bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct epigenetic and transcriptional profiles of Epstein-Barr virus-positive and negative primary CNS lymphomas
Authors: Hai Ling , Friedel Dennis , Hinz Felix , Hoffmann Dirk C , Doubrovinskaia Sofia , Rohdjess Hannah , Weidenauer Katharina , Denisova Evgeniya , Scheffler Georg T , Kessler Tobias , Kourtesakis Alexandros , Herold-Mende Christel , Henegariu Octavian , Baehring Joachim M , Dietrich Jorg , Brors Benedikt , Wick Wolfgang , Sahm Felix , Kaulen Leon D 
Published: November 2024

Abstract

Background
Epstein-Barr virus (EBV)+ and EBV- primary CNS lymphomas (PCNSL) carry distinct mutational landscapes, but their transcriptional and epigenetic profiles have not been integrated and compared. This precludes further insights into pathobiology and molecular differences, relevant for classification and targeted therapy.

Methods
Twenty-three EBV- and 15 EBV+ PCNSL, histologically classified as diffuse large B-cell lymphomas, were subjected to RNA-sequencing and EPIC methylation arrays. Unsupervised clustering analyses were performed. Differentially expressed and differentially methylated genes were identified and integrated.

Results
Two distinct transcriptional clusters were found, which separated EBV- and EBV+ PCNSL (P &lt; .0001). The EBV+ transcriptional signature contained genes (GPR15, FCER2/CD23, SLAMF1/CD150) closely regulated by EBV oncogenes in B cells. Pathway enrichment analysis uncovered enhanced B-cell receptor (BCR) and WNT/beta-catenin signaling in EBV- lymphomas, whereas Interleukin-10, NOTCH, and viral life cycle pathways were upregulated in EBV+ PCNSL. Correspondingly, BCR-associated SYK kinase activity was enriched in EBV- tumors while JAK2 was overrepresented in EBV+ PCNSL. Epigenetic profiling revealed reduced global promoter methylation in EBV+ PCNSL. Two methylation clusters were recognized, which separated EBV- and EBV+ PCNSL (P &lt; .0001). Epigenetic profiles were distinct from 2,788 other brain tumor and nonmalignant reference samples. Promoter region hypermethylation of CD79B, a BCR subunit critical for sustained proliferation in EBV- disease, highly correlated (R = −0.7) with its transcriptional downregulation in EBV+ PCNSL.

Conclusions
EBV+ and EBV- PCNSL harbor distinct transcriptional and epigenetic profiles, corroborating them as distinctive biological subtypes. Uncovered differences provide novel insights into their pathobiology, may guide molecular diagnostics and targeted therapies.
Natural History of High-Risk Human Papillomavirus in Kenyan and South African Women: Implications for Vaccination Campaigns and Cervical Cancer Screening Programs
Authors: Happel Anna-Ursula , Budiawan Elvira , Onono Maricianah , Innes Steve , Palanee-Phillips Thesla , Heuvel Janine , Rakiep Adeebah , Kellow-Webb Sarah , Ongere Joan , Wakhungu Imeldah , Mkhize Zandile , Kapa La-Donna , Sigcu Nompumelelo , Dabee Smritee , Nair Gonasagrie , Scoville Caitlin , Mugo Nelly R , Williamson Anna-Lise , Passmore Jo-Ann S , Jaspan Heather B , Heffron Renee 
Published: November 2024

Abstract

Objective
Human papillomavirus (HPV) vaccines and DNA testing roll out in resource-constrained settings. We evaluated the natural history of HPV infections in African women to contribute to normative guidance.

Methods
Women aged 16 to 35 years were enrolled from 3 sites in South Africa and Kenya and followed quarterly for 18 months. A subset was recalled 5 years postenrollment, when Papanicolaou smears were conducted. Endocervical swabs were tested for 36 HPV genotypes by HPV Direct Flow. Logistic regression models identified correlations between demographic, biological, or behavioral factors and baseline high-risk HPV (HR-HPV).

