bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum percolation in quasicrystals using continuous-time quantum walk
Authors: Chawla Prateek , Ambarish C V , Chandrashekar C M 
Published: November 2019

Abstract
We study the percolation of a quantum particle on quasicrystal lattices and compare it with the square lattice. For our study, we have considered quasicrystal lattices modelled on the pentagonally symmetric Penrose tiling and the octagonally symmetric Ammann-Beenker tiling. The dynamics of the quantum particle are modelled using the continuous-time quantum walk (CTQW) formalism. We present a comparison of the behaviour of the CTQW on the two aperiodic quasicrystal lattices and the square lattice when all the vertices are connected and when disorder is introduced in the form of disconnections between the vertices. Unlike on a square lattice, we see a significant fraction of the quantum state localized around the origin in the quasicrystal lattices. With increase in disorder, the percolation probability of a particle on a quasicrystal lattice decreases significantly faster when compared to the square lattice. This study also sheds light on the fraction of disconnections allowed to see percolation of quantum particle on these quasicrystal lattices.
CATHER: a novel threading algorithm with predicted contacts
Authors: Du Zongyang , Pan Shuo , Wu Qi , Peng Zhenling , Yang Jianyi 
Published: November 2019

Abstract

Motivation
Threading is one of the most effective methods for protein structure prediction. In recent years, the increasing accuracy in protein contact map prediction opens a new avenue to improve the performance of threading algorithms. Several preliminary studies suggest that with predicted contacts, the performance of threading algorithms can be improved greatly. There is still much room to explore to make better use of predicted contacts.

Results
We have developed a new contact-assisted threading algorithm named CATHER using both conventional sequential profiles and contact map predicted by a deep learning-based algorithm. Benchmark tests on an independent test set and the CASP12 targets demonstrated that CATHER made significant improvement over other methods which only use either sequential profile or predicted contact map. Our method was ranked at the Top 10 among all 39 participated server groups on the 32 free modeling targets in the blind tests of the CASP13 experiment. These data suggest that it is promising to push forward the threading algorithms by using predicted contacts.

Availability and implementation
http://yanglab.nankai.edu.cn/CATHER/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Proactive visual and statistical analysis of genomic data in Epiviz
Authors: Cui Zhe , Kancherla Jayaram , Chang Kyle W , Elmqvist Niklas , Corrada Bravo Héctor 
Published: November 2019

Abstract

Motivation
Integrative analysis of genomic data that includes statistical methods in combination with visual exploration has gained widespread adoption. Many existing methods involve a combination of tools and resources: user interfaces that provide visualization of large genomic datasets, and computational environments that focus on data analyses over various subsets of a given dataset. Over the last few years, we have developed Epiviz as an integrative and interactive genomic data analysis tool that incorporates visualization tightly with state-of-the-art statistical analysis framework.

Results
In this article, we present Epiviz Feed, a proactive and automatic visual analytics system integrated with Epiviz that alleviates the burden of manually executing data analysis required to test biologically meaningful hypotheses. Results of interest that are proactively identified by server-side computations are listed as notifications in a feed. The feed turns genomic data analysis into a collaborative work between the analyst and the computational environment, which shortens the analysis time and allows the analyst to explore results efficiently.

We discuss three ways where the proposed system advances the field of genomic data analysis: (i) takes the first step of proactive data analysis by utilizing available CPU power from the server to automate the analysis process; (ii) summarizes hypothesis test results in a way that analysts can easily understand and investigate; (iii) enables filtering and grouping of analysis results for quick search. This effort provides initial work on systems that substantially expand how computational and visualization frameworks can be tightly integrated to facilitate interactive genomic data analysis.

