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At least 703 records · Page 39Linked to original sources
PubMed2003

Cerner Millennium: the Innsbruck experience.

OBJECTIVES: A Clinical Information System, serving more than 2,000 users was to be implemented at three hospitals of TILAK (Tiroler Landeskrankenanstalten GmbH), including the University Hospital of Innsbruck. The system was intended to integrate data from radiology, laboratory, and pathology subsystems with patient data. METHODS: Using Cerner Millennium software and Health Level 7 standards, the first stage of an Electronic Patient Record (EPR) was built. Direct data entry was facilitated using either a Microsoft Word text processor (with subsequent authentication workflow) or structured forms. An enterprise-wide scheduling module allows coordination and storage of patient appointments directly in the EPR. As required by security policy, the Cerner software regulates the varying degrees of information exchange among organizations and departments within the enterprise. RESULTS: First experiences indicate satisfactory acceptance of system functionalities. The introduction of Cerner Millennium at TILAK has achieved essential goals defined at the beginning of the project. Basic functionalities--free text documentation, standardized documentation, scheduling, and some parts of order entry--are offered in a user friendly manner. Integration with existing systems to complete the EPR has been successful using standard interfaces (HL7). CONCLUSION: TILAK concluded that it was possible to successfully implement a Clinical Information System (CIS) developed mainly for the American market in a European healthcare environment. Some adaptations and functional extensions were necessary (e.g., the discharge summary "Arztbrief"). The system had enough flexibility to meet the requirements and specifications of European healthcare processes. A key factor of success was the establishment of a basic level of understanding and communication between the software vendor and the TILAK user community.

Austria↗
PubMed2005

Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach.

High-density oligonucleotide arrays have become a popular assay for concurrent measurement of mRNA expression at the genome scale. Much effort has been devoted to the development of statistical analysis tools aimed at reducing experimental noise and normalizing experimental variation in gene expression analysis. However, these investigations do not detect or catalog systematic problems associated with specific oligonucleotide probes. Here, we present an investigation of problematic probes that yield consistent but inaccurate signals across multiple experiments. By evaluating data integrity among gene, probe sequence, and genomic structure we identified a total of 20,696 (10.5%) nonspecific probes that could cross-hybridize to multiple genes and a total of 18,363 (9.3%) probes that miss the target transcript sequences on the Affymetrix GeneChip U95A/Av2 array. The numbers of nonspecific and mistargeted probes on the U133A array are 29,405 (12.1%) and 19,717 (8.0%), respectively. The poor performance of the mistargeted probes was confirmed in two GeneChip experiments, in which these probes showed a 20-30% decrease in detecting present signals compared with normal probes. Comparison of qualitative expression signals obtained from SAGE and EST data with those from GeneChip arrays showed that the consistency of the two platforms is 30% lower in problematic probes than in normal probes. A Web application was developed to apply our results for improving the accuracy of expression analysis.

Expressed Sequence Tags↗
PubMed2000

Preserving renal function in adults with hypertension and diabetes: a consensus approach. National Kidney Foundation Hypertension and Diabetes Executive Committees Working Group.

Over 11 million Americans have both diabetes and hypertension-comorbid diseases that strongly predispose people to both renal as well as cardiovascular (CV) injury. Hypertension substantially contributes to CV morbidity and mortality in people with diabetes. Diabetes is the most common cause of end-stage renal disease in the United States. Furthermore, hypertension and diabetes are particularly prevalent in certain populations, such as African-Americans and Native Americans. Since the 1994 Working Group Report on Hypertension and Diabetes, a large body of clinical trial data has affirmed the original blood pressure goal of less than 130/85 mmHg recommended to preserve renal function and reduce CV events in people with hypertension and diabetes. Data that are more recent have emerged, however, to support an even lower diastolic blood pressure goal, ie, 80 mmHg, in order to optimally preserve renal function and reduce CV events in people with diabetic nephropathy. A review of clinical trials indicates that more than 65% of people with diabetes and hypertension will require two or more different antihypertensive medications to achieve the new suggested target blood pressure of 130/80 mmHg. The purpose of this report is to update the previous recommendations with a focus on level of blood pressure control, proteinuria reduction, and therapeutic approaches to achieve these goals. We provide an evidence-based approach, integrating data from the major clinical trials that were designed as randomized prospective, long-term studies that had as a primary endpoint either progression of diabetic nephropathy or reduction in CV events. This report also addresses socioeconomic and cultural barriers that hinder achievement of blood pressure goals. Lastly, the report discusses approaches to resolve cultural barriers, both physician- and patient-derived, that interfere with achievement of lower blood pressure goals.

