bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal distributed multi-parameter estimation in noisy environments
Authors: Hamann Arne , Sekatski Pavel , Dür Wolfgang 
Published: March 2024

Abstract
We consider the task of multiple parameter estimation in the presence of strong correlated noise with a network of distributed sensors. The signals and the noises have different spatial dependence but are encoded with the same local generators. We study how to find and improve noise-insensitive strategies. We show that sequentially probing with GHZ states from the decoherence-free subspace that we identify is asymptotically optimal up to a factor of at most 4 in the limit of many repetitions. The implementation of such strategies only requires local read-out and ‘passive’ resources—an initially entangled state of the sensors and tunable local interaction strength.
Monitoring spatiotemporal changes in land use/land cover and its impacts on ecosystem services in southern Zambia
Authors: Liang Diling , Reed James , Fakheran Sima , Moombe Kaala , Siangulube Freddie , Sunderland Terry 
Published: March 2024

Abstract
Ecosystems play a vital role in human well-being, yet the widespread loss of ecosystem services due to human activities, including agricultural expansion and deforestation, remains a significant concern. Despite the wealth of research highlighting the importance of ecosystem conservation in Zambia, a critical gap exists in understanding the interplay between the conservation of ecosystem services and the socio-economic needs of local communities. This study presents a comparative analysis of ecosystem services in two distinct landscapes within southern Zambia: the protected area of Kafue National Park (KNP) and the agricultural landscape of Kalomo district between 2000–2020. Employing a combination of quantitative and qualitative methods, we evaluate the impacts of land/use and land cover (LULC) changes on selected ecosystem services, with a particular focus on carbon storage and the habitat quality of the trumpeter hornbill. The results of the comparison indicate that: (1) the Kalomo district has suffered from extensive land conversion, with forest changing to cropland, while KNP was well protected from encroachment, with forest area increasing over time; (2) carbon stocks and the habitat quality of trumpeter hornbills continually decreased in the Kalomo district but improved in KNP; (3) Kalomo district has suffered rapid environmental degradation due to an imbalance between economic development and environmental conservation, while strict enforcement in KNP has preserved ecosystems. The findings underscore the importance of integrated and inclusive land-use planning and natural resource governance for maintaining and enhancing ecosystem services in Zambia. To progress towards landscape management that is both sustainable and equitable, aligning with the objectives of the Global Biodiversity Framework, it is proposed that a comprehensive approach be adopted in the region. This approach should encompass a more thorough consideration of local livelihood requirements, as well as the wider political-economic and social factors at play.
The issues on the commercialization of perovskite solar cells
Authors: Zhang Lixiu , Wang Yousheng , Meng Xiangchuan , Zhang Jia , Wu Pengfei , Wang Min , Cao Fengren , Chen Chunhao , Wang Zhaokui , Yang Fu , Li Xiaodong , Zou Yu , Jin Xi , Jiang Yan , Li Hengyue , Liu Yucheng , Bu Tongle , Yan Buyi , Li Yaowen , Fang Junfeng , Xiao Lixin , Yang Junliang , Huang Fuzhi , Liu Shengzhong , Yao Jizhong , Liao Liangsheng , Li Liang , Zhang Fei , Zhan Yiqiang , Chen Yiwang , Mai Yaohua , Ding Liming 
Published: March 2024

