bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environment friendly synthesis of Fe3O4 nanoparticles using moringa oleifera seed/pulp extract and their application for dye wastewater treatment
Authors: Vora Rutvi , Patel Hima , Parekh Kinnari 
Published: December 2024

Abstract
A simple, eco-friendly, green synthesis protocol for producing biocompatible iron oxide nanoparticles using the Moringa oleifera (MO) seed/pulp extracts (MSE/MPE) is reported. The crystallite phase formation of magnetite nanoparticles is confirmed using a powder x-ray diffractometer. The morphology, surface properties, and magnetic properties are investigated using a transmission electron microscope (TEM), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and vibrating sample magnetometer (VSM). The particles with optimized properties from MSE and MPE synthesis are used for investigating their photocatalytic activity on methylene blue dye. Results of dye degradation show that the particles synthesized using MSE showed 53.46% degradation, whereas MPE showed 37.87% degradation of methylene blue dye under UV light. The photodegradation process follows pseudo-second-order kinetic model indicating that the dye is degraded to its intermediate compounds, which are chemically adsorbed on the particle surface, as confirmed through FTIR. The results show promising potential of synthesizing such nanoparticles for treatment of wastewater using a greener approach.
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers
Authors: Wojtulewski Adam , Sikora Aleksandra , Dineen Sean , Raoof Mustafa , Karolak Aleksandra 
Published: December 2024

Abstract

Objective
The primary objective of this study is to investigate various applications of artificial intelligence (AI) and statistical methodologies for analyzing and managing peritoneal metastases (PM) caused by gastrointestinal cancers.

Methods
Relevant keywords and search criteria were comprehensively researched on PubMed and Google Scholar to identify articles and reviews related to the topic. The AI approaches considered were conventional machine learning (ML) and deep learning (DL) models, and the relevant statistical approaches included biostatistics and logistic models.

Results
The systematic literature review yielded nearly 30 articles meeting the predefined criteria. Analyses of these studies showed that AI methodologies consistently outperformed traditional statistical approaches. In the AI approaches, DL consistently produced the most precise results, while classical ML demonstrated varied performance but maintained high predictive accuracy. The sample size was the recurring factor that increased the accuracy of the predictions for models of the same type.

Conclusions
AI and statistical approaches can detect PM developing among patients with gastrointestinal cancers. Therefore, if clinicians integrated these approaches into diagnostics and prognostics, they could better analyze and manage PM, enhancing clinical decision-making and patients’ outcomes. Collaboration across multiple institutions would also help in standardizing methods for data collection and allowing consistent results.
Predicting CRISPR-Cas9 off-target effects in human primary cells using bidirectional LSTM with BERT embedding
Authors: Sari Orhan , Liu Ziying , Pan Youlian , Shao Xiaojian 
Published: December 2024

Abstract

Motivation
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system is a ground-breaking genome editing tool, which has revolutionized cell and gene therapies. One of the essential components involved in this system that ensures its success is the design of an optimal single-guide RNA (sgRNA) with high on-target cleavage efficiency and low off-target effects. This is challenging as many conditions need to be considered, and empirically testing every design is time-consuming and costly. In silico prediction using machine learning models provides high-performance alternatives.

Results
We present CrisprBERT, a deep learning model incorporating a Bidirectional Encoder Representations from Transformers (BERT) architecture to provide a high-dimensional embedding for paired sgRNA and DNA sequences and Bidirectional Long Short-term Memory networks for learning, to predict the off-target effects of sgRNAs utilizing only the sgRNAs and their paired DNA sequences. We proposed doublet stack encoding to capture the local energy configuration of the Cas9 binding and applied the BERT model to learn the contextual embedding of the doublet pairs. Our results showed that the new model achieved better performance than state-of-the-art deep learning models regarding single split and leave-one-sgRNA-out cross-validations as well as independent testing.

