bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of andrenine bees reveals a long and complex history of faunal interchanges between the Americas during the Mesozoic and Cenozoic
Authors: Ramos Kelli S. , Martins Aline C. , Melo Gabriel A. R. 
Published: August 2021

ABSTRACTBees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Among the main groups of bees, Andreninae sensu lato comprise about 3000 species widely distributed with greatest and disjunct diversity in arid areas of North America, South America, and the Palearctic region. Here, we present the first comprehensive dated phylogeny and historical biogeographic analysis for andrenine bees, including representatives of all currently recognized tribes. Our analyses rely on a dataset of 106 taxa and 7952 aligned nucleotide positions from one mitochondrial and six nuclear loci. Andreninae is strongly supported as a monophyletic group and the recovered phylogeny corroborates the commonly recognized clades for the group. Thus, we propose a revised tribal classification that is congruent with our phylogenetic results. The time-calibrated phylogeny and ancestral range reconstructions of Andreninae reveal a fascinating evolutionary history with Gondwana patterns that are unlike those observed in other subfamilies of bees. Andreninae arose in South America during the Late Cretaceous around 90 Million years ago (Ma) and the origin of tribes occurred through a relatively long time-window from this age to the Miocene. The early evolution of the main lineages took place in South America until the beginning of Paleocene with North American fauna origin from it and Palearctic from North America as results of multiple lineage interchanges between these areas by long-distance dispersal or hopping through landmass chains. Overall, our analyses provide strong evidence of amphitropical distributional pattern currently observed in Andreninae in the American continent as result at least three periods of possible land connections between the two American landmasses, much prior to the Panama Isthmus closure. The andrenine lineages reached the Palearctic region through four dispersal events from North America during the Eocene, late Oligocene and early Miocene, most probably via the Thulean Bridge. The few lineages with Afrotropical distribution likely originated from a Palearctic ancestral in the Miocene around 10 Ma when these regions were contiguous, and the Sahara Desert was mostly vegetated making feasible the passage by several organisms. Incursions of andrenine bees to North America and then onto the Old World are chronological congruent with distinct periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.
A graph-theoretical approach to DNA similarity analysis
Authors: Nguyen Dong Quan Ngoc , Xing Lin , Le Phuong Dong Tan , Lin Lizhen 
Published: August 2021

AbstractOne of the very active research areas in bioinformatics is DNA similarity analysis. There are several approaches using alignment-based or alignment-free methods to analyze similarities/dissimilarities between DNA sequences. In this work, we introduce a novel representation of DNA sequences, using n-ary Cartesian products of graphs for arbitrary positive integers n. Each of the component graphs in the representing Cartesian product of each DNA sequence contain combinatorial information of certain tuples of nucleotides appearing in the DNA sequence. We further introduce a metric space structure to the set of all Cartesian products of graphs that represent a given collection of DNA sequences in order to be able to compare different Cartesian products of graphs, which in turn signifies similarities/dissimilarities between DNA sequences. We test our proposed method on several datasets including Human Papillomavirus, Human rhinovirus, Influenza A virus, and Mammals. We compare our method to other methods in literature, which indicates that our analysis results are comparable in terms of time complexity and high accuracy, and in one dataset, our method performs the best in comparison with other methods.
Naked mole-rat and Damaraland mole-rat exhibit lower respiration in mitochondria, cellular and organismal levels
Authors: Yap Kang Nian , Wong Hoi Shan , Ramanathan Chidambaram , Rodriguez-Wagner Cristina Aurora , Roberts Michael D. , Freeman David A , Buffenstein Rochelle , Zhang Yufeng 
Published: August 2021

