bluuebunny/crossref_metadata_2025_split huggingface dataset:
No evidence of increase in suicide in Greece during the first wave of Covid-19
Authors: Vandoros Sotiris , Theodorikakou Olga , Katsadoros Kyriakos , Zafeiropoulou Dimitra , Kawachi Ichiro 
Published: November 2020

AbstractBackground and ObjectiveMental health outcomes have reportedly worsened in several countries during the Covid-19 pandemic and associated lockdowns. In the present study we examined whether suicides increased in Greece during the first wave of the pandemic.MethodsWe used daily suicide estimates from a Suicide Observatory in Greece from 2015-2020 and followed three methodologies: A descriptive approach, an interrupted time series analysis, and a differences-in-differences econometric model.ResultsWe did not find any empirical evidence of any increase in suicides during the first wave of Covid-19 and the lockdown in any of the three approaches used.ConclusionsSuicides did not seem to increase during the first wave of covid-19 and lockdown in Greece. However, this does not mean that mental health did not deteriorate, or that we will not observe an increase in suicides during the second wave. Protective factors for Greece during the first wave may include working from home (for those able to tele-work), strong family ties, advertising of a suicide hotline and income support for the unemployed.
Ethical and practical considerations in HIV drug trial closure: perspectives of research staff in Uganda
Authors: Nalubega Sylivia , Cox Karen , Mugerwa Henry , Evans Catrin 
Published: November 2020

AbstractThere is a gap in evidence regarding how research trial closure processes are managed to ensure continuity of HIV care for HIV positive participants following trial closure within low income settings. This research aimed to establish how research staff in Uganda understood and practised post-trial care for HIV positive trial participants. A grounded theory study was conducted using in-depth individual interviews and focus group discussions with 22 research staff from 3 different trials in Uganda, in 2014-2015. The results indicated that researchers engaged in three main activities to support trial participants, including; (i) preparing for post-trial care, which included instituting trial closure guidelines, planning necessary resources, and informing trial participants about post-trial care; (ii) facilitating participants during trial exit by engaging in psychological and practical support activities, and (iii) providing follow up care and support for participants after trial exit, to respond to the needs of trial participants which often arose after trial exit. This study established a need for a holistic approach to post-trial-care of HIV positive trial participants in Uganda, and the need to engage multiple stakeholders including ethics authorities.
Molecular docking-based screening for novel inhibitors of the human immunodeficiency virus type 1 protease that effectively reduce the viral replication in human cells
Authors: Mavian Carla , Coman Roxana M , Zhang Xinrui , Pomeroy Steve , Ostrov David A. , Dunn Ben M , Sleasman John W. , Goodenow Maureen M 
Published: November 2020

AbstractTherapeutic pressure by protease inhibitors (PIs) contributes to accumulation of mutations in the HIV type 1 (HIV-1) protease (PR) leading to development of drug resistance with subsequent therapy failure. Current PIs target the active site of PR in a competitive manner. Identification of molecules that exploit non-active site mechanisms of inhibition is essential to overcome resistance to current PIs. Potential non-active site HIV-1 protease (PR) inhibitors (PI) were identified by in silico screening of almost 140,000 molecules targeting the hinge region of PR. Inhibitory activity of best docking compounds was tested in an in vitro PR inhibition biochemical assay. Five compounds inhibited PR from multiple HIV-1 subtypes in vitro and reduced replicative capacity by PI-sensitive or multi-PI resistant HIV-1 variants in human cells ex vivo. Antiviral activity was boosted when combined with Ritonavir, potentially diminishing development of drug resistance, while providing effective treatment for drug resistant HIV-1 variants.
Aversive Conditioning of Spatial Position Sharpens Neural Population-level Tuning in Visual Cortex and Selectively Reduces Alpha-band Activity
Authors: Friedl Wendel M. , Keil Andreas 
Published: November 2020