Adult↗
PubMed2026

A One Health approach to Antimicrobial Resistance: Concepts, challenges, and advances in omics.

Antimicrobial resistance (AMR) is a global threat driven by the interplay between microbial evolution and human activity. Antimicrobial use in human and veterinary medicine, as well as in agriculture, accelerates the selection and dissemination of resistant bacteria and genes across interconnected human, animal, and environmental reservoirs. These dynamic exchanges render single-sector interventions ineffective. A One Health approach integrating human, animal, and environmental health is therefore essential to understand and mitigate the emergence and spread of AMR. This chapter focuses on bacterial antimicrobial resistance, addressing key concepts, major challenges, and emerging technologies within a One Health framework. Advances in next-generation sequencing and omics technologies have transformed our capacity to resolve AMR at unprecedented scale and resolution. These tools enable the tracking of resistance genes and high-risk clones across ecosystems, uncover transmission pathways, and identify key drivers of dissemination. Such insights support real-time epidemiological surveillance, outbreak detection, and targeted interventions. However, translating these advances into routine practice remains a major challenge, requiring harmonized methodologies, data integration, and cross-sector coordination. Addressing AMR demands sustained collaboration across disciplines and stakeholders, including clinicians, veterinarians, farmers, researchers, policymakers, industry, and the public. And framing AMR as a shared ecological and societal responsibility underscores the urgency of coordinated global action. We call for the urgent integration of One Health principles into surveillance, policy, and innovation to preserve antimicrobial effectiveness and safeguard future health.

Humans↗
PubMed1996

Dinuclear Copper(II) Complexes Incorporating a New Septadentate Polyimidazole Ligand.

The dinuclear copper(II) complexes [Cu(2)(tmihpn)(prz)](ClO(4))(2).2CH(3)CN (6) and [Cu(2)(tmihpn)(O(2)CCH(3))](ClO(4))(2).CH(3)CN (7) were prepared, where tmihpn is the deprotonated form of N,N,N',N'-tetrakis[(1-methylimidazol-2-yl)methyl]-1,3-diaminopropan-2-ol and prz is the pyrazolate anion. The crystal structures of 6 and 7 were determined and revealed that both complexes contain bridging alkoxide ligands as well as bridging pyrazolate and acetate ions, respectively. Crystal data: compound 6, triclinic, P&onemacr;, a = 18.089(2) Å, b = 22.948(3) Å, c = 9.597(2) Å, alpha = 93.37(2) degrees, beta = 94.49(2) degrees, gamma = 81.69(2) degrees, V = 3925.1 Å(3), Z = 4; compound 7, triclinic, P&onemacr;, a = 12.417(2) Å, b = 15.012(3) Å, c = 10.699(2) Å, alpha = 104.76(2) degrees, beta = 102.63(2) degrees, gamma = 99.44(2) degrees, V = 1830.1 Å(3), Z = 2. In compound 6, the coordination geometry around both copper centers resembles a distorted square pyramid, while the stereochemistry around the copper centers in 7 is best described as trigonal bipyramidal. Both complexes display well-resolved isotropically shifted (1)H NMR spectra. Selective substitution studies and integration data have been used to definitively assign several signals to specific ligand protons. Results from the solution (1)H NMR studies suggest that the basal and apical imidazole groups do not exchange rapidly on the NMR time scale and the solid state structures of the complexes are retained in solution. In addition, the magnetochemical characteristics of 6 and 7 were determined and provide evidence for "magnetic orbital switching". Antiferromagnetic coupling in 6 (J = -130 cm(-)(1)) is strong, while the copper centers in compound 7 are ferromagnetically coupled (J = +16.4 cm(-1)). Differences in the magnetic behavior of the two copper centers have been rationalized using the "ligand orbital complementary" concept. The ground state magnetic orbitals involved in spin coupling in 6 (d(x)()()2(-)(y)()()2) are different from those in 7 (d(z)()()2).