Abstract
Perovskite solar cells have aroused a worldwide research upsurge in recent years due to their soaring photovoltaic performance, ease of solution processing, and low cost. The power conversion efficiency record is constantly being broken and has recently reached 26.1% in the lab, which is comparable to the established photovoltaic technologies such as crystalline silicon, copper indium gallium selenide and cadmium telluride (CdTe) solar cells. Currently, perovskite solar cells are standing at the entrance of industrialization, where huge opportunities and risks coexist. However, towards commercialization, challenges of up-scaling, stability and lead toxicity still remain, the proper handling of which could potentially lead to the widespread adoption of perovskite solar cells as a low-cost and efficient source of renewable energy. This review gives a holistic analysis of the path towards commercialization for perovskite solar cells. A comprehensive overview of the current state-of-the-art level for perovskite solar cells and modules will be introduced first, with respect to the module efficiency, stability and current status of industrialization. We will then discuss the challenges that get in the way of commercialization and the corresponding strategies to address them, involving the upscaling, the stability and the lead toxicity issue. Insights into the future direction of commercialization of perovskite photovoltaics was also provided, including the flexible perovskite cells and modules and perovskite indoor photovoltaics. Finally, the future perspectives towards commercialization are put forward.
Acute alcohol ingestion decreases the work done above the end-test power during a 3-min all-out cycling exercise
Authors: dos Santos Danilo França Conceição , Wanner Samuel Penna , de Paula Rodolfo Ferreira , Zanetti Gustavo Oliveira , de Oliveira Donizete Cícero Xavier , Orsatti Fabio Lera , Teixeira-Coelho Francisco 
Published: March 2024

Abstract

Introduction
Alcohol ingestion influences metabolism during a subsequent exercise session, as evidenced by increased blood lactate concentration during fixed-intensity exercise. Therefore, augmented blood concentrations of alcohol may interfere with the anaerobic metabolism during high-intensity, short-duration exercise bout, thereby leading to impaired athletic performance.

Objective
This study investigated whether the acute ingestion of alcohol as ethanol modulates performance parameters derived from the power–duration relationship in a 3-min all-out cycling test that allows for identifying the power output related to heavy and severe exercise intensities.

Methods
Twenty-four recreationally active cyclists (16 men and 8 women) ingested a beverage containing either 0.4 g ethanol.kg−1 body mass (EtOH) or a placebo (PLA) solution. Thirty minutes following ingestion, they completed a 3-min all-out test to measure power output and determine the end-test power (EP) and the work done above EP (WEP).

Results
Alcohol ingestion decreased WEP by 16% (EtOH: 5.6 ± 2.5 kJ vs. PLA: 6.7 ± 2.4 kJ; P = .003) but did not change EP (EtOH: 211 ± 44 W vs. PLA: 212 ± 44 W; P = .671). The alcohol-mediated effect in WEP was not influenced when controlling for participants’ sex or accuracy in identifying the beverage ingested.

Conclusion
Our data indicate that alcohol ingestion impaired the anaerobic work capacity, as evidenced by the reduction in WEP during the 3-min all-out test. Moreover, the ability to exercise at an intensity above the heavy domain may be decreased after ingestion of a moderate alcohol dose.
NIEND: neuronal image enhancement through noise disentanglement
Authors: Zhao Zuo-Han , Liu Lijuan , Liu Yufeng 
Published: March 2024

Abstract

Motivation
The full automation of digital neuronal reconstruction from light microscopic images has long been impeded by noisy neuronal images. Previous endeavors to improve image quality can hardly get a good compromise between robustness and computational efficiency.

Results
We present the image enhancement pipeline named Neuronal Image Enhancement through Noise Disentanglement (NIEND). Through extensive benchmarking on 863 mouse neuronal images with manually annotated gold standards, NIEND achieves remarkable improvements in image quality such as signal-background contrast (40-fold) and background uniformity (10-fold), compared to raw images. Furthermore, automatic reconstructions on NIEND-enhanced images have shown significant improvements compared to both raw images and images enhanced using other methods. Specifically, the average F1 score of NIEND-enhanced reconstructions is 0.88, surpassing the original 0.78 and the second-ranking method, which achieved 0.84. Up to 52% of reconstructions from NIEND-enhanced images outperform all other four methods in F1 scores. In addition, NIEND requires only 1.6 s on average for processing 256 × 256 × 256-sized images, and images after NIEND attain a substantial average compression rate of 1% by LZMA. NIEND improves image quality and neuron reconstruction, providing potential for significant advancements in automated neuron morphology reconstruction of petascale.

