bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes
Authors: Cruz Dávalos Diana Ivette , Arizmendi Cárdenas Yami Ommar , Bravo-Lopez Miriam Jetzabel , Neuenschwander Samuel , Reis Silvia , Bastos Murilo Q. R. , Stenderup Jesper , Yediay Fulya Eylem , Villa-Islas Viridiana , Reyna-Blanco Carlos S. , Rodrigues-Carvalho Claudia , Hünemeier Tábita , Allentoft Morten E. , Amorim Carlos Eduardo G. , Moreno-Mayar J. Víctor , Ávila-Arcos María C. , Malaspinas Anna-Sapfo 
Published: February 2022

AbstractAlthough Brazil was inhabited by more than 3,000 Indigenous populations prior to European colonization, today’s Indigenous peoples represent less than 1% of Brazil’s census population. Some of the decimated communities belonged to the so-called “Botocudos” from central-eastern Brazil. These peoples are thought to represent a case of long-standing genetic continuity bearing a strong craniometric resemblance to that of the oldest Indigenous Americans (“Paleoamericans”). Yet, little is known about their origins and genetic relationship to other Native Americans, as only two “Botocudo” genomes have been sequenced so far and those were surprisingly of Polynesian ancestry. To deepen our knowledge on the genomic history of pre-contact Indigenous Americans and the pathogens they were exposed to, we carbon-dated and sequenced 24 ancient Brazilians (including 22 “Botocudos”) whose remains were hosted at the National Museum of Rio de Janeiro and recovered prior to the tragic 2018 fire. The resulting genomes’ depth of coverage ranged from 0.001× to 24×. Their genetic ancestry was found to be Indigenous American without gene flow from external populations such as Europeans, Africans or Polynesians. Unlike Mesoamericans, the “Botocudos” and Amazonians do not seem to have experienced a population expansion once in the Americas. Moreover, remarkably, their genomes exhibit amongst the lowest levels of heterozygosity worldwide and long runs of homozygosity, which could be explained by unique social practices or a very small effective size. Finally, whole genomes of likely ancient pathogens were recovered, including lineages of Human parvovirus B19 that were possibly introduced after the European contact.Significance statementTo better understand the genetic relationship among Indigenous populations in Brazil, we sequenced the genomes of 24 ancient individuals (22 of which labelled as “Botocudos”, a term used to describe hunter-gatherer tribes) whose remains were hosted at the Museu Nacional of Rio de Janeiro prior to the tragic fire that consumed it in 2018. Unlike two previously published “Botocudo” genomes, the 22 “Botocudos” from this study have Indigenous American-related ancestry without any Polynesian-related ancestry, and they are similarly related to several Native Brazilian populations. Finally, unlike Eurasian hunter-gatherers, the “Botocudos” exhibit among the lowest heterozygosity and longest runs of homozygosity worldwide – compatible with a very small effective size and suggesting a unique social structure among hunter-gatherers in the Americas.
Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria
Authors: Ikhimiukor Odion O. , Oaikhena Anderson O. , Afolayan Ayorinde O. , Fadeyi Abayomi , Kehinde Aderemi , Ogunleye Veronica O , Aboderin Aaron O. , Oduyebo Oyinlola O. , Elikwu Charles J. , Odih Erkison Ewomazino , Komolafe Ifeoluwa , Argimón Silvia , Egwuenu Abiodun , Adebiyi Ini , Sadare Oluwadamiloa A. , Okwor Tochi , Kekre Mihir , Underwood Anthony , Ihekweazu Chikwe , Aanensen David M. , Okeke Iruka N. 
Published: February 2022

