bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinicopathological correlates of vitamin D receptor expression in prostate cancer: results of genomic analysis
Authors: Omenai Sebastian A. , Ebili Henry O. , Ezenkwa Uchenna S. , Ale Ayotunde O. , Akintola Patrick A. , Adetona Adesoji E. , Akunwata Chima U. , Mashor Mbwas I. , Nwanji Ifeanyichukwu D. , Iyapo Oluwadamilare , Ezekekwu Chinedu A. , Akulue John C. , Chidozie Ngozi , Nwadiokwu Ifeanyi J.
Published: February 2025

Objectives:

Prostate cancer (PCa) is the most common malignancy in men. Geography and environmental factors have been associated with varying incidence and mortalities in different groups. Vitamin D has antiproliferative effect on PCa cells, and its effect is mediated through vitamin D receptor (VDR). This study reported the correlation of VDR expression with some clinicopathological and biological features among a cohort of patients with PCa.

Methods:

Genomic and clinicopathological data of 497 patients with PCa reposited in The Cancer Genome Atlas were retrieved using Linux command in running codes and scripts and extrapolated onto SPSS version 28 for statistical analysis. Descriptive and inferential statistics were conducted to determine the proportions and associations of VDR expression with genomic variables and clinicopathological indices. The mechanism of VDR dysregulation was also interrogated.

Results:

Our results showed that high VDR expression was positively correlated with a high Gleason score (P < 0.001), poorer prognostic International Society of Urological Pathology grade groups (P < 0.001), advanced tumor stage (P = 0.01), and poorer response to androgen deprivation therapy (ADT). Age, race, and overall and disease-free survival did not show any correlation with VDR expression (P > 0.05). Furthermore, the major mechanism of dysregulation of VDR in PCa was by aberrant methylation of the VDR promoter region (P < 0.001), and not by copy number alterations (P = 0.42).

Conclusion:

VDR expression is associated with adverse clinicopathological indices, including late-stage disease profile, high-grade indices, and poorer response to ADT. VDR is also mainly deregulated by aberrant epigenetic mechanism. The study is limited by absence of some clinical information such as sunlight exposure.
Hemolytic Anemia With Acanthocytes During Alectinib Treatment of Anaplastic T-Cell Lymphoma: A Case Report and Literature Review
Authors: Boumeghar Kevin , Buchbinder Nimrod , Metot Capucine , Bera Elsa , Picard Véronique , Modot Thomas , Gallais Florian , Daliphard Sylvie , Bobée Victor
Published: February 2025

Alectinib, an ALK inhibitor used for ALK+ non–small cell lung cancer and other malignancies, has been associated with anemia and RBC abnormalities, including acanthocytosis. We report the first case of alectinib-induced acanthocytosis and hemolysis causing anemia during treatment for anaplastic large cell lymphoma in an 11-year-old boy. Extensive testing, including next-generation sequencing, and a specific indirect antiglobulin test conducted with alectinib, was performed to document this hemolytic anemia. Dose reduction improved hemoglobin levels, allowing completion of the 2-year treatment, suggesting a dose-dependent mechanism. Blood counts and morphology normalized after discontinuation of alectinib. A comprehensive literature review and discussion of the underlying mechanisms are also provided.
Operative Time and Accrual of Postoperative Complications in Minimally Invasive Versus Open Myomectomy
Authors: Applebaum Jeremy , Kim Edward K. , Ewy Joshua , Humphries Leigh A. , Shah Divya K.
Published: February 2025

(Abstracted from J Minim Invasive Gynecol 2024;31:747–755)

Uterine fibroids are a common occurrence in women of childbearing age, and key symptoms can include abnormal uterine bleeding, infertility, or pregnancy complications. Myomectomy is the standard procedure for removal of problematic uterine fibroids and is used to relieve symptoms and preserve or improve fertility.
Diagnostic Accuracy of an Integrated AI Tool to Estimate Gestational Age From Blind Ultrasound Sweeps
Authors: Stringer Jeffrey S.A. , Pokaprakarn Teeranan , Prieto Juan C. , Vwalika Bellington , Chari Srihari V. , Sindano Ntazana , Freeman Bethany L. , Sikapande Bridget , Davis Nicole M. , Sebastião Yuri V. , Mandona Nelly M. , Stringer Elizabeth M. , Benabdelkader Chiraz , Mungole Mutinta , Kapilya Filson M. , Almnini Nariman , Diaz Arieska N. , Fecteau Brittany A. , Kosorok Michael R. , Cole Stephen R. , Kasaro Margaret P.
Published: February 2025

(Abstracted from JAMA 2024;332:649–657)

Gestational age (GA) is critical for guiding obstetric decisions related to antenatal care and delivery. In high-income countries, GA is typically measured via fetal biometry using high-resolution ultrasound machines operated by credentialed sonographers.
Practice Variation in Urine Collection Among Emergency Department Providers in Pre–toilet-trained Children With Suspected Urinary Tract Infection
Authors: Wilson Lucy M. , Klassen Terry P. , Crombie Tighe , Gangwani Apoorva , Wai Lai Veronica Ka , Gripp Karen , Doyle Elisabete , Beer Darcy , Hogue Kaitlin , Florescu Oana , Knisley Lisa , Aregbesola Alex
Published: February 2025

Background:

Urinary tract infections are a common cause of acute illness among children presenting to the emergency department (ED). Many techniques exist to collect urine specimens in pre–toilet-trained children. There is wide practice variation regarding the most appropriate collection method. This variation also appears to exist across national health organizations and societies. To date, little is known about the extent of practice variation in urine collection methods or the influence of patient and health care provider characteristics on the choice of collection method.

