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PubMed1996

Affect, attachment, memory: contributions toward psychobiologic integration.

Recent decades have seen a marked expansion in knowledge regarding human neurophysiology, and psychiatry is currently challenged with the task of integrating this information with a psychodynamic understanding of emotional life. In this paper we review portions of the relevant literature regarding the basic brain functions of affect, memory, and attachment, and we consider the implications of these data for integrated psychobiologic conceptualizations of emotional dysfunction and its treatment. In particular, data from these three areas of study point to the possibility that implicit memory of the early attachment relationship, communicated via the language of affect, is an enduring neural structure that influences both emotional self-regulation and behavior related to relatedness. Finally, we consider the implications of this proposition for the nature of psychotherapy, which from a psychobiologic view might be profitably conceptualized as a directed attachment relationship whose purpose is the revision of the implicit emotional memory of attachment.

Affect↗

PubMed2026

Mitochondrial Function-Related Genes in Sleep Disorders: A Multi-Omics Mendelian Randomization Study.

Mitochondrial dysfunction is linked to sleep disorders in previous report, but the potential roles of specific genes remain unclear. This study aimed to dissect different subtype-specific genetic associations and their underlying mechanisms. A multi-omics Summary-data-based Mendelian Randomization (SMR) approach was performed to identify potential causal links between mitochondrial function-related genes and sleep disorders. We integrated GWAS data from FinnGen database (the discovery set), independent GWAS datasets (covering different sleep-disorder subtypes and used for validation), and cis-QTLs (including mQTLs, eQTLs, and pQTLs) to perform systematic exploration. Specially, we performed targeted validation of tissue-specific effects, leveraging gene expression data from disease-relevant brain regions within the GTEx database. Our SMR analysis identified mitochondrial function-related genes potentially modulating sleep disorders across biological layers, initially identifying 102 genes at the methylation level, 48 at the gene expression level, and 6 at the protein abundance level. Integrative analysis subsequently prioritized DCXR and ACADVL and revealed their distinct, subtype-specific associations. DCXR exhibited a protective role in sleep apnea while ACADVL showed a paradoxical risk conferring role in daytime sleepiness. In addition, the analysis identified an epigenetic regulatory mechanism for DCXR in which its expression and protein levels are modulated by DNA methylation. Finally, validation in brain-hypothalamus tissue confirmed DCXR as a significant potential protective factor (OR = 0.929, 95% CI: 0.887-0.973, P_HEIDI = 0.999, FDR = 0.2449). Our findings implicate key mitochondrial genes, particularly DCXR and ACADVL, in the pathophysiology of specific sleep disorder subtypes, highlighting potential avenues for precision medicine. Clinical trial number: Not applicable.

Humans↗

PubMed2026

SeqQC-former: A sequence-quality fusion framework for QC-aware review prioritization of candidate somatic SNVs in cancer genomics.

The accurate prioritization of candidate somatic single-nucleotide variants (SNVs) remains a challenge due to the substantial variability in sequencing quality across genomic loci. SeqQC-Former is a sequence-quality fusion framework that integrates the local nucleotide context with read-level quality-control (QC) covariates derived from matched tumor-normal sequencing data. This integration generates QC-aware prioritization scores for the downstream review of candidate variants. Unlike conventional variant callers, SeqQC-Former is designed not to infer biological truth but to support post-calling review and prioritization under heterogeneous sequencing conditions. The framework was trained and evaluated on a SEQC2-derived dataset comprising 89,447 candidate loci, including 1378 positive and 88,069 negative loci. In chromosome-held-out validation, which aims to reduce potential genomic-position leakage, SeqQC-Former demonstrated strong discrimination (AUROC = 0.9479; AUPRC = 0.9448), indicating good generalization to previously unseen chromosomes. Given that the SEQC2-derived labels contain QC-associated information; these results should be interpreted as an evaluation of QC-aware prioritization capability rather than an independent validation of biological variant correctness. Ablation analyses revealed that structured QC covariates provided the dominant predictive signal under the current SEQC2-derived labeling regime. SeqQC-Former achieved a significantly higher AUROC than classical machine-learning baselines, as determined by DeLong's test (p < 0.01). Application to 53,164 glioblastoma variants demonstrated that external predictions were sensitive to QC scaling and threshold selection, underscoring that model outputs should be interpreted as QC-dependent prioritization scores rather than calibrated probabilities or definitive biological classifications. Overall, SeqQC-Former offers a reproducible post-calling QC-aware prioritization framework for large-scale somatic SNV review and underscores the importance of explicitly modeling sequencing-quality information when interpreting structured cancer genomics datasets.