ABSTRACTBackgroundSalmonellosis causes significant morbidity and mortality in Africa. Despite being endemic in Nigeria, information on circulating lineages of invasive Salmonella is sparse.MethodsSalmonella enterica isolated from blood (n=60) and cerebrospinal fluid (CSF, n=3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools.ResultsIsolates and sequence types (STs) from blood were S. Typhi [ST1, n =1 and ST2, n =43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n=7], S. Durham [ST10, n=2], S. Rissen [ST8756, n=2], S. Chester [ST2063, n=1], S. Dublin [ST10, n=1], S. Infantis [ST603, n=1], S. Telelkebir [ST8757, n=1] and S. Typhimurium [ST313, n=1], S. Typhi ST2 (n=2) and S. Adabraka ST8757 (n=1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n=44), carried an IncY plasmid and had several antibiotic resistance genes (ARGs) including blaTEM-1 (n=38), aph(6)-Id (n=32), tet(A) (n=33), sul2 (n=32), dfrA14 (n=30) as well as quinolone resistance-conferring gyrA_S83Y SNPs (n=37). All S. Enteritidis harboured aph(3’’)-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir.. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir.ConclusionMost invasive salmonelloses in south west Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant Typhi lineage 3.1.1.. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes represented a third of the isolates emphasizing the need for better diagnosis and surveillance.Author SummaryWhole genome sequencing of 63 invasive Salmonella from 5 tertiary hospitals in Nigeria revealed multiple serovars including a dominant antibiotic-resistance-gene harbouring S. Typhi 3.1.1 genotype comprising a gyrA_S83Y and IncY plasmid. We also report invasive non-typhoidal Salmonella harbouring typhoidal toxins.
Mucins form a nanoscale material barrier against immune cell attack
Authors: Park Sangwoo , Colville Marshall J. , Shurer Carolyn R. , Huang Ling-Ting , Kuo Joe Chin-Hun , Paek Justin H. , Goudge Marc C. , Su Jin , DeLisa Matthew P. , Lammerding Jan , Zipfel Warren R. , Fischbach Claudia , Reesink Heidi L. , Paszek Matthew J. 
Published: February 2022

ABSTRACTThe cancer cell glycocalyx serves as a major line of defense against immune surveillance. However, how specific physical properties of the glycocalyx contribute to immune evasion and how these properties are regulated are not well understood. Here, we uncover how the surface density, glycosylation, and crosslinking of cancer-associated mucins contribute to the nanoscale material thickness of the glycocalyx, and further analyze the effect of the glycocalyx thickness on resistance to effector cell attack. Natural Killer (NK) cell-mediated cytotoxicity exhibits a near perfect inverse correlation with the glycocalyx thickness of target cells regardless of the specific glycan structures present. NK cells expressing a chimeric antigen receptor (CAR) have an enhanced ability to breach the glycocalyx and kill target cells. Equipping the NK cell surface with a mucin-digesting enzyme also improves killing with a performance enhancement that rivals or exceeds CARs in some cases. Together, our results provide new considerations for improving cancer immunotherapies.
The predictive value of double-stranded RNA for A-to-I editing detection
Authors: Shur Guy , Tamir Yuval , Eran Alal 
Published: February 2022

Structured AbstractMotivationAdenosine-to-inosine (A-to-I) RNA editing, a crucial reaction for many processes that contribute to transcriptome plasticity, is both widely common across the transcriptome and difficult to predict due to a lack of distinctive genomic characteristics that can be obtained and analyzed computationally. An exception to this is the secondary structure of RNA molecules, which has been shown to have a major impact on the selectivity and specificity of the enzymes responsible for A-to-I editing. Yet, this information is rarely used for the task of editing site prediction.ResultsHere, we demonstrated the value of using base-pairing probabilities of RNA nucleotides to classify genomic sites as A-to-I RNA editing sites, using large-scale truth data which we compiled and make available for use in training future models. Our analysis suggests that the span of four bases from –2 (upstream) to +1 (downstream) of a putative editing site is most informative in this regard. A classifier trained on base-pairing probabilities alone performed with a positive predictive value (PPV) of 0.68, a negative predictive value (NPV) of 0.64, and an area under the receiver operating characteristic curve (AUC) of 0.71. By identifying structure-related features that are informative for detecting A-to-I RNA editing sites and quantifying their predictive value, this work advances our understanding of A-to-I editing determinants.AvailabilityAll source codes and data are available at https://github.com/Ally-s-Lab/P-BEP
SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection
Authors: Greaney Allison M. , Raredon Micha S.B. , Kochugaeva Maria P. , Niklason Laura E. , Levchenko Andre 
Published: February 2022

