bluuebunny/crossref_metadata_2025_split huggingface dataset:
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly
Authors: Lewis T E , Sillitoe I , Lees J G 
Published: October 2018

Abstract

Motivation
Many bioinformatics areas require us to assign domain matches onto stretches of a query protein. Starting with a set of candidate matches, we want to identify the optimal subset that has limited/no overlap between matches. This may be further complicated by discontinuous domains in the input data. Existing tools are increasingly facing very large data-sets for which they require prohibitive amounts of CPU-time and memory.

Results
We present cath-resolve-hits (CRH), a new tool that uses a dynamic-programming algorithm implemented in open-source C++ to handle large datasets quickly (up to ∼1 million hits/second) and in reasonable amounts of memory. It accepts multiple input formats and provides its output in plain text, JSON or graphical HTML. We describe a benchmark against an existing algorithm, which shows CRH delivers very similar or slightly improved results and very much improved CPU/memory performance on large datasets.

Availability and implementation
CRH is available at https://github.com/UCLOrengoGroup/cath-tools; documentation is available at http://cath-tools.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
The extraordinary journey of a metal endoclip to the outside of the chest wall
Authors: Acar Arkin , Ceylan Kenan Can , Kaya Şeyda Örs 
Published: October 2018

Abstract
Metal endoclips are frequently utilized in surgical procedures. Within the medical literature, metal endoclip migration following general surgical procedures is a widely studied complication. However, examples of thoracic metal endoclip migration are, as yet, absent in the medical literature. This case study seeks to provide the first clear example of such thoracic metal endoclip migration.
Generations and Stability of Support for the EU: An Analysis of Six-Wave Panel Data from The Netherlands
Authors: Ringlerova Zuzana 
Published: October 2018

AbstractAs the Brexit referendum has demonstrated, public support for the European Union (EU) is important for the future of the EU. The existing research shows that young citizens tend to be more supportive of the EU than old citizens. How stable, however, is this support? Do individuals who grew up in a strongly integrated EU have more stable support for the EU? Analysis of six-wave panel data from The Netherlands reveals that support for the EU is about equally stable among all generations, young and old. Given the higher level of support for the EU among younger generations, these findings suggest that support for the EU may increase as older, more skeptical generations are replaced by younger generations.
The Role of Bowel Ultrasound in Detecting Subclinical Inflammation in Pregnant Women with Crohn’s Disease
Authors: Leung Yvette , Shim Hang Hock , Wilkens Rune , Tanyingoh Divine , Afshar Elnaz Ehteshami , Sharifi Nastaran , Pauls Mehrnoosh , Novak Kerri L , Kaplan Gilaad G , Panaccione Remo , Wilson Stephanie R , Seow Cynthia H 
Published: October 2018

Abstract

Background and Aims
Maintaining disease remission improves outcomes for pregnant women with Crohn’s disease (CD). As symptoms may correlate poorly with disease activity in the gravid state, we investigated the utility of bowel sonography during pregnancy to assess disease activity.

Methods
We conducted a prospective observational cohort study of pregnant women with CD undergoing bowel sonography between July 1, 2012, and December 1, 2016. Clinically active disease was defined using standardized clinical indices (Harvey Bradshaw Index >4 for active disease). Sonographic findings were graded as inactive (normal, mild) or active (moderate, severe) by expert radiologists.

Results
There were 91 pregnancies in 82 CD patients. Symptoms were present in 12 pregnancies; however, eight (67%) had sonographic findings of inactive disease, and escalation of therapy was not initiated. Conversely, sonographically active disease in seven asymptomatic pregnancies resulted in four women escalating therapy. The remaining three women declined escalation of therapy, one had a miscarriage, and the other two women had persistently active disease on sonography and endoscopy at one-year postpartum.

