bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionized Calcium Binding Adaptor Molecule 1 (IBA1)
Authors: Zhang Xiaoming , Wang Li-Ping , Ziober Amy , Zhang Paul J , Bagg Adam 
Published: September 2020

Abstract

Objectives
Ionized calcium binding adaptor molecule 1 (IBA1), a marker of microglia/macrophages, has not been investigated in human hematopathologic contexts. We evaluated its expression in mature and immature neoplasms of monocytic/histiocytic and dendritic cell (DC) origin.

Methods
Immunohistochemistry for IBA1, CD14, CD68, and CD163 was performed on a total of 114 cases, including a spectrum of monocytic/histiocytic and DC neoplasms (20 tissue based and 59 bone marrow based) and several nonhistiocytic/monocytic/DC neoplasms as control groups (15 tissue based and 20 bone marrow based).

Results
IBA1 expression was observed in all types of mature tissue-based histiocytic/DC neoplasms (20/20) but not in the corresponding control group (0/15). In bone marrow–based cases, IBA1 was expressed in most acute myeloid leukemias (AMLs) with monocytic differentiation (48/53), both blastic plasmacytoid dendritic cell neoplasms (2/2), and all chronic myelomonocytic leukemias (4/4), while it was positive in only one nonmonocytic AML (1/15) and none of the acute lymphoblastic leukemias (0/5). Collectively, IBA1 showed much higher sensitivity and specificity (93.7%, 97.1%) compared with CD14 (65.4%, 88.2%), CD68 (74.4%, 74.2%), and CD163 (52.6%, 90.6%).

Conclusions
IBA1 is a novel, highly sensitive, and specific marker for diagnosing neoplasms of monocytic/histiocytic and DC origin.
Inferring signaling pathways with probabilistic programming
Authors: Merrell David , Gitter Anthony 
Published: September 2020

Abstract

Motivation
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to understand diseases and therapies at the cellular level, it is crucial to have an accurate understanding of the signaling pathways at work. Since signaling pathways can be modified by disease, the ability to infer signaling pathways from condition- or patient-specific data is highly valuable. A variety of techniques exist for inferring signaling pathways. We build on past works that formulate signaling pathway inference as a Dynamic Bayesian Network structure estimation problem on phosphoproteomic time course data. We take a Bayesian approach, using Markov Chain Monte Carlo to estimate a posterior distribution over possible Dynamic Bayesian Network structures. Our primary contributions are (i) a novel proposal distribution that efficiently samples sparse graphs and (ii) the relaxation of common restrictive modeling assumptions.

Results
We implement our method, named Sparse Signaling Pathway Sampling, in Julia using the Gen probabilistic programming language. Probabilistic programming is a powerful methodology for building statistical models. The resulting code is modular, extensible and legible. The Gen language, in particular, allows us to customize our inference procedure for biological graphs and ensure efficient sampling. We evaluate our algorithm on simulated data and the HPN-DREAM pathway reconstruction challenge, comparing our performance against a variety of baseline methods. Our results demonstrate the vast potential for probabilistic programming, and Gen specifically, for biological network inference.

Availability and implementation
Find the full codebase at https://github.com/gitter-lab/ssps.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sex-biased parasitism and expression of a sexual signal
Authors: Rosso Adam A , Nicholson Daniel J , Logan Michael L , Chung Albert K , Curlis John David , Degon Zachariah M , Knell Robert J , Garner Trenton W J , McMillan W Owen , Cox Christian L 
Published: September 2020