Materials and Methods:

A cross-sectional survey was designed and comprised of 3 sections: pediatric emergency medicine physician demographics, pediatric ED demographics, and case scenarios designed to assess the context surrounding urine collection method choice. The survey was disseminated to pediatric emergency medicine physicians across Canada from February 2023 to April 2023. A descriptive analysis of the characteristics of pediatric emergency medicine physicians and the EDs in which they worked was performed. Multivariate logistic regression models were used to examine pediatric emergency medicine physicians and ED factors that influence urine collection methods.

Results:

Of 235 surveys, 96 were returned (41% participation rate). Most respondents were aged 40 to 49 (n=31, 35.6%), female (60.5%), completed residency in Ontario (18.4%) and Quebec (17.2%), and worked at the Children’s Hospital of Eastern Ontario (16%). There was variation in urine collection methods among pediatric emergency medicine physicians with a preference for transurethral catheterization and bladder stimulation versus other methods. Factors such as the length of wait time of patients to be seen in the ED (odds ratio=3.03, 95% CI=1.14-8.09) and year postmedical school (odds ratio=1.67, 95% CI=1.07-2.60) were associated with increased choice of urinary catheterization when selecting a urine collection method.

Conclusions:

The data suggests there is practice variation in urine collection methods among Canadian pediatric emergency medicine physicians. This practice variation is influenced by both individual providers and the demographics of EDs.
Clinical Features and Management Strategies in Children With Mycoplasma Pneumoniae
Authors: Garcia Tamara , Florin Todd A. , Leonard Jan , Shah Samir S. , Ruddy Richard M. , Wallihan Rebecca , Desai Ankita P. , Alter Sherman , El-Assal Osama , Marzec Sarah , Keaton Meghan , Yun Ki Wook , Leber Amy L. , Mejias Asuncion , Cohen Daniel M. , Ramilo Octavio , Ambroggio Lilliam ,   On Behalf of the Children’s Hospitals Initiative for Research in Pneumonia (CHIRP)
Published: February 2025

Objective:

Mycoplasma pneumoniae (Mp) is the most detected bacterial pathogen in children with community-acquired pneumonia (CAP). Our primary objective was to compare the clinical presentation, clinical management, and outcomes of children with and without Mp CAP across 6 children’s hospitals.

Methods:

Eligible children were 2 months old or above and diagnosed with CAP in a prospective multicenter cohort study between October 1, 2015 and June 31, 2018. Children were excluded if they had complex chronic conditions. Children were tested for Mp via polymerase chain reaction assays. Clinical outcomes included hospitalization, and among hospitalized children length of stay, pediatric intensive care unit (PICU) admission, and rehospitalization within 8 weeks of discharge. Negative binomial and logistic regression were performed to determine the association of Mp with clinical outcomes.

Results:

Of the 415 children included, 38 (7.4%) had Mp detected. Children with Mp were older [median interquartile range age 8.8 (3.1, 13.0) vs. 4.6 (interquartile range: 2, 8.2) y], more likely to receive azithromycin (68.4% vs. 22.2%) and more likely to receive antibiotics in the prior 2 weeks (63.2% vs. 35.7%) versus those with non-Mp CAP. Children with Mp CAP were 33% less likely to stay in the hospital for an additional day (95% CI: 0.48-0.94).

Conclusion:

Children with Mp CAP are more likely to have a longer duration of symptoms, but there are no statistical differences in symptom prevalence, laboratory values, or radiographic findings. There was no statistical difference in clinical outcomes for children with Mp CAP suggesting that clinical presentation and outcomes are similar between Mp and non-Mp CAP. Polymerase chain reaction testing for Mp CAP may be the only way to discriminate between non-Mp and Mp CAP.
Therapeutic Scoliosis-Specific Exercises for a Child With Spinal Muscular Atrophy: A Case Report
Authors: Kanner Cara H. , Rodriguez-Torres Rafael , Wallach Rebekah , Bakarania Prachi , Montes Jacqueline
Published: February 2025

Purpose:

The purpose of this study is to report on therapeutic scoliosis-specific exercises (PSSE) for a child with spinal muscular atrophy (SMA) who had spinal fusion.

Methods:

PSSE were recommended after scoliosis was diagnosed and exercises focused on posture and improving strength preoperatively and restoring function postoperatively.

Results:

Gross motor function remained stable before spinal fusion, briefly decreased after the procedure, and then stabilized post-surgery. Distance walked on the 6-minute walk test decreased post-surgery but improved after the addition of PSSE to the Standard of Care.

Conclusions:

Including PSSE as an adjunct to traditional interventions may be beneficial for children with SMA. Evidence supports incorporating PSSE to improve posture preoperatively in idiopathic scoliosis. Its use postoperatively and in children with SMA is not well studied. Controlled studies are needed to understand the impact of pre- and post-op PSSE in children with SMA.
Deep Learning–Based Signal Amplification of T1-Weighted Single-Dose Images Improves Metastasis Detection in Brain MRI
Authors: Haase Robert , Pinetz Thomas , Kobler Erich , Bendella Zeynep , Zülow Stefan , Schievelkamp Arndt-Hendrik , Schmeel Frederic Carsten , Panahabadi Sarah , Stylianou Anna Magdalena , Paech Daniel , Foltyn-Dumitru Martha , Wagner Verena , Schlamp Kai , Heussel Gudula , Holtkamp Mathias , Heussel Claus Peter , Vahlensieck Martin , Luetkens Julian A. , Schlemmer Heinz-Peter , Haubold Johannes , Radbruch Alexander , Effland Alexander , Deuschl Cornelius , Deike Katerina
Published: February 2025

Objectives

Double-dose contrast-enhanced brain imaging improves tumor delineation and detection of occult metastases but is limited by concerns about gadolinium-based contrast agents' effects on patients and the environment. The purpose of this study was to test the benefit of a deep learning–based contrast signal amplification in true single-dose T1-weighted (T-SD) images creating artificial double-dose (A-DD) images for metastasis detection in brain magnetic resonance imaging.