Availability and implementation
The source code for Epiviz Feed application is available at http://github.com/epiviz/epiviz_feed_polymer. The Epiviz Computational Server is available at http://github.com/epiviz/epiviz-feed-computation. Please refer to Epiviz documentation site for details: http://epiviz.github.io/.
Fusion-Bloom: fusion detection in assembled transcriptomes
Authors: Chiu Readman , Nip Ka Ming , Birol Inanc 
Published: November 2019

Abstract

Summary
Presence or absence of gene fusions is one of the most important diagnostic markers in many cancer types. Consequently, fusion detection methods using various genomics data types, such as RNA sequencing (RNA-seq) are valuable tools for research and clinical applications. While information-rich RNA-seq data have proven to be instrumental in discovery of a number of hallmark fusion events, bioinformatics tools to detect fusions still have room for improvement. Here, we present Fusion-Bloom, a fusion detection method that leverages recent developments in de novo transcriptome assembly and assembly-based structural variant calling technologies (RNA-Bloom and PAVFinder, respectively). We benchmarked Fusion-Bloom against the performance of five other state-of-the-art fusion detection tools using multiple datasets. Overall, we observed Fusion-Bloom to display a good balance between detection sensitivity and specificity. We expect the tool to find applications in translational research and clinical genomics pipelines.

Availability and implementation
Fusion-Bloom is implemented as a UNIX Make utility, available at https://github.com/bcgsc/pavfinder and released under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Limited impacts of chronic eye fluke infection on the reproductive success of a fish host
Authors: Nezhybová Veronika , Reichard Martin , Methling Caroline , Ondračková Markéta 
Published: November 2019

AbstractParasitic infections may affect the reproductive success of the host either directly, through behavioural modification, or indirectly, by altering their reproductive investment in response to infection. We determined the effects of infection with the eye fluke Diplostomum pseudospathaceum (Trematoda) on the reproductive traits of European bitterling (Rhodeus amarus, Cyprinidae), an intermediate fish host with a resource-based mating system. Male bitterling infected by Diplostomum exhibited a larger but less pronounced red eye spot (sexually selected signal) than control males, suggesting that infected males were less preferred by females. The frequency of female ovulation and number of offspring were comparable between the infected and the control group, although there was a 1–2 week delay in the peak of ovulation and offspring production in infected fish, which is known to coincide with higher juvenile mortality. Chronic eye fluke infection had minimal metabolic costs (measured as oxygen consumption) and, consistent with these results, reproductive activity did not differ between infected and control fish in an experimental test of intersexual selection. Overall, the impact of eye fluke infection on the reproduction of European bitterling was limited. We consider the potential effect of favourable conditions during experiments (abundant food, access to spawning substrate and lack of predators and co-infections) on experimental outcomes and recognize that the effects of chronic eye fluke infection in natural conditions might be more pronounced.
FOXD3, frequently methylated in colorectal cancer, acts as a tumor suppressor and induces tumor cell apoptosis under ER stress via p53
Authors: Xu Ming , Zhu Jing , Liu Shuiping , Wang Chan , Shi Qinglan , Kuang Yeye , Fang Xiao , Hu Xiaotong 
Published: November 2019

AbstractForkhead box D3 (FOXD3), an important member of the forkhead box transcription factor family, has many biological functions. However, the role and signaling pathways of FOXD3 in colorectal cancer (CRC) are still unclear. We examined FOXD3 expression and methylation in normal colon mucosa, CRC cell lines and primary tumors by reverse transcription–polymerase chain reaction, methylation-specific PCR and bisulfite genomic sequencing. We also evaluated its tumor-suppressive function by examining its modulation of apoptosis under endoplasmic reticulum (ER) stress in CRC cells. The FOXD3 target signal pathway was identified by western blotting, immunofluorescence and chromatin immunoprecipitation. We found that FOXD3 was frequently methylated and silenced in CRC cell lines and was downregulated in CRC tissues compared with paired adjacent non-tumor tissues. Meanwhile, low FOXD3 protein expression was significantly correlated with poor histopathological grading, lymph node metastasis and poor prognosis of patients, indicating its potential as a tumor marker that may be of potential value as a therapeutic target for CRC. Moreover, restoration of FOXD3 expression inhibited the proliferation and migration of tumor cells. FOXD3 also increased mitochondrial apoptosis through the unfolded protein response under ER stress. Furthermore, we found that FOXD3 could bind directly to the promoter of p53 and enhance its expression. Knockdown of p53 impaired the effect of apoptosis induced by FOXD3. In conclusion, we showed for the first time that FOXD3, which is frequently methylated in CRC, acted as a tumor suppressor inducing tumor cell apoptosis under ER stress via p53.
Slowly-Conducting Pyramidal Tract Neurons in Macaque and Rat
Authors: Kraskov A , Soteropoulos D S , Glover I S , Lemon R N , Baker S N 
Published: November 2019

