bluuebunny/crossref_metadata_2025_split huggingface dataset:
SUPPA2 provides fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
Authors: Trincado Juan L. , Entizne Juan C. , Hysenaj Gerald , Singh Babita , Skalic Miha , Elliott David J. , Eyras Eduardo 
Published: November 2016

AbstractDespite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method for differential splicing analysis that addresses these challenges and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data SUPPA2 achieves higher accuracy compared to other methods; especially at low sequencing depth and short read length, with important implications for cost-effective use of RNA-seq for splicing; and was able to identify novel Transformer2-regulated exons. We further analyzed two differentiation series to support the applicability of SUPPA2 beyond binary comparisons. This identified clusters of alternative splicing events enriched in microexons induced during differentiation of bipolar neurons, and a cluster enriched in intron retention events that are present at late stages during erythroblast differentiation. Our data suggest that SUPPA2 is a valuable tool for the robust investigation of the biological complexity of alternative splicing.
Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples
Authors: Shokralla Shadi , F. Gibson Joel , King Ian , J. Baird Donald , H. Janzen Daniel , Hallwachs Winnie , Hajibabaei Mehrdad 
Published: November 2016

ABSTRACTEnvironmental DNA analysis using PCR amplified marker genes has been a key application of high-throughput sequencing (HTS). However, PCR bias is a major drawback to gain accurate qualitative and quantitative biodiversity data. We developed a PCR-free approach using enrichment baits for species-specific mitochondrial cytochrome c oxidase 1(COI) DNA barcodes. The sequence capture was tested on species-rich bulk terrestrial and aquatic benthic samples. Hybridization capture recovered an average of 6 and 4.7 more arthropod orders than amplicon sequencing for terrestrial and benthic samples, respectively. For the terrestrial sample, the four most abundant arthropod orders comprised 94.0% of the sample biomass. These same four orders comprised 95.5% and 97.5% of the COI sequences recovered by amplification and capture, respectively. Hybridization capture recovered three arthropod orders that were detected by biomass analysis, but not by amplicon sequencing and two other insect orders that were not detected by either biomass or amplicon methods. These results indicate the advantage of using sequence capture for a more accurate analysis of biodiversity in bulk environmental samples. The protocol can be easily customized to other DNA barcode markers or gene regions of interest for a wide range of taxa or for a specific target group.
Sexual selection can both increase and decrease extinction probability: reconciling demographic and evolutionary factors
Authors: Martínez‐Ruiz Carlos , Knell Robert J. 
Published: November 2016

Summary

Previous theoretical models of the effect of sexual selection on average individual fitness in a population have mostly predicted that sexually selected populations should adapt faster and clear deleterious mutations more quickly than populations where sexual selection is not operating.

While some laboratory studies have supported these predictions, others have not and studies of field systems have tended to find negative effects of sexual selection, or no effect. The negative effects of sexual selection found in field and other studies are usually ascribed to the costs associated with strong sexual selection acting on the population.

Here, using an individual‐based model that allows feedback between demographic and evolutionary processes, we find that sexual selection can lead to both increases and decreases in population‐level fitness measures such as extinction probability and adaptation rate. Whether fitness increases or decreases depends on a variety of environmental and demographic factors including the nature of environmental change, the carrying capacity of the environment, the average fecundity of the population in question and the strength of condition dependence.

In many cases, our model predicts that sexual selection leads to higher extinction probability in small populations because of an increased risk of demographic stochasticity, but lower extinction probability in larger populations because of faster adaptation rates. This is consistent with field studies that have mostly focussed on very small populations such as recently introduced birds, and tend to find negative effects, and also with laboratory studies that tend to use larger populations and have tended to find positive effects.