AbstractProcessing capabilities for many low-level visual features are experientially malleable, aiding sighted organisms in adapting to dynamic environments. Explicit instructions to attend a specific visual field location influence retinotopic visuocortical activity, amplifying responses to stimuli appearing at cued spatial positions. It remains undetermined, however, both how such prioritization affects surrounding non-prioritized locations, and if a given retinotopic spatial position can attain enhanced cortical representation through experience rather than instruction. This work examined visuocortical response changes as human observers learned, through differential classical conditioning, to associate specific on-screen locations with aversive outcomes. Using dense-array EEG and pupillometry, we tested the pre-registered hypotheses of either sharpening or generalization around an aversively associated location following a single conditioning session. Specifically, competing hypotheses tested if mean response changes would take the form of a gaussian (generalization) or difference-of-gaussian (sharpening) distribution over spatial positions, peaking at the viewing location paired with a noxious noise. Occipital 15 Hz steady-state visual evoked potential (ssVEP) responses were selectively heightened when viewing aversively paired locations and displayed a non-linear, difference-of-gaussian profile across neighboring locations, consistent with suppressive surround modulation of non-prioritized positions. Measures of alpha band (8 – 12.8 Hz) activity and pupil diameter also exhibited selectively heightened responses to noise-paired locations but did not evince any difference across the non-paired locations. These results indicate that visuocortical spatial representations are sharpened in response to location-specific aversive conditioning, while top-down influences indexed by alpha power reduction exhibit all-or-none modulation.Significance StatementIt is increasingly recognized that early visual cortex is not a static processor of physical features, but is instead constantly shaped by perceptual experience. It remains unclear, however, to what extent the cortical representation of many fundamental features, including visual field location, is malleable by experience. Using EEG and an aversive classical conditioning paradigm, we observed sharpening of visuocortical responses to stimuli appearing at aversively associated locations along with location-selective facilitation of response systems indexed by pupil diameter and EEG alpha power. These findings highlight the experience-dependent flexibility of retinotopic spatial representations in visual cortex, opening avenues towards novel treatment targets in disorders of attention and spatial cognition.
Effects of inactivation method on SARS-CoV-2 virion protein and structure
Authors: Loveday Emma K. , Hain Kyle S. , Kochetkova Irina , Hedges Jodi F. , Robison Amanda , Snyder Deann T. , Brumfield Susan K. , Young Mark J. , Jutila Mark A. , Chang Connie B. , Taylor Matthew P. 
Published: November 2020

AbstractThe risk posed by Severe Acute Respiratory Syndrome Coronavirus −2 (SARS-CoV-2) dictates that live-virus research is conducted in a biosafety level 3 (BSL3) facility. Working with SARS-CoV-2 at lower biosafety levels can expedite research yet requires the virus to be fully inactivated. In this study, we validated and compared two protocols for inactivating SARS-CoV-2: heat treatment and ultraviolet irradiation. The two methods were optimized to render the virus completely incapable of infection while limiting destructive effects of inactivation. We observed that 15 minutes of incubation at 65°C completely inactivates high titer viral stocks. Complete inactivation was also achieved with minimal amounts of UV power (70,000 μJ/cm2), which is 100-fold less power than comparable studies. Once validated, the two methods were then compared for viral RNA quantification, virion purification, and antibody recognition. We observed that UV irradiation resulted in a 2-log reduction of detectable genomes compared to heat inactivation. Protein yield following virion enrichment was equivalent for all inactivation conditions, but the resulting viral proteins and virions were negatively impacted by inactivation method and time. We outline the strengths and weaknesses of each method so that investigators might choose the one which best meets their research goals.
COVATOR: A Software for Chimeric Coronavirus Identification
Authors: Habib Peter T. 
Published: November 2020

AbstractThe term chimeric virus was not popular in the last decades. Recently, according to current sequencing efforts in discovering COVID-19 Secrets, the generated information assumed the presence of 6 Coronavirus main strains, but coronavirus diverges into hundreds of sub-strains. the bottleneck is the mutation rate. With two mutation/month, humanity will meet a new sub-strain every month. Tracking new sequenced viruses is urgently needed because of the pathogenic effect of the new substrains. here we introduce COVATOR, A user-friendly and python-based software that identifies viral chimerism. COVATOR aligns input genome and protein that has no known source, against genomes and protein with known source, then gives the user a graphical summary.
Machine Learning in Clinical Psychology and Psychotherapy Education: A Survey of Postgraduate Students at a Swiss University
Authors: Blease Charlotte , Kharko Anna , Annoni Marco , Gaab Jens , Locher Cosima 
Published: November 2020