Humans↗

PubMed1998

US EPA's IRIS pilot program: establishing IRIS as a centralized, peer-reviewed data base with agency consensus. Integrated Risk Information System.

The US EPA's Integrated Risk Information System (IRIS) contains Agency consensus scientific positions and quantitative values on cancer and noncancer health effects that may result from lifetime oral or inhalation exposure to specific chemical substances in the environment. Combined with specific exposure assessment information, the summary health information in IRIS may be used as a source in evaluating potential public health risks from environmental contaminants. IRIS is available to the public via EPA's Internet server at http://www.epa.gov/iris. Originally developed for internal EPA use, IRIS usage has broadened since being made publicly available in 1988 to include the private and public sectors nationally and internationally. Up to 1995, IRIS summaries were generated from within various EPA Offices and Regions and reviewed by Agency Workgroups, one for cancer and one for noncancer endpoints, before entry onto IRIS. In response to the increasing usage and recognition of IRIS and suggestions for improvement, an IRIS Pilot program was initiated in 1995. The purpose of the Pilot was 3-fold: To improve efficiency in getting information on to IRIS; to improve documentation for the positions reported in IRIS summaries, including applying new methodologies and guidance; and to improve opportunity for public input including external peer review. A new infrastructure was put in place, consisting of a cross-Agency team of 'Chemical Managers', a Pilot Program Manager, and a set of Agency 'Consensus Reviewers'. Cancer and noncancer assessments were prepared in an integrated fashion for Pilot chemical substances, documented in 'Toxicological Reviews' and derivative IRIS summaries. Public input was emphasized via an initial data call and rigorous external peer review. A final step was Agency-wide consensus review by senior staff scientists representing EPA's Offices and Regions. EPA's experience with the Pilot is forming the basis for designing operational aspects of the long-term IRIS program.

Benchmarking↗

PubMedDate not supplied

[Application of geographical information systems in epidemiological studies exemplified by the ISAAC study in Munich].

Geographical Information Systems (GIS) are increasingly applied as modern tools for analysis and visualization of health-related spatial data, especially in epidemiological research. GIS are used by medical researchers and executives in the public health service. A community-based survey was conducted according to the phase II protocol of the International Study of Asthma and Allergies in Childhood (ISAAC) in Munich. The spatial patterns of disease incidence were analysed and related to exposure data by GIS. The prevalence study on fourth-grade pupils (n = 3354) and school beginners (n = 2890) was conducted during the school term 1995/96 in Munich. Parental questionnaires and measurements of lung function and immunological parameters were used. The questionnaire data were integrated in a GIS database. In this paper we discuss methodological aspects of GIS-based spatial analysis related to epidemiological data. In addition, we investigate whether there were spatial clusters of children with wheeze in the last 12 months of a magnitude unlikely to occur by chance and which could indicate local health risks. The study was based on permutation tests where global and local methods were applied. No spatial clusters of children with asthma symptoms were identified in the city of Munich.

Asthma↗

PubMed2026

Large-scale functional annotation establishes a reference framework for human LRRK2 variants.

Pathogenic variants in leucine-rich repeat kinase 2 (LRRK2)1are among the most frequent monogenic causes of Parkinson's disease (PD)2 and act through a gain-of-function mechanism of increased kinase activity. LRRK2-targeted therapies are in clinical development, but interpretation of the rapidly expanding catalogue of rare LRRK2 variants remains a barrier to translation. Here, we present functionally annotated data on >350 LRRK2 coding variants using a standardized cellular assay with Rab10 phosphorylation as a readout of kinase activity and integrated these data with curated genetic and clinical annotations from the Movement Disorders Society Genetic Mutation Database (MDSGene). Variants differed in activation magnitude, ranging from modest increases (e.g., p.G2019S) to strongly activating substitutions such as p.Y1699C or p.L1795F. Activating variants occurred across the full length of LRRK2, although the largest effects clustered within the ROC-COR regulatory hub, where structural analysis identified subdomains forming an allosteric scaffold controlling kinase output. All known/established pathogenic variants showed increased activity, whereas benign and likely benign variants remained within the wild-type range. Functional effect sizes correlated with pathway activation in patient-derived immune cells, altogether providing a framework for ACMG-based variant interpretation in which kinase activation can support PS3 functional evidence for reclassification of variants.

Protein phosphorylation↗

PubMed1989

[Six channels telemetry system for recording masticatory forces of complete denture wearers].

