bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allogeneic gene-edited HIV-specific CAR-T cells secreting PD-1 blocking scFv enhance anti-HIV activity in vitro
Authors: Pan Hanyu , Wang Jing , Liang Huitong , Jiang Zhengtao , Zhao Lin , Wang Yanan , Yang Xinyi , Liang Zhiming , Shen Xiaoting , Lin Qinru , Liang Yue , Yang Jinglong , Lu Panpan , Zhu Yuqi , Xiang Weirong , Li Min , Wang Pengfei , Zhu Huanzhang 
Published: January 2022

AbstractHIV-specific chimeric antigen receptor (CAR) T cells have been developed to target latently infected CD4+ T cells that express virus either spontaneously or after intentional latency reversal. However, the T-cell exhaustion and the patient-specific autologous paradigm of CAR-T hurdled the clinical application. Here, we created HIV-specific CAR-T cells using human peripheral blood mononuclear cells and a 3BNC117-E27 CAR (3BE CAR) construct that enables the expression of PD-1 blocking scFv E27 and the single-chain variable fragment of the HIV-1-specific broadly neutralizing antibody 3BNC117 to target native HIV envelope glycoprotein (Env). In comparison with T cells expressing 3BNC117-CAR alone, 3BE CAR-T cells showed greater anti-HIV potency with stronger proliferation capability, higher killing efficiency (up to ~75%) and enhanced cytokine secretion in the presence of HIV envelope glycoprotein-expressing cells. Furthermore, our approach achieved high levels (over 97%) of the TCR-deficient 3BE CAR-T cells with the functional inactivation of endogenous TCR to avoid graft-versus-host disease without compromising their antiviral activity relative to standard anti-HIV CAR-T cells. These data suggest that we have provided a feasible approach to large-scale generation of “off-the-shelf” anti-HIV CAR-T cells in combination with antibody therapy of PD-1 blockade, which can be a powerful therapeutic candidate for the functional cure of HIV.
Dickeya colocasiae sp. nov. isolated from wetland taro, Colocasia esculentum
Authors: Boluk Gamze , Dobhal Shefali , Arizala Dario , Alvarez Anne M. , Arif Mohammad 
Published: January 2022

AbstractBacterial pathogens identified as Dickeya sp. have recently been associated with a corm rot of wetland taro on Oahu, Hawaii, but the species designation of these strains was unclear. A Gram-negative, pectinolytic bacterial strain PL65T isolated from an infected taro corm was subjected to polyphasic analysis to determine its genomic and phenotypic characteristics. Multi-locus sequence analyses (MLSA) based on five housekeeping genes (dnaA, gapA, gyrB, atpD, and purA) revealed that Dickeya zeae and D. oryzae, were the closest relatives. Phylogenetic analysis based on 463 core gene sequences clearly showed two potentially new species within Dickeya oryzae. In silico DNA– DNA hybridization value of strain PL65T with 12 Type strains of Dickeya species was <68%. Average nucleotide identity (ANI) analysis revealed that PL65T was at the margin of the species delineation cut-off values with a 96% ANI value. The metabolic profile of strain PL65T using BIOLOG differentiated it from the type strains of all other known species of Dickeya. Based on the results of genome-to-genome comparisons and phenotypic data presented in this report, we propose establishment of a new species, Dickeya colocasiae sp. nov. with strain PL65T as the type strain (ICMP 24361T).
Population genomic evidence of selection on structural variants in a natural hybrid zone
Authors: Zhang Linyi , Chaturvedi Samridhi , Nice Chris C. , Lucas Lauren K. , Gompert Zachariah 
Published: January 2022

AbstractStructural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between twoLycaeidesbutterfly taxa (L. melissaand Jackson HoleLycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviating from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson HoleLycaeidesancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average then SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess introgression from Jackson HoleLycaeides.Excess Jackson HoleLycaeidesancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might contribute disproportionately to hybrid fitness and thus (partial) reproductive isolation.
Gene regulatory evolution in cold-adapted fly populations neutralizes plasticity and may undermine genetic canalization
Authors: Huang Yuheng , Lack Justin B. , Hoppel Grant T. , Pool John E. 
Published: January 2022

