bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between diagnosis disclosure and adherence to antiretroviral therapy among adolescents living with HIV in sub-Saharan Africa: a protocol for systematic review and meta-analysis
Authors: Mengesha Melkamu Merid , Ajema Dessalegn , Teshome Awugchew , Tura Abera Kenay 
Published: July 2020

AbstractIntroductionMore than eight in ten of the world’s 1.65 million adolescents living with human immunodeficiency virus (ALHIV) live in sub-Saharan Africa (SSA). Suboptimal adherence to antiretroviral therapy (ART) and poor viral suppression are reported among ALHIV which may in turn compromise the gains achieved so far. The evidence on whether knowing one’s own human immunodeficiency virus (HIV) status and self-disclosure to others benefit adherence to ART or not is inconclusive. This review aims to estimate the association between knowing one’s HIV status and self-disclosure on adherence to ART among ALHIV in SSA.MethodsComprehensive search strings will be used to identify relevant observational studies published in English up to May 2020 in major databases: Excerpta Medica database (EMBASE), PubMed, and Ovid/MEDLINE. To access African studies and also to freely access subscription-based articles, the African Index Medicus (AIM) and the WHO HINARI databases will be searched. The AfroLib database will be searched to access the gray literature of African studies. We will use the COVIDENCE software for title/abstract screening, full-text screening, quality assessment, and data extraction. Two authors will independently screen retrieved articles, and a third author authorized to resolve conflicts will handle disagreements. The Joanna Briggs Institute’s (JBI) critical appraisal tools will be used to assess study quality. Appropriate statistical tests will be conducted to quantify the between studies heterogeneity and for the assessment of publication bias. We will check individual study influence analysis and also do subgroup analysis. The STATA version 14.2 will be used for statistical analysis.DiscussionA high-level adherence to ART is required to achieve adequate viral suppression and improve quality of life. Consequently, the evidence on how adherence to ART differs with knowledge of one’s own HIV status and self-disclosure may help guide interventions aimed at improving adherence to ART.
The significance of case detection ratios for predictions on the outcome of an epidemic - a message from mathematical modelers
Authors: Fuhrmann Jan , Barbarossa Maria Vittoria 
Published: July 2020

AbstractIn attempting to predict the further course of the novel coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2, mathematical models of different types are frequently employed and calibrated to reported case numbers. Among the major challenges in interpreting these data is the uncertainty about the amount of undetected infections, or conversely: the detection ratio. As a result, some models make assumptions about the percentage of detected cases among total infections while others completely neglect undetected cases. Here, we illustrate how model projections about case and fatality numbers vary significantly under varying assumptions on the detection ratio. Uncertainties in model predictions can be significantly reduced by representative testing, both for antibodies and active virus RNA, to uncover past and current infections that have gone undetected thus far.
Aboveground carbon stock is related to land cover and woody species diversity in tropical ecosystems of Eastern Ethiopia
Authors: Sintayehu Dejene W. , Belayneh Anteneh , Dechassa Nigussie 
Published: July 2020

Abstract
Background
Current theories on biodiversity-carbon sequestration relationship describe biodiversity as an important factor influencing carbon storage, either through complementarity effect or by mass ratio effect. So far, the expected form of biodiversity-carbon relationships in tropical ecosystems has not been known with certainty. Therefore, we explored the relationship between aboveground carbon stock and different biodiversity measurement indices (i.e., species richness, species diversity, species evenness, and functional diversity) in different land cover types of Eastern Ethiopia. A total of 48 plots were established using stratified random sampling. Vegetation parameters such as diameter at breast height, diameter at stump height, tree height, and species type were recorded.

Results
We found that the average aboveground carbon stock of the study area is 147.6 ± 17.2 t ha−1 (mean, SE) across land cover types. Species richness, Shannon index, and functional diversity together explained 73.5%, 61.4%, 58.9%, and 52.0% of the variation in aboveground carbon storage in woodland, riparian forest, bushland, and farmland, respectively. Functional diversity was a significant predictor explaining the total aboveground carbon stocks (26.7%) across the land cover types. The effects of biodiversity on aboveground carbon storage were mediated by functional diversity and presence and dominance of species. This shows that both the selection effects and the niche complementarity are important for carbon storage. However, the impact of functional diversity effects (niche complementarity) was higher than that of functional dominance effects (selection effects).

