bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of blame-related action tendencies in the vulnerability to major depressive disorder
Authors: Duan Suqian , Lawrence Andrew , Valmaggia Lucia , Moll Jorge , Zahn Roland 
Published: November 2020

AbstractBackgroundPersisting self-blaming emotional biases were previously associated with vulnerability to major depressive disorder (MDD). More specifically self-contempt/disgust biases distinguished remitted MDD, compared with never-depressed control participants. The contribution of action tendencies to MDD vulnerability and their relationship with blame-related emotions to prepare for subsequent behaviour is elusive. Here, we investigated whether maladaptive action tendencies such as “creating a distance from oneself” and “hiding” are associated with MDD vulnerability, as well as with self-disgust/contempt and shame respectively.Methods76 participants with medication-free remitted MDD and 44 healthy control (HC) participants without a personal or family history of MDD completed the value-related moral sentiment task, which measured their blame-related emotions during hypothetical social interactions and a novel task to assess their blame-related action tendencies.ResultsAs predicted, the MDD group exhibited a higher proneness to feeling like hiding and creating a distance from themselves compared with the HC group. Interestingly, apologising for one’s wrongdoing, was associated with all self-blaming emotions including shame, guilt, self-contempt/disgust and self-indignation, but was more common in HC. In contrast, apologising and perceiving to be in control of one’s friend’s wrongdoings were more common in MDD. Although shame was indeed associated with hiding, this was also true of guilt. Self-disgust/contempt was associated with attacking rather than creating a distance from oneself.ConclusionsMDD vulnerability was associated with specific maladaptive action tendencies which were not clearly predicted by the type of emotion, thus unveiling novel cognitive markers and neurocognitive treatment targets.General Scientific summaryThis study confirmed the hypothesis that specific maladaptive action tendencies related to self-blame, such as feeling like hiding and feeling like creating a distance from oneself, were distinctive of people with major depressive disorder, even on remission of symptoms. These action tendencies were not clearly predicted by the type of emotion experienced, showing the importance of assessing them directly. This calls for novel psychological and neurocognitive treatments specifically aiming at maladaptive action tendencies which have so far not been directly addressed in standard assessments and treatments.
The burden of Progressive Fibrotic Interstitial lung disease across the UK
Authors: Simpson Thomas , Barratt Shaney L , Beirne Paul , Chaudhuri Nazia , Crawshaw Anjali , Crowley Louise E , Fletcher Sophie , Gibbons Michael A , Hallchurch Philippa , Horgan Laura , Jakaityte Ieva , Lewis Thomas , McLellan Tom , Miller Ryan , Stanel Stefan , Thillai Muhunthan , Thompson Fiona , Wu Zhe , Molyneaux Philip L , West Alex G 
Published: November 2020

AbstractWhile Idiopathic pulmonary fibrosis (IPF) remains the exemplar progressive fibrotic lung disease, there remains a cohort of non-IPF fibrotic lung diseases (fILD) which adopt a similar clinical behaviour to IPF despite therap. This phenotypically related group of conditions, where progression of disease is similar to that seen in IPF, have recently been described as Progressive Fibrotic Interstitial Lung diseases (PF-ILD). Previous estimates suggest that between 18 to 40% of all fILD will develop progressive disease, however, the exact burden remains unknown. This retrospective, observational study therefore aimed to estimate the incidence of PF-ILD across England.All new referrals seen across nine UK centres for their first outpatient clinic appointment between 1st August 2017 and 31st January 2018 were assessed against the diagnostic criteria for PF-ILD laid out in the INBUILD trial. A total of 1749 patients with fILD were assessed. In this cohort of patients at risk of developing PF-ILD the INBUILD criteria were met in 14.5% (253/1749) of all new non-IPF fILD referrals. The average time from referral to specialist centre to diagnosis of progressive phenotype was 311 days. Of the progression events the majority were driven by a measured drop in FVC, with more than half of patients experiencing a drop of 10%. Almost one quarter of patients (24.1%) were diagnosed with progressive disease on the basis of radiological and symptomatic progression alone without a spirometric deterioration.This study represents a fair and balanced approach to assessing the incidence of objectively measurable and treatable PF-ILDs in the UK. A rate of 14.5% of new referrals with non-IPF ILD is less than that reported in previous studies however our methodology is likely to give a more accurate result than estimates based on extrapolation from general disease statistics, from physician-reported estimates prone to significant biases, or insurance claim processes also substantially prone to bias. This information has implication for workforce planning and the funding of anti-fibrotic therapy in the UK and beyond.
Involvement of Gut Microbiota in the Development of Psoriasis Vulgaris
Authors: Sun Chaonan , Chen Ling , Yang Huan , Sun Hongjiang , Xie Zhen , Zhao Bei , Jiang Xuemei , Qin Bi , Shen Zhu 
Published: November 2020

