bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient base-catalysed Kemp elimination in an engineered ancestral enzyme
Authors: Gutierrez-Rus Luis I. , Alcalde Miguel , Risso Valeria A , Sanchez-Ruiz Jose M. 
Published: July 2022

AbstractThe routine generation of enzymes with completely new active sites is one of the major unsolved problems in protein engineering. Advances in this field have been so far modest, perhaps due, at least in part, to the widespread use of modern natural proteins as scaffolds for de novo engineering. Most modern proteins are highly evolved and specialized, and, consequently, difficult to repurpose for completely new functionalities. Conceivably, resurrected ancestral proteins with the biophysical properties that promote evolvability, such as high stability and conformational diversity, could provide better scaffolds for de novo enzyme generation. Kemp elimination, a non-natural reaction that provides a simple model of proton abstraction from carbon, has been extensively used as a benchmark in de novo enzyme engineering. Here, we present an engineered ancestral β-lactamase with a new active site capable of efficiently catalysing the Kemp elimination. Our Kemp eliminase is the outcome of a minimalist design based on a single function-generating mutation followed by sharply-focused, low-throughput library screening. Yet, its catalytic parameters (kcat/KM=2·105 M−1s−1, kcat=635 s−1) compare favourably with the average modern natural enzyme and with the best proton-abstraction de novo Kemp eliminases reported in the literature. General implications of our results for de novo enzyme engineering are discussed.
Network analysis applied to DASS-21: Emergence of a new dimension
Authors: Alvarenga Marco Antônio Silva , Bandeira Paulo Felipe Ribeiro , Guilhermino Carollina Souza , de Azevedo Tiago Geraldo , Olímpio Kelly Fernandes , Kersul Camila , da Cunha Glacithane Lins , Alves-Teodoro Juliana , Ribeiro Pricila Cristina Correa , Mansur-Alves Marcela , Teodoro Maycoln Lêoni Martins 
Published: July 2022

AbstractThe DASS-21 has been studied in different samples and cultures as a brief tool for screening and referral to specialized interventions, thus presenting the prerogative to be characterized as a complex system (CS). CS is a new approach to data analysis assumes that items on a scale are components integrated as a network. Despite this, to date network analysis has not been applied to verify the psychometric properties of the DASS-21. This was a non-clinical sample consisting of college students and professionals (N = 4017), aged 18 years or older (M = 31.16; SD = 10.308), from different Brazilian regions. The data collection was done through electronic forms composed by a sociodemographic questionnaire and DASS-21. Participants could forward the form to other potential respondents. Uni, bi, and multivariate analyses were used, and, among them, exploratory graph analysis (EGA) and boostrap EGA (BootEGA). EGA e BootEGA generated a model with four factors. The four-factor model from DASS-21 showed better fit rates compared to the others replicated in this research. The new four factor model has excellent composite reliability and is invariant regard to gender and type of activity performed. This research was composed of a non-probabilistic and convenience sample, without equitable geographical distribution of the participants and whose answers to this study were provided only by the web-based forms. The DASS-21 presented a new factor model composed of four distinct dimensions with excellent intrinsic features.
“I was scared dating… who would take me with my status?”- Living with HIV in the UTT era in Johannesburg, South Africa
Authors: Sineke Tembeka , Onoya Dorina , Mokhele Idah , Cele Refiloe , Sharma Shubhi , Sigasa Smangele , Dukashe Mandisa , Hansrod Laila , Inglis Robert , King Rachel , Bor Jacob 
Published: July 2022

