bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differentiation of genome‐wide DNA methylation between japonica and indica rice
Authors: Yan Tao , Kuang Liuhui , Gao Fei , Chen Jian , Li Lin , Wu Dezhi 
Published: January 2025

SUMMARYRice (Oryza sativa L.) subspecies japonica and indica show distinct morphological and genetic differentiation. However, the differences in the genome‐wide DNA methylation and its effects on gene expression and metabolic levels between japonica and indica rice remain unclear. In this study, we investigated the genome‐wide DNA methylation, transcriptomes and metabolomes of 12 representative japonica and indica rice accessions, to reveal the differentiation between rice subspecies. We detected 83 327 differentially methylated regions (DMRs) and 14 903 DMR‐associated genes between two subspecies. Indica rice showed significantly lower levels of the CG, CHG, and CHH methylation compared with japonica rice. Subsequently, we identified 5596 differentially expressed genes between the two subspecies, predominantly enriched in pathways related to carbohydrate and amino acid metabolism. By integrating DNA methylation with transcriptomic data, a significant correlation was established between methylation patterns and the expression level of key agronomic genes in rice. Furthermore, multi‐omics analyses reveal that carbohydrate metabolism pathways, especially the tricarboxylic acid (TCA) cycle metabolites, are remarkable differentiation between rice subspecies. These results provide a foundation for future studies in rice domestication and genetic improvement.
Effect of an adjustable ceiling to prevent premature rising attempts after general anesthesia in healthy ponies and horses: A pilot study
Authors: Lindqvist Anna , Nyman Görel , Rydén Anneli , Wattle Ove 
Published: January 2025

AbstractObjectiveThis study aimed to assess and compare the recovery of ponies and horses following general anesthesia in two different settings: a recovery box with an inflexible, adjustable ceiling, and free recovery without restraints. Our primary objective was to evaluate the effect of adjustable ceilings on the prevention of premature attempts to rise during recovery. The secondary aim was to compare the physiological stress indicators during recovery.Study designProspective, randomized, experimental study.AnimalsSix healthy ponies and 10 healthy horses.MethodsThis study used a crossover design with two settings: an inflexible, adjustable ceiling and free recovery. Recovery was scored using a quality scoring system. Heart rate, and lactate, glucose, and cortisol levels were analyzed and compared between the animals and recoveries.ResultsAll animals had a higher recovery quality (p = .026) with an adjustable ceiling than with free recovery. No differences were observed in glucose level or heart rate between the two settings. However, horses had higher blood lactate, 2.9 ± 1.2 mmol/L versus 1.6 ± 0.7 mmol/L (p = .025), and serum cortisol, 184 ± 81 nmol/L versus 93 ± 20 nmol/L (p = .031) in restricted recovery than free recovery, respectively.ConclusionAn inflexible, adjustable ceiling improved the quality of recovery and prevented premature rising attempts; however, it was associated with increased lactate and cortisol levels, indicating an increased level of stress.Clinical significanceLimiting premature rising attempts with an adjustable ceiling during recovery phase has the potential to improve the quality of recovery in horses. Further research is needed to draw conclusions for clinical use.
Vascular health and exercise in females throughout the lifespan: Exploring puberty, pregnancy and menopause
Authors: Miller Kathleen B. , Moir M. Erin , Fico Brandon G. 
Published: January 2025

AbstractThis narrative review highlights the impact of exercise on vascular health in females over the lifespan with an emphasis on puberty, pregnancy and menopause. These events encompass substantial changes in sex hormone levels, particularly oestrogens and progesterone. They are also accompanied by distinct adaptations of the central, peripheral and cerebral vasculature. Regular exercise is an effective mechanism to reduce vascular risk in females of all ages, especially for those at higher risk for vascular disorders. However, there are large variabilities in the vascular adaptations to exercise in females that may be related to circulating sex hormone levels. In addition, exogenous hormones, such as oral contraceptives taken after puberty or hormonal replacement therapy taken to mitigate symptoms of menopause, may interact with exercise‐induced changes in vascular function. We highlight how more research is needed to understand the optimal exercise interventions to promote vascular health in females across the lifespan, especially during times of hormonal transition.
Assessing the threat of
Yersinia pestis
harboring a multi-resistant IncC plasmid and the efficacy of an antibiotic targeting LpxC
Authors: Lemaitre Nadine , Dewitte Amélie , Rakotomanimana Faniry , Gooden David , Toone Eric , Rajerison Minoarisoa , Zhou Pei , Sebbane Florent 
Published: January 2025