AbstractGiven that sexual signals are often expressed more highly in one sex than the other, they can impose a sex-specific cost of reproduction through parasitism. The two primary paradigms regarding the relationship of parasites to sexual signals are the good genes hypothesis and the immunocompetence handicap hypothesis; however, there are other ecological, morphological and energetic factors that might influence parasite infections in a sex-specific fashion. We tested the relationship between expression of a sexual signal (the dewlap) and ecological, morphological and energetic factors mediating ectoparasite (mite) load between male and female Panamanian slender anoles (Anolis apletophallus). We found that males were more highly parasitized than females because of the preponderance of ectoparasites on the larger dewlap of males. Indeed, ectoparasite infection increased with both body size and dewlap size in males but not in females, and parasite infection was related to energy storage in a sex-specific fashion for the fat bodies, liver and gonads. Our work and previous work on testosterone in anoles suggests that this pattern did not arise solely from immunosuppression by testosterone, but that mites prefer the dewlap as an attachment site. Thus, the expression of this sexual signal could incur a fitness cost that might structure life-history trade-offs.
Optimal estimation of bacterial growth rates based on a permuted monotone matrix
Authors: Ma Rong , Cai T Tony , Li Hongzhe 
Published: September 2020

SummaryMotivated by the problem of estimating bacterial growth rates for genome assemblies from shotgun metagenomic data, we consider the permuted monotone matrix model $Y=\Theta\Pi+Z$ where $Y\in \mathbb{R}^{n\times p}$ is observed, $\Theta\in \mathbb{R}^{n\times p}$ is an unknown approximately rank-one signal matrix with monotone rows, $\Pi \in \mathbb{R}^{p\times p}$ is an unknown permutation matrix, and $Z\in \mathbb{R}^{n\times p}$ is the noise matrix. In this article we study estimation of the extreme values associated with the signal matrix $\Theta$, including its first and last columns and their difference. Treating these estimation problems as compound decision problems, minimax rate-optimal estimators are constructed using the spectral column-sorting method. Numerical experiments on simulated and synthetic microbiome metagenomic data are conducted, demonstrating the superiority of the proposed methods over existing alternatives. The methods are illustrated by comparing the growth rates of gut bacteria in inflammatory bowel disease patients and control subjects.
The Impact of Hypertension and Use of Calcium Channel Blockers on Tuberculosis Treatment Outcomes
Authors: Chidambaram Vignesh , Gupte Akshay , Wang Jann-Yuan , Golub Jonathan E , Karakousis Petros C 
Published: September 2020

Abstract

Background
Hypertension induces systemic inflammation, but its impact on the outcome of infectious diseases like tuberculosis (TB) is unknown. Calcium channel blockers (CCB) improve TB treatment outcomes in preclinical models, but their effect in patients with TB remain unclear.

Methods
This retrospective cohort study, including all patients &gt; 18 years receiving treatment for culture-confirmed, drug-sensitive TB from 2000 to 2016 at the National Taiwan University Hospital, assessed the association of hypertension and CCB use with all-cause and infection-related mortality during the first 9 months of TB treatment, as well as sputum smear microscopy and sputum culture positivity at 2 and 6 months.

Results
Of the 2894 patients, 1052 (36.4%) had hypertension. A multivariable analysis revealed that hypertension was associated with increased mortality due to all causes (hazard ratio [HR], 1.57; 95% confidence interval [CI], 1.23–1.99) and infections (HR, 1.87; 95% CI, 1.34–2.6), but there were no statistical differences in microbiological outcomes when stratified based on hypertensive group. Dihydropyridine-CCB (DHP-CCB) use was associated only with reduced all-cause mortality (HR, 0.67; 95% CI, .45–.98) by univariable Cox regression. There were no associations between DHP-CCB use and infection-related mortality (HR, 0.78; 95% CI, .46–1.34) or microbiological outcomes in univariable or multivariable regression analyses.

Conclusions
Patients with hypertension have increased all-cause mortality and infection-related mortality during the 9 months following TB treatment initiation. DHP-CCB use may lower all-cause mortality in TB patients with hypertension. The presence of hypertension or the use of CCB did not result in a significant change in microbiological outcomes.
Human Papillomavirus Vaccination Prior to Loop Electroexcision Procedure Does Not Prevent Recurrent Cervical High-grade Squamous Intraepithelial Lesions in Women Living With Human Immunodeficiency Virus: A Randomized, Double-blind, Placebo-controlled Trial
Authors: Firnhaber Cynthia , Swarts Avril , Jezile Vuyokazi , Mulongo Masango , Goeieman Bridgette , Williams Sophie , Faesen Mark , Michelow Pamela , Wilkin Timothy 
Published: September 2020

Abstract

Background
Women living with human immunodeficiency virus (HIV), especially in sub-Saharan Africa, are at high risk for cervical high-grade squamous intraepithelial lesions (HSIL) and cervical cancer. These women have high HSIL recurrence rates after loop electroexcision procedure (LEEP). Retrospective studies suggest that human papillomavirus (HPV) vaccination improves response to treatment of cervical HSIL.

Methods
We performed a double-blind, randomized clinical trial enrolling 180 women living with HIV in Johannesburg, South Africa, diagnosed with cervical HSIL by colposcopic biopsy. Women received quadrivalent HPV vaccine or placebo (1:1) at entry, week 4, and week 26. LEEP was performed at week 4. Colposcopic-directed biopsies and cervical cytology were performed at weeks 26 and 52. The primary endpoint, cervical HSIL by histology or cytology at either week 26 or 52, was compared between arms using χ 2 analysis.

Results
Participant characteristics included median age of 39 years and median CD4 count 489 cells/μL, and 94% had HIV suppression. One hundred seventy-four women completed the vaccine/placebo series and had evaluable results at week 26 or 52. The proportion experiencing the primary endpoint was similar in the vaccine and placebo groups (53% vs 45%; relative risk, 1.18 [95% confidence interval, .87–1.6]; P = .29). HSIL recurrence was associated with a LEEP biopsy result of HSIL and detection of HSIL at the margins of the LEEP sample.

Conclusions
This study did not support HPV vaccination to prevent recurrent HSIL after LEEP in women living with HIV. Recurrent HSIL was high despite virologic suppression. Improved treatments are needed for HSIL to reduce the burden of cervical cancer among women living with HIV.

Clinical Trials Registration
NCT01928225.
Diagnostic Delay Is Associated With Complicated Disease and Growth Impairment in Paediatric Crohn’s Disease
Authors: Ricciuto Amanda , Mack David R , Huynh Hien Q , Jacobson Kevan , Otley Anthony R , deBruyn Jennifer , El-Matary Wael , Deslandres Colette , Sherlock Mary E , Critch Jeffrey N , Bax Kevin , Jantchou Prevost , Seidman Ernest G , Carman Nicholas , Rashid Mohsin , Muise Aleixo , Wine Eytan , Carroll Matthew W , Lawrence Sally , Van Limbergen Johan , Benchimol Eric I , Walters Thomas D , Griffiths Anne M , Church Peter C 
Published: September 2020

Abstract

Background
Paediatric data on the association between diagnostic delay and inflammatory bowel disease [IBD] complications are lacking. We aimed to determine the effect of diagnostic delay on stricturing/fistulising complications, surgery, and growth impairment in a large paediatric cohort, and to identify predictors of diagnostic delay.

Methods
We conducted a national, prospective, multicentre IBD inception cohort study including 1399 children. Diagnostic delay was defined as time from symptom onset to diagnosis &gt;75th percentile. Multivariable proportional hazards [PH] regression was used to examine the association between diagnostic delay and stricturing/fistulising complications and surgery, and multivariable linear regression to examine the association between diagnostic delay and growth. Predictors of diagnostic delay were identified using Cox PH regression.

Results
Overall (64% Crohn’s disease [CD]; 36% ulcerative colitis/IBD unclassified [UC/IBD-U]; 57% male]), median time to diagnosis was 4.2 (interquartile range [IQR] 2.0–9.2) months. For the overall cohort, diagnostic delay was &gt;9.2 months; in CD, &gt;10.8 months and in UC/IBD-U, &gt;6.6 months. In CD, diagnostic delay was associated with a 2.5-fold higher rate of strictures/internal fistulae (hazard ratio [HR] 2.53, 95% confidence interval [CI] 1.41–4.56). Every additional month of diagnostic delay was associated with a decrease in height-for-age z-score of 0.013 standard deviations [95% CI 0.005–0.021]. Associations persisted after adjusting for disease location and therapy. No independent association was observed between diagnostic delay and surgery in CD or UC/IBD-U. Diagnostic delay was more common in CD, particularly small bowel CD. Abdominal pain, including isolated abdominal pain in CD, was associated with diagnostic delay.

Conclusions
Diagnostic delay represents a risk factor for stricturing/internal fistulising complications and growth impairment in paediatric CD.

Podcast
This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast
Seeking the historical listener
Authors: Plank Steven 
Published: September 2020

Abstract
This article considers questions relating to the performance practice of listening to music in early modern contexts. The evidence of paintings by Pieter Lastman, Gerard ter Borch and Hendrik Sorgh, poetry by Robert Herrick, William Shakespeare and Edmund Waller, and accounts of performances by Francesco da Milano, Nicola Matteis and Queen Elizabeth I all help to bring into focus questions of attentiveness, affective response and analogical understanding. The source material also interestingly raises the possibility of occasionally understanding the act of listening within a frame of erotic relationship modelled on Laura Mulvey’s well-known concept of the ‘male gaze’.
The species evenness of “prey” bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil
Authors: Qian Hang , Hou Chunli , Liao Hao , Wang Li , Han Shun , Peng Shaobing , Chen Wenli , Huang Qiaoyun , Luo Xuesong 
Published: September 2020

ABSTRACT
To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.
Back to the future: old methods for new estimation and test of the Gutenberg–Richter b-value for catalogues with variable completeness
Authors: Taroni Matteo 
Published: September 2020

SUMMARYIn this short paper we show how to use the classical maximum likelihood estimation procedure for the b-value of the Gutenberg–Richter law for catalogues with different levels of completeness. With a simple correction, that is subtracting the relative completeness level to each magnitude, it becomes possible to use the classical approach. Moreover, this correction allows to adopt the testing procedures, initially made for catalogues with a single level of completeness, for catalogues with different levels of completeness too.
Coenzyme Q10 modulates sulfide metabolism and links the mitochondrial respiratory chain to pathways associated to one carbon metabolism
Authors: González-García Pilar , Hidalgo-Gutiérrez Agustín , Mascaraque Cristina , Barriocanal-Casado Eliana , Bakkali Mohammed , Ziosi Marcello , Abdihankyzy Ussipbek Botagoz , Sánchez-Hernández Sabina , Escames Germaine , Prokisch Holger , Martín Francisco , Quinzii Catarina M , López Luis C 
Published: September 2020

AbstractAbnormalities of one carbon, glutathione and sulfide metabolisms have recently emerged as novel pathomechanisms in diseases with mitochondrial dysfunction. However, the mechanisms underlying these abnormalities are not clear. Also, we recently showed that sulfide oxidation is impaired in Coenzyme Q10 (CoQ10) deficiency. This finding leads us to hypothesize that the therapeutic effects of CoQ10, frequently administered to patients with primary or secondary mitochondrial dysfunction, might be due to its function as cofactor for sulfide:quinone oxidoreductase (SQOR), the first enzyme in the sulfide oxidation pathway. Here, using biased and unbiased approaches, we show that supraphysiological levels of CoQ10 induces an increase in the expression of SQOR in skin fibroblasts from control subjects and patients with mutations in Complex I subunits genes or CoQ biosynthetic genes. This increase of SQOR induces the downregulation of the cystathionine β-synthase and cystathionine γ-lyase, two enzymes of the transsulfuration pathway, the subsequent downregulation of serine biosynthesis and the adaptation of other sulfide linked pathways, such as folate cycle, nucleotides metabolism and glutathione system. These metabolic changes are independent of the presence of sulfur aminoacids, are confirmed in mouse models, and are recapitulated by overexpression of SQOR, further proving that the metabolic effects of CoQ10 supplementation are mediated by the overexpression of SQOR. Our results contribute to a better understanding of how sulfide metabolism is integrated in one carbon metabolism and may explain some of the benefits of CoQ10 supplementation observed in mitochondrial diseases.
The role of medicine donations in the global programme for the elimination of lymphatic filariasis
Authors: Williams Tijana , Taylor Rachel , Iwamoto Minne , Hida Takayuki , Gusovsky Fabian 
Published: September 2020

Abstract
World Health Assembly Resolution 50.29, adopted in 1997, committed the World Health Organization (WHO) and its member states to eliminate lymphatic filariasis (LF) as a public health problem. In 2000, to support this ambitious goal and the health ministries in the &gt;70 LF-endemic countries, the Global Programme to Eliminate Lymphatic Filariasis (GPELF) was created. The resulting WHO elimination strategy consists of two main components: to stop the spread of infection by interrupting transmission and to alleviate the suffering of affected populations (by controlling morbidity). The GPELF has brought together a broad global partnership of public and private actors, including three pharmaceutical companies with headquarters in three different continents. The medicine donations programmes from GlaxoSmithKline, MSD (trade name of Merck & Co. Inc., Kenilworth, NJ, USA) and Eisai have enabled significant achievements during the first 20 y of the GPELF and are positioned to provide essential contributions to the GPELF's goals for the next decade. As we celebrate the progress towards LF elimination during the GPELF's first 20 y, this article reflects on the factors that led to the creation of the three donation programmes, the contributions these programmes have made and some lessons learned along the way. We close by emphasizing our continued commitments to LF elimination and perspectives on the next decade.
Caring for patients in the global programme to eliminate lymphatic filariasis
Authors: Mackenzie Charles D , Mante Sunny 
Published: September 2020

Abstract
Clinical lymphatic filariasis (LF) is a debilitating, disfiguring medical condition with severe psychosocial consequences for patients and their families. Addressing these patients’ medical needs is a major component of the global programme to eliminate lymphatic filariasis (GPELF). In the 20 y of providing a minimal package of care many thousands of surgical operations to correct LF hydrocoeles been performed and national programmes in &gt;90% of LF endemic countries have received the training needed to care for their patients. The creation of educational materials detailing appropriate patient care, together with increased funding, have been key catalysts in increasing awareness of clinical LF in recent years. Nevertheless, the implementation of care for these patients has often faced challenges that have led to delays in fully implementing the patient care component of GPELF; these include locating these often stigmatised individuals, maintaining provision of the necessary consumables (e.g. soaps and creams) and maintaining programme support within already overstretched national LF teams. As the LF global programme moves to achieve success by 2030 it will be vital to continue to focus efforts on the care and rehabilitation of those suffering from lymphoedema and hydrocoeles, learning from the experiences of the past 20 y.
Impact of the COVID-19 pandemic on stress and emotional reactions in Israel: a mixed-methods study
Authors: Levkovich Inbar , Shinan-Altman Shiri 
Published: September 2020

Abstract

Background
The COVID-19 pandemic has had a profound impact worldwide. This study sought to assess the pandemic's psychological impact on the Israeli public.

Methods
Using mixed methods we assessed Israeli adults during the COVID-19 outbreak. In the quantitative study, participants (N=1407) completed an online battery of measures assessing psychological variables and perceived threat related to COVID-19. Statistical analyses included tests for between-group differences and Pearson correlations. The qualitative study entailed in-depth, semistructured interviews conducted by telephone (N=38).

Results
The quantitative findings indicate that about 48% of the public had negative emotional reactions and 20% perceived they were liable to contract the virus. Moreover, a positive correlation was found between these feelings and the degree of perceived threat. Three major themes emerged from the qualitative study: 1) a sense of shock and chaos; 2) gradual adjustment to the new reality; and 3) fears and concerns for self and family members. The study's results revealed the following sources of participants’ emotional responses and sense of threat: health concerns regarding themselves and their loved ones; employment concerns; problems with children and spouses caused by being together at home; and difficulties entailed in working at home.

Conclusions
The study reveals many of the psychological variables and perceived threats related to COVID-19 in Israel. While social distancing may make people feel safer, it can also increase their feelings of isolation, stress and frustration and cause difficulties in many life situations. The findings point to the necessity of addressing the public's perceived susceptibility and emotional reactions about COVID-19.