bluuebunny/crossref_metadata_2025_split huggingface dataset:
Updates in nonhormonal therapy for perimenopausal and menopausal symptoms
Authors: Voedisch Amy J. 
Published: January 2025

Purpose of review
Perimenopausal and menopausal symptoms are common and may significantly impact quality of life. Menopausal hormone therapy is the most effective treatment but may not be appropriate in all cases. Nonhormonal alternatives range from lifestyle changes and dietary supplements to medical interventions and prescription therapies. This review will summarize the newest advancements in nonhormonal therapies for bothersome perimenopausal and menopausal symptoms.

Recent findings
The Menopause Society recently updated their recommendations and guidelines for nonhormonal therapies. Previous recommendations, such as clonidine and pregabalin, are no longer recommended. A new class of medication, neurokinin B antagonists, are now available to target vasomotor symptoms and show promise in addressing sleep and mood issues.

Summary
Well tolerated, effective nonhormonal therapies are available to address perimenopausal and menopausal symptoms for those patients who are not candidates for or chose not to use menopausal hormone therapy.
Sleep disturbance and menopause
Authors: Carmona Nicole E. , Solomon Natalie L. , Adams Karen E. 
Published: January 2025

Purpose of review
Sleep problems are among the most prevalent and bothersome symptoms of menopause. This review characterizes menopausal sleep disturbances, describes biopsychosocial predictors, and summarizes the evidence supporting pharmacological and nonpharmacological treatment options.

Recent findings
Recent studies found that sleep changes are early indicators of perimenopause and sought to disentangle the respective impacts of menopausal status, hot flashes (HFs), and changes in reproductive hormones on peri-/postmenopausal sleep problems. Both HFs and reproductive hormones predicted sleep problems, but neither solely accounted for the myriad changes in sleep, thus highlighting the contribution of additional biopsychosocial risk factors. Inconsistencies across studies were likely due to differences in study design and methodology, participants’ menopausal stage, and the presence of sleep complaints. Recent studies support the use of psychological (cognitive-behavioral therapy for insomnia) and pharmacological (e.g., neurokinin B antagonists) treatments in addition to hormone therapy.

Summary
Sleep problems are common and of critical import to women during the menopausal transition, significantly influencing treatment preferences and satisfaction. Thus, sleep problems should be routinely assessed from a biopsychosocial perspective and treated with evidence-based interventions throughout menopause. Treatment selection should be based on diagnosis and careful assessment.
Increased Incidence and Severity of Group A Streptococcal Infections in Children in Southeast Texas From June 2022 to May 2023
Authors: Hankins Julia D. , Johnson Coreen L. , Sanchez Belkys C. , Serrano Angela V. , Runge Jessica K. , Spinler Jennifer K. , Powell John W. , Luna Ruth Ann , Dunn James J. , Niles Denver T. 
Published: January 2025

Background:
Group A Streptococcus (GAS) infections can cause a range of disease manifestations and severity, including invasive infections that can lead to death. In 2022–2023, there was an increased number of cases of invasive GAS in the United States following a decline in 2020–2022.

Methods:
We investigated this surge at a 3-hospital system of children’s hospitals in Southeast Texas. Cases of invasive GAS (n = 252) were retrospectively reviewed from peak periods of infection, beginning June 2019–May 2020 and continuing each successive year until May 2023. Cases were analyzed based on patient demographics, disease manifestations, coinfections, and hospital course. Isolates grown in culture were sequenced, and the emm types and genes associated with virulence were analyzed.

Results:
Compared with previous years, June 2022–May 2023 had the largest number of invasive GAS cases (n = 154, 2022–2023; 34, 2021–2022; 12, 2020–2021; 52, 2019–2020). Compared with the previous 3 years, patients from 2022 to 2023 were more likely to present with complicated pneumonia (23.4% vs. 7.1%; P = 0.0009), require respiratory support (34.4% vs. 14.3%; P < 0.001), be admitted to the intensive care unit (29.2% vs. 16.3; P = 0.0235), and be infected with emm type 12 isolates (40.6% vs. 10.3%; P = 0.0030).