AbstractAnatomical studies report a large proportion of fine myelinated fibers in the primate pyramidal tract (PT), while very few PT neurons (PTNs) with slow conduction velocities (CV) (&lt;~10 m/s) are reported electrophysiologically. This discrepancy might reflect recording bias toward fast PTNs or prevention of antidromic invasion by recurrent inhibition (RI) of slow PTNs from faster axons. We investigated these factors in recordings made with a polyprobe (32 closely-spaced contacts) from motor cortex of anesthetized rats (n = 2) and macaques (n = 3), concentrating our search on PTNs with long antidromic latencies (ADLs). We identified 21 rat PTNs with ADLs &gt;2.6 ms and estimated CV 3–8 m/s, and 67 macaque PTNs (&gt;3.9 ms, CV 6–12 m/s). Spikes of most slow PTNs were small and present on only some recording contacts, while spikes from simultaneously recorded fast-conducting PTNs were large and appeared on all contacts. Antidromic thresholds were similar for fast and slow PTNS, while spike duration was considerably longer in slow PTNs. Most slow PTNs showed no signs of failure to respond antidromically. A number of tests, including intracortical microinjection of bicuculline (GABAA antagonist), failed to provide any evidence that RI prevented antidromic invasion of slow PTNs. Our results suggest that recording bias is the main reason why previous studies were dominated by fast PTNs.
Increase of Dose Associated With Decrease in Protection Against Controlled Human Malaria Infection by PfSPZ Vaccine in Tanzanian Adults
Authors: Jongo Said A , Church L W Preston , Mtoro Ali T , Schindler Tobias , Chakravarty Sumana , Ruben Adam J , Swanson Phillip A , Kassim Kamaka R , Mpina Maximillian , Tumbo Anneth-Mwasi , Milando Florence A , Qassim Munira , Juma Omar A , Bakari Bakari M , Simon Beatus , James Eric R , Abebe Yonas , KC Natasha , Saverino Elizabeth , Fink Martina , Cosi Glenda , Gondwe Linda , Studer Fabian , Styers David , Seder Robert A , Schindler Tobias , Billingsley Peter F , Daubenberger Claudia , Sim B Kim Lee , Tanner Marcel , Richie Thomas L , Abdulla Salim , Hoffman Stephen L 
Published: November 2019

Abstract

Background
A vaccine would be an ideal tool for reducing malaria’s impact. PfSPZ Vaccine (radiation attenuated, aseptic, purified, cryopreserved Plasmodium falciparum [Pf] sporozoites [SPZ]) has been well tolerated and safe in &gt;1526 malaria-naive and experienced 6-month to 65-year-olds in the United States, Europe, and Africa. When vaccine efficacy (VE) of 5 doses of 2.7 × 105 PfSPZ of PfSPZ Vaccine was assessed in adults against controlled human malaria infection (CHMI) in the United States and Tanzania and intense field transmission of heterogeneous Pf in Mali, Tanzanians had the lowest VE (20%).

Methods
To increase VE in Tanzania, we increased PfSPZ/dose (9 × 105 or 1.8 × 106) and decreased numbers of doses to 3 at 8-week intervals in a double blind, placebo-controlled trial.

Results
All 22 CHMIs in controls resulted in parasitemia by quantitative polymerase chain reaction. For the 9 × 105 PfSPZ group, VE was 100% (5/5) at 3 or 11 weeks (P &lt; .000l, Barnard test, 2-tailed). For 1.8 × 106 PfSPZ, VE was 33% (2/6) at 7.5 weeks (P = .028). VE of dosage groups (100% vs 33%) was significantly different (P = .022). Volunteers underwent repeat CHMI at 37–40 weeks after last dose. 6/6 and 5/6 volunteers developed parasitemia, but time to first parasitemia was significantly longer than controls in the 9 × 105 PfSPZ group (10.89 vs 7.80 days) (P = .039), indicating a significant reduction in parasites in the liver. Antibody and T-cell responses were higher in the 1.8 × 106 PfSPZ group.

Conclusions
In Tanzania, increasing the dose from 2.7 × 105 to 9 × 105 PfSPZ increased VE from 20% to 100%, but increasing to 1.8 × 106 PfSPZ significantly reduced VE.

