bluuebunny/crossref_metadata_2025_split huggingface dataset:
sofia 2 – an automated, parallel H i source finding pipeline for the WALLABY survey
Authors: Westmeier T , Kitaeff S , Pallot D , Serra P , van der Hulst J M , Jurek R J , Elagali A , For B-Q , Kleiner D , Koribalski B S , Lee-Waddell K , Mould J R , Reynolds T N , Rhee J , Staveley-Smith L 
Published: July 2021

ABSTRACT
We present sofia 2, the fully automated 3D source finding pipeline for the WALLABY extragalactic H i survey with the Australian SKA Pathfinder (ASKAP). sofia 2 is a reimplementation of parts of the original sofia pipeline in the c programming language and makes use of OpenMP for multithreading of the most time-critical algorithms. In addition, we have developed a parallel framework called sofia-X that allows the processing of large data cubes to be split across multiple computing nodes. As a result of these efforts, sofia 2 is substantially faster and comes with a much reduced memory footprint compared to its predecessor, thus allowing the large WALLABY data volumes of hundreds of gigabytes of imaging data per epoch to be processed in real time. The source code has been made publicly available to the entire community under an open-source licence. Performance tests using mock galaxies injected into genuine ASKAP data suggest that in the absence of significant imaging artefacts sofia 2 is capable of achieving near-100 per cent completeness and reliability above an integrated signal-to-noise ratio (SNR) of about 5–6. We also demonstrate that sofia 2 generally recovers the location, integrated flux, and w20 line width of galaxies with high accuracy. Other parameters, including the peak flux density and w50 line width, are more strongly biased due to the influence of the noise on the measurement. In addition, very faint galaxies below an integrated SNR of about 10 may get broken up into multiple components, thus requiring a strategy to identify fragmented sources and ensure that they do not affect the integrity of any scientific analysis based on the sofia 2 output.
Exploring the inner-disc region of the atoll source 4U 1705-44 using AstroSat’s SXT and LAXPC observations
Authors: Malu S , Sriram K , Harikrishna S , Agrawal Vivek K 
Published: July 2021

ABSTRACT
For the first time, simultaneous broad-band spectral and timing study of the atoll source 4U 1705-44 was performed using AstroSat Soft X-ray Telescope (SXT) and Large Area X-ray Proportional Counter (LAXPC) data (0.8–70 keV). Based on the HID, the source was in the soft banana state during these observations. Spectral modelling was performed using the full reflection framework and an inner disc radii of 14 Rg was obtained. A hard power-law tail was noticed in the soft state and hot component fluxes and varying power-law indices point towards a varying corona/sub-Keplerian flow. Based on the spectral fits, the boundary layer radius and magnetospheric radius were constrained to be ∼14–18 and ∼9–19 km, respectively. Cross-correlation function studies were performed between the 0.8–3 keV soft SXT light curve and 10–20 keV hard LAXPC light curve and correlated and anticorrelated lags were found, which was used to constrain the coronal height to 0.6–20 km (β = 0.1). Since the inner disc radius is not varying during the observations, we conclude that the detected lags are possibly caused by a varying structure of corona/boundary layer in the inner region of the accretion disc. Based on the observations, a geometrical model is proposed for explaining the detected lags in the atoll source 4U 1705-44.
Integrase Strand Transfer Inhibitors and Weight Gain in Children and Youth With Perinatal Human Immunodeficiency Virus in the DC Cohort
Authors: Koay Wei Li A , Dirajlal-Fargo Sahera , Levy Matthew E , Kulie Paige , Monroe Anne , Castel Amanda D , Rakhmanina Natella Y ,   DC Cohort Executive Committee, D’Angelo Lawrence , Rakhmanina Natella , Kharfen Michael , Serlin Michael , Kumar Princy , Bamdad Aria , Bezabeh Tsedenia , Burrows Pamela Katzen , Reamer Susan , Sapozhnikova Alla , Temprosa Marinella , Younes Naji , Byrne Morgan , Castel Amanda , Greenberg Alan , Jaurretche Maria , Levy Matthew , Monroe Anne , Peterson James , Happ Lindsey Powers , Wilbourn Brittany , Ma Yan , Akselrod Hana , Wilcox Ronald , Rana Sohail , Horberg Michael , Fernandez Ricardo , Hebou Annick , Dieffenbach Carl , Masur Henry , Bordon Jose , Teferi Gebeyehu , Benator Debra , Ruiz Maria Elena , Abbott Stephen 
Published: July 2021