Conclusions:
In June 2022–May 2023, there was a 5-fold surge of invasive GAS infection cases in children at Texas Children’s Hospital compared with the previous 3 years. These cases required greater intensive care unit hospitalization and respiratory support requirements due to higher rates of complicated pneumonia.
Feeding interruptions for extubation and other procedures
Authors: Landais Mickael , Ehrmann Stephan , Guitton Christophe 
Published: January 2025

Purpose of review
The objective of this review is to examine the available evidence concerning feeding interruptions before extubation and other medical procedures in ICUs. We will analyze the physiological mechanisms involved, the potential risks associated with feeding interruptions, as well as the results of recent clinical studies. Additionally, we will explore current practices and recommendations from major professional societies, as well as recent innovations aimed at minimizing feeding interruptions.

Recent findings
Fasting before extubation is a common yet heterogeneous practice, varying across ICUs. Although dysphagia is a frequent complication after extubation, its prevalence decreases over time. However, physiologically, fasting before extubation appears ineffective in reducing gastric content or preventing aspiration. The Ambroisie study demonstrated that continuing enteral nutrition up to extubation is not inferior to a 6 h fasting strategy in terms of extubation failure at 7 days. The management of perioperative nutrition in intubated patients is debated. A retrospective study found no significant difference in postoperative respiratory events between patients fasting for at least 6 h and those fasting less or not at all but further prospective randomized studies are needed for definitive conclusions. For abdominal and digestive surgeries, fasting remains necessary to simplify procedures and reduce contamination risks. For invasive ICU procedures, such as catheter placement, the continuation of enteral nutrition appears reasonable. However, for percutaneous tracheotomy, limited evidence suggests no clear benefit from fasting, though the risk of large-volume aspiration during the procedure raises concerns. The approach to nutrition in this context requires further investigation.

Summary
Fasting before extubation in ICUs is a common practice inherited from anesthesia, aiming to reduce the risk of aspiration. The Ambroisie study demonstrates that continuing enteral nutrition until extubation is not inferior to a 6 h fasting strategy regarding extubation failure at 7 days.
Pessary Placement for Voiding Dysfunction Due to Prolapse Among Neurologically Intact Women
Authors: Ashmore Sarah , Mueller Margaret G. , Kenton Kimberly , Bretschneider C. Emi 
Published: January 2025

Importance
Literature surrounding conservative management of voiding dysfunction (VD) due to pelvic organ prolapse (POP) is limited.

Objective
The objective of this study was to evaluate the effect of pessaries on VD in women with symptomatic POP.

Study Design
This was a retrospective case series of adult women who underwent a pessary fitting for POP and VD between January 2010 to December 2022 at 2 tertiary care centers. Voiding dysfunction was defined as a composite outcome of participant report of obstructive voiding symptoms and postvoid residual volume (PVR) ≥150 mL prior to pessary fitting. Obstructive voiding symptoms were determined by positive response on the Pelvic Floor Distress Inventory-20 to items 5, 6, 19, and/or 20.

Results
Sixty-one participants with POP and VD underwent successful pessary fitting at 2 large academic institutions. Median (range) age was 75 years (35–89) and body mass index of 26.5 (18.0–46.3). Participant reports of “difficult bladder emptying” and “sensation of incomplete bladder emptying” were the most reported symptoms of obstructive voiding. Advanced staged prolapse (prolapse ≥ stage 3) was documented for 84% of participants. Median point C, Ba, and genital hiatus were −2 cm, +3 cm, and 4 cm, respectively, on examination. Median PVR prior to pessary fitting was 263 mL (150–810). Voiding dysfunction resolved in 60 out of 61 participants (98%). Median repeat PVR after pessary placement was 50 mL (0–250).

