bluuebunny/crossref_metadata_2025_split huggingface dataset:
A recurrence based approach for validating structural variation using long-read sequencing technology
Authors: Zhao Xuefang , Weber Alexandra M. , Mills Ryan E. 
Published: February 2017

ABSTRACTAlthough there are numerous algorithms that have been developed to identify structural variation (SVs) in genomic sequences, there is a dearth of approaches that can be used to evaluate their results. The emergence of new sequencing technologies that generate longer sequence reads can, in theory, provide direct evidence for all types of SVs regardless of the length of region through which it spans. However, current efforts to use these data in this manner require the use of large computational resources to assemble these sequences as well as manual inspection of each region. Here, we present VaPoR, a highly efficient algorithm that autonomously validates large SV sets using long read sequencing data. We assess of the performance of VaPoR on both simulated and real SVs and report a high-fidelity rate for various features including overall accuracy, sensitivity of breakpoint precision, and predicted genotype.
Efficiency of genome-wide association study in random cross populations
Authors: Viana José Marcelo Soriano , Mundim Gabriel Borges , Pereira Hélcio Duarte , Andrade Andréa Carla Bastos , Silva Fabyano Fonseca e 
Published: February 2017

ABSTRACTGenome-wide association studies (GWAS) with plant species have employed inbred lines panels. Our objectives were to present additional quantitative genetics theory for GWAS, evaluate the relative efficiency of GWAS in non-inbred and inbred populations and in an inbred lines panel, and assess factors affecting GWAS. Fifty samples of 400 individuals from populations with linkage disequilibrium were simulated. Individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits controlled by 10 quantitative trait loci (QTLs) and 90 minor genes, assuming different degrees of dominance and heritabilities of 40 and 80%. The average SNP density was 0.1 centiMorgan and the QTL heritabilities ranged from 3.2 to 11.8%. To increase the QTL detection power, the additive-dominance model must be fitted for traits controlled by dominance effects but must not be fitted for traits showing no dominance. The power of detection was maximized increasing the sample size to 400 and the false discovery rate (FDR) to 5%. The average power of detection for the low, intermediate, and high heritability QTLs were 9.7, 32.7, and 87.7%, respectively. Under sample size of 400 the observed FDR was equal to or lower than the specified level of significance. The association mapping was highly precise. The analysis of the inbred random cross population provided essentially the same results from the non-inbred population. The inbred lines panel provided the best results concerning the low and intermediate heritability QTL detection power, FDR, and mapping precision. The FDR is mainly affected by population structure, compared to relationship information.
A population MRI brain template and analysis tools for the macaque
Authors: Seidlitz Jakob , Sponheim Caleb , Glen Daniel , Ye Frank Q. , Saleem Kadharbatcha S. , Leopold David A. , Ungerleider Leslie , Messinger Adam 
Published: February 2017

AbstractThe use of standard anatomical templates is common in human neuroimaging, as it facilitates data analysis and comparison across subjects and studies. For non-human primates, previousin vivotemplates have lacked sufficient contrast to reliably validate known anatomical brain regions and have not provided tools for automated single-subject processing. Here we present the “National Institute of Mental Health Macaque Template”, or NMT for short. The NMT is a high-resolutionin vivoMRI template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, we generated maps of tissue segmentation and cortical thickness. Surface reconstructions and transformations to previously published digital brain atlases are also provided. We further provide an analysis pipeline using the NMT that automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies.
Maximum entropy methods for extracting the learned features of deep neural networks
Authors: Finnegan Alex , Song Jun S. 
Published: February 2017

