julilili42/papers huggingface dataset:
MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
2017-11-24

Abstract Background There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing and there is a need to adapt short read tools to long read datasets. Methods We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods. Results All presented methods are implemented in the open source edition of MEGAN and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community.
Characterisation of porous knitted titanium for replacement of intervertebral disc nucleus pulposus
2017-11-24

Abstract Effective restoration of human intervertebral disc degeneration is challenged by numerous limitations of the currently available spinal fusion and arthroplasty treatment strategies. Consequently, use of artificial biomaterial implant is gaining attention as a potential therapeutic strategy. Our study is aimed at investigating and characterizing a novel knitted titanium (Ti6Al4V) implant for the replacement of nucleus pulposus to treat early stages of chronic intervertebral disc degeneration. Specific knitted geometry of the scaffold with a porosity of 67.67 ± 0.824% was used to overcome tissue integration failures. Furthermore, to improve the wear resistance without impairing original mechanical strength, electro-polishing step was employed. Electro-polishing treatment changed a surface roughness from 15.22 ± 3.28 to 4.35 ± 0.87 μm without affecting its wettability which remained at 81.03 ± 8.5°. Subsequently, cellular responses of human mesenchymal stem cells (SCP1 cell line) and human primary chondrocytes were investigated which showed positive responses in terms of adherence and viability. Surface wettability was further enhanced to super hydrophilic nature by oxygen plasma treatment, which eventually caused substantial increase in the proliferation of SCP1 cells and primary chondrocytes. Our study implies that owing to scaffolds physicochemical and biocompatible properties, it could improve the clinical performance of nucleus pulposus replacement.
Aureo Wiki The repository of the Staphylococcus aureus research and annotation community
2017-11-25

In light of continuously accumulating data and knowledge on major human pathogens, comprehensive and up-to-date sources of easily accessible information are urgently required. The AureoWiki database (http://aureowiki.med.uni-greifswald.de) provides detailed information on the genes and proteins of clinically and experimentally relevant S. aureus strains, currently covering NCTC 8325, COL, Newman, USA300_FPR3757, and N315. By implementing a pan-genome approach, AureoWiki facilitates the transfer of knowledge gained in studies with different S. aureus strains, thus supporting functional annotation and better understanding of this organism. All data related to a given gene or gene product is compiled on a strain-specific gene page. The gene pages contain sequence-based information complemented by data on, for example, protein function and localization, transcriptional regulation, and gene expression. The information provided is connected via links to other databases and published literature. Importantly, orthologous genes of the individual strains, which are linked by a pan-genome gene identifier and a unified gene name, are presented side by side using strain-specific tabs. The respective pan-genome gene page contains an orthologue table for 32 S. aureus strains, a multiple-strain genome viewer, a protein sequence alignment as well as other comparative information. The data collected in AureoWiki is also accessible through various download options in order to support bioinformatics applications. In addition, based on two large-scale gene expression data sets, AureoWiki provides graphical representations of condition-dependent mRNA levels and protein profiles under various laboratory and infection-related conditions.
Graphical representations of international and interdisciplinary links in science
2017-11-25

Patterns of connectedness in science among national contexts and scientific disciplines are described in the form of illustrative diagrams. The analyses are based on large-scale citation data covering the historical period between 1985 and 2012. Global illustrations as well as some more differentiated trends are presented for both international and interdisciplinary links. Such graphical illustrations may not only help to better understand patterns of information exchange in science but also promote attention for the field of scientometrics.
Biodiversity–multifunctionality relationships depend on identity and number of measured functions
2017-11-27

Biodiversity ensures ecosystem functioning and provisioning of ecosystem services, but it remains unclear how biodiversity-ecosystem multifunctionality relationships depend on the identity and number of functions considered. Here, we demonstrate that ecosystem multifunctionality, based on 82 indicator variables of ecosystem functions in a grassland biodiversity experiment, increases strongly with increasing biodiversity. Analysing subsets of functions showed that the effects of biodiversity on multifunctionality were stronger when more functions were included and that the strength of the biodiversity effects depended on the identity of the functions included. Limits to multifunctionality arose from negative correlations among functions and functions that were not correlated with biodiversity. Our findings underline that the management of ecosystems for the protection of biodiversity cannot be replaced by managing for particular ecosystem functions or services and emphasize the need for specific management to protect biodiversity. More plant species from the experimental pool of 60 species contributed to functioning when more functions were considered. An individual contribution to multifunctionality could be demonstrated for only a fraction of the species.
Metal‐Catalyzed Synthesis and Use of Thioesters: Recent Developments
2017-11-27

