bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of ovarian response prediction index and follicle-oocyte index on pregnancy outcomes: a retrospective cohort study of 12,218 fresh transfer cycles
Authors: Wang Mao , Tan Li , Ding Yu-Bin , Tang Xiao-Jun , Li Tian , Hu Xin-Yue , Zhong Hu-Cen , Wan Qi , Zhong Zhao-Hui 
Published: March 2024

Objective:
To investigate the potential relationships among the ovarian response prediction index (ORPI), follicle-oocyte index (FOI), and clinical pregnancy rate (CPR) in women undergoing their first in vitro fertilization/intracytoplasmic sperm injection-embryo transfer (IVF/ICSI-ET) fresh cycle transfer.

Methods:
In this retrospective cohort study, we included 12,218 women who underwent their first IVF/ICSI-ET cycle between December 2014 and January 2021. The primary and secondary outcomes of our study were CPR and cumulative live birth rate (CLBR), respectively. The data were divided into three groups according to the ORPI and FOI tertiles. Multivariate logistic regression analyses, stratification analyses, interaction, restricted cubic splines, and receiver operating characteristic (ROC) curves were constructed to identify the relationships among ORPI, FOI, and CPR.

Results:
A statistically significant increase in CPR was detected from the lowest to the highest tertile group (ORPI: 48.12%, 54.07%, and 53.47%, P <0.001; FOI: 49.99%, 52.95%, and 52.71%, P = 0.012). A higher CLBR was observed in the high group (ORPI: 38.63%, 44.62%, and 44.19%, P <0.001; FOI: 41.02%, 43.78%, and 42.59%, P = 0.039). Multivariate logistic regression analysis revealed no statistically significant differences between ORPI, FOI, and neither CPR (odds ratio [OR] [95% confidence interval {CI}], 0.99 [0.97–1.00] vs. [1.02 {0.84–1.24}]) nor CLBR (OR [95% CI], 0.99 [0.97–1.01] vs. 0.99 [0.81–1.20]). No significant association was found among FOI, ORPI, and CPR, even in the subgroups. Restricted cubic spline analyses indicated the existence of a non-linear relationship across the entire range of FOI and ORPI. The ORPI and FOI variables had poor predictive ability (AUC < 0.60) for CPR.

Conclusions:
Both ORPI and FOI are not reliable predictors of clinical pregnancy or live birth outcomes in fresh ETs. Clinicians and researchers should avoid using FOI and ORPI to assess pregnancy outcomes after fresh ET because of their limited relevance and predictive value.
Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries
Authors: Khan Mohd Wasif , de Jesus Vivianne Cruz , Mittermuller Betty-Anne , Sareen Shaan , Lee Victor , Schroth Robert J. , Hu Pingzhao , Chelikani Prashen 
Published: March 2024

SUMMARYEarly childhood caries (ECC) is influenced by microbial and host factors, including social, behavioral, and oral health. In this cross-sectional study, we analyzed interkingdom dynamics in the dental plaque microbiome and its association with host variables. The samples collected from the preschool children underwent 16S rRNA and ITS1 rRNA gene sequencing. The questionnaire data were analyzed for social determinants of oral health. The results indicated a significant enrichment ofStreptococcus mutansandCandida dubliniensisin ECC samples, in contrast toNeisseria oralisin caries-free children. Our interkingdom correlation analysis revealed thatCandida dubliniensiswas strongly correlated with bothNeisseria bacilliformisandPrevotella veroralisin ECC. Additionally, ECC showed significant associations with host variables, including oral health status, age, place of residence, and mode of childbirth. This study provides empirical evidence associating the oral microbiome with socioeconomic and behavioral factors in relation to ECC, offering insights for developing targeted prevention strategies.HIGHLIGHTSCharacterized interkingdom association between cariogenic species of genus Neisseria and CandidaBoth bacterial and fungal species are important for caries status prediction using artificial intelligenceSocioeconomic index is associated with caries status and caries-associated microbial markers
Analytical and Clinical Validation of Direct Detection of Antimicrobial Resistance Markers by Plasma Microbial Cell-free DNA Sequencing
Authors: Christians Fred C. , Akhund-Zade Jamilla , Jarman Kristin , Venkatasubrahmanyam Shivkumar , Noll Nicholas , Blauwkamp Timothy A. , Bercovici Sivan , Zielinska Aga , Carr Amy L. , Craney Arryn , Pike Matthew , Farrell John Joseph , Dadwal Sanjeet , Wood James B. , Matkovich Efrat , McAdams Staci , Nolte Frederick S. 
Published: March 2024

ABSTRACTSequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens with potential to harbor these markers. The AMR markers include SCCmec,mecAandmecCfor methicillin,vanAandvanBfor vancomycin,blaCTX-Mfor oxyimino-cephalosporin and aztreonam, andblaKPCfor carbapenem resistance. The AMR markers are computationally linked to the pathogens detected, using a statistical model based on observed AMR gene and pathogen abundances. Analytical validation showed high reproducibility (100%), inclusivity (54 to100%), and exclusivity (100%), with limits of detection ranging from 425 to 6,107 pathogen mcfDNA molecules/μL for the different markers. Clinical accuracy was assessed with 115 unique plasma samples from patients at 7 study sites with concordant culture results for 12/18 (66.7%) target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results when available. The positive percent agreement (PPA), negative percent agreement (NPA), overall percent agreement (OPA), and diagnostic yield (DY) were estimated for each AMR marker. The results for the combination of SCCmecandmecAfor staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), OPA 40/42 (95.2%), DY 42/60 (70.0%);vanAfor enterococci were PPA 3/3 (100%), NPA 2/2 (100%), OPA5/5 (100%), DY 5/6 (83.3%);blaCTX-Mfor gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), OPA34/35 (97.1%), DY 35/49 (71.4%); andblaKPCfor gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), OPA23/25 (92.3%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy.
Dynamics of Brain Connectivity across the Alzheimer’s Disease Spectrum: a magnetoencephalography study
Authors: Carrasco-Gómez Martín , García-Colomo Alejandra , Cabrera-Álvarez Jesús , Bruña Ricardo , Santos Andrés , Maestú Fernando 
Published: March 2024

AbstractAlzheimer’s disease (AD) represents a major challenge in neurodegenerative disease research, as it is characterized by a complex pathophysiology that involves not only structural but also functional changes in the brain. While changes in static functional connectivity have already been linked to AD, there is still a lack of research studying dynamic functional connectivity (dFC) across the AD continuum, which could be crucial for identifying potential biomarkers for early diagnosis and tracking disease progression. This study leverages the high temporal resolution of MEG to dissect the dynamics of brain connectivity alterations across various stages of AD and their association with cognitive decline and structural brain changes.321 participants were included in this study, categorized into healthy control, subjective cognitive decline (SCD), and mild cognitive impairment (MCI) groups. Amplitude envelope correlation with leakage correction was calculated over MEG signals using a sliding window, and the correlation across epochs was studied to assess dFC at whole-brain and node level. Finally, we explored dFC associations with cognitive scores, grey matter volume, and white matter fractal anisotropy.The study unveils a significant reduction in whole-brain dFC, especially within the alpha and beta frequency bands, as individuals advance along the AD continuum. Notably, the frontal and temporal lobes, as well as regions within the default mode network, exhibited pronounced dFC reductions. Finally, dFC significantly correlated with cognitive performance and changes in structural brain, suggesting the potential of the proposed dFC metric as sensitive indicator for monitoring disease progression.This investigation provides crucial insights into the temporal dynamics of brain connectivity alterations in the early stages of the AD spectrum, underlining the importance of dFC changes as reflective of cognitive and anatomical degeneration. The findings hint towards a strong relationship between connectivity profiles and white matter integrity, especially for high frequency activity in the association cortices.Key PointsDynamic functional connectivity declines over the AD spectrum.Dynamic functional connectivity reductions are most prominent in orbitofrontal, temporal, and DMN-related areas.Cognitive performance, brain volumetrics, and white matter integrity parameters positively correlate with dynamic functional connectivity over the whole AD spectrum, and most significantly among mild cognitive impairment participants.
Bradyrhizobiumand the soybean rhizosphere: Species level bacterial population dynamics in established soybean fields, rhizosphere and nodules
Authors: Sarao Sukhvir K. , Boothe Vincent , Das Bikram K. , Gonzalez Hernandez Jose L. , Brözel Volker S. 
Published: March 2024

