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PubMed2026

Scalable, open-access and multidisciplinary data integration pipeline for climate-sensitive diseases.

Climate-sensitive infectious diseases pose an important challenge for human, animal and environmental health and it has been estimated that over half of known human pathogenic diseases can be aggravated by climate change. While climatic and weather conditions are important drivers of transmission of vector-borne diseases, socio-economic, behavioural, and land-use factors as well as the interactions among them impact transmission dynamics. Analysis of drivers of climate-sensitive diseases require rapid integration of interdisciplinary data to be jointly analysed with epidemiological (including genomic and clinical) data. Current tools for the integration of multiple data sources are often limited to one data type or rely on proprietary data and software. To address this gap, we develop a scalable and open-access pipeline for the integration of multiple spatio-temporal datasets that requires only the declaration of the country and temporal range and resolution of the study. The tool is locally deployable and can easily be integrated into existing climate-disease-modelling applications. We demonstrate the utility of the tool for dengue modelling in Vietnam where epidemiological data are legally required to remain local. We include a pipeline for bias correction of climate data to enhance their quality for downstream modelling tasks. The Dengue Advanced Readiness Tools-Pipeline empowers users by simplifying complex download, correction, and aggregation steps, fostering data-driven discovery of relationships between infectious diseases and their drivers in space and time, and enhancing reproducibility in research. Additional modules and datasets can be added to the existing ones to make the pipeline extendable to use cases other than the ones presented here.

automated workflows↗
PubMed1992

Structural proteins of equine arteritis virus.

We have recently shown that the genome of equine arteritis virus (EAV) contains seven open reading frames (ORFs). We now present data on the structural proteins of EAV and the assignment of their respective genes. Virions are composed of a 14-kDa nucleocapsid protein (N) and three membrane proteins designated M, GS, and GL. M is an unglycosylated protein of 16 kDa, and GS and GL are N-glycosylated proteins of 25 and 30 to 42 kDa, respectively. The broad size distribution of GL results from heterogeneous N-acetyllactosamine addition since it is susceptible to digestion by endo-beta-galactosidase. Using monospecific antisera as well as an antivirion serum, and by expression of individual ORFs, the genes for the structural proteins were identified: ORF 7 codes for N, ORF 6 for M, ORF 5 for GL, and ORF 2 for GS. With the exception of GS, the proteins are about equally abundant in EAV virions, being present at a molar ratio of 3 (N):2 (M):3 (GL). The GS protein, which is expressed at a level similar to that of M in infected cells, is strikingly underrepresented in virus particles (1 to 2%). Our data justify a distinct taxonomic position for EAV, together with lactate dehydrogenase-elevating virus and simian hemorrhagic fever virus; although coronavirus- and toroviruslike in features of transcription and translation, the virion architecture of EAV is fundamentally different.

Amino Acid Sequence↗
PubMedDate not supplied

The use of psychological test data to predict open-heart surgery outcome: a prospective study.

In an attempt to predict survival of open-heart surgery, particularly among high risk subjects who undergo extra-corporeal circulation [ECG] using pump oxygenation perfusion, a preoperative battery including intellectual, personality and neuropsychological instruments and also ratings of cardiac impairment, was administered to 15 control [cardiac surgery without ECG] and 72 experimental [ECG] subjects. Subjects were divided into survivor [S] and fatality [F] groups, and preoperative test data were analyzed using multivariate stepwise discrimination techniques. In a variety of analyses, at least 86% and as high as 100% of subjects were correctly classified as survivors or fatalities on the basis of variables sampled, indicating the outcome of cardiac surgery may be predicted preoperatively with a high degree of accuracy.

Adaptation, Psychological↗
PubMed2026

TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score. RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest. AVAILABILITY AND IMPLEMENTATION: Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.

Software↗
PubMed1992

Effects of isoflurane on acetylcholine receptor channels. 1. Single-channel currents.

We studied the effects of the volatile general anesthetic isoflurane on single acetylcholine (ACh) receptor channels from clonal BC3H-1 cells. Excised patches were exposed to concentrations of isoflurane ranging from 0.18% to 4.0%, in the presence of 200 nM ACh. Isoflurane transformed channel behavior from isolated openings into bursts of brief openings. The channel open time decreased monotonically with the concentration of isoflurane; the mean open time was half of control at 0.4% isoflurane. The duration of bursts also decreased in the presence of isoflurane. The duration of brief closures within bursts was 300-400 musec at concentrations above 0.3% isoflurane. The number of openings per burst increased moderately with isoflurane but did not exceed 3. The frequency of bursts increased with the concentration of isoflurane. The apparent single-channel conductance decreased to 75% of control at 4% isoflurane. These results are discussed in terms of models of channel block. The concentration dependence of the open time, the gap duration, and the conductance are consistent with a sequential open-channel blocking mechanism in which most but not all blocking events were resolved. A model that assumes that isoflurane "blocks" both open and closed channels was then considered. This model is consistent not only with the open time data but also with the burst duration and number of openings per burst. These results indicate that isoflurane has effects on closed as well as open ACh receptor channels.

