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PubMed2026

Interpretable data integration for single-cell and spatial multi-omics.

Integrating single-cell or spatial transcriptomic and epigenomic data enables scrutinizing the transcriptional regulatory mechanisms controlling cell fate. Current integration methods usually align multi-omics data into a shared latent space but fail to reveal the underlying connections between genes and regulatory elements. The correlation- or regression-based regulatory inference methods cannot dissect different transcriptional regulation codes for cells under different spatial and temporal states. To address both problems, we develop a feature-guided optimal transport (FGOT) method, which simultaneously uncovers cellular heterogeneity and their associated transcriptional regulatory links. FGOT also provides post hoc interpretability for existing integration methods. FGOT is applicable for paired/unpaired single-cell multi-omics data and paired spatial multi-omics data. Benchmarking and validating via histone modification data or three-dimensional (3D) genomics data show good robustness and accuracy in integration and inference of regulatory links. The method allows systematic screening of cell-state and spatial-location-specific regulatory elements in diseases at the single-cell level. A record of this paper's transparent peer review process is included in the supplemental information.

Single-Cell Analysis↗

PubMed2002

HLA-DR/DQ haplotype in rheumatoid arthritis: novel allelic associations in UK Caucasians.

OBJECTIVE: To elucidate the relative importance of the HLA-DR and HLA-DQ loci in conferring genetic predisposition to rheumatoid arthritis (RA). METHODS: HLA-DRB1 and HLA-DQB1 alleles were typed in a set of 685 patients with RA using sequence-specific polymerase chain reaction. Allele and phenotype frequencies were compared with those in 2 large sets of historical, ethnically matched healthy controls, using the relative predispositional effect method. RESULTS: Positive association was confirmed with the shared epitope positive HLA-DRB1 alleles associated with RA in Caucasians. A significant susceptibility effect was observed with HLA-DRB1*09, described in other ethnically diverse populations but not in Caucasians. A significant underrepresentation of the HLA-DRB1*0103 variant was noted among the RA cases, supporting the proposed protective role of the DERAA motif at residues 70-74 of the DRbeta molecule. No HLA-DRB1 independent association of the HLA-DQB1 alleles, implicated in predisposing to RA, was evident. CONCLUSION: These data corroborate the shared epitope hypothesis of susceptibility to RA and provide strong evidence for the DRB1 locus as the primary RA susceptibility factor in the HLA region.

Adult↗

PubMed2026

Exploring the shared genetic architecture of sarcopenia using genomic structural equation modeling.

Sarcopenia is a common age-associated condition characterized by the progressive loss of skeletal muscle mass, strength, and physical functionality. While large-scale genome-wide association studies (GWAS) have previously addressed isolated traits of sarcopenia, the multifactorial genetic architecture underlying this condition remains largely undefined. To characterize the common genetic basis of sarcopenia-related traits, genomic structural equation modeling (Genomic-SEM) was implemented. Multiple post-GWAS analytic approaches were integrated to pinpoint susceptibility loci. These analyses encompassed identifying enriched genetic pathways and relevant genomic elements, as well as cell-type-specific enrichment in skeletal muscle satellite stem cells, mesenchymal stem cells, and skeletal muscle satellite cells in limb muscle. Furthermore, based on the integrated GWAS data of sarcopenia-related traits, polygenic risk score (PRS) analysis was conducted to evaluate risk associations at the chromosomal level. A well-fitted Genomic-SEM successfully integrated the GWAS data, revealing the shared genetic architecture of sarcopenia-related traits. We identified 110 single nucleotide polymorphisms (SNPs) reaching genome-wide significance (p < 5 × 10-8), of which 9 represent novel discoveries. Subsequent fine-mapping procedures and gene-set analyses identified 15 causal variants alongside 77 candidate susceptibility genes. This study provides a comprehensive genetic characterization of sarcopenia via Genomic-SEM, offering new insights into the etiological pathways underlying sarcopenia.

Sarcopenia↗

PubMed2005

A cross-cultural investigation of the use of teaching styles.

Teacher beliefs are a major influence on teacher actions. Because context influences beliefs, it was the purpose of this study to explore teachers' beliefs about Mosston's Spectrum of Teaching Styles from an international perspective. Over 1,400 teachers from 7 countries completed a survey related to their self-reported use of and beliefs about various teaching styles. Data suggested a shared core of reproduction teaching style use. The use of and beliefs about the production styles of teaching were more varied. Teachers' use of styles was significantly related to their beliefs about the styles.

Cultural Diversity↗

PubMed2002

The hidden matrilineal structure of a solitary lemur: implications for primate social evolution.