AbstractBradyrhizobiumfixes nitrogen symbiotically with soybean and is an agriculturally significant bacterium. Much is known about theBradyrhizobiumspecies that nodulate soybeans. Conversely, prevalence ofBradyrhizobiumin soil and the rhizosphere is known only to the genus level as culture independent approaches have provided only partial 16S rRNA gene sequences, so that nodulating and non-nodulating species could not be distinguished. To track which species in bulk soil proliferate in the rhizosphere, and then nodulate, we sought to study population dynamics ofBradyrhizobiumin soybean fields and rhizosphere at the species level. Recent advances in Oxford Nanopore Technologies provided us with higher fidelity and increased number of reads which enabled us to trackBradyrhizobiumpopulations at the species level. We found evidence for 74 species ofBradyrhizobiumwithin a community of 10,855 bacterial species in bulk soil and rhizosphere from three different soybean fields in South Dakota. The most predominant species in bulk soil and rhizosphere includedB. liaoningense, B. americanum,andB. diversitatus, however none of these were isolated from nodules. Isolates from nodules includedB. japonicum, B. elkaniiandB. diazoefficiens.These nodulators also maintained populations in bulk soil and rhizosphere, although they were not the most prevalentBradyrhizobium.Our findings reveal the rich diversity and community dynamics ofBradyrhizobiumspecies in soybean field soil as well as in the rhizosphere. Our results showed that many species of the genus maintain populations in soybean field soil, even in the long-term absence of potential nodulating partners.
Spatial and temporal variation in respiratory syncytial virus (RSV) subtype RNA in wastewater, and relation to clinical specimens
Authors: Zambrana Winnie , Huang ChunHong , Solis Daniel , Sahoo Malaya K. , Pinsky Benjamin A. , Boehm Alexandria B. 
Published: March 2024

AbstractRespiratory syncytial virus (RSV) causes a large burden of respiratory illness, globally. It has two subtypes, RSV A and RSV B, but little is known regarding the predominance of these subtypes during different seasons and their impact on morbidity and mortality. Using molecular methods, we quantified RSV A and RSV B RNA in wastewater solids across multiple seasons and metropolitan areas to gain insight into the predominance of RSV subtypes. We determined the predominant subtype for each group using the proportion of RSV A to total RSV (RSV A + RSV B) in each wastewater sample (PA,WW), and conducted a comparative analysis temporally, spatially and against clinical specimens. A median PA,WWof 0.00 in the first season and 0.58 in the second season indicated a temporal shift in the predominant subtype. Spatially, while we observed dominance of the same subtype, PA,WWwas higher in some areas (PA,WW= 0.58 to 0.88). The same subtype predominated in wastewater and clinical samples, but clinical samples showed higher levels of RSV A (RSV A positivity in clinical samples = 79%, median PA,WW= 0.58). These results suggest that wastewater, alongside clinical data, holds promise for enhanced subtype surveillance.ImportanceRespiratory syncytial virus (RSV) causes a large burden of respiratory illness, globally. It has two subtypes, RSV A and RSV B, but little is known regarding the predominance of these subtypes during different seasons and their impact on morbidity and mortality. The study illustrates that information on subtype predominance can be gleaned from wastewater. As a biological composite sample from the entire contributing population, wastewater monitoring of RSV A and B can complement clinical surveillance of RSV.
Heterogeneity in elevated glucose and A1C as predictors of the prediabetes to diabetes transition: Framingham Heart Study, Multi-Ethnic Study on Atherosclerosis, Jackson Heart Study, and Atherosclerosis Risk In Communities
Authors: Patel Chirag J. , Ioannidis John PA , Gregg Edward W. , Vasan Ramachandran S. , Manrai Arjun K. 
Published: March 2024