Journal Article↗
PubMed1994

[Social integration and mortality in Japanese elderly].

The prospective association of social integration reported in 1987 with mortality over three years was examined in a cohort of 2200 Japanese elderly, aged 60 years and over. Social integration data was obtained from a national survey which measured both the quantity and frequency of attachment. Social ties was classified into five types; spouse, child(ren) living together, child(ren) living separately, friend, neighbor, and community group. Ten potential confounding variables-age, educational attainment, address, existence of chronic diseases, activities of daily living, subjective well-being, drinking, sleeping hours, cigarette smoking, and exercise- were controlled using logistic regression analysis for each sex. Men who belong to more community organizations or attend meeting of these groups more frequently had significantly less mortality during the follow-up period. Trends for women were not significant. No association was observed between mortality and other variables of social integration.

Aged↗
PubMed2006

Identification of functional modules in a PPI network by clique percolation clustering.

Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein-protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experimentally determined protein complexes. Our method of analysis can of course be applied to protein-protein interaction data for any species and even other biological networks.

Algorithms↗
PubMed2001

Comparison of prognostic models in patients with advanced Hodgkin disease. Promising results from integration of the best three systems.

BACKGROUND: Several prognostic systems have been elaborated for patients with Hodgkin disease (HD) over the last 12 years, but early identification of a reasonably large group of both low and high risk, advanced stage patients remains unsatisfactory. METHODS: Seven well known models were applied to 516 patients with advanced HD, with 315 patients used for the study sample and 201 patients used for the test sample. Individual performances as well as joint performances were analyzed univariately and multivariately in relation to overall survival, recurrence free survival, and time to treatment failure by means of a proportional hazards model. RESULTS: None of the models identified a group containing > 10% of patients from the total population who had a failure risk of either < or = 10% or > or = 50%. The systems of the International Database on Hodgkin Disease, the Memorial Sloan-Kettering Cancer Center, and the International Prognostic Factor Project showed the best prognostic power; only these three, when analyzed together, predicted clinical outcome with a statistically significant fit to the clinical data. Integration of the three systems in a linear model dramatically improved their individual discriminatory capacity by identifying patients with 10% and 50% failure risks, respectively, in 23% and 24% of the study patient population and in 19% and 25% of the test population, respectively. CONCLUSIONS: As powerful and simple new prognostic factors are awaited that may improve our predictive ability, this integrated index is probably the best way to exploit the significance of those presently available. The program required for the calculations can be downloaded from the Internet at the web site http://www.unimo.it/gisl/default.htm.

Adolescent↗
PubMed2005

Digital biology: an emerging and promising discipline.

This article examines the role of computation and quantitative methods in modern biomedical research to identify emerging scientific, technical, policy and organizational trends. It identifies common concerns and practices in the emerging community of computationally-oriented bio-scientists by reviewing a national symposium, Digital Biology: the Emerging Paradigm, held at the National Institutes of Health in Bethesda, Maryland, November 6th and 7th 2003. This meeting showed how biomedical computing promises scientific breakthroughs that will yield significant health benefits. Three key areas that define the emerging discipline of digital biology are: scientific data integration, multi-scale modeling and networked science. Each area faces unique technical challenges and information policy issues that must be addressed as the field matures. Here we summarize the emergent challenges and offer suggestions to academia, industry and government on how best to expand the role of computation in their scientific activities.

Computational Biology↗
PubMed2005

Using passive air samplers to assess urban-rural trends for persistent organic pollutants and polycyclic aromatic hydrocarbons. 2. Seasonal trends for PAHs, PCBs, and organochlorine pesticides.

