bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons
Authors: Drouin Alexandre , Giguère Sébastien , Déraspe Maxime , Marchand Mario , Tyers Michael , Loo Vivian G. , Bourgault Anne-Marie , Laviolette François , Corbeil Jacques 
Published: March 2016

AbstractBackgroundThe identification of genomic biomarkers is a key step towards improving diagnostic tests and therapies. We present a reference-free method for this task that relies on ak-mer representation of genomes and a machine learning algorithm that produces intelligible models. The method is computationally scalable and well-suited for whole genome sequencing studies.ResultsThe method was validated by generating models that predict the antibiotic resistance ofC. difficile, M. tuberculosis, P. aeruginosa, andS. pneumoniaefor 17 antibiotics. The obtained models are accurate, faithful to the biological pathways targeted by the antibiotics, and they provide insight into the process of resistance acquisition. Moreover, a theoretical analysis of the method revealed tight statistical guarantees on the accuracy of the obtained models, supporting its relevance for genomic biomarker discovery.ConclusionsOur method allows the generation of accurate and interpretable predictive models of phenotypes, which rely on a small set of genomic variations. The method is not limited to predicting antibiotic resistance in bacteria and is applicable to a variety of organisms and phenotypes. Kover, an efficient implementation of our method, is open-source and should guide biological efforts to understand a plethora of phenotypes (http://github.com/aldro61/kover/).
Mixing of Porpoise Ecotypes in South Western UK Waters Revealed by Genetic Profiling
Authors: Fontaine Michaël C. , Thatcher Oliver , Ray Nicolas , Piry Sylvain , Brownlow Andrew , Davison Nicholas J. , Jepson Paul , Deaville Rob , Goodman Simon J. 
Published: March 2016

AbstractContact zones between marine ecotypes are of interest for understanding how key pelagic predators may react to climate change. We analysed the fine scale genetic structure and morphological variation in harbour porpoises around the UK, at the proposed northern limit of a contact zone between southern and northern ecotypes in the Bay of Biscay. Using a sample of 591 stranded animals spanning a decade and microsatellite profiling at 9 loci, clustering and spatial analyses revealed that animals stranded around UK are composed of mixed genetic ancestries from two genetic pools. Porpoises from SW England displayed a distinct genetic ancestry, had larger body-sizes and inhabit an environment differentiated from other UK costal areas. Genetic ancestry blends from one group to the other along a SW-NE axis along the UK coastline, and showed a significant association with body size, consistent with morphological differences between the two ecotypes and their mixing around the SW coast. We also found significant isolation-by-distance among juveniles, suggesting that stranded juveniles display reduced intergenerational dispersal, while adults show larger variance. The fine scale structure of this admixture zone raises the question of how it will respond to future climate change and provides a reference point for further study.
Disentangling the representation of identity from head view along the human face processing pathway
Authors: Guntupalli J. Swaroop , Wheeler Kelsey G. , Gobbini M. Ida 
Published: March 2016

AbstractNeural models of a distributed system for face perception implicate a network of regions in the ventral visual stream for recognition of identity. Here, we report an fMRI neural decoding study in humans that shows that this pathway culminates in a right inferior frontal cortex face area (rIFFA) with a representation of individual identities that has been disentangled from variable visual features in different images of the same person. At earlier stages in the pathway, processing begins in early visual cortex and the occipital face area (OFA) with representations of head view that are invariant across identities, and proceeds to an intermediate level of representation in the fusiform face area (FFA) in which identity is emerging but still entangled with head view. Three-dimensional, view-invariant representation of identities in the rIFFA may be the critical link to the extended system for face perception, affording activation of person knowledge and emotional responses to familiar faces.Significance StatementIn this fMRI decoding experiment, we address how face images are processed in successive stages to disentangle the view-invariant representation of identity from variable visual features. Representations in early visual cortex and the occipital face area distinguish head views, invariant across identities. An intermediate level of representation in the fusiform face area distinguishes identities but still is entangled with head view. The face-processing pathway culminates in the right inferior frontal area with representation of view-independent identity. This paper clarifies the homologies between the human and macaque face processing systems. The findings show further, however, the importance of the inferior frontal cortex in decoding face identity, a result that has not yet been reported in the monkey literature.
Vessel recruitment and derecruitment mechanism and paradoxical behaviour of vasoconstriction during ischaemia
Authors: Lakshmanan Kayalvizhi , Majumdar Sarangam 
Published: March 2016