AbstractIntroductionThere are a number of glycemic definitions for prediabetes; however, the heterogeneity in diabetes transition rates from prediabetes across different glycemic definitions in major US cohorts has been unexplored. We estimate the variability in risk and relative risk of adiposity based on diagnostic criteria like fasting glucose and hemoglobin A1C% (HA1C%).Research Design and MethodsWe estimated transition rate from prediabetes, as defined by fasting glucose between 100-125 and/or 110-125 mg/dL, and HA1C% between 5.7-6.5% in participant data from the Framingham Heart Study, Multi-Ethnic Study on Atherosclerosis, Atherosclerosis Risk in Communities, and the Jackson Heart Study. We estimated the heterogeneity and prediction interval across cohorts, stratifying by age, sex, and body mass index. For individuals who were prediabetic, we estimated the relative risk for obesity, blood pressure, education, age, and sex for diabetes.ResultsThere is substantial heterogeneity in diabetes transition rates across cohorts and prediabetes definitions with large prediction intervals. We observed the highest range of rates in individuals with fasting glucose of 110-125 mg/dL ranging from 2-18 per 100 person-years. Across different cohorts, the association obesity or hypertension in the progression to diabetes was consistent, yet it varied in magnitude. We provide a database of transition rates across subgroups and cohorts for comparison in future studies.ConclusionThe absolute transition rate from prediabetes to diabetes significantly depends on cohort and prediabetes definitions.Twitter SummaryNew study finds variable diabetes risk in prediabetes across US cohorts. Results highlight obesity, Black race, and hypertension as key factors, emphasizing the need for precision in diabetes care. #DiabetesResearch
Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries
Authors: Akaberi Dario , Pourghasemi Lati Monireh , Krambrich Janina , Berger Julia , Neilsen Grace , Strandback Emilia , Turunen S. Pauliina , Wannberg Johan , Gullberg Hjalmar , Moche Martin , Chinthakindi Praveen Kumar , Nyman Tomas , G. Sarafianos Stefan , Sandström Anja , D. Järhult Josef , Sandberg Kristian , Lundkvist Åke , Verho Oscar , Lennerstrand Johan 
Published: March 2024

AbstractIn vitro screening of large compounds libraries with automated high-throughput screening is expensive, time consuming and requires dedicated infrastructures. Conversely, the selection of DNA-encoded chemical libraries (DECL) can be rapidly performed with routine equipment available in most laboratories. In this study we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity-based selection of the DELopen library (open access for academics), containing 4.2 billion compounds. The identified inhibitors were peptide-like compounds containing an N-terminal electrophilic group able to form a covalent bond with the nucleophilic Cys145 of Mpro, as confirmed by x-ray crystallography. This DECL selection campaign enabled the discovery of the unoptimized compound SLL11 displaying an IC50of 30 nM, proving that the rapid exploration of large chemical spaces enabled by DECL technology, allows for the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. Compound MP1, a close analogue of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50= 2.3µM) cell lines. As peptide-like compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds as well as the substitution of selected residues with D-enantiomers will be explored in the future to improve the antiviral activity of these novel compounds.
Applying health equity implementation science frameworks to population genetic screening
Authors: Rao Nandana D. , Fullerton Stephanie M. , Shirts Brian H. , Chen Annie T. , Henrikson Nora B. 
Published: March 2024

ABSTRACTImplementation science frameworks with a focus on health equity have emerged to help guide the introduction of new interventions into healthcare and community settings while limiting health disparities. The purpose of this research was to explore the applicability of such frameworks to guide the equitable implementation of population genetic screening programs. We searched PubMed and reference lists for relevant frameworks and examples of their use in health settings. We then assessed if and how selected frameworks provide guidance for different stages of population genetic screening: recruitment, sample collection, result return, follow-up care and prevention, and cascade screening. Findings were synthesized into a list of health equity considerations specific to each stage. We identified 5 implementation frameworks that focus on health equity. Guidance varied by framework type: determinant (explaining what affects implementation outcomes), process (translating research into practice), or evaluation (assessing implementation). Common characteristics included focusing implementation efforts on populations who have historically experienced health inequities and adapting interventions to fit local contexts. Process models also highlighted the importance of community partnerships. Overall, frameworks offered broad recommendations applicable to population genetic screening program implementation. However, gaps still exist in guidance provided for later stages of population genetic screening. To improve the equitable implementation of genetic screening, future programs may benefit from utilizing one or more of these frameworks or by incorporating the health equity considerations and outcomes compiled in this analysis.
Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits
Authors: Dube Sukoluhle , Al-Mannai Sharefa , Liu Li , Tomei Sara , Sanchez Apryl , Mifsud William , Bedognetti Davide , Hendrickx Wouter , Raynaud Christophe Michel 
Published: March 2024