This is the second of two papers demonstrating the feasibility of using passive air samplers to investigate persistent organic pollutants along an urban-rural transect in Toronto. The first paper investigated spatial trends for polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs). This second paper investigates the seasonality of air concentrations for polycyclic aromatic hydrocarbons (PAHs), PCBs, and OCPs along this transect. Air samplers, consisting of polyurethane foam (PUF) disks housed in stainless steel domed chambers, were deployed for three 4-month integration periods from June 2000 to July 2001. The seasonal variations of derived air concentrations for PAHs, PCBs, and OCPs reflected the different source characteristics for these compounds. PAHs showed a strong urban-rural gradient with maximum concentrations at urban sites during the summer period (July-October). These high summer values in Toronto were attributed to increases in evaporative emissions from petroleum products such as asphalt. PCBs also exhibited a strong urban-rural gradient with maximum air concentrations (approximately 2-3 times higher) during the spring period (April-June). This was attributed to increased surface-air exchange of PCBs that had accumulated in the surface layer over the winter. alpha-HCH was fairly uniformly distributed, spatially and temporally, as expected. This pattern and the derived air concentration of approximately 35 to approximately 100 pg m(-3) agreed well with high volume air data from this region, adding confidence to the operation of the passive samplers and showing that site-to-site differences in sampling rates was not an issue. For other OCPs, highest concentrations were observed during the spring period. This was associated with either (i) their local and/or regional application (gamma-HCH, endosulfan) and (ii) their revolatilization (chlordanes, DDT isomers, dieldrin, and toxaphene). Principal component analysis resulted in clusters for the different target chemicals according to their chemical class/source type. The results of this study demonstrate how such a simple sampling technique can provide both spatial and seasonal information. These data, integrated over seasons, can be used to evaluate contaminant trends and the potential role of large urban centers as sources of some semivolatile compounds to the regional environment, including the Great Lakes ecosystem.

Air↗
PubMed2006

Population pharmacokinetics of tipifarnib in healthy subjects and adult cancer patients.

AIMS: To characterize the population pharmacokinetics of tipifarnib. METHODS: A total of 1083 subjects treated orally with a solution, capsule or tablet formulations of tipifarnib, given as a single dose or as multiple twice-daily doses (range 25-1300 mg) were combined with data from 1, 2 and 24 h intravenous infusions. A total of 3445 concentrations in the index data set were fitted by an open three-compartment linear disposition model with sequential zero-order input into the depot compartment, followed by a first-order absorption process, and lag time, using NONMEM V. The effect of patient covariates on tipifarnib pharmacokinetics was explored. The model was evaluated using goodness of fit plots and relative error measurements for 3894 concentrations in the test data set. Computer simulations were undertaken to evaluate the effect of covariates on tipifarnib pharmacokinetics. RESULTS: Tipifarnib oral bioavailability (26.7%) did not differ between the formulations. The absorption rate from the solution was faster than from the solid forms. Whereas the absorption rate and systemic clearance were more rapid in healthy subjects, the extent of absorption and the steady-state volume of distribution were comparable in cancer patients and healthy subjects. Systemic clearance in cancer patients (21.9 l h-1) exhibited a statistically significant relationship with total bilirubin. The typical volume of the central compartment in cancer patients (54.6 l 70 kg-1) was directly proportional to body weight. The clinical relevance of these covariates in cancer patients is questionable as there was a substantial overlap in simulated concentration-time profiles across a wide range of covariate values. CONCLUSIONS: A population PK approach has been used to integrate data gathered during clinical development and to characterize the pharmacokinetics of tipifarnib. Individualization of dose based on body weight or total bilirubin concentration in adult cancer patients is not warranted.

Administration, Oral↗
PubMed1992

Mixed microprocessor-random logic approach for innovative pacing systems.

Modern pacing systems are becoming more and more sophisticated. Conversion of the information supplied by a sensor into suitable parameters for a rate controlling algorithm and the management of complex timing are common tasks for an integrated circuit (IC) in cardiac pacing. An effective solution consists of using a microprocessor to implement algorithms and pacing modes in a flexible way. The key point of using the same hardware resources for different tasks on a time sharing basis allows the design of a less complex IC when compared to a random logic structure with the same performances. The major design problems in a full microprocessor solution are its relatively low operating speed due to the low frequency clock necessary for low current drain, and the sequential structure of the machine itself. This can lead to unacceptable timing inaccuracy in all situations requiring the management of complex decision trees. In order to take full benefit from the advantages of a microprocessor structure without these drawbacks, a mixed microprocessor-random logic approach has been investigated. This architecture uses a microprocessor core to perform all high level nonreal-time operations (setup of the pacing cycle, data reduction and processing, data integrity checks) while a set of random logic peripherals is used for all critical timing aspects.