AbstractIn this paper, we introduce mathematical aspect of recruitment and derecruitment mechanism of blood vessels acting in such a way as to preserve physiological values of the capillary pressure and perspective of pressure drop effect which has been pointed out by a series of studies documenting a paradoxical vasoconstriction during ischaemia.
Fate mapping caudal lateral epiblast reveals continuous contribution to neural and mesodermal lineages and the origin of secondary neural tube
Authors: Albors Aida Rodrigo , Halley Pamela A. , Storey Kate G. 
Published: March 2016

SummaryThe ability to monitor and manipulate epiblast cells in and around the primitive streak of the mouse embryo is important for investigating how cells maintain potency and how distinct cell fates are established. Here, we report development of a key resource for such studies, a mouse line in which a tamoxifen-inducible Cre recombinase construct replaces an endogenous gene,Nkx1.2, whose expression demarcates the epiblast adjacent to and including the primitive streak. We show that this Nkx1.2CreERT2line drives transgene expression in the endogenousNkx1.2domain. Labelling this caudal epiblast cell population at embryonic day (E) 7.5 confirmed contribution to all three germ layers at later stages. Labelled cells were also retained within the caudal lateral epiblast at E8.5 and E9.5 and E10.5 tailbud. A subset of these cells co-expressed early neural (Sox2) and mesodermal (Bra) markers. These findings support the existence of neuromesodermal progenitors within theNkx1.2cell lineage. Consistent with the retention of such bipotent progenitors throughout body axis elongation, labellingNkx1.2-expressing cells at E10.5 and assessment at E11.5 demonstrated continued contribution to both neural and mesodermal lineages. Furthermore, detailed analysis ofNkx1.2expression revealed a novel domain in tailbud mesenchyme that is contiguous with neural tissue. The presence of labelled Sox2/Bra co-expressing cells in this mesenchyme cell population suggests that this is the retained neuromesodermal progenitor pool, which gives rise to both new paraxial mesoderm and new neural tissue, generated now via secondary neurulation. Here, we introduce this caudal-mostNkx1.2domain as the neuromesodermal lip.
The neural correlates of two forms of spiritual love: an EEG study
Authors: Faber E. S. Louise 
Published: March 2016

AbstractSpiritual practices are gaining an increasingly wider audience as a means to enhance positive affect in healthy individuals and to treat neurological disorders such as anxiety and depression. The current study aimed to examine the neural correlates of two different forms of love generated by spiritual practices using EEG; love generated during a loving kindness meditation performed by Buddhist meditators, and love generated during prayer, in a separate group of participants from a Christian-based faith. The loving kindness meditation was associated with significant increases in delta, alpha 1, alpha 2 and beta power compared to baseline, while prayer induced significant increases in power of alpha 1 and gamma oscillations, together with an increase in the gamma: theta ratio. An increase in delta activity occurred during the loving kindness meditation but not during prayer. In contrast increases in theta, alpha 1, alpha 2, beta and gamma power were observed when comparing both types of practice to baseline, suggesting that increases in these frequency bands are the neural correlates of spiritual love, independent of the type of practice used to attain the state of this type of love. These findings show that both spiritual love practices are associated with widespread changes in neural activity across the brain, in particular at frequency ranges that have been implicated in positive emotional experience, integration of distributed neural activity, and changes in short-term and longterm neural circuitry.
Content analysis of the professional journal of the College of Speech Therapists II: coming of age and growing maturity, 1946–65
Authors: Stansfield Jois , Armstrong Linda 
Published: March 2016