Kin selection affects many aspects of social behaviour, especially in gregarious animals in which relatives are permanently associated. In most group-living primates with complex social behaviour, females are philopatric and organized into matrilines. Models of primate social evolution assume that females in solitary primates are also organized into matrilines. We examined the genetic structure and the mating system of a population of Coquerel's dwarf lemur (Mirza coquereli), a solitary primate from Madagascar, to test this assumption. Our genetic and behavioural analyses revealed that this population of solitary individuals is indeed structured into matrilines, even though this pattern was not predicted by behavioural data. Specifically, females sharing a mitochondrial DNA haplotype were significantly clustered in space and the average genetic and geographical distances among them were negatively correlated. Not all females were philopatric, but there is no evidence for the successful settlement of dispersing females. Although not all adult males dispersed from their natal range, they were not significantly clustered in space and all of them roamed widely in search of oestrous females. As a result, paternity was widely spread among males and mixed paternities existed, indicating that scramble competition polygyny is the mating system of this species. Our data therefore revealed facultative dispersal in both sexes with a strong bias towards female philopatry in this primitive primate. We further conclude that complex kinship structures also exist in non-gregarious species, where their consequences for social behaviour are not obvious.

Animals↗

PubMed1998

Using hospital performance data in quality improvement: the Cleveland Health Quality Choice experience.

BACKGROUND: Cleveland Health Quality Choice is a regional initiative to assess hospital performance which was implemented in 1989. The project developed and validated CHOICE, a severity adjustment system that includes diagnosis-specific models for medical, surgical, and obstetrical patients which are based on clinical data abstracted from patients' medical records. METHODOLOGY: Since 1992 Cleveland Health Quality Choice has disseminated semi-annual reports that profile hospital mortality rates, lengths of stay, and cesarean section rates using the CHOICE severity adjustment models. Hospitals receive tabular and graphical representations of hospital outcomes and electronic patient-level data files that can be used to further examine outcomes in clinical subgroups. RESULTS: Four case studies illustrate how outcomes data derived from the CHOICE models led to the development of successful hospital programs to decrease lengths of stay, cesarean section rates, and hospital mortality rates. Although each case study reflected a unique approach to process improvement, several common characteristics were observed: (1) establishment of interdisciplinary process improvement teams with senior physician and nursing leadership; (2) detailed review of the process of care to identify modifiable clinical practices likely to affect outcomes; (3) development of practice guidelines based on group consensus or published recommendations that were designed to affect modifiable practices; and (4) aggressive sharing of serial data with individual practitioners. CONCLUSIONS: Although outcomes data can provide powerful insight on where to target quality improvement efforts, hospitals must identify influential and modifiable clinical practices. Such efforts are most likely to be successful if driven by interdisciplinary work groups, supported by senior clinicians and administrators, and based on locally accepted practice standards.

Adult↗

PubMed2026

The Computational Revolution in Natural Product Research: A Data-Driven Roadmap for Next-Generation Drug Development.

Natural products (NPs) have historically provided the foundational scaffolds for drug development, yet traditional bioprospecting faces critical limitations: high rediscovery rates, laborious isolation workflows, and substantial attrition during clinical translation. The emergence of big data technologies is fundamentally transforming this landscape, enabling a shift from serendipity-based discovery toward systematic, data-driven approaches. This review examines how the integration of artificial intelligence (AI), machine learning (ML), and multi-omics datasets is accelerating natural product research across three key domains: (1) genome mining for biosynthetic gene cluster identification using platforms such as antiSMASH, (2) cheminformatics-driven prediction of structure-activity relationships and ADMET properties, and (3) metabolomics-guided dereplication to prioritize novel bioactive scaffolds. We evaluate the convergence of genomics, metabolomics, and computational chemistry in enabling in silico lead optimization and the discovery of cryptic metabolites from previously inaccessible microbial taxa. While challenges in data standardization and scalability persist, the synergy between big data and NP research is accelerating clinical translation. Despite persistent challenges in data standardization, scalability, and equitable benefit-sharing, the convergence of big data and NP research is poised to redefine drug development. These advances position computational NP research as a cornerstone of next-generation drug development.

big data analytics↗

PubMedDate not supplied

Data and metadata reporting standards for the U.S. Environmental Protection Agency's PM Supersites Research Program.

The EPA Supersites Research Program needs consistency of metadata and data structures to facilitate information sharing among investigators, analysts, and ultimately secondary data users. Under the auspices of NARSTO a successful mechanism was created to develop and implement reporting standards. The development effort included working closely with Supersites data coordinators, investigators, and technical experts, and also leveraging from existing data standards and practices. Overall, the standards are getting good acceptance from the atmospheric research community.

Cities↗

PubMed2003

MaXML: mouse annotation XML.