AbstractWe conducted a retrospective analysis of 38 children and youth with human immunodeficiency virus (aged 0–19 years) in the United States and report an increased rate of change of BMI-for-age z score after initiating integrase strand transfer inhibitors (+0.19 z score units/year [95% confidence interval, .01–.37]; P = .036) for a median follow-up of 527.5 days.
Updated Experience of Mycobacterium chimaera Infection: Diagnosis and Management in a Tertiary Care Center
Authors: Tan Nicholas Y , Tarabochia Alex D , DeSimone Daniel C , DeSimone Christopher V , Wilson John W , Bagameri Gabor , Bennett Courtney E , Abu Saleh Omar M 
Published: July 2021

Abstract

Background
Despite safety communications from the Food and Drug Administration (FDA) regarding the outbreak of Mycobacterium chimaera infections (MCIs) from contaminated heater-cooler devices, new cases continue to be identified.

Methods
We retrospectively reviewed confirmed cases of MCI that were managed at Mayo Clinic sites (Arizona, Florida, and Minnesota) from 09/2015 to 01/2021. Clinical histories including prior cardiovascular surgery were recorded. Diagnostic workup including ophthalmologic examination, imaging, and laboratory testing was reviewed. Treatment and survival outcomes on follow-up were obtained.

Results
Twelve patients with MCI were included. All patients had aortic valve or graft replacement. Five patients had their surgical procedures following the 10/15/2015 FDA safety communication. The mean time from surgery to symptom onset (range) was 32 (13–73) months. Ten of 11 patients who underwent ophthalmologic examination had chorioretinal abnormalities. Three patients who underwent microbial cell-free deoxyribonucleic acid sequencing tested positive for M. chimaera, which was subsequently confirmed with blood culture growth. Echocardiography and positron emission tomography/computed tomography (PET/CT) revealed evidence of prosthetic valve/graft infection in 7/12 (58.3%) and 6/10 (60.0%) of cases, respectively. Seven patients (58.3%) underwent redo cardiovascular surgery. Of these, 1 patient died 2 days postdischarge, 1 experienced spinal osteomyelitis relapse, and another had interval prosthetic valve fluorodeoxyglucose (FDG) uptake on PET/CT suspicious for recurrent infection. Among 4 patients on medical therapy only, 3 expired or transitioned to hospice during follow-up.

Conclusions
MCI continues to occur despite the FDA communications. Incorporation of ophthalmologic examination and use of advanced tools may improve MCI diagnosis. The mortality in these patients is high even with aggressive surgical/medical management.
Quality of life among older Chinese people living with HIV/AIDS: a cross-sectional study in Hunan
Authors: Chen Dan , Wang Min , Duan Luxi , Chen Xi , Zhang Qiang , Li Xingli 
Published: July 2021

Abstract

Background
There is little research to date in the area of quality of life (QoL) among older Chinese people living with HIV/AIDS (PLWHA). This study aims to explore the QoL and its influential factors among older PLWHA in China.

Methods
Cross-sectional data of 242 adults with HIV/AIDS aged 50–84 y from Hunan were analyzed to evaluate the associations of demographic characteristics, illness-related factors, HIV-related stigma and social support with QoL. The WHO QOL-HIV BREF questionnaire was used to measure QoL on six domains (physical, psychological, independence, social relationships, environment and spirituality).

Results
A total of 242 older PLWHA completed the survey, of whom 150 (62.0%) were males. Multivariate linear regression analyses identified that females, side effects of highly active antiretroviral therapy, chronic non-communicable diseases and higher levels of perceived negative self-image were negatively associated with QoL, especially in the physical, independence and spirituality domains; whereas higher education or annual income, retired and elevated levels of subjective social support or support availability were positively associated with QoL, especially in the psychological, independence, social relationships and environment domains.