ABSTRACT

Self-transmissible IncC plasmids rapidly spread multidrug resistance in many medically important pathogens worldwide. A large plasmid of this type (pIP1202, ~80 Kb) has been isolated in a clinical isolate of
Yersinia pestis
, the agent of plague. Here, we report that pIP1202 was highly stable in
Y. pestis-
infected mice and fleas and did not reduce
Y. pestis
virulence in these animals. Although pIP1202 inflicted a fitness cost in fleas (but not in mice) when the insects fed on blood containing a mixture of plasmid-free and plasmid-bearing strains, such a co-infection scenario has never been reported in nature, indicating that pIP1202 could persist in
Y. pestis
strains. Despite being resistant to commonly used antibiotic treatments, we show that plague caused by
Y. pestis
harboring the pIP1202 plasmid is effectively cured by LPC-233—a potent inhibitor of the essential LpxC enzyme in the lipid A biosynthetic pathway. Taken as a whole, our data highlight the alarming threat posed by
Y. pestis
harboring multidrug-resistant IncC plasmids that may persist in wild animals as a reservoir for long periods without antibiotic pressure and illuminate the impact of antibiotics with a novel mode of action against such a biothreat.
clustur: an R package for clustering features using sparse distance matrices
Authors: Johnson Gregory , Westcott Sarah L. , Schloss Patrick D. 
Published: January 2025

ABSTRACT

The clustur R package implements the
de novo
clustering algorithms found in the mothur software package for assigning 16S rRNA gene sequences to operational taxonomic units (OTUs). Making these algorithms accessible through the R ecosystem will foster their further development, broader application, and integration within other R packages.
ConciliaMed: an interactive mobile and web tool to reconcile chronic medications of patients undergoing elective surgery
Authors: Ciudad-Gutiérrez Pablo , Suárez-Casillas Paloma , Alfaro-Lara Eva Rocío , Santos-Rubio Maria Dolores , Santos-Ramos Bernardo , Guisado-Gil Ana Belén 
Published: January 2025

ObjectiveThe last decade has seen exponential growth in electronic health tools. However, only a limited number of electronic medication reconciliation tools have been developed and implemented in healthcare settings. Here, we present ConciliaMed, a mobile and web-based tool for healthcare professionals to reconcile the chronic medications of patients undergoing elective surgery.MethodsA research team of pharmacists and internists worked together with a technology company to design and develop ConciliaMed. Evidence-based guidelines were collected for inclusion in the tool. A group of experts conducted a simulation with a preliminary version of ConciliaMed to identify bugs and technical improvements and to assess their satisfaction with the application. The final prototype of the tool was disseminated through clinical meetings and the Google Store.ResultsFour easy-to-use and interactive modules can be used to reconcile chronic medications through the app, while the web platform is designed for consultation and learning. A higher level of satisfaction with the tool was achieved by the test participants (4.67±0.58). The triggering of dose and duplication alerts for users or the integration of ConciliaMed with electronic prescription systems were some of the more requested adaptations by the test participants.DiscussionThe ability to generate an editable reconciliation report or transfer information between users are some of the features of ConciliaMed that encourage its use. The integration of ConciliaMed into the healthcare workflow is expected.ConclusionThe web platform is freely available online (https://conciliamed.chronic-pharma.com), as is the mobile application through the Google Store, making it easily accessible to healthcare professionals.
Systematic literature review on Calcium Pyrophosphate Deposition (CPPD) nomenclature: condition elements and clinical states— A Gout, Hyperuricaemia and Crystal-Associated Disease Network (G-CAN) consensus project
Authors: Jauffret Charlotte , Adinolfi Antonella , Sirotti Silvia , Cirillo Daniele , Ingrao Luca , Lucia Alessandro , Cipolletta Edoardo , Filippucci Emilio , Tedeschi Sara , Terkeltaub Robert , Dalbeth Nicola , Pascart Tristan , Filippou Georgios 
Published: January 2025

