bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Human Immunodeficiency Virus–Related Gut Microbiota Alterations on Metabolic Comorbid Conditions
Authors: Gelpi Marco , Vestad Beate , Hansen Simen Hyll , Holm Kristian , Drivsholm Ninna , Goetz Alexandra , Kirkby Nicolai Søren , Lindegaard Birgitte , Lebech Anne-Mette , Hoel Hedda , Michelsen Annika E , Ueland Thor , Gerstoft Jan , Lundgren Jens , Hov Johannes Roksund , Nielsen Susanne Dam , Trøseid Marius 
Published: December 2019

AbstractBackgroundWe aimed to identify a human immunodeficiency virus (HIV)–related microbiota signature, independent of sexual preferences and demographic confounders, in order to assess a possible impact of the microbiome on metabolic comorbid conditions.MethodsBacterial 16S ribosomal RNA analyses were performed on stool samples from 405 HIV-infected and 111 uninfected participants of the Copenhagen Comorbidity in HIV Infection (COCOMO) study. Individuals were stratified according to sexual behavior (men who have sex with men [MSM] vs non-MSM).ResultsAfter excluding MSM-associated microbiota traits and adjusting for confounders, we identified an HIV-related microbiota signature, consisting of lower biodiversity, increased relative abundance of the bacterial clades Gammaproteobacteria and Desulfovibrionaceae and decrease in several Clostridia. This microbiota profile was associated with a 2-fold excess risk of metabolic syndrome, driven by increase in Desulfovibrionaceae and decrease in Clostridia (Butyrivibrio, Coprococcus 2, Lachnospiraceae UCG-001 and CAG-56). This association was accentuated (5-fold excess risk) in individuals with previous severe immunodeficiency, which also modified the association between HIV-related microbiota signature and visceral adipose tissue (VAT) area (P for interaction = .01). Accordingly, HIV-related microbiota was associated with 30-cm2 larger VAT in individuals with history of severe immunodeficiency, but not in those without.ConclusionThe HIV-related microbiota was associated with increased risk of metabolic syndrome and VAT accumulation, particularly in individuals with previous severe immunodeficiency, driven by increased Desulfovibrionaceae and lower abundance of several Clostridia. Our findings suggest a potential interplay between HIV-related microbiota, immune dysfunction and metabolic comorbid conditions. Interventions targeting the gut microbiome may be warranted to reduce cardiovascular risk, particularly in individuals with previous immunodeficiency.
Phase I, II and III Trials in Inflammatory Bowel Diseases: A Practical Guide for the Non-specialist
Authors: D’Amico Ferdinando , Baumann Cedric , Rousseau Hélène , Danese Silvio , Peyrin-Biroulet Laurent 
Published: December 2019

AbstractIn the last few decades several new molecules have been developed in the field of inflammatory bowel diseases. However, the process that leads to the approval and use of a new drug is very long, expensive and complex, consisting of various phases. There is a pre-clinical phase that is performed on animals and a clinical phase that is directed to humans. Each research phase aims to evaluate different aspects of the drug and involves a specific target group of subjects. In addition, many aspects must be considered in the evaluation of a clinical trial: randomization, presence of a control group, blind design, type of data analysis performed, and patient stratification. The objective of this review is to provide an overview of the clinical trial phases of a new drug in order to better understand and interpret their results.
Do green buildings provide benefits to the residential sector in Jordan? Yes, but…
Authors: Alkhalidi Ammar , Aljolani Osama 
Published: December 2019

Abstract
The concept of green buildings has recently arisen in order to contribute to solving some environmental, energy and economic issues. To meet the green building requirements, this paper describes an integrated design approach to improve the energy and water efficiency of the mid-rise residential buildings in Jordan using the eQUEST energy simulation tool. The results show that savings of 77.9% in the annual requirements of electricity, 65.0% in the requirements of diesel oil and 19.5% in the indoor water consumption can be achieved. Finally, the Jordanian green building model had achieved 44 points in the Leadership in Energy and Environmental Design green building rating system and will have the ‘Certified’ classification.
A modified limited memory steepest descent method motivated by an inexact super-linear convergence rate analysis
Authors: Gu Ran , Du Qiang 
Published: December 2019