Materials and Methods

In this prospective, multicenter study, a deep learning–based method originally trained on noncontrast, low-dose, and T-SD brain images was applied to T-SD images of 30 participants (mean age ± SD, 58.5 ± 11.8 years; 23 women) acquired externally between November 2022 and June 2023. Four readers with different levels of experience independently reviewed T-SD and A-DD images for metastases with 4 weeks between readings. A reference reader reviewed additionally acquired true double-dose images to determine any metastases present. Performances were compared using Mid-p McNemar tests for sensitivity and Wilcoxon signed rank tests for false-positive findings.

Results

All readers found more metastases using A-DD images. The 2 experienced neuroradiologists achieved the same level of sensitivity using T-SD images (62 of 91 metastases, 68.1%). While the increase in sensitivity using A-DD images was only descriptive for 1 of them (A-DD: 65 of 91 metastases, +3.3%, P = 0.424), the second neuroradiologist benefited significantly with a sensitivity increase of 12.1% (73 of 91 metastases, P = 0.008). The 2 less experienced readers (1 resident and 1 fellow) both found significantly more metastases on A-DD images (resident, T-SD: 61.5%, A-DD: 68.1%, P = 0.039; fellow, T-SD: 58.2%, A-DD: 70.3%, P = 0.008). They were therefore able to use A-DD images to increase their sensitivity to the neuroradiologists' initial level on regular T-SD images. False-positive findings did not differ significantly between sequences. However, readers showed descriptively more false-positive findings on A-DD images. The benefit in sensitivity particularly applied to metastases ≤5 mm (5.7%–17.3% increase in sensitivity).

Conclusions

A-DD images can improve the detectability of brain metastases without a significant loss of precision and could therefore represent a potentially valuable addition to regular single-dose brain imaging.
Prognostic Role of Enhancing Mural Nodules in Intraductal Papillary Mucinous Neoplasms with High-Risk Stigmata
Authors: Kumano Ryohei , Ohno Eizaburo , Ishikawa Takuya , Yamao Kentaro , Mizutani Yasuyuki , Iida Tadashi , Uetsuki Kota , Yamamura Takeshi , Furukawa Kazuhiro , Nakamura Masanao , Honda Takashi , Kawashima Hiroki
Published: February 2025

Objective:

To evaluate the prognostic impact of invasive nodules (IN) detected by contrast-enhanced endoscopic ultrasound (CE-EUS) in intraductal papillary mucinous neoplasms (IPMNs) with high-risk stigmata (HRS) and their role in guiding surgery.

Summary of Background Data:

IPMNs with HRS are surgical candidates, but their long-term outcomes and the need for surgery in all patients remain unclear.

Methods:

This single-center retrospective study included 257 patients with IPMN and HRS, comparing CE-EUS and CT for detecting IN. It evaluated overall survival (OS) and disease-specific survival (DSS) between surgical and observation groups and identified factors influencing OS through multivariate analysis.

Results:

Median follow-up was 53.4 months. Of 257 patients, 226 (87.9%) underwent surgery and 31 (12.1%) were observed. Non-IN patients showed significantly better 5-year OS and DSS than IN patients in both groups (surgery, OS 87.9% vs. 53.2% and DSS 96.9% vs. 64.3%; observation, OS 84.7% vs. 23.3% and DSS 100% vs. 32.8%). Non-IN group that underwent surgery had better 10-year DSS than those in the observed group (96.9% vs. 66.7%). However, with an age-adjusted Charlson comorbidity index (ACCI) ≥5, there was no significant difference in 5-year OS between the groups (77.1% vs. 79.3%, P=0.7036). CE-EUS showed higher sensitivity than CT detecting IN (P=0.042). Independent predictors of poor OS included ACCI ≥5, nonsurgery, mural nodule ≥10 mm, and IN.

Conclusions:

CE-EUS effectively detected IN, significantly impacting the prognosis of IPMN with HRS. Its superior sensitivity to CT and ability to predict OS/DSS highlight its importance in guiding clinical management.
Outcomes of Retroperitoneal vs Transperitoneal Approach for Open Abdominal Aortic Aneurysm Repair Stratified by Aortic Cross-Clamping Site
Authors: Hamouda Mohammed , Abdelkarim Ahmed , Kricfalusi Mikayla , Brooke Benjamin S , Malas Mahmoud B
Published: February 2025

Background:

The approach for open infrarenal Abdominal Aortic Aneurysm (AAA) repair is mainly surgeon driven based on experience and prior training. While the midline Transperitoneal (TP) remain the most common, the Retroperitoneal (RP) approach is usually utilized in more complex cases where suprarenal cross-clamping is necessary. As prior literature is conflicting on optimal outcomes between the two approaches, we aimed to compare RP vs TP outcomes stratified by aortic clamp level.