A six channels telemetry system for recording masticatory force of complete denture wearers has been developed. This system is consisted of three blocks, the transmission block, the receiver block and the data storage and correction block. The transmission block is embedded in a lower complete denture. System has six load sensors and a standard resistor to correct sensor data. Data from six load sensors and standard resistor as well as standard zero are multiplexed using a division multiplex communication method. The sampling frequency is 666 Hz. And the signal is transmitted by FM modulation. The carrier wave frequency is 64 MHz. Receive data are decoded using start-stop system. The wave form noise is reduced using a signal averaging technique at an integrator. The data are input into the computer with an A/D converter. In this system, the sensor data is corrected at the computer with the standard resistor data. This method could reduce the influence of battery power changes and thermal drift significantly. For the load of 10 kg or less, the total linearity of the system remained at +/- 4% of the calibrated value. The noise level is 300 g.

Denture, Complete↗

PubMed2005

Intelligent client for integrating bioinformatics services.

MOTIVATION: In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological data. The integration of these resources under a common platform is a challenging task. To this end, several groups are developing integration technologies, in which services are usually registered in some sort of catalogue to allow novel discovering and accessing mechanisms to be implemented. However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem. RESULTS: In this work we address the design and implementation of a versatile web client to access BioMOBY compatible services (a system by which a client can interact with multiple sources of biological data regardless of the underlying format or schema) using the service description stored in the BioMOBY catalogue. The automatic interface generator significantly reduces developing time and produces uniform service access mechanisms. The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the National Institute for Bioinformatics in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ

Automation↗

PubMed2002

Integrated visualization of problemcentric urologic patient records.

The collision of computer-based technologies and the medical environment is resulting in an increasingly electronic multimedia patient record, consisting of not only the traditional types of data (e.g., clinic notes and laboratory reports), but also digital images (e.g., computed tomography and magnetic resonance imaging) and other visual representations of patient data (e.g., pulmonary function graphs and urodynamic charts). Given the increasing amount of data made available to physicians, it is not only critical that the totality of a patient's medical record be accessible to a clinician, but that the diverse data be integrated and presented in a manner conducive to patient management: key information should be easily discovered. This paper describes a problemcentric time-based visualization of urologic conditions, whereby a patient's medical history is automatically organized around a medical problem and presented as a graphic chronology. Urology-related data in the patient medical record is organized in accord with an expert constructed knowledge-base, and plotted on a timeline using iconic representations. The user interface permits the physician to quickly view multimedia data and to visualize relationships between events in the patient's history.

Computer Systems↗

PubMed1994

Mid-term report on the Arden Syntax in a clinical event monitor.

In implementing a clinical event monitor (CEM), a decision-support system, we worked with an existing repository of clinical data (Keystone), fed from ancillary systems using HL7. The rules are written in the Arden Syntax, an ASTM standard for expressing medical knowledge as medical logic modules (MLMs). The Arden Syntax leaves unspecified the clinical data model and deductive database access language; we briefly describe our query language and the related medical concepts dictionary (MCD). This paper gives an overview of our implementation of the Arden Syntax, the MCD and the deductive database access language, with reasons for the major design decisions. Overall, less than a quarter of the development effort has gone into the Arden compiler and interpreter; the rest has focused on accessing the data and integrating with other systems. We feel that the Arden Syntax has proved its worth in writing rules; effort should now be focused on medical vocabularies and data models.

Artificial Intelligence↗

PubMed2004

Primer on medical genomics. Part XIV: Introduction to systems biology--a new approach to understanding disease and treatment.

The advent of the "-omics revolution" has forced us to reevaluate our ability to acquire, measure, and handle large data sets. Omic platforms such as expression arrays and mass spectrometry, with their exquisite selectivity, sensitivity, and specificity, are unrivaled technologies for detection, quantitation, and identification of DNA, messenger RNA, proteins, and metabolites derived from complex body tissue and fluids. More recently, attempts have been made to capture the utility of these platform technologies and combine them under the umbrella of systems biology, also referred to as pathway, network, or integrative biology. Applied systems biology is the integrated analysis of genetic, genomic, protein, metabolite, cellular, and pathway events that are in flux and interdependent. It necessitates the use of a variety of analytic platforms as well as biostatistics, bioinformatics, data integration, computational biology, modeling, and knowledge assembly protocols. Such sophisticated analyses may provide new insight into the understanding of disease processes and mechanisms of action of pharmaceutical agents. Ultimately, this requires a perspective on how complex systems behave and are modulated. In this regard, systems biology, more appropriately considered as a process containing a series of modules, aims to provide tools and capabilities to carry out such tasks. We describe the essentials required to carry out systems biology experiments, the method in which integrated data in the form of a systems biology correlation network affords new insight into understanding disease, and the vista of developing more efficient biomarkers and therapeutic agents.