AbstractHow to choose the step size of gradient descent method has been a popular subject of research. In this paper we propose a modified limited memory steepest descent method (MLMSD). In each iteration we propose a selection rule to pick a unique step size from a candidate set, which is calculated by Fletcher’s limited memory steepest descent method (LMSD), instead of going through all the step sizes in a sweep, as in Fletcher’s original LMSD algorithm. MLMSD is motivated by an inexact super-linear convergence rate analysis. The R-linear convergence of MLMSD is proved for a strictly convex quadratic minimization problem. Numerical tests are presented to show that our algorithm is efficient and robust.
Longitudinal analysis of ESBL and carbapenemase carriage among Enterobacterales and Pseudomonas aeruginosa isolates collected in Europe as part of the International Network for Optimal Resistance Monitoring (INFORM) global surveillance programme, 2013–17
Authors: Kazmierczak Krystyna M , de Jonge Boudewijn L M , Stone Gregory G , Sahm Daniel F 
Published: December 2019

Abstract

Objectives
To determine the spread of ESBLs and carbapenemases in Enterobacterales and Pseudomonas aeruginosa in Europe.

Methods
45 335 Gram-negative bacilli were collected in 18 European countries as part of the International Network for Optimal Resistance Monitoring (INFORM) global surveillance programme from 2013 to 2017. Antimicrobial susceptibility was determined using broth microdilution, and 9546 isolates were screened for β-lactamase genes by PCR and sequencing.

Results
ESBLs were identified in 35.5% of Klebsiella pneumoniae and 18.5% of Escherichia coli. ESBL carriage was lowest among isolates in Northern/Western Europe and highest in Eastern Europe. CTX-M-15 was the dominant ESBL in all countries except Greece, where SHV-type ESBLs were more common. Carbapenemases (KPC, OXA-48-like, GES, NDM and VIM) were found in 3.4% of Enterobacterales and were most common among K. pneumoniae (10.5% of those collected). Carbapenemase carriage was lowest in Northern/Western and highest in Southern Europe. KPC-positive Enterobacterales were most abundant but the percentages of OXA-48-like-, NDM- and VIM-positive isolates increased over time and were correlated with an increase in meropenem non-susceptibility. Carbapenemases (VIM, IMP, NDM and GES) were also identified in 5.1% of P. aeruginosa and were commonly found in Eastern Europe. Carbapenemase carriage and meropenem non-susceptibility among P. aeruginosa fluctuated over the 5 years studied and were not well correlated.

Conclusions
ESBL and carbapenemase carriage varied by species and European subregion. Meropenem non-susceptibility in European isolates of Enterobacterales can be attributed to carbapenemase carriage and is increasingly caused by MBLs and OXA-48-like carbapenemases. Carbapenemases or other β-lactamases are not a common cause of meropenem non-susceptibility in P. aeruginosa in Europe.
Interventions to Enhance Adherence to Oral Antineoplastic Agents: A Scoping Review
Authors: Rosenberg Shoshana M , Petrie Keith J , Stanton Annette L , Ngo Lan , Finnerty Emma , Partridge Ann H 
Published: December 2019

Abstract

Background
As new targeted oral antineoplastic therapies have emerged in recent years, the development of effective strategies that promote optimal adherence to cancer medication regimens has become an important priority.

Methods
We conducted a scoping literature review to search for English language articles published through July 15, 2019, to identify studies that reported the testing and/or evaluation of interventions to improve adherence to oral antineoplastic agents.

Results
A total of 56 articles were selected for review. Of the studies evaluated, 14 were randomized trials. All interventions except two targeted adult patients. Thirty-three studies enrolled fewer than 100 patients. Most interventions were education- and counseling-based and centered on provision of information about the drug and strategies to manage side effects. Only eight studies used an mHealth tool and/or text messages to target nonadherence. Among studies with a comparison sample, fewer than one-half (44.7%) reported statistically significant improvements in adherence or persistence associated with the intervention; however, some pharmacist-directed programs, particularly those that integrated monitoring or routine follow-up with a provider, did demonstrate efficacy.

Conclusion
Although the development of adherence-promoting interventions for oral antineoplastic therapies has increased recently, few have been rigorously tested. The nascent literature suggests those that are pharmacist directed and use regular monitoring show promise, though additional prospective studies are needed. Study methodology, population selection, and potential challenges that may be encountered in the implementation and dissemination phases should be considered when developing new interventions to address nonadherence to oral antineoplastic treatment.
Molecular Subtypes and Genomic Profile of Primary Central Nervous System Lymphoma
Authors: Bödör Csaba , Alpár Donát , Marosvári Dóra , Galik Bence , Rajnai Hajnalka , Bátai Bence , Nagy Ákos , Kajtár Béla , Burján Adrienn , Deák Beáta , Schneider Tamás , Alizadeh Hussain , Matolcsy András , Brandner Sebastian , Storhoff James , Chen Ning , Liu Mingdong , Ghali Nadeem , Csala Irén , Bagó Attila G , Gyenesei Attila , Reiniger Lilla 
Published: December 2019

Abstract
Primary central nervous system lymphomas (PCNSL) are aggressive non-Hodgkin lymphomas affecting the central nervous system (CNS). Although immunophenotyping studies suggested an uniform activated B-cell (ABC) origin, more recently a spectrum of ABC and germinal center B-cell (GC) cases has been proposed, with the molecular subtypes of PCNSL still being a matter of debate. With the emergence of novel therapies demonstrating different efficacy between the ABC and GC patient groups, precise assignment of molecular subtype is becoming indispensable. To determine the molecular subtype of 77 PCNSL and 17 secondary CNS lymphoma patients, we used the NanoString Lymphoma Subtyping Test (LST), a gene expression-based assay representing a more accurate technique of subtyping compared with standard immunohistochemical (IHC) algorithms. Mutational landscapes of 14 target genes were determined using ultra-deep next-generation sequencing. Using the LST-assay, a significantly lower proportion (80% vs 95%) of PCNSL cases displayed ABC phenotype compared with the IHC-based characterization. The most frequently mutated genes included MYD88, PIM1, and KMT2D. In summary, we successfully applied the LST-assay for molecular classification of PCNSL, reporting higher proportion of cases with GC phenotype compared with IHC analyses, leading to a more precise patient stratification potentially applicable in the diagnostic algorithm of PCNSL.
Soil and climate equally contribute to changes in the species compositions of Brazilian dry forests across 300 km
Authors: Arruda Daniel M , Magnago Luiz F S , Solar Ricardo R C , Duque-Brasil Reinaldo , Rodrigues Priscyla M S , Santos Rubens M , Schaefer Carlos E G R 
Published: December 2019

Abstract

Aims
Understanding the factors that control biodiversity distributions at different spatial scales has been a key challenge for conservation efforts. That biodiversity, reflected in differences in species compositions among sites (beta diversity), can be derived from species replacement (turnover) and is driven by multiple factors. Here, we sought to tackle this issue through two questions related to threatened Brazilian seasonally dry forests: (i) what is the contribution of species turnover to beta diversity? and (ii) which factors drive variations in species compositions among forest patches?

Methods
We sampled tree species and environmental variables (soils and climate) in 17 dry forest patches spaced almost 300 km apart. We used the beta diversity partitioning framework to determine the contribution of turnover. We used redundancy analysis, with properly controlled spatial structure, to assess the contributions of the environmental and spatial factors to the variations of the species composition.

Important Findings
Beta diversity among the patches was mainly represented by the turnover component (98.2%), with Simpson dissimilarity superior to other regions of the country (means of 0.89 and 0.71 in multiple site and pairwise measures, respectively). The environmental factors measured explained more than space, representing 30.3% of the variation of the species composition, of which 28.1% was nonspatially structured. We suggest that 300 km represents a threshold at which edaphic and climatic predictors have similar effects in determining community turnover (14.9% and 12.6%, respectively, without spatial structure). Thus, conservation strategies should be considered across landscapes to effectively protect tropical forest diversity, as even considering the different climatic aspects covered by the scale, landscaped edaphic varieties are important drivers of species turnover.
Outbreaks of Kingella kingae Infections in Daycare Centers Suggest Tissue Tropism of the Causative Strains
Authors: Yagupsky Pablo , El Houmami Nawal , Fluss Ronen 
Published: December 2019

Abstract

Background
Although Kingella kingae is recognized as an important pediatric pathogen, our knowledge of the virulence factors involved in the invasion of specific host’s tissues is limited. Outbreaks of K kingae infections in daycare centers represent natural experiments in which a single virulent strain, introduced into a cohort of susceptible young children, causes multiple infections. If K kingae strains exhibit tissue tropism, the syndromes observed in a given cluster of cases would be relatively homogeneous.

Methods
Clinical data of all the K kingae outbreaks known to date were gathered and analyzed. The clinical syndromes diagnosed in the affected attendees were classified as septic arthritis, osteomyelitis, tenosynovitis, soft tissue infection, bacteremia with no focal disease, endocarditis, and meningitis, and computed separately. To assess the similarity of the clinical syndromes detected within outbreaks, we used the Cramer V statistic, which is a measure of the association between 2 nominal variables and, for the purposes of the study, between the detected clinical syndromes and the outbreaks.

Results
A total of 23 outbreaks involving 61 attendees were identified. The mean±SD attack rate in the affected classrooms was 15.8% ± 4.8%, and the K kingae colonization rate among the attendees was 54.8% ± 25.3%. Seventy-two separate foci of infection were diagnosed. Osteomyelitis and septic arthritis were the most common clinical syndromes and were diagnosed in 26 children each, followed by tenosynovitis in 4 children. The clinical syndromes diagnosed among attendees to the same classroom showed a statistically significant tendency to be similar (P = .015).

Conclusions
The distribution of clinical syndromes in clusters of K kingae infections differs from that of sporadic cases. The causative strains combine enhanced virulence and high transmissibility, and show tropism toward bones, joints, and tendon sheaths. This information can be used to identify virulence factors associated with invasion of these specific host tissues.
True aneurysm of the digital artery: a case report and systematic literature review
Authors: Sheikh Zara , Selvakumar Sadasivam , Goon Patrick 
Published: December 2019

Abstract
Aneurysmal disease can occur in any vessel in the body and occur most commonly the aorta, cerebral and popliteal arteries; however, aneurysms of the digital artery remain a rare presentation. They form an important differential diagnosis in any patient presenting with a mass in the hand. This report presents the case of a 64-year-old man with a true aneurysm of the common palmar digital artery who underwent successful repair, following excision and end to end anastomosis. Only 21 cases of true digital artery aneurysm have been reported; we review the literature pertaining to the diagnosis and management of digital artery aneurysms since they were first described by Baruch et al in 1977.
Azole resistance in Candida from animals calls for the One Health approach to tackle the emergence of antimicrobial resistance
Authors: Castelo-Branco Débora de Souza Collares Maia , Paiva Manoel de Araújo Neto , Teixeira Carlos Eduardo Cordeiro , Caetano Érica Pacheco , Guedes Gláucia Morgana de Melo , Cordeiro Rossana de Aguiar , Brilhante Raimunda Sâmia Nogueira , Rocha Marcos Fábio Gadelha , Sidrim José Júlio Costa 
Published: December 2019

Abstract
This study initially aimed at investigating the occurrence of azole resistance among Candida spp. from animals and analyzing the involvement of efflux pumps in the resistance phenomenon. Then, the dynamics of antifungal resistance was assessed, by comparing the antifungal epidemiological cutoff values (ECVs) against C. albicans and C. tropicalis from humans and animals. Fifty azole-resistant isolates (24 C. albicans, 24 C. tropicalis; 2 C. parapsilosis sensu lato) were submitted to the efflux pump inhibition assay with promethazine and significant MIC reductions were observed for fluconazole (2 to 250-fold) and itraconazole (16 to 4000-fold). Then, the antifungal ECVs against C. albicans and C. tropicalis from human and animal isolates were compared. Fluconazole, itraconazole and voriconazole ECVs against human isolates were lower than those against animal isolates. Based on the antifungal ECVs against human isolates, only 33.73%, 50.39% and 63.53% of C. albicans and 52.23%, 61.85% and 55.17% of C. tropicalis from animals were classified as wild-type for fluconazole, itraconazole and voriconazole, respectively. Therefore, efflux-mediated mechanisms are involved in azole resistance among Candida spp. from animals and this phenomenon seems to emerge in animal-associated niches, pointing to the existence of environmental drivers of resistance and highlighting the importance of the One Health approach to control it.
Efficient gravitational lens optical scalars calculation of black holes with angular momentum
Authors: Boero Ezequiel F , Moreschi Osvaldo M 
Published: December 2019

