bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cervical cancer incidence stratified by age in women with HIV compared with the general population in the United States, 2002–2016
Authors: Stier Elizabeth A. , Engels Eric , Horner Marie-Josèphe , Robinson William T. , Qiao Baozhen , Hayes Jennifer , Bayakly Rana , Anderson Bridget J. , Gonsalves Lou , Pawlish Karen S. , Zavala Diego , Monterosso Analise , Shiels Meredith S. 
Published: May 2021

Objective:
Recommendations for the age of initiating screening for cervical cancer in women with HIV (WWH) in the United States have not changed since 1995 when all women (regardless of immune status) were screened for cervical cancer from the age of onset of sexual activity, which often occurs in adolescence. By 2009, recognizing the lack of benefit as well as harms in screening young women, guidelines were revised to initiate cervical cancer screening for the general population at age 21 years. By comparing cervical cancer incidence in young WWH to that of the general population, we assessed the potential for increasing the recommended age of initiating cervical cancer screening in WWH.

Design:
We compared age-specific invasive cervical cancer (ICC) rates among WWH to the general population in the United States HIV/AIDS Cancer Match Study.

Methods:
We estimated standardized incidence ratios as the observed number of cervical cancer cases among WWH divided by the expected number, standardized to the general population by age, race/ethnicity, registry, and calendar year.

Results:
ICC rates among WWH were elevated across all age groups between ages 25 and 54 years (SIR = 3.80; 95% CI 3.48--4.15) but there were zero cases among ages less than 25 years.

Conclusion:
The absence of ICC among WWH less than 25 years supports initiating cervical cancer screening at age 21 years, rather than adolescence, to prevent cancers in WWH at ages with higher risk of ICC.
Hospital Adoption of Electronic Decision Support Tools for Preeclampsia Management
Authors: Bui Linh N. , Marshall Cassondra , Miller-Rosales Chris , Rodriguez Hector P. 
Published: May 2021

Background:
Electronic health record (EHR)–based clinical decision support tools can improve the use of evidence-based clinical guidelines for preeclampsia management that can reduce maternal mortality and morbidity. No study has investigated the organizational capabilities that enable hospitals to use EHR-based decision support tools to manage preeclampsia.

Objective:
To examine the association of organizational capabilities and hospital adoption of EHR-based decision support tools for preeclampsia management.

Methods:
Cross-sectional analyses of hospitals providing obstetric care in 2017. In total, 739 hospitals responded to the 2017-2018 National Survey of Healthcare Organizations and Systems (NSHOS) and were linked to the 2017 American Hospital Association (AHA) Annual Survey Database and the Area Health Resources File (AHRF). A total of 425 hospitals providing obstetric care across 49 states were included in the analysis. The main outcome was whether a hospital adopted EHR-based clinical decision support tools for preeclampsia management. Hospital organizational capabilities assessed as predictors include EHR functions, adoption of evidence-based clinical treatments, use of quality improvement methods, and dissemination processes to share best patient care practices. Logistic regression estimated the association of hospital organizational capabilities and hospital adoption of EHR-based decision support tools to manage preeclampsia, controlling for hospital structural and patient sociodemographic characteristics.

Results:
Two-thirds of the hospitals (68%) adopted EHR-based decision support tools for preeclampsia, and slightly more than half (56%) of hospitals had a single EHR system. Multivariable regression results indicate that hospitals with a single EHR system were more likely to adopt EHR-based decision support tools for preeclampsia (17.4 percentage points; 95% CI, 1.9 to 33.0; P < .05) than hospitals with a mixture of EHR and paper-based systems. Compared with hospitals having multiple EHRs, on average, hospitals having a single EHR were also more likely to adopt the tools by 9.3 percentage points, but the difference was not statistically significant (95% CI, −1.3 to 19.9). Hospitals with more processes to aid dissemination of best patient care practices were also more likely to adopt EHR-based decision-support tools for preeclampsia (0.4 percentage points; 95% CI, 0.1 to 0.6, for every 1-unit increase in dissemination processes; P < .01).