Although the sequencing of the human genome and several model organisms is almost complete, the number of genes in the human is still in debate. cDNA (complementary DNA) is generated from mRNA that is transcribed from the genome and can be regarded as a gene itself; therefore, decoding cDNA sequences is important in characterizing genes. Recently, biologists have been able to describe more knowledge about genes in order to characterize them, and this information is generally called 'annotation.' Furthermore, annotation is important in understanding the systems of organisms in various fields of research. We therefore constructed the MaXML (Mouse annotation XML) format with which mouse cDNA annotation data can be exchanged and shared between laboratories more efficiently. Defining strict data types for annotations is difficult, but we consider XML a feasible format for describing them. We have used the MaXML format to express mouse annotation data in FANTOM DB. We have also developed tools and systems utilizing these MaXML data, including a parser and a server to provide data on-the-fly.

Animals↗

PubMed2024

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples.

Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.

Humans↗

PubMed2005

Genetic insights into disease mechanisms of autoimmunity.

Educating the immune system to distinguish between self and non-self is critical to ensure that an immune response is mounted against foreign antigens and not against self. A breakdown in these mechanisms can lead to the onset of autoimmune disease. Clinical and molecular data suggest that shared immunogenetic mechanisms lead to the autoimmune process. The most studied genes and molecules are the human leukocyte antigen (HLA) region and the cytotoxic T-lymphocyte-associated 4 molecule (CTLA-4). Recently progress has been achieved in narrowing down the primary variants within both gene regions, but further work is needed to determine the function and extent of the aetiological variant(s) present. Recent exciting results also suggest a role for the newly discovered lymphoid-specific phosphatase (LYP) protein. As well as these general mechanisms, disease-specific mechanisms are beginning to be elucidated, for example the role of autoimmune regulatory element 1 (AIRE1) in autoimmune polyendocrinopathy-candidiasis ectodermal dystrophy (APECED). Taken together, these data suggest that both general and disease-specific mechanisms lead to the clinical outcome of autoimmune disease and that increased understanding of these mechanisms will improve our knowledge of how autoimmune disease occurs, eventually leading to the development of novel therapeutic agents.

Antigens, CD↗

PubMed2002

The impact of the Balanced Budget Act on the utilization and financial condition of children's services in California hospitals.

The objective of this study was to evaluate the utilization and financial performance of children's services after the Balanced Budget Act of 1997. The author analyzed these performance factors by hospital ownership, HMO penetration, and disproportionate share hospitals. Using data from California hospitals and conducting an analysis from 1997 to 1999, the author found that public hospitals were able to increase their profits from pediatric and neonatal intensive care services. The study also revealed that DSH hospitals located in high HMO penetration markets reduced their operating losses in nursery and pediatric services.

Budgets↗

PubMed2004

eL-DASionator: an LDAS upload file generator.

BACKGROUND: The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as flat text files in a defined format. The popular Ensembl ContigView uses the same format for the transient upload and display of user data. RESULTS: In order to easily generate LDAS upload files we developed a software tool that is accessible via a web-interface http://atgc.lirmm.fr/eldasionator.html. Users can submit their DNA sequences of interest. Our program (i) aligns these sequences to the reference sequences of Ensembl, (ii) determines start and end positions of each sequence on the reference sequence, and (iii) generates a formatted annotation file. This file can be used to load any LDAS annotation server or it can be uploaded to the Ensembl ContigView. CONCLUSION: The eL-DASionator is an on-line tool that is intended for life-science researchers with little bioinformatics background. It conveniently generates LDAS upload files, and makes it possible to generate annotations in a standard format that permits comfortable sharing of this data.

Base Sequence↗

PubMed1998

Developing a team for multicultural, multi-institutional research on fatigue and quality of life.

PURPOSE/OBJECTIVES: To describe the process of establishing a multisite team to conduct research with a multicultural focus on fatigue. DATA SOURCES: Articles, book chapters, personal experience. DATA SYNTHESIS: Teamwork facilitated development of a productive professional working group, sharing of resources, and data collection culminating in a research proposal for studying cancer-related fatigue in a multicultural population. CONCLUSIONS: Establishing a common goal by investing time, committing to the process, and establishing trust was the secret to effective team functioning. IMPLICATIONS FOR NURSING PRACTICE: The prospect of multi-institutional collaboration has implications for oncology nurses in the areas of research and practice. Goals that could not be achieved easily in the setting of a single institution are reached more easily with multisite collaboration and teamwork.

Cooperative Behavior↗

PubMed2002

Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted field.