Results
At enrollment, 158 of 311 women (median age, 23 years; IQR, 20–27) had at least 1 HR-HPV genotype. HPV-52 (13.5%), HPV-16 (9.5%), HPV-58 (9.0%), HPV-18 (8.4%), and HPV-35 (8.4%) were most common. Coinfection with low-risk HPVs (odds ratio, 2.65; 95% CI, 1.59–4.45) were associated with HR-HPV positivity, while reported condom use (odds ratio, 0.57; 95% CI, .34–.98) and older age were protective. Of women with HR-HPV at enrollment, 87.3% cleared at least 1 HR-HPV infection over 18 months and 64.6% cleared all such infections. Few (1.9%) had evidence of high-grade cervical abnormalities, among which HPV-35 was the most prevalent during the study.

Conclusions
The high prevalence of HR-HPV emphasizes that HPV vaccination, screening, and testing campaigns in Africa are important. Nonvaccine HPV-35 was as common as HPV-18, suggesting the need to supplement current vaccines with this genotype. HR-HPV clearance was also common, highlighting that clear messaging is needed from health care providers to patients while discussing HPV DNA testing results.
Phylogenetic analyses support flush-pursuit foraging and flocking behaviors as evolutionary drivers of flash plumage signals in North American passerines
Authors: Benedict Lauryn , Jones Harrison , Robinson Scott , P. McEntee Jay 
Published: November 2024

ABSTRACT
Animal coloration patterns are wildly variable. Despite this, there are plumage traits that occur similarly across taxonomic groups, suggesting the possible action of widespread selective regimes. Here, we investigate why so many avian species have “flash” plumage signals—color patches that are not visible when an animal is still but become visible with movement. Flash patches have been hypothesized to warn conspecifics of danger and coordinate prey escape behaviors among flocking species. Other hypotheses suggest that flash signals function in prey capture, species recognition, or social (including sexual) selection. To test these hypotheses, we scored 326 species of North American passerines for the presence of 3 flash and 2 static patches on bird rumps, wings, and tails. We combined those data with social and ecological information from available datasets and used phylogenetically controlled analyses to test the hypotheses that flash color patch evolution is driven by (1) flocking-associated behaviors, (2) social selection, and/or (3) foraging strategy. Our data show that flash signals are common among North American passerines, occurring in 54% of species, and that most wing and tail patches are white in color. We recovered evidence that rump flash patches can be predicted by winter flocking, migration, and diets specialized on plants, consistent with functions in flock cohesion or species recognition, as previously reported in shorebirds. Flash plumage patch evolution was not predicted by breeding system or territoriality and was therefore not consistent with social selection as a broad evolutionary driver. In contrast, we found evidence that the flush-pursuit foraging strategy predicts the presence of avian wing and tail flash patches. These results fit with multiple single-taxon studies that have shown flash plumage signals to function in flush-pursuit foraging. Our results underscore that natural selection, not just social selection, can drive the evolution of conspicuous coloration in animals.
Using unsupervised machine learning to find profiles of domestic abuse perpetrators
Authors: Hadjimatheou Katerina , Quiroz Flores Alejandro , Weir Ruth , Skevington Taylor 
Published: November 2024

Abstract
In this article we use unsupervised machine learning to discover hidden structures and patterns in a longitudinal police dataset of domestic abuse suspects, to provide a police force with an overarching or ‘baseline’ picture of how domestic abuse manifests locally. 3 algorithms were used to analyse 12 variables in a longitudinal dataset of over 40,000 suspects, organising them into discreet “clusters” or profiles with common characteristics and highlighting the differences and continuities between these. The quantitative findings, which highlighted clusters of abuse that had not previously been ‘on the radar’ of domestic abuse services in the specific force area, were then contextualised through qualitative interviews with a range of stakeholders to help identify priorities for intervention and further research. Our study shows how cutting-edge quantitative methods can be applied to improve understanding of prevalence and features of police-recorded abuse; draw attention to previously under-addressed types of abuse; serve as the groundwork for further, more in-depth research; and provide an evidence-base for local decision-making.
Perceptions of grant peer reviewers: a mixed methods study
Authors: Schmaling Karen B , Evenson Gabriel R , Marble Blake K , Gallo Stephen A 
Published: November 2024