AbstractBackgroundThere is increasing use of for machine learning-enabled tools (e.g., psychotherapy apps) in mental health care.ObjectiveThis study aimed to explore postgraduate clinical psychology and psychotherapy students’ familiarity and formal exposure to topics related to artificial intelligence and machine learning (AI/ML) during their studies.MethodsIn April-June 2020, we conducted a mixed-methods web-based survey using a convenience sample of 120 clinical psychology and psychotherapy enrolled in a two-year Masters’ program students at a Swiss university.ResultsIn total 37 students responded (response rate: 37/120, 31%). Among the respondents, 73% (n=27) intended to enter a mental health profession. Among the students 97% reported that they had heard of the term ‘machine learning,’ and 78% reported that they were familiar with the concept of ‘big data analytics’. Students estimated 18.61/3600 hours, or 0.52% of their program would be spent on AI/ML education. Around half (46%) reported that they intended to learn about AI/ML as it pertained to mental health care. On 5-point Likert scale, students moderately agreed (median=4) that AI/M should be part of clinical psychology/psychotherapy education.ConclusionsEducation programs in clinical psychology/psychotherapy may lag developments in AI/ML-enabled tools in mental healthcare. This survey of postgraduate clinical psychology and psychotherapy students raises questions about how curricula could be enhanced to better prepare clinical psychology/psychotherapy trainees to engage in constructive debate about ethical and evidence-based issues pertaining to AI/ML tools, and in guiding patients on the use of online mental health services and apps.
Assessment of functional capacity with cardiopulmonary exercise testing in non-severe COVID-19 patients at three months follow-up
Authors: Clavario Piero , De Marzo Vincenzo , Lotti Roberta , Barbara Cristina , Porcile Annalisa , Russo Carmelo , Beccaria Federica , Bonavia Marco , Bottaro Luigi Carlo , Caltabellotta Marta , Chioni Flavia , Santangelo Monica , Hautala Arto J. , Ameri Pietro , Canepa Marco , Porto Italo 
Published: November 2020

ABSTRACTIntroductionLong-term effects of Coronavirus Disease of 2019 (COVID-19) and their sustainability in a large number of patients are of the utmost relevance. We aimed to determine: 1)functional capacity of non-severe COVID-19 survivors by cardiopulmonary exercise testing (CPET); 2)those characteristics associated with worse CPET performance.MethodsWe prospectively enrolled the first 150 consecutive subjects with laboratory-confirmed COVID-19 infection discharged alive from March to April 2020 at Azienda Sanitaria Locale (ASL)3, Genoa, Italy. At 3-month from hospital discharge, complete clinical evaluation, trans-thoracic echocardiography, cardiopulmonary exercise testing (CPET), pulmonary function test (PFT), and dominant leg extension (DLE) maximal strength evaluation were performed.ResultsExcluding severe and incomplete/missing cases, 110 patients were analyzed. Median percent predicted peak oxygen uptake (%pVO2) was 90.9(79.2-109.0)%. Thirty-eight(34.5%) patients had %pVO2 below, whereas 72(65.5%) above the 85% predicted value (indicating normality). Median PFT parameters were within normal limits.Eight(21.1%) patients had a mainly respiratory, 9(23.7%) a mainly cardiac, 3(7.9%) a mixed-cardiopulmonary, and 18(47.4%) a non-cardiopulmonary limitation of exercise. Eighty-one(73.6%) patients experimented at least one symptom, without relationship with %pVO2 (p>0.05).Multivariate linear regression analysis showed age (β=0.46, p=0.020), percent weight loss (β=-0.77, p=0.029), active smoke status (β=-7.07, p=0.019), length of hospital stay (β=-0.20, p=0.042), and DLE maximal strength (β=1.65, p=0.039) independently associated with %pVO2.ConclusionsHalf of non-severe COVID-19 survivors show functional capacity limitation mainly explained by muscular impairment, albeit cardiopulmonary causes are possible. These findings call for future research to identify patients at higher risk of long-term effects, that may benefit from careful surveillance and targeted rehabilitation.Take-home messagesat 3-month cardiopulmonary exercise testing 38/110(34.5%) non-severe COVID-19 survivors had percent predicted peak oxygen uptake (%pVO2) < 85% (indicating normality). Half of them had functional capacity limitation mainly explained by muscular impairment.
Deaths among COVID Cases in the United States: Racial and Ethnic Disparities Persist
Authors: Fabic Madeleine Short , Choi Yoonjoung , Bishai David 
Published: November 2020