Algorithms↗
PubMed2005

Brain reserve and dementia: a systematic review.

BACKGROUND: Behavioural brain reserve is a property of the central nervous system related to sustained and complex mental activity which can lead to differential expression of brain injury. Behavioural brain reserve has been assessed using autobiographical data such as education levels, occupational complexity and mentally stimulating lifestyle pursuits. So far there have been several epidemiological reports but no systematic review to put conflicting results into context. Our aim was to quantitatively review evidence for the effect of brain reserve on incident dementia. METHOD: Cohort studies of the effects of education, occupation, premorbid IQ and mental activities on dementia risk were of interest. Abstracts were identified in MEDLINE (1966-September 2004), CURRENT CONTENTS (to September, 2004), PsychINFO (1984-September 2004), Cochrane Library Databases and reference lists from relevant articles. Twenty-two studies met inclusion criteria. Key information was extracted by both reviewers onto a standard template with a high level of agreement. Studies were combined through a quantitative random-effects meta-analysis. RESULTS: Higher brain reserve was associated with a lowered risk for incident dementia (summary odds ratio, 0.54; 95% confidence interval, 0.49-0.59). This effect was found over a median of 7.1 years follow-up and resulted from integrating data across more than 29000 individuals. Notably, increased complex mental activity in late life was associated with lower dementia rates independent of other predictors; a dose-response relationship was also evident between extent of complex mental activities in late life and dementia risk. CONCLUSIONS: This study demonstrates robust evidence that complex patterns of mental activity in the early, mid- and late-life stages is associated with a significant reduction in dementia incidence. Randomized control trials based on brain-reserve principles are now required.

Brain↗
PubMed2003

Language functional magnetic resonance imaging in preoperative assessment of language areas: correlation with direct cortical stimulation.

OBJECTIVE: The aim of this study was to analyze the usefulness of preoperative language functional magnetic resonance imaging (fMRI), by correlating fMRI data with intraoperative cortical stimulation results for patients with brain tumors. METHODS: Naming and verb generation tasks were used, separately or in combination, for 14 right-handed patients with tumors in the left hemisphere. fMRI data obtained were analyzed with SPM software, with two standard analysis thresholds (P < 0.005 and then P < 0.05). The fMRI data were then registered in a frameless stereotactic neuronavigational device and correlated with direct brain mapping results. We used a statistical model with the fMRI information as a predictor, spatially correlating each intraoperatively mapped cortical site with fMRI data integrated in the neuronavigational system (site-by-site correlation). Eight patients were also studied with language fMRI postoperatively, with the same acquisition protocol. RESULTS: We observed high variability in signal extents and locations among patients with both tasks. The activated areas were located mainly in the left hemisphere in the middle and inferior frontal gyri (F2 and F3), the superior and middle temporal gyri (T1 and T2), and the supramarginal and angular gyri. A total of 426 cortical sites were tested for each task among the 14 patients. In frontal and temporoparietal areas, poor sensitivity of the fMRI technique was observed for the naming and verb generation tasks (22 and 36%, respectively) with P < 0.005 as the analysis threshold. Although not perfect, the specificity of the fMRI technique was good in all conditions (97% for the naming task and 98% for the verb generation task). Better correlation (sensitivity, 59%; specificity, 97%) was achieved by combining the two fMRI tasks. Variation of the analysis threshold to P < 0.05 increased the sensitivity to 66% while decreasing the specificity to 91%. Postoperative fMRI data (for the cortical brain areas studied intraoperatively) were in accordance with brain mapping results for six of eight patients. Complete agreement between pre- and postoperative fMRI studies and direct brain mapping results was observed for only three of eight patients. CONCLUSION: With the paradigms and analysis thresholds used in this study, language fMRI data obtained with naming or verb generation tasks, before and after surgery, were imperfectly correlated with intraoperative brain mapping results. A better correlation could be obtained by combining the fMRI tasks. The overall results of this study demonstrated that language fMRI could not be used to make critical surgical decisions in the absence of direct brain mapping. Other acquisition protocols are required for evaluation of the potential role of language fMRI in the accurate detection of essential cortical language areas.

