bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of single-dose HPV vaccination on HPV 16 and 18 prevalence in South African adolescent girls with and without HIV
Authors: Delany-Moretlwe Sinead , Machalek Dorothy A , Travill Danielle , Petoumenos Kathy , Nyemba Dorothy C , Mbulawa Zizipho Z A , Ndlovu Nontokozo , Kaldor John M , Rees Helen 
Published: November 2024

Abstract

Background
The World Health Organization has endorsed single-dose human papillomavirus (HPV) vaccination, but data on the impact on HPV prevalence in high HIV burden settings are limited.

Methods
A single-dose bivalent HPV vaccine was delivered to adolescent girls in grade 10 in a schools-based campaign in 1 district in South Africa. Impact on HPV 16 and 18 prevalence was evaluated using repeat cross-sectional surveys. A clinic-based survey in girls aged 17-18 years established HPV 16 and 18 prevalence in a prevaccine population (n = 506, including 157 living with HIV) in 2019 and was repeated in the same age group and sites in a single-dose eligible population in 2021 (n = 892, including 117 with HIV). HPV DNA was detected on self-collected vaginal swabs using the Seegene Anyplex II HPV 28. Population impact was estimated overall and by HIV status using prevalence ratios adjusted for differences in sexual behavior between surveys.

Results
Single-dose vaccination campaign coverage was 72% (4807 of 6673) of eligible girls attending high school (n = 66) in the district. HPV 16 and 18 prevalence was 35% lower in the postvaccine survey overall (adjusted prevalence ratio = 0.65, 95% confidence interval [CI] = 0.51 to 0.83; P &lt; .001) and 37% lower in those living with HIV (adjusted prevalence ratio = 0.63, 95% CI = 0.41 to 0.95; P  = .026). No protective effect was seen for nonvaccine oncogenic HPV types 33, 35, 39, 51, 52, 56, 58, 59, or 68 overall (adjusted prevalence ratio = 1.14, 95% CI = 1.03 to 1.26; P = .011) or in those living with HIV (adjusted prevalence ratio = 1.00, 95% CI = 0.83 to 1.21. P = 0.99).

Conclusion
These data provide reassuring evidence of single-dose impact on population-level HPV 16 and 18 prevalence in a South African population, irrespective of HIV status.
Post-criticality and the pursuit of an empirical philosophy of education: epistemology, methodology, ethics
Authors: Schildermans Hans , Vlieghe Joris , Wortmann Kai 
Published: November 2024

Abstract
This article examines the relevance of post-criticality as a research stance across various traditions in educational research. After problematizing the dominance of critical approaches centred on deconstruction and denunciation, the authors advocate instead for an empirical philosophy of education. This article sets the stage for a suite of articles, published in this issue, which explore affirmative, engaged methodologies that prioritize proximity to educational practices over detached critique. Collectively, the articles investigate how post-critical methodologies can produce richer understandings of educational realities and foster meaningful connections between theory and practice.
α-separability and adjustable combination of amplitude and phase model for functional data
Authors: Wang Tian , Ding Jimin 
Published: November 2024

Abstract
We consider separating and joint modelling amplitude and phase variations for functional data in an identifiable manner. To rigorously address this separability issue, we introduce the notion of α-separability upon constructing a family of α-indexed metrics. We bridge α-separability with the uniqueness of Fréchet mean, leading to the proposed adjustable combination of amplitude and phase model. The parameter α allows user-defined modelling emphasis between vertical and horizontal features and provides a novel viewpoint on the identifiability issue. We prove the consistency of the sample Fréchet mean and variance, and the proposed estimators. Our method is illustrated in simulations and COVID-19 infection rate data.
Splenic artery pseudoaneurysm rupture post-laparoscopic sleeve gastrectomy
Authors: Babic Stephanie M , Ramachandran Roshan N 
Published: November 2024

Abstract
A splenic artery pseudoaneurysm (SAP) is a rare vascular entity that is becoming increasingly recognized as a potential complication of bariatric surgery. This is a case of a 36-year-old woman brought by ambulance to a regional emergency department with abdominal pain, collapse, and gross haemodynamic instability 2 years post-laparoscopic sleeve gastrectomy. She received aggressive resuscitation in the emergency department but could not be stabilized and so underwent an emergency laparotomy. Intra-operatively, she was found to have a ruptured SAP with active bleeding, which was managed with a splenectomy. A high index of suspicion is required in any patient presenting with abdominal pain and circulatory collapse in the context of previous bariatric surgery. In rural or regional settings without immediate access to interventional radiology services, the most appropriate management option will almost invariably be an emergency laparotomy and splenectomy due to the risk of deterioration during patient transfer.
Comparative Genomics Provides Insights into Adaptive Evolution and Demographics of Bats
Authors: Liu Gaoming , Pan Qi , Zhu Pingfen , Guo Xinyu , Zhang Zhan , Li Zihao , Zhang Yaolei , Zhang Xiaoxiao , Wang Jiahao , Liu Weiqiang , Hu Chunyan , Yu Yang , Wang Xiao , Chen Weixiao , Li Meng , Yu Wenhua , Liu Xin , Seim Inge , Fan Guangyi , Zhou Xuming 
Published: November 2024