AbstractThe relationships between adaptive evolution, phenotypic plasticity, and canalization remain incompletely understood. Theoretical and empirical studies have made conflicting arguments on whether adaptive evolution may enhance or oppose the plastic response. Gene regulatory traits offer excellent potential to study the relationship between plasticity and adaptation, and they can now be studied at the transcriptomic level. Here we take advantage of three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. We measure the transcriptome-wide plasticity in gene expression levels and alternative splicing (intron usage) between warm and cold laboratory environments. We find that suspected adaptive changes in both gene expression and alternative splicing tend to neutralize the ancestral plastic response. Further, we investigate the hypothesis that adaptive evolution can lead to decanalization of selected gene regulatory traits. We find strong evidence that suspected adaptive gene expression (but not splicing) changes in cold-adapted populations are more vulnerable to the genetic perturbation of inbreeding than putatively neutral changes. We find some evidence that these patterns may reflect a loss of genetic canalization accompanying adaptation, although other processes including hitchhiking recessive deleterious variants may contribute as well. Our findings augment our understanding of genetic and environmental effects on gene regulation in the context of adaptive evolution.Significance StatementIt is unclear whether adaptive evolution is concordant or discordant with regulatory plasticity, especially for splicing plasticity which is rarely studied. Here we analyzed RNA-seq data from three pairs of natural fly populations that represent separate adaptive evolution to cold climate. We found that adaptive evolution is generally discordant with the ancestral plasticity between cold and warm temperatures for gene expression abundance and splicing. We also investigate the hypothesis that adaptation leads to decanalization of the selected traits. By comparing the expression variance between inbred and outbred samples, we found evidence that adaptation may lead to genetic decanalization for expression abundance but not for splicing. Our study reveals the relationship between adaptation, plasticity and canalization in three instances in nature.
FRET monitoring of transcription factor activities in living bacteria
Authors: Wang Pengchao , Zhang Guangming , Xu Zeling , Chen Zhe , Liu Xiaohong , Wang Chenyin , Zheng Chaogu , Wang Jiangyun , Zhang Hongmin , Yan Aixin 
Published: January 2022

AbstractBacteria adapt to the constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor the in situ TF-promoter interactions in living bacteria are lacking. Herein, we developed a whole-cell TF-promoter binding assay based on the intermolecular Förster resonance energy transfer (FRET) between a fluorescent unnatural amino acid CouA which is genetically encoded into defined sites in TFs and the live cell fluorescent nucleic acid stain SYTO 9. We show that this new FRET pair monitors the intricate TF-promoter interactions elicited by various types of signal transduction systems with specificity and sensitivity. Furthermore, the assay is applicable to identify novel modulators of the regulatory systems of interest and monitor TF activities in bacteria colonized inC. elegans. In conclusion, we established a tractable and sensitive TF-promoter binding assay in living bacteria which not only complements currently available approaches for DNA-protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria-host interface.
THE EFFECT OF HAND HYGIENE INTERVENTION ON THE KNOWLEDGE AND SKILLS LEVEL OF SCHOOL CHILDREN
Authors: Mufida Nurlela , Rumambo Pandin Moses Glorino 
Published: January 2022

ABSTRACTBackgroundHand washing is an alternative, effective and inexpensive method that can be used to prevent infectious diseases. Washing hands with soap can improve children’s health. The purpose of this study was to determine the effect of hand hygiene intervention on the level of knowledge and skills of elementary school students. The method used to conduct this research is a critical review, namely by reviewing articles from databases such as Google Scholar, Pubmed, Direct, Medline. The search keywords used were: quantitative studies on delivery, intervention, hand hygiene, skills, children, and primary school. The selected articles are articles that meet the standard writing criteria, which were published between 2017-2021, both in English and Indonesian. Based on these evaluation criteria, 20 (twenty) studies were obtained. From the results of a literature search, several studies on the use of intervention strategies to provide hand hygiene health education found that although there were other intervention strategies to improve hand hygiene, there were significant differences in both knowledge and skills after being given the intervention.
A prospective, single-center study to evaluate the clinical performance of Meril ABFind in individuals vaccinated against COVID-19
Authors: Shastri Jayanthi , Agrawal Sachee , Chatterjee Nirjhar , Gupta Harsha 
Published: January 2022

