bluuebunny/crossref_metadata_2025_split huggingface dataset:
Telmesani Radiological Classification of the Location of the Vertical Segment of the Facial Nerve: Impact on Surgical Approach in Cochlear Implant Surgery
Authors: Telmesani Laila Mohammed , Alrammah Mona Khalid 
Published: August 2017

Objective:
This study was conducted to establish a radiological classification of the location of the vertical segment of the facial nerve (VSFN) and to see if this has implications on the surgical technique needed to access the round window niche (RWN) in cochlear implant (CI) surgery.

Study Design:
Observational case series study.

Setting:
Tertiary referral center.

Patients:
One hundred twenty seven patients underwent CI surgery, and high resolution computed tomography (HRCT) of 140 temporal bones was studied. The data that were collected consisted of the patient's age, sex, radiological inner ear malformations (IEM), and the surgical technique used to access the RWN.

Main Outcome Measures:
The radiologic location of the VSFN in relation to the lateral semicircular canal in the coronal plane of HRCT and its implication on the surgical approach used to access the RWN in CI surgery.

Results:
A statistically significant association is present between the radiological location of the VSFN and the surgical approach used (p < 0.001).
There was insignificant correlation between the locations of the VSFN and the patient's age, sex, and IEM as the p > 0.05.

Conclusions:
On HRCT (0.6 mm) in the coronal plane, the position of the VSFN in relation to the lateral semicircular canal is correlated with the alternative approaches that must be taken during CI surgery.
Postoperative renal dysfunction after noncardiac surgery
Authors: Vaara Suvi T. , Bellomo Rinaldo 
Published: August 2017

Purpose of review
The narrative review aims to discuss recent results and important knowledge gaps regarding acute kidney injury (AKI) in postoperative patients undergone major noncardiac surgery.

Recent findings
Postoperative AKI affects approximately one-fifth of patients after major surgery, but the incidence varies according to the type of surgery. Preexisting chronic kidney disease is a major risk factor for postoperative AKI. It carries a substantial risk for postoperative adverse outcomes, as well as long-term mortality and morbidity. To prevent postoperative AKI, avoiding intraoperative hypotension and hypoperfusion as well as nephrotoxic substances are important. Currently, no efficient pharmacotherapy for prevention or treatment of AKI is available. In general, goal-directed management protocols have reduced the incidence of postoperative AKI. Additionally, a restrictive fluid management regimen might reduce organ edema and be beneficial also for the kidney function.

Summary
AKI is a frequent postoperative complication with a substantial risk for both short and long-term adverse events, and its incidence is likely to rise because of increasing major surgical procedures. Studies investigating better strategies to prevent and treat AKI in this population are urgently needed.
The Surgeon’s Fist with the Thumb Up to Guide the Design and Inset of the Osteoseptocutaneous Fibula Flap in Mandibular Reconstruction
Authors: AL Deek Nidal F. , Tsao Chung-Kan , Wei Fu-Chan 
Published: August 2017

Summary:
Successful reconstruction of an oromandibular defect with the osteoseptocutaneous fibula flap necessitates flawless design and inset, which is an experience-demanding endeavor. Laterality of the fibula flap has been thought to pose a certain challenge to reconstruction. To address this concern and guide flap design and inset, the authors proposed using the surgeon’s fist with the thumb up to replicate key anatomical landmarks of the fibula flap: the peroneal vessels and proximal bone end, and the posterior crural septum including the septal vessels, the skin, and the lateral surface of the fibula bone. This method facilities recipient vessels selection and skin paddle design, orientation, and inset to avoid complications regardless of laterality.
Smaller Diameter Anastomotic Coupling Devices Have Higher Rates of Venous Thrombosis in Microvascular Free Tissue Transfer
Authors: Hanson Summer E. , Mitchell Matthew B. , Palivela Nihanth , Peng S. Andrew , Feng Lei , Largo Rene D. , Butler Charles E. , Garvey Patrick B. 
Published: August 2017

Background:
Smaller anastomotic coupling devices may increase the risk of complications in free flap reconstructions; however, the relationship between coupler size and venous thrombosis rates has not been adequately evaluated. The authors hypothesized that smaller diameter coupling devices are associated with higher rates of venous thrombosis than larger diameter devices in free tissue transfer.

