bluuebunny/crossref_metadata_2025_split huggingface dataset:
Barrier crossing in small avian migrants: individual tracking reveals prolonged nocturnal flights into the day as a common migratory strategy
Authors: Adamík Peter , Emmenegger Tamara , Briedis Martins , Gustafsson Lars , Henshaw Ian , Krist Miloš , Laaksonen Toni , Liechti Felix , Procházka Petr , Salewski Volker , Hahn Steffen 
Published: February 2016

AbstractOver decades it has been unclear how individual migratory songbirds cross large ecological barriers such as seas or deserts. By deploying light-level geolocators on four songbird species weighing only about 12 g, we found that these otherwise mainly nocturnal migrants seem to regularly extend their nocturnal flights into the day when crossing the Sahara Desert and the Mediterranean Sea. The proportion of the proposed diurnally flying birds gradually declined over the day with similar landing patterns in autumn and spring. The prolonged flights were slightly more frequent in spring than in autumn, suggesting tighter migratory schedules when returning to breeding sites. Often we found several patterns for barrier crossing for the same individual in autumn compared to the spring journey. As only a small proportion of the birds flew strictly during the night and even some individuals might have flown non-stop, we suggest that prolonged endurance flights are not an exception even in small migratory species. We emphasise an individual’s ability to perform both diurnal and nocturnal migration when facing the challenge of crossing a large ecological barrier to successfully complete a migratory journey.
Visualising the molecular alteration of the calcite (104) – water interface by sodium nitrate
Authors: Hofmann Sascha , Voïtchovsky Kislon , Spijker Peter , Schmidt Moritz , Stumpf Thorsten 
Published: February 2016

AbstractThe reactivity of calcite, one of the most abundant minerals in the earth’s crust, is determined by the molecular details of its interface with the contacting solution. Recently, it has been found that trace concentrations of NaNO3 severely affect calcite’s (104) surface and its reactivity. Here we combine molecular dynamics (MD) simulations, X-ray reflectivity (XR) and in situ atomic force microscopy (AFM) to probe the calcite (104) – water interface in the presence of NaNO3. Simulations reveal density profiles of different ions near calcite’s surface, with NO3− able to reach closer to the surface than CO32− and in higher concentrations. Reflectivity measurements show a structural destabilisation of the (104) surfaces’ topmost atomic layers in NaNO3 bearing solution, with distorted rotation angles of the carbonate groups and substantial displacement of the lattice ions. Nanoscale AFM results confirm the alteration of crystallographic characteristics, and the ability of dissolved NaNO3 to modify the structure of interfacial water was observed by AFM force spectroscopy. Our experiments and simulations consistently evidence a dramatic deterioration of the crystals’ surface, with potentially important implications for geological and industrial processes.
Alpha-synuclein: relating metals to structure, function and inhibition
Authors: McDowall J S , Brown D R 
Published: February 2016

Abstract
Alpha-synuclein has long been studied due to its involvement in the progression of Parkinson’s disease (PD), a common neurodegenerative disorder, although a consensus on the exact function of this protein is elusive. This protein shows remarkable structural plasticity and this property is important for both correct cellular function and pathological progression of PD. Formation of intracellular oligomeric species within the substantia nigra correlates with disease progression and it has been proposed that formation of a partially folded intermediate is key to the initiation of the fibrillisation process. Many factors can influence changes in the structure of alpha-synuclein such as disease mutations and interaction with metals and neurotransmitters. High concentrations of both dopamine and metals are present in the substantia nigra making this an ideal location for both the structural alteration of alpha-synuclein and the production of toxic oxygen species. The recent proposal that alpha-synuclein is a ferrireductase is important as it can possibly catalyse the formation of such reactive species and as a result exacerbate neurodegeneration.
Characterisation of high‐frequency modulator response via measurements of optical modulation sidebands
Authors: Ng W. , Sarkissian R. , Mahalingam H. 
Published: February 2016

The authors report an approach to characterise the radiofrequency (RF)‐response and bandwidth of photonic modulators by measuring their modulation sidebands in the optical domain. After taking into account the RF‐response measured independently for photodetectors, they demonstrated excellent agreement with swept‐frequency measurements over a broad frequency range of ∼6 to 40 GHz. They also evaluated the dynamic half‐wave voltage (Vπ) of a Mach–Zehnder (MZ) LiNbO3 modulator by modelling and measuring the asymmetry of its RF‐drive on the two MZ arms. Since there are no RF‐bandwidth constraints in the authors’ reported approach, the technique can be extended to measure the RF‐response of optical modulators at frequencies beyond those supported by microwave instrumentation such as network analysers.
Effect of bath temperature and concentration of buffer salt on the optoelectronic characteristics of CdS thin films synthesised by chemical bath deposition method
Authors: Kakhaki Zahra Makhdoumi , Youzbashi Amirali , Sangpour Parvaneh , Naderi Nima , Kazemzadeh Asghar 
Published: February 2016