Conclusions
Bowel ultrasound may detect subclinical inflammation in asymptomatic pregnant women with CD and stratify CD activity in symptomatic patients. Therefore, bowel sonography should be considered as a useful adjunct for the assessment of the pregnant woman with Crohn’s disease.
Confirmational Holism and Theory Choice: Arrow Meets Duhem
Authors: Cresto Eleonora , Tajer Diego 
Published: October 2018

Abstract
In a recent paper Samir Okasha has suggested an application of Arrow’s impossibility theorem to theory choice. When epistemic virtues are interpreted as ‘voters’ in charge of ranking competing theories, and there are more than two theories at stake, the final ordering is bound to coincide with the one proposed by one of the voters (the dictator), provided a number of seemingly reasonable conditions are in place. In a similar spirit, Jacob Stegenga has shown that Arrow’s theorem applies to the amalgamation of evidence; the ‘voters’ here are the different sources of evidence. As with Okasha’s proposal, it is not clear how to avoid Arrow’s pessimistic conclusion.
In this paper we develop a novel argument that purports to show that, in typical examples, Arrow’s result does not obtain when dealing with evidence amalgamation. The reason is that we cannot escape the well-known Duhem problem: the evidence actually confirms (or disconfirms) complex conjunctions that include various auxiliary hypotheses. We argue that confirmational holism induces us to restrict the domain of a reasonable amalgamation function, thus violating one of Arrow’s conditions. The upshot is that we are now able to see the Duhem problem under a different, positive light – namely, as a phenomenon that makes the aggregation of the evidence possible in the first place, when there are at least three options on the table.
Accretion disc MHD winds and blazar classification
Authors: Boula Stella , Kazanas Demosthenes , Mastichiadis Apostolos 
Published: October 2018

ABSTRACT
The Fermi Gamma-Ray Space Telescope observations of blazars show a strong correlation between the spectral index of their γ-ray spectra and their synchrotron peak frequency $\nu _{\rm {pk}}^{\rm {syn}}$; additionally, the rate of Compton dominance of these sources also seems to be a function of $\nu _{\rm {pk}}^{\rm {syn}}$. In this work, we adopt the assumption that the non-thermal emission of blazars is primarily due to radiation by a population of Fermi-accelerated electrons in a relativistic outflow (jet) along the symmetry axis of the blazar’s accretion disc. Furthermore, we assume that the Compton component is related to an external photon field of photons, which are scattered from particles of the magnetohydrodynamic wind emanating from the accretion disc. Our results reproduce well the aforementioned basic observational trends of blazar classification by varying just one parameter, namely the mass accretion rate on to the central black hole.
Deep forest
Authors: Zhou Zhi-Hua , Feng Ji 
Published: October 2018

AbstractCurrent deep-learning models are mostly built upon neural networks, i.e. multiple layers of parameterized differentiable non-linear modules that can be trained by backpropagation. In this paper, we explore the possibility of building deep models based on non-differentiable modules such as decision trees. After a discussion about the mystery behind deep neural networks, particularly by contrasting them with shallow neural networks and traditional machine-learning techniques such as decision trees and boosting machines, we conjecture that the success of deep neural networks owes much to three characteristics, i.e. layer-by-layer processing, in-model feature transformation and sufficient model complexity. On one hand, our conjecture may offer inspiration for theoretical understanding of deep learning; on the other hand, to verify the conjecture, we propose an approach that generates deep forest holding these characteristics. This is a decision-tree ensemble approach, with fewer hyper-parameters than deep neural networks, and its model complexity can be automatically determined in a data-dependent way. Experiments show that its performance is quite robust to hyper-parameter settings, such that in most cases, even across different data from different domains, it is able to achieve excellent performance by using the same default setting. This study opens the door to deep learning based on non-differentiable modules without gradient-based adjustment, and exhibits the possibility of constructing deep models without backpropagation.
Hepatitis B Virus (HBV) Infection and Re-activation During Nucleos(t)ide Reverse Transcriptase Inhibitor–Sparing Antiretroviral Therapy in a High–HBV Endemicity Setting
Authors: Abdullahi Adam , Fopoussi Olga Mafotsing , Torimiro Judith , Atkins Mark , Kouanfack Charles , Geretti Anna Maria 
Published: October 2018