Methods:
The authors reviewed a prospectively maintained database for all patients who underwent microsurgical free tissue transfer at their institution from 2001 to 2013. The primary outcome measured was venous thrombosis, and the primary objective was to assess the relationship between venous coupler diameter and the rate of venous thrombosis. The secondary objective was to compare venous thrombosis rates between coupled and hand-sewn venous anastomoses.

Results:
A total of 5643 consecutive free flap reconstructions were evaluated; 3257 (57.7 percent) had coupled venous anastomoses. The 1.5-mm-diameter coupler had an overall thrombosis rate of 6.9 percent, significantly higher than that of all other coupler sizes (p = 0.04). In multivariable regression with generalized estimating equations analysis, both use of a 1.5-mm coupler (OR, 7.75; 95 percent CI, 3.20 to 18.76; p < 0.0001) and preoperative radiation therapy (OR, 1.62; 95 percent CI, 1.04 to 2.52; p = 0.03) were significant independent predictors of venous thrombosis.

Conclusions:
The authors found a significantly higher rate of venous thrombosis with the 1.5-mm-diameter coupler than with larger diameter devices or hand-sewn venous anastomoses. This evidence suggests that surgeons should choose an outflow vessel that does not require a coupler diameter smaller than 2.0 mm or perform a hand-sewn anastomosis in situations where this is not possible.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Upper Extremity Innervation Patterns and Clinical Implications for Nerve and Tendon Transfer
Authors: Lee Ellen Y. , Sebastin Sandeep J. , Cheah Andre , Kumar V. P. , Lim Aymeric Y. T. 
Published: August 2017

Background:
The authors previously studied the intramuscular innervation of 150 upper limb muscles and demonstrated that certain patterns of intramuscular innervation allowed muscles to be split into compartments with independent function. This study aims to determine the location, extramuscular course, and number of motor nerve branches of upper limb peripheral nerves. The authors want to combine this information with their previous work to create a blueprint of upper limb neuromuscular anatomy that would be useful in reconstructive surgery.

Methods:
Ten fresh frozen cadaveric upper limbs were dissected. The origin of branches from the peripheral nerve trunk, their course, and the number of motor nerves per muscle were determined. The authors reviewed all the images of the Sihler-stained muscles from their earlier study.

Results:
Motor nerve branches arise at the intersection of nerve trunk and muscle belly and are clustered near the origin of muscle groups. Two patterns of extramuscular innervation were noted, with one group having a single motor nerve and another group with consistently more than one motor nerve. A modified classification of muscles was proposed based on the orientation of muscle fibers to the long axis of the limb, the number of muscle compartments, and the number of heads of origin or the tendons of insertion.

Conclusions:
Motor nerve clusters can be located based on fixed anatomical landmarks. Muscles with multiple motor nerves have morphology that allows them to be split into individual compartments. The authors created a muscle and nerve blueprint that helps in planning nerve and split muscle transfers.
Analytical Validation of Multiplex Biomarker Assay to Stratify Colorectal Cancer Samples into Molecular Subtypes
Authors: Ragulan Chanthirika , Eason Katherine , Fontana Elisa , Nyamundanda Gift , Patil Yatish , Poudel Pawan , Lawlor Rita T. , Rio Maguy Del , Si-Lin Koo , Siew Tan Wah , Sclafani Francesco , Begum Ruwaida , Mendes Larissa S. Teixeira , Martineau Pierre , Scarpa Aldo , Tan Iain Beehuat , Cunningham David , Sadanandam Anguraj 
Published: August 2017