ObjectivesThe Gout, Hyperuricaemia and Crystal-Associated Disease Network (G-CAN) has developed a calcium pyrophosphate deposition (CPPD) nomenclature project. This systematic literature review constituted its first step and aimed to provide a state-of-the-art analysis of the medical literature of the last 20 years.MethodsA systematic literature search was undertaken in thePubMed,CochraneandEmbasedatabases between 2000 and 2022, restricted to studies on humans and in the English language. Eight reviewers independently and manually extracted labels related to CPPD concepts, according to an a priori list generated by the authors: pathogenic conditions and pathogenic crystal labels, elementary imaging condition elements and asymptomatic and symptomatic condition states. For each concept, labels were analysed to determine their frequency.ResultsAmong the 2375 articles identified, 886 articles were included, of which 394 (44.5%) were case reports and 169 (19.0%) were scoping reviews. Overall, the most common labels used to designate the pathogenic condition were ‘pseudogout’in 365/783 (46.6%), ‘chondrocalcinosis’in 207/783 (26.4%) and ‘calcium pyrophosphate deposition disease’in 181/783 (23.1%) occurrences. The most common abbreviation was ‘CPPD’ in 312/390 (80.0%), but with different meanings. CPPD clinical phenotypes were often described as ‘pseudo-form’ labels.ConclusionThose results demonstrate the heterogeneity of labels used to describe CPPD condition concepts, with wide variation in condition labels in the medical literature. This work provides the rationale and basis to achieve agreement about CPPD technical nomenclature.
Association between HIV risk perception, knowledge of biomedical prevention and sexual behaviour among sub-Saharan African immigrants living in a precarious situation in France
Authors: Coulibaly Karna , Gosselin Anne , Derche Nicolas , Mbiribindi Romain , Desgrées du Loû Annabel 
Published: January 2025

ObjectivesSub-Saharan African immigrants are particularly affected by HIV in France, with many acquiring the infection after migration due to precarious circumstances that increase their vulnerability. This study aimed to explore the association between HIV risk perception, knowledge of biomedical HIV prevention methods and sexual behaviours among sub-Saharan African immigrants living in precarious conditions in the greater Paris area.MethodsThis cross-sectional study analysed data from 614 participants in the MAKASI project, conducted in the greater Paris area (2019–2020). Sociodemographic characteristics, living conditions, knowledge of biomedical HIV prevention methods (postexposure prophylaxis, treatment as prevention and pre-exposure prophylaxis (PrEP)) and sexual behaviours were described by sex using Pearson’s χ2tests. HIV risk perception, defined as self-reported exposure to HIV comparable to or greater than the general population, was analysed by participant characteristics. A multivariable logistic regression model identified factors associated with HIV risk perception using variables with a significance threshold of 20%.ResultsMost participants (76.5%) were men, with a median age of 34 years (IQR: 29–41) and living in precarious conditions. Forty-one per cent of respondents reported perceiving their HIV exposure risk as comparable to or greater than the general population. Participants aware of PrEP (adjusted OR (aOR) =2.60 (1.17–5.80); p<0.020) and those who had sex with occasional partners without a condom within in the 3 months preceding the survey (aOR=1.89 (1.12–3.18); p<0.017) were more likely to report the same or greater risk of HIV exposure.ConclusionsOur findings reveal that PrEP knowledge and sex with occasional partners, particularly participants who did not use condoms, are associated with increased HIV risk perception among sub-Saharan African immigrants. Further research should explore the relationship between PrEP uptake and HIV risk perception in this population.Trial registration numberNCT04468724
Olaparib, temozolomide and concomitant radiotherapy for partially or biopsy-only glioblastoma first-line treatment: results from the OLA-TMZ-RTE-01 phase 1 study
Authors: Stefan Dinu , Lesueur Paul , Lequesne Justine , Feuvret Loic , Bronnimann Charlotte , Castéra Marie , Brachet Pierre-Emmanuel , Hrab Ioana , Ducloie Mathilde , Lacroix Joëlle , Lecornu Marie , Braux Grégoire , Christy François , Sunyach Marie-Pierre , Cohen-Jonathan Moyal Elizabeth , Kao William , Faisant Maxime , Emery Evelyne , Grellard Jean-Michel , Sichel Francois , Laurent Carine , Fontanilles Maxime , Clarisse Bénédicte 
Published: January 2025

