bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations Between Hospital Nursing Resources and Breastfeeding Outcomes
Authors: Mason Aleigha , Lake Eileen T. , Clark Rebecca R. S. 
Published: September 2024

Purpose:
To summarize how nursing resources and missed nursing care are associated with hospital breastfeeding outcomes, including human milk provision.

Background:
Nurses are the primary providers of breastfeeding support in the hospital. Nursing resources, eg, staffing and the work environment, enable nurses to carry out their work successfully. If resources are constrained, nurses may miss providing breastfeeding support. There is a gap in the literature about the relationships among nursing resources, missed nursing care, and breastfeeding outcomes.

Methods:
The Cumulative Index to Nursing and Allied Health Literature and PubMed were searched with keywords such as: “nurse staffing,” “nurse work environment,” “missed nursing care,” “breastfeeding,” “human milk,” and “lactation.” We included peer-reviewed studies of US samples in English published between 2014 and 2022.

Results:
Of 312 references, 8 met inclusion criteria: 5 quantitative and 3 qualitative. Better nurse staffing and breastfeeding support were associated with improved breastfeeding outcomes in the qualitative and quantitative literature. Missed care partially mediated the relationship between staffing and exclusive breast milk feeding rates. Better nurse work environments were associated with increased breastfeeding support and provision of human milk.

Conclusions:
Empirical evidence supports an association between the nurse work environment, nurse staffing, breastfeeding support, and outcomes. Implications for practice and research: Poor staffing may be associated with decreased breastfeeding support and outcomes. Hospital administrators and nurse managers may consider improving nurse staffing and the work environment to improve breastfeeding outcomes. Future research should simultaneously examine staffing and the work environment and address breastfeeding outcome disparities.
The Barriers and Perceived Benefits to Vulvar Self-Examination in the Management of Vulvar Lichen Sclerosus
Authors: Adamson Sarah R. , Willems Anneliese , Chew Christopher Y. , Saunders Helen , Keogh Louise , Veysey Emma 
Published: September 2024

Objectives
It is common practice to advise people with vulvar lichen sclerosus to perform vulvar self-examination (VSE) to optimize topical therapy and detect changes that may represent active disease, scarring, and/or squamous cell carcinoma development. The aim of this study was to better understand people's willingness and potential barriers to performing VSE.

Materials and Methods
A cross-sectional survey was undertaken of all patients with vulvar LS presenting to a tertiary referral vulvar dermatology clinic in Australia, from June 2022 to January 2023. Patients who did not speak and read English were excluded. Ethics approval was obtained.

Results
Seventy-eight (66%) of 118 eligible patients completed the survey. Fifty-three (68%) of patients had examined their vulva at least once. Forty-one (49%) had been recommended VSE by a medical practitioner. All those recommended VSE had performed VSE at least once. In contrast, only 10 (27%) of the 37 patients not recommended VSE by a health professional had ever performed VSE. Seventy-nine percent of all patients reported that they were very likely or likely to perform VSE if it was recommended.
Patients with higher education level and tampon use were more likely to perform VSE. Self-reported back problems were associated with being less likely to perform VSE.

Conclusions
More widespread VSE may result in earlier detection of the complications of vulvar lichen sclerosus. Most women would perform VSE if recommended by a health care provider; however, currently only half are receiving this advice. Further research should be performed to determine whether VSE affects clinical outcomes.
Multimodality Evaluation of Persistent Hyperparathyroidism in a Rare Case of Ectopic Submandibular Parathyroid Adenoma
Authors: Edamadaka Yeshwanth , Malhotra Gaurav , Daga Aaditya , Memon Saba S. , Lila Anurag R. , Bandgar Tushar 
Published: September 2024

Abstract
A 53-year-old woman of primary hyperparathyroidism with both ultrasound neck examination and planar 99mTc-MIBI scan being negative revealed a tracer-avid focus in the left submandibular region in early (15 minutes postinjection) 99mTc-MIBI SPECT/CT views, raising a suspicion of rare ectopic parathyroid adenoma. This finding was correlated on 4D-CT and confirmed on histopathology following surgical excision. Submandibular region is an unusual location for ectopic parathyroid adenoma. Nevertheless, high degree of suspicion with utilization of multimodality imaging including 99mTc MIBI-SPECT/CT and 4D-CT improves preoperative detection of parathyroid adenoma at rare ectopic sites as seen in this case of persistent hyperparathyroidism.
Novel therapies for pediatric low grade glioma
Authors: Demaliaj Dardan , Gardner Sharon L. 
Published: September 2024

