bluuebunny/crossref_metadata_2025_split huggingface dataset:
First direct detection of a polarized companion outside a resolved circumbinary disk around CS Chamaeleonis
Authors: Ginski C. , Benisty M. , van Holstein R. G. , Juhász A. , Schmidt T. O. B. , Chauvin G. , de Boer J. , Wilby M. , Manara C. F. , Delorme P. , Ménard F. , Pinilla P. , Birnstiel T. , Flock M. , Keller C. , Kenworthy M. , Milli J. , Olofsson J. , Pérez L. , Snik F. , Vogt N. 
Published: May 2018

Aims. To understand planet formation it is necessary to study the birth environment of planetary systems. Resolved imaging of young planet forming disks allows us to study this environment in great detail and find signs of planet-disk interaction and disk evolution. In the present study we aim to investigate the circumstellar environment of the spectroscopic binary T Tauri star CS Cha. From unresolved mid-to far-infrared photometry it is predicted that CS Cha hosts a disk with a large cavity. In addition, spectral energy distribution modeling suggests significant dust settling, pointing toward an evolved disk that may show signs of ongoing or completed planet formation.
Methods. We observed CS Cha with the high contrast imager SPHERE at the ESO Very Large Telescope (VLT) in polarimetric differential imaging mode to resolve the circumbinary disk in near-infrared scattered light. These observations were followed up by VLT/NACO L-band observations and complemented by archival VLT/NACO K-band and Hubble Space Telescope WFPC2 I-band data.
Results. We resolve the compact circumbinary disk around CS Cha for the first time in scattered light. We find a smooth, low inclination disk with an outer radius of ~55 au (at 165 pc). We do not detect the inner cavity but find an upper limit for the cavity size of ~15 au. Furthermore, we find a faint comoving companion with a projected separation of 210 au from the central binary outside of the circumbinary disk. The companion is detected in polarized light and shows an extreme degree of polarization (13.7 ± 0.4% in the J band). The J- and H-band magnitudes of the companion are compatible with masses of a few MJup. However, K-, L-, and I-band data draw this conclusion into question. We explore with radiative transfer modeling whether an unresolved circum-companion disk can be responsible for the high polarization and complex photometry. We find that the set of observations is best explained by a heavily extincted low-mass (~20 MJup) brown dwarf or high-mass planet with an unresolved disk and dust envelope.
Felsenkeller 5 MV underground accelerator: Towards the Holy Grail of Nuclear Astrophysics 12C(α, γ)16O
Authors: Bemmerer Daniel , Cowan Thomas E. , Grieger Marcel , Hammer Sebastian , Hensel Thomas , Junghans Arnd R. , Koppitz Martina , Ludwig Felix , Müller Stefan E. , Rimarzig Bernd , Reinicke Stefan , Schwengner Ronald , Stöckel Klaus , Szücs Tamás , Takács Marcell P. , Turkat Steffen , Wagner Andreas , Wagner Louis , Zuber Kai 
Published: May 2018

Low-background experiments with stable ion beams are an important tool for putting the model of stellar hydrogen, helium, and carbon burning on a solid experimental foundation. The pioneering work in this regard has been done by the LUNA collaboration at Gran Sasso, using a 0.4 MV accelerator. The present contribution reviews the status of the project for a higher-energy underground accelerator in Felsenkeller, Germany. Results from γ-ray, neutron, and muon background measurements in the Felsenkeller underground site in Dresden, Germany, show that the background conditions are satisfactory.
Two tunnels of the Felsenkeller site have recently been refurbished for the installation of a 5MV high-current Pelletron accelerator. Civil construction work has completed in March 2018. The accelerator will provide intense, 50 μA, beams of 1H+, 4He+, and 12C+ ions, enabling research on astrophysically relevant nuclear reactions with unprecedented sensitivity.
Co-occurrence of Noonan and Cardiofaciocutaneous Syndrome Features in a Patient with KRAS Variant
Authors: Vallejos Carla , Bolanos-Garcia Víctor , Ponce Diana , Unanue Nancy , Garay Francisco , Cassorla Fernando , Aracena Mariana , Rodríguez Fernando 
Published: May 2018