Abstract
Background: Radio-chemotherapy remains the mainstay of glioblastoma first-line treatment after extended surgery, but the prognosis is still poor. PARP inhibitors like olaparib may improve glioblastoma outcomes. We implemented a phase 1-2a trial to assess the safety and efficacy of olaparib combined with standard radio-chemotherapy as a first-line treatment in unresected glioblastoma patients. We herein present results of phase 1. Methods: Based on the Stupp regimen, two sequential dose escalations of olaparib were performed to distinguish the radiotherapy period and the maintenance period for assessing the maximum tolerated dose (MTD) of olaparib separately for each treatment period. Dose escalations were performed by a TITE-CRM (TIme-To-Event Continual Reassessment Method). Results: A total of 30 pts were enrolled: 20 (66.7%) men, median age 59 years [range 25-70], 12 (42.9%) Eastern Cooperative Oncology Group (ECOG) performance status of 0. Among them, 16 and 11 pts were assessable for determining MTD in each period. Hematological dose-limiting toxicities were experienced by 4 and 1 patients in each sequential dose escalation, respectively. MTD was olaparib 100 mg twice daily for 3 days a week in concomitant during both the radio-chemotherapy and maintenance periods of the standard treatment. Median progression-free and overall survival was 6.2 and 19.8 months, respectively. The 2-year survival rate was 36.7% [22.9-58.7]. Conclusions: Intermittent dosing of olaparib at radiosensitizing concentrations in concomitant with the Stupp protocol has an acceptable safety profile with promising outcomes in unresectable glioblastoma patients. Further efficacy determination is ongoing in the phase 2a step.
Abstract TMP64: Ultra-Early Hematoma Expansion is Associated with Ongoing Hematoma Growth and Functional Outcomes: A STOP-MSU Secondary Analysis
Authors: Mutimer Chloe , Wu Teddy , Zhao Henry , churilov leonid , Campbell Bruce , Cheung Andrew , Meretoja Atte , Kleinig Timothy , Choi Philip , Ma Henry , Cloud Geoffrey , Grimley Rohan , Shah Darshan , Ranta Anna , Mahawish Karim , Yogendrakumar Vignan , Sharma Gagan , Davis Stephen , Donnan Geoffrey , Yassi Nawaf 
Published: January 2025

Introduction:
Hematoma expansion (HE) is strongly associated with mortality and disability in intracerebral hemorrhage (ICH). While it is accepted that the majority of this expansion occurs early after onset, there is limited data on HE and associations with outcome in the ultra-early time window (within 3 hours of symptom onset). We aimed to (a) estimate the incidence of HE within the ultra-early period of ICH, (b) describe hematoma growth dynamics over time, and (c) investigate the associations between ultra-early HE and clinical outcomes after ICH.

Methods:
We performed a planned secondary analysis of the STOP-MSU international multicenter randomized controlled trial. The trial compared tranexamic acid (TXA) with placebo in 201 patients with primary ICH presenting within 2 hours of symptom onset. Repeat CT imaging 1 hour after treatment commencement was optional, and patients who underwent this ultra-early re-imaging were included in this descriptive study. Hematoma expansion was defined as growth by either >33% or >6ml from the baseline hematoma volume.

Results:
We included 105 patients with ultra-early re-imaging (median age 66 years, 40% female, 53% TXA). Median time from onset to baseline imaging was 74min (IQR 56-87min), and between baseline and ultra-early re-imaging was 95min (IQR 74-132min). Forty-one patients (39%) had ultra-early HE. These patients had larger baseline hematoma volumes (15.9ml vs 9.1ml, p=0.03) and similar rates of intraventricular hemorrhage (22% vs 29.7%, p=0.38), compared to those without ultra-early HE. No effect of TXA on ultra-early HE was observed (TXA 41.1% vs placebo 36.5%, p=0.61).