ABSTRACT
We provide new very simple and compact expressions for the efficient calculation of gravitational lens optical scalars for Kerr space–time, which are exact along any null geodesic. These new results are obtained recurring to well-known results on geodesic motion that exploit obvious and hidden symmetries of Kerr space–time and contrast with the rather long and cumbersome expressions previously reported in the literature, providing a helpful improvement for the sake of an efficient integration of the geodesic deviation equation on Kerr geometry. We also introduce a prescription for the observer frame that captures a new notion of centre of the black hole, which can be used for any position of the observer, including those near the black hole. We compare the efficient calculation of weak lens optical scalars with the exact equations, finding an excellent agreement.
Inferring the parallax of Westerlund 1 from Gaia DR2
Authors: Aghakhanloo Mojgan , Murphy Jeremiah W , Smith Nathan , Parejko John , Díaz-Rodríguez Mariangelly , Drout Maria R , Groh Jose H , Guzman Joseph , Stassun Keivan G 
Published: December 2019

ABSTRACT
Westerlund 1 (Wd1) is potentially the largest star cluster in the Galaxy. That designation critically depends upon the distance to the cluster, yet the cluster is highly obscured, making luminosity-based distance estimates difficult. Using Gaia Data Release 2 (DR2) parallaxes and Bayesian inference, we infer a parallax of $0.35^{+0.07}_{-0.06}$ mas corresponding to a distance of $2.6^{+0.6}_{-0.4}$ kpc. To leverage the combined statistics of all stars in the direction of Wd1, we derive the Bayesian model for a cluster of stars hidden among Galactic field stars; this model includes the parallax zero-point. Previous estimates for the distance to Wd1 ranged from 1.0 to 5.5 kpc, although values around 5 kpc have usually been adopted. The Gaia DR2 parallaxes reduce the uncertainty from a factor of 3 to 18 per cent and rules out the most often quoted value of 5 kpc with 99 per cent confidence. This new distance allows for more accurate mass and age determinations for the stars in Wd1. For example, the previously inferred initial mass at the main-sequence turn-off was around 40 M⊙; the new Gaia DR2 distance shifts this down to about 22 M⊙. This has important implications for our understanding of the late stages of stellar evolution, including the initial mass of the magnetar and the LBV in Wd1. Similarly, the new distance suggests that the total cluster mass is about four times lower than previously calculated.
The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay
Authors: Silla Toomas , Schmid Manfred , Dou Yuhui , Garland William , Milek Miha , Imami Koshi , Johnsen Dennis , Polak Patrik , Andersen Jens S , Selbach Matthias , Landthaler Markus , Jensen Torben Heick 
Published: December 2019

Abstract
Recruitment of the human ribonucleolytic RNA exosome to nuclear polyadenylated (pA+) RNA is facilitated by the Poly(A) Tail eXosome Targeting (PAXT) connection. Besides its core dimer, formed by the exosome co-factor MTR4 and the ZFC3H1 protein, the PAXT connection remains poorly defined. By characterizing nuclear pA+-RNA bound proteomes as well as MTR4-ZFC3H1 containing complexes in conditions favoring PAXT assembly, we here uncover three additional proteins required for PAXT function: ZC3H3, RBM26 and RBM27 along with the known PAXT-associated protein, PABPN1. The zinc-finger protein ZC3H3 interacts directly with MTR4-ZFC3H1 and loss of any of the newly identified PAXT components results in the accumulation of PAXT substrates. Collectively, our results establish new factors involved in the turnover of nuclear pA+ RNA and suggest that these are limiting for PAXT activity.