Conclusions
The study findings suggest that interventions to improve QoL should focus on reducing HIV-related stigma and side effects and on enhancing economic situations and social support.
Contribution ofSchistosoma mansonito systemic inflammation and microbial translocation among people with HIV in Zambia
Authors: Furch Briana D , Mwakamui Simutanyi , Sianongo Sandie , Zyambo Kanekwa , Heimburger Douglas C , Koethe John R , Kelly Paul 
Published: July 2021

AbstractBackgroundSchistosoma mansoni is hyperendemic in many rural areas of Zambia where up to 77% of people are positive for infection via serologic evaluation. Zambia also has a high prevalence of HIV infection. Individually, S. mansoni and HIV infection impair gastrointestinal barrier integrity and induce inflammation, but the effects of coinfection are not well understood. We set out to test the hypothesis that HIV would exacerbate intestinal barrier failure in patients with S. mansoni infection.MethodsAdults attending medical outpatient clinics in Kaoma, Western Province, Zambia, were enrolled in a case-control study to determine the relative contributions of schistosomiasis and HIV to microbial translocation (measured as soluble CD14 [sCD14] and lipopolysaccharide binding protein [LBP]) and inflammation (measured as CRP).ResultsAmong 152 adults evaluated, 74 (49%) were HIV-seropositive, 45 (29%) were shedding schistosome ova (Kato-Katz), 120 (81%) were seropositive for schistosome antibodies (i.e. prior or current infection, with or without egg shedding) and 16 (11%) were HIV/schistosome coinfected (defined by Kato-Katz). HIV infection was associated with higher circulating sCD14 concentrations (p=0.003 by Kruskal–Wallis test), but schistosomiasis was not. HIV infection was associated with greater exposure to schistosomes assessed serologically (OR=2.48, 95% CI 1.05 to 5.86; p=0.03), but reduced likelihood of egg shedding (OR 0.47, 95% CI 0.21 to 1.01; p=0.03).ConclusionsThere was no evidence for a compounding or synergistic effect of coinfection on microbial translocation that appeared to be correlated with HIV infection. Further studies are needed to understand how the increase in LBP secondary to HIV infection may decrease schistosome egg excretion in coinfected individuals.
Autozygosity Mapping by Genome-wide Single Nucleotide Polymorphism Array Identifies a Novel Homozygous HR Mutation in a Consanguineous Family with Universal Hereditary Hair Loss
Authors: Zeinali Sirous , Youssefian Leila , Vahidnezhad Hassan , Saeidian Amir Hossein , Sotoudeh Soheila , Bagherian Hamideh , Uitto Jouni 
Published: July 2021

Abstract

Objective:
Isolated hereditary hypotrichosis is caused by mutations in as many as 11 different genes. The conventional mutation detection strategy consists of sequencing of individual candidate genes separately, a time consuming and costly approach. In this study, we perform genome-wide single nucleotide polymorphism (SNP) array to identify candidate genes of hereditary hypotrichosis.

Methods:
A consanguineous family with two patients with hereditary hypotrichosis was enrolled, and autozygosity mapping by genome-wide SNP array was utilized to identify candidate genes.

Results:
Autozygosity mapping delineated runs of homozygosity, and alignment of the 11 genes identified the hairless (HR) gene as the candidate gene. Nucleotide sequencing revealed a novel homozygous mutation c.381delT, p.Ser127ArgfsTer40.

Conclusion:
This study illustrates how autozygosity mapping by a high-density SNP array streamlines mutation detection in heritable skin diseases.
Regulatory involvement of the PerR and SloR metalloregulators in theStreptococcus mutansoxidative stress response
Authors: Ruxin Talia R. , Schwartzman Julia A. , Davidowitz Cleo R. , Haney Robet A. , Spatafora Grace A. 
Published: July 2021