Conclusions
Implementation of protected area-based ecosystem conservation practices in the country seems feasible to mitigate climate change and Reducing Emissions from Deforestation and Forest Degradation (REDD+) programme should emphasize on biodiversity conservation.
The effect of temporary closure and enhanced terminal disinfection using aerosolized hydrogen peroxide of an open-bay intensive care unit on the acquisition of extensively drug-resistant Acinetobacter baumannii
Authors: Moghnieh Rima , Tamim Hani , Jadayel Marwa , Abdallah Dania , Al-Kassem Rasha , Kadiri Hind , Hafez Hani , Al-Hassan Salam , Ajjour Lina , Lakkis Rawad , Jisr Tamima , Samaha Nadia-Lara , Haddad Nicholas 
Published: July 2020

Abstract
Background
At Makassed Hospital’s open-bay intensive care unit (ICU), enhanced terminal disinfection (ETD) using hydrogen peroxide (H2O2) was performed without a predefined schedule in extensively-drug-resistant Acinetobacter baumannii (XDR-AB) outbreaks. In this study, we aimed to check for the value of the temporary closure of the ICU and the use of ETD with aerosolized H2O2 and Ag+ on minimizing the rate of XDR-AB acquisition in patients admitted to the ICU of our facility, which might consequently help us determine the optimal schedule for such procedure in this unit.

Methods
This is a retrospective medical file review of patients admitted to the ICU between January 2016 and May 2018. We divided this period into numerical weeks (NW) after each closure and ETD episode. Risk factors of acquisition (RFA) were determined by comparing the characteristics of patients who acquired XDR-AB to those who didn’t. The proportion of patients residing in each NW was included in the RFA analysis.

Results
Out of 335 patients, 13% acquired XDR-AB. The overall incidence of XDR-AB acquisition was 14.6 cases/1000 patient days. RFA were XDR-AB contact pressure ≥ 3 days [Odds Ratio (OR) = 9.86, 95% Confidence Interval (CI) (3.65–26.64), P < 0.0001)], mechanical ventilation [OR = 4.99, 95%CI (1.76–14.15), P = 0.002)], and having a wound [OR = 3.72, 95%CI (0.99–13.96), P = 0.05)]. Patients who stayed during NW 7,11 and 14 were at risk of acquisition where the odds significantly increased by 6.5, 9.7 and 14.4 folds respectively (P = 0.03,0.01, and 0.01, respectively). We considered NW 7 as the most suitable time for temporary closure of the ICU and ETD with aerosolized H2O2.

Conclusion
Contact pressure, mechanical ventilation, and presence of a wound were RFA of XDR-AB. Temporary closure of the ICU with ETD using aerosolized H2O2 decreased the rate of XDR-AB acquisition, yet this effect fades away with time. The ETD was shown to be most efficiently done when repeated every 7 calendar weeks in our open-bay ICU as part of a prevention bundle.
Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases
Authors: Le Bastard Quentin , Chapelet Guillaume , Birgand Gabriel , Hillmann Benjamin M. , Javaudin François , Hayatgheib Niki , Bourigault Céline , Bemer Pascale , De Decker Laure , Batard Eric , Lepelletier Didier , Montassier Emmanuel 
Published: July 2020

Abstract
Background
The prevalence of extended beta-lactamase producing Enterobacteriaceae (ESBL-E) has been constantly increasing over the last few decades. These microorganisms that have acquired broad antibiotic resistance are now common human pathogens. Changes in the gut microbiome, induced by antibiotics or other drugs, enable expansion of these microorganisms, but the mechanisms are not yet fully understood.

Objectives
The main objective was to identify specific bacteria and functional pathways and genes characterizing the gut microbiome of nursing home residents carrying ESBL-E, using metagenomics.