These findings go at least some way towards an understanding of the apparent contradictions between theoretical predictions, laboratory studies and field data.
Technologies of Translocality: Vegetables, Meat and Dresses in Arab Muslim Detroit
Authors: Kinder Kimberley 
Published: November 2016

AbstractThe diversification of US suburbs in terms of race, ethnicity and immigration has created invaluable opportunities for scholars to study technologies of translocality‐in‐the‐making. Translocal landscapes are described as spaces of ‘here' studded with ‘parts of elsewhere' (Allen and Cochrane, )—but which pieces of the landscape count as meaningfully ‘of elsewhere', how do those parts get there, and what range of meanings can they signify? This article is based on qualitative, in‐depth interviews and explores these questions in the context of an Arab Muslim ethnic enclave and retail district in an inner‐ring suburb of Detroit. The findings indicate that ‘parts of elsewhere' are more internally pluralized, multifunctional, multidirectional and aesthetically diverse than commonly recognized. The implications of these findings challenge scholars to develop more robust frameworks to explain how translocal geographies are produced, why they matter, and how they can be recognized.
Organizational Factors Affect Safety‐Net Hospitals’ Breast Cancer Treatment Rates
Authors: Bickell Nina A. , Moss Alexandra DeNardis , Castaldi Maria , Shah Ajay , Sickles Alan , Pappas Peter , Lewis Theophilus , Kemeny Margaret , Arora Shalini , Schleicher Lori , Fei Kezhen , Franco Rebeca , McAlearney Ann Scheck 
Published: November 2016

ObjectiveTo identify key organizational approaches associated with underuse of breast cancer care.SettingNine New York City area safety‐net hospitals.Study DesignMixed qualitative–quantitative, cross‐sectional cohort.MethodsWe used qualitative comparative analysis (QCA) of key stakeholder interviews, defined organizational “conditions,” calibrated conditions, and identified solution pathways. We defined underuse as no radiation after lumpectomy in women <75 years or mastectomy in women with ≥4 positive nodes, or no systemic therapy in women with tumors ≥1 cm. We used hierarchical models to assess organizational and patient factors’ impact on underuse.Principal FindingsUnderuse varied by hospital (8–29 percent). QCA found lower underuse sites designated individuals to track and follow‐up no‐shows; shared clinical information during handoffs; had fully integrated electronic medical records enabling transfer of responsibility across specialties; had strong system support; allocated resources to cancer clinics; had a patient‐centered culture paying close organizational attention to clinic patients. High underuse sites lacked these characteristics. Multivariate modeling found that hospitals with strong approaches to follow‐up had low underuse rates (RR = 0.28; 0.08–0.95); individual patient characteristics were not significant.ConclusionsAt safety‐net hospitals, underuse of needed cancer therapies is associated with organizational approaches to track and follow‐up treatment. Findings provide varying approaches to safety nets to improve cancer care delivery.
Sibship Analysis Based on Parental Genotype Reconstruction from Any Number of Reference Siblings
Authors: Huang Jian , Huang YuSong 
Published: November 2016

AbstractPrevious analyses of alleged siblings have calculated the conditional probability of a test sibling's genotype given a reference sibling's genotype; however, more genetic information is available when two or more reference siblings are tested. Based on the root concept of identity by descent (IBD), we present a sibship method of parental genotype reconstruction (PGR) that can use any number of reference sibs. Nine PGR patterns, along with their respective IBD proportions of full‐sibs and half‐sibs, were identified and used to calculate joint sibship probabilities and likelihood ratio formulas. In addition, a correction PGR was developed for situations involving the same genotype repeating in the reference sibs. The method is simple and can be applied to any number of alleged full or half‐siblings.
Computational Study of Fracture Characteristics in Infant Skulls Using a Simplified Finite Element Model
Authors: Jiang Binhui , Zhu Feng , Cao Libo , Presley Barbara R. , Shen Ming , Yang King H. 
Published: November 2016