Animals↗

PubMed1999

[Computer program for retinopathy of prematurity screening].

BACKGROUND: The goal of retinopathy of prematurity (ROP) screening is complete detection of all preterm infants with threshold ROP. AIM: We wanted to develop software to facilitate registration of ROP findings, checking due dates of re-examination, and evaluation of screening data. By means of complete and faultless registration and evaluation of the data of preterm infants, the effectiveness and safety of the screening should increase. METHODS: We developed software that runs under Microsoft Windows 3.1 or Windows 95 and is programmed in Microsoft Access Basic and Microsoft Visual Basic. The software allows all screening data to be registered and evaluated. Intuitive handling, third level of normalization in database architecture, and automatic plausibility checks guarantee the utmost integrity of data and efficacy of database. RESULTS AND CONCLUSION: To date, the software has been used routinely in 2000 examinations in 1000 preterm infants. Our software facilitates clinical management and evaluation of ROP screening, which therefore becomes more safe.

Diagnosis, Computer-Assisted↗

PubMed1990

Methods for estimating release rates during high frequency quantal secretion and for testing such methods.

The rate of spontaneous quantal release must be estimated in some investigations of synaptic transmission, even when frequencies are so high that individual quanta cannot be distinguished. An obvious method is to measure the time integrals of the summed MEPPs and then dividing this value by the integral of an average MEPP. The method was tested by recording miniature end-plate potentials (MEPPs) at frog neuromuscular junctions, counting the number of MEPPS, and then adding together records from the same junction to simulate high frequencies. The estimates from the integral method agreed well with the actual counts. The method can readily be used with a microcomputer and does not require stationary data. Methods based on fluctuation analysis were also used to estimate quantal frequencies, but they did not always give good estimates. This was not a thorough test of the fluctuation method, but an example of testing with MEPP data. The integral method might be reasonably reliable, but there are further potential complications, like changes in MEPP size and short-circuiting of the end-plate membrane, which may make it difficult to obtain reliable measurements of high frequency quantal secretion without voltage clamping and protocols that permit measurements of individual MEPCs during the course of the frequency measurements.

Animals↗

PubMed1997

A Neural Global Workspace Model for Conscious Attention.

Considerable progress is being made in interdisciplinary efforts to develop a general theory of the neural correlates of consciousness. Developments of Baars' Global Workspace theory over the past decade are examples of this progress. Integrating experimental data and models from cognitive psychology, AI and neuroscience, we present a neurocognitive model in which consciousness is defined as a global integration and dissemination system - nested in a large-scale, distributed array of specialized bioprocessors - which controls the allocation of the processing resources of the central nervous system. It is posited that this global control is effected via cortical 'gating' of a strategic thalamic nucleus. The basic circuitry of this neural system is reasonably well understood, and can be modeled, to a first approximation, employing neural network principles.

Journal Article↗

PubMed2003

The clinical reasoning characteristics of diagnostic experts.

The aim of this study was to identify and describe the clinical reasoning characteristics of diagnostic experts. A group of 21 experienced general practitioners were asked to complete the Diagnostic Thinking Inventory (DTI)and a set of 10 clinical reasoning problems (CRP) to evaluate their clinical reasoning. Both the DTI and the CRPs were scored, and the CRP response patterns of each GP examined in terms of the number and type of errors contained in them. Analysis of these data showed that six GPs were able to reach the correct diagnosis using significantly less clinical information than their colleagues. These GPs also made significantly fewer interpretation errors but scored lower on both the DTI and the CRPs. Additionally, this analysis showed that more than 20% of misdiagnoses occurred despite no errors being made in the identification and interpretation of relevant clinical information. These rests indicate that these six GPs diagnose efficiently,effectively and accurately using relatively few clinical data and can therefore be classified as diagnostic experts. They also indicate that a major cause of misdiagnoses is failure to properly integrate clinical data. We suggest that increased emphasis on this step in the reasoning process should prove beneficial to the development of clinical reasoning skill in undergraduate medical students.

Adult↗

PubMed2003

An application framework for computer-aided patient positioning in radiation therapy.

