bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of a Trustworthy Cloud-Native National Digital Health Information Infrastructure for Secure Data Management and Use
Authors: Zao John Kar-Kin , Wu Joseph Tsung-Shu , Kanyimbo Kennedy , Delizy Florian , Gan Tchin-Tze , Kuo Hung-I , Hsia Chih-Hao , Lo Chuan-Hsi , Yang Shang-Hui , Richard Clément Jean Alexandre , Rajab Billy , Monawe Maganizo , Kamanga Blessings , Mtambalika Nikotelhe , Yu Kwong-Leung Joseph , Chou Chih-Feng , Neoh Choo-Aun , Gallagher Joseph , O'Donoghue John , Mtegha Rebecca , Lee Hsin-Yi , Mbewe Alinafe 
Published: November 2024

Abstract
Since 2022, Malawi Ministry of Health (MoH) designated the development of a National Digital Health Information System (NDHIS) as one of the most important pillars of its national health strategy. This system is built upon a distributed computing infrastructure employing the following state-of-art technologies: (i) digital healthcare devices to capture medical data; (ii) Kubernetes-based Cloud-Native Computing architecture to simplify system management and service deployment; (iii) Zero-Trust Secure Communication to protect confidentiality, integrity and access rights of medical data transported over the Internet; (iv) Trusted Computing to allow medical data to be processed by certified software without compromising data privacy and sovereignty. Trustworthiness, including reliability, security, privacy and business integrity, of this system was ensured by a peer-to-peer network of trusted medical information guards deployed as the gatekeepers of the computing facility on this system. This NDHIS can facilitate Malawi to attain universal health coverage by 2030 through its scalability and operation efficiency. It shall improve medical data quality and security by adopting a paperless approach. It will also enable MoH to offer data rental services to healthcare researchers and AI model developers around the world. This project is spearheaded by the Digital Health Division (DHD) under MoH. The trustworthy computing infrastructure was designed by a taskforce assembled by the DHD in collaboration with Luke International in Norway, and a consortium of hardware and software solution providers in Taiwan. A prototype that can connect community clinics with a district hospital has been tested at Taiwan Pingtung Christian Hospital.
Commentary on ‘the interplay of the innovation cycle, build time, lifetime, and deployment rate of new energy technologies: a case study of nuclear fusion energy’ designing innovation strategies for rapid feasible technological change
Authors: Jewell Jessica 
Published: November 2024

Abstract
How fast can new technologies come online and what is the most effective policy strategy to accelerate their growth? A recent article by Lopes Cardozo and Ward contribute to shedding light on this very interesting question particularly tricky to answer for technologies which are not yet commercial. Taking the case of nuclear fusion, the authors aim to identify the best innovation strategy for the technology. They embed this analysis in a useful concept of a `forced transition' which echoes the general belief that energy transitions will need to be driven by policies rather than pure market forces. Their work introduces two significant theoretical advances: the Fastest Feasible Growth (FFG) model and foregrounding generational changes for analyzing technological deployment. While the authors' insights offer valuable contributions to both growth modeling and experience curve analysis, their work raises important questions for future research. These include the empirically validating of the relationship between technological generations and growth; identifying the conditions under which technological expansion would be faster then their FFG model; the duration of the exponential growth phase; the applicability of the model beyond the global scale; and conceptualising technological generations.
An undiscovered circadian clock to regulate phytoplankton photosynthesis
Authors: Su Yixi , Hu Jingyan , Xia Mengsheng , Chen Jiwei , Meng Weizhao , Qian Cheng , Shu Yuexuan , Wang Chao , Wang Xianwei , Salehi-Ashtiani Kourosh , Brynjólfsson Sigurður , Lin Jianping , Li Yongquan , Zhang Haisheng , Wang Lizhong , Fu Weiqi 
Published: November 2024

Abstract
Circadian clocks exist in all types of organisms and coordinate key biological processes, e.g. photosynthesis in phytoplankton (microalgae) and land plants. We asked whether a circadian rhythm sustains in phytoplankton when living under constant illumination without environmental cues. Here, we report the first transcriptomic architecture of persistent oscillatory gene expression in the model marine diatom, Phaeodactylum tricornutum living under constant illumination and temperature without environmental cues. We show that cyclic expression of a considerable number of genes involved in light harvesting and carbon fixation sustained after 24 h of constant illumination (free-running), which could pose additional constraints on cell growth under constant light conditions. Over long-term adaptation to constant illumination, the majority of the rhythmic genes identified under diel light conditions lose their oscillatory expression in the absence of external entrainers, and the genes potentially controlled by persistent circadian clocks are primarily involved in transcriptional regulation and cell division. We find constant illumination leads to an increased average expression of transcription factors and cell division genes, while genes involved in the Calvin–Benson cycle and pigment biosynthesis are kept at low expression levels, which plays a role in the down-regulation of photosynthetic efficiency. By manipulation of the dark rest period, we confirm a fine-tuned light/dark cycle could dramatically improve photosynthetic efficiency in microalgae. Our results unveil a novel persistent circadian rhythm on photosynthetic regulation in marine phytoplankton and provide critical insights into the interaction between environmental signals and inheritable internal circadian clocks in diatoms.
Over-the-scope clips for Nonvariceal upper gastrointestinal bleeding: a systematic review and meta-analysis of randomized studies
Authors: Ni Yuanzhi , Ali Kamran , Tang Penghao , Hayat Khizar , Cheng Zhiwen , Xu Benfeng , Qin Zhiwen , Zhang Wu 
Published: November 2024

