bluuebunny/crossref_metadata_2025_split huggingface dataset:
Menopausal hormone therapy use among active duty service women
Authors: Janvrin Miranda L. , Banaag Amanda , Brown Jill , Shvartsman Katerina , Koehlmoos Tracey P. 
Published: December 2024

Abstract

Objective
Menopausal hormone therapy (HT) has been shown to be effective in alleviating symptoms of menopause. While previous literature has described the frequency of HT use for the relief of menopausal symptoms in both the general and veteran female populations, there is currently no literature describing this frequency within the female active duty population. This study aims to address this gap in knowledge by conducting a retrospective cross-sectional study of HT receipt in active duty service women (ADSW) ages 45 to 64 during fiscal years (FYs) 2018 to 2022.

Methods
We used the Military Health System (MHS) Data Repository (MDR) to conduct a retrospective study of ADSW ages 45 to 64 in the US Army, Air Force, Navy, and Marine Corps during FY 2018 to 2022. Study analyses included descriptive statistics on participant demographics and HT type. Logistic regressions were performed to assess for significant associations between participant demographics and receipt of HT.

Results
We identified a total of 13,629 women aged 45 to 64 on active duty service in the US Army, Air Force, Navy, and Marine Corps during FY 2018 to 2022, of whom 1,290 (9.5%) received HT. Significantly lower odds for receipt of HT was observed among ADSW ages 45 to 49, 60 to 64, of Asian/Pacific Islander race, and all ranks below Senior Officer. No significant associations were observed by Service branch.

Conclusions
The prevalence of HT use among ADSW ages 45 to 65 is lower than HT use among the US veteran population age 45 and older but higher than among the US general population age 45 and older.
The role of short luteal phases on cycle regularity during the perimenopausal transition
Authors: Visby Madsen Caroline , Adornetto Gianluca , Kirkegaard Kirstine 
Published: December 2024

Abstract

Objective
The aim of the study was to explore the correlation between short luteal phases and cycle irregularity in perimenopausal women.

Methods
In this feasibility pilot study, daily salivary-progesterone measurements from presumed perimenopausal women have been analyzed using the inne minilab—an at-home system for ovulation and cycle tracking. Data were collected between 2020 to August 2022 from 29 women from Germany and Austria from users over the age of 42 years. Mean age was 44.5 years. The women were divided into two groups based on the presence of short luteal phases. Wilcoxon rank sum test was used to compare the two groups with regard to perimenopausal characteristics: cycle length variability, occurrence, and frequency of short cycles, long cycles, and anovulatory cycles.

Results
A significant correlation (P value =0.02) was found between short luteal phases and short cycle length under 23 days, with a median of two short cycles in the short luteal phase positive group compared to a median of 0 short cycles in the negative group. However, this correlation did not persist when adjusting for number of observations per participant. No difference was found when comparing other cycle characteristics

Conclusions
These findings could suggest that it may not be feasible to utilize the occurrence of short luteal phases in the context of expressing the likelihood of cycle irregularity, length, or anovulation. However, because of the small sample size in this study, the null findings could be due to lack of power. Larger studies would be needed to determine how short luteal phases may be correlated to cycle regularity.
Primary Care Screening for Nonalcoholic Fatty Liver Disease Among People With HIV in the United States: A Real-World Provider Survey
Authors: Price Jennifer C. , Hirose Kyoko , Chalasani Naga , Crandall Holly , Heath Sonya , Loomba Rohit , Naggie Susanna , Sterling Richard K. , Sulkowski Mark , Wilson Laura , Lake Jordan E. 
Published: December 2024

Abstract
Nonalcoholic fatty liver disease (NAFLD) is highly prevalent in people with HIV (PWH) and increases the risk of hepatic fibrosis and hepatocellular carcinoma. We sent an online survey to providers of the American Academy of HIV Medicine. Of respondents (n = 214, 8% response rate), 65% reported screening for NAFLD in PWH, with 28% routinely screening all patients. Most respondents refer patients to hepatology if workup suggests another coexisting liver disease or cirrhosis, with the primary goals of referral being additional diagnostic testing (60%) or specific treatments (75%). The most common barriers to screening were feeling unsure of what tests to order (28%) and how to conclusively diagnose NAFLD (29%). Most respondents were interested in society guidelines (73%) and NAFLD education for patients (57%) and providers (55%). Our findings support the development of NAFLD clinical practice guidelines for HIV providers and the inclusion of PWH in clinical trials of novel agents.
Unusual Presentation of a Pediatric Burkitt’s Lymphoma With Infiltration of the Interatrial Septum
Authors: Abdelmohsen Gaser , Alamri Aliaa , Algiraigri Ali , Elnakeeb Mohamed , Maghrabi Khadijah 
Published: December 2024