AbstractNaked mole-rats (NMR) and Damaraland mole-rats (DMR) are the only two eusocial mammals known. Both species exhibit extraordinary longevity for their body size, high tolerance to hypoxia and oxidative stress and high reproductive output; these collectively defy the concept that all life-history traits should be negatively correlated. However, when life-history traits share similar underpinning physiological mechanisms, these may be positively associated with each other. Here, we propose that the bioenergetic properties of mole-rats share a potential common mechanism. We adopted a top-down perspective measuring the bioenergetic properties at the organismal, cellular, and molecular level in both species and the biological significance of these properties were compared with the same measures in Siberian hamsters and C57BL/6 mice, chosen for their similar body size to the mole-rat species. We found mole-rats shared several bioenergetic properties that differed from their comparator species, including low basal metabolic rates, a high dependence on glycolysis rather than on oxidative phosphorylation for ATP production, and low proton conductance across the mitochondrial inner membrane. These shared mole-rat features could be a result of evolutionary adaptation to tolerating variable oxygen atmospheres, in particular hypoxia, and may in turn be one of the molecular mechanisms underlying their extremely long lifespans.
Knockout of circRNAs by base editing back-splice sites of circularized exons
Authors: Gao Xiang , Ma Xu-Kai , Li Xiang , Li Guo-Wei , Liu Chu-Xiao , Zhang Jun , Wang Ying , Wei Jia , Chen Jia , Chen Ling-Ling , Yang Li 
Published: August 2021

AbstractA large number of circular RNAs (circRNAs) are produced from back-splicing of exon(s) of precursor mRNAs and generally co-expressed with their cognate linear RNAs from the same gene loci. Methods for circRNA-specific knockout are lacking, largely due to complete sequence-overlaps between circular and cognate linear RNAs. Here, we report to use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress both circular and linear RNAs expression, which confirms the requirement of canonical splice site signals for back-splice. Importantly, by targeting back-splice sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular, but not linear cognate RNAs. As hundreds of exons were found to be predominantly back-spliced to produce circRNAs, this study provides an efficient method to deplete circRNAs for function study.
A Novel Mouse Wound Model for Scar Tissue Formation in Abdominal-Muscle Wall
Authors: Jimi Shiro , Saparov Arman , Koizumi Seiko , Miyazaki Motoyasu , Takagi Satoshi 
Published: August 2021

AbstractScar tissue formation is a result of excess healing reactions after wounding. Hypertrophic scars scarcely develop in a mouse. In the present study, we established a novel experimental model of a scar-forming wound by resecting a small portion of the abdominal wall on the lower center of the abdomen, which exposed contractive forces by the surrounding muscle tissue. As a tension-less control, a back-skin excision model was used with a splint fixed onto the excised skin edge, and granulation tissue formed on the muscle facia supported by the back skeleton. One week after the resection, initial healing reactions such as fibroblast proliferation took place in both models.However, after 21 days, lesions with collagen-rich granulation tissues forming multiple nodular/spherical-like structures developed only in the abdominal-wall model. The lesions are analogous to scar lesions in humans. Such lesions, however, did not develop in the back-skin excision model. Therefore, this animal model is unique in that fibrous scar tissues form under a physiological condition without using any artificial factors and is valuable for studying the pathogenesis and preclinical treatment of scar lesions.Summary StatementScar lesions are hardly developed in animals. We thus developed a scar lesion in mice without using any artificial factors. The model is reliable, reproducible, and valuable.
An Intrinsically Disordered Peptide Tag that Confers an Unusual Solubility to Aggregation-Prone Proteins
Authors: Jo Byung Hoon 
Published: August 2021

ABSTRACTThere is a high demand for the production of recombinant proteins in Escherichia coli for biotechnological applications but their production is still limited by their insolubility. Fusion tags have been successfully used to enhance the solubility of aggregation-prone proteins; however, smaller and more powerful tags are desired for increasing the yield and quality of target proteins. Herein, NEXT tag, a 53 amino acid-length solubility enhancer, is described. The NEXT tag showed outstanding ability to improve both in vivo and in vitro solubilities with minimal effect on passenger proteins. The C-terminal region of the tag was mostly responsible for in vitro solubility, while the N-terminal region was essential for in vivo soluble expression. The NEXT tag appeared to be intrinsically disordered and seemed to exclude neighboring molecules and prevent protein aggregation by acting as an entropic bristle. This novel peptide tag should have general use as a fusion partner to increase the yield and quality of difficult-to-express proteins.IMPORTANCEProduction of recombinant protein in Escherichia coli still suffers from the insolubility problem. Conventional solubility enhancers with large sizes represented by maltose-binding protein (MBP) have remained as the first-choice tags, however, the success in the soluble expression of tagged protein is largely unpredictable. In addition, the large tags can negatively affect the function of target proteins. In this work, NEXT tag, an intrinsically disordered peptide, was introduced as a small but powerful alternative to MBP. The NEXT tag could significantly improve both expression level and solubility of target proteins including a thermostable carbonic anhydrase and a polyethylene terephthalate (PET)-degrading enzyme that are remarkable enzymes for environmental bioremediation.
Nontypeable Haemophilus influenzae infection impedes Pseudomonas aeruginosa colonization and persistence in mouse respiratory tract
Authors: Lindgren Natalie , Novak Lea , Hunt Benjamin C. , McDaniel Melissa S. , Swords W. Edward 
Published: August 2021