AbstractNew architectures of multilayer artificial neural networks and new methods for training them are rapidly revolutionizing the application of machine learning in diverse fields, including business, social science, physical sciences, and biology. Interpreting deep neural networks, however, currently remains elusive, and a critical challenge lies in understanding which meaningful features a network is actually learning. We present a general method for interpreting deep neural networks and extracting network-learned features from input data. We describe our algorithm in the context of biological sequence analysis. Our approach, based on ideas from statistical physics, samples from the maximum entropy distribution over possible sequences, anchored at an input sequence and subject to constraints implied by the empirical function learned by a network. Using our framework, we demonstrate that local transcription factor binding motifs can be identified from a network trained on ChIP-seq data and that nucleosome positioning signals are indeed learned by a network trained on chemical cleavage nucleosome maps. Imposing a further constraint on the maximum entropy distribution also allows us to probe whether a network is learning global sequence features, such as the high GC content in nucleosome-rich regions. This work thus provides valuable mathematical tools for interpreting and extracting learned features from feed-forward neural networks.
‘Tuning Out' or ‘Tuning in'? Mobile Music Listening and Intensified Encounters with the City
Authors: Watson Allan , Drakeford‐Allen Dominiqua 
Published: February 2017

AbstractMobile music listening has become an increasingly pervasive part of urban life. Yet it represents an area of enquiry with which urban studies scholars have yet to engage meaningfully. This essay considers the role of mobile music devices in creating new sonic, emotional and social interactions with and within the city. While academic work in this area has emphasized the use of these devices as a ‘tuning out' of the physicality of the city, we suggest that they might also be used as part of a ‘tuning in' that enhances the meaning and intensity of engagements with the city. In making this case, the essay considers two areas of academic enquiry that highlight the use of mobile music devices in intensified engagements with the city: first, recent writing on the sonic ecologies of the city that emphasize ‘city sounds' as part of the urban experience; and secondly, recent advances in the field of urban computing that provide technologies for location‐aware music exchanges and mediated social interactions. The essay emphasizes mobile music listening as one area of critical enquiry that can help develop our understanding of the ways in which the pervasiveness of mobile devices is recalibrating the experience of urban spatiality.
Identification and pharmacological characterization of succinate receptor agonists
Authors: Geubelle Pierre , Gilissen Julie , Dilly Sébastien , Poma Laurence , Dupuis Nadine , Laschet Céline , Abboud Dayana , Inoue Asuka , Jouret François , Pirotte Bernard , Hanson Julien 
Published: February 2017

Background and PurposeThe succinate receptor (formerly GPR91 or SUCNR1) is described as a metabolic sensor that may be involved in homeostasis. Notwithstanding its implication in important (patho)physiological processes, the function of succinate receptors has remained ill‐defined because no pharmacological tools were available. We report on the discovery of the first family of potent synthetic agonists.Experimental ApproachWe screened a library of succinate analogues and analysed their activity on succinate receptors. Also, we modelled a pharmacophore and a binding site for this receptor. New agonists were identified based on the information provided by these two approaches. Their activity was studied in various bioassays, including measurement of cAMP levels, [Ca2+]i mobilization, TGF‐α shedding and recruitment of arrestin 3. The in vivo effects of activating succinate receptors with these new agonists was evaluated on rat BP.Key ResultsWe identified cis‐epoxysuccinic acid and cis‐1,2‐cyclopropanedicarboxylic acid as agonists with an efficacy similar to that of succinic acid. Interestingly, cis‐epoxysuccinic acid was 10‐ to 20‐fold more potent than succinic acid on succinate receptors. For example, cis‐epoxysuccinic acid reduced cAMP levels with a pEC50 = 5.57 ± 0.02 (EC50 = 2.7 μM), compared with succinate pEC50 = 4.54 ± 0.08 (EC50 = 29 μM). The rank order of potency of the three agonists was the same in all in vitro assays. Both cis‐epoxysuccinic and cis‐1,2‐cyclopropanedicarboxylic acid were as potent as succinate in increasing rat BP.Conclusions and ImplicationsWe describe new agonists at succinate receptors that should facilitate further research on this understudied receptor.
Dynamic diversification history with rate upshifts in Holarctic bell‐flowers (Campanula and allies)
Authors: Jones Katy E. , Korotkova Nadja , Petersen Jörn , Henning Tilo , Borsch Thomas , Kilian Norbert 
Published: February 2017

