bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remote underwater video for monitoring reef fish spawning aggregations
Authors: Saulnier Erwan , Breckwoldt Annette , Robert Marianne , Pelletier Dominique 
Published: December 2024

Abstract
Fish spawning aggregations (FSAs) are critical events in the life cycle of many commercially and ecologically important species, yet FSAs are often exploited and highly vulnerable to fishing due to their predictability in time and space. Although FSAs are increasingly recognized as a conservation and management priority, monitoring these ephemeral dynamic events remains challenging. Here, we assessed the ability of remote underwater video (RUV) to monitor reef FSAs, using blacksaddled coral grouper (Plectropomus laevis) as a case study. We deployed RUV systems monthly on a year-round basis in a reef channel of the New Caledonian barrier reef where P. laevis was assumed to form spawning aggregations. Specifically, we investigated whether RUV could both track spatiotemporal changes in fish abundance and detect spawning signs to validate the purpose of potential gatherings. Our analysis revealed strong seasonal changes in P. laevis abundance, characterized by a 5-fold increase between October and February, and marked variations among sampled habitats. The probability of occurrence of males in courtship colouration showed spatiotemporal patterns fairly similar to those in abundance. Finally, we recorded clear courtship behaviours between November and April, providing evidence that P. laevis aggregate monthly to spawn during a protracted reproductive season. This study advances our understanding of the spawning aggregation dynamics of this understudied grouper, and highlights the potential of RUV to monitor and ultimately inform management of reef FSAs.
AI-Augmented Kidney Stone Composition Analysis with Auto-Release Improves Quality, Efficiency, Cost–Effectiveness, and Staff Satisfaction
Authors: Day Patrick L , Rokke Denise , Schneider Laura , Abbott Jillian , Holmen Brenda , Johnson Patrick , Wieczorek Mikolaj A , Kunze Katie L , Carter Rickey E , Bornhorst Joshua , Jannetto Paul J 
Published: December 2024

Abstract

Background
We sought to evaluate key performance indicators related to an internally developed and deployed artificial intelligence (AI)-augmented kidney stone composition test system for potential improvements in test quality, efficiency, cost-effectiveness, and staff satisfaction.

Methods
We compared quality, efficiency, staff satisfaction, and financial data from the 6 months after the AI-augmented laboratory test system was deployed (test period) with data from the same 6-month period in the previous year (control period) to determine if AI-augmentation improved key performance indicators of this laboratory test.

Results
In the 6 months following the deployment (test period) of the AI-augmented kidney stone composition test system, 44 830 kidney stones were analyzed. Of these, 92% of kidney stones were eligible for AI-assisted interpretation. Out of these AI-eligible stones, 45% were able to be auto-released by the AI-augmented test system without human secondary review. Furthermore, the new AI-augmented kidney stone test system resulted in an apparent 40% reduction in incorrect laboratory results. Additionally, the new AI-augmented test system improved laboratory efficiency by 20%, improved staff satisfaction, and reduced the average analysis cost per kidney stone by $0.23.

Conclusions
The AI-augmented test system improved test quality, efficiency, cost-effectiveness and staff satisfaction related to this kidney stone composition test.
Observation of Tropilaelaps mercedesae (Mesostigmata: Laelapidae) on Western honey bees (Apis mellifera) exiting colonies
Authors: Tokach Rogan , Aurell Dan , Chuttong Bajaree , Williams Geoffrey R 
Published: December 2024

Abstract
Tropilaelaps mercedesae (Delfinado and Baker) is an emerging parasitic mite that can severely impact the Western honey bee (Apis mellifera L.). While T. mercedesae has been reported to be expanding its geographical range, the routes of inter-colony dispersal between A. mellifera colonies are still largely unknown. In this study, we used funnel traps to collect foraging honey bees exiting their colonies before performing an alcohol wash to collect any phoretic T. mercedesae mites. We found T. mercedesae on exiting adult honey bees; however, they were only detected when a colony had an elevated T. mercedesae brood infestation. We show that T. mercedesae can exit colonies through phoresy on adult A. mellifera which demonstrates the potential of these mites to be spread through the natural movement of A. mellifera honey bees among colonies.
The copyright and design protection interplay post-Cofemel: continuity or recalibration?
Authors: Sipetas Spyros 
Published: December 2024