Adolescent↗
PubMed1997

Evaluation of virtual source beam configurations for rapid tomographic reconstruction of gas and vapor concentrations in workplaces.

Beam path average data from an Open Path Fourier Transform Infrared (OP-FTIR) spectrometer can be used to reconstruct two-dimensional concentration maps of the gas and vapor contaminants in workplaces and the environment using computed tomographic (CT) techniques. However, a practical limitation arises because in the past, multiple-source and detector units were required to produce a sufficient number of intersecting beam paths in order to reconstruct concentration maps. Such a system can be applied to actual field monitoring situations only with great expense and difficulty. A single monostatic OP-FTIR system capable of rapid beam movement can eliminate this deficiency. Instead of many source and detector units, a virtual source arrangement has been proposed using a number of flat mirrors and retroreflectors to obtain intersecting folded beam paths. Three virtual source beam configurations generated for a single-beam steerable FTIR system were tested using 54 flat mirrors and four retroreflectors or 54 flat mirrors and 56 retroreflectors mounted along the perimeter walls of a typical 24- x 21-ft test room. The virtual source CT configurations were numerically evaluated using concentration maps created from tracer gas concentration distributions measured experimentally in a test chamber. Synthetic beam path integral data were calculated from the test maps and beam configurations. Computer simulations of different beam configurations were used to determine the effects of beam geometry. The effects of noise and peak reducing artifacts were evaluated. The performance of the tomographic reconstruction strategy was tested as a function of concentration and concentration gradients.

Air Pollution, Indoor↗
PubMed2002

Building a genome database using an object-oriented approach.

GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

Databases, Genetic↗
PubMed2004

Retracted: Effects of Vitamin K2 on Osteoporosis

The article entitled “Effects of Vitamin K2 on Osteoporosis, published in Curr Pharm Des 2004; 10(21): 2557-76, by Iwamoto J, Takeda T and Sato Y.” has been retracted by the Editorial office of the journal Current Pharmaceutical Design, as the text, data and some figures used/referred in this review article are from sources which have been retracted or under investigation on the basis of data fabrication and falsification, authorship misconduct, duplicate publication, unethical research practices, text recycling/self-plagiarism, and unresolved concerns about data integrity and research conduct. The authors were informed of this complaint and were requested to give justification on the matter in their defense. However, no reply was received from their side in this regard. Some sources that have been retracted are as follows: REFERENCE: 1. Iwamoto J, Takeda T, Ichimura S. Combined treatment with vitamin K2 and bisphosphonate in postmenopausal women with osteoporosis. Yonsei Med J 2003; 44: 751-6. Available at: https://eymj.org/DOIx.php?id=10.3349/ymj.2019.60.1.115. 2. Sato Y, Honda Y, Kuno H, Oizumi K. Menatetrenone ameliorates osteopenia in disuse-affected limbs of vitamin D- and K-deficient stroke patients. Bone 1998; 23: 291-6. Available at: https://www.sciencedirect.com/science/article/pii/S8756328298001082. 3. Sato Y, Honda Y, Kaji M, Asoh T, Hosokawa K, Kondo I, et al. Amelioration of osteoporosis by menatetrenone in elderly female Parkinson's disease patients with vitamin D deficiency. Bone 2002; 31: 114-8. Available at: https://pubmed.ncbi.nlm.nih.gov/ 12110423/. Bentham Science apologizes to its readers for any inconvenience this may have caused. The Bentham Editorial Policy on Article. Retraction can be found at https://benthamscience.com/editorial-policies-main.php BENTHAM SCIENCE DISCLAIMER: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript, the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.

Animals↗
PubMed2024

ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.

The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.

Humans↗