Abstract While thioesters are common intermediates in biochemical processes, they are much less appreciated in organic synthesis, also compared to other carboxylic acid derivatives. However, their chemistry and reactivity is intriguing and diversified, reaching much further than the acyl substitution and aldol chemistry. Herein, we focus on metal‐catalyzed reactions for the synthesis of thioesters as well as their transformations. Reactions such as thiocarbonylation, cross‐coupling, decarbonylation, allylic substitution or dual photoredox/metal catalysis are discussed. On one hand, new atom economic methods allow for convenient synthesis of thioesters from well available starting materials. On the other hand, various synthetically important compounds can by synthesized due to the multifaceted reactivity of thioesters that we aimed to depict.
Neurologic Phenotypes Associated With Mutations in RTN4IP1 (OPA10) in Children and Young Adults
2017-11-27

A broad clinical spectrum of neurologic features, ranging from isolated optic atrophy to severe early-onset encephalopathies, is associated with RTN4IP1 biallelic mutations and should prompt RTN4IP1 screening in both syndromic neurologic presentations and nonsyndromic recessive optic neuropathies.
Symphyseal fixation in open book injuries cannot fully compensate anterior SI joint injury—A biomechanical study in a two-leg alternating load model
2017-11-27

Symphyseal locked plating significantly reduces relative movement of the sacroiliac joint in open book injuries type Tile B1.1 or B1.2 (APC II) but cannot fully restore the situation of the intact sacroiliac joint.
Successful treatment of thrombotic microangiopathy associated with dengue infection: A case report and literature review
2017-11-27

Abstract Dengue infection has been associated with multiple renal complications, including glomerulonephritis, acute tubular necrosis, tubulointerstitial nephritis, and thrombotic microangiopathy ( TMA ), this last one being a rare complication of dengue, with only a few reported cases. TMA associated with dengue can be explained by an alteration in the activity of the enzyme ADAMTS 13, leading to thrombotic thrombocytopenic purpura; or it can be secondary to direct or indirect endothelial injury by the virus, which leads to hemolytic uremic syndrome. Here, we present a case of severe TMA , not related to ADAMTS 13, which was clearly associated with dengue infection.
Editorial: Role of Protein-Protein Interactions in Metabolism: Genetics, Structure, Function
2017-11-27

25293039] from the Japanese Society for the Promotion of Science. MK was funded by a joint ANR/FCT program; France: ANR-13-ISV5-0001 (DODYCOEL), and Portuguese national funds, through the Fundacao para a Ciencia e a Tecnologia (Project FCT-ANR/BEX-BCM/0002/2013). WB was supported by the National Institutes of Health (USA) Grants ES004344 and ES013648 from NIEHS, USPHS. UZ was supported by grants from the Robert Bosch Foundation, Stuttgart, Germany.
Variables that influence BRAF mutation probability: A next-generation sequencing, non-interventional investigation of BRAFV600 mutation status in melanoma
2017-11-27

This exploratory study highlights that testing center, melanoma subtype, and age in combination with UV exposure and melanoma subtype significantly influence BRAFV600 mutation probability in patients with melanoma. Further validation of this model, in terms of reproducibility and broader relevance, is required.
The exomic landscape of t(14;18)‐negative diffuse follicular lymphoma with 1p36 deletion
2017-11-28

Summary Predominantly diffuse t(14;18) negative follicular lymphoma ( FL ) with 1p36 deletion shows distinctive clinical, morphological and molecular features that distinguish it from classical FL . In order to investigate whether it possesses a unique mutation profile, we performed whole exome sequencing of six well‐characterised cases. Our analysis showed that the mutational landscape of this subtype is largely distinct from classical FL . It appears to harbour several recurrent mutations, affecting STAT 6, CREBBP and basal membrane protein genes with high frequency. Our data support the view that this FL subtype should be considered a separate entity from classical FL .
What Makes an Israelite an Israelite? Judean Perspectives on the Samarians in the Persian Period
2017-11-28

Within Persian-period Yehud the boundaries of the collective entity Israel were a matter of dispute. The debate was triggered by the question of whether the population in the area of the former Northern Kingdom should be regarded as Israelite or not. But while there was no consensus regarding their status, the same underlying criterion for defining an Israelite is used either to include or exclude the Samarians in/from Israel—not the faith in YHWH or the adherence to the law but the social construction of a common descent which finds its expression in the system of the twelve tribes of Israel. Against the widespread view, post-exilic Israel is best described as an ethnos and not as a Kultgemeinde.
Soundpeaking – Hydropeaking induced changes in river soundscapes
2017-11-28