AbstractPreviously, we classified colorectal cancers (CRCs) into five CRCA subtypes with different prognoses and potential treatment responses, using a 786-gene signature. We merged our subtypes and those described by five other groups into four consensus molecular subtypes (CMS) that are similar to CRCA subtypes. Here we demonstrate the analytical development and application of a custom NanoString platform-based biomarker assay to stratify CRC into subtypes. To reduce costs, we switched from the standard protocol to a custom modified protocol (NanoCRCA) with a high Pearson correlation coefficient (>0.88) between protocols. Technical replicates were highly correlated (>0.96). The assay included a reduced robust 38-gene panel from the 786-gene signature that was selected using an in-laboratory developed computational pipeline of class prediction methods. We applied our NanoCRCA assay to untreated CRCs including fresh-frozen and formalin-fixed paraffin-embedded (FFPE) samples (n=81) with matched microarray or RNA-Seq profiles. We further compared the assay results with CMS classification, different platforms (microarrays/RNA-Seq) and gene-set classifiers (38 and 786 genes). NanoCRCA classified fresh-frozen samples (n=39; not including those showing a mixture of subtypes) into all five CRCA subtypes with overall high concordance across platforms (89.7%) and with CMS subtypes (84.6%), independent of tumour cellularity. This analytical validation of the assay shows the association of subtypes with their known molecular, mutational and clinical characteristics. Overall, our modified NanoCRCA assay with further clinical assessment may facilitate prospective validation of CRC subtypes in clinical trials and beyond.Novelty and ImpactWe previously identified five gene expression-based CRC subtypes with prognostic and potential predictive differences using a 786-gene signature and microarray platform. Subtype-driven clinical trials require a validated assay suitable for routine clinical use. This study demonstrates, for the first time, how molecular CRCA subtype can be detected using NanoString Technology-based biomarker assay (NanoCRCA) suitable for clinical validation. NanoCRCA is suitable for analysing FFPE samples, and this assay may facilitate patient stratification within clinical trials.
Whole Root Transcriptomic Analysis Reveals a Role for Auxin Pathways in Resistance toRalstonia solanacearumin Tomato
Authors: French Elizabeth , Kim Bong Suk , Rivera-Zuluaga Katherine , Iyer-Pascuzzi Anjali S. 
Published: August 2017

SummaryThe soilborne pathogenRalstonia solanacearumis the causal agent of bacterial wilt, and causes significant crop loss in the Solanaceae family. The pathogen first infects roots, which are a critical source of resistance in tomato (Solanum lycopersicumL.). Roots of both resistant and susceptible plants are colonized by the pathogen, yet rootstocks can provide significant levels of resistance. Currently, mechanisms of this ‘root-mediated resistance’ remain largely unknown. To identify the molecular basis of this resistance, we analyzed the genome-wide transcriptional response of roots of resistant (Hawaii 7996) and susceptible (West Virginia700) tomatoes at multiple time points after inoculation withR. solanacearum. We found that defense pathways in roots of the resistant Hawaii7996 are activated earlier and more strongly than roots of susceptible West Virginia700. Further, auxin signaling and transport pathways are suppressed in roots of the resistant variety. Functional analysis of an auxin transport mutant in tomato confirmed a role for auxin pathways in bacterial wilt. Together, our results suggest that roots mediate resistance toR. solanacearumthrough genome-wide transcriptomic changes that result in strong activation of defense genes and alteration of auxin pathways.
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments
Authors: Oliveira Francislon S. , Brestelli John , Cade Shon , Zheng Jie , Iodice John , Fischer Steve , Aurrecoechea Cristina , Kissinger Jessica C. , Brunk Brian P. , Stoeckert Christian J. , Fernandes Gabriel R. , Roos David S. , Beiting Daniel P. 
Published: August 2017

ABSTRACTMicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to constructin silicoexperiments using an intuitive graphical ‘strategy’ approach. The current release of the database integrates microbial census data with sample details for nearly 14,000 samples originating from human, animal and environmental sources, including over 9,000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate.
An atlas of genetic associations in UK Biobank
Authors: Canela-Xandri Oriol , Rawlik Konrad , Tenesa Albert 
Published: August 2017