ABSTRACTBACKGROUNDSouth Africa rolled out Universal Test-and-Treat (UTT) in 2016, extending treatment eligibility to all persons living with HIV (PLHIV). Through this study, we sought to understand the experience of people living with HIV in the UTT era in South Africa.METHODSIn May 2021, we conducted in-depth interviews (IDI) (N = 27) with adult (≥ 18 years) PLHIV referred by HIV counsellors at three peri-urban primary healthcare clinics. We also conducted three focus group discussions (FGDs) (N = 27) with adult PLHIV recruited from clinics or from civil society organisations through snowball sampling. Follow-up interviews were conducted with 29 IDI and FGD participants, to gain a deeper understanding of their journey living with HIV. Participants were asked to reflect on their HIV diagnosis, what their HIV status meant to them in light of the UTT era and how, if at all, being HIV-positive affected their lives. Interviews and focus group discussions were audio-recorded, transcribed, translated to English, and analysed thematically.RESULTSThe study included 4 men and 23 women recruited from clinics and 12 men and 16 women recruited from civil society (total N= 54). Participants reported that PLHIV could live a long life with antiretroviral therapy (ART) and that ART was widely accessible. However, they reported that HIV elicited feelings of guilt and shame as a sexually transmitted disease. Participants used the language of “blame” in discussing HIV transmission, citing their own reckless behaviour or blaming their partner for infecting them. Participants feared transmitting HIV to others and felt a responsibility to avoid transmission. To manage transmission anxieties, participants avoided sexual relationships, chose HIV-positive partners, and/or insisted on using condoms. Many participants feared – or had previously experienced – rejection by their partners due to their HIV status and reported hiding their medication, avoiding disclosure to their partners, or avoiding relationships altogether. Most participants also reported having low to no knowledge about treatment-as-prevention (TasP). Participants who were aware of TasP expressed less anxiety about transmitting HIV to others and greater confidence in having relationships.CONCLUSIONDespite the normalization of HIV as a chronic disease, PLHIV still experience transmission anxiety and fears of rejection by their partners. Disseminating information on treatment-as-prevention could reduce the psychosocial burdens of living with HIV, encourage open communication with partners, and remove barriers to HIV testing and treatment adherence.
Sociodemographic factors affecting not receiving COVID-19 vaccine in Japan among people who originally intended to vaccinate: a prospective cohort study
Authors: Matsuyama Akiko , Mori Takahiro , Ogami Akira , Mafune Kosuke , Tateishi Seiichiro , Kuwamura Mami , Muramatsu Keiji , Fujino Yoshihisa , Mori Koji ,   the CORoNaWork project
Published: July 2022

AbstractBackgroundVaccine hesitancy is a major issue for acquiring herd immunity. However, some individuals may go unvaccinated owing to inhibitory factors other than vaccine hesitancy. If there is even a small number of such people, support is needed for equitable vaccine distribution and acquiring herd immunity. We investigated sociodemographic factors that affected not undergoing COVID-19 vaccination in Japan among individuals who initially had strong intention to vaccinate.MethodsWe conducted this prospective cohort study on workers aged 20–65 years from December 2020 (baseline), to December 2021 using a self-administered questionnaire survey. There were 27,036 participants at baseline and 18,560 at follow-up. We included 6,955 participants who answered yes to this question at baseline: “Would you like to receive a COVID-19 vaccine as soon as it becomes available?” We applied multilevel logistic regression analyses to examine the association between sociodemographic factors and being unvaccinated at follow-up.ResultsIn all, 289 participants (4.2%) went unvaccinated. The odds ratios (ORs) for being unvaccinated were significantly higher for participants aged 30–39 and 40–49 than those aged 60–65 years. Being divorced, widowed, or single, having low income, and having COVID-19 infection experience also had higher ORs.ConclusionsWe found that some participants who initially had strong intention to vaccinate may have gone unvaccinated owing to vaccine side effects and the financial impact of absenteeism due to side effects. It is necessary to provide information repeatedly about the need for vaccination as well as social support to ensure that those who intend to vaccinate are able to do so.
Protocol for the Tessa Jowell BRAIN MATRIX Platform Study
Authors: Watts Colin , Savage Joshua , Patel Amit , Mant Rhys , Wykes Victoria , Pohl Ute , Bulbeck Helen , Apps John , Sharpe Rowena , Thompson Gerard , Waldman Adam , Ansorge Olaf , Billingham Lucinda ,   the TJBM Investigators
Published: July 2022