ABSTRACTStreptococcus mutansis a commensal of the human oral microbiome that can instigate dental caries under conditions of dysbiosis. This study investigatesS. mutansmetalloregulators and their involvement in mediating a response to oxidative stress. Oxidative stress in the oral cavity can derive from temporal increases in reactive oxygen species (ROS) after meal consumption, and from endogenous bacterial ROS-producers that colonize the dentition as constituents of dental plaque. We hypothesize that the PerR (SMU.593) and SloR (SMU.186) metalloregulatory proteins inS. mutanscontribute to oxidative stress tolerance by regulating the expression of genes responsive to H2O2challenge. The results of qRT-PCR experiments withS. mutanscultures exposed to 0.5mM H2O2revealperRtranscription that is responsive to the peroxide stressor, andsloRtranscription that is subject to PerR repression. The results of gel shift assays support direct binding of a PerR homolog to theS. mutans sloRpromoter at Fur and PerR consensus sequences on the UA159 chromosome. In addition, transcription of theS. mutans tpxanddprantioxidant genes is upregulated in aperR/sloRdouble knockout mutant, consistent with heightened resistance of theS. mutansGMS802perR-deficient strain when challenged with H2O2. Cumulatively, these results reveal a relationship of reciprocity between the PerR and SloR metalloregulators during theS. mutansresponse to oxidative stress and begin to elucidate the fitness strategies that evolved to fosterS. mutanssurvival and persistence in the transient environments of the human oral cavity.IMPORTANCEIn 2020, untreated dental caries, especially in the permanent dentition, ranked among the most prevalent infectious diseases worldwide. Moreover, caries disproportionately affects children and individuals of low socioeconomic status. Untreated caries can lead to systemic health problems and has been associated with extended school and work absences, inappropriate use of emergency departments, and an inability for military forces to deploy. In combination with public health policy, research aimed at alleviatingS. mutans-inducedtooth decay is important because it can improve oral health, as well as overall health, especially for underserved populations. This research is focused on theS. mutansSloR and PerR metalloregulatory proteins that can help inform the development of therapeutics aimed at alleviating and potentially preventing dental caries.
Transcranial direct current stimulation combined with alcohol cue inhibitory control training reduces the risk of early alcohol relapse: a randomized placebo-controlled clinical trial
Authors: Dubuson Macha , Kornreich Charles , Vanderhasselt Anne , Baeken Chris , Wyckmans Florent , Dousset Clémence , Hanak Catherine , Veeser Johannes , Campanella Salvatore , Chatard Armand , Jaafari Nemat , Noël Xavier 
Published: July 2021

AbstractBackgroundApproximately half the people with alcohol use disorder (AUD) relapse into alcohol reuse in the few weeks following withdrawal treatment. Brain stimulation and cognitive training represent recent forms of complementary interventions in the context of AUD.ObjectiveTo evaluate the clinical efficacy of transcranial direct current stimulation (tDCS) over the dorsolateral prefrontal cortex (DLPFC) combined with alcohol cue inhibitory control training (ICT) as part of rehabilitation.MethodsA randomized clinical trial was conducted on patients (n=125) withsevere AUD at a withdrawal treatment unit. Each patient was randomly assigned to one of four conditions, in a 2 [verum vs. sham tDCS] x 2 [alcohol cue vs. neutral ICT] factorial design. The primary outcome of the treatment was the measured abstinence rate after two weeks or more (up to one year).ResultsVerum tDCS improved the abstinence rate at the 2-week follow-up compared to the sham condition, independently of the training condition (79.7% [95% CI = 69.8-89.6] vs. 60.7% [95% CI = 48.3-73.1]; p = 0.02). A priori contrasts analyses revealed higher abstinence rates for the verum tDCS associated with alcohol cue ICT (86.1% [31/36; 95% CI= 74.6-97.6]) than for the other three conditions (64% [57/89; 95% CI = 54-74]). These positive clinical effects on abstinence did not persist beyond two weeks after the intervention.ConclusionsAUD patients who received tDCS applied to DLPFC showed a significantly higher abstinence rate during the weeks following rehabilitation. When combined with alcohol-specific ICT, brain stimulation may provide better clinical outcomes.Trial RegistrationClinicalTrials.gov number NCT03447054
DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression
Authors: Kong Tim , Laranjeira Angelo Brunelli Albertoni , Yang Kangning , Fisher Daniel A. C. , Yu LaYow , Wang Anthony Z , Ruzinova Marianna , Fowles Jared S. , Allen Maggie J. , Celik Hamza , Challen Grant A. , Huang Sidong , Oh Stephen T. 
Published: July 2021

AbstractChronic myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed bulk transcriptome profiling accompanied by single cell RNA-sequencing on CD34+ stem/progenitor cells from serial patient samples obtained at the chronic MPN and sAML phases, and identified aberrantly increased expression of dual-specificity phosphatase 6 (DUSP6) underlying disease transformation. Genetic and pharmacologic targeting of DUSP6 led to inhibition of S6 and JAK/STAT signaling, resulting in potent suppression of cell proliferation, while also reducing inflammatory cytokine production in primary samples. Furthermore, ectopic DUSP6 expression augmented proliferation and mediated JAK2 inhibitor resistance, while DUSP6 inhibition reduced colony-forming potential of JAK2 inhibitor-persistent patient cells. Mechanistically, DUSP6 perturbation dampened S6 signaling via inhibition of RSK1, which we identified as a second indispensable candidate associated with poor clinical outcome. Lastly, DUSP6 inhibition potently suppressed disease development across Jak2 V617F and MPL W515L MPN mouse models, and sAML patient-derived xenografts. These findings underscore DUSP6 in driving disease transformation and therapeutic resistance, and highlight the DUSP6-RSK1 axis as a novel, druggable pathway in myeloid malignancies.
Polygenic risk for psychiatric disorder reveals distinct association profiles across social behaviour in the general population
Authors: Schlag Fenja , Allegrini Andrea , Buitelaar Jan , Verhoef Ellen , van Donkelaar Marjolein , Plomin Robert , Rimfeld Kaili , Fisher Simon Edward , Pourcain Beate St 
Published: July 2021