Background:
Burkitt’s lymphoma (BL) is the most common subtype of non-Hodgkin lymphoma in children, typically presenting with extranodal masses in areas such as the abdomen, face, and neck. Cardiac involvement in BL is extremely rare, especially in pediatric patients, and has significant implications for diagnosis, management, and prognosis.

Case Presentation:
A 6-year-old male patient with Burkitt’s lymphoma, presenting with an uncommon infiltration of the interatrial septum, is described. The patient initially presented with a painful right facial mass, bilateral periorbital edema, and a history of fever, weight loss, and lower limb pain. Imaging revealed extensive disease, including a right masticator muscle mass, mandibular infiltration, and multiple soft tissue and skeletal lesions, along with significant thickening of the interatrial septum. A diagnosis of Stage III Burkitt’s lymphoma was confirmed through biopsy and immunohistochemical analysis. The patient was treated according to the ANHL1131 protocol, including Rituximab and multi-agent chemotherapy. Remarkably, the cardiac infiltration showed substantial regression on follow-up echocardiography after chemotherapy.

Conclusions:
This case underscores the importance of a comprehensive cardiac evaluation in pediatric patients with Burkitt’s lymphoma, particularly when presenting with atypical manifestations such as interatrial septum involvement. The findings demonstrate that systemic chemotherapy can effectively treat cardiac infiltration, even in complex cases with extensive disease. This report highlights the need for awareness of rare cardiac presentations in pediatric lymphoma and the critical role of advanced imaging modalities in diagnosis and management. Continuous monitoring and early implementation of cardioprotective strategies are essential to optimize outcomes in such cases.
Lymphogranuloma Venereum Surveillance in Chlamydia trachomatis Positive Male Rectal Swabs Collected from I Want The Kit in Maryland, United States
Authors: Hardick Justin , Conte Madison , Young Mattlyn , Ramdeep Nisha , Manabe Yukari C , Hamill Matthew M 
Published: December 2024

Abstract

Background
Infection with Chlamydia trachomatis (CT) can have distinct clinical presentations, such as trachoma, or lymphogranuloma venereum (LGV). Certain populations are at greater risk for LGV acquisition and transmission, which requires a longer duration of therapy than other urogenital CT sexually transmitted infections (STIs). Commercial assays are not available in the United States to distinguish LGV from non-LGV serovars.

Methods
LGV real-time PCR was performed on rectal CT-positive samples (N = 93) obtained from men (N = 80) who ordered from a mail-in self-collection STI service between April 2021 and February 2024. pmpH gene sequencing was performed on all samples to confirm LGV versus non-LGV, and multi-locus sequence typing (MLST) was performed on LGV-positive samples (N = 7) for additional confirmation.

Results
LGV was detected in 7.5% (7/93) of samples by real-time PCR, with pmpH sequencing and MLST confirming 100% (7/7) of these results. Overall, pmpH sequencing data was obtained for 92% (86/93) of samples with the following serovar distribution based on BLAST analysis: 54% (47/86) J, 28% (24/86) F, 9% (8/86) E and 8% (7/86) L. No individual had more than one LGV positive sample. No statistically significant associations with demographic factors were identified.

Conclusions
LGV was detected in CT-positive rectal swabs from users of an online, mail-in, self-collect STI testing platform in Maryland. These data suggest that increased LGV reflexive testing may be warranted. These data also illustrate that mail-in programs for routine STI testing may be leveraged for public health surveillance purposes.
Comparison of Chlamydia trachomatis Seroprevalence and Risk Factors for Infection Among Women by Gender/Sex of Sex Partner, United States, 2013–2016
Authors: Paris Keely S. , Khosropour Christine M. , Balkus Jennifer E. , Waters Mary Bridget , Kreisel Kristen M. , Manhart Lisa E. 
Published: December 2024

ABSTRACT

Objectives
Women who report sex with women are thought to have lower risk for Chlamydia trachomatis (CT) infection than women who report sex with men only (WSM-only), but comparisons of lifetime burden are limited.