AbstractBackgroundFollowing a content analysis of the first 10 years of the UK professional journal Speech, this study was conducted to survey the published work of the speech (and language) therapy profession in the 20 years following the unification of two separate professional bodies into the College of Speech Therapists.AimTo understand better the development of the speech (and language) therapy profession in the UK in order to support the development of an online history of the speech and language therapy profession in the UK.Methods & ProceduresThe 40 issues of the professional journal of the College of Speech Therapists published between 1946 and 1965 (Speech and later Speech Pathology and Therapy) were examined using content analysis and the content compared with that of the same journal as it appeared from 1935 to the end of the Second World War (1945).Outcomes & ResultsMany aspects of the journal and its authored papers were retained from the earlier years, for example, the range of authors’ professions, their location mainly in the UK, their number of contributions and the length of papers. Changes and developments included the balance of original to republished papers, the description and discussion of new professional issues, and an extended range of client groups/disorders.Conclusions & ImplicationsThe journal and its articles reflect the growing maturity of the newly unified profession of speech therapy and give an indication both of the expanding depth of knowledge available to speech therapists and of the rapidly increasing breadth of their work over this period.
Do overeducated individuals have increased risks of ill health?: a Swedish population‐based cohort study
Authors: Hultin Hanna , Lundberg Michael , Lundin Andreas , Magnusson Cecilia 
Published: March 2016

AbstractPrevious studies indicate that the increasing educational level in many post‐industrial nations may imply that subgroups of the population work in occupations for which they are overeducated. We aimed to investigate whether overeducation is associated with future self‐rated health and psychological distress. The analytical sample consisted of 21,159 participants from the Stockholm Public Health Cohort. Individuals with upper secondary or university education, who in 2006 or 2007 had occupations requiring less education, were considered overeducated. The outcomes were self‐rated health (SRH) and psychological distress in 2010. Overeducated women had an increased risk of less than goodSRH, compared to university‐educated women in matching occupations (adjusted odds ratios (OR): 2.44 confidence intervals (CI): 1.32–4.51 for overeducated women with secondary school education), but not compared to less educated women in the same occupational class (adjustedOR: 0.87CI:0.32–2.38 for overeducated women with secondary school education). We found no increased risk of less than goodSRHfor overeducated men, and no association between overeducation and psychological distress for either sex. The results indicate that overeducation is notper seassociated with onset of less than goodSRHor psychological distress in a short‐term perspective, and the findings support education expansion as a means of improving public health.
Comparative efficacy of tocilizumab, abatacept and rituximab after non‐TNF inhibitor failure: results from a multicentre study
Authors: Pascart Tristan , Philippe Peggy , Drumez Elodie , Deprez Xavier , Cortet Bernard , Duhamel Alain , Houvenagel Eric , Flipo René‐Marc 
Published: March 2016

AbstractAimsThe aim of this study was to compare the efficacy of tocilizumab, rituximab and abatacept after a non‐tumor necrosis factor inhibitor (non‐TNFi) failure for the treatment of rheumatoid arthritis (RA).Materials and methodsThis retrospective multi‐centre study included patients treated for RA with abatacept, rituximab or tocilizumab after having received in the previous line the first non‐TNFi. Data were collected from patient charts. The primary endpoint was the delta Disease Activity Index of 28 joints – erythrocyte sedimentation rate (DAS28‐ESR) and DAS28‐CRP (C‐reactive protein) at 12 months. The relative change in primary outcome measures from baseline were calculated.ResultsOne hundred patients started a second non‐TNFi between 2006 and 2013, including 15 patients treated with rituximab, 36 with tocilizumab and 49 with abatacept. The change of DAS28‐ESR was significantly different between the three groups (P = 0.001). In post hoc pairwise comparisons, patients treated with tocilizumab had a higher decrease of the DAS28‐ESR than patients treated by abatacept (median [interquartile range: IQR]: 36% [0; 54%] vs. 0% [0; 20%], P = 0.002). A similar non‐significant difference was found between tocilizumab and rituximab (median [IQR] decrease: 36% [0; 54%] vs. 0% [−11; 34%], P = 0.07). Similar results were found with the 12 months change in DAS28‐CRP.ConclusionsThis study suggests a better efficacy of tocilizumab compared with abatacept and rituximab in situations of non‐TNFi failure.
The American Board of Emergency Medicine ConCert Examination: Emergency Physicians' Perceptions of Learning and Career Benefits
Authors: Marco Catherine A. , Wahl Robert P. , Counselman Francis L. , Heller Barry N. , Harvey Anne L. , Joldersma Kevin B. , Kowalenko Terry , Coombs Andrea B. , Reisdorff Earl J. 
Published: March 2016