AbstractWe report the case of a 3-year-old girl, who is the third child of nonconsanguineous parents, with short stature, hypertrophic cardiomyopathy, and mild dysmorphic features; all suggestive of Noonan syndrome. In addition, the patient presents with feeding difficulties, deep palmar and plantar creases, sparse hair, and delayed psychomotor and language development, all characteristics frequently observed in cardiofaciocutaneous syndrome. Molecular analysis of the Ras/ MAPK pathway genes using high-resolution melting curve analysis and gene sequencing revealed a de novo KRAS amino acid substitution of leucine to tryptophan at codon 53 (p.L53W). This substitution was recently described in an Iranian patient with Noonan syndrome. The findings described in this report expand the phenotypic heterogeneity observed in RASopathy patients harboring a KRAS substitution, and advocate for the inclusion of genes with low mutational frequency in genetic screening protocols for Noonan syndrome and other RASopathies.
Establishing Intellectually Impaired Victims’ Understanding about ‘Truth’ and ‘Lies’: Police Interview Guidance and Practice in Cases of Sexual Assault
Authors: Richardson Emma , Stokoe Elizabeth , Antaki Charles 
Published: May 2018

AbstractEffective police interviews are central to the justice process for sexual assault victims, but little is known about either actual communication between police officers and witnesses or the alignment between guidance and real practice. This study investigated how police officers, in formal interviews, follow ‘best evidence’ guidance to obtain victims’ demonstrable understandings of ‘truth and lies’. We conducted qualitative conversation analysis of 20 evidentiary interviews between police officers and victims who were ‘vulnerable’ adults or children. Analysis revealed that interviewers initiated conversation about truth and lies inappropriately in three ways: (i) by eliciting confirmations rather than demonstrations of understanding; (ii) by eliciting multiple demonstrations and confirmations of understanding, or (iii) by re-introducing ‘truth and lies’ conversations at incorrect points in the interview. Both (ii) and (iii) imply prior or forthcoming dishonesty on the part of the victim. In the context of encouraging victims to report sexual assault and achieve justice, the article reveals potential communicative barriers in which victims—or their evidence—may be discredited right at the start of the process.
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources
Authors: Sulakhe Dinanath , D’Souza Mark , Wang Sheng , Balasubramanian Sandhya , Athri Prashanth , Xie Bingqing , Canzar Stefan , Agam Gady , Gilliam T Conrad , Maltsev Natalia 
Published: May 2018

Abstract
In recent years, the emphasis of scientific inquiry has shifted from whole-genome analyses to an understanding of cellular responses specific to tissue, developmental stage or environmental conditions. One of the central mechanisms underlying the diversity and adaptability of the contextual responses is alternative splicing (AS). It enables a single gene to encode multiple isoforms with distinct biological functions. However, to date, the functions of the vast majority of differentially spliced protein isoforms are not known. Integration of genomic, proteomic, functional, phenotypic and contextual information is essential for supporting isoform-based modeling and analysis. Such integrative proteogenomics approaches promise to provide insights into the functions of the alternatively spliced protein isoforms and provide high-confidence hypotheses to be validated experimentally. This manuscript provides a survey of the public databases supporting isoform-based biology. It also presents an overview of the potential global impact of AS on the human canonical gene functions, molecular interactions and cellular pathways.
Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity
Authors: Schmitt Oliver , Eipert Peter , Schwanke Sebastian , Lessmann Felix , Meinhardt Jennifer , Beier Julia , Kadir Kanar , Karnitzki Adrian , Sellner Linda , Klünker Ann-Christin , Ruß Frauke , Jenssen Jörg 
Published: May 2018