Availability and implementation
The study is conducted based on Vaa3D and Python 3.10. Vaa3D is available on GitHub (https://github.com/Vaa3D). The proposed NIEND method is implemented in Python, and hosted on GitHub along with the testing code and data (https://github.com/zzhmark/NIEND). The raw neuronal images of mouse brains can be found at the BICCN’s Brain Image Library (BIL) (https://www.brainimagelibrary.org). The detailed list and associated meta information are summarized in Supplementary Table S3.
HyperTMO: a trusted multi-omics integration framework based on hypergraph convolutional network for patient classification
Authors: Wang Haohua , Lin Kai , Zhang Qiang , Shi Jinlong , Song Xinyu , Wu Jue , Zhao Chenghui , He Kunlun 
Published: March 2024

Abstract

Motivation
The rapid development of high-throughput biomedical technologies can provide researchers with detailed multi-omics data. The multi-omics integrated analysis approach based on machine learning contributes a more comprehensive perspective to human disease research. However, there are still significant challenges in representing single-omics data and integrating multi-omics information.

Results
This article presents HyperTMO, a Trusted Multi-Omics integration framework based on Hypergraph convolutional network for patient classification. HyperTMO constructs hypergraph structures to represent the association between samples in single-omics data, then evidence extraction is performed by hypergraph convolutional network, and multi-omics information is integrated at an evidence level. Last, we experimentally demonstrate that HyperTMO outperforms other state-of-the-art methods in breast cancer subtype classification and Alzheimer’s disease classification tasks using multi-omics data from TCGA (BRCA) and ROSMAP datasets. Importantly, HyperTMO is the first attempt to integrate hypergraph structure, evidence theory, and multi-omics integration for patient classification. Its accurate and robust properties bring great potential for applications in clinical diagnosis.

Availability and implementation
HyperTMO and datasets are publicly available at https://github.com/ippousyuga/HyperTMO
Psychometric evaluation of the multidimensional Uraemic Pruritus in Dialysis patients (UP-Dial) scale: comparison of haemodialysis and peritoneal dialysis patients with chronic pruritus
Authors: Nochaiwong Surapon , Ruengorn Chidchanok , Thavorn Kednapa , Noppakun Kajohnsak , Sood Manish M , Knoll Greg A , Bernstein Jonathan A , Szepietowski Jacek C , Chuamanochan Mati 
Published: March 2024

Abstract

Background
High-quality patient-reported outcome (PRO) measures for dialysis patients with chronic pruritus are urgently needed. However, no known, well-validated multidimensional tools have been investigated to measure pruritus symptoms in dialysis patients.

Objectives
To examine the psychometric properties of a multidimensional tool of chronic pruritus, the Uraemic Pruritus in Dialysis patients (UP-Dial) 14-item scale, by comparing haemodialysis and peritoneal dialysis modality.

Methods
This validation study used data from the Thai Renal Outcomes Research-Uraemic Pruritus, a prospective, multicentre, longitudinal study. Data for this study were collected from 1 February 2019 to 31 May 2022. The adult sample of 226 haemodialysis and 327 peritoneal dialysis patients fulfilled the criteria of chronic pruritus based on the International Forum for the Study of Itch. Psychometric properties of the UP-Dial included validity and reliability, as measured across haemodialysis and peritoneal dialysis patients. Patients completed a set of anchor-based measurement tools, including global itching, Dermatology Life Quality Index (DLQI), EuroQoL-5 dimension-5 level (EQ-5D-5L), Kidney Disease Quality of Life-36 (KDQOL-36), Pittsburgh Sleep Quality Index (PSQI), global fatigue, Somatic Symptom Scale-8 (SSS-8) and Patient Health Questionnaire-9 (PHQ-9).