SummaryDespite much concerted effort to better understand SARS-CoV-2 viral infection, relatively little is known about the dynamics of early viral entry and infection in the airway. Here we analyzed a single-cell RNA sequencing dataset of early SARS-CoV-2 infection in a humanized in vitro model, to elucidate key mechanisms by which the virus triggers a cell-systems-level response in the bronchial epithelium. We find that SARS-CoV-2 virus preferentially enters the tissue via ciliated cell precursors, giving rise to a population of infected mature ciliated cells, which signal to basal cells, inducing further rapid differentiation. This feed-forward loop of infection is mitigated by further cell-cell communication, before interferon signaling begins at three days post-infection. These findings suggest hijacking by the virus of potentially beneficial tissue repair mechanisms, possibly exacerbating the outcome. This work both elucidates the interplay between barrier tissues and viral infections, and may suggest alternative therapeutic approaches targeting non-immune response mechanisms.
Quantitative risk assessment of COVID-19 and serious illness among spectators at mass gathering events with vaccine-testing package implementation
Authors: Murakami Michio , Fujita Tsukasa , Iwasaki Yuichi , Onishi Masaki , Naito Wataru , Imoto Seiya , Yasutaka Tetsuo 
Published: February 2022

AbstractWhile mass gathering events have resumed in conjunction with vaccine-testing (VT) packages, their effects on reducing COVID-19 risk remain unclear. Here, we used an environmental exposure model to analyze the effects of vaccinations and proof of negative test results on reducing infection risk and serious illness among spectators at mass gathering events. We then analyzed the difference in risk with and without VT and regular seat zoning. Risk of infection and serious illness were quantified using a model incorporating parameters such as vaccination coverage, vaccine prevention effectiveness, and sensitivity of polymerase chain reaction (PCR) or qualitative antigen tests. When vaccine prevention effectiveness was 50% (corresponding to 4 months for the delta variant and 1–2 months for the omicron variant after the second vaccine dose), the risk of infection and serious illness among vaccinated spectators were 0.32–0.40 and 0.13–0.16 times of those who tested negative, respectively. In contrast, the risks of infection and serious illness among vaccinated spectators without measures such as mask wearing were 4.0 and 1.6 times higher than those among unvaccinated spectators with such measures, respectively. The risk of infection with an 80% vaccination coverage and a vaccine prevention effectiveness of 20% (corresponding to 5–6 months for the delta variant or 3–4 months for the omicron variant after the second vaccine dose) was comparable to that of a 20% vaccine coverage and a vaccine prevention effectiveness of 80% (corresponding to 1–3 months for delta variant after the second vaccine dose). Regarding zoning, there was little difference in risk with a vaccination coverage of ≥80%. Adherence to individual measures after vaccination and maintenance of high vaccine effectiveness among spectators at stadiums are important for reducing risk of infection and serious illness. Furthermore, seat zoning did not affect overall infection risk reduction.
The impact of retracted randomised controlled trials on systematic reviews and clinical practice guidelines: a meta-epidemiological study
Authors: Kataoka Yuki , Banno Masahiro , Tsujimoto Yasushi , Ariie Takashi , Taito Shunsuke , Suzuki Tomoharu , Oide Shiho , Furukawa Toshi A. 
Published: February 2022