Abstract

Motivation
Structural connectomics supports understanding aspects of neuronal dynamics and brain functions. Conducting metastudies of tract-tracing publications is one option to generate connectome databases by collating neuronal connectivity data. Meanwhile, it is a common practice that the neuronal connections and their attributes of such retrospective data collations are extracted from tract-tracing publications manually by experts. As the description of tract-tracing results is often not clear-cut and the documentation of interregional connections is not standardized, the extraction of connectivity data from tract-tracing publications could be complex. This might entail that different experts interpret such non-standardized descriptions of neuronal connections from the same publication in variable ways. Hitherto, no investigation is available that determines the variability of extracted connectivity information from original tract-tracing publications. A relatively large variability of connectivity information could produce significant misconstructions of adjacency matrices with faults in network and graph analyzes. The objective of this study is to investigate the inter-rater and inter-observation variability of tract-tracing-based documentations of neuronal connections. To demonstrate the variability of neuronal connections, data of 16 publications which describe neuronal connections of subregions of the hypothalamus have been assessed by way of example.

Results
A workflow is proposed that allows detecting variability of connectivity at different steps of data processing in connectome metastudies. Variability between three blinded experts was found by comparing the connection information in a sample of 16 publications that describe tract-tracing-based neuronal connections in the hypothalamus. Furthermore, observation scores, matrix visualizations of discrepant connections and weight variations in adjacency matrices are analyzed.

Availability
The resulting data and software are available at http://neuroviisas.med.uni-rostock.de/neuroviisas.shtml
MASCOT: parameter and state inference under the marginal structured coalescent approximation
Authors: Müller Nicola F , Rasmussen David , Stadler Tanja 
Published: May 2018

Abstract

Motivation
The structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many sub-populations, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states. We showed that our approximation provides unbiased migration rate and population size estimates across a wide parameter range.

Results
We extend this approach by providing a new algorithm to calculate the probability of the state of internal nodes that includes the information from the full phylogenetic tree. We show that this algorithm is able to increase the probability attributed to the true sub-population of a node. Furthermore we use improved integration techniques, such that our method is now able to analyse larger datasets, including a H3N2 dataset with 433 sequences sampled from five different locations.

Availability and implementation
The presented methods are part of the BEAST2 package MASCOT, the Marginal Approximation of the Structured COalescenT. This package can be downloaded via the BEAUti package manager. The source code is available at https://github.com/nicfel/Mascot.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nextstrain: real-time tracking of pathogen evolution
Authors: Hadfield James , Megill Colin , Bell Sidney M , Huddleston John , Potter Barney , Callender Charlton , Sagulenko Pavel , Bedford Trevor , Neher Richard A 
Published: May 2018

Abstract

Summary
Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike.

Availability and implementation
All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.
Diagnostic Yield of Next-generation Sequencing in Very Early-onset Inflammatory Bowel Diseases: A Multicentre Study
Authors: Charbit-Henrion Fabienne , Parlato Marianna , Hanein Sylvain , Duclaux-Loras Rémi , Nowak Jan , Begue Bernadette , Rakotobe Sabine , Bruneau Julie , Fourrage Cécile , Alibeu Olivier , Rieux-Laucat Frédéric , Lévy Eva , Stolzenberg Marie-Claude , Mazerolles Fabienne , Latour Sylvain , Lenoir Christelle , Fischer Alain , Picard Capucine , Aloi Marina , Dias Jorge Amil , Hariz Mongi Ben , Bourrier Anne , Breuer Christian , Breton Anne , Bronsky Jiri , Buderus Stephan , Cananzi Mara , Coopman Stéphanie , Crémilleux Clara , Dabadie Alain , Dumant-Forest Clémentine , Gurkan Odul Egritas , Fabre Alexandre , Fischer Aude , Diaz Marta German , Gonzalez-Lama Yago , Goulet Olivier , Guariso Graziella , Gurcan Neslihan , Homan Matjaz , Hugot Jean-Pierre , Jeziorski Eric , Karanika Evi , Lachaux Alain , Lewindon Peter , Lima Rosa , Magro Fernando , Major Janos , Malamut Georgia , Mas Emmanuel , Mattyus Istvan , Mearin Luisa M , Melek Jan , Navas-Lopez Victor Manuel , Paerregaard Anders , Pelatan Cecile , Pigneur Bénédicte , Pais Isabel Pinto , Rebeuh Julie , Romano Claudio , Siala Nadia , Strisciuglio Caterina , Tempia-Caliera Michela , Tounian Patrick , Turner Dan , Urbonas Vaidotas , Willot Stéphanie , Ruemmele Frank M , Cerf-Bensussan Nadine 
Published: May 2018