Results
From the patient’s perspective, face validity was satisfactory for both dialysis samples. Psychometric analyses of the UP-Dial for each dialysis sample had good convergent validity. Spearman rho correlations indicate a positively strong correlation (0.73–0.74) with global itching, a positively moderate correlation (0.33–0.58) with DLQI, PSQI, global fatigue, SSS-8 and PHQ-9, and a negatively moderate correlation (–0.39 to –0.58) with EQ-5D-5L and KDQOL-36. The discriminant validity was satisfactory with a group of moderate and severe burden of pruritus for both dialysis samples. For scale reliability, the UP-Dial revealed excellent internal consistency (Cronbach’s α = 0.89 and McDonald’s ω = 0.90) and reproducibility (intraclass correlation 0.84–0.85) for both dialysis samples. Regarding psychometric properties, no statistically significant differences between dialysis samples were observed (all P &gt; 0.05).

Conclusions
The findings reaffirm good measurement properties of the UP-Dial 14-item scale in haemodialysis and peritoneal dialysis patients with chronic pruritus. These suggest a transferability of the UP-Dial as a PRO measure in clinical trial and practice settings.
Blockade of interleukin-13 signalling improves skin barrier function and biology in patients with moderate-to-severe atopic dermatitis
Authors: Sander Nicole , Stölzl Dora , Fonfara Melina , Hartmann Jan , Harder Inken , Suhrkamp Ina , Jakaša Ivone , van den Bogaard Ellen , van Vlijmen-Willems Ivonne , Szymczak Silke , Rodriguez Elke , Gerdes Sascha , Weidinger Stephan 
Published: March 2024

Abstract

Background
Interleukin (IL)-13 is a key driver of inflammation and barrier dysfunction in atopic dermatitis (AD). While there is robust evidence that tralokinumab – a monoclonal antibody that neutralizes IL-13 – reduces inflammation and clinical disease activity, less is known about its effects on barrier function.

Objectives
To characterize the effects of tralokinumab treatment on skin barrier function.

Methods
Transepidermal water loss (TEWL), stratum corneum hydration (SCH), natural moisturizing factor content, histopathological characteristics, biomarker expression and microbiome composition were evaluated in lesional, nonlesional and sodium lauryl sulfate-irritated skin of 16 patients with AD over the course of 16 weeks of tralokinumab treatment.

Results
All clinical severity scores decreased significantly over time. At week 16, mean TEWL in target lesions decreased by 33% (P = 0.01) and SCH increased by 58% (P = 0.004), along with a histological reduction in spongiosis (P = 0.003), keratin 16 expression and epidermal thickness (P = 0.001). In parallel, there was a significant decrease in several barrier dysfunction-associated and proinflammatory proteins such as fibronectin (P = 0.006), CCL17/TARC (P = 0.03) and IL-8 (P = 0.01), with significant changes seen as early as week 8. Total bacterial load and Staphylococcus aureus abundance were significantly reduced from week 2.

Conclusions
Tralokinumab treatment improved skin physiology, epidermal pathology and dysbiosis, further highlighting the pleiotropic role of IL-13 in AD pathogenesis.
Exploration of a Potential DOOR Endpoint for Hospital-acquired Bacterial Pneumonia and Ventilator-associated Bacterial Pneumonia Using Six Registrational Trials for Antibacterial Drugs
Authors: Kinamon Tori , Waack Ursula , Needles Mark , Rubin Daniel , Collyar Deborah , Doernberg Sarah B , Evans Scott R , Hamasaki Toshimitsu , Holland Thomas L , Howard-Anderson Jessica , Chambers Henry , Fowler Vance G , Nambiar Sumati , Kim Peter , Boucher Helen W , Gopinath Ramya 
Published: March 2024

Abstract

Background
Desirability of outcome ranking (DOOR) is an innovative approach to clinical trial design and analysis that uses an ordinal ranking system to incorporate the overall risks and benefits of a therapeutic intervention into a single measurement. Here we derived and evaluated a disease-specific DOOR endpoint for registrational trials for hospital-acquired bacterial pneumonia and ventilator-associated bacterial pneumonia (HABP/VABP).