Conclusion
Pessary placement resolved VD due to POP in 98% of participants. Clinicians can offer pessary placement as nonsurgical management for participants with VD due to POP.
SH2D2A is an indicator of favourable prognosis in bladder cancer and is enriched in activated Treg cells
Authors: Gilmour Brian C. , Visser Johan Georg , Köhn-Luque Alvaro , Borowicz Paweł , Lossius Andreas , Spurkland Anne 
Published: January 2025

AbstractGiven the expanding availability of RNA-seq and other such high dimensional data it is now possible to consider a complementary approach working in the opposite directioni.e., from transcriptomics up towards protein function. This approach may prove fruitful in producing information on the function of cytosolic-bound proteins such as adapter proteins. To test the validity of this method, we made use of several public datasets to interrogate the cancer-specific role of the adapter protein SH2D2A: a protein enriched in T and NK cells and a known interactor of the kinase LCK, whose function remains uncertain. We found that SH2D2A is a favourable marker for prognosis in urothelial bladder cancer (BLCA). Digging further, we identified a population of SH2D2A+FOXP3+IL2RAhiactivated Tregs as the main expressors of SH2D2A in BLCA. This suggests that the expression of SH2D2A in these Tregs contributes to a beneficial prognostic effect. Further comprehension of SH2D2A’s function in these cells holds the potential for advancing treatment in BLCA and diversifying possible targets for immunotherapies.
Benchmarking of automated cancer cell annotation methods for scRNA-seq data reveals Consensus annotation as the preferred method
Authors: Abdelaal Tamim , Klijn Christiaan , Hancock Matt 
Published: January 2025

AbstractTargeted cancer therapies have shown therapeutic advantages due to tumor-specific drug activity. Single-cell RNA-sequencing has been widely used in cancer studies to define different cellular identities. However, accurate identification of tumor vs other normal cells is essential to define novel tumor-specific targets. Recent methods have been developed to perform the task of tumor cell annotation, which can be divided into two categories: CNV-based methods, which use transcriptome measurements to infer copy number variations and identify cells with alterations as tumor, and Reference-based methods which train a classifier using previously annotated tumor data and use it to annotate new datasets. We benchmarked the state-of-the-art method of each category, SCEVAN and scATOMIC, respectively, together with Consensus annotation method where a cell is considered tumor if both methods agree on that. Across 20 cancer datasets spanning 9 cancer types with a total of 379 samples, the Consensus annotation outperformed other methods in terms of precision score. SCEVAN works well when clear CNVs are detected, otherwise cells are randomly split between normal and tumor producing many false positives. While scATOMIC efficiently detects all normal cells except normal epithelial cells, where all epithelial cells (normal and malignant) are considered cancerous. The Consensus annotation method overcomes the limitations of both methods, being able to detect normal epithelial cells together with other normal cell types as non-tumor, also annotating malignant epithelial cells as tumor even with weak CNVs. This produces overall higher precision with the least number of false positives, leading to confident tumor-specific potential therapeutic targets. Implementation is available in the MACE R package through GitLab (https://gitlab.com/genmab-public/mace/).
Targeting anemia-induced CD71+reticulocytes protects mice fromPlasmodiuminfection
Authors: Zeydabadinejad Sareh , Kim Jong Sung Anthony , Zheng Anna , Kandalgaonkar Mrunmayee Rajendra , Ababio Prince Boakye , Vijay-Kumar Matam , Yeoh Beng San , Saha Piu 
Published: January 2025