AbstractBackgroundAccurate rapid antibody detection kits requiring minimum infrastructure are beneficial in detecting post-vaccination antibodies in large populations. ChAdOx1-nCOV (COVISHIELD™) and BBV-152 (Covaxin™) vaccines are primarily used in India.MethodsIn this single-centre prospective study, performance of Meril ABFind was investigated by comparing with Abbott SARS-CoV-2 IgG II Quant (Abbott Quant), GenScript cPass SARS-CoV-2 neutralization antibody detection kit (GenScript cPass), and COVID Kawach MERILISA (MERILISA) in 62 vaccinated health care workers (HCW) and 40 pre-pandemic samples.ResultsIn the vaccinated subjects, Meril ABFind kit displayed high sensitivity of 93.3% (CI, 89.83%-96.77%), 94.92% (CI, 91.88%-97.96%), and 90.3% (CI, 86.20%-94.4%) in comparison to Abbott Quant, MERILISA, and GenScript cPass respectively. The results of the Meril ABFind in the COVISHIELD-vaccinated group were excellent with 100% sensitivity in comparison to the other three kits. In the Covaxin-vaccinated group, Meril ABFind displayed sensitivity ranging from 80% to 88.9%. In control samples, there were no false positives detected by Meril ABFind, while Abbott Quant, MERILISA, and GenScript cPass reported 2.5%, 10.0%, and 12.5% false positives, respectively. In the pre-pandemic controls, specificity of Meril ABFind was 100%, Abbott Quant 97.5%, MERILISA 90%, and GenScript cPass 87.5%.ConclusionThe Meril ABFind kit demonstrated satisfactory performance when compared with the three commercially available kits and was the only kit without false positives in the pre-pandemic samples. This makes it a viable option for rapid diagnosis of post vaccination antibodies.
Using Mobile Phone-based Text Message to Recruit Representative Samples: Assessment of a Cross-Sectional Survey about the COVID-19 Vaccine Hesitation
Authors: Sartorao Filho C.I. , Sartorao Neto C.I. , Sartorao A.L.V. , Terribile D.C. , Mello R. , Mello B.B. , Zoqui M.C. , Duarte D.O. , Cachoni L.E.G. , Bisseto V.C.Q. , Ribeiro E.A.C. 
Published: January 2022

AbstractBackgroundLimited research has examined mobile phone-based platforms for survey recruitment, especially during the COVID-19 pandemic in Brazil. Our objective was to investigate the feasibility and representativeness of mobile phone-based advertisement during a preliminary study about COVID-19 vaccine hesitation in Brazil. Moreover, we evaluate whether the older population can be reached through mobile phone-based platforms of the survey.MethodsWe conducted a study in December 2021 based on a preliminary survey about the COVID-19 vaccine hesitation in Assis, Brazil, Sao Paulo state. From a list of the adult population hesitant for the second dose of the COVID-19 vaccine, we sent a mobile phone-based advertisement inviting the participants to answer the survey for one week. The respondent’s data were collected in a Google form platform. The comparison between the target population and the respondents was made using the Chi-squared test and the Welch’s test, using a P-value of .05 as significative.ResultsThe response rate was 9.99% after one week. The mean age of the respondent group was 33.97 (SD 14.99) and 35.05 (SD 14.19) of the population, with a P-value of .192 and a Cohen’s d coefficient of 0.0754, corresponding to a small effect size between groups. We demonstrate that the mobile phone-based survey is a feasible and representative strategy during the pandemics in Brazil. Moreover, the older population respondent was representative.ConclusionWe achieved a representative sample of respondents using the mobile phone-based survey in Brazil. Furthermore, it was representative in all sociodemographic and health characteristics assessed. Finally, these findings suggest the method is a highly feasible and economical means of recruiting for survey research.
Implementation of a Rapid RT-LAMP Saliva-based SARS-CoV-2 Testing Program in the Workplace
Authors: Cook Bradley W.M. , Kobasa Kaitlyn , Tamayo Marielou , Theriault Natasha , Pappas Diane Gordon , Theriault Steven S. 
Published: January 2022