AbstractCampanula s.l. is one of the most speciose flowering plant lineages of the Holarctic (ca. 600 species). In the present study we sequenced three regions of the plastid genome (petD, rpl16 and trnK/matK) across a broad sample of Campanula s.l., which markedly improved phylogenetic resolution and statistical support compared to previous studies. Based on this robust phylogenetic hypothesis we estimated divergence times using BEAST, diversification rate shifts using Bayesian Analysis of Macroevolutionary Mixture (BAMM) and TreePar, and ancestral ranges using Biogeography with Bayesian (and likelihood) Evolutionary Analyses in R. Campanula s.l. is estimated to have originated during the Early Eocene but the major diversification events occurred between the Late Oligocene and Middle Miocene. Two upward diversification rate shifts were revealed by BAMM, specific to the crown nodes of two Campanula clades: CAM17, a mostly South European‐SW Asian lineage originating during the Middle Miocene and containing nearly half of all known Campanula species; and CAM15B, a SW Asian–Sino‐Himalayan lineage of nine species originating in the early Pleistocene. The dynamic diversification history of Campanula and the inferred rate shifts are discussed in a geo‐historical context.
Patient‐reported control of chronic rhinosinusitis symptoms is positively associated with general health‐related quality of life
Authors: Gray S.T. , Hoehle L.P. , Phillips K.M. , Caradonna D.S. , Sedaghat A.R. 
Published: February 2017

ObjectiveIn chronic rhinosinusitis (CRS), although patient‐reported severity of sinonasal symptoms is significantly associated with diminishment of patients’ general health‐related quality of life (QOL), it remains unclear whether patient‐perceived control of CRS symptomatology is associated with patients’ QOL. In this study, we sought to determine the association between patient‐perceived control of CRS symptomatology and QOL.DesignProspective cross‐sectional study.SettingAcademic, tertiary care centre.ParticipantsA cohort of 166 adults with CRS who were asked to categorise their level of CRS symptom control as “Not at all,” “A little,” “Somewhat,” “Very” and “Completely.”Main outcome measureGeneral health‐related QOL, as reflected by the five‐dimensional EuroQol quality of life survey‐derived visual analogue scale (EQ5D‐VAS) and health utility values (EQ5D‐HUV).ResultsWe found that higher EQ5D‐VAS scores were associated with CRS patients who classified their symptom control as “Very” (adjusted β=15.74, 95% CI: 5.44 to 26.04, P=.003) and “Completely” (adjusted β=14.24, 95% CI: 2.98 to 25.52, P=.014) compared to patients who classified their symptom control as “Not at all.” This was also true for higher EQ5D‐HUV which was associated with patient‐reported CRS symptom control of “A little” (adjusted β=0.10, 95% CI: 0.01 to 0.18, P=.024), “Somewhat” (adjusted β=0.08, 95% CI: 0.00 to 0.17, P=.049), “Very” (adjusted β=0.13, 95% CI: 0.05 to 0.21, P=.002) and “Completely” (adjusted β=0.18, 95% CI: 0.09 to 0.27, P<.001).ConclusionsHigher levels of patient‐reported CRS symptom control are therefore associated with better QOL. These findings suggest that CRS symptom control should be targeted for improving patients’ QOL.
Management of the international development aid system: The Case of Tanzania
Authors: Furukawa Mitsuaki 
Published: February 2017

AbstractThis article tries to clarify Government behaviours as to how to manage aid in Tanzania. Contrary to the Organisation for Economic Co‐operation and Development (OECD) Development Assistance Committee (DAC) donor intentions, the development aid structure, carefully constructed under the poverty reduction regime in Tanzania, has led to Tanzanian‐owned initiatives toward a national development plan (NDP). Furthermore, this article shows that, in the process of creating an international development aid system, the Tanzanian Government has learned to manage aid in a recipient‐driven manner not only from DAC donors, but also from China.
Association Between Migraine and Atopic Diseases in Childhood: A Potential Protective Role of Anti‐Allergic Drugs
Authors: Aupiais Camille , Wanin Stephanie , Romanello Silvia , Spiri Daniele , Moretti Raffaella , Boizeau Priscilla , Massano Davide , Zuccotti Gian Vincenzo , Crichiutti Giovanni , Kanagarajah Lakshmi , Houdouin Veronique , Alberti Corinne , Titomanlio Luigi 
Published: February 2017