Abstract Underwater soundscapes and their unique acoustic signatures are mainly generated through movement of streambed sediment, subsequent particle collisions, and turbulence created by water flowing over submerged obstructions such as rocks and woody debris. This study characterized river soundscapes in Alpine rivers of Trentino, (North East Italy) with the combined use of hydrophones and a new microelectricalmechanical systems based device (Hydroflown) that is capable of measuring particle velocity components of the sound field. Pool and riffle habitats affected and unaffected by hydropeaking were characterized in terms of their particle velocity and sound pressure levels across 10 octave bands (acoustic signature) to assess temporal variations in overall sound levels, changes in frequency composition, and relationship to hydromorphological habitat parameters. Data revealed that soundscapes affected by hydropeaking are highly homogenized, and sound pressure levels are strongly correlated with turbine discharge, which results in rapid, multiple‐fold spikes in low frequency amplitude levels within the typical hearing range of common teleost fish species. The outcomes of this study provide the basis for further examination of the resulting behavioural and physiological responses of organisms to anthropogenic changes in river soundscapes.
Structural brain abnormalities in the common epilepsies assessed in a worldwide ENIGMA study
2017-11-29

Progressive functional decline in the epilepsies is largely unexplained. We formed the ENIGMA-Epilepsy consortium to understand factors that influence brain measures in epilepsy, pooling data from 24 research centres in 14 countries across Europe, North and South America, Asia, and Australia. Structural brain measures were extracted from MRI brain scans across 2149 individuals with epilepsy, divided into four epilepsy subgroups including idiopathic generalized epilepsies (n =367), mesial temporal lobe epilepsies with hippocampal sclerosis (MTLE; left, n = 415; right, n = 339), and all other epilepsies in aggregate (n = 1026), and compared to 1727 matched healthy controls. We ranked brain structures in order of greatest differences between patients and controls, by meta-analysing effect sizes across 16 subcortical and 68 cortical brain regions. We also tested effects of duration of disease, age at onset, and age-by-diagnosis interactions on structural measures. We observed widespread patterns of altered subcortical volume and reduced cortical grey matter thickness. Compared to controls, all epilepsy groups showed lower volume in the right thalamus (Cohen's d = -0.24 to -0.73; P < 1.49 × 10-4), and lower thickness in the precentral gyri bilaterally (d = -0.34 to -0.52; P < 4.31 × 10-6). Both MTLE subgroups showed profound volume reduction in the ipsilateral hippocampus (d = -1.73 to -1.91, P < 1.4 × 10-19), and lower thickness in extrahippocampal cortical regions, including the precentral and paracentral gyri, compared to controls (d = -0.36 to -0.52; P < 1.49 × 10-4). Thickness differences of the ipsilateral temporopolar, parahippocampal, entorhinal, and fusiform gyri, contralateral pars triangularis, and bilateral precuneus, superior frontal and caudal middle frontal gyri were observed in left, but not right, MTLE (d = -0.29 to -0.54; P < 1.49 × 10-4). Contrastingly, thickness differences of the ipsilateral pars opercularis, and contralateral transverse temporal gyrus, were observed in right, but not left, MTLE (d = -0.27 to -0.51; P < 1.49 × 10-4). Lower subcortical volume and cortical thickness associated with a longer duration of epilepsy in the all-epilepsies, all-other-epilepsies, and right MTLE groups (beta, b < -0.0018; P < 1.49 × 10-4). In the largest neuroimaging study of epilepsy to date, we provide information on the common epilepsies that could not be realistically acquired in any other way. Our study provides a robust ranking of brain measures that can be further targeted for study in genetic and neuropathological studies. This worldwide initiative identifies patterns of shared grey matter reduction across epilepsy syndromes, and distinctive abnormalities between epilepsy syndromes, which inform our understanding of epilepsy as a network disorder, and indicate that certain epilepsy syndromes involve more widespread structural compromise than previously assumed.
Ethnic identity and the choice to play for a national team: a study of junior elite football players with a migrant background
2017-11-29

In German (junior) elite football, there are a comparatively large number of highly talented players with a migrant background. These players were born in Germany and joined the Talent Development Programme of the German Football Association (DFB). Many of these players can decide for which national association they want to play in international games. In media and public discourse, this decision is usually explained by the degree of self-identification with a specific ethnic group. However, this assumption is not empirically evident. Using the example of junior elite players with a Turkish background, this article focuses therefore on the question, which role ethnic identity plays in this decision. Based on social identity theory, we conducted semistructured interviews with 10 adolescent elite football players with Turkish background who played for the German and/or the Turkish Football Association. Our findings suggest that – in contrast to media narratives – ethnic identity only plays a marginal role in the decision to play for a national football association.
Protostegid marine turtle remains from the Cenomanian (Late Cretaceous) of the Kassenberg (Mülheim an der Ruhr, Western Germany)
2017-11-29

Postcranial remains of protostegid turtles from the lowermost Cenomanian of Mülheim an der Ruhr (Western Germany) are described. The material includes fragments from the carapace and appendicular skeleton of a taxon with a medium carapace length of approximately 20-30 cm. The turtle remains supplement the record of this group from the Cenomanian of Germany and the fossil fauna of the Kassenberg.
First-in-human phase I study of ISTH0036, an antisense oligonucleotide selectively targeting transforming growth factor beta 2 (TGF-β2), in subjects with open-angle glaucoma undergoing glaucoma filtration surgery
2017-11-30

