bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rotavirus Vaccine Effectiveness Stratified By National-Level Characteristics: An Introduction to the 24-Country MNSSTER-V Project, 2007–2023
Authors: Burnett Eleanor , Umana Jazmina , Anwari Palwasha , Mujuru Hilda A , Groome Michelle J , Van Trang Nguyen , Iniguez Volga , Gheorghita Stela , Sahakyan Gayane , Nazurdinov Anvar , Michael Fausta , Mandomando Inacio , Desormeaux Anne Marie , Eraliev Umid , Enweronu-Laryea Christabel , Nalunkuma Cissy , Bonkoungou Isidore , Muhsen Khitam , Luhata Lungayo Christophe , Omore Richard , Goldfarb David M , Robinson Annick Lalaina , McCracken John , Uwimana Jeannine , N’Zue Kofi , Rey-Benito Gloria , Weldegebriel Goitom , Mwenda Jason M , Parashar Umesh D , Tate Jacqueline E 
Published: November 2024

Abstract

Background
Rotavirus vaccines are moderately protective against illness in settings with high compared with low mortality rates. Vaccine effectiveness (VE) evaluations may clarify our understanding of these disparities, but estimates among key subpopulations and against rare outcomes are not available in many analyses due to sample size. We combined 25 data sets from test-negative design case-control evaluations in 24 countries that enrolled children with medically attended diarrhea, laboratory-confirmed rotavirus stool testing, and documented vaccination status. We calculated rotavirus VE stratified by country-level characteristics.

Methods
Children 3–59 months old with birthdates and surveillance hospital arrival dates were included; other variables were standardized as available. Children were considered vaccinated if they received ≥1 dose of rotavirus vaccine &gt;14 days before arrival. We summarized child- and country-level characteristics, including national &lt;5-year-old mortality rate (U5M). Following the manufacturer recommended dose schedule, complete- and partial-series adjusted VE were estimated using logistic regression models.

Results
We included 6626 rotavirus-positive children (case patients) and 19 459 rotavirus negative children (controls). Adjusted complete-series VE was significantly higher among children from countries in the low and medium U5M stratum (74% [95% confidence interval, 64%–81%]) compared with all groups within the high U5M stratum (range, 52% [42%–60%]) to 46% [31%–57%]). Partial-series estimates were lower than complete-series estimates.

Conclusions
These findings are consistent with the published literature, though they suggest heterogeneity in vaccine performance within broad child mortality rate levels. Our findings also highlight the importance of complete-series vaccination.
Flourishing as an aim of higher education: exploring the aspirations and challenges of the educational philosophy of the University of Humanistic Studies (UvH)
Authors: de Ruyter Doret 
Published: November 2024

Abstract
This study paper intends to look into the multidimensional world of producing tactile and sensory fashion clothes particularly suited for those who have visual impairments. This research focuses on the fundament principle of this approach is that visually impaired individuals and communities should be the centre stage of the development process of tactile and sensory products. In addition, it analyses the potential advantages that may be received from the incorporation of tactile and sensory components into clothes, in terms of accessibility also as a method of enabling visually impaired persons to express themselves via clothing. In this study, we take a deeper look at the challenges that arose throughout the development. By embracing this innovative approach, the fashion industry can pave the way for more inclusive and empowering solutions that transcend traditional boundaries and contribute to a more diverse and accessible fashion landscape.
The Dynamic Atom-Probe: Past, Present, and Perspectives
Authors: Kruse Norbert , Visart de Bocarmé Thierry 
Published: November 2024

Abstract
The present communication aims at demonstrating the wealth of information accessible by 1D-atom probe experiments using pulsed field desorption mass spectrometry (PFDMS), ultimately combined with video-field ion microscopy, while subjecting metallic samples to elevated gas pressures and studying surface reaction kinetics. Two case studies are being presented here: (a) the microkinetics of nickel tetracarbonyl (Ni(CO)4) formation through reaction of carbon monoxide with nickel and (b) the nitric oxide decomposition and reaction with hydrogen on platinum at variable steady electric fields mimicking electrocatalytic conditions. In both cases, surface areas with 140–150 atomic sites of the stepped Ni (001) and Pt (111) sample surfaces were probed. Under (a), we demonstrate variable repetition frequencies of field pulses to inform kinetic and mechanistic details of the surface reaction while under (b), we reveal the occurrence of field-induced processes impacting the surface reaction mechanism of nitric oxide with hydrogen and therefore opening new pathways not available under purely thermal conditions (in the absence of electric fields). Some aspects of PFDMS technical achievements will be discussed as they may provide clues for designing dynamic atom probe tomography instrumentation.
“It Really Hurts When I Get Up.”: A 24-Year-Old Male with Progressive Sacral Pain and Stiffness
Authors: Mohan Niveditha 
Published: November 2024