Methods
Through comprehensive examination of data from nearly 4000 participants enrolled in six registrational trials for HABP/VABP submitted to the Food and Drug Administration (FDA) between 2005 and 2022, we derived and applied a HABP/VABP specific endpoint. We estimated the probability that a participant assigned to the study treatment arm would have a more favorable overall DOOR or component outcome than a participant assigned to comparator.

Results
DOOR distributions between treatment arms were similar in all trials. DOOR probability estimates ranged from 48.3% to 52.9% and were not statistically different. There were no significant differences between treatment arms in the component analyses. Although infectious complications and serious adverse events occurred more frequently in ventilated participants compared to non-ventilated participants, the types of events were similar.

Conclusions
Through a data-driven approach, we constructed and applied a potential DOOR endpoint for HABP/VABP trials. The inclusion of syndrome-specific events may help to better delineate and evaluate participant experiences and outcomes in future HABP/VABP trials and could help inform data collection and trial design.
Directed acyclic graphs in clinical research
Authors: Dekkers Olaf M , Laugesen Kristina , Groenwold Rolf H H 
Published: March 2024

Abstract
Directed acyclic graphs (DAGs), or causal diagrams, are graphical representations of causal structures that can be used in medical research to understand and illustrate potential bias, including bias arising from confounding, selection, and misclassification. Further, they provide guidance for researchers about how to address a potential bias.
Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse
Authors: Baldarelli Richard M , Smith Cynthia L , Ringwald Martin , Richardson Joel E , Bult Carol J ,   Mouse Genome Informatics Group, Anagnostopoulos Anna , Begley Dale A , Bello Susan M , Christie Karen , Finger Jacqueline H , Hale Paul , Hayamizu Terry F , Hill David P , Knowlton Michelle N , Krupke Debra M , McAndrews Monica , Law Meiyee , McCright Ingeborg J , Ni Li , Onda Hiroaki , Sitnikov Dmitry , Smith Constance M , Tomczuk Monika , Wilming Laurens , Xu Jingxia , Zhu Yunxia , Blodgett Olin , Campbell Jeffrey W , Corbani Lori E , Frost Peter , Giannatto Sharon C , Miers David B , Motenko Howie , Neuhauser Steven B , Shaw David R , Butler Nancy E , Ormsby Janice E 
Published: March 2024

Abstract
Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic and genomic aspects of human biology and disease using the laboratory mouse as a model system. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are core MGI databases that share data and system architecture. MGI serves as the central community resource of integrated information about mouse genome features, variation, expression, gene function, phenotype, and human disease models acquired from peer-reviewed publications, author submissions, and major bioinformatics resources. To facilitate integration and standardization of data, biocuration scientists annotate using terms from controlled metadata vocabularies and biological ontologies (e.g. Mammalian Phenotype Ontology, Mouse Developmental Anatomy, Disease Ontology, Gene Ontology, etc.), and by applying international community standards for gene, allele, and mouse strain nomenclature. MGI serves basic scientists, translational researchers, and data scientists by providing access to FAIR-compliant data in both human-readable and compute-ready formats. The MGI resource is accessible at https://informatics.jax.org. Here, we present an overview of the core data types represented in MGI and highlight recent enhancements to the resource with a focus on new data and functionality for MGD and GXD.
What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Authors: Basenko Evelina Y , Shanmugasundram Achchuthan , Böhme Ulrike , Starns David , Wilkinson Paul A , Davison Helen R , Crouch Kathryn , Maslen Gareth , Harb Omar S , Amos Beatrice , McDowell Mary Ann , Kissinger Jessica C , Roos David S , Jones Andrew 
Published: March 2024

Abstract
FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.