Abstract

Background & Aims
Nonvariceal upper gastrointestinal bleeding (NVUGIB) is a common and potentially life-threatening condition. Over-the-scope clips (OTSCs) have emerged as a promising endoscopic treatment option for NVUGIB. We aimed to analyze the efficacy and safety of OTSCs compared to standard endoscopic treatments (ST) in patients with NVUGIB.

Methods
We conducted a comprehensive search of PubMed, Embase, Scopus, and Cochrane Library databases from inception to June 2024 for randomized controlled trials (RCTs) comparing OTSCs with ST for NVUGIB. The primary outcomes were initial hemostasis and persistent bleeding. Secondary outcomes included rebleeding rates, mortality, hospital stays and others. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using random/fixed-effects models.

Results
Six RCTs involving 621 patients were included in the meta-analysis. OTSCs demonstrated significantly higher initial hemostasis (OR 4.80, 95% CI 1.78–12.96; P = 0.002) and lower persistent bleeding rates (OR 0.17, 95% CI 0.05–0.56; P = 0.003) compared to ST group. The rebleeding rate was significantly lower in the OTSC group 7-days re-bleeding (OR 0.27, 95% CI 0.14–0.53; P = 0.001); 30-days rebleeding (OR 0.40, 95%CI 0.22, 0.70; P = 0.002). No significant differences were observed in mortality (OR 0.65, 95% CI 0.31–1.33; P = 0.38) and hospital stay (mean difference 0.79 days 95%CI -0.57, 2.15) between the two groups.

Conclusions
OTSCs are more effective than ST for achieving hemostasis and preventing rebleeding in patients with NVUGIB, without increasing mortality.
Key message What is Already Known Previous studies have shown that nonvariceal upper gastrointestinal bleeding (NVUGIB) is a serious medical condition that needs effective endoscopic interventions. The success rates of standard treatments for achieving hemostasis and preventing rebleeding are not consistent. What This Study Adds According to this study, over-the-scope clips (OTSCs) have the same mortality rate as standard endoscopic treatments, but they significantly improve initial hemostasis and lower rebleeding rates. Impact on Research, Practice, or Policy The findings support the use of OTSCs as a preferred intervention for NVUGIB, which could affect clinical guidelines and encourage additional research focused on improving endoscopic techniques and patient outcomes in the management of gastrointestinal bleeding.
CONTExT-RA: a cross-sectional study evaluating disease activity, quality of life and the socio-demographic profile of Irish patients with rheumatoid arthritis
Authors: Murphy Grainne , O’Rourke Killian , Camon Angela , Kane David , O’Shea Finbar , Conway Richard , Sheehy Claire , Saddiq Moneeb , Moran Deirdre 
Published: November 2024

Abstract

Objectives
CONTExT-RA is a cross-sectional, non-interventional multicentre study which enrolled patients diagnosed with RA and receiving DMARD treatment in a secondary care setting. The study evaluated disease control and associated disease burden amongst this Irish population.

Methods
Patients with RA attending six Irish rheumatology centres were invited to participate. Each consented patient attended a single routine study visit. Disease activity was assessed using Clinical Disease Activity Index (CDAI). The primary endpoint was EuroQol-5 dimensions (EQ-5D-5L) stratified by CDAI, compared using a non-parametric Wilcoxon Rank-Sum test.

Results
130 patients were included. Using CDAI, 34 (26.2%) patients were in clinical remission (CR), 42 (32.3%) had low disease activity (LDA), 41 (31.5%) had moderate disease activity (MDA) and 13 (10.0%) had high disease activity (HDA). QoL (EQ-5D-5L index (median)) scores were significantly (P &lt; 0.001) greater for patients in CR or CR/LDA than for those with MDA/HDA, 0.866 (0.920), 0.777 (0.822) vs 0.578 (0.691), respectively. Patients in CR reported higher levels of work productivity, mean (s.d.) rating of 1.7 (2.52) vs those in MDA/HDA of 4.2 (3.28) (higher rating indicates greater impairment). Similar findings were observed for non-work-related activities.