AbstractRising SARS-CoV-2 cases, testing delays and the risk of pre-symptomatic and asymptomatic transmission provided the impetus for an in-house rapid testing program. Employees and their household contacts were encouraged to self-collect saliva samples which were pooled for routine testing using an established colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. In brief, individual or a maximum of four saliva samples were pooled, heat-inactivated to render microorganisms, especially SARS-CoV-2, non-infectious prior to being added to RT-LAMP assay tubes containing either human sample control gene, RNase P or a region of the SARS-CoV-2 gene, ORF1ab. During the second wave of SARS-CoV-2 infections in November 2020, two samples from an employee and a member of their household tested positive via RT-LAMP within two days of each other. A delayed clinical qRT-PCR test confirmation of both individuals 5 days later underscores the power of routine rapid testing with with-in-the-hour turnaround times. Workplace rapid testing programs using RT-LAMP are flexible in their design, have a reduced cost compared to qRT-PCR, may involve non-invasive self-saliva collection for increased safety for the testing personnel, and can be performed with minimal training.
Waning COVID-19 Vaccine Effectiveness for BNT162b2 and CoronaVac in Malaysia: An Observational Study
Authors: Suah Jing Lian , Husin Masliyana , Keng Tok Peter Seah , Tng Boon Hwa , Thevananthan Thevesh , Low Ee Vien , Appannan Maheshwara Rao , Zin Faizah Muhamad , Zin Shahanizan Mohd , Yahaya Hazlina , Peariasamy Kalaiarasu M. , Sivasampu Sheamini 
Published: January 2022

SUMMARYBackgroundEvaluation of vaccine effectiveness over time against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (COVID-19) is important. Evidence on effectiveness over time for the CoronaVac vaccine is lacking despite its widespread use globally. In Malaysia, a diverse set-up of COVID-19 vaccines was rolled out nationwide, and the waning of vaccine protection is a concern. We aimed to investigate and compare waning vaccine effectiveness against COVID-19 infections, COVID-19 related ICU admission and COVID-19 related deaths for BNT162b2 and CoronaVac vaccines.MethodsIn this observational study, we consolidated nationally representative data on COVID-19 vaccination and patients’ outcomes. Data on all confirmed COVID-19 cases from 1 to 30 September 2021 were used to compare vaccine effectiveness between the ‘early’ group (fully vaccinated in April to June 2021) and the ‘late’ group (fully vaccinated in Jul to Aug 2021). We used a negative binomial regression model to estimate vaccine effectiveness against COVID-19 infections for both ‘early’ and ‘late’ groups, by comparing the rates of infection for individuals vaccinated in the two different periods relative to the unvaccinated. Among confirmed COVID-19 cases, we used logistic regression to estimate and compare vaccine effectiveness against ICU admission and deaths between the two different periods.FindingsFor BNT162b2, vaccine effectiveness against COVID-19 infections declined from 90.8% (95% CI 89.4, 92.0) in the late group to 79.1% (95% CI 75.8, 81.9) in the late group. Vaccine effectiveness for BNT162b2 against ICU admission and deaths were comparable between the two different periods. For CoronaVac, vaccine effectiveness waned against COVID-19 infections from 74.4% in the late group (95% CI 209 70.4, 77.8) to 30.0% (95% CI 18.4, 39.9) in the early group. It also declined significantly against ICU admission, dropping from 56.1% (95% CI 51.4, 60.2) to 29.9% (95% CI 13.9, 43.0). For deaths, however, CoronaVac’s effectiveness did not wane after three to five months of full vaccination.InterpretationVaccine effectiveness against COVID-19 infections waned after three to five months of full vaccination for both BNT162b2 and CoronaVac in Malaysia. Additionally, for CoronaVac, protection against ICU admission declined as well. Evidence on vaccine effectiveness over time informs evolving policy decisions on vaccination.
Frequency of Hematologic and Solid Malignancies in the Family History of Patients with Myeloid Neoplasms
Authors: Ali Alaa , Yassin Batool , Almothaffar Ali 
Published: January 2022