AbstractSkull fracture characteristics are associated with loading conditions (such as the impact point and impact velocity) and could provide indication of abuse or accident‐induced head injuries. However, correlations between fracture characteristics and loading conditions in infant and toddler are ill‐understood. A simplified computational model representing an infant head was built to simulate skull responses to blunt impacts. The fractures were decided through a first principal strain‐based element elimination strategy. Simulation results were qualitatively compared with test data from porcine heads. This simplified model well captured the fracture pattern, initial fracture position, and direction of fracture propagation. The model also very well described fracture characteristics found in studies with human infant cadaveric specimens. A series of parametric studies was conducted, and results indicated that the parameters studied had substantial effects on fracture patterns. Additionally, the jagged shapes of sutures were associated with strain concentrations in the skull.
Characterization of hangover following intravenous alcohol exposure in social drinkers: methodological and clinical implications
Authors: Vatsalya Vatsalya , Stangl Bethany L. , Schmidt Veronica Y. , Ramchandani Vijay A. 
Published: November 2016

AbstractHangover refers to the cluster of physiological and behavioral symptoms that occur following the end of a drinking episode. While hangover has been studied after the typical oral consumption of alcohol, the occurrence of hangover following intravenous (IV) alcohol administration in human laboratory studies has not been previously reported. This study characterizes hangover symptoms and post‐infusion drinking behavior following acute IV alcohol administration in social drinkers. Twenty‐one to thirty‐year‐old healthy social drinkers (n = 24) underwent an alcohol clamp session at breath alcohol concentration of 0.06 percent. Hangover symptoms as well as any post‐infusion drinking that occurred between the end of the session and the following morning were assessed using the Acute Hangover Scale, and examined for influences of recent drinking history, family history of alcoholism and Sex. Results indicated a 79 percent prevalence of hangover symptoms, with the most common symptoms being ‘tired’, ‘thirsty’ and ‘headache’. Recent drinking measures showed significant effects on Average Hangover Scale scores, with heavier drinkers showing greater hangover symptoms. There was a significant sex difference in average hangover scores, with females reporting higher scores than males. Subjective measures of stimulation and intoxication were also associated with Average Hangover Scale scores. The probability of post‐infusion drinking was not predicted by hangover scores, but was related to recent drinking history; subjective response to alcohol was a significant mediator of this relationship. These findings demonstrate that hangover symptoms are experienced following IV alcohol administration, and extend previous studies of influences of risk factors for alcohol use disorders including recent drinking on hangover.
PPARγ agonism attenuates cocaine cue reactivity
Authors: Miller William R , Fox Robert G , Stutz Sonja J , Lane Scott D , Denner Larry , Cunningham Kathryn A , Dineley Kelly T 
Published: November 2016

AbstractCocaine use disorder is a chronic relapsing condition characterized by compulsive drug seeking and taking even after prolonged abstinence periods. Subsequent exposure to drug‐associated cues can promote intense craving and lead to relapse in abstinent humans and rodent models. The responsiveness to these cocaine‐related cues, or ‘cue reactivity’, can trigger relapse and cocaine‐seeking behaviors; cue reactivity is measurable in cocaine‐dependent humans as well as rodent models. Cue reactivity is thought to be predictive of cocaine craving and relapse. Here we report that PPARγ agonism during abstinence from cocaine self‐administration reduced previously active lever pressing in Sprague Dawley rats during cue‐reactivity tests, while administration of the PPARγ antagonist, GW9662, reversed this effect. PPARγ agonism also normalized nuclear ERK activity in the medial prefrontal cortex and hippocampus which was reversed with GW9662. Our results support the utility of PPARγ agonism as a relapse prevention strategy to maintain abstinence in the presence of cocaine‐associated cues.
Mixed‐amphetamine salts increase abstinence from marijuana in patients with co‐occurring attention‐deficit/hyperactivity disorder and cocaine dependence
Authors: Notzon Daniel P. , Mariani John J. , Pavlicova Martina , Glass Andrew , Mahony Amy L. , Brooks Daniel J. , Grabowski John , Levin Frances R. 
Published: November 2016