Availability and implementation
The CrisprBERT is available at GitHub: https://github.com/OSsari/CrisprBERT.
SampleExplorer: using language models to discover relevant transcriptome data
Authors: Chin Wee Loong , Lassmann Timo 
Published: December 2024

Abstract

Motivation
Over the last two decades, transcriptomics has become a standard technique in biomedical research. We now have large databases of RNA-seq data, accompanied by valuable metadata detailing scientific objectives and the experimental procedures used. The metadata is crucial in understanding and replicating published studies, but so far has been underutilized in helping researchers to discover existing datasets.

Results
We present SampleExplorer, a tool allowing researchers to search for relevant data using both text and gene set queries. SampleExplorer embeds sample metadata and uses a transformer-based language model to retrieve similar datasets. Extensive benchmarking (see Supplementary Materials and Methods) using the ARCHS4 database demonstrates that SampleExplorer provides an effective approach for retrieving biologically relevant samples from large-scale transcriptomicdata. This tool provides an efficient approach for discovering relevant gene expression datasets in large public repositories. It improves sample and dataset identification across diverse experimental contexts, helping researchers leverage existing transcriptomic data for potential replication or verification studies.

Availability and implementation: SampleExplorer is available as a Python package compatible with versions 3.9 to 3.11, available for installation via the Python Package Index (PyPI). The codebase and documentation are accessible at https://github.com/wlchin/SampleExplorer. Supplementary data (Supplementary Materials and Methods) provides detailed methodological information, including an algorithmic description of the retrieval process and data preparation steps.
Development of pH-responsive crosslinked peptides that form stable α-helices under weakly acidic conditions
Authors: Amano Miwo , Chiba Junya , Yasukagawa Tetsuya , Yokoyama Satoru , Zhou Yue , Ohishi Yuki , Inouye Masahiko 
Published: December 2024

Abstract
α-Helical structures in protein surface are frequently related to protein–protein interactions that play important roles in signal transduction. We have developed various crosslinking agents that stabilize the α-helical structure of short peptides. In this article, we report pH-responsive crosslinked peptides that promote helical conformation of the peptides under weakly acidic conditions. We incorporated critical sequence of a synthetic estrogen receptor activity-regulating peptide into our pH-responsive crosslinked peptide. The pH control could provide total structural regulation of the target peptide.
A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy
Authors: Velotta Jonathan P , Iqbal Azwad R , Glenn Emma S , Franckowiak Ryan P , Formenti Giulio , Mountcastle Jacquelyn , Balacco Jennifer , Tracey Alan , Sims Ying , Howe Kerstin , Fedrigo Olivier , Jarvis Erich D , Therkildsen Nina O 
Published: December 2024

Abstract
Transitions across ecological boundaries, such as those separating freshwater from the sea, are major drivers of phenotypic innovation and biodiversity. Despite their importance to evolutionary history, we know little about the mechanisms by which such transitions are accomplished. To help shed light on these mechanisms, we generated the first high-quality, near-complete assembly and annotation of the genome of the American shad (Alosa sapidissima), an ancestrally diadromous (migratory between salinities) fish in the order Clupeiformes of major cultural and historical significance. Among the Clupeiformes, there is a large amount of variation in salinity habitat and many independent instances of salinity boundary crossing, making this taxon well-suited for studies of mechanisms underlying ecological transitions. Our initial analysis of the American shad genome reveals several unique insights for future study including: (i) that genomic repeat content is among the highest of any fish studied to date; (ii) that genome-wide heterozygosity is low and may be associated with range-wide population collapses since the 19th century; and (iii) that natural selection has acted on the branch leading to the diadromous genus Alosa. Our analysis suggests that functional targets of natural selection may include diet, particularly lipid metabolism, as well as cytoskeletal remodeling and sensing of salinity changes. Natural selection on these functions is expected in the transition from a marine to diadromous life history, particularly in the tolerance of nutrient- and ion-devoid freshwater. We anticipate that our assembly of the American shad genome will be used to test future hypotheses on adaptation to novel environments, the origins of diadromy, and adaptive variation in life history strategies, among others.
Times needed to evolve mating cues under allopatry and parapatry
Authors: Sibly Richard M , Curnow Robert N 
Published: December 2024