Abstract
Inflammatory arthritis of the spine, such as ankylosing spondylitis, can cause significant disability and most commonly affects those under age 45. There are medications that prevent disease progression, making early identification critical. Only about 2% of those who are positive for the HLA-B27 allele actually have an inflammatory arthropathy. The vast majority of individuals with ankylosing spondylitis can be identified through history, physical examination, and imaging. A range of musculoskeletal and non-musculoskeletal features of inflammatory arthritis are important to identify in the diagnostic evaluation. Imaging is the cornerstone of diagnosis, particularly plain radiographs and magnetic resonance imaging of the spine and sacroiliac joints. Appropriate care includes education, exercise, physical therapy, behavioral health care, and smoking cessation. Nonsteroidal anti-inflammatory medications are commonly used as the initial therapy in most patients, and tumor necrosis factor (TNF) inhibitors have been shown to prevent disease progression with symptom control in many patients.
“I Need to Exercise to Lose Weight, but My Back Hurts.”: Low Back Pain with a BMI of 47
Authors: Watson Alex , Standaert Christopher J. 
Published: November 2024

Abstract
Already one of the most common health conditions, low back pain (LBP) is even more prevalent in those with obesity. This population has higher rates of chronic pain in general—approximately 33% vs. 10% in the average population. In part, this is related to a combination of adipose tissue secreting pro-inflammatory cytokines, diet, sedentary lifestyle, and behavioral issues, such as kinesiophobia (fear of movement). Obesity-related diseases, further complicate an already impaired health state and present additional barriers to exercise and other forms of care. There is reason to believe that obesity may contribute to the development of degenerative spinal issues, and obesity is associated with worse outcomes for treatment of these conditions. Language, understanding, and a comprehensive approach to managing LBP in patients with obesity is essential. A treatment approach including exercise (especially aquatic therapy), behavioral support, dietary intervention, medications, and bariatric surgery consultation may be the most effective approach.
Dark energy survey year 3 results: likelihood-free, simulation-based wCDM inference with neural compression of weak-lensing map statistics
Authors: Jeffrey N , Whiteway L , Gatti M , Williamson J , Alsing J , Porredon A , Prat J , Doux C , Jain B , Chang C , Cheng T -Y , Kacprzak T , Lemos P , Alarcon A , Amon A , Bechtol K , Becker M R , Bernstein G M , Campos A , Rosell A Carnero , Chen R , Choi A , DeRose J , Drlica-Wagner A , Eckert K , Everett S , Ferté A , Gruen D , Gruendl R A , Herner K , Jarvis M , McCullough J , Myles J , Navarro-Alsina A , Pandey S , Raveri M , Rollins R P , Rykoff E S , Sánchez C , Secco L F , Sevilla-Noarbe I , Sheldon E , Shin T , Troxel M A , Tutusaus I , Varga T N , Yanny B , Yin B , Zuntz J , Aguena M , Allam S S , Alves O , Bacon D , Bocquet S , Brooks D , da Costa L N , Davis T M , De Vicente J , Desai S , Diehl H T , Ferrero I , Frieman J , García-Bellido J , Gaztanaga E , Giannini G , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , Huterer D , James D J , Lahav O , Lee S , Marshall J L , Mena-Fernández J , Miquel R , Pieres A , Malagón A A Plazas , Roodman A , Sako M , Sanchez E , Cid D Sanchez , Smith M , Suchyta E , Swanson M E C , Tarle G , Tucker D L , Weaverdyck N , Weller J , Wiseman P , Yamamoto M 
Published: November 2024