AbstractBackgroundPsoriasis is a common chronic recurrent dermatitis. Accumulating observations show gut microbiota dysbiosis in psoriasis.ObjectivesWe intend to further investigate the relationship between intestinal microbiota and psoriasis development.MethodsWe first performed an epidemiological investigation on differences of gastrointestinal discomfort symptoms between psoriatic patients and general population. Then variation of gut microbiota in psoriatic patients (un)treated with Acitretin was analyzed by 16S rRNA sequencing. We last compared recovery status and vital cytokines of mouse psoriasiform models, which were transplanted with fecal microbiota from psoriatic patients or healthy controls.Results(1) 85.53% of psoriatic patients versus 58.08% of healthy controls presented with at least one gastrointestinal symptom. The prevalence of investigated symptoms (e.g. abdominal distension, constipation) were significantly higher in patients, compared with controls (p<0.05). Increased fart and constipation were significantly correlated with psoriasis (p<0.05, respectively). (2) The abundance of Ruminococcaceae family, Coprococcus_1 genus and Blautia genus were significantly decreased with psoriasis improvement, which had been demonstrated significantly increased in psoriasis. (3) Mice receiving psoriatic microflora transplantation showed significantly delayed recovery of psoriasiform dermatitis and less reduction of IL-17A, than those receiving healthy microflora or blank control (p<0.05 and p<0.01, respectively).ConclusionsMultiple evidences we provided here demonstrate the involvement of gut microbiota in psoriasis development. The strategy based on gut microbiota is expected to be a promising supplementary for long-term management of psoriasis.
Making prognostic algorithms useful in shared decision-making: Patients and clinicians’ requirements for the Predict:Breast Cancer interface
Authors: Farmer G.D. , Pearson G.M. , Skylark W.J. , Freeman A.L.J. , Spiegelhalter D.J. 
Published: November 2020

AbstractObjectivesTo develop a new interface for the widely used prognostic breast cancer tool: PREDICT. To facilitate shared decision-making around post-surgery breast cancer treatments. To derive insights into communicating the outputs of prognostic models to patients and their clinicians.MethodWe applied user-centred design principles in developing a new interface for PREDICT. The research involved online surveys, focus groups, meetings, and usability testing with patients, clinicians and the public.ResultsThe new interface has been launched and delivers around 30,000 sessions per month. We identified several principles that are useful when communicating the output of prognostic models, including multiple presentation formats, and contextualising statistics. A programme of future work based on patient and clinician feedback has been developed, including the provision of quantitative data on the adverse effects of adjuvant breast cancer treatments.ConclusionsFor prognostic algorithms to fulfil their potential to assist with shared decision-making they need carefully designed interfaces. User-centred design puts patients and clinicians needs at the forefront, allowing them to derive the maximum benefit from prognostic models.
Socioeconomic determinants of mobility responses during the first wave of COVID-19 in Italy: from provinces to neighbourhoods
Authors: Gauvin Laetitia , Bajardi Paolo , Pepe Emanuele , Lake Brennan , Privitera Filippo , Tizzoni Michele 
Published: November 2020

AbstractAs the second wave of SARS-CoV-2 infections is surging across Europe, it is crucial to identify the drivers of mobility responses to mitigation efforts during different restriction regimes, for planning interventions that are both economically and socially sustainable while effective in controlling the outbreak. Here, using anonymous and privacy enhanced cell phone data from Italy, we investigate the determinants of spatial variations of reductions in mobility and co-location in response to the adoption and the lift of restrictions, considering both provinces and city neighbourhoods. In large urban areas, our analysis uncovers the desertification of historic city centers, which persisted after the end of the lockdown. At the province level, the local structure of the labour market mainly explained the variations in mobility responses, together with other demographic factors, such as population’s age and sex composition. In the future, targeted interventions should take into account how the ability to comply with restrictions varies across geographic areas and socio-demographic groups.
Characteristic of IgA and IgG antibody response to SARS-CoV-2 infection in an Italian referral Covid-19 Hospital
Authors: Annamaria Carnicelli , Barbara Fiori , Rosalba Ricci , Alfonso Piano , Nicola Bonadia , Eleonora Taddei , Massimo Fantoni , Rita Murri , Antonella Cingolani , Christian Barillaro , Lucio Cutuli Salvatore , Debora Marchesini , Davide Antonio Della Polla , Evelina Forte , Mariella Fuorlo , Luca Di Maurizio , Paola Amorini , Francesco Franceschi , Maurizio Sanguinetti 
Published: November 2020