AbstractUsing COVID-19 Case Surveillance Public Use Data by the Centers for Disease Control and Prevention, we estimate monthly age-adjusted case fatality rates (CFR) for four major groups: non-Hispanic (NH) whites, NH Blacks, NH Asians, and Hispanics. Available data show that CFRs across race/ethnic groups have become more equal over time. Nevertheless, racial and ethnic disparities persist. NH whites consistently experience lower CFRs; NH Blacks generally experience higher case fatality among younger patients; and NH Asians generally experience higher case fatality among older patients. Age-adjusted CFRs reveal dramatically different racial and ethnic disparities that are hidden by crude CFRs. Such adjustment is imperative for understanding COVID-19’s toll.
Genomic landscapes of canine splenic angiosarcoma (hemangiosarcoma) contain extensive heterogeneity within and between patients
Authors: Wong Shukmei , Ehrhart EJ , Stewart Samuel , Zismann Victoria , Cawley Jacob , Halperin Rebecca , Briones Natalia , Richter Keith , Sivaprakasam Karthigayini , Perdigones Nieves , Contente-Cuomo Tania , Facista Salvatore , Trent Jeffrey M. , Murtaza Muhammed , Khanna Chand , Hendricks William P. D. 
Published: November 2020

ABSTRACTCancer genomic heterogeneity presents significant challenges for understanding oncogenic processes and for cancer’s clinical management. Variation in driver mutation frequency between patients with the same tumor type as well as within individual patients’ cancers can limit the power of mutations to serve as diagnostic, prognostic, and predictive biomarkers. We have characterized genomic heterogeneity between and within patients in canine splenic hemangiosarcoma (HSA), a common naturally occurring cancer in pet dogs that is similar to human angiosarcoma (AS). HSA is a clinically, physiologically, and genomically complex canine cancer that may serve as a valuable model for understanding the origin and clinical impact of cancer heterogeneity. We conducted a prospective collection of 52 splenic masses from 44 dogs (28 HSA, 15 benign masses, and 1 stromal sarcoma) presenting to emergency care with hemoperitoneum secondary to a ruptured splenic mass. Multi-platform genomic analysis included matched tumor/normal cancer gene panel and exome sequencing. We found candidate somatic cancer driver mutations in 14/28 (50%) HSAs. Among recurrent candidate driver mutations,TP53was most commonly mutated (29%) followed byPIK3CA(14%),AKT1(11%), andCDKN2AIP(11%). We also identified significant intratumoral genomic heterogeneity, consistent with a branched evolution model, through multi-region exome sequencing of three distinct tumor regions from selected primary splenic tumors. These data provide new perspective on the genomic landscape and comparative value of understanding HSA in pet dogs, particularly as a naturally occurring cancer bearing intratumoral heterogeneity.
SARS-CoV-2-specific T cell memory is long-lasting in the majority of convalsecent COVID-19 individuals
Authors: Li Ziwei , Liu Jing , Deng Hui , Yang Xuecheng , Wang Hua , Feng Xuemei , Zelinskyy Gennadiy , Trilling Mirko , Sutter Kathrin , Lu Mengji , Dittmer Ulf , Wang Baoju , Yang Dongliang , Zheng Xin , Liu Jia 
Published: November 2020