Animals↗
PubMed2026

Artificial Intelligence for Colorectal Surgeons-Part II: Research Applications, Challenges in Adoption, and Practical Resources.

BACKGROUND: This is part II of a 2-part series examining artificial intelligence in colorectal surgery. Part I established foundational concepts and clinical applications. Implementation, however, requires understanding research methodologies, available resources, and the specific challenges currently limiting widespread adoption. These topics are the focus of part II. OBJECTIVE: To examine artificial intelligence's transformation of surgical research, provide practical implementation resources, address adoption challenges, and explore future directions in colorectal surgery. METHODS: Comprehensive literature review focusing on artificial intelligence research methodology, implementation barriers, educational resources, and emerging technologies relevant to colorectal surgeons. RESULTS: Artificial intelligence streamlines clinical trial design through predictive modeling and natural language processing, reducing enrollment challenges that contribute to failed or inadequate trial accrual. Machine learning enables heterogeneity analysis within clinical trials, identifying treatment-responsive subgroups. Foundation models unlock analysis of unstructured electronic health record data at scale. Professional societies and universities offer specialized artificial intelligence education programs, with open-access data sets facilitating research participation. However, implementation faces multifaceted challenges: technical infrastructure demands, with real-time processing requiring dedicated graphics processing unit clusters; regulatory frameworks struggling with continuously evolving algorithms; undefined liability distribution for artificial intelligence-assisted decisions; algorithmic bias risking health care disparities; and the "black box" problem limiting clinical trust. Economic barriers include substantial initial costs without clear reimbursement pathways. Future directions include multimodal artificial intelligence integrating imaging, genomics, and histopathology; cognitive robotic systems with real-time decision support; digital twin technology for patient-specific surgical simulation; and global surgical artificial intelligence networks enabling distributed learning across institutions. CONCLUSIONS: Although artificial intelligence offers transformative potential for colorectal surgery research and practice, successful implementation requires addressing technical, regulatory, ethical, and economic challenges. The surgeon's evolving role demands both traditional expertise and computational fluency. Future advances in multimodal integration, autonomous systems, and global collaboration will fundamentally reshape surgical practice but will require thoughtful implementation prioritizing patient benefit and clinical value.

Humans↗
PubMed1992

Molecular cloning and characterization of gravity specific cDNA in rice (Oryza sativa L.) suspension callus.

Rice (Oryza sativa L. var. Nipponbare) suspension callus was exposed to gravity stress at 450,000 g for 2 hours, after which poly(A)+RNA was isolated and a cDNA library was constructed. Three different gravity specific cDNAs, namely, GSC 128, GSC 233 and GSC 381 of 0.67, 0.60 and 0.68 kilobase pairs and transcripts of 1.9, 1.6 and 2.0 kb, respectively, were isolated by differential screening and Northern hybridization. The maximum level of transcript was achieved after 4 hours of exposure to gravity at 450,000 g for GSC 128, 2 hours for GSC 233 and 8 hours for GSC 381 followed by a gradual decrease to undetectable levels with the extension of gravitation time. Callus (GSC 128), shoot and callus (GSC 381) and root and callus (GSC 233) specific expression of transcripts was identified. Although the protection of callus by treatment with ABA, kinetin and sucrose extended the period of expression of mRNA in suspension callus after gravity exposure, the expression of gravity-inducible mRNA was exclusively regulated by the degree of callus viability or survival after the stress. In addition, we demonstrated that the level of GSC 381 transcript was markedly increased by exposing the cell to periodical gravity stress, suggesting that this mRNA is expressed and translated into special proteins which are closely related to the survival of the cell against gravity stress. The sequence of GSC 233 and GSC 381, consisting of 417 and 531 base pairs of the longest open reading frames, encode polypeptides with calculated molecular weights of 15.29 and 19.47 kDa, respectively. A sequence homology search against a data bank revealed that GSC 233 and GSC 381 differed from other stress inducible genes in terms of the coding sequence and expression characteristics.

Adaptation, Physiological↗
PubMed1991

[Electronic data processing assisted documentation of tumor after care in an ambulatory setting--a simplification of daily routine].

A data collection system on microcomputer was developed for patients with malignant diseases in ambulant aftercare. At the same time when patient data are collected to be sent to a central medicostatistical plotting station, as it is usual in Austrian hospitals, a file for further aftercare is opened. By data transfer to other software products, statistical data evaluation is possible. Patients can also be called to hospital for different reasons.

Aftercare↗
PubMed1978

Fenestrations in endothelium of rat liver sinusoids revisited by freeze-fracture.