AbstractBackgroundStudies demonstrated that there are several germline mutations that lead to a familial predisposition for acute myeloid leukemia and Myelodysplastic syndrome. According to the American Society of Clinical Oncology ,the minimum cancer family history was defined as including first- and second-degree family history, type of primary cancer, and age at diagnosis.The current study aimed to estimate the frequency of positive family history for hematologic and solid malignancies in patients with Myeloid Neoplasms / Aplastic anemia.Patients and MethodsA cross section study was carried out at the Center of Blood Diseases, Medical City Campus during the period from March-December 2020. A purposeful sample of all adult patients with Myeloid Neoplasms [Acute Myeloid Leukemia, Myelodysplastic Syndrome, Chronic Myeloid Leukemia and Aplastic Anemia] were included in the study. A data collection form was prepared, based on the Hereditary Hematopoietic Malignancies Screening form adopted by the University of Chicago, and modified by the researchers; The data were collected by direct interview with the patients. Patients with hematologic malignancy and one or more first-degree relatives, or ≥2 second-degree relatives, with hematologic malignancies and individuals with Myelodysplastic Syndrome or Acute Myeloid Leukemia and two first or second-degree relatives with a diagnosis of solid tumor malignancy were considered potential carriers of such genetic predisposition.ResultsA total of 153 patients were included; males were nearly equal to females with a male to female ratio of nearly 1:1. Acute Myeloid Leukemia was found in 57.5%, Aplastic Anemia was found in 19%, Chronic Myeloid Leukemia in 17% and only four patients (6.5%) were known cases of Myelodysplastic Syndrome. Nine patients (5.9%) reported family history of hematological malignancies, 29 (19.0%) reported family history of solid malignancies and only one patient reported family history of both hematological and solid malignancies.Regarding the official medical reports of the patients, no patient had been interviewed properly about this crucial point.ConclusionPositive family history for hematological and solid malignancies in Iraqi patients with myeloid neoplasms is prevalent. Our current approach to this critical issue in Iraq needs to be re-considered.
Prevalence and determinants of oral and cervicogenital HPV infection: baseline analysis of the MHOC cohort study
Authors: Brouwer Andrew F. , Campredon Lora P. , Walline Heather M. , Marinelli Brittany M. , Goudsmit Christine M. , Thomas Trey B. , Delinger Rachel L. , Lau Yan Kwan , Andrus Emily C. , Yost Monica L. , McCloskey Jodi K. , Sullivan Taylor S. , Mortensen Alex S. , Huang Suiyuan , Murphy Keith , Cheng Bonnie , Stanek Kayla , Nair Thankam , Carey Thomas E. , Meza Rafael , Eisenberg Marisa C. 
Published: January 2022

AbstractWe determined baseline oral and cervicogenital human papillomavirus (HPV) prevalence and determinants of infection in the Michigan HPV and Oropharyngeal Cancer (MHOC) study. We enrolled 394 college-age and older-adult participants of both sexes in Ann Arbor, Michigan and the surrounding area. All participants provided an oral sample at baseline, and 130 females provided a cervicogenital sample. Samples were tested for 18 HPV genotypes using polymerase chain reaction (PCR) MassArray. Participants filled out sociodemographic and behavioral questionnaires. Prevalence ratios for HPV oral or cervicogenital prevalence by predictor variables were estimated in univariable log-binomial models. Analysis was conducted 2018–20. In the full cohort, baseline oral HPV prevalence was 10.0% for any detected genotype (among the 338 valid oral tests at baseline) and 6.5% for high-risk types, and cervicogenital prevalence was 20.0% and 10.8%, respectively (among the 130 first valid cervicogenital tests). Oral HPV prevalence did not vary by sex, with 10.5% of women and 9.0% of men having an infection. We found a high prevalence of oral and cervicogenital HPV infection among those reporting no recent sexual partners compared to those with a single recent sexual partner, but prevalence increased with the number of recent partners for most sexual behaviors. We observed an ecological fallacy masking the direction of impact of vaccination on HPV prevalence in the full cohort compared to the college-aged and older-adult populations considered separately. Substance use was not significantly associated with oral or cervicogenital HPV infection. Many studies report substantially higher oral HPV infection prevalence in men than in women. That difference may not be uniform across populations in the US.