Conclusion
Disease control for many patients with RA, treated in secondary care in Ireland, is sub-optimal with only 1 in 4 in CDAI remission. The impact of poor disease control on QoL is significant, and the superior outcomes for patients in CR provide compelling evidence that by achieving greater disease control, the burden of disease on patients can be greatly reduced.
Interrater reliability of RheuMetric checklist scales for physician global assessment, inflammation, damage and patient distress
Authors: Schmukler Juan , Castrejon Isabel , Li Tengfei , Block Joel A , Pincus Theodore 
Published: November 2024

Abstract

Objective
To analyse interrater reliability of four RheuMetric checklist 0–10 visual numerical scales (VNSs) of physician global assessment (DOCGL), inflammation or reversible findings (DOCINF), organ damage or irreversible findings (DOCDAM) and patient distress or findings explained by fibromyalgia, depression or anxiety (DOCDIS).

Methods
A retrospective study was performed of data from a rheumatology fellows’ continuity clinic at Rush University. Each rheumatology patient seen in routine care with any diagnosis completed a multidimensional health assessment questionnaire (MDHAQ). Both the rheumatology fellow and attending rheumatologist independently completed RheuMetric estimates at the same visit for DOCGL, DOCINF, DOCDAM, DOCDIS and the proportion of DOCGL explained by each subglobal estimate (totalling 100%). Agreement between the two assessors was compared using paired t-tests, Spearman correlation coefficients, intraclass correlation coefficients (ICCs), Lin’s concordance correlation coefficients (LCCCs) and Bland–Altman plots.

Results
In 112 patients, mean levels of DOCINF were highest in inflammatory diseases, DOCDAM in osteoarthritis (OA) and DOCDIS in primary fibromyalgia (FM). However, mean DOCDAM was as high as DOCINF in inflammatory diseases. No statistically significant differences were seen between scores from attending rheumatologists and fellows. Agreement within 2/10 ranged from 60% for DOCGL to 71% for DOICINF and DOCDAM. Spearman correlations were 0.49–0.65, ICCs were 0.46–0.63 and LCCCs were 0.46–0.62 between rheumatologist and fellow, indicating moderate agreement; reliability was slightly higher for each subglobal VNS than for DOCGL.

Conclusion
RheuMetric 0–10 DOCGL, DOCINF, DOCDAM and DOCDIS have moderate interrater reliability and are feasible in routine care to estimate patient status beyond DOCGL for improved management decisions.
A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon
Authors: Petrone Mary E , Charon Justine , Grigg Matthew J , William Timothy , Rajahram Giri S , Westaway Jacob , Piera Kim A , Shi Mang , Anstey Nicholas M , Holmes Edward C 
Published: November 2024

Abstract
The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa affect the pathogen life cycle and disease outcomes. However, only one RNA virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere via metagenomic sequencing suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. From this, we identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group ‘ormycoviruses’. By characterizing 15 additional ormycoviruses identified in the transcriptomes of arthropods, we show that this group of viruses exhibits a complex ecology as noninfecting passengers at the arthropod–mammal interface. With the addition of viral diversity discovered using the artificial intelligence–based analysis of metagenomic data, we also demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to advances in large-scale virus discovery, we characterize the diversity and confirm the putative genomic architecture of an unclassified viral taxon. This approach can be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.
Functional determinants and evolutionary consequences of pleiotropy in complex and Mendelian traits
Authors: Barbitoff Yury A. , Bogaichuk Polina M. , Pavlova Nadezhda S. , Predeus Alexander V. 
Published: November 2024

AbstractPleiotropy, a phenomenon of multiple phenotypic effects of the same genetic alteration, is one of the most important features of genotype-to-phenotype networks. Over the last century, biologists have actively debated the prevalence, mechanisms, and consequences of pleiotropy. In this work, we employed data on genotype-to-phenotype associations from the Human Phenotype Ontology and Mouse Genome Database, as well as genome-wide associations from the UK Biobank cohort to investigate the similarities and dissimilarities in the patterns of pleiotropy between species and different trait types (i.e., Mendelian traits and complex traits). We found that the pleiotropic effects of genes correlate well between species, but have a much weaker correlation when different data sources are compared for the same species. In all cases, however, highly pleiotropic genes possessed a common set of features, such as the broad expression across tissues, involvement in many biological processes, or a high number of protein-protein interactions of the respective gene products. Furthermore, we observed a universal tendency of highly pleiotropic genes to be under greater negative selection pressure combined with a significant enrichment of recent positive selection signals at pleiotropic loci. Taken together, our results pinpoint a common mechanism underlying pleiotropic effects in different trait domains, and suggest that high degree of pleiotropy plays a role in adaptation, despite imposing additional constraint on genetic variation.
DistortCorrect Stitcher: Microscopy Image Stitching with Integrated Optical Distortion Correction
Authors: Cang Hu , Fan Huaxun , Sun Sha , Zhang Kai 
Published: November 2024