Abstract
The Cofemel judgment of the Court of Justice of the European Union (CJEU) was issued against a backdrop of uncertainty regarding the protectability of fashion designs by copyright as works of applied art. The initial reflex to this decision, thought to have a radical effect on the copyright–design protection overlap, was a concern that copyright might overtake design rights. This article investigates whether such an outcome has indeed materialized in the post-Cofemel reality of the fashion industry, employing an empirical analysis. Through an evaluation of EUIPO design registration data and interviews with legal practitioners working with fashion brands, the IP landscape in this domain is explored, drawing conclusions concerning the preferred means of protection for fashion designs, before and after Cofemel. Did the CJEU affect the fashion industry’s legal practice or is this Sisyphean task of iterative referrals regarding the fate of works of applied art in vain? And more specifically, was Cofemel’s effect revolutionary, after all, or was the discourse surrounding its significant impact merely an echo chamber within IP scholarship? Overall, the article reflects on the future of fashion design protection from a copyright perspective, also focusing on pending CJEU referrals on works of applied art, while also considering the treatment of derivative works under copyright law and their relevance to the fashion industry.
Gynecologic cancer clinical trial eligibility criteria as a marker for equitable clinical trial access
Authors: Oluloro Ann , Swisher Elizabeth M , Gray Heidi J , Goff Barbara , Doll Kemi M 
Published: December 2024

Abstract

Background
Racial and ethnic minorities remain underrepresented in gynecologic cancer clinical trials despite disproportionately worse oncologic outcomes. Research shows differential racial enrollment patterns because of comorbidity-based exclusion criteria. Our objective was to evaluate contemporary trends in comorbidity-based exclusion criteria among National Cancer Institute–sponsored gynecologic cancer clinical trials and protocol adherence to broadened eligibility criteria guidelines as an assessment of equitable enrollment access.

Methods
The ClinicalTrials.gov registry was queried for National Cancer Institute–sponsored gynecologic cancer clinical trials (1994-2021). Study characteristics and comorbidity-based exclusion criteria were abstracted from protocols. Descriptive statistics and temporal trends were calculated using χ2 testing with STATA v17 software.

Results
Among 279 clinical trials identified, 65% completed enrollment, 53% were phase II, and 48% focused on ovarian cancer. Pharmaceutical agents (85%) were the primary therapeutic interventions. Several inequitably restrictive exclusion criteria increased over time such as hepatitis infection (17% in 1994-2000 vs 49% in 2015-2021, P &lt; .001) and cardiovascular disease (47% in 1994-2000 vs 66% in 2015-2021, P = .002). A previously rare exclusion, “mental illness and/or social situations,” dramatically increased from 5% to 51% (P &lt; .001) over 3 decades. Adherence to broadened eligibility criteria recommendations was mixed. Renal function, cardiovascular disease, and performance status criteria were not broadened, but HIV, prior or concurrent malignancies, and brain metastasis criteria were.

Conclusions
Some, but not all, of the known restrictive comorbidity-based exclusion criteria have increased in gynecologic cancer clinical trial design, despite calls for improving racial and ethnic minority representation. Exclusion criteria are critical for trial safety, however, they must be carefully considered given the differential racial impact on eligibility.
The Ontological Security Politics of US Naval Ship Museums
Authors: Steele Brent J , Subotić Jelena 
Published: December 2024