AbstractObjectivesTo investigate whether and when the correction is done in Systematic Reviews (SRs) and Clinical Practice Guidelines (CPGs) when their included Randomised Controlled Trials (RCTs) have been retracted.DesignA meta-epidemiological study.Data sourcesThe Retraction Watch Database.Eligibility criteria for selecting studiesSRs and CPGs citing the retracted RCTs on Web of Science.Review methodsWe investigated how often the retracted RCTs were cited in SRs and CPGs. We also investigated whether and when such SRs and CPGs corrected themselves by visually inspecting their current web pages. We summarized the proportion of correction and the time from retraction to correction.ResultsWe identified 98 retracted RCTs as well as 360 articles (335 SRs and 25 CPGs) citing them. Among the 360 articles, 157 (44%) were published after the retraction, 203 (56%) were published before retraction. Among 77 articles published citing already retracted RCTs in their evidence synthesis without caution, none corrected themselves after publication. Of 203 articles published before retraction, 149 included RCTs that were later retracted in their evidence synthesis. Among them, one SR was retracted due to plagiarism. Only 5% of SRs (6/130) and 11% of CPGs (2/18) corrected their results.ConclusionsA large number of SRs and CPGs included already retracted RCTs without caution and never corrected themselves. When SRs and CPGs had included RCTs which were later retracted, only a small minority corrected their evidence syntheses. The scientific community, including publishers and researchers, should make systematic and concerted efforts to remove the impact of retracted RCTs.What is already known on this topic-Systematic Reviews (SRs) and Clinical Practice Guidelines (CPGs) aggregating randomised controlled trials (RCTs) are important sources of information for clinical decision making.-There are anecdotal reports of publications citing retracted RCTs and point to the problem of their continued citation after retraction.-However, there are no studies that comprehensively examined the fate of retracted RCTs on SRs and CPGs in their evidence synthesis.What this study adds-A considerable number of SRs and CPGs cited already retracted RCTs and none corrected themselves later.-Only a small minority of SRs (5%, 6/130) and CPGs (11%, 2/18) which cited RCTs that were later retracted corrected their findings after the retraction was announced.-The results indicate that publishers and researchers should make efforts to remove the impact of retracted RCT.
Presentation and Short-term Course of New Onset Cannabis Induced Psychotic Disorder in Males
Authors: D’Souza Deepak Cyril , Raj Justin , Ganesh Suhas , Goyal Nishant , KL Vidya , Tikka Sai Krishna , Shreekantiah Umesh , Murthy Pratima , Ram Daya , Sharma Priyamvada , Sinha Vinod K , Cortes-Briones Jose 
Published: February 2022

AbstractIntroductionCannabis use has been associated with several psychosis outcomes including acute and persistent psychosis termed Cannabis Induced Psychotic Disorder (CIPD). The clinical and cognitive profile, course of CIPD, and the extent to which it is different from psychosis unrelated to cannabis exposure (PsyNoCan) is not clear.MethodsThe acute presentation and short-term (∼4 weeks) course of hospitalized male patients with new onset CIPD were compared prospectively to PsyNoCan using measures of psychosis, depression, mania, memory and other cognitive processes at admission, and after 4 weeks of inpatient hospitalization. A subsample of CIPD patients were followed up after 4-6 months of discharge. Cognitive test performance was benchmarked for comparison in healthy controls and individuals with Cannabis Use Disorder.ResultsCompared to PsyNoCan (n=53), CIPD (n=66) had a significantly lower severity of psychotic symptoms at admission but no differences in mood symptoms. After 4 weeks of hospitalization, the CIPD group had less psychosis. While both groups had significant cognitive deficits at baseline compared to healthy controls, cognitive test performance improved to a greater extent in CIPD. Amongst 16 CIPD cases with longitudinal follow-up data, 10 relapsed with psychosis within 6 months after resuming cannabis use.ConclusionCIPD in males has a distinct presentation and short-term course, characterized by less severe psychosis, and greater resolution of psychopathology and cognitive deficits relative to PsyNoCan. Relapse of cannabis use may predict poorer long-term outcomes with greater psychotic relapses. The longer-term course, prognosis and biology of CIPD, and its presentation in females needs further study.
Clonal dynamics of SARS-CoV-2-specific T cells in children and adults with COVID-19
Authors: Khoo Weng Hua , Jackson Katherine , Phetsouphanh Chansavath , Zaunders John J. , Alquicira-Hernandez José , Yazar Seyhan , Ruiz-Diaz Stephanie , Singh Mandeep , Dhenni Rama , Kyaw Wunna , Tea Fiona , Merheb Vera , Lee Fiona X. Z. , Burrell Rebecca , Howard-Jones Annaleise , Koirala Archana , Zhou Li , Yuksel Aysen , Catchpoole Daniel R. , Lai Catherine L. , Vitagliano Tennille L. , Rouet Romain , Christ Daniel , Tang Benjamin , West Nicholas P. , George Shane , Gerrard John , Croucher Peter I. , Kelleher Anthony D. , Goodnow Christopher G. , Sprent Jonathan D. , Powell Joseph D. , Brilot Fabienne , Nanan Ralph , Hsu Peter S. , Deenick Elissa K. , Britton Philip N. , Phan Tri Giang 
Published: February 2022