Conclusion:
Standardized EHRs and policies to disseminate evidence are foundational hospital capabilities that can help advance the use of EHR-based decision support tools for preeclampsia management in the approximately one-third of US hospitals that still do not use them.
Sphingobacterium lumbrici sp. nov., a novel bacterium isolated from wormcast of Eisenia foetida
Authors: Zhang Xiao-Fei , Shi Rui , Chen Min , Zhou Xing-Kui , Wei Yu-Qian , Cha Qi-Yan , Li Ni , Su Yuan-Xiao , Ma Li , Mo Ming-He , Cao Yi 
Published: May 2021

A novel Gram-stain-negative, rod-shaped, non-motile, yellowish bacterium, designated strain 1.3611T, was isolated from the wormcast of Eisenia foetida. The strain grew optimally at 30–37 ℃, at pH 7.0 and with 0–1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain 1.3611T showed the highest degree of 16S rRNA gene sequence similarity to

Sphingobacterium olei

HAL-9T (97.0 %), followed by

Sphingobacterium alkalisoli

Y3L14T (95.8 %). The respiratory quinone of strain 1.3611T was menaquinone-7 (MK-7) and its major cellular fatty acids were iso-C15 : 0 (41.3 %), summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c, 22.1 %) and iso-C17 : 0 3-OH (16.2 %). The major polar lipids were sphingophospholipid, phosphatidylethanolamine, four unidentified glycolipids, two unidentified phospholipids and five unidentified polar lipids. The genomic DNA G+C content was 39.0 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genomes of strain 1.3611T and

S. olei

HAL-9T were 37.9 and 88.9 %, respectively. According to the phenotypic and chemotaxonomic phylogenetic results, strain 1.3611T should represent a novel species of the genus

Sphingobacterium

, for which the name Sphingobacterium lumbrici sp. nov. is proposed, with strain 1.3611T (=KCTC 62980T=CCTCC AB 2018349T) as the type strain.
Portable and label-free quantitative Loop-mediated Isothermal Amplification (qLAMP) for reliable COVID-19 diagnostics in 3 minutes: An Arduino-based detection system assisted by a pH microelectrode
Authors: Moisés Alvarez Mario , Bravo-González Sergio , González-González Everardo , Santiago Grissel Trujillo-de 
Published: May 2021

AbstractLoop-mediated isothermal amplification (LAMP) has been recently studied as an alternative method for cost-effective diagnostics in the context of the current COVID-19 pandemic. Recent reports document that LAMP-based diagnostic methods have a comparable sensitivity and specificity to that of RT-qPCR. We report the use of a portable Arduino-based LAMP-based amplification system assisted by pH microelectrodes for the accurate and reliable diagnosis of SARS-CoV-2 during the first 3 minutes of the amplification reaction. We show that this simple system enables a straightforward discrimination between samples containing or not containing artificial SARS-CoV-2 genetic material in the range of 10 to 10,000 copies per 50 µL of reaction mix. We also spiked saliva samples with SARS-CoV-2 synthetic material and corroborated that the LAMP reaction can be successfully monitored in real time using microelectrodes in saliva samples as well. These results may have profound implications for the design of real-time and portable quantitative systems for the reliable detection of viral pathogens including SARS-CoV-2.
Chromosome X-wide analysis of positive selection in human populations: from common and private signals to selection impact on inactivated genes and enhancers-like signatures
Authors: Villegas-Mirón Pablo , Acosta Sandra , Nye Jessica , Bertranpetit Jaume , Laayouni Hafid 
Published: May 2021

AbstractThe ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic bases of population-specific adaptations genome-wide. Here we present the analysis of recent selective sweeps specifically in the X chromosome in different human populations from the third phase of the 1000 Genomes Project using three different haplotype-based statistics. We describe numerous instances of genes under recent positive selection that fit the regimes of hard and soft sweeps, showing a higher amount of detectable sweeps in sub-Saharan Africans than in non-Africans (Europe and East Asia). A global enrichment is seen in neural-related processes while numerous genes related to fertility appear among the top candidates, reflecting the importance of reproduction in human evolution. Commonalities with previously reported genes under positive selection are found, while particularly strong new signals are reported in specific populations or shared across different continental groups. We report an enrichment of signals in genes that escape X chromosome inactivation, which may contribute to the differentiation between sexes. We also provide evidence of a widespread presence of soft-sweep-like signatures across the chromosome and a global enrichment of highly scoring regions that overlap potential regulatory elements. Among these, enhancers-like signatures seem to present putative signals of positive selection that might be in concordance with selection in their target genes. Also, particularly strong signals appear in regulatory regions that show differential activities, which might point to population-specific regulatory adaptations.
SELP Asp603Asn and severe thrombosis in COVID-19 males: implication for anti P-selectin monoclonal antibodies treatment
Authors: Fallerini Chiara , Daga Sergio , Benetti Elisa , Picchiotti Nicola , Zguro Kristina , Catapano Francesca , Baroni Virginia , Lanini Simone , Bucalossi Alessandro , Marotta Giuseppe , Baldassarri Margherita , Fava Francesca , Beligni Giada , Di Sarno Laura , Alaverdian Diana , Palmieri Maria , Croci Susanna , Isidori Andrea M. , Furini Simone , Frullanti Elisa ,   GEN-COVID Multicenter Study, Renieri Alessandra , Mari Francesca 
Published: May 2021