Background and ObjectivesThe prevalence of ADHD is greater in substance use disorders than the general population, and ADHD and substance use disorders share neurobiological features such as dysregulation of reward circuitry. We tested the hypothesis that stimulants would decrease marijuana use in a randomized controlled trial of extended release mixed amphetamine salts (MAS‐XR) for treatment of co‐occurring ADHD and cocaine use disorders.MethodsMarijuana users were defined as participants reporting use in the 30 days before study initiation, collected with timeline follow‐back. The original 14‐week trial utilized a 3‐arm randomized design, comparing placebo, MAS‐XR 60 mg, and MAS‐XR 80 mg. For this analysis, both MAS‐XR groups were combined, leaving n = 20 in the placebo group and n = 37 in the MAS‐XR group. The primary outcome was proportion of subjects reporting any marijuana use per study week. Comparisons between groups were made using a logistic mixed effects model incorporating multiple predictors and modeling time‐by‐treatment interactions.ResultsThere were no significant baseline differences in marijuana use frequency and quantity. There was a significant decrease in the proportion of participants using marijuana over time in the MAS‐XR group, but no difference in the proportion of marijuana‐use days over time.Discussion and ConclusionsTreatment of ADHD and comorbid cocaine use disorders with MAS‐XR is associated with increased weekly abstinence from marijuana but not with a decrease in the proportion of marijuana using days per week.Scientific SignificanceStimulant treatment of ADHD and cocaine use disorders may diminish co‐occurring cannabis use. (Am J Addict 2016;25:666–672)
Development of Australia's first older adult‐specific early intervention for alcohol‐related harm: Feasibility and proof of concept
Authors: Bright Stephen J , Williams Cylie M 
Published: November 2016

ObjectivesThe rate of older Australians at risk of experiencing alcohol‐related harm increased by 31% over the past 10 years, yet there are no Australian age‐specific early interventions. We describe the development of Australia's first age‐specific early intervention protocol.MethodsThrough examining effective overseas older adult‐specific interventions, in addition to other relevant literature, an early intervention protocol was developed.ResultsThe Older Wiser Lifestyles (OWL) early intervention protocol extends protocols that have been developed overseas through providing: (i) interventions that are tailored to the person's readiness to change, including the provision of harm reduction strategies for people who are precontemplative; and (ii) individualised psychoeducational materials regarding medical conditions and medications.ConclusionThe OWL protocol has been successfully implemented in a service, and preliminary data warrant a clinical trial of the intervention. Australian health‐care providers should consider the OWL protocol as a simple method to reduce the risk from alcohol consumption among older adults.
Systemic treatment in advanced biliary cancers: A multicenter Australian analysis and review
Authors: Brungs Daniel , Aghmesheh Morteza , Sjoquist Katrin , Goldstein David 
Published: November 2016

AbstractAimWhile first‐line palliative chemotherapy (CT1) improves survival and quality of life in advanced biliary cancer (ABC), there is no randomized evidence to support second‐line chemotherapy (CT2) in ABC. We aim to explore to role of CT2 in ABC.MethodsWe performed a retrospective review of all patients who received one or more lines of chemotherapy for ABC at four Australian cancer centers between 2008 and 2011. A Cox proportional hazard model was developed to determine the impact of clinicopathologic variables on overall survival (OS) from time of progression on CT1.ResultsWe identified 73 patients who received palliative chemotherapy for ABC. Twenty‐five patients (34%) received two or more lines of chemotherapy. Patients with a preserved performance status on progression on first‐line chemotherapy (CT1) were more likely to receive second‐line chemotherapy (CT2) (P < 0.001). Disease control rate with CT2 was 36%, and mean progression‐free survival was 3.2 months (95% confidence interval 1.5–4.9 months). The following variables were significant in the univariate analysis of OS from time of progression on CT1: lines of chemotherapy (P = 0.0001), Eastern Cooperative Oncology Group performance status at progression on CT1 (P < 0.0001) and disease control with CT1 (P = 0.027). Lines of chemotherapy received and performance status remained significant in the multivariate analysis for OS from progression on CT1.ConclusionSecond‐line chemotherapy is feasible in a subset of patients with ABC. Even after accounting for confounding variables, CT2 appears to increase OS in ABC, although we are unable to exclude other unmeasured factors such as tumor biology. These findings warrant further evaluation with prospective trials.
Systematic review and meta‐analysis of studies of biliary reconstruction in adult living donor liver transplantation
Authors: Chok Kenneth S. H. , Lo Chung Mau 
Published: November 2016