Abstract

Background and Aims
An expanding number of monogenic defects have been identified as causative of severe forms of very early-onset inflammatory bowel diseases [VEO-IBD]. The present study aimed at defining how next-generation sequencing [NGS] methods can be used to improve identification of known molecular diagnosis and to adapt treatment.

Methods
A total of 207 children were recruited in 45 paediatric centres through an international collaborative network [ESPGHAN GENIUS working group] with a clinical presentation of severe VEO-IBD [n = 185] or an anamnesis suggestive of a monogenic disorder [n = 22]. Patients were divided at inclusion into three phenotypic subsets: predominantly small bowel inflammation, colitis with perianal lesions, and colitis only. Methods to obtain molecular diagnosis included functional tests followed by specific Sanger sequencing, custom-made targeted NGS, and in selected cases whole exome sequencing [WES] of parents-child trios. Genetic findings were validated clinically and/or functionally.

Results
Molecular diagnosis was achieved in 66/207 children [32%]: 61% with small bowel inflammation, 39% with colitis and perianal lesions, and 18% with colitis only. Targeted NGS pinpointed gene mutations causative of atypical presentations, and identified large exonic copy number variations previously missed by WES.

Conclusions
Our results lead us to propose an optimised diagnostic strategy to identify known monogenic causes of severe IBD.
Deformations of Pre-symplectic Structures and the Koszul L∞-algebra
Authors: Schätz Florian , Zambon Marco 
Published: May 2018

AbstractWe study the deformation theory of pre-symplectic structures, that is, closed 2-forms of fixed rank. The main result is a parametrization of nearby deformations of a given pre-symplectic structure in terms of an $L_{\infty }$-algebra, which we call the Koszul $L_{\infty }$-algebra. This $L_{\infty }$-algebra is a cousin of the Koszul dg Lie algebra associated to a Poisson manifold. In addition, we show that a quotient of the Koszul $L_{\infty }$-algebra is isomorphic to the $L_{\infty }$-algebra that controls the deformations of the underlying characteristic foliation. Finally, we show that the infinitesimal deformations of pre-symplectic structures and of foliations are both obstructed.
‘I Stand on My Own Two Feet but Need Someone Who Really Cares’: Social Networks and Social Capital among Unaccompanied Minors for Becoming Established in Swedish Society
Authors: Eriksson Malin , Wimelius Malin E , Ghazinour Mehdi 
Published: May 2018

AbstractSettling in a new host country as an unaccompanied minor holds a lot of challenges such as adaptation of new social norms, learning a new language and understanding a new culture. Social networks may foster good conditions for settlement in the host community but little is known about the availability, quality and significance of social networks for unaccompanied minors (UM) in Sweden. The aim of this qualitative grounded-theory situational study was to explore experiences of social networks among UM and the significance of those networks for becoming established in Sweden, based on data from in-depth interviews with 11 young persons. Unaccompanied young persons were broadly found to be involved in three different kinds of networks: professional carers, like-ethnic friends and ‘Swedes’ in general. Networks with professionals (i.e. linking social capital) were perceived as both a secure base and a source of rejection, and could either facilitate or obstruct the establishment. Supporting networks with like-ethnic friends (bonding social capital) proved to be the most available and important resource for becoming established, while access to networks with Swedes (bridging social capital) was in general low but still perceived as important for becoming established, not least for reducing language and cultural barriers.
APOL1 risk genotype in European steroid-resistant nephrotic syndrome and/or focal segmental glomerulosclerosis patients of different African ancestries
Authors: Gribouval Olivier , Boyer Olivia , Knebelmann Bertrand , Karras Alexandre , Dantal Jacques , Fourrage Cécile , Alibeu Olivier , Hogan Julien , Dossier Claire , Tête Marie Josèphe , Antignac Corinne , Servais Aude 
Published: May 2018