ABSTRACTPatients with cystic fibrosis (CF) experience lifelong respiratory infections which are a significant cause of morbidity and mortality. These infections are polymicrobial in nature, and the predominant bacterial species undergo a predictable series of changes as patients age. Young patients have populations dominated by opportunists that are typically found within the microbiome of the human nasopharynx, such as nontypeable Haemophilus influenzae (NTHi); these are eventually supplanted and the population within the CF lung is later dominated by pathogens such as Pseudomonas aeruginosa (Pa). In this study, we investigated how initial colonization with NTHi impacts colonization and persistence of Pa in the respiratory tract.Analysis of polymicrobial biofilms in vitro by confocal microscopy revealed that NTHi promoted greater levels of Pa biofilm volume and diffusion. However, sequential respiratory infection of mice with NTHi followed by Pa resulted in significantly lower Pa as compared to infection with Pa alone. Coinfected mice also had reduced airway tissue damage and lower levels of inflammatory cytokines as compared with Pa infected mice. Similar results were observed after instillation of heat-inactivated NTHi bacteria or purified NTHi lipooligosaccharide (LOS) endotoxin prior to Pa introduction. Based on these results, we conclude that NTHi significantly reduces susceptibility to subsequent Pa infection, most likely due to priming of host innate immunity rather than a direct competitive interaction between species. These findings have potential significance with regard to therapeutic management of early life infections in patients with CF.
Quality of life profile of methadone maintenance treatment patients in Ho Chi Minh City, Vietnam
Authors: Trang Vu Thu , Tu Le Ngoc , Tuong Vi Vu Thi , Long Khuong Quynh , Cam Hong Le Huynh Thi , Thu Van Tieu Thi , Van Dung Do 
Published: August 2021

AbstractAimTo determine the health-related quality of life (HRQoL) of methadone maintenance treatment patients in Ho Chi Minh City, Vietnam.Subject and MethodsA cross-sectional study was conducted in 967 patients treating at two methadone clinics in Ho Chi Minh City, in 2018. Patient’s health-related quality of life was estimated using the EQ-5D-5L and Visual analogue scale (VAS). Tobit regressions were used to identify factors related to patient’s health-related quality of life.ResultsOverall, the mean EQ-5D-5L utility and EQ-VAS indexes were 0.96 (SD = 0.12) and 75.8 (SD=15.5), respectively. Factors related with a higher EQ-5D-5L score included peoples who are single, and have a higher monthly income (more than 4 million VND per month), while patients aged under 30 years old, have full-time employment, and have higher education were associated with a higher EQ-VAS score. HIV was associated with lower scores of both EQ-5D-5L and EQ- VAS (β = -0.07 (95%CI: -0.13; -0.01), and β = -7.10 (95%CI: -9.23; -4.98), respectively).ConclusionHRQoL measurement provides valuable information for the policymaker to adopt suitable decisions on opioid dependence treatment. The finding shows that patients with education, job situation, and socioeconomic status are the related elements with higher HRQoL, which suggested that the policymakers and physicians should pay more attention to these aspects while working on treatment plan for drug users.
Factorial Structure of the Transactional eHealth Literacy Among Vietnamese Youth: An Instrument Validation Study
Authors: Vu Giang Thu , Vu Thuc Minh Thi , van Kessel Robin , Han Wong Brian Li , Nguyen Tham Thi , Thi Nguyen Thao Phuong , Nguyen Son Hoang , Do Ha Ngoc , Tran Bach Xuan , Latkin Carl A. , Ho Cyrus , Ho Roger 
Published: August 2021