Of 92 patients with both ultra-early and 24 hour re-imaging available, 31 patients had ultra-early HE. Of these, 9 (29%) had further growth at 24 hours, compared to 4/61 patients (6.6%) with no ultra-early growth (p<0.01). Median hematoma growth rate significantly reduced over time compared to the onset-to-baseline imaging period (clustered median regression p<0.01) (Figure 1).
Ultra-early hematoma expansion was associated with poor functional outcomes (mRS 3-6; aOR 3.87 [1.21-12.40], p=0.02) and mortality (aOR 6.16 [95% CI 2.15-17.68], p<0.01), adjusted for treatment group.

Conclusions:
Most hematoma growth occurs in the ultra-early period. The presence of ultra-early HE is associated with ongoing hematoma growth, poor functional outcomes and mortality, and could be a therapeutic target for clinical trials.
Philology’s Deep History
Authors: Ungureanu Delia 
Published: January 2025

Abstract
The story of David Damrosch’s Comparing the Literatures: Literary Studies in a Global Age is inextricably bound to the story of the past twelve years of the Institute for World Literature. Many of the ideas the book puts forth were created and developed through the network of people and ideas IWL brings together. I will briefly look at three ideas developed through IWL that underlie Comparing the Literatures and then I will argue that David Damrosch’s distinctive approach to comparative and world literature is philology’s deep history, in the footsteps of Auerbach’s 1951 essay Philologie der Weltliteratur. I will look at David Damrosch’s commitment to philology’s deep history throughout his career, from What Is World Literature? to Comparing the Literatures and I will illustrate it with a few case studies of my own.
Comparative Literature in Taiwan in the Age of World Literature
Authors: Chang Chung-An 
Published: January 2025

Abstract
Comparative literature in Taiwan flourished in the 1970s, focusing on the comparison of classical Chinese and Western literary classics. In the 1990s, this focus shifted to theory-based research centered on local sociopolitical issues. The literariness of actual comparisons and appreciation of literary works suffered as a result of this shift. The high level of specialization in the present academic system hinders interdisciplinary research, and, in this vein, translation studies has come to question the value of comparative literature. The resurgence of world literature has opened up new possibilities and repivoted attention back toward literariness and translation of texts away from the focus on contentious ideological issues. From the perspective of a Sinosphere with multiple literary centers, comparatists in Taiwan have an opportunity to leverage their diverse and rich cultural resources for the fostering of literary dialogues. Such discourse can connect literary works worldwide, and in the process revive the momentum of a discipline that promotes cross-cultural understanding and profound appreciation for the diversity of human civilizations.
A Re-deliberation of Minzu Literature and World Literature
Authors: Gong Haomin 
Published: January 2025

Abstract
This essay examines the tension between minzu (roughly an equivalent of “ethnic” and “national”) and world literature by investigating Tibetan-Chinese writer Alai’s Gesar and his other writings. For Alai, the tension between minzu and world literature is a moot question. He challenges many assumptions of both minzu and world literature through his metafictional rewriting of Gesar and alerts us to the power of differentiation. Alai’s unique views urge us to reflect on the politics of a non-Western ethnic writer writing in, to, and for the world.
Delayed primary flexor tendon repair in zone II injuries: results of using WALANT and controlled true active motion
Authors: Emir Zeynep , Güngör Sedanur , Çevik Kadir , Ayhan Egemen 
Published: January 2025

Early repair of flexor tendon injuries is ideal, but delays are common. We studied the outcomes of flexor tendon repairs delayed from 5 days to 6 months and carried out under wide-awake local anaesthesia with no tourniquet (WALANT). Twenty-four patients (29 fingers) who underwent primary flexor tendon repair on zone II using a four- to six-strand core suture technique, followed by controlled early active motion therapy. Clinical assessments, including total active motion (TAM) and Disabilities of the Arm, Shoulder and Hand, were made 6, 8 and 12 weeks after operation. All outcomes improved significantly over time. At the final assessment, 93% of fingers showed excellent TAM outcomes. Extension deficit was between 5° and 20° in eight of 26 fingers. The results of this study suggest that delayed primary flexor tendon repair under WALANT can achieve excellent functional outcomes, although longer follow-up is needed for extension deficit recovery. Level of evidence: IV