bipolar depression compared to major depressive disorder with comorbid borderline personality disorder
Authors: Zimmerman Mark , Martinez Jennifer H , Young Diane , Chelminski Iwona , Dalrymple Kristy 
Published: October 2012

Zimmerman M, Martinez JH, Young D, Chelminski I, Dalrymple K. Sustained unemployment in psychiatric outpatients with bipolar depression compared to major depressive disorder with comorbid borderline personality disorder. Bipolar Disord 2012: 14: 856–862. © 2012 John Wiley & Sons A/S.Published by Blackwell Publishing Ltd.Objectives:  The morbidity associated with bipolar disorder is, in part, responsible for repeated calls for improved detection and recognition. No such clinical commentary exists for improved detection of borderline personality disorder in depressed patients. Clinical experience suggests that borderline personality disorder is as disabling as bipolar disorder; however, no studies have directly compared the two disorders. For this reason we undertook the current analysis from the Rhode Island Methods to Improve Diagnostic Assessment and Services (MIDAS) project comparing unemployment and disability rates in patients with bipolar disorder and borderline personality disorder.Methods:  Patients were interviewed with semi‐structured interviews. We compared three non‐overlapping groups of depressed patients: (i) 181 patients with DSM–IV major depressive disorder and borderline personality disorder, (ii) 1068 patients with major depressive disorder without borderline personality disorder, and (iii) 84 patients with bipolar depression without borderline personality disorder.Results:  Compared to depressed patients without borderline personality disorder, depressed patients with borderline personality disorder were significantly more likely to have been persistently unemployed. A similar difference was found between patients with bipolar depression and major depressive disorder without borderline personality disorder. No differences were found between patients with bipolar depression and depression with borderline personality disorder.Conclusions:  Both bipolar disorder and borderline personality disorder were associated with impaired occupational functioning and thus carry a significant public health burden. Efforts to improve detection of borderline personality disorder in depressed patients might be as important as the recognition of bipolar disorder.
Noradrenaline stimulates cell proliferation by suppressing potassium channels via Gi/o‐protein‐coupled α1B‐adrenoceptors in human osteoblasts
Authors: Kodama D , Togari A 
Published: October 2012

Background and PurposeRecent studies demonstrated that the sympathetic nervous system regulates bone metabolism via β2‐adrenoceptors. Although α‐adrenoceptors are also expressed in osteogenic cells, their functions in bone metabolism have been less studied. We previously demonstrated that noradrenaline suppressed potassium currents via α1B‐adrenoceptors in the human osteoblast SaM‐1 cell line. The aim of this study was to investigate the signal transduction pathway and the physiological role of noradrenaline in human osteoblasts in more detail.Experimental ApproachTo investigate signal transduction through α1B‐adrenoceptors, we used whole‐cell patch clamp recording and Ca fluorescence imaging. Potassium channels regulate membrane potential and cell proliferation activity in non‐excitable cells, so we evaluated cell proliferation activity by BrdU incorporation and WST assay.Key ResultsIn SaM‐1 cells, bath‐applied noradrenaline elevated intracellular Ca2+ concentration and this effect was abolished by both chloroethylclonidine, an α1B‐adrenoceptor antagonist, and U73122, a PLC inhibitor. However, the inhibitory effect of noradrenaline on whole‐cell current was unaffected by U73122. In contrast, in cells pretreated with either Pertussis toxin, a Gi/o‐protein‐coupled receptor inhibitor, or gallein, a Gβγ‐protein inhibitor, the inhibitory effect of noradrenaline on whole‐cell current was significantly suppressed. Noradrenaline‐induced enhancement of cell proliferation was inhibited by CsCl, a non‐selective potassium channel blocker, gallein and H89, a PKA inhibitor, but not by U73122.Conclusions and ImplicationsNoradrenaline facilitated cell proliferation by regulation of potassium currents in human osteoblasts via Gi/o‐protein‐coupled α1B‐adrenoceptors, not via coupling to Gq‐proteins.