AbstractObjectiveAs part of the American Board of Emergency Medicine (ABEM) Maintenance of Certification (MOC) program, ABEM‐certified physicians are required to pass the Continuous Certification (ConCert) examination at least every 10 years. With the 2015 ConCert examination, ABEM sought to better understand emergency physicians' perceptions of the benefits of preparing for and taking the examination and the career benefits of staying ABEM‐certified.MethodsThis was a prospective survey study. A voluntary postexamination survey was administered at the end of the 2015 ABEM ConCert examination (September 21–26, 2015). Physicians were asked about the benefits of preparing for the examination and maintaining ABEM certification. Examination performance was compared to perceptions of learning and career benefits.ResultsOf the 2,601 on‐time test takers, 2,511 respondents participated (96.5% participation rate). The majority of participants (92.0%) identified a benefit to preparing for the ConCert examination, which included reinforced medical knowledge (73.9%), increased knowledge (66.8%), and making them a better clinician (39.4%). The majority of respondents (90.8%) identified a career benefit of maintaining ABEM certification, which included more employment options (73.8%), more positively viewed by other physicians (56.8%), and better financial outcomes (29.8%). There was a statistically significant association between the perception of knowledge reinforcement and examination performance (p < 0.001). There was also a statistically significant association between the perception that staying certified created more career opportunities and examination performance (p < 0.001).ConclusionsMost emergency physicians identified benefits of preparing for and taking the ABEM ConCert examination, which included reinforcing or adding medical knowledge and making them better clinicians. Most physicians also found career benefits to remaining ABEM‐certified, which included greater employment choices, higher financial compensation, and higher esteem from other physicians. The belief that preparing for and taking the examination reinforced medical knowledge was associated with better examination performance.
Potentially Avoidable Pediatric Interfacility Transfer Is a Costly Burden for Rural Families: A Cohort Study
Authors: Mohr Nicholas M. , Harland Karisa K. , Shane Dan M. , Miller Sarah L. , Torner James C. 
Published: March 2016

AbstractObjectivesInterhospital transfer is a common strategy to provide high‐quality regionalized care in rural emergency departments (EDs), but several reports have highlighted problems with selection of children for transfer. The purpose of this study is to characterize the burden of potentially avoidable transfer (PAT) and to estimate the medical and family‐oriented costs associated with PAT.MethodsThis study was a cohort study of all children treated in Iowa EDs between 2004 and 2013. PAT was defined as a child who was transferred and then either discharged from the receiving ED or admitted for ≤ 1 day, without having any separately billed procedures performed. Costs of care were estimated from 1) medical costs, 2) ambulance transfer, and 3) family costs (travel and lodging).ResultsOver 10 years, 2,117,317 children were included (1% transferred to another hospital). Only 63% were transferred to a designated children's hospital, and PATs were identified in 39% of all transfers. PAT was associated with $909 in additional cost. The conditions most strongly associated with PAT were seizure (additional cost $1,138), fracture ($814), isolated traumatic brain injury without extra‐axial bleeding ($1,455), respiratory infection ($556), and wheezing ($804). Few of these charges are attributable to nonmedical family costs ($21).ConclusionsPotentially avoidable pediatric interhospital transfer is common and is responsible for significant healthcare‐related costs. Future work should focus on improving selection of children who benefit from interhospital transfer for high‐yield conditions, to reduce the costly and distressing burden that PAT places on rural patients and their families.
Serum S100B as a Surrogate Biomarker in the Diagnoses of Burnout and Depression in Emergency Medicine Residents
Authors: Gulen Bedia , Serinken Mustafa , Eken Cenker , Karcıoglu Özgür , Kucukdagli Okkes Taha , Kilic Elif , Akpinar Guleser , Nogay Suleyman , Kuh Mahmut 
Published: March 2016