Purpose of review
Current biological findings provide new insights into the genetics driving growth of low-grade gliomas in pediatric patients. This has provided new targets for novel therapies. The purpose of this paper is to review novel therapies for pediatric low-grade gliomas that have been published in the past 24 months.

Recent findings
Low-grade gliomas are often driven by mitogen activated protein kinase (MAPK) alterations either with BRAF V600E point mutations or BRAF fusions. Current advances have also highlighted novel fusions of fibroblast growth factor receptor (FGFR), myeloblastosis family of transcription factors (MYB), meningioma 1 tumor suppressor (MN1), neurotrophic receptor kinase family of receptors (NTRK), Kristen RAS (Rat Sarcoma Virus) oncogene homolog in mammals (KRAS), Receptor tyrosine kinase ROS proto oncogene 1 (ROS1), protein kinase C alpha (PRKCA), and platelet derive growth factor receptor (PDGFR) amplification. Novel therapies have been employed and are showing encouraging results in pediatric low-grade gliomas. Current trials are underway with newer generation pan RAF inhibitors and mitogen activated protein kinase - kinase (MEK) inhibitors. Other early phase clinical trials have provided safety data in pediatric patients targeting FGFR fusion, NTRK fusion, PDGFR amplification and ROS1 mutations.

Summary
Historical treatment options in pediatric low-grade gliomas have utilized surgery, radiation therapy and conventional chemotherapy. Recently greater insight into their biology has found that alterations in MAPK driven pathways are often the hallmark of tumorigenesis. Targeting these novel pathways has led to tumor control and shrinkage without the use of conventional chemotherapy. Caution should be taken however, since these treatment options are still novel, and we do not fully appreciate the long-term effects. Nonetheless a new era of targeted medicine is here.
Reconstructing the diversity dynamics of paleo-grasslands using deep learning on superresolution images of fossil Poaceae pollen
Authors: Adaimé Marc-Élie , Kong Shu , Urban Michael A. , Street-Perrott F. Alayne , Verschuren Dirk , Punyasena Surangi W. 
Published: September 2024

AbstractDespite its abundance in the fossil record, grass pollen is largely overlooked as a source of ecological and evolutionary data because most Poaceae species cannot be differentiated using traditional optical microscopy. However, deep learning techniques can quantify the small variations in grass pollen morphology visible under superresolution microscopy. We use the abstracted morphological features output by deep learning to estimate the taxonomic diversity and physiology of fossil grass pollen assemblages. Using a semi-supervised learning strategy, we trained convolutional neural networks (CNNs) on pollen images of 60 widely distributed grass species and unlabeled fossil Poaceae. Semi-supervised learning improved the CNN models’ capability to generalize feature recognition in fossil pollen specimens. Our models successfully captured both the taxonomic diversity of an assemblage and morphological differences between C3and C4species. We applied our trained models to fossil grass pollen assemblages from a 25,000-year lake-sediment record from eastern equatorial Africa and correlated past shifts in grass diversity with atmospheric CO2concentration and proxy records of local temperature, precipitation, and fire occurrence. We quantified grass diversity for each time window using morphological variability, calculating both Shannon entropy and morphotype counts from the specimens’ CNN features. Reconstructed C3:C4ratios suggest a gradual increase in C4grasses with rising temperature and fire activity across the late-glacial to Holocene transition. Our results demonstrate that quantitative machine-learned features of pollen morphology can significantly advance palynological analysis, enabling robust estimation of grass diversity and C3:C4ratio in ancient grassland ecosystems.SignificanceThe pollen of most grass species are morphologically indistinguishable using traditional optical microscopy, but we show that they can be differentiated through deep learning analyses of superresolution images. Abstracted morphological features derived from convolutional neural networks can be used to quantify the biological and physiological diversity of grass pollen assemblages, withouta prioriknowledge of the species present, and used to reconstruct past changes in the taxonomic diversity and relative abundance of C4grasses in ancient grasslands. This approach unlocks ecological information that had been previously unattainable from the fossil pollen record and demonstrates that deep learning can solve some of the most intractable identification problems in the reconstruction of past vegetation dynamics.
Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts
Authors: Willemsen Anouk , Manzano-Marín Alejandro , Horn Matthias 
Published: September 2024