Abstract
Bats possess a range of distinctive characteristics, including flight, echolocation, impressive longevity, and the ability to harbor various zoonotic pathogens. Additionally, they account for the second-highest species diversity among mammalian orders, yet their phylogenetic relationships and demographic history remain underexplored. Here, we generated de novo assembled genomes for 17 bat species and 2 of their mammalian relatives (the Amur hedgehog and Chinese mole shrew), with 12 genomes reaching chromosome-level assembly. Comparative genomics and ChIP-seq assays identified newly gained genomic regions in bats potentially linked to the regulation of gene activity and expression. Notably, some antiviral infection-related gene under positive selection exhibited the activity of suppressing cancer, evidencing the linkage between virus tolerance and cancer resistance in bats. By integrating published bat genome assemblies, phylogenetic reconstruction established the proximity of noctilionoid bats to vesper bats. Interestingly, we found 2 distinct patterns of ancient population dynamics in bats and population changes since the last glacial maximum does not reflect species phylogenetic relationships. These findings enriched our understanding of adaptive mechanisms and demographic history of bats.
The evolution of dbSNP: 25 years of impact in genomic research
Authors: Phan Lon , Zhang Hua , Wang Qiang , Villamarin Ricardo , Hefferon Tim , Ramanathan Aravinthan , Kattman Brandi 
Published: November 2024

Abstract
The Single Nucleotide Polymorphism Database (dbSNP), established in 1998 by the National Center for Biotechnology Information (NCBI), has been a critical resource in genomics for cataloging small genetic variations. Originally focused on single nucleotide polymorphisms (SNPs), dbSNP has since expanded to include a variety of genetic variants, playing a key role in genome-wide association studies (GWAS), population genetics, pharmacogenomics, and cancer research. Over 25 years, dbSNP has grown to include more than 4.4 billion submitted SNPs and 1.1 billion unique reference SNPs, providing essential data for identifying disease-related genetic variants and studying human diversity. Integrating large-scale projects like 1000 Genomes, gnomAD, TOPMed, and ALFA has expanded dbSNP’s catalog of human genetic variation, increasing its usefulness for research and clinical applications. Keeping up with advancements such as next-generation sequencing and cloud-based infrastructure, dbSNP remains a cornerstone of genetic research supporting continued discoveries in precision medicine and population genomics. DATABASE URL: https://www.ncbi.nlm.nih.gov/snp.
Overcoming nucleotide bias in the nonenzymatic copying of RNA templates
Authors: Duzdevich Daniel , Carr Christopher E , Colville Ben W F , Aitken Harry R M , Szostak Jack W 
Published: November 2024

Abstract
The RNA World hypothesis posits that RNA was the molecule of both heredity and function during the emergence of life. This hypothesis implies that RNA templates can be copied, and ultimately replicated, without the catalytic aid of evolved enzymes. A major problem with nonenzymatic template-directed polymerization has been the very poor copying of sequences containing rA and rU. Here, we overcome that problem by using a prebiotically plausible mixture of RNA mononucleotides and random-sequence oligonucleotides, all activated by methyl isocyanide chemistry, that direct the uniform copying of arbitrary-sequence templates, including those harboring rA and rU. We further show that the use of this mixture in copying reactions suppresses copying errors while also generating a more uniform distribution of mismatches than observed for simpler systems. We find that oligonucleotide competition for template binding sites, oligonucleotide ligation and the template binding properties of reactant intermediates work together to reduce product sequence bias and errors. Finally, we show that iterative cycling of templated polymerization and activation chemistry improves the yields of random-sequence products. These results for random-sequence template copying are a significant advance in the pursuit of nonenzymatic RNA replication.
CRISPR-AsCas12f1 couples out-of-protospacer DNA unwinding with exonuclease activity in the sequential target cleavage
Authors: Song Xiaoxuan , Chen Ziting , Sun Wenjun , Yang Hao , Guo Lijuan , Zhao Yilin , Li Yanan , Ren Zhiyun , Shi Jin , Liu Cong , Ma Peixiang , Huang Xingxu , Ji Quanjiang , Sun Bo 
Published: November 2024