Abstract
Peer review is integral to the evaluation of grant proposals. Reviewer perceptions and characteristics have received limited study, especially their associations with reviewers’ evaluations. This mixed methods study analyzed the unstructured comments of 270 experienced peer reviewers after they scored proposals based on mock overall evaluations written by the primary reviewer. Comments were coded for topical content and emotional valence blind to participants’ characteristics. The most frequent comments were about their experiences with peer review with negative valence. Additional themes were identified within the content codes, including concerns about favoritism and inappropriate behavior observed in other reviewers. Reviewers who made negative comments gave poorer scores than reviewers who did not. Reviewer mindsets are understudied: negative moods and cognitions may affect reviewers’ overall evaluative severity. Future studies should further investigate these associations.
Evaluating participatory research projects through a harmonized, online, self-reflection, and impact-assessment methodology
Authors: Santoro Lamelas Valeria , Valente Riccardo , Gresle Anne-Sophie 
Published: November 2024

Abstract
Participatory research can be promoted by scientific intermediary units, such as Science Shops. The overarching goal of these initiatives is thereby to foster a process of co-creation of the research questions to address societal needs that are relevant to scientific research and society at large. The InSPIRES project was a Horizon Europe initiative from 2017 to 2021 with the primary objective of expanding the implementation of Science Shops across Europe and internationally. Within the framework of this project, a harmonized, self-reflection and impact assessment methodology has been developed to evaluate five dimensions of participatory research: knowledge democracy, citizen-led research, participatory dynamics, integrity, and transformative change. In this article, we report the results of 58 projects implemented in Africa, Asia and Europe. We present the results of quantitative and qualitative data analysis with a view towards encouraging the debate on the challenges involved in designing a standardized evaluation tool to capture the multiplicity of processes involved in participatory research. Results showed that the participatory research processes increase access to knowledge and promote the forging of alliances and relations of trust through respectful dialogue from multiple standpoints. The analysis also retraces some critical points with regard to the democratization of knowledge and the scope for social transformation, which would require further scrutiny. All in all, the proposed InSPIRES assessment tool proved to be a straightforward approach to systematically evaluate key dimensions of participatory research across different phases and project roles that could serve as a starting point for future similar initiatives.
Implementation of OSL nanoDot dosimetry in different treatment techniques for head and neck cancer
Authors: Negrete-Hernandez Ingrid M , Lozano Ivonne B , Roman-Lopez Jesus , Guzman-Castañeda Jesus I 
Published: November 2024

Abstract
In recent decades, technological advances have been made in the field of radiotherapy and with it the emergence of new dosimetric systems for their calibration and commissioning, among other uses. Such is the case of the measurement in the build-up region, where there is no charged-particle equilibrium, which is reflected in the increase in surface dose for patient treatments and potential skin toxicities as a secondary effect. This study utilizes optically stimulated dosemeters (nanoDot) and the radiochromic film (EBT3) to measure skin doses in patients with head and neck cancer who received radiotherapy. Accurately depicting 15 patients with different diagnoses from 3 linear accelerators using 3D, intensity modulated radiation therapy, or volumetric arc therapy/RapidArc technology, these results were compared with those calculated in the treatment planning system (TPS) and obtaining a percentage of variation for the EBT3 ranged from 0.30% to 6.15%, while that observed for the nanoDot was from 0.51% to 4.88%. This difference may be attributed to the reproducibility of placement in patients. Therefore, for clinical use, nanoDot dosemeters are a viable alternative for in vivo dosimetry where rapid validation of planning system results is required.
Academia–industry collaboration, intellectual property rights enforcement, and scientific performance: evidence from Chinese Academy of Sciences
Authors: Du Xinyue , Feng Feng 
Published: November 2024