AbstractThromboembolism is a frequent cause of severity and mortality in COVID-19. However, the etiology of this phenomenon is not well understood. A cohort of 1,186 subjects, from the GEN-COVID consortium, infected by SARS-CoV-2 with different severity were stratified by sex and adjusted by age. Then, common coding variants from whole exome sequencing were mined by LASSO logistic regression. The homozygosity of the cell adhesion molecule P-selectin gene (SELP) rs6127 (c.1807G>A; p.Asp603Asn) which increases platelet activation is found to be associated with severity in the male subcohort of 513 subjects (Odds Ratio= 2.27, 95% Confidence Interval 1.54-3.36). As the SELP gene is downregulated by testosterone, the odd ratio is increased in males older than 50 (OR 2.42, 95% CI 1.53-3.82). Asn/Asn homozygotes have increased D-dimers values especially when associated with poly Q≥23 in the androgen receptor (AR) gene (OR 3.26, 95% CI 1.41-7.52). These results provide a rationale for the repurposing of antibodies against P-selectin as adjuvant therapy in rs6127 male homozygotes especially if older than 50 or with impaired AR gene.Key points○The functional polymorphism rs6127 (p.Asp603Asn) in the testosterone-regulated SELP gene associates with COVID-19 severity and thrombosis.○Conditions with decreased testosterone (old males), or decreased testosterone efficacy (AR gene polyQ ≥ 23) strengthen the association.
Estimating the wave 1 and wave 2 infection fatality rates from SARS-CoV-2 in India
Authors: Purkayastha Soumik , Kundu Ritoban , Bhaduri Ritwik , Barker Daniel , Kleinsasser Michael , Ray Debashree , Mukherjee Bhramar 
Published: May 2021

AbstractObjectiveThere has been much discussion and debate around the underreporting of COVID-19 infections and deaths in India. In this short report we first estimate the underreporting factor for infections from publicly available data released by the Indian Council of Medical Research on reported number of cases and national seroprevalence surveys. We then use a compartmental epidemiologic model to estimate the undetected number of infections and deaths, yielding estimates of the corresponding underreporting factors. We compare the serosurvey based ad hoc estimate of the infection fatality rate (IFR) with the model-based estimate. Since the first and second waves in India are intrinsically different in nature, we carry out this exercise in two periods: the first wave (April 1, 2020 - January 31, 2021) and part of the second wave (February 1, 2021 – May 15, 2021). The latest national seroprevalence estimate is from January 2021, and thus only relevant to our wave 1 calculations.ResultsBoth wave 1 and wave 2 estimates qualitatively show that there is a large degree of “covert infections” in India, with model-based estimated underreporting factor for infections as 11.11 (95% credible interval (CrI) 10.71-11.47) and for deaths as 3.56 (95% CrI 3.48 - 3.64) for wave 1. For wave 2, underreporting factor for infections escalate to 26.77 (95% CrI 24.26 – 28.81) and to 5.77 (95% CrI 5.34 – 6.15) for deaths. If we rely on only reported deaths, the IFR estimate is 0.13% for wave 1 and 0.03% for part of wave 2. Taking underreporting of deaths into account, the IFR estimate is 0.46% for wave 1 and 0.18% for wave 2 (till May 15). Combining waves 1 and 2, as of May 15, while India reported a total of nearly 25 million cases and 270 thousand deaths, the estimated number of infections and deaths stand at 491 million (36% of the population) and 1.21 million respectively, yielding an estimated (combined) infection fatality rate of 0.25%. There is considerable variation in these estimates across Indian states. Up to date seroprevalence studies and mortality data are needed to validate these model-based estimates.
Correlation of the commercial anti-SARS-CoV-2 receptor binding domain antibody test with the chemiluminescent reduction neutralizing test and possible detection of antibodies to emerging variants
Authors: Morinaga Yoshitomo , Tani Hideki , Terasaki Yasushi , Nomura Satoshi , Kawasuji Hitoshi , Shimada Takahisa , Igarashi Emiko , Saga Yumiko , Yoshida Yoshihiro , Yasukochi Rei , Kaneda Makito , Murai Yushi , Ueno Akitoshi , Miyajima Yuki , Fukui Yasutaka , Nagaoka Kentaro , Ono Chikako , Matsuura Yoshiharu , Fujimura Takashi , Ishida Yoichi , Oishi Kazunori , Yamamoto Yoshihiro 
Published: May 2021