The freeze-fracture appearance of fenestrations of sinusoidal endothelial cells has been reassessed in perfusion-fixed rat liver. Fenestrations, limited to the attenuated portions of the endothelial cell cytoplasm are usually round or oval in shape, with diameters ranging from 40-600 nm. Within a given fenestrated region, they are disposed in clusters forming sieve plates. In addition, the presence of wide, irregularly shape openings suggest that adjacent fenestrations may coalesce and result in the larger openings. Our data thus confirm the existence of both small and large fenestrae in the endothelial wall, in contradistinction to previous studies showing only regular, medium sized (100 nm) openings.

Animals↗
PubMed1991

Isolation and characterization of a cDNA encoding a chicken beta thyroid hormone receptor.

We have isolated and characterized a cDNA encoding a chicken beta homolog of c-erbA, or thyroid hormone receptor (TR). Chicken liver cDNA libraries were screened with a rat TR beta-1 cDNA probe, and several cDNA inserts were isolated and characterized. The sequence of one cDNA predicts a 369-amino-acid open reading frame (ORF), with a protein sequence that possesses 96% identity with that of rat TR beta-1, but only 88% identity with chicken TR alpha. These data indicate that the cDNA likely encodes a beta form of TR that has the expected putative DNA and T3 binding domains. The chicken TR beta (chTR beta) in vitro translated protein binds T3 with high affinity, and binds both the thyroid hormone response element (TRE) from the rat growth hormone gene and the Xenopus vitellogenin A2 gene estrogen response element (ERE), similarly to that of the rat TR beta-1. Northern blot analysis revealed the expression of a 7.0-kb RNA in several tissues including cerebellum, pituitary, kidney, and liver. This chicken liver TR beta cDNA sequence varies in both the 5' and 3' untranslated regions from the chicken kidney TR beta cDNA sequence recently reported (Forrest et al., 1990). The 5' untranslated cDNA sequence divergence occurs near a potential splice site junction of the human TR beta gene, suggesting that this chicken liver cDNA may represent an alternatively spliced RNA product of the chicken TR beta gene.

Amino Acid Sequence↗
PubMed2025

Privacy-preserving framework for genomic computations via multi-key homomorphic encryption.

MOTIVATION: The affordability of genome sequencing and the widespread availability of genomic data have opened up new medical possibilities. Nevertheless, they also raise significant concerns regarding privacy due to the sensitive information they encompass. These privacy implications act as barriers to medical research and data availability. Researchers have proposed privacy-preserving techniques to address this, with cryptography-based methods showing the most promise. However, existing cryptography-based designs lack (i) interoperability, (ii) scalability, (iii) a high degree of privacy (i.e. compromise one to have the other), or (iv) multiparty analyses support (as most existing schemes process genomic information of each party individually). Overcoming these limitations is essential to unlocking the full potential of genomic data while ensuring privacy and data utility. Further research and development are needed to advance privacy-preserving techniques in genomics, focusing on achieving interoperability and scalability, preserving data utility, and enabling secure multiparty computation. RESULTS: This study aims to overcome the limitations of current cryptography-based techniques by employing a multi-key homomorphic encryption scheme. By utilizing this scheme, we have developed a comprehensive protocol capable of conducting diverse genomic analyses. Our protocol facilitates interoperability among individual genome processing and enables multiparty tests, analyses of genomic databases, and operations involving multiple databases. Consequently, our approach represents an innovative advancement in secure genomic data processing, offering enhanced protection and privacy measures. AVAILABILITY AND IMPLEMENTATION: All associated code and documentation are available at https://github.com/farahpoor/smkhe.

Computer Security↗
PubMed1992

Dihydrolipoamide dehydrogenase from Haloferax volcanii: gene cloning, complete primary structure, and comparison to other dihydrolipoamide dehydrogenases.

We used the N-terminal amino acid sequence of dihydrolipoamide dehydrogenase from Haloferax volcanii, to design and synthesize two oligonucleotide probes that were used to identify and clone a 4.3 kilobase pair (kbp) fragment from MboI restriction endonuclease digestion of Hf. volcanii genomic DNA. The nucleotide sequence of a 1.5-kbp region of this clone was determined and this revealed an open reading frame that translated into a protein with good homology to dihydrolipoamide dehydrogenase from other sources. The first 48 amino acids were identical with the N-terminal sequence data obtained from the purified protein. The complete primary structure of the halophilic dihydrolipoamide dehydrogenase was analyzed in terms of its homologies to dihydrolipoamide dehydrogenases from other sources and its molecular adaptations to high intracellular ionic strength.

Amino Acid Sequence↗
PubMed1992

The nucleotide sequence between genes 31 and 30 of bacteriophage T4.

The nucleotide sequence of the 2994 bp T4 phage DNA fragment between genes 31 and 30 is presented. The fragment contains 7 complete open reading frames in the direction of early transcription and two early promoters, PE128.6 and PE128.2, which we show to cause difficulties in cloning DNA from this genomic region. Our data complete the nucleotide sequence and the organization of genes in the genomic region between T4 genes 31 and 30.

Amino Acid Sequence↗