AbstractThe progression into the Digital Age has brought an array of novel skill requirements. Unlike traditional literacy, there are currently few measures that can reliably measure eHealth literacy. The Transactional Model of eHealth Literacy and subsequent Transactional eHealth Literacy Instrument may provide a feasible option for measuring eHealth literacy. However, this instrument has yet to be validated, which is the aim of this study. We conducted an online cross-sectional study among 236 Vietnamese young people. Using exploratory factor analysis, we ensured that a model consisting of four factors had the best fit (RMSEA = 0.116; CFI = 0.907) and the highest internal consistency (Cronbach’s α = 0.96). A confirmatory factor analysis tested measurement invariance at four levels: configural, metric, scalar, and strict invariance. Only metric invariance was partially invariant, while the rest tested fully invariant. Even with partial metric invariance, there is reason to assume that functional, communicative, critical, and translational eHealth literacy (the four levels according to the transactional model) are consistently measured when deploying the Transactional eHealth Literacy Instrument across groups. In other words, this study suggests the instrument can be used for comparisons across groups and has the potential to generate high-quality data usable for informing change agents as to whether a particular population is proficient enough to adopt novel eHealth innovations.
Prevalence and effect of bacterial co-infections on clinical outcomes in hospitalized COVID-19 patients at a tertiary care centre of India
Authors: Pathak Ashutosh , Singh Sweta , Singh Sanjay , Patel Sangram Singh , Fatima Nida , Garg Atul , Ghoshal Ujjala , Sahu Chinmoy 
Published: August 2021

AbstractBackgroundBacterial co-infections are a leading cause of morbidity and mortality during viral infections including COVID-19. Systematic testing of COVID-19 patients having bacterial co-infections is essential to select the correct antibiotic for treatment in order to reduce mortality and also prevent spread of antimicrobial resistance (AMR). The present study aims to evaluate the prevalence, demographic parameters, antibiotic sensitivity patterns and outcomes in hospitalized COVID-19 patients with bacterial co-infections.MethodsA total of 1019 COVID-19 patients were selected for the study. We analyzed the prevalence, antibiotic sensitivity pattern and clinical outcomes in COVID-19 patients having bacterial co-infections.ResultsOut of a total 1019 COVID-19 patients screened, 5.2% of patients demonstrated clinical signs of bacterial co-infection. Bacteremia was found in majority of the patients followed by respiratory and urinary infections. Escherichia coli, Pseudomonas aeruginosa and Klebsiella spp. were most common isolates among the Gram-negative and Coagulase-negative Staphylococci (CONS) and Staphylococcus aureus among the Gram-positive bacterial infections. Antibiotic sensitivity profiling revealed that colistin, imipenem and fosfomycin were the most effective drugs against the Gram-negative isolates while vancomycin, teicoplanin and doxycycline against the Gram-positive isolates. Analysis of clinical outcomes revealed that the mortality rate was higher (39%) among the patients with bacterial co-infections as compared to the group without co-infection (17%).ConclusionsThis study reveals that the rate of bacterial co-infections is significantly increasing among COVID-19 patients and leading to increase in mortality. Systematic testing of bacterial co-infections is therefore essential in COVID-19 patients for better clinical outcomes and to reduce AMR.
Serendipitous COVID-19 Vaccine-Mix in Uttar Pradesh, India: Safety and Immunogenicity Assessment of a Heterologous Regime
Authors: Kant Rajni , Dwivedi Gaurav , Zaman Kamran , Sahay Rima R , Sapkal Gajanan , Kaushal Himanshu , Nyayanit Dimpal A. , Yadav Pragya D , Deshpande Gururaj , Singh Rajeev , Chaowdhary Sandeep , Gupta Nivedita , Kumar Sanjay , Abraham Priya , Panda Samiran , Bhargava Balram 
Published: August 2021