Abstract

Background
Apolipoprotein L1 (APOL1) risk variants are strongly associated with sporadic focal segmental glomerulosclerosis (FSGS) in populations with African ancestry. We determined the frequency of G1/G2 variants in steroid-resistant nephrotic syndrome (SRNS)/FSGS patients with African or French West Indies ancestry in France and its relationships with other SRNS genes.

Methods
In a cohort of 152 patients (139 families), the APOL1 risk variants were genotyped by direct Sanger sequencing and pathogenic mutations were screened by next-generation sequencing with a panel including 35 SRNS genes.

Results
The two risk allele [high-risk (HR)] genotypes were found in 43.1% (66/152) of subjects compared with 18.9% (106/562) in a control population (P < 0.0001): 33 patients homozygous for APOL1 G1 alleles, 4 homozygous for G2 and 29 compound heterozygous for G1 and G2. Compared with patients in the low-risk (LR) group, patients in the HR group were more likely to originate from the French West Indies than from Africa [45/66 (68.2%) versus 30/86 (34.9%); P < 0.0001]. There were more familial cases in the HR group [27 (41.5%) versus 8 (11.4%); P < 0.0001]. However, causative mutations in monogenic SRNS genes were found in only 1 patient in the HR group compared with 16 patients (14 families) in the LR group (P = 0.0006). At diagnosis, patients in the HR group without other mutations were more often adults [35 (53.8%) versus 19 (27.1%); P = 0.003] and had a lower estimated glomerular filtration rate (78.9 versus 98.8 mL/min/1.73 m2; P = 0.02).

Conclusions
The HR genotype is frequent in FSGS patients with African ancestry in our cohort, especially in those originating from the West Indies, and confer a poor renal prognosis. It is usually not associated with other causative mutations in monogenic SRNS genes.
Real-time Utilization of Metagenomic Sequencing in the Diagnosis and Treatment Monitoring of an Invasive Adenovirus B55 Infection and Subsequent Herpes Simplex Virus Encephalitis in an Immunocompetent Young Adult
Authors: Fang Xueling , Xu Mi , Fang Qiang , Tan Haiqin , Zhou Jiale , Li Ziqin , Li Fan , Yang Shangxin 
Published: May 2018

Abstract

Background
Metagenomic sequencing has shown tremendous promise in solving difficult infectious diseases cases. In this study, we utilized this technology to help guide the care of a critically ill patient with severe pneumonia, fever of unknown origin, and subsequent encephalitis in the intensive care unit (ICU).

Methods
Shotgun metagenomic sequencing was performed on the patient’s blood, bronchoalveolar lavage (BAL), and cerebral spinal fluid by using an Illumina MiniSeq sequencer.

Results.
A high load of human adenovirus B55 (HAdV-B55), a highly pathogenic adenovirus associated with numerous recently reported outbreaks and deaths in China, was detected in both blood and BAL, which explained the severity of the condition. The patient was treated with intravenous ribavirin, which cleared the virus after 26 days. Metagenomic sequencing also helped diagnose an unexpected herpes simplex virus–1 encephalitis during hospitalization, which led to timely treatment.

Conclusions.
This was the first successful case utilizing metagenomic sequencing to guide diagnosis and treatment in the ICU setting in China. We have proven the concept that metagenomic sequencing can play an important role in determining clinical approaches and ultimately in improving patient outcomes. We also hope to share our successful treatment protocol for the severe pneumonia and viremia caused by HAdV-B55.