AbstractBackgroundWe monitored the evolution of markers of hepatitis B virus (HBV) infection in virologically suppressed HIV-positive patients switching to nucleoside reverse transcriptase inhibitor (NRTI)–sparing antiretroviral therapy within a randomized trial in Cameroon.Methods  HBV surface antigen (HBsAg), HBV DNA, and antibodies against surface (anti-HBs), core (total anti-HBc), and e-antigen (anti-HBe) were measured retrospectively in samples collected at study entry and over 48 weeks after NRTI discontinuation.ResultsParticipants (n = 80, 75% females) had a plasma HIV-1 RNA &lt;60 copies/mL, a median CD4 count of 466 cells/mm3, and undetectable HBsAg and HBV DNA at study entry. After NRTI discontinuation, 3/20 (15.0%) anti-HBc-negative patients showed evidence indicative or suggestive of incident HBV infection (163 cases/1000 person-years); 6/60 (10.0%) anti-HBc-positive patients showed evidence indicative or suggestive of HBV reactivation (109 cases/1000 person-years). In one case of reactivation, anti-HBs increased from 14 to &gt;1000 IU/L; sequencing showed HBV genotype A3 and 3 escape mutations in surface (Y100C, K122R, Y161FY). Alongside new-onset detection of HBsAg or HBV DNA, 1 patient experienced acute hepatitis and 6 patients experienced mild or marginal increases in serum transaminase levels.ConclusionsEvolving treatment strategies for sub-Saharan Africa must be accompanied by the formulation and implementation of policy to guide appropriate assessment and management of HBV status.
Pathophysiological Events Associated With Pancreatitis in Response to Tobacco
Authors: Luaces-Regueira María , Castiñeira-Alvariño Margarita , Castro-Manzanares María , Campos-Toimil Manuel , Domínguez-Muñoz J. Enrique 
Published: October 2018

Objectives
The aim of this study was to comparatively analyze the effects of different concentrations of cigarette smoke condensate (CSC, a standardized tobacco extract) and ethanol on intracellular enzyme activation, cell necrosis, alteration of cytosolic calcium concentration ([Ca2+]c), and amylase secretion in pancreatic acinar cells.

Methods
The effects of CSC (1 μg/mL to 0.4 mg/mL) and ethanol (10–100 mM) on intracellular enzyme activity, cell necrosis, and [Ca2+]c were measured by fluorescence assays in isolated pancreatic acinar cells. Amylase secretion was evaluated by spectrophotometry. Supramaximal concentrations of cholecystokinin (10–100 nM) were used as positive control.

Results
Neither CSC nor ethanol induced trypsin or elastase activation. Both CSC (0.1–0.4 mg/mL) and ethanol (10–75 mM) significantly increased [Ca2+]c. Amylase secretion was increased only in CSC-treated cells (0.3 and 0.4 mg/mL). After 60 minutes, CSC (0.3 and 0.4 mg/mL) significantly increased acinar cell necrosis at a similar percentage to that induced by cholecystokinin. Ethanol did not induce any significant cell necrosis.

Conclusions
Cigarette smoke condensate induces acinar cell injury and increases [Ca2+]c and amylase secretion, independently of intracellular enzyme activation, suggesting that tobacco could induce several main early events of pancreatitis in pancreatic acinar cells. However, ethanol only induces increases [Ca2+]c, having no effect on cell injury, amylase secretion, or intracellular enzyme activation.
Prognostic Impact of Portal System Invasion in Pancreatic Cancer Based on Image Classification
Authors: Morimoto Daishi , Yamada Suguru , Murotani Kenta , Sonohara Fuminori , Takami Hideki , Suenaga Masaya , Hayashi Masamichi , Niwa Yukiko , Tashiro Mitsuru , Hattori Norifumi , Iwata Naoki , Kanda Mitsuro , Tanaka Chie , Kobayashi Daisuke , Nakayama Goro , Koike Masahiko , Fujiwara Michitaka , Fujii Tsutomu , Kodera Yasuhiro 
Published: October 2018

Objectives
This study aimed to clarify the correlation between image classification and the pathological degree of portal system invasion (PSI) and to evaluate the prognostic impact of PSI in pancreatic cancer (PC).

Methods
Pancreatic cancer patients with surgical resections (head, n = 244; body and tail, n = 80) were enrolled in this study.

Results
Based on imaging findings, portal vein (PV) invasion was classified as type A (absent), B (unilateral narrowing), C (bilateral narrowing), or D (stenosis or obstruction with collaterals). Splenic vein (SPV) invasion was classified as type α (absent), β (stenosis), or γ (obstruction). The pathological grade of venous invasion was classified as grade 0 (no invasion), 1 (tunica adventitia), 2 (tunica media), or 3 (tunica intima). In PV and SPV invasions, image classification and pathological grade showed significant correlation (PV: ρ = 0.696; SPV: ρ = 0.681). Patients with PV invasion deeper than type B exhibited significantly poorer survival than type A (P < 0.0001). In contrast, there was no difference in survival among types α, β, and γ.

Conclusions
Image classification was correlated with the pathological grade of PSI in PC. Although not applicable for SPV invasion, image classification of PV invasion is a robust indicator for PC prognosis.
Dysbiosis in Snoring Children
Authors: Collado Maria Carmen , Katila Maija Kristiina , Vuorela Nina Maria , Saarenpää‐Heikkilä Outi , Salminen Seppo , Isolauri Erika 
Published: October 2018

ABSTRACTBackground and Objectives:Early microbial colonization has a key impact on infant health through nutritional, immunological, and metabolic programming. The origin of child snoring is multifactorial and complex, and may thereby also generate long‐term health problems. The link between child snoring and gut microbes remains unclear, although indirect evidence exists regarding this relationship. This study aimed to characterize the connection between gut microbiota and child snoring.Methods:In a prospective, observational CHILD‐SLEEP birth cohort study, gut microbiota in a subcohort of 43 of these children at 2 years of life was profiled with 16S ribosomal RNA gene amplicon sequencing.Results:A higher abundance of the Proteobacteria phylum, the Enterobacteriaceae family, and Erysipelotrichaceae family, as well as a higher ratio of Firmicutes to Bacteroidetes were detected in snorers as compared to controls. Furthermore, snorers showed significantly lower microbial diversity and richness than non‐snorers.Conclusions:The snoring children manifest different gut microbiota as compared with healthy children. Considering that snoring and sleep disorders can be a source of long‐term consequences, including cardiovascular, metabolic, immunological, neurocognitive and behavioral consequences, our results proposes early microbiota as a new treatment target.
Distinct Dynamics of Stem and Progenitor Cells in Blood of Polytraumatized Patients
Authors: Vogel Mona , Christow Hannes , Manz Isabel , Denkinger Michael , Amoah Amanda , Schütz Desiree , Brown Andreas , Möhrle Bettina , Schaffer Annika , Kalbitz Miriam , Gebhard Florian , Mayer Benjamin , Huber-Lang Markus , Geiger Hartmut 
Published: October 2018

ABSTRACTEndogenously mobilized stem and progenitor cells (SPCs) or exogenously provided SPCs are thought to be beneficial for trauma therapy. However, still little is known about the synchronized dynamics of the number of SPCs in blood after severe injury and parameters like cytokine profiles that correlate with these numbers. We determined the number of hematopoietic stem cells, common myeloid progenitors, granulocyte-macrophage progenitors, and mesenchymal stem/stromal cells in peripheral blood (PB) 0 to 3, 8, 24, 48, and 120 h after polytrauma in individual patients (injury severity score ≥ 21). We found that the number of blood SPCs follows on average a synchronous, inverse bell-shaped distribution, with an increase at 0 to 3 h, followed by a strong decrease, with a nadir in SPC numbers in blood at 24 or 48 h. The change in numbers of SPCs in PB between 48 h and 120 h revealed two distinct patterns: Pattern 1 is characterized by an increase in the number of SPCs to a level higher than normal, pattern 2 is characterized by an almost absent increase in the number of SPCs compared to the nadir. Changes in the concentrations of the cytokines CK, MDC, IL-8, G-CSF Gro-α, VEGF, and MCP-1 correlated with changes in the number of SPCs in PB or were closely associated with Pattern 1 or Pattern 2. Our data provide novel rationale for investigations on the role of stem cell mobilization in polytraumatized patients and its likely positive impact on trauma outcome.
Psychological burden of haematological cancer on patient and family: is it time for a multisystem approach?
Authors: Statham Clare , Davis Carol 
Published: October 2018

Purpose of review
Literature addressing the psychological impact of haematological cancers on patients and their families is sparse. New evidence might prompt a change in approach to the assessment and management of psychological burden.

Recent findings
The diagnosis, treatment and surveillance of haematological cancers often have a profound psychological impact on patients and their families and can result in clinically significant problems and increased carer stress. These may manifest at any stage from diagnosis to death or living as a survivor. Some high-risk subgroups have been identified.