Abstract
Public research institutes (PRIs) are an important part of the academic research world and also tasked with collaborating with industry to contribute to knowledge economics. This raises conflicts between disseminating public knowledge and appropriating through secrecy or intellectual property. However, there is little empirical evidence on the effect of PRIs’ academia–industry collaboration on scientific performance. Our research fills this gap by providing an empirical analysis at the Chinese Academy of Sciences (CAS). Based on a newly compiled dataset about CAS, this study explores the effect of academia–industry collaboration on scientific performance and the moderating role of intellectual property rights (IPR) enforcement. The empirical results reveal that there is an inverse U-shaped relationship between academia–industry collaboration and scientific performance and IPR enforcement steepens this curvilinear relationship. These findings suggest that policymakers should be mindful of possible adverse consequences for scientific performance and strengthen the IPR enforcement, when encouraging academia–industry collaboration.
A critique of the use of species and below-species taxonomic terms for viruses—time for change?
Authors: Simmonds Peter 
Published: November 2024

Abstract
The International Committee for the Taxonomy of Viruses (ICTV) regulates assignment and names of virus species and higher taxa through its taxonomy proposal and ratification process. Despite using similar taxonomic ranks to those used elsewhere in biology, the ICTV has maintained the principle that species and other taxa are strictly categories with a formal nomenclature, whereas the viruses as objects are referenced through a parallel inventory of community-assigned virus names. This is strikingly different from common and scientific name synonyms for species used elsewhere in biology. The recent introduction of binomial names for virus species resembling biological scientific names has intensified this confusion in terms within the virology community and beyond. The ICTV taxonomy furthermore does not engage with or regulate classification below species and consequently lacks taxonomic terms or descriptions for important viral pathogens such as polioviruses, severe acute respiratory syndrome coronavirus type 2, HIV-1, and avian influenza as examples. The consequent reliance on community-adopted virus names, genotypes, and other categories often lacks clarity for clinical, biocontainment, and other regulatory purposes. This article proposes a revision of rules and procedures for species and below-species level classification. It recasts virus and virus species names as ‘common’ and ‘scientific’ names that are used in other biology nomenclature codes, each with expanded reference to both object and taxon. It further advocates the creation of a formal below-species taxonomic rank to define a new inventory of approved taxa and specified nomenclature below species. Adoption of the proposed changes will realign virus taxonomy with other biological nomenclatural codes and provide greater transparency and clarity in virology, medical, and regulatory fields.
Effect of a Machine Learning-Derived Early Warning Tool With Treatment Protocol on Hypotension During Cardiac Surgery and ICU Stay: The Hypotension Prediction 2 (HYPE-2) Randomized Clinical Trial
Authors: Schuurmans Jaap , Rellum Santino R. , Schenk Jimmy , van der Ster Björn J. P. , van der Ven Ward H. , Geerts Bart F. , Hollmann Markus W. , Cherpanath Thomas G. V. , Lagrand Wim K. , Wynandts Paul R. , Paulus Frederique , Driessen Antoine H. G. , Terwindt Lotte E. , Eberl Susanne , Hermanns Henning , Veelo Denise P. , Vlaar Alexander P. J. 
Published: November 2024

OBJECTIVES:
Cardiac surgery is associated with perioperative complications, some of which might be attributable to hypotension. The Hypotension Prediction Index (HPI), a machine-learning-derived early warning tool for hypotension, has only been evaluated in noncardiac surgery. We investigated whether using HPI with diagnostic guidance reduced hypotension during cardiac surgery and in the ICU.

DESIGN:
Randomized clinical trial conducted between May 2021 and February 2023.

SETTING:
Single-center study conducted in an academic hospital in the Netherlands.

PATIENTS:
Adults undergoing elective on-pump coronary artery bypass grafting, with or without single heart valve surgery, were enrolled if a mean arterial pressure (MAP) greater than or equal to 65 mm Hg was targeted during the surgical off-pump phases and ICU stay. After eligibility assessment, 142 of 162 patients approached gave informed consent for participation.

INTERVENTIONS:
Patients randomized 1:1 received either diagnostic guidance in addition to standard care if HPI reached greater than or equal to 75 (n = 72) or standard care alone (n = 70).

MEASUREMENTS AND MAIN RESULTS:
The primary outcome was the severity of hypotension, measured as time-weighted average (TWA) of MAP less than 65 mm Hg. Secondary outcomes encompassed hypertension severity and intervention disparities. Of 142 patients randomized, 130 were included in the primary analysis. The HPI group showed 63% reduction in median TWA of hypotension compared with the standard care group, with a median of differences of –0.40 mm Hg (95% CI, –0.65 to –0.27; p < 0.001). In the HPI group, patients spent a median 28 minutes (95% CI, 17–44 min) less in hypotension, with a measurement duration of 322 minutes in the HPI group and 333 minutes in the standard care group. No significant differences were observed in hypertension severity, treatment choice, or fluid, vasopressors, and inotrope amounts.