AbstractMalaria, caused byPlasmodiumspp., is a global health concern linked to anemia and increased mortality. Compensatory erythropoiesis seen during acute anemia results in an increased circulating reticulocyte count (i.e., immature RBC) a key factor in understanding the relationship between pre-existing anemia andPlasmodiumburden. Reticulocytes in mice are marked by transferrin receptor (CD71+) and glycophorin A-associated protein (Ter119+). To model acute anemia with increased reticulocytes, C57BL/6 mice were either bled (i.e.phlebotomized) or administered phenylhydrazine, before being infected withPlasmodium yoelii(P. yoelii), a mouse-specific strain with a preference for reticulocytes. InP. yoelii-infected anemic mice, we observed heightened parasitemia and significant body weight loss compared with non-anemicP. yoelii-infected mice. Additionally, serum inflammatory cytokines, erythropoietin, and liver injury markers, along with hemozoin deposition significantly increased in anemicP. yoelii-infected mice. RBC transfusion from healthy normal donors toP. yoelii-infected anemic recipient mice ameliorated anemia by reducing overall reticulocyte count and increasing mature RBC count. RBC transfusion rescued body weight loss, decreased parasitemia, and reduced serum erythropoietin levels. Finally, to confirm the role of reticulocytes inP. yoeliiinfection, reticulocytes were depleted using anti-CD71 monoclonal antibody inP. yoelii-infected mice. We observed improvement in hematologic parameters and stark reduction in parasitemia in both pre-existing anemic and non-anemicP. yoelii-infected mice. Collectively, our results suggest that pre-existing anemia may increase the risk ofPlasmodiuminfection due to the greater reticulocytes population. Anti-CD71 treatment inPlasmodiuminfection may offer a novel therapeutic strategy to combatPlasmodiuminfection and malaria.Grant supportThis work was supported by grants from the Crohn’s and Colitis Foundation (CCF) and American Heart Association (AHA) Career Development Award (854385 and 855256 respectively) to Piu Saha; grant from the National Institutes of Health (NIH) to Matam Vijay-Kumar (DK134053) and Liver Scholar Award from American liver Foundation to Beng San Yeoh.
SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data
Authors: Saldanha Oliver Lester , Goepp Vivien , Pfeiffer Kevin , Kim Hyojin , Zhu Jie Fu , Kramann Rafael , Hayat Sikander , Kather Jakob Nikolas 
Published: January 2025

AbstractRapid technological advancements have made it possible to generate single-cell data at a large scale. Several laboratories around the world can now generate single-cell transcriptomic data from different tissues. Unsupervised clustering, followed by annotation of the cell type of the identified clusters, is a crucial step in single-cell analyses. However, there is no consensus on the marker genes to use for annotation, and celltype annotation is currently mostly done by manual inspection of marker genes, which is irreproducible, and poorly scalable. Additionally, patient-privacy is also a critical issue with human datasets. There is a critical need to standardize and automate celltype annotation across datasets in a privacy-preserving manner. Here, we developed SwarmMAP that uses Swarm Learning to train machine learning models for cell-type classification based on single-cell sequencing data in a decentralized way. SwarmMAP does not require any exchange of raw data between data centers. SwarmMAP has a F1-score of 0.93, 0.98, and 0.88 for cell type classification in human heart, lung, and breast datasets, respectively. Swarm Learning-based models yield an average performance of0.907which is on par with the performance achieved by models trained on centralized data (p-val=0.937, Mann-WhitneyUTest). We also find that increasing the number of datasets increases cell-type prediction accuracy and enables handling higher cell-type diversity. Together, these findings demonstrate that Swarm Learning is a viable approach to automate cell-type annotation. SwarmMAP is available athttps://github.com/hayatlab/SwarmMAP.
Plant domestication does not reduce diversity in root microbiomes
Authors: Hernández-Terán Alejandra , Escalante Ana E. , Rebolleda-Gómez Maria 
Published: January 2025