Abstract
The time needed for the evolution of mating cues that distinguish species, such as species-specific songs or plumage coloration in birds, has received little attention. Aiming to gain some understanding of the timing of the evolutionary process we here present models of how mating cues evolve in populations split into subpopulations between which there may (parapatry) or may not (allopatry) be migration. Mating cues can be either neutral or directly selected. In models in which evolution commences with a substitution at a neutral mating-cue locus, under allopatry there is no selection on the mating cue, but under parapatry, selection may be induced on the mating cue by the selective conditions in the subpopulations, and the migration rates between them. We use simulation to calculate how selection pressures on mating cues then depend on selective conditions in subpopulations and migration rates between them. In the second part of the paper, we demonstrate quantitatively how the resulting selection pressures on new mating cues together with mutation rate affect speciation time. Our results suggest that species-specific songs or plumage colorations that are selectively neutral evolve faster under parapatry than under allopatry, and this may explain the short speciation times that are sometimes reported. Although our modelling assumptions are restrictive so that caution is needed in comparing the results to empirical data, we hope that our main results, showing quantitatively how parapatry can reduce speciation times, will encourage further work relaxing model assumptions or studying different models of mate choice.
Giant periscapular lipoma unmasked by post-bariatric surgery weight loss: a case report
Authors: Mohammad Hussain , Almajed Suaad , Nawaf Norah , AlMulla Nawar , Lari Ali , Jarragh Ali 
Published: December 2024

Abstract
Giant lipomas, rare benign tumours composed of mature adipose tissue, represent only 1% of all lipomas, typically exceeding 10 cm in diameter or weighing over 1000 g. These tumours can cause nerve compression, discomfort, or functional impairment, necessitating surgical excision. We report a 52-year-old male with a giant intramuscular lipoma in the periscapular region, initially identified following significant weight loss after bariatric surgery. Clinical evaluation revealed a 15 × 20 cm mass, confirmed via computed tomography (CT) scan. Surgical excision was performed, followed by histopathological analysis, which confirmed a benign lipoma. Postoperative management was complicated by seroma formation, requiring drainage. This case underscores the importance of early diagnosis, imaging, and appropriate surgical management for large lipomas to prevent complications and recurrence while ensuring optimal cosmetic outcomes.
A field resource for the glioma cerebrospinal fluid proteome: impacts of resection and location on biomarker discovery
Authors: Riviere-Cazaux Cecile , Graser Christopher J , Warrington Arthur E , Hoplin Matthew D , Andersen Katherine M , Malik Noor , Palmer Elizabeth A , Carlstrom Lucas P , Dasari Surendra , Munoz-Casabella Amanda , Ikram Samar , Ghadimi Keyvan , Himes Benjamin T , Jusue-Torres Ignacio , Sarkaria Jann N , Meyer Fredric B , Van Gompel Jamie J , Kizilbash Sani H , Sener Ugur , Michor Franziska , Campian Jian L , Parney Ian F , Burns Terry C 
Published: December 2024

Abstract

Background
While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples for monitoring biomarker discovery, including anatomical location and post-surgical changes, remains unknown.

Methods
Aptamer-based proteomics was performed on 147 CSF samples from 74 patients; 71 of whom had grade 2–4 astrocytomas or grade 2–3 oligodendrogliomas. This included pre- versus post-resection intracranial CSF samples obtained at early (1–16 days; n = 20 patients) or delayed (86–153 days; n = 11 patients) time points for patients with glioma. Paired lumbar versus intracranial glioma CSF samples were also obtained (n = 14 patients).

Results
Significant differences were identified in the CSF proteome between lumbar, subarachnoid, and ventricular CSF in patients with gliomas. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome, with distinct sets of proteins present at different time points since resection. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies, such as bevacizumab and immunotherapies.