Summary
The range of diagnostic groups, wide range of data analysis time-points relative to time of diagnosis, heterogeneity of outcome measures and differing methodologies (mainly prevalence studies) confound generalization of the findings. Targeted screening of the most at-risk subpopulations at times of greatest risk seems sensible to facilitate early intervention; further work is required to establish how often to screen and the best way of doing that. None of these articles define thresholds for intervention. Clearly more psychological support is needed for patients with haematological cancers and their families, but these articles do not provide evidence to suggest what this should comprise. There remains a need for large, longitudinal multicentre studies.
Levodopa’s effects on expression of reinforcement learning
Authors: J.P. Grogan , H.K. Isotalus , A. Howat , N. Irigoras Izagirre , L.E. Knight , E.J. Coulthard 
Published: October 2018

ABSTRACTDopamine has been implicated in learning from rewards and punishment, and in the expression of this learning. However, many studies do not fully separate retrieval and decision mechanisms from learning and consolidation. Here, we investigated the effects of levodopa (dopamine precursor) on choice performance (isolated from learning or consolidation). We gave 31 healthy older adults 150mg of levodopa or placebo (double-blinded, randomised) 1 hour before testing them on stimuli they had learned the value of the previous day. We found that levodopa did not affect the overall accuracy of choices, nor the relative expression of positively or negatively reinforced values. This contradicts several studies and suggests that dopamine may not play a role in the choice performance for values learned through reinforcement learning in humans.
Multi-omic profiling of transcriptome and DNA methylome in single nuclei with molecular partitioning
Authors: Luo Chongyuan , Liu Hanqing , Wang Bang-An , Bartlett Anna , Rivkin Angeline , Nery Joseph R. , Ecker Joseph R. 
Published: October 2018

AbstractSingle-cell transcriptomic and epigenomic analyses provide powerful strategies for unbiased determination of cell types in mammalian tissues. Although previous studies have identified cell types using individual molecular signatures, the generation of consensus cell type classification requires the integration of multiple data types. Most existing single-cell techniques can only make one type of molecular measurement. Here we describe single-nucleus methylcytosine and transcriptome sequencing (snmCT-seq), a multi-omic method that requires no physical separation of DNA and RNA molecules. We demonstrated that snmCT-seq profiles generated from single cells or nuclei robustly distinguish human cell types and accurately measures cytosine DNA methylation and gene expression signatures of each cell type.
Unleashing floret fertility by a mutated homeobox gene improved grain yield during wheat evolution under domestication
Authors: Sakuma Shun , Golan Guy , Guo Zifeng , Ogawa Taiichi , Tagiri Akemi , Sugimoto Kazuhiko , Bernhardt Nadine , Brassac Jonathan , Mascher Martin , Hensel Goetz , Ohnishi Shizen , Jinno Hironobu , Yamashita Yoko , Ayalon Idan , Peleg Zvi , Schnurbusch Thorsten , Komatsuda Takao 
Published: October 2018

AbstractFloret fertility is a key trait to determine the number of grains per inflorescence in cereals. During wheat (Triticum sp.) evolution, floret fertility has been increased and current bread wheat (T. aestivum L.) produces three to five grains per spikelet; however, little is known about the genetic basis controlling floret fertility. Here we identify the quantitative trait locus Grain Number Increase 1 (GNI1), encoding a homeodomain leucine zipper class I (HD-Zip I) transcription factor. GNI1 evolved in the Triticeae through gene duplication and functionalization. GNI1 was predominantly expressed in the most apical floret primordia and parts of the rachilla, suggesting that GNI1 inhibits rachilla growth and development. GNI1 expression decreased during wheat evolution, and as a consequence, more fertile florets and grains per spikelet are being produced. Genetic analysis revealed that the reduced-function allele of GNI1-A contributes to increase the number of fertile florets per spikelet. The knockdown of GNI1 in transgenic hexaploid wheat improved fertile floret and grain number. Furthermore, wheat plants carrying the impaired allele increased grain yield under field conditions. Our findings illuminate that gene duplication and functionalization generated evolutionary novelty for floret fertility (i.e. reducing floral numbers) while the mutations towards increased grain production were under selection during wheat evolution under domestication.
Significance StatementGrain number is a fundamental trait for cereal grain yield; but its underlying genetic basis is mainly unknown in wheat. Here we show for the first time a direct link between increased floret fertility, higher grain number per spike and higher plot-yields of wheat in the field. We have identified GNI1 gene encoding an HD-Zip I transcription factor responsible for increased floret fertility. The wild type allele imposes an inhibitory role specifically during rachilla development, indicating that expression of this protein actively shuts-down grain yield potential; whereas, the reduced-function allele enables more florets and grains to be produced. GNI1 evolved through gene duplication in Triticeae and its mutations were under parallel human selection during wheat and barley evolution under domestication.