AbstractIntroductionAntibody response play a fundamental role in the natural history of infectious disease. A better understanding of the immune response in patients with SARS-CoV-2 infection could be important for identifying patients at greater risk of developing a more severe form of disease and with a worse prognosis.MethodsWe performed a cross-sectional analysis to determine the presence and the levels of both anti-SARS-CoV-2 IgG and IgA in a cohort of hospitalized patients with confirmed infection at different times in the natural history of the disease. Patients enrolled when admitted at the emergency department were prospectively followed up during hospital stay.ResultsOverall, 131 patients were considered with a total of 237 samples processed. Cross-sectional analysis showed that seroconversion for IgA seems to occur between days 5 and 15 while IgG response seems to occur slightly later, peaking at day 20 after symptoms onset. Both IgA and IgG were maintained beyond two months. Severe patients showed a higher IgA response compared with mild patients when analyzing optical density (8.3 versus 5.6, p < 0.001). Prospective analysis conducted on 55 patients confirmed that IgA appear slightly earlier than IgG. After stratifying for the severity of disease, both the IgA and IgG response was more vigorous in severe cases. Moreover, while IgG tended to stabilize, there was a relevant decline after the first month of IgA levels in mild cases.ConclusionIgA and IgG antibody response is closely related although seroconversion for IgA occurs earlier. Both IgA and IgG are maintained beyond two months. Severe patients showed a more vigorous IgA and IgG response. IgA levels seem to decline after one month since the onset of symptoms in mild cases.
5-Alpha-Reductase Inhibitors Reduce Remission Time of COVID-19: Results From a Randomized Double Blind Placebo Controlled Interventional Trial in 130 SARS-CoV-2 Positive Men
Authors: Cadegiani Flávio Adsuara , McCoy John , Wambier Carlos Gustavo , Goren Andy 
Published: November 2020

BackgroundSARS-CoV-2 entry into type II pneumocytes is depended on the TMPRSS2 proteolytic enzyme. The only known promoter of TMPRSS2 in humans is an androgen response element. As such, androgen sensitivity may be a risk factor for COVID-19. Previously, we have reported a retrospective cohort analysis demonstrating the protective effect of 5-alpha-reductase inhibitors (5ARis) in COVID-19. Men using 5ARis were less likely to be admitted to the ICU than men not taking 5ARis. Additionally, men using 5ARis had drastically reduced frequency of symptoms compared to men not using 5ARis in an outpatient setting. Here we aim to determine if 5ARis will be a beneficial treatment if given after SARS-CoV-2 infection.MethodsA double-blinded, randomized, prospective, investigational study of dutasteride for the treatment of COVID-19 (NCT04446429). Subjects confirmed positive for SARS-CoV-2 were treated in an outpatient setting. Endpoints for the study were remission times for a predetermined set of symptoms: fever or feeling feverish, cough, shortness of breath, sore throat, body pain or muscle pain/ache, fatigue, headache, nasal congestion, nasal discharge (runny nose), nausea or vomiting, diarrhea, loss of appetite, and loss of taste or smell (Ageusia or Anosmia).ResultsA total of 130 SARS-CoV-2 positive men were included in the study, 64 subjects in the dutasteride arm and 66 subjects in the placebo-controlled group. The differences in the average remission times for fatigue and anosmia or ageusia was statistically different between the groups (5.8 versus 10.1 days for fatigue and 7.3 versus 13.4 days for anosmia or ageusia, in dutasteride and placebo groups, respectively), however, the total remission time was significantly reduced for the men given dutasteride; 9.0 days versus 15.6 days in the placebo group (p < 0.001). Excluding loss of taste and smell the average total remission time was 7.3 days in the dutasteride group versus 11.7 in the placebo arm (p < 0.001).ConclusionThe total remission time for men using 5ARis was significantly reduced compared to men not taking 5ARis.
RT-LAMP assay for ultra-sensitive detection of SARS-CoV-2 in saliva and VTM clinical samples
Authors: Ganguli A. , Mostafa A. , Berger J. , Stewart de Ramirez S. A. , Baltaji A. , Roth K. , Aamir M. , Aedma S. , Mady M. , Mahajan P. , Sathe S. , Johnson M. , White K. , Kumar J. , Valera E. , Bashir R. 
Published: November 2020