Study Design:

The Vascular Quality Initiative database was queried for all patients who underwent open AAA repair from January 2012 to February 2024. Patients were stratified according to aortic cross-clamp site: infrarenal, interrenal, suprarenal, and supraceliac. We used multivariate logistic regression to analyze outcomes of RP vs TP within each clamp site while adjusting for baseline and clinically relevant variables.

Results:

A total of 8,842 patients were included. Compared to TP, RP approach was associated with higher odds of postoperative dialysis [aOR=1.74,(95%CI 1.07-2.83),p=0.025) with infrarenal cross-clamping. However, at higher clamping sites RP was associated with lower odds of bowel ischemia [aOR=0.40,(95%CI 0.20-0.80),p=0.009] with interrenal clamping; lower odds of dialysis [aOR=0.66,(95%CI 0.44-0.99),p=0.048], bowel ischemia [aOR=0.52,(95%CI 0.32-0.85),p=0.009) and 30-day mortality [aOR=0.48,(95%CI 0.30-0.79),p=0.004) with suprarenal clamping; and lower in-hospital [aOR=0.35,(95%CI 0.16-0.80),p=0.013) and 30-day mortality [aOR=0.41,(95%CI 0.17-0.98),p=0.046] with supraceliac clamping.

Conclusion:

In this large multi-institutional study, we identified that differential outcomes of RP vs TP approaches for open AAA are modified by aortic cross-clamping level. RP is associated with lower postoperative complications and better survival compared to TP in cases requiring more proximal cross-clamping sites. However, TP approach is associated with lower risk of renal complications in cases restricted to infrarenal clamping.
Change targets, messaging, and content delivery for a community-engaged social media campaign addressing HIV-related stigma in Peru: a qualitative study
Authors: Nunez Alyson , Curtis Marguerite , Wong Milagros , Kosyluk Kristin A. , Galea Jerome T. , Franke Molly F. , Errea Renato A.
Published: February 2025

Mitigating HIV-related stigma is critical to improving HIV outcomes and reaching global HIV targets. We conducted formative community-engaged research to identify key characteristics of a social media campaign to address HIV-related stigma among youth in Lima, Peru. Focus groups and in-depth interviews with young people living with HIV (men who have sex with men, transgender women, sex workers, persons with perinatally-acquired HIV, cisgender women, and Venezuelan migrants), HIV advocates, and healthcare providers were carried out from November 2022 to July 2023. Audio recordings were transcribed verbatim and analysed for emergent themes using framework analysis. Two change targets were identified for campaign messaging: 1) changing how HIV and people living with HIV (PLWH) are perceived, and 2) changing attitudes and actions towards PLWH. Messages aligning with the first change target included education to raise awareness that HIV does not discriminate; HIV is a chronic, treatable condition; and “undetectable equals untransmittable” (U=U). Messages aligning with the second target included normalizing open conversations about HIV, encouraging support versus pity for PLWH, fostering unity among HIV-affected communities, and promoting inclusion of PLWH. Participants provided recommendations to achieve these messaging objectives, including how, to whom and by whom messages are delivered.
Acute obstructive uropathy in male C57Bl/6 mice after general anesthesia with fentanyl, midazolam and medetomidine
Authors: Wallace Damian J. , Holmgren Carl , Czubayko U. , Klesing Jeanine , Machado Daniela Martin , Kerr Jason N. D.
Published: February 2025

The selective alpha-2 adrenoreceptor agonist medetomidine is commonly used as a component of combination solutions for general anesthesia in rodents and small animals. However, it has also been reported to increase the risk of obstructive uropathy in male mice. Here we report that in a recent cohort of mice undergoing two sequential surgical procedures using the anesthetic combination of fentanyl, midazolam and medetomidine (FMM) for general anesthesia, 60% of the male mice developed severe obstructive uropathy within 48 hours of the second surgery. We also report one case of an older male mouse developing severe obstructive uropathy after a single general anesthesia with FMM. In a subsequent pilot study involving five male mice undergoing similar surgical procedures, also with two sequential surgeries, but using xylazine as the alpha-2 adrenoreceptor agonist in the narcotic combination, none of the animals developed obstructive uropathy in the post-operative period or thereafter. We suggest that replacement of medetomidine with xylazine should be considered for general anesthesia in male mice undergoing multiple successive anesthesia events or in for procedures in older males.
Adaptation of protein stability to thermally heterogeneous environments
Authors: Priklopil Tadeas , Bomblies Kirsten , Widmer Alex
Published: February 2025