ABSTRACT
We present simulation-based cosmological wcold dark matter (wCDM) inference using dark energy survey year 3 weak-lensing maps, via neural data compression of weak-lensing map summary statistics: power spectra, peak counts, and direct map-level compression/inference with convolutional neural networks (CNN). Using simulation-based inference, also known as likelihood-free or implicit inference, we use forward-modelled mock data to estimate posterior probability distributions of unknown parameters. This approach allows all statistical assumptions and uncertainties to be propagated through the forward-modelled mock data; these include sky masks, non-Gaussian shape noise, shape measurement bias, source galaxy clustering, photometric redshift uncertainty, intrinsic galaxy alignments, non-Gaussian density fields, neutrinos, and non-linear summary statistics. We include a series of tests to validate our inference results. This paper also describes the Gower Street simulation suite: 791 full-sky pkdgrav3 dark matter simulations, with cosmological model parameters sampled with a mixed active-learning strategy, from which we construct over 3000 mock dark energy survey lensing data sets. For wCDM inference, for which we allow $-1&lt; w&lt; -\frac{1}{3}$, our most constraining result uses power spectra combined with map-level (CNN) inference. Using gravitational lensing data only, this map-level combination gives $\Omega _{\rm m}= 0.283^{+0.020}_{-0.027}$, ${S_8 = 0.804^{+0.025}_{-0.017}}$, and $w &lt; -0.80$ (with a 68 per cent credible interval); compared to the power spectrum inference, this is more than a factor of two improvement in dark energy parameter ($\Omega _{\rm DE}, w$) precision.
Origin of high dark remnant fractions in Milky Way globular clusters: the crucial role of initial black hole retention
Authors: Rostami-Shirazi Ali , Baumgardt Holger , Zonoozi Akram Hasani , Ghasemi S Mojtaba , Haghi Hosein 
Published: November 2024

ABSTRACT
Comparing the dynamical and stellar masses of Milky Way (MW) globular clusters (GCs) reveals a discrepancy exceeding a factor of 2. Since this substantial invisible mass is concentrated in the cluster centre, it is attributed to stellar remnants. The majority of mass in remnants consists of white dwarfs (WDs). Allocating over half of a GC’s current mass to WDs could significantly restrict the dynamical evolution scenarios governing stellar clusters. As the most massive stars in GCs, black holes (BHs) exert a substantial effect on the escape rate of lower mass stars, such as WDs. This paper aims to identify which scenarios of BH natal kicks can accurately reproduce the notable dark remnant fraction observed in MW GCs. We compare the observed remnant fraction of MW GCs with a comprehensive grid of direct N-body simulations while adjusting the natal kick received by BHs. Our results reveal that simulations employing low natal kicks to BHs are the only ones capable of mirroring the remnant fraction of MW GCs. According to the Spitzer instability, the presence of a BH population prompts the formation of a BH sub-system (BHSub) at the centre of a star cluster. The BHSub serves as an energetic power plant, continually releasing kinetic energy through few-body encounters between single and binary BHs, and transferring the generated energy to the entire stellar population. This energy induces a significant difference in the ejection rate of stellar remnants and luminous stars, ultimately increasing the fraction of dark remnants within the star cluster.
Radio frequency interference from radio navigation satellite systems: simulations and comparison to MeerKAT single-dish data
Authors: Engelbrecht Brandon N , Santos Mario G , Fonseca José , Li Yichao , Wang Jingying , Irfan Melis O , Harper Stuart E , Grainge Keith , Bull Philip , Carucci Isabella P , Cunnington Steven , Pourtsidou Alkistis , Spinelli Marta , Wolz Laura 
Published: November 2024