Abstract
This article explores the politics of United States naval warship museums. Specifically, it investigates the role of museum tour guides in re-embodying and reinforcing, but also contesting and countering, US hegemonic narratives at these popular tourist sites. To explain the politics of these sites, this article is built around three interrelated arguments. First, insights from ontological security studies illuminate identity politics at work, calling particular attention on the routines, narratives, and expertise found throughout these locations. Second, the importance of naval power and the historical narratives at work here are more nuanced than the existing scholarship in critical security studies has considered so far. While hegemonic politics and militarized narratives are embedded, often times overtly, throughout these sites, there are also endogenous tensions within them as well. Examining the role of tour guides, curators, and directors in these settings reveals a contentious politics of US identity representation. Third, we may be witnessing a generational shift in expertise happening in real time. A new generation of experts brings with them new historical sensibilities and attitudes toward the military and US hegemony writ large. We illustrate these dynamics with three short vignettes from ship museums Iowa, Missouri, and Midway.
Correlates of nocturnal hypoxemia in children with sickle cell disease
Authors: Rani Seema , Mahon Brendan , Afolabi-Brown Olufunke , Bernstein Bruce A , Apollonsky Nataly , Miller Robin E 
Published: December 2024

Abstract

Objectives
Nocturnal hypoxemia (NH) and obstructive sleep apnea (OSA), more prevalent in children with sickle cell disease, are associated with sickle cell disease-related comorbidities. This study aimed to identify clinical and laboratory factors associated with NH in children with sickle cell disease.

Methods
This was an institutional review board-approved exploratory retrospective chart review of 81 children with SCD followed by the Sickle Cell Center at St. Christopher’s Hospital for Children, Philadelphia, PA, referred for an overnight polysomnogram 2008-2014. Demographic, hematologic, respiratory, SCD-related comorbidities and therapies, surgical history, and emergent healthcare utilization data were collected. Data were analyzed by IBM SPSS. Bivariate analyses identified clinical variables that were significantly, individually associated with NH. Clinical variables significantly associated with NH in bivariate analyses were entered in logistic regression models with OSA status to identify factors independently associated with NH, adjusting for OSA status.

Results
Fifteen children (19%) had NH, 18 (22%) had OSA, and 8 (10%) had both. Children with OSA more likely had NH. Lower hemoglobin level, higher reticulocyte count, lower diastolic blood pressure, and lower oxygen saturation were independently, significantly associated with NH, irrespective of the patient’s OSA status.

Conclusions
NH was present even in the absence of OSA. Identifying factors associated with NH is valuable to guide management of this cohort due to the known complications associated with NH in SCD.
Diagnosis and management of sigmoid leiomyosarcoma presenting with intussusception: a case report
Authors: El-Boghdadly Sami A , Alshareef Alaa M , Almisfer Abdulrahman K , Momen Ibrahim M 
Published: December 2024

Abstract
Sigmoid leiomyosarcoma is a rare type of cancer that originates from smooth muscles of the sigmoid colon. This case report details a 50-year-old female found to have this condition, presenting to the emergency department with intussusception. A CT scan revealed two intraluminal masses, with the largest 10 cm from the anal verge. A colonoscopy and biopsy revealed a large obstructing mass with atypical spindle-shaped cells. This case shows a rare type of cancer presenting in a rare complication and highlights the approach done in the multi-disciplinary tumor board meeting involving gastroenterologists, radiologists, surgeons, and oncologists, leading to prompt diagnosis and surgical resection.
Cell- and tissue-specific glycosylation pathways informed by single-cell transcriptomics
Authors: Chrysinas Panagiotis , Venkatesan Shriramprasad , Ang Isaac , Ghosh Vishnu , Chen Changyou , Neelamegham Sriram , Gunawan Rudiyanto 
Published: December 2024

Abstract
While single-cell studies have made significant impacts in various subfields of biology, they lag in the Glycosciences. To address this gap, we analyzed single-cell glycogene expressions in the Tabula Sapiens dataset of human tissues and cell types using a recent glycosylation-specific gene ontology (GlycoEnzOnto). At the median sequencing (count) depth, ∼40–50 out of 400 glycogenes were detected in individual cells. Upon increasing the sequencing depth, the number of detectable glycogenes saturates at ∼200 glycogenes, suggesting that the average human cell expresses about half of the glycogene repertoire. Hierarchies in glycogene and glycopathway expressions emerged from our analysis: nucleotide-sugar synthesis and transport exhibited the highest gene expressions, followed by genes for core enzymes, glycan modification and extensions, and finally terminal modifications. Interestingly, the same cell types showed variable glycopathway expressions based on their organ or tissue origin, suggesting nuanced cell- and tissue-specific glycosylation patterns. Probing deeper into the transcription factors (TFs) of glycogenes, we identified distinct groupings of TFs controlling different aspects of glycosylation: core biosynthesis, terminal modifications, etc. We present webtools to explore the interconnections across glycogenes, glycopathways and TFs regulating glycosylation in human cell/tissue types. Overall, the study presents an overview of glycosylation across multiple human organ systems.
Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data
Authors: Zhao Jianshu , Pierre Both Jean , Konstantinidis Konstantinos T 
Published: December 2024