AbstractImmunization program against COVID-19 in India started with two vaccines; AstraZeneca’s ChAdOx1-nCov-19 (termed Covishield in India) and inactivated whole virion BBV152 (Covaxin); homologous prime-boost approach was followed. However, eighteen individuals, under the national program, inadvertently received Covishield as the first jab and Covaxin as the second. We compared the safety and immunogenicity profile of them against that of individuals receiving either Covishield or Covaxin (n=40 in each group). Lower and similar adverse events following immunization in all three groups underlined the safety of the combination vaccine-regime. Immunogenicity profile against Alpha, Beta and Delta variants in heterologous group was superior; IgG antibody and neutralising antibody response of the participants was also significantly higher compared to that in the homologous groups. The findings suggest that immunization with a combination of an adenovirus vector platform-based vaccine followed by an inactivated whole virus vaccine was not only safe but also elicited better immunogenicity.
Trends in accident-related admissions to pediatric intensive care units during the first COVID-19 lockdown in Germany
Authors: Bruns Nora , Willemsen Lea , Holtkamp Katharina , Kamp Oliver , Dudda Marcel , Kowall Bernd , Stang Andreas , Hey Florian , Blankenburg Judith , Hemmen Sabir , Eifinger Frank , Fuchs Hans , Haase Roland , Andrée Clemens , Heldmann Michael , Potratz Jenny , Kurz Daniel , Schumann Anja , Müller-Knapp Merle , Mand Nadine , Doerfel Claus , Dahlem Peter , Rothoeft Tobias , Ohlert Manuel , Silkenbäumer Katrin , Dohle Frank , Indraswari Fithri , Niemann Frank , Jahn Peter , Merker Michael , Braun Nicole , Nunez Francisco Brevis , Engler Matthias , Heimann Konrad , Wolf Gerhard , Wulf Dominik , Hollborn Claudia , Freymann Holger , Allgaier Nicolas , Knirsch Felix , Dercks Martin , Reinhard Julia , Hoppenz Marc , Felderhoff-Müser Ursula , Dohna-Schwake Christian 
Published: August 2021

AbstractObjectiveTo compare the number of accident- and injury-related admissions to pediatric intensive care units (PICU) during the first German COVID-19 lockdown with previous years. To investigate if shifts in types of accidents or injuries occurred, especially regarding non-accidental injuries.DesignRetrospective observational multicenter study.Setting37 German PICUs.Patients1444 children and adolescents < 18 years admitted to German PICUs due to trauma or injuries during the first German lockdown period (16.3.-31.5.2020) and during the same periods of the years 2017-2019.InterventionsNone.Measurements and main resultsStandardized morbidity ratios (SMR) and 95% confidence intervals (CI) were calculated for the severity of disease, admission reasons, types of accidents, injury patterns, surgeries and procedures, and outcomes. Disease severity did not differ from previous years. We found an increase in ingestions (SMR 1.41 (CI 0.88 – 2.16)) and a decrease in aspirations (0.77 (0.41 – 1.32)) and burns (0.82 (0.59 – 1.12)). The total number of admissions for trauma remained constant, but traffic accidents (0.76 (0.56 – 1.01) and school/kindergarten accidents (0.25 (0.05 – 0.74) decreased. Household (1.32 (1.05 – 1.64)) and leisure accidents (1.32 (1.05 – 1.65)) increased. Injured structures did not change, but less neurosurgeries (0.69 (0.42 – 1.07)) and more visceral surgeries (2.00 (1.14 – 3.24)) were performed. Non-accidental non-suicidal injuries declined (0.85 (0.50 – 1.37)). Suicide attempts increased in adolescent boys (1.57 (0.58 – 3.42)), while there was a decrease in adolescent girls (0.86 (0.53 – 1.31)).ConclusionsOur study showed shifts in trauma types and associated surgeries during the lockdown period that are generally in line with current literature. The decreased number of non-accidental non-suicidal injuries we observed does not suggest a fundamental increase in severe child abuse during the lockdown period. The decrease in suicide attempts among adolescent girls confirms previous findings, while the increase among boys has not been described yet and deserves further investigation.