The advent of molecular technologies that allow the collection and analysis of large amounts of genetic data is rapidly transforming the field of genetic epidemiology. Whether monitoring infectious outbreaks or identifying genotypic variations that underlie disease susceptibility, genetic epidemiology relies heavily on the analysis of multiple, independently derived results. By allowing the simultaneous monitoring of thousands of genetic or expression data points, microarrays are emerging as particularly powerful tools. Several recent reviews have described array manufacturing and the types of scientific questions that can exploit this technology, but few have addressed how the intended use of an array can dictate its design. This review will focus on this latter issue, with particular emphasis on the genetic epidemiology of infectious disease. The design of arrays for genotyping, expression profiling, and fingerprinting are presented, and examples of recent epidemiological studies are used to illustrate the applications' strong points and limitations. In addition to discussing arrays' ability to provide global views of gene identity or function, the review will describe design options for creating arrays that detect multiple genetic variations. It will also examine the reliability of array-generated fingerprints, assay accessibility, and possibilities for sharing and comparing data across studies. Although many challenges lie ahead, microarrays' multiple abilities appear uniquely poised to accelerate the advance of genetic epidemiology's multiple fronts.

Base Sequence↗

PubMed2006

Basal forebrain cholinergic system of the anuran amphibian Rana perezi: evidence for a shared organization pattern with amniotes.

The organization of the basal forebrain cholinergic system (BFCS) in the frog was studied by means of choline acetyltransferase (ChAT) immunohistochemistry. The BFCS was observed as a conspicuous cholinergic cell population extending through the diagonal band, medial septal nucleus, bed nucleus of the stria terminalis, and pallidal regions. Abundant fiber labeling was also found around the labeled cell bodies. The combination of retrograde tract tracing with dextran amines and ChAT immunohistochemistry revealed intraseptal and intra-BFCS cholinergic connections. In addition, an extratelencephalic cholinergic input from the laterodorsal tegemental nucleus was demonstrated. The possible influence of monoaminergic inputs on the BFCS neurons was examined by means of tyrosine hydroxylase and serotonin immunohistochemistry combined with ChAT immunolabeling. Our results showed that catecholaminergic fibers overlapped the BFCS, with the exception of the medial septal nucleus. Serotoninergic innervation was widespread, but less abundant in the caudal extent of the BFCS. Taken together, our results on the localization of the cholinergic neurons in the basal forebrain and their relationship with cholinergic, catecholaminergic, and serotoninergic afferents have shown numerous common features with amniotes. In particular, anurans and mammals (for which most data is available) share a strikingly comparable organization pattern of the BFCS.

Animals↗

PubMed1999

General practice integration in Australia. Primary health services provider and consumer perceptions of barriers and solutions.

OBJECTIVE: To identify practical examples of barriers and possible solutions to improve general practice integration with other health service providers. METHOD: Twelve focus groups, including one conducted by teleconference, were held across Australia with GPs and non GP primary health service providers between May and September, 1996. Focus groups were embedded within concept mapping sessions, which were used to conceptually explore the meaning of integration in general practice. Data coding, organising and analysis were based on the techniques documented by Huberman and Miles. RESULTS: Barriers to integration were perceived to be principally due to the role and territory disputes between the different levels of government and their services, the manner in which the GP's role is currently defined, and the system of GP remuneration. Suggestions on ways to improve integration involved two types of strategies. The first involves initiatives implemented 'top down' through major government reform to service structures, including the expansion of the role of divisions of general practice, and structural changes to the GP remuneration systems. The second type of strategy suggested involves initiatives implemented from the 'bottom up' involving services such as hospitals (e.g. additional GP liaison positions) and the use of information technology to link services and share appropriate patient data. CONCLUSION: The findings support the need for further research and evaluation of initiatives aimed at achieving general practice integration at a systems level. There is little evidence to suggest which types of initiatives improve integration. However, general practice has been placed in the centre of the health care debate and is likely to remain central to the success of such initiatives. Clarification of the future role and authority of general practice will therefore be required if such integrative strategies are to be successful at a wider health system level.

Australia↗

PubMedDate not supplied

Assessing the educational literature in the responsible conduct of research for core content.

To determine core content for RCR instruction, content analysis was conducted using key instructional resources for ORI's nine RCR "core instructional areas". Topics discussed in these key RCR resources were identified and their frequency across resources was tabulated. Topics covered most frequently were judged to be core content. Although key educational resources cited a variety of references, specific topics and issues addressed were generally consistent across the materials examined. Nonetheless, key resources varied in organization and depth of coverage for core instructional areas. Recent resources were more systematic and comprehensive than earlier works. This was particularly evident in materials about human participant research, conflicts of interest, and data management and sharing. Key resources presented additional "non-core" issues, such as scientific values, ethical principles, creativity and objectivity, moral reasoning, genetics, epidemiological issues, and scientists' societal roles, suggesting that ORI's core instructional areas should be reconfigured or expanded. Because educational material available on RCR and professionalism was so comprehensive, we recommend that ORI consider research integrity, not research misconduct, as one core instructional area. We also recommend that compliance with research regulations be restored as a core instructional area to accentuate ethical, financial and legal requirements related to acceptance of federal funding.

Authorship↗