BackgroundMigraine is a common cause of headache in childhood. Several studies have investigated the association between migraine and atopic diseases, mostly in the adult population.ObjectiveThis study aimed to investigate this association in children.MethodsA case‐control study was conducted across 3 European tertiary care hospitals between June 2014 and August 2014. Cases (n = 229) were children aged 6‐18 years consulting for a migraine episode. Controls in the same age range (n = 406) were consulting for a minor injury and did not have a history of recurrent headache. Logistic regression analyses tested the effect of atopic diseases and anti‐allergic therapies on occurrence of migraine.ResultsChildren with migraine were more likely to have persistent asthma compared to absence of asthma (odds ratio [OR]: 4.57, 95% confidence interval [CI]: 2.04‐10.24) and less likely to have been treated by inhaled or nasal corticosteroid (OR: 0.34, 95% CI: 0.15‐0.76) or antihistamine therapy (OR: 0.33, 95% CI: 0.18‐0.60). The median number of monthly migraine episodes was higher in children with persistent asthma (3; interquartile [IQR]: 1‐4; range: 0.5‐10) compared to children with intermittent asthma (2; IQR: 1‐3; range: 0.1‐4) or non‐asthmatic children (2; IQR: 1‐3; range: 0.1‐12) (P < .01).ConclusionPersistent childhood asthma was associated with increased risk of migraine and higher frequency of migraine attacks. History of anti‐asthmatic or anti‐allergic therapies was associated with decreased risk of migraine in children and adolescents. The role of these therapies on the pathogenesis and occurrence of migraine needs to be further elucidated because of the huge potential impact in terms of public health.
Tb3Al2.5 Ga2.5O12 transparent ceramic for magneto‐optical application
Authors: Hao Deming , Feng Yue , Tang Yanru , Yi Xuezhuan , Zhang Shuai , Chen Chong , Lin Hui , Zhou Shengming 
Published: February 2017

AbstractThe optical quality and microstructure of the Tb3Al2.5 Ga2.5O12 transparent ceramic were investigated and compared with those of terbium gallium garnet (Tb3Ga5O12 TGG) and terbium aluminum garnet (Tb3Al5O12 TAG). The transmission of the Tb3Al2.5 Ga2.5O12 ceramic was as high as 80% in the visible and near‐infrared (IR) regions, which was close to the theoretical value. The Verdet constant of the Tb3Al2.5 Ga2.5O12 ceramic measured at 632.8 nm and room temperature was −150.6 rad/Tm, which was 12% larger than that of the TGG single crystal and 13% smaller than that of the TAG single crystal, and the Tb3Al2.5 Ga2.5O12 ceramic showed the highest transparency among these three samples.
Job satisfaction and resilience in psychiatric nurses: A study at the Institute of Mental Health, Singapore
Authors: Zheng Zhimin , Gangaram Poornima , Xie Huiting , Chua Stephanie , Ong Samantha Bee Cheng , Koh Sioh Eng 
Published: February 2017

AbstractJob satisfaction ranks highly as one of the main factors influencing turnover rates among nurses. Mental health nursing has been reported to be a particularly stressful specialty, yet little is known about the level of job satisfaction among psychiatric nurses in Singapore. Resilience is defined as a means of adapting to stress at the workplace, and could serve as a factor influencing job satisfaction. The present study aimed to explore the current level of job satisfaction among psychiatric nurses working in the only tertiary psychiatric institution in Singapore, the influencing factors, and the relationship between resilience and job satisfaction. A survey questionnaire consisting of the following was administered to all eligible nurses working in the Institute of Mental Health between the period of 16–24 December 2014: (i) The McCloskey and Mueller Satisfaction Scale; (ii) The Resilience Scale; and (iii) sociodemographic data form. A total of 874 nurses were eligible for participation in the study, and a total of 748 nurses responded, totalling 85.6% response. A mean satisfaction score of 95.21 and mean resilience score of 125.74 were obtained. Mean satisfaction and resilience scores were the highest for nurses with longer working experience and those of older age. A positive and significant association between satisfaction and resilience scores (P = 0.001) was obtained. Psychiatric nurses in Singapore are generally satisfied with their job, but this can be further improved with the strengthening of personal resilience.
Evaluation of the effect of indomethacin and piroxicam administration before embryo transfer on pregnancy rate
Authors: Kumbasar Serkan , Gül Özer , Şık Aytek 
Published: February 2017