Proper protein folding is essential for biological function, and its disruption can lead to disease, reduced fitness, or death. The ability of a protein to maintain its folded conformation is thus critical for life, making it a key target of adaptive evolution. However, protein stability is sensitive to environmental factors, particularly temperature, which can threaten phenotypic integrity and organismal survival under thermal changes. Despite its importance, the influence of complex thermal environments – characterized here by mean temperature, thermal fluctuations, and environmental heterogeneity – on the evolution of protein stability remains poorly understood. To address this, we developed a mathematical framework that combines two well-established models: a population genetic model describing species distributed across habitats with distinct thermal environments, and a thermodynamic model of protein stability incorporating temperature-dependent enthalpy and entropy contributions. We focus on two-state proteins that alternate between folded and unfolded states and assume that allelic fitness is maximized in proteins that achieve an optimal balance between flexibility and rigidity. Using this framework, we performed an invasion analysis of mutations (sensuadaptive dynamics framework) affecting three thermodynamic parameters that fully determine protein stability profiles. Where possible, we derived analytical expressions for evolutionarily optimal thermodynamic parameters and complemented these with numerical solutions. Our results show that mean temperature and thermal fluctuations have orthogonal effects on thermodynamic parameters, underscoring the need to consider both when studying protein stability adaptation. We further examined thermally heterogeneous environments, where subpopulations connected by migration experience different mean temperatures, identifying conditions that favor either local (specialist) or global (generalist) adaptation. Our results may explain why one thermodynamic parameter shows little association with thermal adaptation and suggest that local adaptation is more likely for proteins with stability profiles limited to narrow temperature ranges. Additionally, our analysis reveals whether a locally adapted protein originated in a colder or warmer habitat. Finally, we identified trade-offs in thermodynamic parameters that influence local or global adaptation. This study offers key predictions about protein evolution in complex thermal environments and lays the groundwork for developing practical tools to understand how temperature shapes adaptation and biodiversity.
Robust constrained weighted least squares for in vivo human cardiac diffusion kurtosis imaging
Authors: Coveney Sam , Afzali Maryam , Mueller Lars , Teh Irvin , Szczepankiewicz Filip , Jones Derek K. , Schneider Jurgen E
Published: February 2025

Robust estimation with convexity constraints significantly improves signal fitting for in vivo human cardiac diffusion kurtosis imaging.

Purpose

Cardiac diffusion tensor imaging (cDTI) is an emerging technique to investigate the microstructure of heart tissue. At sufficiently high b-values, additional information on microstructure can be observed, but the data require a representation beyond DTI such as diffusion kurtosis imaging (DKI). cDTI is highly prone to image corruption, which researchers usually attempt to handle with shot-rejection. However, this can be handled more generally with robust estimation techniques. Recent work has also demonstrated the need to perform constrained fitting for DKI, as fitted parameters can otherwise violate necessary constraints on the signal behaviour, causing significant errors in estimated measures.

Methods

We developed robust constrained weighted least squares (RCWLS) by combining robust estimation with convexity constraints specifically for DKI. Using in vivo cardiac DKI data from 11 healthy volunteers collected with a Connectom scanner, we tested various combinations of fitting techniques, with/without robustness and with/without constraints.

Results

RCWLS was the only tested technique that convincingly showed radial kurtosis to be larger than axial kurtosis for all subjects, something that is expected in myocardium due to increased restrictions to diffusion in the plane perpendicular to the primary myocyte direction. RCWLS also showed the best correction of corrupted regions in diffusion parameter maps for individual subjects.

Conclusion

Fitting techniques utilizing both robust estimation and constraints are essential to facilitate applicability of in vivo cardiac DKI.
Modelling the Impact of Dominant Transport Pathways on Antarctic Krill Fishing Activity in the Southern Ocean
Authors: Kelly Cian , Ellingsen Ingrid , Daae Ragnhild , Alver Morten Omholt
Published: February 2025

Antarctic krill (Euphasia superba) are a key component in the Southern Ocean ecosystem, especially in the Atlantic sector, where the majority of the population is concentrated. The Norwegian commercial krill fishery exclusively targets three subareas in the Antarctic: the western Antarctic Peninsula, and the northern shelves of both the South Orkney Islands and South Georgia. Given it’s reliance on oceanic transport from other regions and the potential impact of rising sea temperatures on the northern habitat, the South Georgian krill population is particularly sensitive to altering environmental conditions. The relative distance from the peninsular regions to South Georgia means that choosing to trawl in this region implies a higher risk, which is why it is exclusively targeted in winter when extensive sea-ice makes peninsular regions unsafe and inaccessible to commercial fishery operations. In this article, we show that relative to operations at South Orkney and the Antarctic Pensinsula, average catches at South Georgia have been lower with higher variability over the past 15 years. Using a Lagrangian modelling approach, we illustrate that variability in advection from source regions in the Antarctic Peninsula are correlated with proceeding catch values at South Georgia. This was not the case for source release sites at the South Orkney Islands. The dominant transport pathways for krill were strongly determined by position of regional fronts and the source sites of recruits to South Georgia were related to the position of fronts at both the Antarctic Peninsula and South Orkney Islands. This study highlights the importance of advective patterns on the variability in krill fishing activity and supports the hypothesis that South Georgia is a sink region for krill in the Southern Ocean while the western Antarctic Peninsula is a central source site.
Accuratede novotranscription unit annotation from run-on and sequencing data
Authors: Munn Paul R. , Chia Jay , Danko Charles G.
Published: February 2025

Functional element annotations are critical tools used to provide insight into the molecular processes governing cell development, differentiation, and disease. Run-on and sequencing assays measure the production of nascent RNAs and can provide an effective data source for discovering functional elements. However, the accurate inference of functional elements from run-on sequencing data remains an open problem because the signal is noisy and challenging to model. Here we investigated computational approaches that convert run-on and sequencing data into annotations representing transcription units, including genes and non-coding RNAs. We developed a convolutional neural network, calledconvolutional discovery ofgeneanatomy usingPRO-seq (CGAP), trained to identify different anatomical features of a transcription unit, which were then stitched together into transcript annotations using a hidden Markov model (HMM). Comparison with existing methods showed a significant performance improvement using our novel CGAP-HMM approach. We developed a voting system that ensembles the top three annotation strategies, resulting in large and significant improvements in transcription unit annotation accuracy over the best performing individual method. Finally, we also report a conditional generative adversarial network (cGAN) as a generative approach to transcription unit annotation that shows promise for further development. Collectively our work provides novel tools forde novotranscription unit annotation from run-on and sequencing data that are accurate enough to be useful in many applications.
Multiple Xpa In vivo crystallization routes in HEK 293 human cells
Authors: Leymarie O. , Skobelkina A. , Montaville P. , Brewee C. , Isabet T. , Chauvet H. , Pereiro E. , Chavas L. , Jamme F.
Published: February 2025