AbstractThe COVID-19 pandemic has underscored the shortcomings in the deployment of state-of-the-art diagnostic platforms. Although several PCR-based techniques have been rapidly developed to meet the growing testing needs, such techniques often need samples collected through a swab, the use of RNA extraction kits, and expensive thermocyclers in order to successfully perform the test. Isothermal amplification-based approaches have also been recently demonstrated for rapid SARS-CoV-2 detection by minimizing sample preparation while also reducing the instrumentation and reaction complexity. There are limited reports of saliva as the sample source and some of these indicate inferior sensitivity when comparing RT-LAMP with PCR-based techniques. In this paper, we demonstrate an improved sensitivity assay to test saliva using a 2-step RT-LAMP assay, where a short 10-minute RT step is performed with only B3 and BIP primers before the final reaction. We show that while the 1-step RT-LAMP demonstrate satisfactory results, the optimized 2-step approach allows for single molecule sensitivity per reaction and performs significantly better than the 1-step RT-LAMP and conventional 2-step RT-LAMP approaches with all primers included in the RT Step. Importantly, we demonstrate RNA extraction-free RT-LAMP based assays for detection of SARS-CoV-2 from VTM and saliva clinical samples.
Non-alcoholic fatty liver disease (NAFLD) prevalence in Latin American and the Caribbean: Protocol for a systematic review
Authors: Rojas Yesmi Arcelia Ortega , Vidal Cuéllar Claudia Lucía , Aparicio Barrón Karina Mercedes , Larco Rodrigo Carrillo 
Published: November 2020

ABSTRACTBackgroundNon-alcoholic fatty liver disease (NAFLD) is the most common worldwide cause of chronic liver disease and it carries a significant economic burden for the healthcare system. The worldwide prevalence of NAFLD appears to be 25%, with the highest rates in Latin America and the Caribbean (LAC) and the middle west. Prevalence of NAFLD in LAC has not been well represented in multiple global meta-analyses because they did not include regional search engines or excluded papers in Spanish. Furthermore, older estimates may not represent the current epidemiological situation given the recent rise of several risk factors like obesity, unhealthy diet and lifestyles in LAC.ObjectiveTo estimate the prevalence of NAFLD in the general adult population of LAC.MethodsSystematic review and meta-analysis. We will conduct a search in OVID (MEDLINE, Embase, Global Health), Cochrane Library, and LILACS. Search terms include those related to non-alcoholic fatty liver disease, along with countries in LAC. We seek observational studies with a random sample of the general population, closed populations, and patients; results will be presented for each of these groups. Titles and abstracts will be screened by two reviewers independently. After the screening phase, we will download the full-text of the selected publications and two reviewers will comprehensively read these papers. If there is any discrepancy in any of these two selection phases, it will be solved by consensus by the two reviewers or by a third party. An extraction data form in a spreadsheet will be developed and tested with a random sample of five selected studies. The data extracted will include study details, sample size, method of NAFLD diagnosis and prevalence of NAFLD. Data extraction will be conducted by two reviewers independently. We will use the risk of bias tool proposed by Hoy and colleagues. We will report the main features of the selected reports in tables, this will include the prevalence estimates. We will pool the prevalence estimates. We will only conduct the meta-analysis if there are three or more individual estimates and there is not large heterogeneity amongst them. We will conduct all statistical analyses using Stata 16.0ConclusionsThis systematic review and meta-analysis will provide updated evidence about the prevalence of NAFLD in LAC. Thereby, we will increase NAFLD awareness as a public health problem in LAC, and our results can inform strategies and interventions to reduce NAFLD burden in LAC. We will also pinpoint research needs and discuss future steps so that more robust evidence about NAFLD becomes available in LAC.
K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology
Authors: Ziarsolo Peio , Hasing Tomas , Hilario Rebeca , Garcia-Carpintero Victor , Blanca Jose , Bombarely Aureliano , Cañizares Joaquin 
Published: November 2020

AbstractK-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
Authors: Rougny Adrien , Touré Vasundra , Albanese John , Waltemath Dagmar , Shirshov Denis , Sorokin Anatoly , Bader Gary D. , Blinov Michael L. , Mazein Alexander 
Published: November 2020

AbstractA comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the BricKs Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.
Population genetics of transposable element load: a mechanistic account of observed overdispersion
Authors: Smith Ronald D. , Puzey Joshua R. , Conradi Smith Gregory D. 
Published: November 2020

AbstractIn an empirical analysis of transposable element (TE) abundance within natural populations ofMimulus guttatusandDrosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 300). To obtain insight regarding those evolutionary genetic mechanisms that are may underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analyses of time-dependent and equilibrium population distributions of TE load reveal that overdispersion is likely to arise via copy-and-paste proliferation dynamics, especially when the elementary processes of proliferation and excision are first-order and approximately balanced. Parameter studies and analytic work confirm this result and further suggest that overdispersed population distributions of TE abundance are unlikely to be a consequence of purifying selection on total element load.