ABSTRACT
Radio frequency interference (RFI) is emitted from various sources, terrestrial or orbital, and creates a nuisance for ground-based 21-cm experiments. In particular, single-dish observations will be highly susceptible to RFI due to their wide primary beam and sensitivity. This work aimed to simulate the contamination effects from the Radio Navigational Satellite System (RNSS) within the 1100–1350 (MHz) frequency band. The simulation can be divided into two parts: (i) satellite positioning, emission power, and the beam response on the telescope, and (ii) calibration of the satellite signals to data to improve the original model. We utilize previously observed single-dish L-band data from the Meer-Karoo Array Telescope (MeerKAT), which requires special calibration to account for regions contaminated by satellite-based RFI. We find that we can recreate the satellite contamination with high accuracy around its peak frequencies provided the satellite is not too close to the telescope’s pointing direction. The simulation can predict satellite movements and signals for past and future observations, aiding in RFI avoidance and testing novel cleaning methods. The predicted signal sits below the noise in the target cosmology window in the L band (970–1015 MHz) making it difficult to confirm any out-of-band emission from satellites. However, in our simulations, this contamination still overwhelmed the 21-cm auto-power spectrum. Nevertheless, it is possible to detect the signal in cross-correlations after mild foreground cleaning. Whether such out of band contamination does exist will require further characterization of the satellite signals far away from their peak frequencies.
Testing for allocation strategies and evolutionary tradeoffs in the bivalve shell
Authors: Edie Stewart M , Collins Katie S , Jablonski David 
Published: November 2024

ABSTRACT
Tradeoffs are a fundamental aspect of evolution, such that organismal morphologies often reflect a combination of developmental constraints and functional requirements. The net result is a striking variety of allocation strategies—where and how resources are shunted into aspects of the body plan to meet these competing demands. The bivalve shell records aspects of the animal's allocation strategies as the relative investment in the carbonate valves and the internal soft parts, generally reflected by the volume of the internal cavity. The carbonate volume can be further partitioned among different components of the shell, including the sculptural elements thought to evolve partly under ecological controls. Assuming there are general limits to energy acquisition, bivalve individuals may show different allocations between the volumes of the inner cavity and shell, and possibly for the sculpture. Using 3D scans of 385 valves representing 339 extant marine species occurring in the Florida Keys, USA, we find a variety of allocation strategies but that tradeoffs in shell construction are uncommon. Instead, species with relatively high allocations to their shell thickness also have prominent sculpture, suggesting a structural relationship. Neither outer shell mineralogy nor microstructure appears to partition the tradeoff space, suggesting varied pathways to the fabrication of both convergent and divergent shell forms. Framing new morphological and physiological analyses of bivalves by allocation strategies recorded in their well-fossilized shells opens new opportunities for understanding an under-studied, macroevolutionary dynamic: how tradeoffs have shaped the class's 500 million-year evolutionary and ecological history.
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2024
Authors: Thakur Matthew , Brooksbank Catherine , Finn Robert D , Firth Helen V , Foreman Julia , Freeberg Mallory , Gurwitz Kim T , Harrison Melissa , Hulcoop David , Hunt Sarah E , R. Leach Andrew , Levchenko Mariia , Marques Diana , McDonagh Ellen M , Mithani Aziz , Parkinson Helen , Perez-Riverol Yasset , Perova Zinaida , Sarkans Ugis , Tirunagari Santosh , Tzampatzopoulou Eleni , Venkatesan Aravind , Vizcaino Juan-Antonio , Wingfield Benjamin , Zdrazil Barbara , McEntyre Johanna 
Published: November 2024

Abstract
The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory, Europe’s only intergovernmental life sciences organization. This overview summarizes the latest developments in services that EMBL-EBI data resources provide to scientific communities globally (https://www.ebi.ac.uk/services).
CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data
Authors:   CZI Cell Science Program, Abdulla Shibla , Aevermann Brian , Assis Pedro , Badajoz Seve , Bell Sidney M , Bezzi Emanuele , Cakir Batuhan , Chaffer Jim , Chambers Signe , Cherry J Michael , Chi Tiffany , Chien Jennifer , Dorman Leah , Garcia-Nieto Pablo , Gloria Nayib , Hastie Mim , Hegeman Daniel , Hilton Jason , Huang Timmy , Infeld Amanda , Istrate Ana-Maria , Jelic Ivana , Katsuya Kuni , Kim Yang Joon , Liang Karen , Lin Mike , Lombardo Maximilian , Marshall Bailey , Martin Bruce , McDade Fran , Megill Colin , Patel Nikhil , Predeus Alexander , Raymor Brian , Robatmili Behnam , Rogers Dave , Rutherford Erica , Sadgat Dana , Shin Andrew , Small Corinn , Smith Trent , Sridharan Prathap , Tarashansky Alexander , Tavares Norbert , Thomas Harley , Tolopko Andrew , Urisko Meghan , Yan Joyce , Yeretssian Garabet , Zamanian Jennifer , Mani Arathi , Cool Jonah , Carr Ambrose 
Published: November 2024