The importance of exact patient positioning in radiation therapy increases with the ongoing improvements in irradiation planning and treatment. Therefore, new ways to overcome precision limitations of current positioning methods in fractionated treatment have to be found. The Department of Medical Physics at the German Cancer Research Centre (DKFZ) follows different video-based approaches to increase repositioning precision. In this context, the modular software framework FIVE (Fast Integrated Video-based Environment) has been designed and implemented. It is both hardware- and platform-independent and supports merging position data by integrating various computer-aided patient positioning methods. A highly precise optical tracking system and several subtraction imaging techniques have been realized as modules to supply basic video-based repositioning techniques. This paper describes the common framework architecture, the main software modules and their interfaces. An object-oriented software engineering process has been applied using the UML, C + + and the Qt library. The significance of the current framework prototype for the application in patient positioning as well as the extension to further application areas will be discussed. Particularly in experimental research, where special system adjustments are often necessary, the open design of the software allows problem-oriented extensions and adaptations.

Computer Terminals↗

PubMed2025

UALCAN Mobile, an app for cancer proteogenomic data analysis.

Cancer is a complex disease affecting various organs and is a major cause of death worldwide. During cancer initiation, disease progression, and tumor metastasis, various genomic and proteomic alterations are observed. Recent technological advances have led to the generation of large amounts of molecular data, including genomics and transcriptomics. These large-scale datasets can be utilized to analyze and identify sub-class-specific cancer biomarkers and targets. However, there is a need for the development of user-friendly tools for large-scale data analysis, disseminating the analyzed data in a visualizable format to cancer researchers with no programming skills. We developed UALCAN, a comprehensive platform that allows users to integrate disparate data to better understand the genes, proteins, and pathways perturbed in cancer and make discoveries of potential biomarkers and targets. In the current study, we describe the development of the UALCAN Mobile application (app) that will provide cancer transcriptomic data obtained from The Cancer Genome Atlas (TCGA) project to evaluate protein-coding gene expression based on various stratifications, including stage, grade, race, gender, and molecular-subtypes across over 30 types of cancers. In addition, the UALCAN mobile provides data analysis options for epigenetic changes due to DNA promoter methylation and Clinical Proteomic Tumor Analysis Consortium (CPTAC) cancer proteomic data. The app provides access to large cancer molecular datasets on the go. To find changes in the expression of causative genes and proteins and to identify biomarkers and therapeutic targets, UALCAN mobile app will be extremely valuable. The "UALCAN Mobile" app is free to use and can be downloaded from both the iOS/Apple and the Android Play Store and has been downloaded over 100 times in each of iOS and android app stores.

app↗

PubMed2024

Multi-organ gene expression analysis and network modeling reveal regulatory control cascades during the development of hypertension in female spontaneously hypertensive rat.

Hypertension is a multifactorial disease with stage-specific gene expression changes occurring in multiple organs over time. The temporal sequence and the extent of gene regulatory network changes occurring across organs during the development of hypertension remain unresolved. In this study, female spontaneously hypertensive (SHR) and normotensive Wistar Kyoto (WKY) rats were used to analyze expression patterns of 96 genes spanning inflammatory, metabolic, sympathetic, fibrotic, and renin-angiotensin (RAS) pathways in five organs, at five time points from the onset to established hypertension. We analyzed this multi-dimensional dataset containing ~15,000 data points and developed a data-driven dynamic network model that accounts for gene regulatory influences within and across visceral organs and multiple brainstem autonomic control regions. We integrated the data from female SHR and WKY with published multiorgan gene expression data from male SHR and WKY. In female SHR, catecholaminergic processes in the adrenal gland showed the earliest gene expression changes prior to inflammation-related gene expression changes in the kidney and liver. Hypertension pathogenesis in male SHR instead manifested early as catecholaminergic gene expression changes in brainstem and kidney, followed by an upregulation of inflammation-related genes in liver. RAS-related gene expression from the kidney-liver-lung axis was downregulated and intra-adrenal RAS was upregulated in female SHR, whereas the opposite pattern of gene regulation was observed in male SHR. We identified disease-specific and sex-specific differences in regulatory interactions within and across organs. The inferred multi-organ network model suggests a diminished influence of central autonomic neural circuits over multi-organ gene expression changes in female SHR. Our results point to the gene regulatory influence of the adrenal gland on spleen in female SHR, as compared to brainstem influence on kidney in male SHR. Our integrated molecular profiling and network modeling identified a stage-specific, sex-dependent, multi-organ cascade of gene regulation during the development of hypertension.

Animals↗