AbstractThe need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents six high-quality amoeba genomes from known and potential giant virus hosts belonging to two distinct eukaryotic clades:AmoebozoaandDiscoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long and short-read sequencing, we obtained highly contiguous and complete genomes ofAcanthamoeba castellanii, Acanthamoeba griffini,Acanthamoeba terricola,Naegleria clarki,Vermamoeba vermiformis, andWillaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the six amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of giant virus host range. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in non-matching hosts. Moreover, this study emphasises the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.
nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer
Authors: Hendley Audrey M. , Ashe Sudipta , Urano Atsushi , Ng Martin , Phu Tuan Anh , Peng Xianlu L. , Luan Changfei , Finger Anna-Marie , Jang Gun Ho , Kerper Natanya R. , Berrios David I. , Jin David , Lee Jonghyun , Riahi Irene R. , Gbenedio Oghenekevwe M. , Chung Christina , Roose Jeroen P. , Yeh Jen Jen , Gallinger Steven , Biankin Andrew V. , O’Kane Grainne M. , Ntranos Vasilis , Chang David K. , Dawson David W. , Kim Grace E. , Weaver Valerie M. , Raffai Robert L. , Hebrok Matthias 
Published: September 2024

ABSTRACTThe pleiotropic roles of nSMase2-generated ceramide include regulation of intracellular ceramide signaling and exosome biogenesis. We investigated the effects of eliminating nSMase2 on early and advanced PDA, including its influence on the microenvironment. Employing the KPC mouse model of pancreatic cancer, we demonstrate that pancreatic epithelial nSMase2 ablation reduces neoplasia and promotes a PDA subtype switch from aggressive basal-like to classical. nSMase2 elimination prolongs survival of KPC mice, hinders vasculature development, and fosters a robust immune response. nSMase2 loss leads to recruitment of cytotoxic T cells, N1-like neutrophils, and abundant infiltration of anti-tumorigenic macrophages in the pancreatic preneoplastic microenvironment. Mechanistically, we demonstrate that nSMase2-expressing PDA cell small extracellular vesicles (sEVs) reduce survival of KPC mice; PDA cell sEVs generated independently of nSMase2 prolong survival of KPC mice and reprogram macrophages to a proinflammatory phenotype. Collectively, our study highlights previously unappreciated opposing roles for exosomes, based on biogenesis pathway, during PDA progression.Graphical abstract
Invisible people: Exploring how well remote-sensed datasets reveal the distribution of forest-proximate populations
Authors: Rakotoarisoa Mirindra , Jones Julia P. G. , Rakotonarivo O. Sarobidy , Rajaonarivelo Manoa , Schüßler Dominik 
Published: September 2024

AbstractAccurate information on the location and density of people living at the forest frontier is vital for effective and equitable forest conservation. We compare the location of settlements and estimated population density from three global-scale, remote-sensed datasets (World Settlement Footprint 2015, Open Buildings, WorldPop) with a fine-scale, manually-derived dataset of 3,136 human settlements, of which 95% had fewer than 150 households. The study region is located in north-eastern Madagascar, contains three protected areas and the largest unprotected block of humid forest of the island. The Open Buildings dataset detected a much higher proportion (94%) of settlements than did World Settlement Footprint (15%). Population density from WorldPop matches poorly with that estimated from our manually-derived dataset. The accuracy of all three datasets is worse in more remote, forested areas, further away from basic infrastructure. Open Buildings appears to best reveal the distribution of low density scattered populations in forested areas. However, further testing in other climatic regions is still needed. Making good use of appropriate remote-sensed data could revolutionize the inclusion of local communities in conservation policy and practice, improve the quality of inference in conservation research, particularly in times of a planned expansion of the global protected area network.
Dynamics of serum BDNF After Aerobic Exercise in Subacute Stroke Patients: A Sub-Analysis of the randomized controlled Phys-Stroke trial
Authors: Rackoll Torsten , Doppelbauer Lea , Neumann Konrad , Heinrich Nave Alexander ,   the Phys-Stroke study group
Published: September 2024