Conclusions
The intracranial glioma CSF proteome serves as a rich and dynamic reservoir of potential biomarkers that can be used to evaluate the effects of resection and other therapies over time. All data within this study, including detailed individual clinical annotations, are shared as a resource for the neuro-oncology community to collectively address these unanswered questions and further understand glioma biology through CSF proteomics.
Maternal-Infant Respiratory Syncytial Virus and Influenza A Virus Antibody Transfer in Preterm and Full-term Infants
Authors: Rumfelt Kalee E , Pike Mindy , Stolarczuk Jennifer E , Lekander Ava , Lauring Adam S , Eckert Linda O , Englund Janet A , Martin Emily T , Kachikis Alisa B 
Published: December 2024

Abstract

Background
Immunization against influenza and respiratory syncytial virus (RSV) protects pregnant individuals and their infants against infection via transplacental transport of immunoglobulin G (IgG). We sought to evaluate the quantity and efficiency of maternal influenza- and RSV-specific IgG transfer in pregnancies with preterm and full-term deliveries.

Methods
Delivery samples from 115 maternal-infant pairs (2018-2021) were analyzed for RSV prefusion F and IAV-H3 and IAV-H1 antibodies using electrochemiluminescence assays. We used Wilcoxon rank sum tests, t tests, Pearson correlation coefficients (PCCs), and linear regression to evaluate distributions of IgG results by maternal influenza vaccination status and preterm birth (&lt;37 weeks).

Results
Approximately 70% of pregnant persons received influenza vaccine. Maternal and cord antibody concentrations were highest in the influenza-vaccinated group for IAV-H3 and IAV-H1 regardless of preterm birth status (maternal H3, P = .004; cord H3, P = .03; maternal H1, P = .0001; cord H1, P = .0002). Preterm infants had significantly lower cord to maternal IgG transfer ratios for IAV-H3 and RSV when compared with full-term infants (P ≤ .05). Correlations between maternal and cord IgG concentrations were significant (P ≤ .001) for all 3 viruses, with the strongest correlation for H3 (PCC: IAV-H3, 0.77; IAV-H1, 0.68; RSV, 0.62). Associations between maternal IgG transfer and preterm birth were significant for IAV-H3 and RSV (IAV-H3, β = −0.42; RSV, β = −0.63; P ≤ .05).

Conclusions
Maternal antibody following vaccination or infection is readily transferred across the placenta. Preterm infants have higher influenza IgG following maternal influenza vaccination and are at highest risk of lower IgG transfer ratios without vaccination.
Urogenital Schistosoma haematobium Cases at the Hospital for Tropical Diseases, London (1998-2018), and Suggested Pragmatic Follow-up Pathway for Non-endemic Settings
Authors: Warrell Clare E , Polley Spencer , Bodhani Rashmita , Coltart Cordelia E M , Rafferty Hannah , Nabarro Laura E , Godbole Gauri , Bustinduy Amaya L , Hsieh Michael H , Chiodini Peter L 
Published: December 2024

Abstract

Background
Characteristics of confirmed urogenital Schistosoma haematobium infections and outcomes in non-endemic regions are scarce in the literature and there is a minimal evidence base for appropriate management in this setting. Specific schistosomal urinary and urological complications include risk of hydronephrosis, renal impairment, and malignant transformation. Therefore, approach to follow-up should be robust and systematic.

Methods
This is a retrospective case-note review of all patients with confirmed S haematobium infection (defined as visible ova in terminal urine and/or histopathological diagnosis on biopsy) at the Hospital for Tropical Diseases (HTD), London, between 1998 and 2018. Outcomes of follow-up were reviewed and formulated into a pragmatic guideline for follow-up of these patients in this setting.

Results
A majority of the 186 patients with confirmed S haematobium infection presented before 2012. Young, male migrants were at highest risk of complications from chronic infection and were most prone to being lost to follow-up. One patient was referred with squamous cell carcinoma of the bladder found on biopsy with S haematobium infection.