CdS thin films were deposited onto glass substrate by the chemical bath deposition method, using cadmium chloride (CdCl2) as a source of cadmium, thiourea (CS(NH2)2) as a source of sulphur, ammonium nitrate (NH4NO3) as buffer salt and ammonia as pH controller and complexing agent. The effects of the deposition temperature and the concentration of ammonium nitrate on the structural, compositional, optical and optoelectrical properties of CdS thin films were investigated. The optimised sample was utilised for fabrication of photodetectors. A high photosensitivity and a short response time was reported for the photodetectors based on the sample with the bath temperature of 65°C and concentration of ammonium nitrate of 1.5 M compare with the other samples.
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM
Authors: Wong Alan S. L. , Choi Gigi C. G. , Cui Cheryl H. , Pregernig Gabriela , Milani Pamela , Adam Miriam , Perli Samuel D. , Kazer Samuel W. , Gaillard Aleth , Hermann Mario , Shalek Alex K. , Fraenkel Ernest , Lu Timothy K. 
Published: February 2016

Significance
The systematic discovery of new gene and drug combinations that modulate complex biological phenotypes and human diseases requires scalable and multiplexed screening technologies. We leverage the programmability of the CRISPR-Cas9 system for multiplexed targeting of specific genomic loci and the versatility of the combinatorial genetics en masse (CombiGEM) technology to rapidly assemble barcoded combinatorial genetic perturbation libraries that can be tracked with high-throughput sequencing. CombiGEM-CRISPR enables simple, massively parallel screening of barcoded combinatorial gene perturbations in human cells, and the translation of these hits into effective drug combinations. This approach is broadly applicable for performing pooled combinatorial genetic perturbations to map out how the orchestrated action of genes controls complex phenotypes and to translate these findings into novel drug combinations.
FastLSU: a more practical approach for the Benjamini–Hochberg FDR controlling procedure for huge-scale testing problems
Authors: Madar Vered , Batista Sandra 
Published: February 2016

AbstractMotivation: We address a common problem in large-scale data analysis, and especially the field of genetics, the huge-scale testing problem, where millions to billions of hypotheses are tested together creating a computational challenge to control the inflation of the false discovery rate. As a solution we propose an alternative algorithm for the famous Linear Step Up procedure of Benjamini and Hochberg.Results: Our algorithm requires linear time and does not require any P-value ordering. It permits separating huge-scale testing problems arbitrarily into computationally feasible sets or chunks. Results from the chunks are combined by our algorithm to produce the same results as the controlling procedure on the entire set of tests, thus controlling the global false discovery rate even when P-values are arbitrarily divided. The practical memory usage may also be determined arbitrarily by the size of available memory.Availability and implementation: R code is provided in the supplementary material.Contact: sbatista@cs.princeton.eduSupplementary information: Supplementary data are available at Bioinformatics online.
DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures
Authors: Wright Erik S. , Vetsigian Kalin H. 
Published: February 2016

Abstract
Summary: For numerous experimental applications, PCR primers must be designed to efficiently amplify a set of homologous DNA sequences while giving rise to amplicons with maximally diverse signatures. We developed DesignSignatures to automate the process of designing primers for high-resolution melting (HRM), fragment length polymorphism (FLP) and sequencing experiments. The program also finds the best restriction enzyme to further diversify HRM or FLP signatures. This enables efficient comparison across many experimental designs in order to maximize signature diversity.
Availability and implementation: DesignSignatures is accessible as a web tool at www.DECIPHER.cee.wisc.edu, or as part of the DECIPHER open source software package for R available from BioConductor.
Contact: kalin@discovery.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Characterization of clinical signs in the human interactome
Authors: Chagoyen Monica , Pazos Florencio 
Published: February 2016

Abstract
Motivation: Many diseases are related by shared associated molecules and pathways, exhibiting comorbidities and common phenotypes, an indication of the continuous nature of the human pathological landscape. Although it is continuous, this landscape is always partitioned into discrete diseases when studied at the molecular level. Clinical signs are also important phenotypic descriptors that can reveal the molecular mechanisms that underlie pathological states, but have seldom been the subject of systemic research. Here, we quantify the modular nature of the clinical signs associated with genetic diseases in the human interactome.
Results: We found that clinical signs are reflected as modules at the molecular network level, to at least to the same extent as diseases. They can thus serve as a valid complementary partition of the human pathological landscape, with implications for etiology research, diagnosis and treatment.
Contact: monica.chagoyen@cnb.csic.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data
Authors: Chen Jinyu , Zhang Shihua 
Published: February 2016