AbstractObjectivesBurnout syndrome is recognized as a major global problem among emergency healthcare workers as it causes prevalent fatigue, job separations, and disappointment. The objective of this study was to investigate the relationship of the glial marker S100B in sera of emergency physicians with burnout syndrome and depression.MethodsThis was a prospective observational study of emergency medicine residents in three distinct university‐based departments of emergency medicine. S100B levels were measured before and after the shifts. In addition, the resident completed the Maslach Burnout Inventory (MBI) and the Beck Depression Inventory (BDI) prior to starting the shift. S100B levels were compared to the occurrence of burnout syndrome and depression as measured by the MBI and BDI.ResultsForty‐eight of 53 emergency medicine residents actively working in the three university‐based EDs participated in the study. The majority of the sample had BDI scores compatible with severe depression (n = 37, 77.1%). The median scores of MBI for emotional exhaustion, depersonalization, and personal accomplishment were 29 (interquartile range [IQR] = 25 to 33), 14 (IQR = 12 to 18), and 26.5 (IQR = 22 to 31), respectively. S100B levels were found to correlate best with scores of BDI and emotional exhaustion in burnout syndrome. The difference between median S100B levels recorded in the residents with severe depression and moderate depression was found statistically significant (median [IQR] = 150 [145 to 151] vs. 135 [128 to 140]; p = 0.0005). This is also true for S100B levels detected before and after night shifts (median [IQR] = 146 [136.5 to 153.2] and 149.5 [139–158], respectively; difference = 3, 95% confidence interval = 2 to 4 [p = 0.001]).ConclusionsS100B levels correlate with depression scores and emotional exhaustion in burnout syndrome. The findings suggest that S100B can be used as a marker to screen emergency medicine residents and detect individuals with high risk for depression and burnout syndrome.
Standardization of allergen products: 3. Validation of candidate European Pharmacopoeia standard methods for quantification of major birch allergen Bet v 1
Authors: Kaul S. , Zimmer J. , Dehus O. , Costanzo A. , Daas A. , Buchheit K. H. , Asturias J. A. , Barber D. , Carnés J. , Chapman M. , Dayan‐Kenigsberg J. , Döring S. , Führer F. , Hanschmann K. M. , Holzhauser T. , Ledesma A. , Moingeon P. , Nony E. , Pini C. , Plunkett G. , Reese G. , Sandberg E. , Sander I. , Strecker D. , Valerio C. , van Ree R. , Vieths S. 
Published: March 2016

AbstractBackgroundThe BSP090 project aims at establishing European Pharmacopoeia Reference Substances in combination with the corresponding ELISA methods for the quantification of major allergens in allergen products. Two sandwich ELISAs proved suitable for quantification of Bet v 1, the major birch pollen allergen, in preceding phases of BSP090.MethodsTwo Bet v 1‐specific ELISA systems were compared with respect to accuracy and precision in a ring trial including 13 laboratories. Model samples containing recombinant rBet v 1.0101 as well as native birch pollen extracts were measured independently at least three times in each facility. The assessment was completed with a comparative quantification of Bet v 1 in 30 marketed birch allergen products in one laboratory, simulating the future use as reference method.ResultsIn the collaborative study, both candidate ELISAs confirmed their suitability to quantify recombinant and native Bet v 1. ELISA‐A showed higher precision and lower interlaboratory variability, yet ELISA‐B exhibited slightly higher accuracy. Subsequent parallel measurement of Bet v 1 in a panel of ‘real‐life’ birch allergen products indicated better repeatability of ELISA‐B. Both systems detected substantial differences in Bet v 1 content between allergen products, but the effect was more pronounced using ELISA‐B due to persistently higher values compared to ELISA‐A.ConclusionsIn the collaborative study, no deciding differences were observed between the two candidate ELISAs. Further comparison under conditions simulating the intended use combined with the criterion of long‐term availability enabled the selection of one Bet v 1‐specific ELISA for proposal as European Pharmacopoeia standard method.