AbstractDuring the very early phase of stroke recovery, the brain is hypothesized to be in a neuroplastic state that is responsive to external stimuli. Here, brain-derived neurotrophic factor (BDNF) is thought to play an important role. BDNF, a member of the neurotrophin family, is implicated in processes such as synaptogenesis and long-term potentiation. Post-stroke, reduced BDNF levels are observed compared to the healthy population. An intervention that has been shown to elevate BDNF is Aerobic exercise. Yet, the impact of aerobic exercise in stroke patients remains unclear. This sub-analysis of the multicenter, randomized, controlled ’Physical Fitness Training in Patients with Subacute Stroke’ trial aimed to investigate serum BDNF dynamics and the effects of a four-week aerobic exercise intervention on long- term BDNF levels.Data from 200 patients, with missing data imputed, revealed a modest increase in serum BDNF levels up to three months post-stroke (22.6 ng/ml, 95% CI 19.2 to 26) which plateaued until six months (24.3 ng/ml, 95% CI 20.6 to 27.9). Despite higher baseline BDNF levels in the exercise group, no treatment effect was observed until six months (training 24.6 ng/ml, 95% CI 20.2 to 29 vs relaxation: 24.3 ng/ml, 95% CI 19.8 to 28.8,p= 0.95). A sex-related interaction was identified in the relaxation group, with female patients exhibiting higher BDNF increases until end of follow up (20.9 ng/ml, 95% CI 15.7 to 26.2 (males) vs 31.0 ng/ml, 95% CI 22.9 to 39.0 (females),p= 0.039). Dose-response analyses and associations with recurrent events yielded no substantial differences.While serum BDNF levels increased early after stroke in the first three months, aerobic exercise did not demonstrate a significant impact on BDNF levels within this dataset. Further investigations with more measurements during the early subacute phase are warranted to elucidate the interplay between exercise, BDNF, and recovery.
SNRK regulates TGFβ levels in atria to control cardiac fibrosis
Authors: Thirugnanam Karthikeyan , Rizvi Farhan , Jahangir Arshad , Homar Peter , Shabnam Fathima , Palecek Sean P. , Kumar Suresh N. , Pan Amy , Bai Xiaowen , Sekine Hidekazu , Ramchandran Ramani 
Published: September 2024

AbstractAtrial fibrosis is central to the pathology of heart failure (HF) and atrial fibrillation (AF). Identifying precise mechanisms underlying atrial fibrosis will provide effective strategies for clinical intervention. This study investigates a metabolic serine threonine kinase gene,sucrose non-fermenting related kinase (SNRK),that we previously reported to control cardiac metabolism and function. Conditional knockout ofSnrkin mouse cardiomyocytes (SnrkcmcKO) leads to atrial fibrosis and subsequently HF. The precise mechanism underlying cardiomyocyte SNRK-driven repression of fibrosis is not known. Here, using mouse, rat, and human tissues, we demonstrate that SNRK expression is high in atria, especially in atrial cardiomyocytes. SNRK expression correlates with lower levels of pro-fibrotic protein transforming growth factor-beta 1 (TGFβ1) in the atrial cardiomyocytes. In HL-1 adult immortalized mouse atrial cells, using siRNA approaches, we show thatSnrkknockdown cells show more TGFβ1 secretion, which was also observed in heart lysates fromSnrkcardiac-specific knockout mice in vivo. These effects were exacerbated upon infusion of Angiotensin II. Results fromSnrkknockdown cardiomyocytes co-cultured with cardiac fibroblasts suggest that SNRK represses TGFβ1 signaling (Smad 2/3) in atrial CMs and prevents paracrine cardiac fibroblast activation (α-SMA marker). In conclusion, high SNRK expression in atria regulates cardiac homeostasis, by preventing the release of TGFβ1 secretion to block cardiac fibrosis. These studies will assist in developing heart chamber-specific fibrosis therapy for non-ischemic HF and AF.
Enabling Epitope Analysis of Glycoproteins via HDX-MS Using Antigens with Uniformed N-linked Glycans
Authors: Ota Takeshi , Takayama Masahiro , Ishihara Takeshi , Sato Masaaki , Ono Sawaka , Futamata Ryota , Fujitani Masaya , Rokushima Masatomo 
Published: September 2024