CONCLUSIONS:
Using HPI combined with diagnostic guidance on top of standard care significantly decreased hypotension severity in elective cardiac surgery patients compared with standard care.
The Application of Sleep Deprivation Combined With Chloral Hydrate on Pediatric Dermatological Surgery
Authors: Yanling Dang , Lijuan Yang , Yingxin Ma , Dewu Zhang 
Published: November 2024

BACKGROUND
In small dermatological surgeries for infant and child patients, it is required that the child be in a quiet state. However, general anesthesia not only requires the participation of professional anesthesiologists for surgery but also has a high cost and anesthesia risks. Parents have a low acceptance rate. At present, chloral hydrate combined with local anesthesia for sedation has been widely used in various pediatric examination and treatment projects.

OBJECTIVE
To retrospectively analyze the impact of sleep deprivation on pediatric dermatological surgery performed under local anesthesia following chloral hydrate enema.

METHOD
A retrospective review was conducted on 280 pediatric patients who underwent dermatological surgery or tissue pathology biopsy from September 2022 to March 2023. The study analyzed the success rate of local anesthesia following chloral hydrate enema under different states of wakefulness and whether the surgical processes for infants and toddlers were conducted smoothly.

RESULTS
Among the 215 patients who underwent sleep deprivation, the successful completion rate of the surgery reached 87%. By contrast, only 29.2% of the 65 patients who did not experience sleep deprivation completed the surgery. The patients' vital signs remained stable throughout the surgery, and no adverse reactions occurred when the patients were awakened 30 minutes to 1 hour after the surgery.

CONCLUSION
Sleep deprivation in infants and toddlers can enhance the anesthetic and immobilization effects in dermatological surgery, significantly reducing the patients' negative emotions, such as crying and fear, increasing the patient's cooperation during the surgery, and improving parental satisfaction. The clinical operation is convenient and thus worth promoting extensively.
Rates of Receiving Medication for Opioid Use Disorder and Opioid Overdose Deaths During the Early Synthetic Opioid Crisis: A County-level Analysis
Authors: Santaella-Tenorio Julian , Rivera-Aguirre Ariadne , Hepler Staci A. , Kline David M. , Cantor Jonathan , DeYoreo Maria , Martins Silvia S. , Krawczyk Noa , Cerda Magdalena 
Published: November 2024

Background:
Medications for opioid use disorder are associated with a lower risk of drug overdoses at the individual level. However, little is known about whether these effects translate to population-level reductions. We investigated whether county-level efforts to increase access to medication for opioid use disorder in 2012–2014 were associated with opioid overdose deaths in New York State during the first years of the synthetic opioid crisis.

Methods:
We performed an ecologic county-level study including data from 60 counties (2010–2018). We calculated rates of people receiving medication for opioid use disorder among the population misusing opioids in 2012–2014 and categorized counties into quartiles of this exposure. We modeled synthetic and nonsynthetic opioid overdose death rates using Bayesian hierarchical models.

Results:
Counties with higher rates of receiving medications for opioid use disorder in 2012-2014 had lower synthetic opioid overdose deaths in 2016 (highest vs. lowest quartile: rate ratio [RR] = 0.33, 95% credible interval [CrI] = 0.12, 0.98; and second-highest vs. lowest: RR = 0.20, 95% CrI = 0.07, 0.59) and 2017 (quartile second-highest vs. lowest: RR = 0.22, 95% CrI = 0.06, 0.83), but not 2018. There were no differences in nonsynthetic opioid overdose death rates comparing higher quartiles versus lowest quartile of exposure.

Conclusions:
A spatio-temporal modeling approach incorporating counts of the population misusing opioids provided information about trends and interventions in the target population. Higher rates of receiving medications for opioid use disorder in 2012–2014 were associated with lower rates of synthetic opioid overdose deaths early in the crisis.