Subjects and methods
We included 144 residents living in two different nursing homes. All fecal samples were screened for ESBL-E and gut microbiome was characterized using shallow shotgun metagenomic DNA sequencing.

Results
Ten nursing home residents were colonized by ESBL-E, namely Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae species, and were compared to non-carriers. We found that ESBL-E carriers had an alteration in within-sample diversity. Using a bootstrap algorithm, we found that the gut microbiome of ESBL-E carriers was depleted in butyrate-producing species, enriched in succinate-producing species and enriched in pathways involved in intracellular pH homeostasis compared to non-carriers individuals. Several energy metabolism pathways were overrepresented in ESBL-E carriers suggesting a greater ability to metabolize multiple microbiota and mucus layer-derived nutrients.

Conclusions
The gut microbiome of ESBL-E carriers in nursing homes harbors specific taxonomic and functional characteristics, conferring an environment that enables Enterobacteriaceae expansion. Here we describe new functional features associated with ESBL-E carriage that could help us to elucidate the complex interactions leading to colonization persistence in the human gut microbiota.
Movements, habitat utilization, and post-release survival of cobia (Rachycentron canadum) that summer in Virginia waters assessed using pop-up satellite archival tags
Authors: Jensen Douglas R. , Graves John E. 
Published: July 2020

Abstract
Background
Cobia (Rachycentron canadum) is a cosmopolitan marine fish that inhabits tropical, sub-tropical, and temperate marine and estuarine waters and supports a major recreational fishery along the U.S. Atlantic and Gulf of Mexico coasts. Recent changes in U.S. cobia management have sparked controversy and highlighted limitations in our understanding of the species’ biology. This study utilized pop-up satellite archival tags (PSATs) to assess the movements, habitat utilization, and post-release survival of cobia that summer in Virginia waters.

Results
PSATs were deployed on 36 cobia caught in Virginia state waters using standard recreational techniques in August 2016 and August–September 2017. All fish larger than 37-in total length were tagged, and several of these were hooked deeply. No mortalities were inferred for the 20 cobia whose PSATs reported and remained attached for at least 10 days. Premature release of tags was an issue, and only five PSATs remained attached for the full 180-day deployment period. Some fish undertook long seasonal movements, with one individual entering Florida waters well beyond the current stock demarcation boundary. Several fish overwintered in waters offshore of North Carolina near the continental shelf break. Cobia demonstrated a strong affinity for waters ≥ 20 °C, even in the coldest months. They displayed distinct seasonal differences in habitat utilization, spending high proportions of their time near the surface during the summer months and extended periods at depths ≥ 20 m in the winter months.

Conclusions
Cobia are hardy fish with low post-release mortality when handled respectfully. Their migratory patterns are clearly temperature driven, and seasonal changes in habitat utilization means varied vulnerability to fishing gears. Further understanding of cobia migratory patterns, particularly in conjunction with spawning activity, is needed to best manage this species.
Impairment in dynein-mediated nuclear translocation by BICD2 C-terminal truncation leads to neuronal migration defect and human brain malformation
Authors: Tsai Meng-Han , Cheng Haw-Yuan , Nian Fang-Shin , Liu Chen , Chao Nian-Hsin , Chiang Kuo-Liang , Chen Shu-Fang , Tsai Jin-Wu 
Published: July 2020