AbstractIntroductionGliomas are the most common primary tumour of the central nervous system (CNS), with an estimated annual incidence of 6.6 per 100,000 individuals in the USA and around 14 deaths per day from brain tumours in the UK. The genomic and biological landscape of brain tumours has been increasingly defined and, since 2016, the WHO classification of tumours of the CNS incorporates molecular data, along with morphology, to define tumour subtypes more accurately. The Tessa Jowell BRAIN MATRIX Platform (TJBM) study aims to create a transformative clinical research infrastructure that leverages UK NHS resources to support research that is patient centric and attractive to both academic and commercial investors.Methods and analysisThe TJBM study is a programme of work with the principal purpose to improve the knowledge of glioma and treatment for glioma patients. The programme includes a platform study and subsequent interventional clinical trials (as separate protocols). The platform study described here is the backbone data-repository of disease, treatment and outcome data from clinical, imaging and pathology data being collected in glioma patients from secondary care hospitals. The primary outcome measure of the platform is time from biopsy to integrated histological-molecular diagnosis using whole genome sequencing and epigenomic classification. Secondary outcome measures include those that are process-centred, patient-centred and framework-based. Target recruitment for the study is 1000 patients with interim analyses at 100 and 500 patients.Ethics and disseminationThe protocol was approved by West Midlands - Edgbaston Research Ethics Committee. Participants will be required to provide written informed consent. The results of this study will be disseminated through national and international presentations and peer-reviewed publications.Trial registration numberClinicalTrials.gov Identifier: NCT04274283; 18-Feb-2020ISRCTN 14218060; 03-Feb-2020Strengths and limitations of this studyThe TJBM study is a programme of work, which will improve the knowledge of glioma, and treatment for glioma patients.This platform study is a backbone data-repository of disease, treatment and outcome data from clinical, imaging and pathology dataThe TJBM study will aim to provide rapid and accurate molecular diagnosis, a network of clinical hubs with robust protocols for the collection, processing, analysis and storage of tissue, images, and clinical and quality of life dataGliomas occur at all ages and their specific subtype is difficult to predict preoperatively, therefore, the patient population eligible for the study is broad but currently excludes <16-year-old patients
Germline genomic and phenomic landscape of clonal hematopoiesis in 323,112 individuals
Authors: Uddin Md Mesbah , Yu Zhi , Weinstock Joshua S. , Nakao Tetsushi , Niroula Abhishek , Urbut Sarah M. , Koyama Satoshi , Zekavat Seyedeh M. , Paruchuri Kaavya , Silver Alexander J. , Mack Taralynn M. , Wong Megan Y. , Haidermota Sara M. , Bhattacharya Romit , Jorshery Saman Doroodgar , Raddatz Michael A. , Honigberg Michael C. , Hornsby Whitney E. , Zhang Martin Jinye , Sankaran Vijay G. , Griffin Gabriel K. , Gibson Christopher J. , Kresge Hailey A. , Ellinor Patrick T. ,   Veterans Affairs’ Million Veteran Program, Cho Kelly , Sun Yan V. , Wilson Peter W.F. , Pyarajan Saiju , Genovese Giulio , Xu Yaomin , Savona Michael R. , Reiner Alexander P. , Jaiswal Siddhartha , Ebert Benjamin L. , Bick Alexander G. , Natarajan Pradeep 
Published: July 2022

AbstractWith age, acquired mutations can cause clonal expansion of hematopoietic stem cells (HSC). This clonal hematopoiesis of indeterminate potential (CHIP) leads to an increased predisposition to numerous diseases including blood cancer and cardiovascular disease. Here, we report multi- ancestry genome-wide association meta-analyses of CHIP among 323,112 individuals (19.5% non-European; 5.3% have CHIP). We identify 15 genome-wide significant regions and nominate additional loci through multi-trait analyses, and highlight variants in genes involved in self- renewal and proliferation of HSC, telomere maintenance, and DNA damage response pathways. We then use Mendelian randomization to establish a causal relationship between CHIP and coronary artery disease. Next, we systematically profile consequences of CHIP across the phenome, which revealed strong associations with hematopoietic, neoplastic, and circulatory conditions corroborated by polygenic enrichment of CHIP loci in immune cells and cardiomyocytes. These findings expand the genomic and phenomic landscape of CHIP.
A new and efficient enrichment method for metagenomic sequencing of monkeypox virus
Authors: Aja-Macaya Pablo , Rumbo-Feal Soraya , Poza Margarita , Cañizares Angelina , Vallejo Juan A. , Bou Germán 
Published: July 2022