ABSTRACTAn unaddressed key question in the currentcoronavirus disease 2019(COVID-19) pandemic is the duration of immunity for which specific T cell responses against thesevere acute respiratory syndrome coronavirus 2(SARS-CoV-2) are an indispensable element. Being situated in Wuhan where the pandemic initiated enables us to conduct the longest analyses of memory T cell responses against SARS-CoV-2 in COVID-19 convalescent individuals (CIs). Magnitude and breadth of SARS-CoV-2 memory CD4 and CD8 T cell responses were heterogeneous between patients but robust responses could be detected up to 9 months post disease onset in most CIs. Loss of memory CD4 and CD8 T cell responses were observed in only 16.13% and 25.81% of CIs, respectively. Thus, the overall magnitude and breadth of memory CD4 and CD8 T cell responses were quite stable and not inversely correlated with the time from disease onset. Interestingly, the only significant decrease in the response was found for memory CD4 T cells in the first 6-month post COVID-19 disease onset. Longitudinal analyses revealed that the kinetics of SARS-CoV-2 memory CD4 and CD8 T cell responses were quite heterogenous between patients. Loss of memory CD4 T cell responses was observed more frequently in asymptomatic cases than after symptomatic COVID-19. Interestingly, the few CIs in which SARS-CoV-2-specific IgG responses disappeared showed more durable memory CD4 T cell responses than CIs who remained IgG-positive for month. Collectively, we provide the first comprehensive characterization of the long-term memory T cell response in CIs, suggesting that SARS-CoV-2-specific T cell immunity is long-lasting in the majority of individuals.
Early Dietary Exposures Epigenetically Program Mammary Cancer Susceptibility through IGF1-mediated Expansion of Mammary Stem Cells
Authors: Zheng Yuanning , Luo Linjie , Lambertz Isabel U. , Fuchs-Young Robin 
Published: November 2020

AbstractDietary exposures at early developmental stages have been shown to program lifetime breast cancer susceptibility. We previously reported that manipulation of gestational and postweaning diets leads to different mammary tumor outcomes in carcinogen-treated mice. The high tumor incidence (HT) groups (average 61.5% tumor incidence) received a low-fat, low-sugar, mildly restricted (12%v/v) (DR) diet during gestation, followed by a high-fat, high-sugar (HF) diet postweaning. Conversely, the low tumor incidence (LT) groups (average 20% tumor incidence) received the HF diet during gestation, followed by the DR diet postweaning. Herein, we extended these findings by demonstrating that HT animals had an expanded mammary stem cell (MaSC) population compared to LT animals before puberty, and this expansion persisted into adulthood. IGF1 expression was increased in mammary stromal cells from HT animals, which promoted the self-renewal capacity of MaSCs in a paracrine fashion. This increased IGF1 expression was programmed prepubertally through DNA hypomethylation of the IGF1 promoter 1, mediated by decreased DNMT3b levels. IGFBP5 mRNA and protein levels were also reduced in mammary tissues from HT animals, indicating an increased bioavailability of tissue IGF1. In association with these changes, mammary tissues from carcinogen-treated HT animals developed an increased proportion of mammary adenosquamous carcinomas compared to carcinogen-treated LT animals. This study provides novel mechanistic insights into how early dietary exposures program mammary cancer risk and tumor phenotypes by increasing IGF1 expression through epigenetic alterations, thereby expanding the MaSC population, resulting in a higher number of carcinogen targets susceptible to transformation in adulthood.SignificanceEarly high-fat dietary exposure programs lifetime mammary cancer susceptibility before puberty through epigenetic alterations of IGF1 promoters and IGF1-mediated paracrine regulation of mammary stem cell homeostasis.
Multidimensionality in the thermal niches of dung beetles could limit species’ responses to temperature changes
Authors: Calatayud Joaquín , Hortal Joaquín , Noriega Jorge Ari , Arcones Ángel , Espinoza Verónica R. , Guil Noemí , Lobo Jorge M. 
Published: November 2020

AbstractUnderstanding the consequences of climate change requires understanding how temperature controls species’ responses across key biological aspects, as well as the coordination of thermal responses across these aspects. We study the role of temperature in determining the species’ diel, seasonal, and geographical occurrence, using dung beetles as a model system. We found that temperature has relatively low −but not negligible− effects in the three spatiotemporal scales, once accounting for alternative factors. More importantly, the estimated thermal responses were largely incongruent across scales. This shows that species have multidimensional thermal niches, entailing that adjustments to fulfil temperature requirements for one biological aspect, such as seasonal ontogenetic cycles, may result in detrimental effects on other aspects, like diel activity. These trade-offs can expose individuals to inadequate temperatures, reducing populations’ performance. Paradoxically, the relatively weak effects of temperature we found may have serious consequences for species’ responses to warming if temperature regulates essential aspects of species’ biology in divergent ways.