ABSTRACTDomestication has profoundly shaped human civilization and the genetic makeup of numerous plant and animal species. While the effects of plant domestication at the genetic and phenotypic levels are well-documented, its impact on plant microbiome remains less understood. Root microbiomes play crucial roles in nutrient acquisition, pathogen defense, and biotic stress tolerance, yet the influence of domestication on their diversity and assembly is still debated. Two primary hypotheses have been proposed: 1) the reduction in microbial diversity resulting from the domestication process, and 2) the diminished ability of host plants to control their microbiomes. To evaluate these hypotheses, we conducted a meta-analysis of multiple crops, comparing the root microbiomes of domesticated plants and their wild relatives. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased microbial diversity and more structured communities, while others show no significant change. Overall, this study provides evidence that plant domestication does not lead to a uniform reduction in microbial diversity or a consistently diminished ability of plants to influence their microbiomes. Based on these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation in such experiments, analyzing not only diversity but also microbiome function, and considering how root morphology might affect microbiome recruitment. Finally, we highlight the need for research on the potential adaptive or maladaptive consequences that introgression between wild and domesticated plants could have from a microbiome perspective.SIGNIFICANCE STATEMENTPlant domestication has had profound impacts on plant traits and their genetic makeup. These traits are likely to influence microbial interactions with the plants, but the overall effect of domestication on plant microbiomes is still subject to debate. In this work, we challenge two primary hypotheses regarding the effects of domestication on root microbiomes; we compared published microbiomes of wild and domesticated plants and found that domestication does not reduce microbial diversity or the plant’s contribution to their associated microbial communities. Instead, these effects vary between plant species and environmental conditions. This work provides insights into how domestication shapes plant-microbe relationships and discusses new approaches that are critical for advancing this area of research.
Engaging Private Pharmacies in Referring Tuberculosis Suspects in Pakistan: Findings and Implications
Authors: Saleem Zikria , Kiani Ayyaz 
Published: January 2025

ABSTRACTBackgroundWorld Health Organization (WHO) considers local pharmacies as an underused source that can contribute more effectively to the health care programs of the community. This study was aimed to evaluate the impact of involving private pharmacies for timely referral to facilitate TB case detection in Pakistan.MethodsIn this study, 398 pharmacies in five major districts of Pakistan were contacted. Patients having apparent TB symptoms or chronic cough for more than two weeks were referred for TB case detection to the nearby center of National TB Control Program (NTP). The patients were monitored and followed up to analyze the results of the diagnostic tests by involving pharmacy students.ResultsOut of 398 enrolled pharmacies, only 224 pharmacies (56.28%) were producing referrals. A total of 994 TB suspects were referred for tests out of which 839 (84.4%) actually appeared for the TB examination tests while 155 (15.5%) were missing. Of total 839 tested suspects, 189 (22.5%) were diagnosed with smear positive TB.ConclusionCommunity pharmacies under the thematic model of public private partnership can be the key players in tracing, preventing and early diagnosis of TB. This project can be extended and implemented in all provinces of Pakistan with more technical and financial inputs in the existing system in order to completely eradicate TB.
Multilayer regulation underlies the functional precision and evolvability of the olfactory system
Authors: Mermet Jérôme , Cruchet Steeve , Borbora Asfa Sabrin , Lee Daehan , Chai Phing Chian , Jang Andre , Menuz Karen , Benton Richard 
Published: January 2025

AbstractSensory neurons must be reproducibly specified to permit accurate neural representation of external signals but also able to change during evolution. We studied this paradox in theDrosophilaolfactory system by establishing a single-cell transcriptomic atlas of all developing antennal sensory lineages, including latent neural populations that normally undergo programmed cell death (PCD). This atlas reveals that transcriptional control is robust, but imperfect, in defining selective sensory receptor expression. A second layer of precision is afforded by the intersection of expression of functionally-interacting receptor subunits. A third layer is defined by stereotyped PCD patterning, which masks promiscuous receptor expression in neurons fated to die and removes “empty” neurons lacking receptors. Like receptor choice, PCD is under lineage-specific transcriptional control; promiscuity in this regulation leads to previously-unappreciated heterogeneity in neuronal numbers. Thus functional precision in the mature olfactory system belies developmental noise that might facilitate the evolution of sensory pathways.
Evidence of dengue virus transmission and a diverseAedesmosquito virome on the Democratic Republic of Congo-Angola border
Authors: He Wenqiao , Bobanga Thierry , Piantadosi Anne , Popkin-Hall Zachary R. , Vulu Fabien , Collins Matthew H. , Kashamuka Melchior M. , Tshefu Antoinette K. , Juliano Jonathan J. , Parr Jonathan B. 
Published: January 2025

AbstractAedesmosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collectedAedesmosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools of 115 mosquitoes confirmed high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.