AbstractBackgroundSerological tests are beneficial for recognizing the immune response against SARS-CoV-2. To identify protective immunity, optimization of the chemiluminescent reduction neutralizing test (CRNT), using pseudotyped SARS-CoV-2, is critical. Whether commercial antibody tests are comparably accurate is unknown.MethodsSerum samples collected before variants were locally found were obtained from confirmed COVID-19 patients (n = 74), confirmed non-COVID-19 individuals (n = 179), and unscreened individuals (suspected healthy individuals, n = 229). The convalescent phase was defined as the period after day 10 from disease onset. The CRNT against pseudotyped viruses displaying the wild-type spike protein and a commercially available anti-receptor binding domain (RBD) antibody test were assayed. The CRNT was also assayed, using South African (SA) and United Kingdom (UK)-derived variants.ResultsThe CRNT (cut off value, 50% inhibition) and the anti-RBD antibody test (cut off value, 0.8 U/mL) concurred regarding symptomatic COVID-19 patients in the convalescent phase and clearly differentiated between patients and suspected healthy individuals (sensitivity; 95.8% and 100%, specificity; 99.1% and 100%, respectively). Anti-RBD antibody test results correlated with neutralizing titer (r = 0.47, 95% CI 0.20-0.68). Compared with the wild-type, CRNT reduction was observed for the SA and UK-derived variants. Of the samples with ≥100 U/mL by the anti-RBD antibody test, 77.8% and 88.9% showed ≥50% neutralization against the UK and the SA variants, respectively.ConclusionThe CRNT and commercial anti-RBD antibody test effectively classified convalescent COVID-19 patients. The strong positive results using the commercial antibody test can reflect neutralizing activity against emerging variants.
Translational control of fungal gene expression during the wheat-Fusarium graminearum interaction
Authors: Kage Udaykumar , Gardiner Donald M , Stiller Jiri , Kazan Kemal 
Published: May 2021

SummaryTo date, translational regulation of key genes controlling infection-related processes in fungal pathogens during their interactions with plants has not been studied. Here, we employed ribosome profiling (ribo-seq) to study translational responses and how such responses are coordinated with transcriptional changes in the fungal pathogen Fusarium graminearum (Fg), which causes Fusarium head blight (FHB), a destructive disease of cereal crops worldwide.Transcription and translation were not always coordinated with approximately 22% of Fg genes showing a discordant relationship during wheat infection. Nitrite reductase, which we show here as an important component of fungal virulence, is only regulated at the translational level in Fg. In addition, more than 1000 new open reading frames (ORFs), many of which are short and highly conserved, were identified in the Fg genome.Like in higher eukaryotes, translation is controlled by upstream ORFs (uORFs) in Fg during infection. Similarly, miRNAs control both transcription and translation in Fg during wheat infection. However, Fgdicer2-dependent miRNAs do not have a significant effect on transcriptional gene expression at the global outset.The ribo-seq study undertaken here for the first time in any fungal pathogen discovered novel insights about the biology of an important plant pathogen.
Single-Molecule Dynamics of SARS-CoV-2 5’ Cap Recognition by Human eIF4F
Authors: Hong Hea Jin , Guevara Matthew G. , Lin Eric , O’Leary Seán E. 
Published: May 2021