Abstract
Type V-F CRISPR-Cas12f is a group of hypercompact RNA-guided nucleases that present a versatile in vivo delivery platform for gene therapy. Upon target recognition, Acidibacillus sulfuroxidans Cas12f (AsCas12f1) distinctively engenders three DNA break sites, two of which are located outside the protospacer. Combining ensemble and single-molecule approaches, we elucidate the molecular details underlying AsCas12f1-mediated DNA cleavages. We find that following the protospacer DNA unwinding and non-target strand (NTS) DNA nicking, AsCas12f1 surprisingly carries out bidirectional exonucleolytic cleavage from the nick. Subsequently, DNA unwinding is extended to the out-of-protospacer region, and AsCas12f1 gradually digests the unwound DNA beyond the protospacer. Eventually, the single endonucleolytic target-strand DNA cleavage at 3 nt downstream of the protospacer readily dissociates the ternary AsCas12f1-sgRNA–DNA complex from the protospacer adjacent motif-distal end, leaving a staggered double-strand DNA break. The coupling between the unwinding and cleavage of both protospacer and out-of-protospacer DNA is promoted by Mg2+. Kinetic analysis on the engineered AsCas12f1-v5.1 variant identifies the only accelerated step of the protospacer NTS DNA trimming within the sequential DNA cleavage. Our findings provide a dynamic view of AsCas12f1 catalyzing DNA unwinding-coupled nucleolytic cleavage and help with practical improvements of Cas12f-based genome editing tools.
Transfer RNA supplementation rescues HARS deficiency in a humanized yeast model of Charcot-Marie-Tooth disease
Authors: Wilhelm Sarah D P , Kakadia Jenica H , Beharry Aruun , Kenana Rosan , Hoffman Kyle S , O’Donoghue Patrick , Heinemann Ilka U 
Published: November 2024

Abstract
Aminoacyl-tRNA synthetases are indispensable enzymes in all cells, ensuring the correct pairing of amino acids to their cognate tRNAs to maintain translation fidelity. Autosomal dominant mutations V133F and Y330C in histidyl-tRNA synthetase (HARS) cause the genetic disorder Charcot-Marie-Tooth type 2W (CMT2W). Treatments are currently restricted to symptom relief, with no therapeutic available that targets the cause of disease. We previously found that histidine supplementation alleviated phenotypic defects in a humanized yeast model of CMT2W caused by HARS V155G and S356N that also unexpectedly exacerbated the phenotype of the two HARS mutants V133F and Y330C. Here, we show that V133F destabilizes recombinant HARS protein, which is rescued in the presence of tRNAHis. HARS V133F and Y330C cause mistranslation and cause changes to the proteome without activating the integrated stress response as validated by mass spectrometry and growth defects that persist with histidine supplementation. The growth defects and reduced translation fidelity caused by V133F and Y330C mutants were rescued by supplementation with human tRNAHis in a humanized yeast model. Our results demonstrate the feasibility of cognate tRNA as a therapeutic that rescues HARS deficiency and ameliorates toxic mistranslation generated by causative alleles for CMT.
Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina
Authors: Zeng Xin , Gyoja Fuki , Cui Yang , Loza Martin , Kusakabe Takehiro G , Nakai Kenta 
Published: November 2024

Abstract
Despite known single-cell expression profiles in vertebrate retinas, understanding of their developmental and evolutionary expression patterns among homologous cell classes remains limited. We examined and compared approximately 240 000 retinal cells from four species and found significant similarities among homologous cell classes, indicating inherent regulatory patterns. To understand these shared patterns, we constructed gene regulatory networks for each developmental stage for three of these species. We identified 690 regulons governed by 530 regulators across three species, along with 10 common cell class-specific regulators and 16 highly preserved regulons. RNA velocity analysis pinpointed conserved putative driver genes and regulators to retinal cell differentiation in both mouse and zebrafish. Investigation of the origins of retinal cells by examining conserved expression patterns between vertebrate retinal cells and invertebrate Ciona intestinalis photoreceptor-related cells implied functional similarities in light transduction mechanisms. Our findings offer insights into the evolutionarily conserved regulatory frameworks and differentiation drivers of vertebrate retinal cells.
Building electrode/electrolyte interphases in aqueous zinc batteries via self-polymerization of electrolyte additives
Authors: Geng Yaheng , Xin Wenli , Zhang Lei , Han Yu , Peng Huiling , Yang Min , Zhang Hui , Xiao Xilin , Li Junwei , Yan Zichao , Zhu Zhiqiang , Cheng Fangyi 
Published: November 2024