AbstractThe rapidly advancing field of imaging-based spatial transcriptomics demands microscopy images with larger fields of view (FOV) and high spatial resolution to accurately and efficiently quantify RNA molecules at the single-cell level. This challenge requires advanced image processing algorithms to seamlessly stitch multiple microscopic images while overcoming the inherent FOV limitations of microscopes. However, image stitching accuracy is often compromised by optical distortions, which are typically uncorrected or require cumbersome hardware-based calibration. Here, we present DistortCorrect Stitcher, a powerful software package that simultaneously estimates and corrects optical distortion during the stitching process. By iteratively integrating image stitching with distortion correction, our method significantly enhances alignment accuracy without relying on external calibration, providing a robust solution for processing spatial transcriptomics data. DistortCorrect Stitcher maintains high stitching fidelity across large tissue areas, ensuring that the molecular data remain reliable and biologically meaningful. This integrated approach has broad implications for improving spatial biology analysis and enabling more accurate high-throughput assays, thereby accelerating advancements in the field.
GreedyMini: Generating low-density DNA minimizers
Authors: Golan Shay , Tziony Ido , Kraus Matan , Orenstein Yaron , Shur Arseny 
Published: November 2024

AbstractMinimizers is the most populark-mer selection scheme in algorithms and data structures analyzing high-throughput sequencing (HTS) data. In a minimizers scheme, the smallestk-mer by some predefined order is selected as the representative of a sequence window containingwconsecutivek-mers, which results in overlapping windows often selecting the samek-mer. Minimizers that achieve the lowest frequency of selectedk-mers over a random DNA sequence, termed the expected density, are desired for improved performance of HTS analyses. Yet, no method to date exists to generate minimizers that achieve minimum expected density. Moreover, forkandwvalues used by common HTS algorithms and data structures there is a gap between the densities achieved by existing selection schemes and a recent theoretical lower bound. Here, we presentGreedyMini, a toolkit of methods to generate minimizers with low expected or particular density, to improve minimizers, to extend minimizers to larger alphabets,k, andw, and to measure the expected density of a given minimizer efficiently. We demonstrate over various combinations ofkandwvalues, including those of popular HTS methods, thatGreedyMinican generate DNA minimizers that achieve expected densities very close to the lower bound, and both expected and particular densities much lower compared to existing selection schemes. Additionally, we show that thek-mer rank-retrieval time byGreedyMiniis comparable to that of commonk-mer hash functions. We expectGreedyMinito improve the performance of many HTS algorithms and data structures and advance the research ofk-mer selection schemes.
To impute or not to impute in untargeted metabolomics - that is the compositional question
Authors: Krutkin Dennis Dimitri , Thomas Sydney , Zuffa Simone , Rajkumar Prajit , Knight Rob , Dorrestein Pieter C. , Kelley Scott T. 
Published: November 2024

ABSTRACTUntargeted metabolomics often produce large datasets with missing values, arising from biological or technical factors, which can undermine statistical analyses and lead to biased biological interpretations. Imputation methods, such as k-Nearest Neighbors (kNN) and Random Forest (RF) regression are commonly used but their effects vary depending on the type of missing data e.g. Missing Completely At Random (MCAR) and Missing Not At Random (MNAR). Here, we determined the impacts of degree and type of missing data on the accuracy of kNN and RF imputation using two datasets: a targeted metabolomic dataset with spiked-in standards and an untargeted metabolomic dataset. We also assessed the effect of compositional data approaches (CoDA), such as the centered log-ratio (CLR) transform, on data interpretation, since these methods are increasingly being used in metabolomics.Overall, we found that kNN and RF performed more accurately when the proportion of missing data across samples for a metabolic feature was low. However, these imputations could not handle MNAR data and generated wildly inflated values or imputed values where none should exist. Furthermore, we show that the proportion of missing values had a strong impact on the accuracy of imputation which affected the interpretation of the results. Our results suggest extreme caution should be used with imputation even with modestly levels of missing data or when the type of missingness is unknown.
A unifying principle for multispecies coexistence under resource fluctuations
Authors: Richardson James A. , Engelstädter Jan , Letten Andrew D. 
Published: November 2024

AbstractResource fluctuations are ubiquitous in nature and yet are generally assumed to play a limited role in the maintenance of biodiversity. We challenge this assumption by analyzing resource competition dynamics under conditions where traditional theory fails. We show that multi-species coexistence can be sustained when species are able to specialise on different temporal patterns of resource variability, including the asymmetries and periodic extremes commonly observed in natural systems. We further show how this partitioning of the statistical moments of the resource distribution provides a unified framework for explaining coexistence in variable resource environments. A theory of diversity maintenance based on moment partitioning highlights the potential for anthropogenic changes in resource regimes to drive cascading biodiversity losses.