AbstractBackgroundFFPE tissue samples are commonly used in biomedical research and are a valuable source for next-generation sequencing in oncology, however, extracting RNA from these samples can be difficult the quantity and quality achieved can impact the downstream analysis. This study compared the effectiveness of seven different commercially available RNA extraction kits specifically designed for use with FFPE samples in terms of the quantity and quality of RNA recovered.MethodsThis study used 9 samples of FFPE tissue from three different types of tissue (Tonsil, Appendix and lymph node of B-cell lymphoma) to evaluate RNA extraction methods. Three sections of 20μm of each sample were combined per sample. The slices were distributed in a systematic manner to prevent any biases. Each of the 7 commercially available RNA extraction kits were used according to manufacturer’s instructions, with each sample being tested in triplicate resulting in a total of 189 extractions. The concentration, RNA integrity number (RIN) and DV200 of each extraction was analysed using a LabChip to determine the quantity and quality of the recovered RNA.ResultsThis study found that despite processing the FFPE samples in the same standardized way, there were disparities in the quantity and quality of RNA recovered across the different tissue types. Additionally, the study found notable differences in the quantity of RNA recovered when using different extraction kits. In terms of quality, three of the kits performed better than the other four in terms of RNA integrity number (RIN) and DV200 values.ConclusionThough many laboratories have developed their own protocols for specific tissue types, using commercially available kits is still a popular option. Although these kits use similar processes and extraction procedures, the amount and quality of RNA obtained can vary greatly between kits. In this study, among the kits tested, while the Roche kit, provided a nearly systematic better-quality recovery than other kits, the ReliaPrep FFPE Total RNA miniprep from Promega yielded the best ratio of both quantity and quality on the tested tissue samples.
Estimating the selection pressure of tumor growth on tumor tissue microbiomes
Authors: Li Lianwei , Ma Zhanshan (Sam) 
Published: March 2024

AbstractBackgroundThe relationships between tumor and its microbiome are still puzzling, with possible bidirectional interactions. Tumor microbiomes may suppress or stimulate tumor growth on the one hand; on the other hand, tumor growth may exert selection pressure on its microbiomes. There is not any consensus on the mode and/or extension of the bidirectional interactions. The objective of this study is to estimate the selection pressure from the primary tumors on tumor microbiomes by comparing with the selection pressure from the solid normal tissues on their corresponding tissue microbiomes across 20+ cancer types.MethodsWe apply Sloan near neutral theory and big datasets of tumor tissue microbiomes from the TCGA (The Cancer Genome Atlas) databases to achieve the above objective. The near neutral theory model can determine the proportions of above-neutral, neutral and below-neutral species in microbial communities, corresponding with positive, neutral and negative selection pressures from host tissues. By comparing the proportions between the primary tumors and solid normal tissues, we can infer the selection pressure of tumor growth on tissue microbiomes.ResultsWe find that approximately 65% of species in solid normal tissue microbiomes are neutral, and the proportion is only 40% in the primary tumor microbiomes. In contrast, the proportion of positively selected species exceeds 60% in the primary tumor microbiomes. Furthermore, simulations with neutral theory model reveal that most abundant species are mostly neutral, while non-neutral species are in the long tail of the species abundance distributions.ConclusionsTumor growth exerts strong positive selection on resident microbiomes, driving the abundances of certain species above the levels expected by the neutral process. Nevertheless, neutral species are still among the most abundant species, suggesting the necessity to pay close attention to the low-abundance or rare species because they are likely to play a critical role in oncogenesis.