Clinical Trials Registration
NCT02613520.
Asymmetrical elevation of esophagogastric junction pressure suggests hiatal repair contributes to antireflux surgery dysphagia
Authors: Myers J C , Jamieson G G , Szczesniak M M , Estremera-Arévalo F , Dent J 
Published: November 2019

ABSTRACT
The radial distribution of esophago-gastric junction (EGJ) pressures with regard to troublesome dysphagia (TDysph) after antireflux surgery is poorly understood. Before and after antireflux surgery, end-expiratory and peak-inspiratory EGJ pressures were measured at eight angles of 45° radial separation in patients with reflux disease. All 34 patients underwent posterior crural repair, then either 90° anterior (N = 13) or 360° fundoplication (N = 21). Dysphagia was assessed prospectively using a validated questionnaire (score range 0–45) and TDysph defined as a dysphagia score that was ≥5 above pre-op baseline. Compared with before surgery, for 90° fundoplication, end-expiratory EGJ pressures were highest in the left-anterolateral sectors, the position of the partial fundoplication. In other sectors, pressures were uniformly elevated. Compared with 90° fundoplication, radial pressures after 360° fundoplication were higher circumferentially (P = 0.004), with a posterior peak. Nine patients developed TDysph after surgery with a greater increase in end-expiratory and peak-inspiratory EGJ pressures (P = 0.03 and 0.03, respectively) and significantly higher inspiratory pressure at the point of maximal radial pressure asymmetry (P = 0.048), compared with 25 patients without TDysph. Circumferential elevation of end-expiratory EGJ pressure after 90° and 360° fundoplication suggests hiatal repair elevates EGJ pressure by extrinsic compression. The highly localized focal point of elevated EGJ pressure upon inspiration in patients with TDysph after surgery is indicative of a restrictive diaphragmatic hiatus in the presence of a fundoplication.
Zinc Deficiency Activates the IL-23/Th17 Axis to Aggravate Experimental Colitis in Mice
Authors: Higashimura Yasuki , Takagi Tomohisa , Naito Yuji , Uchiyama Kazuhiko , Mizushima Katsura , Tanaka Makoto , Hamaguchi Masahide , Itoh Yoshito 
Published: November 2019

Abstract

Background and Aims
Patients with inflammatory bowel disease [IBD], especially Crohn’s disease, often develop zinc deficiency. However, the precise mechanisms by which zinc deficiency affects IBD pathology, particularly intestinal macrophage function, remain unclear. We studied the effects of zinc deficiency on the development and progression of colitis in mice.

Methods
To induce colitis, mice were treated with 2,4,6-trinitrobenzene sulphonic acid. Rag1−/− mice were then given injections of naïve CD4+CD62L+ T cells. The respective degrees of mucosal injury of mice that had received a zinc chelator (TPEN; N,N,N′,N′-tetrakis [2-pyridylmethyl]ethylenediamine) and of control mice were subsequently compared. Colonic lamina propria mononuclear cells were isolated by enzymatic digestion and were examined using flow cytometry. To generate mouse bone marrow-derived macrophages [BMDMs], bone marrow cells were stimulated with mouse macrophage-colony stimulating factor.

Results
Zinc deficiency aggravates colonic inflammation through the activation of type 17 helper T [Th17] cells in mice. Flow cytometric analysis revealed that zinc deficiency significantly increases the proportion of pro-inflammatory [M1] macrophages in colonic lamina propria mononuclear cells obtained from inflamed colon. Interferon-γ plus lipopolysaccharide-mediated M1 skewing alters the expression of zinc transporters in BMDMs and thereby decreases the intracellular free zinc. TPEN treatment mimicking the effects of the M1 skewing up-regulates IL-23p19 expression, which is strongly related to Th17 development. Furthermore, the nuclear accumulation of interferon-regulatory factor 5 is closely involved in IL-23p19 induction in zinc-deficient macrophages.