Phase changes of macromolecules in living cells gained recently a major interest in cell biology as liquid liquid phase separation or liquid solid phase transition phenomenon being observed in increasing number of biological or pathological processes. Comprehensive characterization of these phases remains challenging and requires new methodological approaches for their complete description across spatial and temporal scales. We propose a combination of imaging methods applied to a model system and report thein vivocrystallization pathways of a macromolecule from its solution to crystalline states at the cell population level down to the meso scale. Combining various live fluorescence based techniques and a high resolution cryo imaging technique within unaltered cryopreserved cells, we could described the unexpectedly wide landscape of thein vivocrystalline states of the fluorescent coral derived protein xpa, gain information of crystal growth dynamicsin cellulo, and provide hypothesis of the crystal nucleation requirements of this stochastic process.
Mapping the dimerization specificity of bZIP transcription factors in bread wheat
Authors: Kaur Raminder , Sharma Nishtha , Jain Prateek , Verma Mamta , Apkari Ashish , Rishi Vikas
Published: February 2025

Dimerization plays a pivotal role in target-binding interactions among various transcription factors (TFs), including bZIPs, bHLHs, MYBs, and zinc finger TFs. The bZIP family is defined by an α-helix class of TFs containing a basic region that binds to the major groove of double-stranded DNA (dsDNA), followed by a leucine zipper motif that mediates dimerization through coiled-coil structures, forming homo- or heterodimers. In polyploid bread wheat (Triticum aestivumcv.), bZIPs and their homeologs interact through the dimerization motifs to form specific bZIP pairs with distinct regulatory functions. The dimerization pattern of bZIPs is critical for gene regulation, however, the mechanisms underlying their specificity remain poorly understood. Here, we focus on the dimerization specificity of coiled-coil α- helical bZIP proteins in bread wheat, highlighting the leucine zipper region as a key dimerization motif. We identified 265 bZIPs containing the bZIP motif, following dimerization criteria established in humans,Drosophila, andArabidopsisbased on the presence of specific amino acids at the ’a’, ’d’, ’e’, and ’g’ positions in heptads. Eight key bZIP TFs were cloned, expressed, and purified for the structural analysis. This study not only provides the dimerization trend exhibited by bZIPs during thermal stability analysis but also provides the reversibility pattern followed by the thermal denaturation exposure at 85°C. Our study also points towards that how amino acid substitutions and the length of the leucine zipper influence the formation of coiled-coil structures among bZIP homeologs of polyploid wheat. Overall, the study advances our understanding of the role of leucine zippers, in determining the specificity and stability of bZIP dimers, which in turn governs DNA binding and gene regulation in plants.
Assembly and annotation ofSolanum dulcamaraandSolanum nigrumplant genomes, two nightshades with different susceptibilities toRalstonia solanacearum
Authors: Ortega Sara Franco , James Sally , Gilbert Lesley , Hogg Karen , Stevens Harry , Daff Jason , Friman Ville-Petri , Harper Andrea L.
Published: February 2025

To understand why close wild plant relatives of crops, such asSolanum dulcamara, are resistant toRalstonia solanacearumwe need genetic resources to perform comparative studies and identify key genes and pathways. Wede-novoassembled and annotated the genome of resistantS. dulcamaraand susceptibleSolanum nigrumplants using a hybrid approach including Oxford Nanopore Technologies and Illumina sequencing. Comparative genomic analysis was then performed to find differences between the genome ofS. dulcamaraand other susceptible Solanaceous species including potato, tomato, aubergine, andS. nigrumand one susceptible and one resistantS. americanumaccession. We identified genes associated with auxin-transport only inS. dulcamaraand a collection of pattern recognition receptors (PRRs) was identified in orthogroups only found in plant species with resistant/tolerant phenotype, suggesting novel plant receptors in these accessions that may improve recognition of pathogen-associated molecular patterns (PAMPs) associated withR. solanacearum. We also identified differences in methylation frequency across the gene bodies in both species, which may be associated with epigenetic regulation of resistance. Future work should assess the functional role of these PRRs during bacterial wilt development to determine if they could offer potential novel targets for breeding improved wilt resistance.
Understanding of ATP-lid conformational dynamics in the N-terminal domain of Hsp90 and its mutants by use of a computational biochemistry approach
Authors: Gohda Keigo
Published: February 2025

Chaperone Hsp90 regulates the activation and maturation of various protein, and is an attractive target for drug discovery. In catalytic cycle of Hsp90, ATP hydrolysis is a key event that drives structural changes, including the interchange of the dimeric Hsp90 structure between open and closed forms. For ATP hydrolysis, ATP-lid closure in the ATP-binding site from the up- to down-conformation is an indispensable co-ordinated structural change. However, the atomistic mechanism underlying lid closure remains unclear. In this study, a computational biochemistry approach was applied to wild-type apo and ATP-complex structures, and the lid-mutants A107N and T101I ATP-complex, to understand lid closure.