Abstract
Dimension reduction (DR or embedding) algorithms such as t-SNE and UMAP have many applications in big data visualization but remain slow for large datasets. Here, we further improve the UMAP-like algorithms by (i) combining several aspects of t-SNE and UMAP to create a new DR algorithm; (ii) replacing its rate-limiting step, the K-nearest neighbor graph (K-NNG), with a Hierarchical Navigable Small World (HNSW) graph; and (iii) extending the functionality to DNA/RNA sequence data by combining HNSW with locality sensitive hashing algorithms (e.g. MinHash) for distance estimations among sequences. We also provide additional features including computation of local intrinsic dimension and hubness, which can reflect structures and properties of the underlying data that strongly affect the K-NNG accuracy, and thus the quality of the resulting embeddings. Our library, called annembed, is implemented, and fully parallelized in Rust and shows competitive accuracy compared to the popular UMAP-like algorithms. Additionally, we showcase the usefulness and scalability of our library with three real-world examples: visualizing a large-scale microbial genomic database, visualizing single-cell RNA sequencing data and metagenomic contig (or population) binning. Therefore, annembed can facilitate DR for several tasks for biological data analysis where distance computation is expensive or when there are millions to billions of data points to process.
Optimal Representative Strain selector—a comprehensive pipeline for selecting next-generation reference strains of bacterial species
Authors: Tarracchini Chiara , Fontana Federico , Petraro Silvia , Lugli Gabriele Andrea , Mancabelli Leonardo , Turroni Francesca , Ventura Marco , Milani Christian 
Published: December 2024

Abstract
Although it is common practice to use historically established ‘reference strains’ or ‘type strains’ for laboratory experiments, this approach often overlooks how effectively these strains represent the full ecological, genetic and functional diversity of the species within a specific ecological niche. In this context, this study proposes the Optimal Representative Strain (ORS) selector tool (https://zenodo.org/doi/10.5281/zenodo.13772191), an innovative bioinformatic pipeline capable of evaluating how a strain represents its whole species from a genetic and functional perspective, in addition to considering its ecological distribution in a particular ecological niche. Based on publicly available genomes, the strain that best fits all these three microbiological aspects is designated as an optimal representative strain. Moreover, a user-friendly software called Local Alternative Optimal Representative Strain selector was developed to allow researchers to screen their local library of bacterial strains for an optimal available alternative based on the reference optimal representative strain. Five different bacterial species, i.e. Lacticaseibacillus paracasei, Lactobacillus delbrueckii, Streptococcus thermophilus, Bacteroides thetaiotaomicron and Lactococcus lactis, were tested in three different environments to evaluate the performance of the bioinformatic pipeline in selecting optimal representative strains.
Improved characterization of 3′ single-cell RNA-seq libraries with paired-end avidity sequencing
Authors: Chamberlin John T , Gillen Austin E , Quinlan Aaron R 
Published: December 2024

Abstract
Prevailing poly(dT)-primed 3′ single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site or in principle the polyadenylation site. Direct sequencing across this site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the ‘barcode’ end. Here, we evaluate the capability of ‘avidity base chemistry’ DNA sequencing from Element Biosciences to sequence through the primer and enable accurate paired-end read alignment and precise quantification of polyadenylation sites. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The additional sequence enables direct and independent assignment of reads to polyadenylation sites, which bypasses the complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and demonstrate necessary adjustments to adapter trimming and sequence alignment regardless of platform, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site measurement but do not rule out the potential for similar performance from other emerging platforms.
Stereotactic Radiosurgery and Fractionated Radiation therapy in the management of pituitary tumors
Authors: Mantziaris Georgios , Trifiletti Daniel M , Pikis Stylianos , Sheehan Jason P 
Published: December 2024