AbstractMany complex psychiatric disorders are characterised by a spectrum of social difficulties. These symptoms lie on a behavioural dimension that is shared with social behaviour in the general population, with substantial contributions of genetic factors. However, shared genetic links may vary across psychiatric disorders and social symptoms. Here, we systematically investigate heterogeneity in shared genetic liabilities with attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorders (ASD), bipolar disorder (BP), major depression (MD) and schizophrenia, across a spectrum of different social symptoms. Specifically, longitudinally assessed low-prosociality and peer-problem scores in two UK population-based/community-based cohorts (ALSPAC, N ≤ 6174, 4-17 years; TEDS, N ≤ 7112, 4-16 years; parent- and teacher-reports) were regressed on polygenic risk scores for ADHD, ASD, BP, MD, and schizophrenia, as informed by genome-wide summary statistics from large consortia, using negative binomial regression models. Across ALSPAC and TEDS, we replicated univariate polygenic associations between social behaviour and risk for ADHD, MD, and schizophrenia. Modelling univariate genetic effects across both cohorts with random-effect meta-regression revealed evidence for polygenic links between social behaviour and ADHD, ASD, MD, and schizophrenia risk, but not BP, where differences in age, reporter and social trait captured 45-88% in univariate effect variation. For ADHD, MD, and ASD polygenic risk, we identified stronger association with peer problems than low prosociality, while schizophrenia polygenic risk was solely associated with low prosociality. The identified association profiles suggest marked differences in the social genetic architecture underlying different psychiatric disorders when investigating population-based social symptoms across 13 years of child and adolescent development.
Coping under stress: Prefrontal control predicts stress burden during the COVID-19 crisis
Authors: Monninger Maximilian , Pollok Tania M. , Aggensteiner Pascal-M. , Kaiser Anna , Reinhard Iris , Hermann Andrea , Meyer-Lindenberg Andreas , Brandeis Daniel , Banaschewski Tobias , Holz Nathalie E. 
Published: July 2021

AbstractBackgroundThe coronavirus (COVID-19) pandemic has confronted millions of people around the world with an unprecedented stressor, affecting physical and mental health. Accumulating evidence suggests that emotional and cognitive self-regulation is particularly needed to effectively cope with stress. Therefore, we investigated the predictive value of affective and inhibitory prefrontal control for stress burden during the COVID-19 crisis.MethodPhysical and mental health burden were assessed using an online survey, which was administered to 104 participants of an ongoing German at-risk birth cohort during the first wave in April 2020. Two follow-ups were carried out during the pandemic, one capturing the relaxation during summer and the other the beginning of the second wave of the crisis. Prefrontal activity during emotion regulation and inhibitory control were assessed prior to the COVID-19 crisis.ResultsIncreased inferior frontal gyrus activity during emotion regulation predicted lower stress burden at the beginning of the first and the second wave of the crisis. In contrast, inferior and medial frontal gyrus activity during inhibitory control predicted effective coping only during the summer, when infection rates decreased but stress burden remained unchanged. These findings remained significant when controlling for sociodemographic and clinical confounders such as stressful life events prior to the crisis or current psychopathology.ConclusionsWe demonstrate that differential stress-buffering effects are predicted by the neural underpinnings of emotion regulation and cognitive regulation at different stages during the pandemic. These findings may inform future prevention strategies to foster stress coping in unforeseen situations.HighlightsHealth threatening stressors, such as the COVID-19 pandemic, significantly worsen well-being.Results reveal high levels of stress during the course of the pandemic with an increase of stress burden towards the second wave.Self-regulation is an important coping strategy to restore allostasis.Higher prefrontal activity during emotion regulation predicted less stress during the peaks of infection rates in the first and second waveHigher prefrontal inhibitory control predicted less stress burden between both waves when infection rates were low.Our findings highlight the importance of prefrontal regulation as effective coping mechanisms in the face of unprecedented stressors.