ABSTRACTCoronaviruses initiate translation through recognition of the viral RNA 5’ m7GpppAmcap by translation factor eIF4F. eIF4F is a heterotrimeric protein complex with cap-binding, RNA-binding, and RNA helicase activities. Modulating eIF4F function through cellular regulation or small-molecule inhibition impacts coronavirus replication, including for SARS-CoV-2. Translation initiation involves highly coordinated dynamics of translation factors with messenger or viral RNA. However, how the eIF4F subunits coordinate on the initiation timescale to define cap-binding efficiency remains incompletely understood. Here we report that translation supported by the SARS-CoV-2 5’-UTR is highly sensitive to eIF4A inhibition by rocaglamide. Through a single-molecule fluorescence approach that reports on eIF4E–cap interaction, we dissect how eIF4F subunits contribute to cap-recognition efficiency on the SARS-CoV-2 5’ UTR. We find that free eIF4A enhances cap accessibility for eIF4E binding, but eIF4G alone does not change the kinetics of eIF4E–RNA interaction. Conversely, formation of the full eIF4F complex significantly alters eIF4E–cap interaction, suggesting that coordinated eIF4E and eIF4A activities establish the net eIF4F–cap recognition efficiency. Moreover, the eIF4F complex formed with phosphomimetic eIF4E(S209D) binds the viral UTR more efficiently than with wild-type eIF4E. These results highlight a dynamic interplay of eIF4F subunits and mRNA that determines cap-recognition efficiency.
Whole genome phylogeny of Cyanobacteria documents a distinct evolutionary trajectory of marine picocyanobacteria
Authors: Strunecký Otakar , Wachtlová Markéta , Koblížek Michal 
Published: May 2021

AbstractDuring their 2.7 Gyr long evolution cyanobacteria radiated into a large number of different lineages. To better understand the evolution of cyanobacteria we compared a whole genome phylogenetic tree using 1,047 concatenated single copy orthologues ofProchlorococcus marinusMIT9313 obtained from 93 reference prokaryotic species with traditional phylogenies inferred from 16S rRNA gene and 109 genes found in all used genomes. In contrast to the traditional phylogeny, our genome wide analysis shows a split between picocyanobacteria encompassing all marineProchlorococcusspecies, marine “Synechococcus” species, and members of freshwaterCyanobiumgenus (altogether referred here as the “PSC” clade) and the remaining groups of extant cyanobacteria. To determine the influence of the horizontal gene transfer on the overall tree topology we removed the 374 genes identified as potentially transferred genes. A newly calculated tree utilizing the remaining 673 genes displayed the same topology as the former whole genome tree with the PSC clade as a basal group of all cyanobacteria. The picocyanobacteria also exhibited distinctly larger similarity to reference bacteria’s cell and genome size, carboxyzome architecture, various metabolic pathways, and chlorophyll synthesis than to the other cyanobacteria. Potentially horizontally transferred genes were found in connected chains throughout fundamental metabolic pathways suggesting that evolution of these genes was severely limited and or brought to a standstill. The environment related genes connected with metabolism of nitrogen, sulfur, and scarce seawater metals were more conserved in PSC group as they were already best tuned for its poor and stable environment. Other genes were found predominantly sequentially static as they were already accurately adapted with rare beneficial mutations. The PSC clade thus represents an isolated cyanobacterial lineage which followed a distinct evolutionary trajectory driven by its specific environment.
Microscopic characterization of local strain field in healing tissue in the central third defect of mouse patellar tendon at early-phase of healing
Authors: Maeda Eijiro , Kuronayagi Kaname , Matsumoto Takeo 
Published: May 2021

AbstractTendons exhibit a hierarchical collagen structure, wherein higher-level components, such as collagen fibres and fascicles, are elongated, slid, and rotated during macroscopic stretching. These mechanical behaviours of collagen fibres play important roles in stimulating tenocytes, imposing stretching, compression, and shear deformation. It was hypothesised that a lack of local fibre behaviours in healing tendon tissue may result in a limited application of mechanical stimuli to cells within the tissue, leading to incomplete recovery of tissue structure and functions in regenerated tendons. Therefore, the present study aimed to measure the microscopic strain field in the healing tendon tissue. A central third defect was created in the patellar tendon of mice, and the regenerated tissue in the defect was examined by tensile testing, collagen fibre analysis, and local strain measurement using confocal microscopy at 3 and 6 weeks after surgery. Healing tissue at 3 weeks exhibited a significantly lower strength and disorganised collagen fibre structure compared with the normal tendon. These characteristics at 6 weeks remained significantly different from those of the normal tendon. Moreover, the magnitude of local shear strain in the healing tissue under 4% tissue strain was significantly smaller than that in the normal tendon. Differences in the local strain field may be reflected in the cell nuclear shape and possibly the amount of mechanical stimuli applied to the cells during tendon deformation. Accordingly, restoration of a normal local mechanical environment in the healing tissue may be key to a better healing outcome of tendon injury.