AbstractDuring brain development, the nucleus of migrating neurons follows the centrosome and translocates into the leading process. Defects in these migratory events, which affect neuronal migration, cause lissencephaly and other neurodevelopmental disorders. However, the mechanism of nuclear translocation remains elusive. Using whole exome sequencing (WES), we identified a novel nonsense BICD2 variant p.(Lys775Ter) (K775X) from a lissencephaly patient. Interestingly, most BICD2 missense variants have been associated with human spinal muscular atrophy (SMA) without obvious brain malformations. By in utero electroporation, we showed that BicD2 knockdown in mouse embryos inhibited neuronal migration. Surprisingly, we observed severe blockage of neuronal migration in cells overexpressing K775X but not in those expressing wild-type BicD2 or SMA-associated missense variants. The centrosome of the mutant was, on average, positioned farther away from the nucleus, indicating a failure in nuclear translocation without affecting the centrosome movement. Furthermore, BicD2 localized at the nuclear envelope (NE) through its interaction with NE protein Nesprin-2. K775X variant disrupted this interaction and further interrupted the NE recruitment of BicD2 and dynein. Remarkably, fusion of BicD2-K775X with NE-localizing domain KASH resumed neuronal migration. Our results underscore impaired nuclear translocation during neuronal migration as an important pathomechanism of lissencephaly.
Fyn depletion ameliorates tauP301L-induced neuropathology
Authors: Liu Guanghao , Fiock Kimberly L. , Levites Yona , Golde Todd E. , Hefti Marco M. , Lee Gloria 
Published: July 2020

AbstractThe Src family non-receptor tyrosine kinase Fyn has been implicated in neurodegeneration of Alzheimer’s disease through interaction with amyloid β (Aβ). However, the role of Fyn in the pathogenesis of primary tauopathies such as FTDP-17, where Aβ plaques are absent, is poorly understood. In the current study, we used AAV2/8 vectors to deliver tauP301L to the brains of WT and Fyn KO mice, generating somatic transgenic tauopathy models with the presence or absence of Fyn. Although both genotypes developed tau pathology, Fyn KO developed fewer neurofibrillary tangles on Bielschowsky and Thioflavin S stained sections and showed lower levels of phosphorylated tau. In addition, tauP301L-induced behavior abnormalities and depletion of synaptic proteins were not observed in the Fyn KO model. Our work provides evidence for Fyn being a critical protein in the disease pathogenesis of FTDP-17.
Molecular and clinicopathologic features of gliomas harboring NTRK fusions
Authors: Torre Matthew , Vasudevaraja Varshini , Serrano Jonathan , DeLorenzo Michael , Malinowski Seth , Blandin Anne-Florence , Pages Melanie , Ligon Azra H. , Dong Fei , Meredith David M. , Nasrallah MacLean P. , Horbinski Craig , Dahiya Sonika , Ligon Keith L. , Santi Mariarita , Ramkissoon Shakti H. , Filbin Mariella G. , Snuderl Matija , Alexandrescu Sanda 
Published: July 2020

AbstractFusions involving neurotrophic tyrosine receptor kinase (NTRK) genes are detected in ≤2% of gliomas and can promote gliomagenesis. The remarkable therapeutic efficacy of TRK inhibitors, which are among the first Food and Drug Administration-approved targeted therapies for NTRK-fused gliomas, has generated significant clinical interest in characterizing these tumors. In this multi-institutional retrospective study of 42 gliomas with NTRK fusions, next generation DNA sequencing (n = 41), next generation RNA sequencing (n = 1), RNA-sequencing fusion panel (n = 16), methylation profile analysis (n = 18), and histologic evaluation (n = 42) were performed. All infantile NTRK-fused gliomas (n = 7) had high-grade histology and, with one exception, no other significant genetic alterations. Pediatric NTRK-fused gliomas (n = 13) typically involved NTRK2, ranged from low- to high-histologic grade, and demonstrated histologic overlap with desmoplastic infantile ganglioglioma, pilocytic astrocytoma, ganglioglioma, and glioblastoma, among other entities, but they rarely matched with high confidence to known methylation class families or with each other; alterations involving ATRX, PTEN, and CDKN2A/2B were present in a subset of cases. Adult NTRK-fused gliomas (n = 22) typically involved NTRK1 and had predominantly high-grade histology; genetic alterations involving IDH1, ATRX, TP53, PTEN, TERT promoter, RB1, CDKN2A/2B, NF1, and polysomy 7 were common. Unsupervised principal component analysis of methylation profiles demonstrated no obvious grouping by histologic grade, NTRK gene involved, or age group. KEGG pathway analysis detected methylation differences in genes involved in PI3K/AKT, MAPK, and other pathways. In summary, the study highlights the clinical, histologic, and molecular heterogeneity of NTRK-fused gliomas, particularly when stratified by age group.
Hydrogen sulfide removal from geothermal fluids by Fe(III)-based additives
Authors: Regenspurg S. , Iannotta J. , Feldbusch E. , Zimmermann F. J. , Eichinger F. 
Published: July 2020