This first-in-human trial demonstrates that intravitreal injection of ISTH0036 at the end of TE is safe. Regarding IOP control, single-dose ISTH0036 administration of 67.5 μg or 225 μg at the time of TE resulted in IOP values persistently < 10 mmHg over the three month postoperative observation period.
The role of soil chemical properties, land use and plant diversity for microbial phosphorus in forest and grassland soils
2017-11-30

Abstract Management intensity modifies soil properties, e.g ., organic carbon (C org ) concentrations and soil pH with potential feedbacks on plant diversity. These changes might influence microbial P concentrations (P mic ) in soil representing an important component of the P cycle. Our objectives were to elucidate whether abiotic and biotic variables controlling P mic concentrations in soil are the same for forests and grasslands, and to assess the effect of region and management on P mic concentrations in forest and grassland soils as mediated by the controlling variables. In three regions of Germany, Schwäbische Alb, Hanich‐Dün, and Schorfheide‐Chorin, we studied forest and grassland plots (each n = 150) differing in plant diversity and land‐use intensity. In contrast to controls of microbial biomass carbon (C mic ), P mic was strongly influenced by soil pH, which in turn affected phosphorus (P) availability and thus microbial P uptake in forest and grassland soils. Furthermore, P mic concentrations in forest and grassland soils increased with increasing plant diversity. Using structural equation models, we could show that soil C org is the profound driver of plant diversity effects on P mic in grasslands. For both forest and grassland, we found regional differences in P mic attributable to differing environmental conditions (pH, soil moisture). Forest management and tree species showed no effect on P mic due to a lack of effects on controlling variables ( e.g ., C org ). We also did not find management effects in grassland soils which might be caused by either compensation of differently directed effects across sites or by legacy effects of former fertilization constraining the relevance of actual practices. We conclude that variables controlling P mic or C mic in soil differ in part and that regional differences in controlling variables are more important for P mic in soil than those induced by management.
The performance of tranchet blows at the Late Middle Paleolithic site of Grotte de la Verpillière I (Saône-et-Loire, France)
2017-11-30

This paper focuses on the technological characteristics of Keilmesser with a lateral tranchet blow modification on the cutting edge. It examines the underlying technological production of these bifacial objects: this implies the evaluation of their working stage succession, as well as produced forms necessary for the execution of tranchet blow performance. Furthermore, it offers a techno-morphological description of these enigmatic tools. The Keilmesser with tranchet blow and corresponding blanks of tranchet blows from Grotte de la Verpillière I in Germolles (Saône-et-Loire, France) are used as case study. The collection of Keilmesser with tranchet blow and corresponding blanks of tranchet blow has been massively expanded with new fieldwork and the review of ancient assemblages. The majority of the pieces were made on blanks from local raw material. The evaluation of the underlying production concept shows that a Keilmesser with tranchet blow, regardless of the wide range of morphologies and matrix size, always consists of specific parts that are necessary for the production sequence and the assumed function. The production of these pieces follows highly specific working stages, some of which can be interchanged in sequence. However, it is always the goal to obtain a low-angled cutting edge. The performance of a tranchet blow is not only an integral part of production, but it is rather the aim of the entire production.
CD20-CD19 Bispecific CAR T Cells for the Treatment of B-Cell Malignancies
2017-12-01

The treatment of leukemia/lymphoma by chimeric antigen receptor (CAR) redirected T cells with specificity for CD19 induced complete remissions in the majority of patients, with a realistic hope for cure. However, recent follow-up data revealed a substantial risk of relapse through leukemic cells that lack the CAR targeted antigen. In this situation, a bispecific CAR with binding domains for CD19 and CD20 is aimed at recognizing leukemic cells with only one cognate antigen. The anti-CD20-CD19 bispecific CAR induced a full T-cell response upon engagement of CD19 or CD20 on target cells showing a true "OR" gate recognition in redirecting T-cell activation. T cells with the anti-CD20-CD19 CAR efficiently killed patients' chronic lymphocytic leukemia cells in vitro. The bispecific CAR T cells cleared pediatric acute lymphocytic leukemia with a mixed CD19<sup>+</sup>CD20<sup>+</sup>/CD20<sup>-</sup> phenotype from the blood and bone marrow of transplanted mice, while anti-CD20 CAR T cells left CD20<sup>-</sup> leukemic cells behind without curing the disease. Data indicate the superior anti-leukemic activity in the control of leukemia, implying that the anti-CD20-CD19 bispecific CAR T cells may reduce the risk of relapse through antigen-loss leukemic cells in the long term.