AbstractBackgroundThe methodology described in previous literature for monkeypox virus (MPXV) sequencing shows low efficiency when using metagenomic approaches. The aim of the present study was to evaluate a new fine-tuned method for extraction and enrichment of genomic MPXV DNA using clinical samples and to compare it to a non-enrichment metagenomic approach.ResultsA new procedure that allows sample enrichment in MPXV DNA, avoiding wasting the sequencing quota in human DNA, was designed. This procedure consisted of host DNA depletion using a saponin/NaCl combination treatment and DNase. After typical quality control, samples using the enrichment method contained around 98 % of reads not classified as human DNA, while the non-enrichment protocol showed around 5-10 %. When reads not belonging to Orthopoxvirus were removed, enriched samples kept about 50 % of the original read counts, while non-enriched ones kept only 2-7 %.ConclusionsResults showed a very significant improvement in sequencing efficiency, increasing the number of reads belonging to MPXV, the depth of coverage and the trustworthiness of the consensus sequences. This, in turn, would allow for more samples to be included in a single cartridge, reducing costs and time to diagnosis, which can be very important factors when dealing with a contagious disease.
Outlier expression of isoforms by targeted RNA sequencing as clinical markers of genomic variants in B lymphoblastic leukemia and other tumor types
Authors: Tsai Harrison K. , Gogakos Tasos , Lip Va , Tsai Jonathan , Li Yen-Der , Fisch Adam , Weiss Jonathan , Grimmett Leslie , Tran Thai Hoa , Caron Maxime , Langlois Sylvie , Sinnett Daniel , Pikman Yana , Kim Annette S. , Nardi Valentina , Silverman Lewis B. , Harris Marian H. 
Published: July 2022

AbstractRecognition of aberrant gene isoforms indicative of underlying DNA events can impact molecular classification and risk stratification of B lymphoblastic leukemia (B-ALL). Aberrant ERG isoforms have been proposed as markers of the favorable-risk DUX4-rearranged (DUX4r) subtype while deletion-mediated IKZF1 isoforms are associated with adverse prognosis in non-DUX4r B-ALL. The high-risk IKZF1plus signature depends on gene deletions including PAX5 while intragenic PAX5 amplifications (PAX5amp) are recurrent in the provisional B-ALL with PAX5-alteration subtype. In this study, we screened for outlier expression of isoforms within targeted RNA sequencing assays designed for fusions. Outlier analysis of known and novel IKZF1, ERG, and PAX5 isoforms was 97.0% (32/33), 90% (9/10), and 100% (6/6) sensitive and 97.8% (226/231), 100% (35/35), and 88.5% (23/26) specific for IKZF1 intragenic or 3’ deletions, DUX4r, and PAX5 intragenic deletions respectively, where false positives were favored to represent low-level deletions below the limit of DNA-based detection. Outlier analysis also identified putative PAX5amp cases and revealed partial tandem duplication (PTD) spanning IKZF1 N159Y in the B-ALL with mutated N159Y subtype. To demonstrate utility in other tumor types, outlier analysis was 100% (9/9) sensitive and 100% (255/255) specific for KMT2A-PTD in hematologic samples and 100% (7/7) sensitive and 100% (79/79) specific for FGFR1 tyrosine kinase domain duplication in brain tumors. These findings support the use of aberrant isoform analysis in targeted RNA sequencing data as a robust strategy for the detection of clinically significant DNA events.
Monkeypox self-diagnosis abilities, determinants of vaccination intention and self-isolation intention after diagnosis among MSM in the Netherlands
Authors: Wang Haoyi , d’Abreu de Paulo Kennedy J.I. , Gültzow Thomas , Zimmermann Hanne M.L. , Jonas Kai. J. 
Published: July 2022