ABSTRACT
Aqueous zinc batteries offer promising prospects for large-scale energy storage, yet their application is limited by undesired side reactions at the electrode/electrolyte interface. Here, we report a universal approach for the in situ building of an electrode/electrolyte interphase (EEI) layer on both the cathode and the anode through the self-polymerization of electrolyte additives. In an exemplified Zn||V2O5·nH2O cell, we reveal that the glutamate additive undergoes radical-initiated electro-polymerization on the cathode and polycondensation on the anode, yielding polyglutamic acid-dominated EEI layers on both electrodes. These EEI layers effectively mitigate undesired interfacial side reactions while enhancing reaction kinetics, enabling Zn||V2O5·nH2O cells to achieve a high capacity of 387 mAh g−1 at 0.2 A g−1 and maintain &gt;96.3% capacity retention after 1500 cycles at 1 A g−1. Moreover, this interphase-forming additive exhibits broad applicability to varied cathode materials, encompassing VS2, VS4, VO2, α-MnO2, β-MnO2 and δ-MnO2. The methodology of utilizing self-polymerizable electrolyte additives to construct robust EEI layers opens a novel pathway in interphase engineering for electrode stabilization in aqueous batteries.
Efficacy and Safety of DTG/3TC for Prophylaxis of HIV Perinatal Transmission: A Pilot Study (PREGNANCY)
Authors: Brites Carlos , Luz Estela , Nóbrega Isabella , Luz Ivana , Zajdenverg Roberto , de Ruiter Annemiek , Jones Bryn , Lorenzo Cynthia R , Travassos Ana Gabriela 
Published: November 2024

Abstract

Background
The prevention of perinatal human immunodeficiency virus (HIV) transmission depends on the safe and effective use of antiretroviral therapy (ART). Simplifying treatment reduces drug exposure for both mother and child. We evaluated the safety and efficacy of dolutegravir (DTG) plus lamivudine (3TC) for antiretroviral-naive pregnant women with HIV.

Methods
This proof-of-concept trial enrolled ART-naive pregnant women ≥15 years old with HIV infection and a gestational age between 14 and 28 weeks. Participants received a fixed-dose combination of DTG/3TC. Baseline HIV genotyping was performed. Participants were monitored at baseline, every 4 weeks, and at delivery. Infants were assessed at birth, 4 weeks, and 6 weeks of age. Outcomes included the proportion of women achieving an undetectable HIV type 1 plasma viral load (&lt;50 copies/mL) at delivery, therapy modification frequency, perinatal HIV transmission rate, and adverse events.

Results
Between January 2019 and March 2021, 20 women were enrolled. At baseline, the median CD4 cell count was 401.6 ± 113.6 cells/μL, increasing to 690.2 ± 266 cells/μL at delivery. Median viral load was 9514 copies/mL. All women achieved an undetectable viral load after an average of 40 days. No cases of perinatal HIV transmission were detected. No therapy modifications were necessary during the study, and no adverse events were related to the ART.

Conclusions
In this pilot trial, DTG/3TC demonstrated safety and efficacy, with all participants achieving viral suppression before delivery. There were no cases of perinatal HIV transmission and no drug-related adverse events. DTG/3TC can be an option for initial treatment of drug-naive pregnant women with HIV.
Diagnostic Value of Cross-priming Amplification Combined With CRISPR-Cas12b in Detecting Cell-free DNA in Tuberculous Pleural Effusion
Authors: Peng Lijun , Fang Tingting , Dai Lingshan , Cai Long 
Published: November 2024

Abstract

Background
Diagnosis of tuberculous pleural effusion (TPE) remains challenging. Studies have shown that detecting cell-free Mycobacterium tuberculosis (cf-TB) DNA in pleural effusion can improve TPE diagnosis. This study aimed to evaluate the diagnostic value of our recently developed TB One-Pot assay, which combines cross-priming amplification with CRISPR-Cas12b, in detecting cf-TB for TPE.

Methods
Pleural effusion samples were collected from inpatients with suspected TPE at Hangzhou Red Cross Hospital. After centrifugation, the precipitate was used for culture, Xpert, and pleural effusion cytologic testing, while the supernatant was used for biochemical and cf-TB assays, including TB One-Pot and the quantitative polymerase chain reaction method (cf-TB-PCR). Assessment of diagnostic performance was based on a comprehensive reference standard.