Abstract
Hundreds of millions of single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the level of single cells. Meta-analyses that span diverse datasets building on recent advances in large language models and other machine-learning approaches pose exciting new directions to model and extract insight from single-cell data. Despite the promise of these and emerging analytical tools for analyzing large amounts of data, the sheer number of datasets, data models and accessibility remains a challenge. Here, we present CZ CELLxGENE Discover (cellxgene.cziscience.com), a data platform that provides curated and interoperable single-cell data. Available via a free-to-use online data portal, CZ CELLxGENE hosts a growing corpus of community-contributed data of over 93 million unique cells. Curated, standardized and associated with consistent cell-level metadata, this collection of single-cell transcriptomic data is the largest of its kind and growing rapidly via community contributions. A suite of tools and features enables accessibility and reusability of the data via both computational and visual interfaces to allow researchers to explore individual datasets, perform cross-corpus analysis, and run meta-analyses of tens of millions of cells across studies and tissues at the resolution of single cells.
Donor-derived cell-free DNA monitoring for early diagnosis of antibody-mediated rejection after kidney transplantation: a randomized trial
Authors: Akifova Aylin , Budde Klemens , Amann Kerstin , Buettner-Herold Maike , Choi Mira , Oellerich Michael , Beck Julia , Bornemann-Kolatzki Kirsten , Schütz Ekkehard , Bachmann Friederike , Halleck Fabian , von Hoerschelmann Ellen , Koch Nadine , Schrezenmeier Eva , Seelow Evelyn , Waiser Johannes , Zukunft Bianca , Eckardt Kai-Uwe , Halbritter Jan , Kettritz Ralph , Del Moral Covadonga López , Lachmann Nils , Stauch Diana , Niemann Matthias , Schmidt Danilo , Halloran Philip F , Osmanodja Bilgin 
Published: November 2024

ABSTRACT

Background
Donor-derived cell-free DNA (dd-cfDNA) shows good diagnostic performance for the detection of antibody-mediated rejection (AMR) in kidney transplant recipients (KTR). However, the clinical benefits of dd-cfDNA monitoring need to be established. Early diagnosis of AMR at potentially reversible stages may be increasingly important due to emerging treatment options for AMR. We hypothesized that monitoring dd-cfDNA in KTR with de novo donor-specific anti-HLA antibodies (dnDSA) and performing kidney biopsy in case of increased dd-cfDNA may reduce time to AMR diagnosis in comparison with clinical indication biopsy.

Methods
In this diagnostic, single-center, open-label, randomized clinical trial, we assigned 40 KTR with prevalent dnDSA and estimated glomerular filtration rate ≥20 mL/min/1.73 m2, but without previous biopsy-proven AMR, to either dd-cfDNA-guided biopsy (intervention group) or clinician-guided biopsy (control group) over a 12-month period. In both groups, dd-cfDNA was assessed at inclusion and 1, 3, 6, 9 and 12 months. In the intervention group, dd-cfDNA &gt;50 copies/mL indicated a biopsy. Biopsies for clinical indication could be performed at any point during the study period in both groups. A protocol biopsy was scheduled after 12 months for patients without dd-cfDNA-guided biopsy or clinical indication biopsy until study completion. The primary endpoint was time from study inclusion to diagnosis of active or chronic active AMR.

Results
Thirty-nine of 40 patients had functioning grafts at study completion. From these, 26 patients underwent biopsy, 13 in each group. AMR was diagnosed earlier in the intervention group than in the control group [median 2.8 months, interquartile range (IQR) 1.7–5.3 vs median 14.5 months, IQR 13.3–16.7, P = .003]. Longitudinal dd-cfDNA monitoring had 77% positive predictive value and 85% negative predictive value for AMR.

Conclusions
Dd-cfDNA-guided biopsy in KTR with prevalent dnDSA can reduce the time to AMR diagnosis and hereby expedite therapy initiation.

Trial registration
ClinicalTrials.gov, NCT04897438.