ABSTRACTGenome-wide association studies have revealed many loci contributing to the variation of complex traits, yet the majority of loci that contribute to the heritability of complex traits remain elusive. Large study populations with sufficient statistical power are required to detect the small effect sizes of the yet unidentified genetic variants. However, the analysis of huge cohorts, like UK Biobank, is complicated by incidental structure present when collecting such large cohorts. For instance, UK Biobank comprises 107,162 third degree or closer related participants. Traditionally, GWAS have removed related individuals because they comprised an insignificant proportion of the overall sample size, however, removing related individuals in UK Biobank would entail a substantial loss of power. Furthermore, modelling such structure using linear mixed models is computationally expensive, which requires a computational infrastructure that may not be accessible to all researchers. Here we present an atlas of genetic associations for 118 non-binary and 599 binary traits of 408,455 related and unrelated UK Biobank participants of White-British descent. Results are compiled in a publicly accessible database that allows querying genome-wide association summary results for 623,944 genotyped and HapMap2 imputed SNPs, as well downloading whole GWAS summary statistics for over 30 million imputed SNPs from the Haplotype Reference Consortium panel. Our atlas of associations (GeneATLAS,http://geneatlas.roslin.ed.ac.uk) will help researchers to query UK Biobank results in an easy way without the need to incur in high computational costs.
Large-scale cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets
Authors: Lam Max , Trampush Joey W. , Yu Jin , Knowles Emma , Davies Gail , Liewald David C. , Starr John M. , Djurovic Srdjan , Melle Ingrid , Sundet Kjetil , Christoforou Andrea , Reinvang Ivar , DeRosse Pamela , Lundervold Astri J. , Steen Vidar M. , Espeseth Thomas , Räikkönen Katri , Widen Elisabeth , Palotie Aarno , Eriksson Johan G. , Giegling Ina , Konte Bettina , Roussos Panos , Giakoumaki Stella , Burdick Katherine E. , Payton Antony , Ollier William , Chiba-Falek Ornit , Attix Deborah K. , Need Anna C. , Cirulli Elizabeth T. , Voineskos Aristotle N. , Stefanis Nikos C. , Avramopoulos Dimitrios , Hatzimanolis Alex , Arking Dan E. , Smyrnis Nikolaos , Bilder Robert M. , Freimer Nelson A. , Cannon Tyrone D. , London Edythe , Poldrack Russell A. , Sabb Fred W. , Congdon Eliza , Conley Emily Drabant , Scult Matthew A. , Dickinson Dwight , Straub Richard E. , Donohoe Gary , Morris Derek , Corvin Aiden , Gill Michael , Hariri Ahmad R. , Weinberger Daniel R. , Pendleton Neil , Bitsios Panos , Rujescu Dan , Lahti Jari , Hellard Stephanie Le , Keller Matthew C. , Andreassen Ole A. , Deary Ian J. , Glahn David C. , Malhotra Anil K. , Lencz Todd 
Published: August 2017

AbstractNeurocognitive ability is a fundamental readout of brain function, and cognitive deficits are a critical component of neuropsychiatric disorders, yet neurocognition is poorly understood at the molecular level. In the present report, we present the largest genome-wide association studies (GWAS) of cognitive ability to date (N=107,207), and further enhance signal by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with cognitive ability, 34 of which were novel. A total of 350 genes were implicated, and this list showed significant enrichment for genes associated with Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis of gene results implicated the biological process of neurogenesis, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker; and LY97241, a potassium channel inhibitor. Transcriptome-wide analysis revealed that the implicated genes were strongly expressed in neurons, but not astrocytes or oligodendrocytes, and were more strongly associated with fetal brain expression than adult brain expression. Several tissue-specific gene expression relationships to cognitive ability were observed (for example, DAG1 levels in the hippocampus). Finally, we report novel genetic correlations between cognitive ability and disparate phenotypes such as maternal age at first birth and number of children, as well as several autoimmune disorders.
Impairment of zebrafish reproduction upon exposure to TDCPP
Authors: Liu Xiecheng , Jia Guofeng 
Published: August 2017