Results
A total of 115 patients were included: 88 TPE cases (diagnosed per the comprehensive reference standard) and 27 non-TPE cases. The sensitivity of TB One-Pot in detecting pleural cf-TB for diagnosing TPE was 64.8%, with an area under the curve (AUC) of 0.805, significantly superior to culture and Xpert (P &lt; .05). When compared with cf-TB-PCR (sensitivity, 53.4%; AUC, 0.767) and the adenosine deaminase assay (sensitivity, 52.3%; AUC, 0.761), TB One-Pot demonstrated slightly higher sensitivity and AUC, but the differences were not statistically significant (P &gt; .05). The specificity of TB One-Pot was 96.3%, while the specificity of the other tests was 100%, with no statistically significant differences (P &gt; .05).

Conclusions
cf-TB provides direct evidence of the etiology of TPE. TB One-Pot for detecting cf-TB in diagnosing TPE outperforms existing TB laboratory tests and may represent a more effective approach for TPE diagnosis in resource-limited settings.
Genomic alterations associated with early-stage disease and early recurrence in patients with colorectal cancer
Authors: Pappas Leontios , Quintanilha Julia C F , Huang Richard S P , Parikh Aparna R 
Published: November 2024

Abstract

Background
The molecular characterization of early-stage (1-3) colorectal cancer (CRC) remains incomplete, as opposed to metastatic disease, where comprehensive genomic profiling (CGP) is routinely performed. This study aimed to characterize the genomics of stages 1-3 versus IV CRC, and the genomics of patients recurring within 1 year of diagnosis.

Patients and Methods
Patients from a de-identified CRC clinico-genomic database who received Foundation Medicine testing (FoundationOne/FoundationOne CDx) during routine clinical care at approximately 280 US cancer clinics between March 2014 and June 2023 were included. Genomic alterations (GA) were compared by Fisher’s exact test.

Results
A total of 4702 patients were included; 1902 with stages 1-3 and 2800 with stage 4 disease. Among patients with stages 1-3 disease, 546 recurred within 1 year. Patients staged 1-3 had higher prevalence of microsatellite instability (MSI-H, 11.4% vs 4.5%, P &lt; .001), tumor mutational burden (TMB) ≥ 10 Mut/Mb (14.6% vs 6.8%, P &lt; .001), GA in RNF43 (11.2% vs 5.7%, P &lt; .001), MSH6 (3.9% vs 1.7%, P &lt; .001), MLH1 (2.3% vs 0.7%, P &lt; .001), and MSH2 (1.5% vs 0.6%, P &lt; .01) compared to those with stage 4 disease. Patients who recurred within 1 year had higher prevalence of MSI-H (13.2% vs 4.4%, P &lt; .001), TMB ≥ 10 Mut/Mb (16.2% vs 6.9%, P &lt; .001), BRAF V600E (17.2% vs 7.9%, P &lt; .003), GA in RNF43 (13.7% vs 5.3%, P &lt; .001), MSH6 (4.2% vs 1.6%, P = .035), and BRCA1/2 (6.2% vs 3.0%, P = .030). On recurrence, more patients received targeted therapy when CGP was performed before versus after first-line therapy (43% vs 19%, P &lt; .001).

Conclusions
Early-stage CRC patients can have distinct genomic profiles and CGP in this population can help expand access to targeted therapies.
Predicative Classes and Strict Potentialism
Authors: Linnebo Øystein , Shapiro Stewart 
Published: November 2024

Abstract
While sets are combinatorial collections, defined by their elements, classes are logical collections, defined by their membership conditions. We develop, in a potentialist setting, a predicative approach to (logical) classes of (combinatorial) sets. Some reasons emerge to adopt a stricter form of potentialism, which insists, not only that each object is generated at some stage of an incompletable process, but also that each truth is “made true” at some such stage. The natural logic of this strict form of potentialism is semi-intuitionistic: where each set-sized domain is classical, the domain of all sets or all classes is intuitionistic.
Complexity data science: A spin-off from digital twins
Authors: Emmert-Streib Frank , Cherifi Hocine , Kaski Kimmo , Kauffman Stuart , Yli-Harja Olli 
Published: November 2024

Abstract
Digital twins offer a new and exciting framework that has recently attracted significant interest in fields such as oncology, immunology, and cardiology. The basic idea of a digital twin is to combine simulation and learning to create a virtual model of a physical object. In this paper, we explore how the concept of digital twins can be generalized into a broader, overarching field. From a theoretical standpoint, this generalization is achieved by recognizing that the duality of a digital twin fundamentally connects complexity science with data science, leading to the emergence of complexity data science as a synthesis of the two. We examine the broader implications of this field, including its historical roots, challenges, and opportunities.