Methods
Among 1,418 sexually-experienced women aged 18-39 years participating in the National Health and Nutrition Examination Survey (2013-2016), we estimated weighted CT seroprevalence and Wald-based 95% confidence intervals (CI) in women who reported ever having sex with a woman (all reported having sex with men also) (WSWM) compared to WSM-only. We defined seropositivity as detection of Pgp3 antibodies and used stratified Poisson regression with robust standard errors to estimate prevalence ratios.

Results
Over half (58.3%) were White non-Hispanic; 16.2% were WSWM. WSWM were somewhat younger (mean = 27.8 vs. 29.0 years, p = 0.07), younger at sexual debut (mean = 15.6 vs. 17.5 years, p < 0.001), and had more lifetime male sexual partners (mean = 15.9 vs. 6.4, p < 0.001) than WSM-only. Weighted CT seroprevalence was 38.9% (95%CI = 30.4-47.4) in WSWM and 28.6% (95%CI = 24.4-32.9) in WSM-only. Correlates of higher CT seroprevalence in both groups were Black non-Hispanic race/ethnicity, Hispanic ethnicity, and CT infection in the prior year. Having ≥5 lifetime male partners compared to 1-2 partners was associated with higher seroprevalence among WSWM (PR = 4.5; 95%CI = 1.77-11.44) and WSM-only (PR = 2.7; 95%CI = 1.87-3.69). Among WSWM, bisexual identity was associated with lower seroprevalence. Among WSM-only, low income and younger age at sexual debut were associated with higher seroprevalence.

Conclusion
Lifetime CT burden was higher in WSWM than WSM-only. Number of lifetime male partners was the strongest predictor of seropositivity for WSWM.
Targeted Peptide Receptor Radionuclide Therapy With 177Lu-DOTATATE Alters Joints Inflammation
Authors: Usmani Sharjeel , Rasheed Rashid , Ahmed Najeeb , Omar Yehia , Numani Shah P. 
Published: December 2024

Abstract
High and frequent expression of somatostatin receptors in differentiated neuroendocrine neoplasms has paved the way for receptor-based, targeted peptide receptor radionuclide therapy especially for nonoperable or metastatic disease. Besides tumors, radiation, in one form or another, has been tested to treat inflammatory disease as well, and this goes back to the early 1990s when the first case of pneumonia treated with radiation showed complete resolution. Currently, radiotracers help in not only in vivo inflammation detection, characterization, and staging but also, and more importantly, for selection of treatment in individual patients. The same concept could be applied to treatment of infection, by coupling the radioisotopes to ligands that target sterile or nonsterile inflammation. In our case, targeted peptide receptor radionuclide therapy showed remarkable resolution of inflammatory joint disease.
Multiple interacting photonic modes in strongly coupled organic microcavities
Authors: Herrera Felipe , Barnes William L. 
Published: December 2024

Room-temperature cavity quantum electrodynamics with molecular materials in optical cavities offers exciting prospects for controlling electronic, nuclear and photonic degrees of freedom for applications in physics, chemistry and materials science. However, achieving strong coupling with molecular ensembles typically requires high molecular densities and substantial electromagnetic-field confinement. These conditions usually involve a significant degree of molecular disorder and a highly structured photonic density of states. It remains unclear to what extent these additional complexities modify the usual physical picture of strong coupling developed for atoms and inorganic semiconductors. Using a microscopic quantum description of molecular ensembles in realistic multimode optical resonators, we show that the emergence of vacuum Rabi splitting in linear spectroscopy is a necessary but not sufficient metric of coherent admixing between light and matter. In low-finesse multi-mode situations, we find that molecular dipoles can be partially hybridized with photonic dissipation channels associated with off-resonant cavity modes. These vacuum-induced dissipative processes ultimately limit the extent of light-matter coherence that the system can sustain.
This article is part of the theme issue ‘The quantum theory of light’.
The not quite Loudon–Fearn–Rarity–Tapster dip and its impact on the development of photonic quantum information
Authors: Rarity John G. 
Published: December 2024