Abstract
Motivation: The underlying relationship between genomic factors and the response of diverse cancer drugs still remains unclear. A number of studies showed that the heterogeneous responses to anticancer treatments of patients were partly associated with their specific changes in gene expression and somatic alterations. The emerging large-scale pharmacogenomic data provide us valuable opportunities to improve existing therapies or to guide early-phase clinical trials of compounds under development. However, how to identify the underlying combinatorial patterns among pharmacogenomics data are still a challenging issue.
Results: In this study, we adopted a sparse network-regularized partial least square (SNPLS) method to identify joint modular patterns using large-scale pairwise gene-expression and drug-response data. We incorporated a molecular network to the (sparse) partial least square model to improve the module accuracy via a network-based penalty. We first demonstrated the effectiveness of SNPLS using a set of simulation data and compared it with two typical methods. Further, we applied it to gene expression profiles for 13 321 genes and pharmacological profiles for 98 anticancer drugs across 641 cancer cell lines consisting of diverse types of human cancers. We identified 20 gene-drug co-modules, each of which consists of 30 cell lines, 137 genes and 2 drugs on average. The majority of identified co-modules have significantly functional implications and coordinated gene-drug associations. The modular analysis here provided us new insights into the molecular mechanisms of how drugs act and suggested new drug targets for therapy of certain types of cancers.
Availability and implementation: A matlab package of SNPLS is available at http://page.amss.ac.cn/shihua.zhang/
Contact: zsh@amss.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Cosmopolitanism and Music in the Nineteenth Century
Authors: Magaldi Cristina 
Published: February 2016

Abstract
This essay explores cosmopolitanism during the nineteenth century, not merely as a concept intertwined with the nation-state, but rather as an experience shaped by shared perceptions of the world and shared views of modernity. It discusses the potential of the concept of a cosmopolitan cultural network during the nineteenth century, within and beyond Europe, to steer music historiography and critique away from a focus on issues of national identity and nationalistic music aesthetics. It argues that cosmopolitans from the margins of Europe expanded on European musics’ many aesthetic possibilities, while they problematized boundaries between local and universal, between originals and copies, between margins and centers, and ultimately between the European and the non-European.
Patterns of Food Consumption in Early Modern Iran
Authors: Matthee Rudolph 
Published: February 2016

Abstract
This article examines patterns of food consumption in early modern Iran from a historical perspective and in a global context. The discussion focuses on the period of the Safavid and the Qajar dynasties, or the early sixteenth to early twentieth centuries. The article first considers Iran’s cultural linkage to the world between the seventh-century Arab invasion and the advent of modern communications in relatively recent times. It then looks at the origins and movement of food in Iran before analyzing the diet of Iranians, especially fresh fruit and vegetables. It also explores regional variations in food consumption patterns in Iran and concludes with an overview of the changes that have occurred in food consumption patterns in the country since the 1960s.
The Mock Academic Faculty Position Competition: A Pilot Professional and Career Development Opportunity for Postdoctoral Fellows
Authors: Henderson Rita Isabel , Syed Naweed 
Published: February 2016

Problem
Medical educators face a dilemma in countries like Canada, where policy makers and strategic planners have prioritized highly qualified personnel and expanded recruitment of advanced trainees at a time when early-career specialists face prolonged job insecurity as they transition to professional employment. The University of Calgary Cumming School of Medicine hatched the Mock Academic Faculty Position competition to test the school’s existing capacity to address the pressing career development needs of highly trained graduates.

Approach
The competition was piloted in May–June 2014. Approximately 180 postdoctoral fellows were invited to compete; 34 submitted portfolios. The Postdoctoral Program Office established a longlist of 12 applicants. Through reviews, a selection committee identified 3 finalists to participate in a daylong event consisting of a research presentation and committee interview. The event was followed by approximately 70 audience members at any given time who were invited to complete anonymous evaluation forms and/or exit interviews.

Outcomes
The selection committee deduced a vast majority of applicants did not sell their skills effectively or demonstrate research programs independent from supervisors. Exit interviews conducted with 40 audience members indicated 36 (90%) picked the same finalist as the selection committee, 34 (85%) found the process “nerve racking,” and 28 (70%) had no previous idea of what goes on inside an academic committee interview.

Next Steps
A key recommendation for future iterations is early attention to systematizing feedback to ensure more direct impact for nonfinalists. Alternative initiatives for those gearing up for industry or public-sector work are being prepared.
Does a Weekly Didactic Conference Improve Resident Performance on the Pediatric Domain of the Orthopaedic In-Training Examination?
Authors: Franklin Corinna C. , Bosch Patrick P. , Grudziak Jan S. , Dede Ozgur , Ramirez Rey N. , Mendelson Steven A. , Ward W. Timothy , Brooks Maria , Kenkre Tanya , Lubahn John D. , Deeney Vincent F. , Roach James W. 
Published: February 2016

Background:
Performance on the Orthopaedic In-training Examination (OITE) has been correlated with performance on the written portion of the American Board of Orthopaedic Surgery examination. Herein we sought to discover whether adding a regular pediatric didactic lecture improved residents’ performance on the OITE’s pediatric domain.