Conclusions
We put forward a pragmatic pathway for S haematobium investigation and follow-up for patients presenting to nonendemic settings with the current resource capabilities of the United Kingdom.
The Prevalence of Multidrug Resistance in Enterobacterales Is Higher in Patients Undergoing Hematopoietic Stem Cell Transplantation
Authors: Andermann Tessa M , Brown Dylan , Holowka Thomas , Bartelt Luther A , Serody Jonathan S , Armistead Paul M , Jamieson Katarzyna J , Conlon Brian P , Rao Gauri G , Alby Kevin , van Duin David , Henderson Heather I 
Published: December 2024

Abstract

Background
Antimicrobial resistance is a global public health emergency. Patients undergoing hematopoietic stem cell transplantation (HCT) are at increased risk for severe infections with multidrug-resistant (MDR) organisms, although more data are needed on the relative burden of MDR Enterobacterales (MDR-E) in immunocompromised populations. In this study, we compare the prevalence of Enterobacterales resistance in cultures from patients undergoing HCT with that of non-HCT patients seeking care at a large healthcare system in North Carolina, USA.

Methods
We analyzed electronic health data from 52 067 patients aged ≥18 years with a culture positive for Enterobacterales species (2000–2023). Of these, 271 had undergone HCT prior to culture-recovered Enterobacterales. We compared resistance trends over time for specific antibacterial classes using a 5-year moving average and used generalized linear models to estimate prevalence ratios and differences of MDR-E in HCT versus non-HCT patients.

Results
HCT recipients overall had a higher prevalence of MDR-E (37.7% vs 19.4%) and resistance for all individual antibiotic classes analyzed. Comparing HCT vs non-HCT groups, the highest prevalence ratio was observed for resistance to aminoglycosides (2.10 [95% confidence interval {CI}, 1.65–2.68]); the largest adjusted absolute difference in nonsusceptibility was observed with quinolones (20.4 [95% CI, 14.9–25.8]). MDR-E infections were associated with double all-cause mortality at 1 year.

Conclusions
This large longitudinal study highlights how antimicrobial resistance has consistently been a substantial problem in HCT recipients over the prior 2 decades. Targeting antimicrobial resistance mitigation efforts will be key in reducing the risk of MDR infections in HCT.
Central sleep apnea and cardiovascular disease state-of-the-art
Authors: Javaheri Shahrokh , Giannoni Alberto , Somers Virend K , Malhotra Atul , Emdin Michele , Costanzo Maria R 
Published: December 2024

Abstract
Central sleep apnea, a rare polysomnographic finding in the general population, is prevalent in certain cardiovascular conditions including systolic and diastolic left ventricular dysfunction, atrial fibrillation, coronary artery disease, carotid artery stenosis, stroke, and use of certain cardiac-related medications. Polysomnographic findings of central sleep apnea with adverse cardiovascular impacts include nocturnal hypoxemia and arousals, which can lead to increased sympathetic activity both at night and in the daytime. Among cardiovascular diseases, central sleep apnea is most prevalent in patients with left ventricular systolic dysfunction; a large study of more than 900 treated patients has shown a dose-dependent relationship between nocturnal desaturation and mortality. Multiple small randomized controlled trials have shown mitigation of sympathetic activity when central sleep apnea is treated with nocturnal oxygen, continuous positive airway pressure, and adaptive servoventilation. However, two early randomized controlled trials with positive airway pressure devices have shown either a neutral effect on survival or excess premature mortality in the active treatment arm, compared to untreated central sleep apnea. In contrast, the results of the most recent trial using an advanced adaptive servoventilation device showed improved quality of life and no signal for mortality suggesting that treatment of central sleep apnea was at least safe. In addition to positive airway pressure devices, multiple medications have been shown to improve central sleep apnea, but no long-term trials of pharmacologic therapy have been published. Currently, phrenic nerve stimulation is approved for the treatment of central sleep apnea, and the results of a randomized controlled trial showed significant improvement in sleep metrics and quality of life.