This paper presents a short history of the discovery by Rodney Loudon and Heidi Fearn of the counter-intuitive destructive interference effect occurring when two indistinguishable photons meet at a beamsplitter. This effect, commonly known as the Hong Ou Mandel effect, underpins much of present day photonic quantum information processing. Here I try to review its development from inception to present day proposals of million qubit photonic quantum computers.
This article is part of the theme issue ‘The quantum theory of Light’.
Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability
Authors: Jocher Jessica , Janssen Philipp , Vieth Beate , Edenhofer Fiona C. , Dietl Tamina , Térmeg Anita , Geuder Johanna , Enard Wolfgang , Hellmann Ines 
Published: December 2024

AbstractThe identification of cell types remains a major challenge. Even after a decade of single-cell RNA sequencing (scRNA-seq), reasonable cell type annotations almost always include manual non-automated steps. The identification of orthologous cell types across species complicates matters even more, but at the same time strengthens the confidence in the assignment. Here, we generate and analyze a dataset consisting of embryoid bodies (EBs) derived from induced pluripotent stem cells (iPSCs) of four primate species: humans, orangutans, cynomolgus, and rhesus macaques. This kind of data includes a continuum of developmental cell types, multiple batch effects (i.e. species and individuals) and uneven cell type compositions and hence poses many challenges. We developed a semi-automated computational pipeline combining classification and marker based cluster annotation to identify orthologous cell types across primates. This approach enabled the investigation of cross-species conservation of gene expression. Consistent with previous studies, our data confirm that broadly expressed genes are more conserved than cell type-specific genes, raising the question how conserved - inherently cell type-specific - marker genes are. Our analyses reveal that human marker genes are less effective in macaques and vice versa, highlighting the limited transferability of markers across species. Overall, our study advances the identification of orthologous cell types across species, provides a well-curated cell type reference for futurein vitrostudies and informs the transferability of marker genes across species.
Synchronous 3D patterning of diverse CNS progenitors generates motor neurons of broad axial identity
Authors: Buchner Felix , Dokuzluoglu Zeynep , Thomas Joshua , Caldarelli Antonio , Kavali Shrutika , Rost Fabian , Grass Tobias , Rodríguez-Muela Natalia 
Published: December 2024

AbstractIn vitro human organoid models have become transformative tools for studying organogenesis, enabling the generation of spinal cord organoids (SCOs) that mimic aspects of spinal cord biology. However, current models do not produce spinal motor neurons (spMNs) with a wide range of axial identities along spinal cord segments within a single structure, limiting their utility in understanding human neural axial specification and the selective vulnerability of spMN subpopulations in motor neuron diseases. Here, we present a novel approach to enhance spMN axial heterogeneity in an advanced SCO model derived from neural stem cells (NSCs) and retinoic acid (RA)-primed neuromesodermal progenitors (NMPs). RA priming guided NMP differentiation into caudal neural progenitors, generating SCOs enriched in spMNs with posterior axial identities. To further diversify spMN populations, we optimized differentiation by synchronously patterning NSCs with RA-primed NMPs. Incorporating an endothelial-like network and skeletal muscle cells enhanced the organoids’ physiological complexity and neural maturation and organoid cell viability. This comprehensive approach, termed CASCO, provides a robust platform to study human spMN specification and model neurodegenerative diseases.
Neuronal alpha-Synuclein Disease stage progression over five years
Authors: Simuni Tanya , Gochanour Caroline , Nair Anuprita R , Brumm Michael C , Coffey Christopher , Poston Kathleen L , Chahine Lana M , Weintraub Daniel , Tanner Caroline M , Gonzalez-Latapi Paulina , Kopil Catherine M , Xiao Yuge , Chowdhury Sohini , Dam Tien , Pagano Gennaro , Stephenson Diane , Siderowf Andrew , Dunn Billy , Marek Kenneth 
Published: December 2024