BackgroundThe chance of biliary complication after living donor liver transplantation (LDLT) is considerable. The objective of this study was to investigate the impact of biliary reconstruction method on post‐LDLT biliary complications. Data sources are from PubMed and Web of Science.MethodsA systematic search was conducted using the search term ‘[biliary complications] OR [biliary complication] OR [biliary stricture] OR [bile leak] AND [living donor liver transplantation]’. Cross‐referencing was allowed so as to encompass more potentially relevant studies. All English papers on adult LDLT published between 1990 and 2014 were considered for review. Papers focusing on biliary reconstruction method in relation to post‐LDLT biliary complications were included.ResultsThe meta‐analysis recruited six retrospective studies but no randomized trial or prospective study. The six studies covered 1286 patients with 260 cases (20.2%) of biliary anastomotic stricture (BAS) and 118 cases (9.2%) of biliary leakage (BL). For biliary reconstruction, 365 patients (28.4%) underwent hepaticojejunostomy (HJ) and 909 (70.7%) underwent duct‐to‐duct anastomosis (DDA), while 12 (0.9%) underwent both and were thus excluded from the analysis. A lower rate of BAS was found in patients with HJ compared with patients with DDA (Mantel–Haenszel odds ratio 0.448, 95% confidence interval 0.311–0.643; P = 0.000). Rates of BL were similar in the two groups (Mantel–Haenszel odds ratio 1.27, 95% confidence interval 0.821–1.966; P = 0.283).ConclusionIn the comparison of HJ and DDA in adult LDLT, the latter was found to be associated with a bigger chance of BAS but not BL.
Contraceptive use in the Nordic countries
Authors: Lindh Ingela , Skjeldestad Finn E. , Gemzell‐Danielsson Kristina , Heikinheimo Oskari , Hognert Helena , Milsom Ian , Lidegaard Øjvind 
Published: November 2016

AbstractIntroductionThe aim was to compare contraceptive use in the Nordic countries and to assess compliance with recommendations from the European Medicines Agency regarding the use of combined oral contraception containing low‐dose estrogen and levonorgestrel, norethisterone or norgestimate.Material and methodsData on hormonal contraceptive prescriptions and sales figures for copper intrauterine devices were obtained from national databases and manufacturers in Denmark, Finland, Iceland, Norway and Sweden in 2010–2013.ResultsContraceptive use was highest in Denmark (42%) and Sweden (41%), followed by Finland (40%). Combined oral contraception was the most used method in all countries, with the highest use in Denmark (26%). The second most used method was the levonorgestrel‐releasing intrauterine system, with the highest use in Finland (15%) and ≈10% in the other countries. Copper intrauterine devices (7%) and the progestin‐only pill (7%) were most often used in Sweden. Combined oral contraception use decreased with increasing age and levonorgestrel‐releasing intrauterine system and progestin‐only pills use increased. The use of long‐acting reversible methods of contraception (=levonorgestrel‐releasing intrauterine system, copper intrauterine devices, and implants) increased with time and was highest in Sweden (20%) and Finland (18%). The highest use of European Medicines Agency recommended combined oral contraception was in Denmark, increasing from 13 to 50% between 2010 and 2013. In Finland, recommended combined oral contraception remained below 1%.ConclusionsContraceptive use was highest in Denmark and Sweden, levonorgestrel‐releasing intrauterine system use was highest in Finland and all long‐acting methods were most common in Sweden. The use of combined oral contraception recommended by the European Medicines Agency was highest in Denmark.