Methods:
In 2012, a didactic lecture series was started in the University of Pittsburgh Medical Center (UPMC) Hamot Orthopaedic Residency Program (Hamot). This includes all topics in pediatric orthopaedic surgery and has teaching faculty present, and occurs weekly with all residents attending. A neighboring program [UMPC Pittsburgh (Pitt)] shares in these conferences, but only during their pediatric rotation. We sought to determine the effectiveness of the conference by comparing the historic scores from each program on the pediatric domain of the OITE examination to scores after the institution of the conference, and by comparing the 2 programs’ scores.

Results:
Both programs demonstrated improvement in OITE scores. In 2008, the mean examination score was 19.6±4.3 (11.0 to 30.0), and the mean percentile was 57.7±12.6 (32.0 to 88.0); in 2014, the mean examination score was 23.5±4.2 (14.0 to 33.0) and the mean percentile was 67.1±12.1 (40.0 to 94.0). OITE scores and percentiles improved with post graduate year (P<0.0001). Compared with the preconference years, Hamot residents answered 3.99 more questions correctly (P<0.0001) and Pitt residents answered 2.93 more questions correctly (P<0.0001). Before the conference, site was not a predictor of OITE score (P=0.06) or percentile (P=0.08); there was no significant difference found between the mean scores per program. However, in the postconference years, site did predict OITE scores. Controlling for year in training, Hamot residents scored higher on the OITE (2.3 points higher, P=0.003) and had higher percentiles (0.07 higher, P=0.004) than Pitt residents during the postconference years.

Conclusions:
This study suggests that adding a didactic pediatric lecture improved residents’ scores on the OITE and indirectly suggests that more frequent attendance is associated with better scores.

Level of Evidence:
Level III—retrospective case-control study.
Surgical Site Infections following Spine Surgery for Non-idiopathic Scoliosis
Authors: Salsgiver Elizabeth , Crotty Jennifer , LaRussa Samuel J. , Bainton Nicole M. , Matsumoto Hiroko , Demmer Ryan T. , Thumm Brian , Vitale Michael G. , Saiman Lisa 
Published: February 2016

Background:
Surgical site infections (SSIs) following spine surgery in children and adolescents with nonidiopathic scoliosis are associated with increased morbidity and health care costs. Potentially modifiable risk factors for SSIs merit additional study in this population.

Methods:
A single-center, retrospective cohort study was performed from August 2008 through December 2013 in children and adolescents undergoing surgery for nonidiopathic scoliosis to determine the trends in SSI rate and causative microorganisms. A standardized perioperative antimicrobial prophylaxis regimen was developed from September-October 2008. Potential risk factors for SSIs were assessed by multivariable analysis using Poisson regression models. Fusion procedures and growing construct procedures were analyzed separately.

Results:
In all, 268 patients underwent 536 surgical procedures of whom 192 underwent 228 fusion procedures, 89 underwent 308 growing construct procedures, and 13 underwent both procedures during the study period. Twenty-one SSIs (3.9% of surgical procedures and 7.8% of patients) occurred within 90 days of surgery, 17 SSIs occurred after fusion procedures (4.5% of procedures and 8.9% of patients), and 4 SSIs occurred after growing construct procedures (1.3% of procedures and 4.5% of patients). There were 9 polymicrobial SSIs (42.9%). Of the 31 bacterial pathogens isolated, 48% were Gram-negative organisms. Among patients undergoing fusion procedures, SSIs were associated with underdosing of preoperative cefazolin [relative risk (RR)=4.99; 95% confidence interval (CI), 1.89-17.43; P=0.012] and tobramycin (RR=5.86; 95% CI, 1.90-18.06; P=0.002), underdosing of intraoperative (RR=5.65; 95% CI, 2.13-14.97; P=0.001) and postoperative (RR=3.86; 95% CI, 1.20-12.40; P=0.023) tobramycin, and any preoperative or intraoperative underdosing (RR=4.89; 95% CI, 1.70-14.12; P=0.003), after adjustment for duration of surgery. No factors were associated with SSIs in those undergoing growing construct procedures. During the study period, the SSIs rate declined (P<0.0001).

Conclusions:
Underdosing of tobramycin and preoperative cefazolin were associated with an increased SSI risk among patients undergoing fusion procedures. Future multicenter studies should further investigate the generalizability of these findings.

Level of Evidence:
Level II—retrospective study.