ABSTRACTBackgroundNeuronal alpha-Synuclein Disease (NSD) is defined by presence of an in vivo biomarker of neuronal alpha-synuclein (n-asyn) pathology, independent of presence of clinical syndrome. The NSD integrated staging system (NSD-ISS) describes progression across the disease continuum as stages 0 to 6. The objective of this analysis was to assess 5-year longitudinal change in the NSD-ISS.MethodsAnalysis included a subset of participants from the Parkinson’s Progression Markers Initiative (PPMI) enrolled before 2020 as Parkinson’s disease, prodromal, or healthy controls who met NSD criteria. Staging was defined based on biomarkers of n-asyn and dopaminergic dysfunction in early stages, clinical features (cognition, other non-motor features, and parkinsonism), and increasing degree of functional impairment in stages 3-6. Stages were examined annually for 5 years, along with the determinants of progression and effects of dopaminergic medication.Findings576 participants were n-asyn positive and included in the analysis. Of these, 494 were enrolled as Parkinson’s disease, 74 as prodromal and 8 as healthy controls. At baseline 56% of participants were in stage 3, 24% stage 2B, 13% stage 4, 4% stage 2A, and <1% in the other stages. At year 5, the percent of individuals in stage 2B, 3, and 4 were 11%, 50%, and 34% respectively, indicating progression through NSD stages. Median (95% CI) time to next stage increase from baseline was 1·19 (1·07-2·01) for stage 2B, 4·98 (4·07-5·35) for stage 3, and 9·77 (7·04-NA) for stage 4. Progression was driven by functional impairment in predominantly motor domain (95%) for stage 2B to 3, increasing degree of non-motor dysfunction for stage 3 to 4 (46%), and combination of motor, non-motor and cognitive domains for stage 4 to 5. Initiation of dopaminergic medications lead to stage regression in 8% participants in stage 3 and 41% in stage 4.InterpretationOur analysis supports the validity of the NSD-ISS in defining stages of disease progression and support the utility of the NSD-ISS as a potential tool to identify clinical trial cohorts for drug development. Further validation in interventional studies is a crucial next step.FundingThe Michael J. Fox Foundation for Parkinson’s Research (MJFF).
Differential aggregation patterns ofEndozoicomonaswithin tissues of the coralAcropora loripes
Authors: Gotze Cecilie R , Dungan Ashley M , van de Meene Allison , Damjanovic Katarina , Philip Gayle K , Maire Justin , Hoj Lone , Blackall Linda L , van Oppen Madeleine JH 
Published: December 2024

AbstractBacteria in the genusEndozoicomonasare well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterising bacterial aggregates associated with the common reef-building coral,Acropora loripes, from the central Great Barrier Reef, Australia. A conventional cultivation-based method was employed to establish a pure culture collection of 11 undescribedEndozoicomonasstrains isolated fromA. loripes. Subsequent 16S rRNA gene sequence analysis revealed their classification into two distinct phylogenetic clades. To resolve their spatial distributionin hospite, clade-specific fluorescencein situhybridisation probes were designed. Aggregates were consistently observed in the gastrodermal tissue layers surrounding the upper and lower gastrovascular cavity and were predominantly formed by cells from the same phylogenetic clade, with a minor proportion of aggregates formed byEndozoicomonasfrom both targeted clades. Furthermore, a clear distinction in aggregation pattern was observed; one clade exhibited clusters with regular and contained growth patterns, whereas the other formed clusters lacking clear boundaries and having irregular shapes. Scanning electron microscopy revealed the presence of a membrane of unknown origin associated with bacterial aggregates in two instances, suggesting potential structural or functional differences in these aggregates. These contrasting morphological features underscore the need for comprehensive investigations into the underlying mechanisms governing bacterial aggregate formation in corals.
Zero-shot retention time prediction for unseen post-translational modifications with molecular structure encodings
Authors: Dens Ceder , Yeung Darien , Krokhin Oleg , Laukens Kris , Bittremieux Wout 
Published: December 2024

AbstractMass spectrometry-based proteomics relies on accurate peptide property prediction models to enhance peptide identification and characterization, especially when dealing with peptidoforms. However, current approaches are limited in their ability to generalize to peptides with novel post-translational modifications (PTMs) due to insufficient training data. To address this challenge, we introduce MoSTERT (Molecular Structure Transformer Encoder for Retention Time prediction) and its enhanced variant, MoSTERT-2S, two transformer-based models designed for zero-shot prediction of retention times of peptides with unseen PTMs. Unlike conventional models, MoSTERT encodes peptide residues at the molecular structure level, allowing it to handle diverse PTMs. MoSTERT-2S further improves accuracy by employing a two-step strategy: first predicting the retention time of the unmodified peptide, then estimating the retention time shift induced by the PTMs.Evaluation on an external dataset demonstrates that MoSTERT-2S achieves state-of-the-art performance, reducing prediction errors compared to existing methods. Its ability to accurately predict retention times for peptides with a wide variety of PTMs not seen during training highlights its potential for advancing proteomic workflows analyzing proteoforms and protein modifications.