AbstractA new method to remove hydrogen sulfide from geothermal fluids during well operation was tested in situ at a geothermal site in Vienna (Austria). For this purpose, ferric iron was added either as granulated iron hydroxide or as FeCl3 solution into a reaction vessel containing the thermal water directly removed from the wells. From the container, the water would be pumped through a particle filter. Physicochemical parameters as well as sulfide were measured constantly over time before and after the filter. It was found that the sulfide was fully removed from the water by both iron additives. While the addition of FeCl3 led first to the formation of black iron(II) sulfide (FeS), which subsequently oxidized in presence of oxygen to Fe(III) hydroxide, no visible change of the granulated iron hydroxide was observed. The reaction time was longer when using the Fe(III) hydroxide additive as compared to the FeCl3 (completed in less than 20 min) but could be enhanced by increasing the amount of added particles. In all experiments the pH was constantly rising during the reaction from about 6.3 to 7.5, which was explained by loss of protons due to purging out of the gaseous H2S. The redox value, which was measured over time, remained rather constant after addition of granulated iron hydroxide (about −350 mV), but strongly increased from −350 mV to −50 mV after adding the FeCl3 suggesting a strong electron-consuming reaction. This can be explained by a two-step reaction: first, the Fe(III) was reduced to Fe(II) by oxidation of either sulfide or thiosulfate to sulfate. Afterward, the Fe(II) oxidized again by dissolved oxygen forming orange Fe(III) hydroxides. The application of the investigated method during operation of geothermal wells could prevent H2S-induced corrosion and would eliminate the toxic effects of this gas.
Homozygous LMNA p.R582H pathogenic variant reveals increasing effect on the severity of fat loss in lipodystrophy
Authors: Soyaltin Utku Erdem , Simsir Ilgin Yildirim , Akinci Baris , Altay Canan , Adiyaman Suleyman Cem , Lee Kristen , Onay Huseyin , Oral Elif Arioglu 
Published: July 2020

Abstract
Background
Classical heterozygous pathogenic variants of the lamin A/C (LMNA) gene cause autosomal dominant familial partial lipodystrophy type 2 (FPLD2). However, recent reports indicate phenotypic heterogeneity among carriers of LMNA pathogenic variants, and a few patients have been associated with generalized fat loss.

Case presentation
Here, we report a patient with a lamin A specific pathogenic variant in exon 11, denoted LMNA (c.1745G > A; p.R582H), present in the homozygous state. Fat distribution was compared radiographically to an unrelated heterozygote LMNA p.R582H patient from another pedigree, a healthy female control, a series of adult female subjects with congenital generalized lipodystrophy type 1 (CGL1, n = 9), and typical FPLD2 (n = 8). The whole-body MRI of the index case confirmed near-total loss of subcutaneous adipose tissue with well-preserved fat in the retroorbital area, palms and soles, mons pubis, and external genital region. This pattern resembled the fat loss pattern observed in CGL1 with only one difference: strikingly more fat was observed around mons pubis and the genital region. Also, the p.R582H LMNA variant in homozygous fashion was associated with lower leptin level and earlier onset of metabolic abnormalities compared to heterozygous p.R582H variant and typical FPLD2 cases. On the other hand, the heterozygous LMNA p.R582H variant was associated with partial fat loss which was similar to typical FPLD2 but less severe than the patients with the hot-spot variants at position 482.

Conclusions
Our observations and radiological comparisons demonstrate an additive effect of LMNA pathogenic variants on the severity of fat loss and add to the body of evidence that there may be complex genotype-phenotype relationships in this interesting disease known as FPLD2. Although the pathological basis for fat loss is not well understood in patients harboring pathogenic variants in the LMNA gene, our observation suggests that genetic factors modulate the extent of fat loss in LMNA associated lipodystrophy.