A total of 15-μs molecular dynamic simulation, including the equilibration and production phases, was conducted for every structure starting from the lid up-conformation, but no lid-closures were observed. However, a very early event, i.e.,a sign, of lid closure have been captured. In the simulations of wild-type and A107N ATP-complex structures, lid segment showed conformational fluctuations, and helix-7 (H7) segment in lid segment was unwound. This conformational instability of lid segment energetically weakened its interaction with facing region, suggesting the up-to-down transition was triggered by the instability of lid segment, particularly H7 segment. The interaction energy between lid segment and facing region was ranked in the order A107N > wild-type > T101I, which was correlated with experimental results such as the orders of ATP-hydrolytic activity and rapidity of conformational changes of lid segment, measured in ATP-spiking experiments by fluorescence resonance energy transfer method (i.e., A107N > wild-type > T101I).
Right atrial dilatation associates with conduction velocity, incidence of arrhythmias and clinical outcomes in pulmonary hypertension
Authors: Reddy S Ashwin , Middleton Jennifer T , De Bie Eckart MDD , Nethercott Sarah L , Polwarth Gary J , Bullock Katherine , Patel Kiran Hk , Bajaj Nikesh , Statton Ben K , Zahra Syeda Anum , Ehnesh Mahmoud , Roney Caroline H , Ng Fu Siong , Kiely David G , Swift Andrew J , Church Colin , Coghlan Gerry , Gräf Stefan , Lawrie Allan , Lordan James , Mackenzie Ross Robert V , Wilkins Martin R , Wort S John , Taboada Dolores , Bunclark Katherine , Cannon John E , Sheares Karen S , Pepke-Zaba Joanna ,   National Cohort Study of Idiopathic and Heritable PAH Collaboration,   UniPHy Clinical Trials Network, Martin Claire A , Rothman Alex MK , Toshner Mark R
Published: February 2025

Introduction

The mechanism, frequency and clinical impact of arrhythmias in pulmonary hypertension (PH) are unclear. We sought to clarify the electrophysiological mechanism in PH and correlate with arrhythmia incidence and clinical outcomes.

Methods

Invasive (n=10) and non-invasive (n=30) electrophysiological mapping techniques determined myocardial conduction velocity, scar burden and atrioventricular (AV) nodal refractoriness, which were then related to cardiac structure and function.

Implantable cardiac monitors (ICMs) were implanted into 80 patients with pulmonary arterial hypertension (PAH). Arrhythmia and clinical worsening episodes were prospectively assessed over 186 patient-years follow-up, and features associated with arrhythmia incidence were identified. Two cohorts encompassing all causes of PH (n=564 and n=3348) were interrogated to assess the relationship between defined arrhythmia risk variables and outcomes.

Results

Right atrial (RA) dilatation was associated with slower conduction velocity (R=0.52, p=0.01) and more prolonged AV nodal refractoriness (R=0.82, p=0.03). In the ICM study, 79 arrhythmia events were noted in 40% of participants. Only RA size was independently associated with significant arrhythmia (HR 1.03, 95% CI 1.01-1.06, p=0.01). Arrhythmia incidence associated with clinical worsening, and 20% of patients received ICM-uncovered targeted arrhythmia treatment. 69% of patients with treated arrhythmia were asymptomatic (median time-to-arrhythmia-detection 7 months). In both longitudinal PH cohorts, right atrial (RA) size was associated with worse survival independent of RA pressure and pulmonary vascular resistance.

Interpretation

The dominant mechanism associated with disordered cardiac electrophysiology in pulmonary hypertension patients is RA enlargement. RA size was the only significant variable associated with longitudinal arrhythmias in PAH and in two large prospective cohorts with representative populations of all causes of pulmonary hypertension, RA size is predictive of outcomes independent of pulmonary vascular resistance. Randomised trials are needed to clarify if screening and treating arrhythmias in pulmonary hypertension improves outcomes.
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea
Authors: Huang Wen-Cong , Probst Maraike , Hua Zheng-Shuang , Szantho Lenard L. , Szollosi Gergely J. , Ettema Thijs , Rinke Chris , Williams Tom A. , Spang Anja
Published: February 2025

The Asgard archaea are a diverse archaeal phylum that includes the host lineage from which eukaryotes evolved. Due to the importance of the Asgard archaea for our understanding of cellular evolution and eukaryotic complexity, recent efforts have focused on better characterizing the genomic diversity of this lineage and its relatives from the TACK archaea. Newly discovered lineages, the Njordarchaeales and Panguiarchaeales, are difficult to place, branching either with Korarchaeota or Asgard archaea. The phylogenetic position of these taxa is important because they include genome-reduced and potentially symbiotic lineages, which may help to inform our understanding of genome evolution and the evolution of symbiotic interactions within Asgard archaea and their relatives. To resolve the placement of Njordarchaeales and Panguiarchaeales in the archaeal tree, we performed a range of phylogenetic analyses revealing that the Njordarchaeales and Pangiuarchaeales constitute the newly-identified class Njordarchaeia within the Asgard archaea. Members of the Njordarchaeia exhibit hallmarks of adaptations to (hyper-) thermophilic lifestyles, which may contribute conflicting signals to phylogenetic analyses. Panguiarchaeum appears to be metabolically distinct from its relatives, displaying reduced metabolic potential and various auxotrophies. Gene tree-species tree reconciliation recovers a complex common ancestor of Asgard archaea that encoded the Wood Ljungdahl pathway, however the subsequent loss of this pathway during the reductive evolution of Panguiarchaeum may have been associated with the switch to a symbiotic lifestyle based on H2 syntrophy. Our analyses identify Panguiarchaeum as the first described Asgard archaea lineage with streamlined genomes that show indications for a symbiotic lifestyle.
Asynchronous viral spread of two unrelated viruses determines Lettuce Big Vein Disease symptom development
Authors: Schravesande Willem E. W. , de Heer Peter M. , Heilijgers Maurice , Verhage Adriaan , van den Burg Harrold A.
Published: February 2025