SUMMARYChildren infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop less severe coronavirus disease 2019 (COVID-19) than adults. The mechanisms for the age-specific differences and the implications for infection-induced immunity are beginning to be uncovered. We show by longitudinal multimodal analysis that SARS-CoV-2 leaves a small footprint in the circulating T cell compartment in children with mild/asymptomatic COVID-19 compared to adult household contacts with the same disease severity who had more evidence of systemic T cell interferon activation, cytotoxicity and exhaustion. Children harbored diverse polyclonal SARS-CoV- 2-specific naïve T cells whereas adults harbored clonally expanded SARS-CoV-2-specific memory T cells. More naïve interferon-activated CD4+T cells were recruited into the memory compartment and recovery was associated with the development of robust CD4+memory T cell responses in adults but not children. These data suggest that rapid clearance of SARS-CoV-2 in children may compromise their cellular immunity and ability to resist reinfection.HIGHLIGHTSChildren have diverse polyclonal SARS-CoV-2-specific naïve T cellsAdults have clonally expanded exhausted SARS-CoV-2-specific memory T cellsInterferon-activated naïve T cells differentiate into memory T cells in adults but not childrenAdults but not children develop robust memory T cell responses to SARS-CoV-2
Task-based fMRI in early Multiple Sclerosis: what is the best head motion correction approach?
Authors: Soares Júlia F. , Abreu Rodolfo , Cláudia Lima Ana , Sousa Lívia , Batista Sónia , Castelo-Branco Miguel , Duarte João Valente 
Published: February 2022

AbstractFunctional MRI (fMRI) is one of the most common brain imaging modalities used for understanding brain organization and connectivity abnormalities associated with multiple sclerosis (MS). The fMRI signal is highly perturbed by head motion, which degrades data quality and influences all image-derived metrics. Numerous correction approaches have been proposed over the years to overcome the problems induced by head motion, however, despite a few efforts, there are still current and persistent controversies regarding the best correction strategy. The lack of a systematic comparison between different correction approaches motivates the search for optimal correction models, particularly in studies with clinical populations prone to characterize by higher motion. Moreover, motion correction strategies gain more relevance in task-based designs, which are less explored compared to resting-state and may have a crucial role in describing the functioning of the brain and highlighting specific connectivity changes.We acquired fMRI data from a group of patients with early MS and matched healthy controls (HC) during performance of a visual task, characterized motion in both groups, and compared the most used motion correction methods. We compared task-activation metrics obtained from models without motion correction, models containing 6 or 24 motion parameters (MPs) as nuisance regressors, models containing 6 or 24 MPs and motion outliers detected with FD or DVARS as nuisance regressors (scrubbing) and models with 6 or 24 MPs where motion outliers were corrected through volume interpolation. To our knowledge, volume interpolation is a frequently used approach but was never compared with other existent methods.Our results showed that there were no differences in motion between groups, suggesting that recently diagnosed MS patients do not present problematic motion. In general, models with 6 MPs present higher Z-scores than models with 24 MPs, suggesting the 6 MPs as the best trade-off between motion correction and preservation of valuable information. However, correction approaches differ between groups, regarding the combination of MPs with correction of motion outliers. Models with 6 MPs and outliers’ volume interpolation or scrubbing with FD presented higher Z-scores in the MS group, while models with 6 MPs and scrubbing with DVARS or volume interpolation were the best combinations for the HC group. Differences between groups in motion correction strategies draw attention to the intrinsic impact of MS on fMRI analyses, which should be carefully addressed.This work paves the way towards finding an optimal motion correction strategy, which is required to improve the accuracy of fMRI analyses, crucially in clinical studies in MS and other patient populations.
Flagellar energy costs across the Tree of Life
Authors: Schavemaker Paul E , Lynch Michael 
Published: February 2022

AbstractFlagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli, Pyrococcus furiosus, and Chlamydomonas reinhardtii. Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature, yield flagellar costs for another ∼200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum.