bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substance use in individuals at clinical high risk of psychosis
Authors: Buchy L. , Cadenhead K. S. , Cannon T. D. , Cornblatt B. A. , McGlashan T. H. , Perkins D. O. , Seidman L. J. , Tsuang M. T. , Walker E. F. , Woods S. W. , Heinssen R. , Bearden C. E. , Mathalon D. , Addington J. 
Published: March 2015

BackgroundA series of research reports has indicated that the use of substances such as cannabis, alcohol and tobacco are higher in youth at clinical high risk (CHR) of developing psychosis than in controls. Little is known about the longitudinal trajectory of substance use, and findings on the relationship between substance use and later transition to psychosis in CHR individuals are mixed.MethodAt baseline and 6- and 12-month follow-ups, 735 CHR and 278 control participants completed the Alcohol and Drug Use Scale and a cannabis use questionnaire. The longitudinal trajectory of substance use was evaluated with linear mixed models.ResultsCHR participants endorsed significantly higher cannabis and tobacco use severity, and lower alcohol use severity, at baseline and over a 1-year period compared with controls. CHR youth had higher lifetime prevalence and frequency of cannabis, and were significantly younger upon first use, and were more likely to use alone and during the day. Baseline substance use did not differentiate participants who later transitioned to psychosis (n = 90) from those who did not transition (n = 272). Controls had lower tobacco use than CHR participants with a prodromal progression clinical outcome and lower cannabis use than those with a psychotic clinical outcome at the 2-year assessment.ConclusionsIn CHR individuals cannabis and tobacco use is higher than in controls and this pattern persists across 1 year. Evaluation of clinical outcome may provide additional information on the longitudinal impact of substance use that cannot be detected through evaluation of transition/non-transition to psychosis alone.
The pattern of support networks among the community dwelling elderly in urban Ireland: variations with mental disorder
Authors: Kirby Michael , Denihan Aisling , Bruce Irene , Coakley Davis , Lawlor Brian A 
Published: March 2015

AbstractObjectives: The changing family and social patterns in modern society are likely to influence the availability of informal support for older people. The aims of this study were to determine the support network distribution of a community dwelling elderly population in Dublin, and of those with mental disorders (dementia, depression and anxiety).Methods: Interviews with 1,001 community dwelling older people using GMS-AGECAT. In addition, a support network assessment instrument was administered, which identifies five different support network types. The local integrated and wider community focused networks are characterised by extensive community involvement, family dependent networks by close family support, and the local self contained and private restricted networks by low levels of family and community involvement.Results: Of the elderly population, 83% had support networks characterised by close community and/or family involvement. Subjects with cognitive impairment had lower levels of informal support from the community, as indicated by a lower proportion of local integrated (44% v 63%) and a higher proportion of private restricted (6% v 12%) networks. Late life depression was also associated with decreased levels of community integration.Conclusions: The elderly in Dublin appear to have high levels of informal support. The extensive support may be a factor in the lower rates of depression found in Dublin than in London and New York. While the overall level of informal support available to older people with mental disorders in the community remains high, a proportion have low levels of family and community involvement and consequently their mental health problems may go unrecognised.
Predictors of early vaginal stenosis during pelvic radiotherapy for locally advanced cervix cancer: a study from a tertiary cancer centre in Eastern India
Authors: Gangopadhyay Aparna , Biswas Jaydip 
Published: March 2015

AbstractAimTo explore possible predictors of early vaginal stenosis among patients with locally advanced cervix cancer on pelvic chemoradiation.Patients and methodsA total of 232 patients with locally advanced cervix cancer, who received pelvic radiotherapy at our institute from November 2011 to October 2013, were prospectively studied. Possible predictors chosen were age, tumour stage, initial vaginal involvement, concomitant chemotherapy and development of vaginitis of Radio Therapy Oncology Group grade 2 or more during radiotherapy. Multiple logistic regression was carried out to assess predictors and the relative risk of predictors was calculated.ResultsInitial vaginal involvement and addition of concomitant chemotherapy are predictors of early vaginal stenosis in locally advanced cervix cancer patients on pelvic chemoradiation. Relative risk for early vaginal stenosis with vaginal involvement at presentation was 16·31, whereas that for concomitant chemotherapy was 9·95.ConclusionAmong patients with locally advanced cervix cancer receiving pelvic chemoradiation, two factors, namely, initial vaginal involvement and concomitant chemotherapy are predictive of early vaginal stenosis. Patients with these factors should be assessed at regular intervals for early vaginal stenosis during pelvic chemoradiation to assess the optimal timing of intracavitary brachytherapy. This is particularly of importance in the absence of facilities for interstitial brachytherapy to ensure appropriate target coverage.
Impact of breathing on post-mastectomy radiotherapy: a dosimetric comparison between intensity-modulated radiotherapy and 3D tangential radiotherapy
Authors: Aaron J. , Sasidharan B. , Ebenezer S. , Thangakunam B. , Antonisamy B. , Selvamani B. 
Published: March 2015

AbstractPurposeTo quantify the effect of breathing motion on post-mastectomy radiotherapy with three-dimensional (3D) tangents and intensity-modulated radiotherapy (IMRT)Materials and methodsPatients trained for breath-hold underwent routine free breathing (FB) computed tomography (CT) simulation for radiotherapy as well as additional CT scans with breath held at the end of normal inspiration (NI scan) and expiration (NE scan) for study. The FB scan was used to develop both tangents and IMRT plans. To simulate breathing, each plan was copied and applied on NI and NE scans. The respiratory parameters of the patients as well as the dosimetric data with both the plans were analysed.ResultsBreathing motion resulted in mean fall in target coverage (V95) with IMRT by more than 5% when compared with tangents, and this effect significantly correlated with higher tidal volume. There was also a decrease in the mean target minimal dose by 20–25% with IMRT when compared with 10–12% with tangents, attributable to breathing motion. However, the cardiac dose crossed the limit (V25<10%) with breathing in the 3D tangents plan.ConclusionsDosimetric coverage of the chest wall is sensitive to breathing motion for the IMRT technique when compared with standard tangents, especially in patients with large tidal volume.
The environmental genomics of metazoan thermal adaptation
Authors: Porcelli D , Butlin R K , Gaston K J , Joly D , Snook R R 
Published: March 2015

AbstractContinued and accelerating change in the thermal environment places an ever-greater priority on understanding how organisms are going to respond. The paradigm of ‘move, adapt or die’, regarding ways in which organisms can respond to environmental stressors, stimulates intense efforts to predict the future of biodiversity. Assuming that extinction is an unpalatable outcome, researchers have focussed attention on how organisms can shift in their distribution to stay in the same thermal conditions or can stay in the same place by adapting to a changing thermal environment. How likely these respective outcomes might be depends on the answer to a fundamental evolutionary question, namely what genetic changes underpin adaptation to the thermal environment. The increasing access to and decreasing costs of next-generation sequencing (NGS) technologies, which can be applied to both model and non-model systems, provide a much-needed tool for understanding thermal adaptation. Here we consider broadly what is already known from non-NGS studies about thermal adaptation, then discuss the benefits and challenges of different NGS methodologies to add to this knowledge base. We then review published NGS genomics and transcriptomics studies of thermal adaptation to heat stress in metazoans and compare these results with previous non-NGS patterns. We conclude by summarising emerging patterns of genetic response and discussing future directions using these increasingly common techniques.
Limited role of functional differentiation in early diversification of animals
Authors: Knope M.L. , Heim N.A. , Frishkoff L.O. , Payne J.L. 
Published: March 2015

AbstractThe origin of most animal phyla and classes during the Cambrian explosion has been hypothesized to represent an ‘early burst’ of evolutionary exploration of functional ecological possibilities. However, the ecological history of marine animals has yet to be fully quantified, preventing an assessment of the early-burst model for functional ecology. Here we use ecological assignments for 18,621 marine animal genera to assess the relative timing of functional differentiation versus taxonomic diversification from the Cambrian to the present day. We find that functional diversity increased more slowly than would be expected given the history of taxonomic diversity. Contrary to previous inferences of rapid ecological differentiation from the early appearances of all well-fossilized phyla and classes, explicit coding of functional characteristics demonstrates that Cambrian genera occupied comparatively few modes of life. Functional diversity increased in the Ordovician and, especially, during the recoveries from the end-Permian and end-Cretaceous mass extinctions. Permanent shifts in the relationship between functional and taxonomic diversity following the era-bounding extinctions indicates a critical role for these biotic crises in coupling taxonomic and functional diversity.
Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells
Authors: Shibata Mikihiro , Uchihashi Takayuki , Ando Toshio , Yasuda Ryohei 
Published: March 2015

AbstractVisualization of morphological dynamics of live cells with nanometer resolution under physiological conditions is highly desired, but challenging. It has been demonstrated that high-speed atomic force microscopy is a powerful technique for visualizing dynamics of biomolecules under physiological conditions. However, application of high-speed atomic force microscopy for imaging larger objects such as live mammalian cells has been complicated because of the collision between the cantilever and samples. Here, we demonstrate that attaching an extremely long (~3 μm) and thin (~5 nm) tip by amorphous carbon to the cantilever allows us to image the surface structure of live cells with the spatiotemporal resolution of nanometers and seconds. We demonstrate that long-tip high-speed atomic force microscopy is capable of imaging morphogenesis of filopodia, membrane ruffles, pit formation and endocytosis in COS-7, HeLa cells and hippocampal neurons.
Generation of OAM waves with circular phase shifter and array of patch antennas
Authors: Wei Wenlong , Mahdjoubi Kourosh , Brousseau Christian , Emile Olivier 
Published: March 2015

The design of an ‘orbital angular momentum (OAM) antenna’ based on an original phase shifter and power divider combination at 2.5 GHz is presented. A prototype is manufactured and characterised based on return loss, radiation and phase patterns. Both simulation and experimental results evidence the properties of waves carrying OAM. This OAM antenna is simple, compact and easy to realise, which makes it suitable for radio communications and radar applications.
Noninvasive in vivo imaging reveals differences between tectorial membrane and basilar membrane traveling waves in the mouse cochlea
Authors: Lee Hee Yoon , Raphael Patrick D. , Park Jesung , Ellerbee Audrey K. , Applegate Brian E. , Oghalai John S. 
Published: March 2015

Significance
The membranes within the cochlea vibrate in response to sound. However, measuring these vibrations to study the sense of hearing has been a technological challenge because invasive techniques have been required. Herein, we describe a new technique capable of depth-resolved displacement measurements in 3D space with picometer sensitivity within the unopened mouse cochlea. We used this technique to make, to our knowledge, the first measurements of the tectorial membrane, the structure that overlies the sensory hair cell stereociliary bundles, within a healthy cochlea. We found that the tectorial membrane sustains traveling wave propagation differently than the more commonly measured basilar membrane. This finding provides a clearer understanding of the mechanical stimulus at the level of the inner hair cell responsible for non-linear sound encoding.
Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators
Authors: Yan Qinghong , Weyn-Vanhentenryck Sebastien M. , Wu Jie , Sloan Steven A. , Zhang Ye , Chen Kenian , Wu Jia Qian , Barres Ben A. , Zhang Chaolin 
Published: March 2015

Significance
Alternative splicing (AS) plays an important role in the mammalian brain, but our atlas of AS events is incomplete. Here, we conducted comprehensive analysis of deep RNA-Seq data of mouse cortex to identify new AS events and evaluate their functionality. We expanded the number of annotated AS events more than 10-fold and demonstrated that, like many known events, thousands of newly discovered events are regulated, conserved, and likely functional. In particular, some can regulate gene expression levels through nonsense-mediated decay, a known mechanism for RNA binding protein autoregulation. Surprisingly, we discovered a number of chromatin regulators as novel targets of this mechanism, revealing a new regulatory link between epigenetics and AS that primarily emerged in the mammalian lineage.
Reproductive Complexity in a Long‐Lived Deepwater Fish, the Blackgill Rockfish
Authors: Lefebvre Lyndsey S. , Field John C. 
Published: March 2015

AbstractFish populations are regulated by complex biological processes and ecosystem interactions. To inform stock assessments and management models, a clear understanding of a species’ reproductive biology is necessary, particularly in long‐lived species, for which estimates of sustainable yield are sensitive to such parameters. Deviations from traditional views of iteroparity in marine fishes (e.g., prolonged adolescent periods and skipped spawning) complicate estimates of maturity and, in turn, spawning output. The Blackgill Rockfish Sebastes melanostomus, an important component of California's commercial rockfish fishery, is a slow‐growing deepwater species whose population is currently thought to be increasing after being fished to below conservation target levels. The objectives of this study were to describe the annual reproductive cycle, update maturity estimates, and detect unusual patterns of ovarian development by using both macroscopic and histological methods. Females were collected between 2010 and 2013 at locations off central and southern California. The annual reproductive cycle was protracted: vitellogenesis was initiated 7 months prior to the first appearance of fertilized eggs, and parturition occurred in December–May. A prolonged adolescent period, potentially lasting up to 12 years, was characterized by the presence of previtellogenic secondary‐growth oocytes year‐round and abortive maturation events. The cold temperatures and low oxygen levels characteristic of the species’ habitat are hypothesized to be the main drivers behind this slow development. Macroscopic staging was found to be sufficient for maturity estimates when samples were temporally restricted. Estimates of length and age at 50% maturity were 33.6 cm and 25.7 years based on histological staging. Estimates of regional maturity based on commercial samples collected between 2001 and 2009 showed a trend of decreasing size at maturity with decreasing latitude. This study highlights the importance of histological examination in accurately assessing ovarian development and consequent baseline maturity information for managed fish populations.Received June 17, 2014; accepted December 16, 2014
Does Catch‐and‐Release Angling Alter the Behavior and Fate of Adult Atlantic Salmon During Upriver Migration?
Authors: Lennox Robert J. , Uglem Ingebrigt , Cooke Steven J. , Næsje Tor F. , Whoriskey Frederick G. , Havn Torgeir B. , Ulvan Eva M. , Solem Øyvind , Thorstad Eva B. 
Published: March 2015

AbstractTo reproduce, Atlantic Salmon Salmo salar return to freshwater rivers and migrate upriver to spawning areas. This migration is the basis for recreational fisheries, which for conservation reasons are increasingly characterized by catch‐and‐release angling. The effectiveness of catch and release for Atlantic Salmon conservation is contingent on the ability of individuals to recover from angling, resume migration, and reach spawning grounds at appropriate times. We monitored 27 caught and released Atlantic Salmon in River Gaula in 2013, a prominent and relatively pristine Norwegian river, by affixing external radio transmitters to them. Those fish were compared with a control group of 33 individuals caught and radio‐tagged at sea in bag nets before river entry. Whereas none of the control fish died during the study period, there were three mortalities among the caught‐and‐released fish (11%; significant difference). All mortalities were qualitatively associated with poor angler care, emphasizing the responsibility of anglers in practicing effective catch and release of Atlantic Salmon. Both control and caught and released Atlantic Salmon spent similar time resting below and in transiting a large natural barrier to migration, an 80‐m gorge. The angled and released Atlantic Salmon were distributed in similar locations throughout the river during the spawning season compared with control fish, but those caught and released later in the season appeared to migrate shorter total distances than control fish. Among the caught and released Atlantic Salmon, 17% were recaptured by anglers, which was similar to the rate of recapture of the control fish (21%). Ultimately, individual and population fitness was not likely to be significantly compromised as a result of catch and release because individuals were recorded in spawning areas at appropriate times. Catch and release can therefore be considered a tenable strategy for balancing the costs and benefits associated with the recreational fishery.Received September 26, 2014; accepted December 16, 2014
hiHMM: Bayesian non-parametric joint inference of chromatin state maps
Authors: Sohn Kyung-Ah , Ho Joshua W. K. , Djordjevic Djordje , Jeong Hyun-hwan , Park Peter J. , Kim Ju Han 
Published: March 2015

AbstractMotivation: Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications.Results: Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets.Conclusion: The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis.Availability and implementation: Source codes are available at https://github.com/kasohn/hiHMM. Chromatin data are available at http://encode-x.med.harvard.edu/data_sets/chromatin/.Contact: peter_park@harvard.edu or juhan@snu.ac.krSupplementary information: Supplementary data are available at Bioinformatics online.
IVA: accurate de novo assembly of RNA virus genomes
Authors: Hunt Martin , Gall Astrid , Ong Swee Hoe , Brener Jacqui , Ferns Bridget , Goulder Philip , Nastouli Eleni , Keane Jacqueline A. , Kellam Paul , Otto Thomas D. 
Published: March 2015

Abstract
Motivation: An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challenging due to the combination of viral population diversity and extremely uneven read depth caused by amplification bias in the inevitable reverse transcription and polymerase chain reaction amplification process of current methods.
Results: We developed a new de novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.
Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva
Contact: iva@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Mammalian genome evolution is governed by multiple pacemakers
Authors: Duchêne Sebastián , Ho Simon Y. W. 
Published: March 2015

Abstract
Genomic evolution is shaped by a dynamic combination of mutation, selection and genetic drift. These processes lead to evolutionary rate variation across loci and among lineages. In turn, interactions between these two forms of rate variation can produce residual effects, whereby the pattern of among-lineage rate heterogeneity varies across loci. The nature of rate variation is encapsulated in the pacemaker models of genome evolution, which differ in the degree of importance assigned to residual effects: none (Universal Pacemaker), some (Multiple Pacemaker) or total (Degenerate Multiple Pacemaker). Here we use a phylogenetic method to partition the rate variation across loci, allowing comparison of these pacemaker models. Our analysis of 431 genes from 29 mammalian taxa reveals that rate variation across these genes can be explained by 13 pacemakers, consistent with the Multiple Pacemaker model. We find no evidence that these pacemakers correspond to gene function. Our results have important consequences for understanding the factors driving genomic evolution and for molecular-clock analyses.
Availability and implementation: ClockstaR-G is freely available for download from github (https://github.com/sebastianduchene/clockstarg).
Contact: simon.ho@sydney.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.