AbstractTDCPP is one of the most common organophosphate flame retardant, which has been widely used in many products. It has been detected in the environment and biota; however, its potential affect to the wildlife and human health remains largely unknown. In this study, we aimed to investigate the effect of long-term exposure to TDCPP on fish reproduction. Zebrafish eggs were treated with various concentration of TDCPP (0, 1, 10 and 100 μg/L) from 1 day post-fertilization (hpf) to 6 months. The fecundity of female fish was significantly decreased as indicated by reduced embryos production. The egg quality was decreased and the malformation rates were increased in the F1 generation. Taken together, long-term exposure to TDCPP affects the reproduction of zebrafish.
Genome-wide analysis of self-reported risk-taking behaviour and cross-disorder genetic correlations in the UK Biobank cohort
Authors: Strawbridge Rona J. , Ward Joey , Cullen Breda , Tunbridge Elizabeth M. , Hartz Sarah , Bierut Laura , Horton Amy , Bailey Mark E. S. , Graham Nicholas , Ferguson Amy , Lyall Donald M. , Mackay Daniel , Pidgeon Laura M. , Cavanagh Jonathan , Pell Jill P. , O’Donovan Michael , Escott-Price Valentina , Harrison Paul J. , Smith Daniel J. 
Published: August 2017

AbstractRisk-taking behaviour is a key component of several psychiatric disorders and could influence lifestyle choices such as smoking, alcohol use and diet. As a phenotype, risk-taking behaviour therefore fits within a Research Domain Criteria (RDoC) approach, whereby identifying genetic determinants of this trait has the potential to improve our understanding across different psychiatric disorders. Here we report a genome wide association study in 116 255 UK Biobank participants who responded yes/no to the question “Would you consider yourself a risk-taker?” Risk-takers (compared to controls) were more likely to be men, smokers and have a history of psychiatric disorder. Genetic loci associated with risk-taking behaviour were identified on chromosomes 3 (rs13084531) and 6 (rs9379971). The effects of both lead SNPs were comparable between men and women. The chromosome 3 locus highlightsCADM2, previously implicated in cognitive and executive functions, but the chromosome 6 locus is challenging to interpret due to the complexity of the HLA region. Risk-taking behaviour shared significant genetic risk with schizophrenia, bipolar disorder, attention deficit hyperactivity disorder and post-traumatic stress disorder, as well as with smoking and total obesity. Despite being based on only a single question, this study furthers our understanding of the biology of risk-taking behaviour, a trait which has a major impact on a range of common physical and mental health disorders.
Positively selected effector genes and their contribution to virulence in the smut fungusSporisorium reilianum
Authors: Schweizer Gabriel , Münch Karin , Mannhaupt Gertrud , Schirawski Jan , Kahmann Regine , Dutheil Julien Y. 
Published: August 2017

AbstractPlants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example are secreted fungal effector proteins and their host targets, which play an important role in pathogenic interactions. Biotrophic smut fungi (Basidiomycota) are well-suited to investigate the evolution of plant pathogens, because several reference genomes and genetic tools are available for these species. Here, we used the genomes ofSporisorium reilianumf. sp.zeaeandS. reilianumf. sp.reilianum, two closely related formae speciales infecting maize and sorghum, respectively, together with the genomes ofUstilago hordei,Ustilago maydisandSporisorium scitamineumto identify and characterize genes displaying signatures of positive selection. We identified 154 gene families having undergone positive selection during species divergence in at least one lineage, among which 77% were identified in the two investigated formae speciales ofS. reilianum. Remarkably, only 29% of positively selected genes encode predicted secreted proteins. We assessed the contribution to virulence of nine of these candidate effector genes inS. reilianumf. sp.zeaeby deleting individual genes, including a homologue of the effector genepit2previously characterized inU. maydis. Only thepit2deletion mutant was found to be strongly reduced in virulence. Additional experiments are required to understand the molecular mechanisms underlying the selection forces acting on the other candidate effector genes, as well as the large fraction of positively selected genes encoding predicted cytoplasmic proteins.