AbstractAimThe aim of this study was to evaluate the effect of non‐steroidal anti‐inflammatory drug (NSAID) administration before embryo transfer (ET) on pregnancy rates in women undergoing in vitro fertilization/intracytoplasmic sperm injection ET.MethodsOur study included 255 patients diagnosed with primary or secondary infertility caused by a male or tubal‐related factor, endometriosis or unexplained factors. The patients were divided randomly into three groups. Two groups were administered oral piroxicam (10 mg capsules) or 100 mg indomethacin (rectal suppository), respectively, 1–2 h before ET. As a control, the third group did not receive any form of treatment before ET. Basal levels of follicle‐stimulating hormone, luteinizing hormone, and level 17β‐estradiol on the day of human chorionic gonadotropin administration, the collected and transferred number of embryos, and the number of grade A embryos obtained were determined in all patients.ResultsThe implantation, clinical pregnancy, and miscarriage rates of the groups were compared. The clinical pregnancy rate per ET and the implantation rate were 35.2% and 12.15% in the piroxicam group, 31.7% and 10.9% in the indomethacin group, and 32.9% and 12.5% in the control, respectively. The miscarriage rates of groups 1, 2 and 3 were 12%, 11.7% and 11.7%, respectively (P = 0.964). The differences in clinical pregnancy rates among the groups were not statistically significant (P = 0.887). There were also no significant differences in the implantation rates (P = 0.842).ConclusionThese results suggest that NSAID administration before ET has no additional effect on pregnancy outcome in patients undergoing in vitro fertilization.
Modified tube gastropexy using a mushroom‐tipped silicone catheter for management of gastric dilatation‐volvulus in dogs
Authors: Belch A. , Rubinos C. , Barnes D. C. , Nelissen P. 
Published: February 2017

ObjectivesTo report the short‐ and long‐term complications and clinical outcomes of a cohort of dogs managed for gastric dilatation‐volvulus using a modified right‐sided tube gastropexy technique.Materials and MethodsRetrospective case series.ResultsOf 31 dogs treated, 29 (93·5%) had an excellent short‐term outcome, and gastric dilatation‐volvulus did not recur in any dog. Twenty‐six dogs (84%) were initially fed via the gastrostomy tube postoperatively; three (9·7%) suffered a major complication including septic peritonitis (n=1), and premature tube removal (n=2). Fourteen dogs (45·1%) had minor complications including mild, self‐limiting discharge from the stoma site in 13.Clinical SignificanceModified tube gastropexy using a mushroom‐tipped silicone catheter is an effective and safe surgical method for the management of gastric dilatation‐volvulus. The gastrostomy tube allowed early enteral feeding and easy administration of medications, including gastroprotectants.
The age, breed and sex pattern of diagnosis for veterinary care in insured cats in Japan
Authors: Isomura R. , Yamazaki M. , Inoue M. , Kwan N. C. L. , Matsuda M. , Sugiura K. 
Published: February 2017

ObjectivesTo estimate the annual prevalence of different diagnostic categories by age, breed and sex in insured cats in Japan for which veterinary care claims had been made, and to identify if there is a pattern in these host factors.Materials and MethodsData from 48,187 cats insured for veterinary care in Japan in the period from April 2012 to March 2013 comprising 26,003 males and 22,184 females were analysed to calculate the annual prevalence of 18 diagnostic categories of disease by age, breed and sex.ResultsThe prevalence was highest for urinary system disorders (12·2% for males and 10·0% for females), followed by digestive disorders (11·6% for males and 10·7% for females) and dermatological diseases (8·7% for males and 9·0% for females). The male cats had a higher prevalence than female cats for most diagnostic categories. The prevalence of cardiovascular, urinary, endocrine and neoplastic disorders increased with age; infectious and parasitic diseases had high prevalence at young ages, and the prevalence of respiratory, musculoskeletal disorders and injuries had bimodal peaks. Dermatological disorders had a high prevalence at all ages. A large variation in prevalence was observed between breeds for otic, dermatological, dental and cardiovascular disorders.Clinical SignificanceThe findings can be used to increase awareness of patterns of health disorders in different categories of cat.