Conclusions
Zinc deficiency aggravates colonic inflammation through activation of the IL-23/Th17 axis. This activation is controlled by subcellular distribution of interferon-regulatory factor 5.
Potential of Colorado Potato Beetle (Coleoptera: Chrysomelidae) to Adapt to Alternative Host Plants
Authors: Hiiesaar Külli , Williams Ingrid H , Jõgar Katrin , Karise Reet , Ploomi Angela , Metspalu Luule , Mänd Marika 
Published: November 2019

Abstract
Twelve selected cultivated or wild solanaceae (Solanum dulcamara, Solanum nigrum, Solanum villosum, Solanum lycopersicum, Solanum muricatum, Solanum melongena, Datura innoxia, Datura metel, Physalis spp., Capsicum annuum, Nicotiana alata, and Petunia spp.) (all species Solanales: Solanaceae) were tested as potential alternative host plants against Solanum tuberosum for a local population of the Colorado potato beetle Leptinotarsa decemlineata Say (CPB) in Estonia. Some CPB populations in America and southern Europe accept most of these plants. However, geographically isolated populations of beetles can differ in their acceptance of new host plants. Migrants from the southern Europe supplement Estonian beetle population regularly, so individuals may differ in their host plant preferences. S. melongena and S. dulcamara were well accepted by the beetles, Lycopersicum spp. (Solanales: Solanaceae) and N. alata were intermediate, and S. villosum and S. nigrum were least accepted. The beetles rejected S. muricatum, Physalis spp., C. annuum, Petunia spp., and D. metel. First-instar larvae completed a full life cycle only on S. dulcamara, N. alata, S. lycopesicum, S. melongena, although their development rate was slower, mortality was higher and emerging adults were underweight relative to those that fed on S. tuberosum. The fourth-instar larvae were less sensitive in relation to food. We found that S. dulcamara as a native plant could provide resources for CPB during early and late season. At the same time, the cultivated S. melongena would be suitable plant species for further testing as dead-end crop for integrated pest management.
The ‘de Winter’ electrocardiogram pattern as a ST-elevation myocardial infarction equivalent: a case report
Authors: Grandjean Thierry , Degrauwe Sophie , Tessitore Elena , Iglesias Juan F 
Published: November 2019

Abstract

Background
A ‘STEMI equivalent’ electrocardiogram (ECG) pattern reflects an acute thrombotic occlusion of a large epicardial coronary artery without ST-segment elevation. These ECG patterns are less known by caregivers.

Case summary
We describe the case of a 56-year-old patient suffering from acute chest pain, presenting in our emergency department with a ‘de Winter’ ECG pattern: an upsloping ST-segment depression with tall symmetrical T waves associated with left anterior descending artery occlusion.

Discussion
The ‘de Winter’ ECG pattern, as other ‘STEMI equivalent’, must be recognized promptly and treated as soon as possible with emergent reperfusion by percutaneous coronary intervention.
A case report: a 22-year-old septic patient with central venous pO2 of 198 mmHg
Authors: Ehlers Ulrike Elisabeth , Mutter Michael , Fahner Peter Jurriaan , Pfammatter Thomas 
Published: November 2019

Abstract

Background
Central venous saturation and central venous pressure can be determined with central venous catheters. Therefore, the tip of the catheter should be located in the superior vena cava. The location can be monitored by electrocardiography or X-ray. The central venous pressure curve is displayed on the monitor. The reference value of central venous saturation is &gt;70%. Venous pO2 is normally 35–45 mmHg and central venous pressure 1–9 mmHg.

Case summary
We treated a 22-year-old patient with septic shock. Central venous saturation was 100% with a pO2 of 198 mmHg. The arterial blood gas analysis was comparatively low with saturation of 98% and pO2 of 111 mmHg. On chest X-ray, the central venous catheter tip appeared on the left side of the heart. On echocardiography, aortic positioning was not evident. On the monitor, a ‘venous pressure-like’ curve was seen, that did not stand in exact correlation to the electrocardiogram curve. The computed tomography (CT) image showed placement of the catheter in the upper left pulmonary vein. The patient had a partial anomalous pulmonary venous return.

Discussion
The C-wave of the central venous pressure curve normally occurs after the R-wave of the electrocardiogram. If C-waves appeared before R-waves, the central venous catheter placement is not central venous and must be checked. In our case, the apparent ‘venous’ pO2 in blood gas examination was higher than arterial pO2. The catheter position had to be in an oxygenated vessel proximal to the left ventricle. A vascular anomaly was a possible diagnosis and was confirmed on CT imaging.