Lettuce big-vein disease (LBVD) is a major disease affecting lettuce cultivation worldwide. LBVD is caused by two unrelated negative-stranded RNA viruses, that is, Mirafiori lettuce big-vein virus (MiLBVV) and Lettuce big-vein associated virus (LBVaV) both vectored by the soilborne fungusOlpidium virulentus. Despite extensive research, a synergistic effect between the two viruses has not been observed, while both viruses individually have been suggested to be the causal agent for the disease. By performing lettuce reinfections using a large soil sample collection carrying LBVD infestedO. virulentusspores, the presence of LBVaV was consistently established in diseased lettuce heads, while MiLBVV infections were apparently less prevalent. Yet, aboveground infections with MiLBVV corresponded with strong disease symptoms. Strikingly, the spread of LBVaV from the root to shoot always preceded that of MiLBVV. The LBVaV systemic spread was highly synchronized between plants, while MiLBVV spread was always delayed and asynchronous. A pan-genome analysis revealed independent segment reassortments for both viruses indicative of mixed field infections over the sampled period. Yet, RNA segment abundance was highly conserved for both viruses between all re-infections, suggesting that segment abundance has a regulatory role for the two individual viruses, but that segment abundance is not impacted by the presence of the other two viruses. The pan-genome analysis also revealed different evolutionary rates of the viral ORFs suggesting that mutagenesis of certain ORFs compromises viral fitness and thus revealing a potential weak spot for both viruses.

Importance

Lettuce big-vein disease (LBVD) is an important viral disease complex affecting lettuce cultivation worldwide. Here we reveal a synergistic interaction between the two principal associated segmented RNA viruses, Mirafiori lettuce big-vein virus (MiLBVV) and Lettuce big-vein associated virus (LBVaV). We show unequivocally that MiLBVV is the main virus responsible for severe disease symptoms in lettuce heads. Yet, MiLBVV root-to-shoot movement was in our conditions always preceded by LBVaV movement into the lettuce heads. Arguably, LBVaV thus facilitates the root-to-shoot movement of MiLBVV. Moreover, both viruses undergo segment reassortment increasing their genome plasticity and the reassortment events appeared to be independent events with mixed infections. Finally, we provide data that both viruses regulate gene expression via the copy number of their RNA segments, but that the genome formula does not change in dual infections. We thus provide evidence for a synergistic interaction needed for strong LBVD symptoms.
Atomistic modelling of lysophospholipids from the Campylobacter jejuni lipidome
Authors: Newman Kahlan E. , Brandner Astrid F. , Essex Jonathan W. , Khalid Syma
Published: February 2025

Lysophospholipids are an important class of lipids in both prokaryotic and eukaryotic organisms. These lipids typically constitute a very small proportion (<1%) of the bacterial lipidome, but can constitute 20-45% of theCampylobacter jejunilipidome under stress conditions. It is thus of importance to include these lipids in modelC. jejunimembrane simulations for an accurate representation of the lipidic complexity of these systems. Here, we present atomistic models for four lysophospholipids from theC. jejunilipidome, each derived from existing phospholipid models. Herein we use molecular dynamics simulations to evaluate the ability of these models to reproduce the expected micellar, hexagonal, and lamellar phases at varying levels of hydration. Mixtures of phospholipids and lysophospholipids emulating theC. jejunilipidome under ideal growth conditions were found to self-assemble into bilayers in solution. The properties of these mixed bilayers were compared to those containing only phospholipids: the presence of the selected lysophospholipids causes a subtle thinning of the bilayer and a reduction in area per lipid, but no significant change in lipid diffusion. We further test the mixed bilayer model running simulations in which a native inner membrane protein is embedded within the bilayer. Finally, we show that lysophospholipids facilitate the formation of pores in the membrane, with lysophospholipid-containing bilayers more susceptible to electroporation than those containing only phospholipids.
In vivo pulse-chase inC. elegansreveals intestinal histone turnover changes upon starvation
Authors: Borchers Christopher , Osburn Kara , Roh Hyun Cheol , Aoki Scott T.
Published: February 2025

The ability to study protein dynamics and function in the authentic context of a multicellular organism is paramount to better understand biological phenomena in animal health and disease. Pulse-chase of self-labeling fusion protein tags provide the opportunity to label proteins of interest and track those proteins over time. There are currently several challenges associated with performing in vivo protein pulse-chase in animals, such as cost, reproducibility, and accurate detection methods. TheC. elegansmodel organism has attributes that alleviate many of these challenges. This work tests the feasibility of applying the Halo modified enzyme (HaloTag) for in vivo protein pulse-chase inC. elegans. HaloTag intestinal histone reporters were created in the worm and used to demonstrate that reporter protein could be efficiently pulse-labeled by soaking animals in ligand. Labeled protein stability could be monitored over time by fluorescent confocal microscopy. Further investigation revealed reporter protein stability was dependent on the animal’s nutritional state. Chromatin Immunoprecipitation and sequencing (ChIP-seq) of the reporters showed incorporation in chromatin with little change hours into starvation, implying a lack of chromatin regulation at the time point tested. Collectively, this work presents a straightforward method to label and track proteins of interest inC. elegansthat can address a multitude of biological questions surrounding protein stability and dynamics in this animal model.