AbstractMonkeypox is a zoonotic disease and leads to a smallpox-like disease in humans. The current epidemic in European countries requires informed responses. We investigated the ability to self-diagnose a potential monkeypox infection, and determinants of vaccination intention and self-isolation intention after exposure among MSM in the Netherlands. We found that about half were able to self-diagnose monkeypox, that 72% had a high intention to get vaccinated and 44% to self-isolate after monkeypox exposure. Determinants went beyond mere risk behaviour criteria.Data availabilityData is available upon request.Ethical statementThe study was assessed and approved by the ERCPN of Maastricht University (ref.188_11_02_2018_S32). Informed consent was provided by all participants.FundingThere was no funding source for this study.Authors’ contributionsAll authors conceptualised this research; KJJ collected the data for this research; HW and KJIDDP analysed the data; all authors drafted the manuscript; all authors critically revised the manuscript for intellectual content; All authors read and approved the final version of the manuscript.
A power-based sliding window approach to evaluate the clinical impact of rare genetic variants
Authors: Cirulli Elizabeth T. , Schiabor Barrett Kelly M. , Bolze Alexandre , Grzymski Joseph J. , Lee William , Washington Nicole L. 
Published: July 2022

AbstractSystematic determination of rare and novel variant pathogenicity remains a major challenge, even when there is an established association between a gene and phenotype. Here we present Power Window (PW), a novel sliding window technique that identifies the clinically impactful regions of a gene using population-scale clinico-genomic datasets. By sizing windows based on the number of variant carriers, rather than the number of variants or nucleotides, statistical power is held constant during analysis, enabling the localization of clinical impact as well as the removal of unassociated gene regions. This method can be used to focus on: specific variant types such as loss of function (LoF) or other coding; parts of a gene, such as those expressed in different tissues; or isolating gene regions with opposite directions of effect. Using a training set of 300K exomes from the UKBiobank (UKB), we developed PW-based LoF and coding models for well-established gene-disease associations and tested their accuracy in two additional cohorts (128k exomes from the UKB and 30k exomes from the Healthy Nevada Project (HNP)). The significant PW models retained a mean of 64% of the rare variant carriers in each gene (range 16-98%), with quantitative traits showing a mean effect size improvement of 48% compared to aggregating rare variants across the entire gene, and the odds ratios for binary traits improving by a mean of 2.4-fold. PW showcases that EHR-based statistical analyses can accurately distinguish between novel coding variants that will have high phenotypic penetrance in a population and those that will not, unlocking new potential for population genetic screening.
Hepatectomy combined with targeted and immunotherapy for CNLC stage IIIb hepatocellular carcinoma: a single-arm clinical trials protocol
Authors: Huang Jun-Tao , Zhong Jian-Hong , Zhang Jie , Gong Wen-Feng , Ma Liang , Li Le-Qun , Xiang Bang-De 
Published: July 2022

ABSTRACTIntroductionCurrent clinical guidelines recommend systematic antitumor therapy as the primary treatment option for patients with stage IIIb hepatocellular carcinoma (HCC) based on the China liver cancer staging (CNLC) criteria. Several different targeted therapeutics have been applied in combination with immunotherapeutic regimens to date in patients with advanced HCC. The present study was developed to evaluate the relative safety and efficacy of hepatectomy in combination with targeted apatinib treatment and immunotherapeutic camrelizumab treatment CNLC-IIIb stage HCC patients with the goal of providing evidence regarding the potential value of this therapeutic regimen in individuals diagnosed with advanced HCC.Methods and analysisThis is a single-arm multicenter clinical trial in which patients undergo hepatectomy in combination with targeted treatment (apatinib) and immunotherapy (camrelizumab). Patients will undergo follow-up every 2-3 months following treatment initiation to record any evidence of disease progression and adverse event incidence for a minimum of 24 months following the discontinuation of treatment until reaching study endpoint events or trial termination. The primary endpoint for this study is patient mortality.Ethics and disseminationThis study protocol was approved by the Ethics Committee of the Guangxi Medical University Cancer Hospital for Human Study (reference number KS2022[124]). The results of this study will be submitted for publication in a peer-reviewed journal.Trial registration numberNCT05062837.Strengths and limitations of this studyThis study will be the first to assess the relative safety and efficacy of hepatectomy combined with targeted and immunotherapeutic treatment in CNLC-IIIb HCC patients.As a multicenter study, the results of this analysis will be representative, generalizable, and reliable.As this study will entail a prolonged follow-up period, it is critical that participants be thoroughly informed prior to enrollment, with individuals exhibiting high compliance being chosen for study inclusion.