Abstract
Pituitary tumors require a diverse, multidisciplinary approach in their management. Stereotactic radiosurgery (single or hypofractionated) and fractionated radiotherapy are integral parts of the armamentarium. With the introduction of highly conformal, stereotactic ionizing radiation approaches, the reported tumor control rates and clinical outcomes have improved significantly. This review details the indications, risks, and outcomes of pituitary radiosurgery and radiation therapy, and presents in brief the differences in treatment approaches between stereotactic radiosurgery, fractionated radiation therapy, and proton therapy.
Clinical value of the MGMT promoter methylation score in IDHmt low-grade glioma for predicting benefit from temozolomide treatment
Authors: Darlix Amélie , Bady Pierre , Deverdun Jérémy , Lefort Karine , Rigau Valérie , Le Bars Emmanuelle , Meriadec Justine , Carrière Mathilde , Coget Arthur , Santarius Thomas , Matys Tomasz , Duffau Hugues , Hegi Monika E 
Published: December 2024

Abstract

Background
Diffuse IDH mutant low-grade gliomas (IDHmt LGG) (World Health Organization grade 2) typically affect young adults. The outcome is variable, with survival ranging from 5 to over 20 years. The timing and choice of initial treatments after surgery remain controversial. In particular, radiotherapy is associated with early and late cognitive toxicity. Over 90% of IDHmt LGG exhibit some degree of promoter methylation of the repair gene O(6)-methylguanine-DNA methytransferase (MGMTp) that when expressed blunts the effect of alkylating agent chemotherapy, for example, temozolomide (TMZ). However, the clinical value of MGMTp methylation predicting benefit from TMZ in IDHmt LGG is unclear.

Methods
Patients treated in the EORTC-22033 phase III trial comparing TMZ versus radiotherapy served as training set to establish a cutoff based on the MGMT-STP27 methylation score. A validation cohort was established with patients treated in a single-center first-line with TMZ after surgery/surgeries.

Results
The MGMT-STP27 methylation score was associated with better progression-free survival (PFS) in the training cohort treated with TMZ, but not radiotherapy. In the validation cohort, an association with next treatment-free survival (P = .045) after TMZ was observed, and a trend using RANO criteria (P = .07). A cutoff value set above the 95% confidence interval of being methylated was significantly associated with PFS in the TMZ-treated training cohort, but not in the radiotherapy arm. However, this cutoff could not be confirmed in the test cohort.

Conclusions
While the MGMTp methylation score was associated with better outcomes in TMZ-treated IDHmt LGG, a cutoff could not be established to guide treatment decisions.
Cadence
Authors: Caplin William E. 
Published: December 2024

Abstract
This work is the most comprehensive examination to date of how formal units in European art music of the tonal era achieve closure by means of cadence, a highly conventional device for ending middle-ground thematic units. Rooted in the author’s broader “theory of formal functions,” the book first develops concepts of cadence for music of the high classical style and then extends these ideas to gauge cadential practice in earlier and later style periods. Throughout the study, various manifestations of cadence are defined in terms of their morphology (their harmonic and melodic profiles) as well as their function (the specific formal contexts in which they are deployed). Following an introductory chapter on concepts of closure in general (in psychology, literature, and music), Part I of the book examines the “classical cadence” by first laying out a series of general concepts that inform the rest of the study and then defining the harmonic and melodic content of the basic cadence types—perfect authentic, imperfect authentic, and half cadences. Along the way, readers learn how promised cadences can fail to be realized by various deviation techniques (deception, evasion, abandonment, and dominant arrival) and how cadential expansion can significantly loosen the formal organization of thematic units. Part II broadens the stylistic horizon to consider how formal closure is achieved in the style periods of the high baroque, the galant, the early Romantic, and the mid- to late nineteenth century. Specific compositional procedures especially characteristic of these styles are shown to impact how closure is achieved by cadential, but also noncadential, means.