AbstractHydrogen deuterium exchange mass spectrometry (HDX-MS) is widely used for epitope analysis of the antibodies. However, epitope analysis of glycoproteins is challenging because of the heterogeneity of attached N-linked glycans. Recent studies have reported methods where N-linked glycans were removed at low pH following hydrogen deuterium exchange reactions, but the methods for glycoproteins remain controversial. Here, we demonstrate the utility of using antigens with uniformed N-linked glycans in glycoprotein epitope analysis by HDX-MS. By treating HEK293 cells with kifunensine, we were able to prepare antigens mainly with N-linked high-mannose-type glycans. Analysis of epitopes of a monoclonal antibody S309 using antigens prepared with this method allowed us to identify an epitope that included the previously reported N-linked glycan attachment sites for this anti-body. We propose that using antigens with uniformed glycans should be effective for epitope analysis of glycoproteins, such as virus spike proteins covered by glycan shields. Moreover, we believe that this approach accelerates research on vaccines and neutralizing antibodies against viruses that escape host immunity through glycan shields or mutations.
Neuropathological evidence of reduced amyloid beta and neurofibrillary tangles in multiple sclerosis cortex
Authors: Pansieri J. , Pisa M. , Yee S. , Gutnikova A. , Ridgeon E. , Hickman R. , Spencer J I , Esiri M. M. , DeLuca G. C. 
Published: September 2024

AbstractMultiple sclerosis (MS) and Alzheimer’s disease (AD) are neurodegenerative diseases demonstrating age-related accumulation of disability. Inflammation lasting decades is a paradigmatic feature of MS pathology that variably relates to neurodegeneration, while the accumulation of Aβ plaques and neurofibrillary tangles (NFT) are cornerstones of AD pathology. However, few studies investigated the accumulation of amyloids in MS.We investigated Aβ deposition and NFT density in temporal or frontal cortices derived from a large post-mortem cohort of MS (n=78) and age and sex-matched control (n=65) cases. We found reduced Aβ burden in MS cases compared with controls, particularly in cases below 65-years-of-age. NFT were similarly reduced in MS compared to controls, notably in cases above 65 years-of-age. Higher Aβ deposition predicted greater NFT density in MS. These findings suggest that MS-related factors may influence Aβ and NFT deposition and/or clearance. This work highlights new therapeutic perspectives relevant for both MS and AD.
Continual integration of single-cell multimodal data with MIRACLE
Authors: Zhou Jiahao , He Zhen , Wang Jing , Hu Shuofeng , Kan Tongtong , Dong Guohua , Shi Jinhui , Liu Runyan , Ou-Yang Le , Bo Xiaochen , Ying Xiaomin 
Published: September 2024

AbstractSingle-cell sequencing technologies have revolutionized our understanding of cellular heterogeneity and facilitated the construction of multi-omics cell atlases via data integration. However, updating these atlases with new data conventionally requires reintegration of all data and is computationally intensive, hindering timely updates and dynamic adjustments in biological and medical research. To address this challenge, we present Multimodal Integration with Continual Learning (MIRACLE), a novel online learning framework for the adaptive and efficient integration of single-cell multimodal data. MIRACLE employs dynamic architectures and data rehearsal strategies to support continual learning, allowing diverse data to be integrated while minimizing information loss over time. Our evaluations demonstrate that MIRACLE achieves accurate online integration with reduced computational requirements, effectively updating and expanding atlases with new cross-tissue and cross-modal data, and precisely identifying novel cell types and transferring labels across datasets. MIRACLE provides an efficient and flexible tool for single-cell community to integrate, share and explore biological knowledge from single-cell multimodal data.