Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “virtual screening”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,423 records · Page 79Linked to original sources

Human papilloma virus and cervical screening.

PURPOSE OF REVIEW: There are around 450,000 cases of cervical cancer per year with 300,000 deaths, making it one of the largest causes of death in women worldwide. Dramatic decreases in cervical cancer mortality rates have been seen following the introduction of screening in several industrialised countries. This is despite using a screening test (the cervical smear) that has a fairly poor sensitivity of approximately 55%. Research has centred on finding a better primary or adjunctive test. Issues of cost and acceptability also need to be addressed. It is now widely understood that virtually all cervical cancers are initiated by oncogenic high-risk type human papilloma virus infections, namely human papilloma viruses 16, 18, 30, 31, 33, and 45. RECENT FINDINGS: The confirmed negative predictive value (99%) of a negative human papilloma virus test makes it potentially valuable in the triage of minor smear abnormalities and as post-treatment surveillance. In addition to evidence of its value in triage, there is a growing debate about its use as a primary tool in cervical screening, particularly in settings that do not currently have a structured programme. However, the psychological impact of human papilloma virus testing is less clear. Ultimately, advances in vaccination may hold the key to the eradication of cervical cancer. SUMMARY: This article assesses the recent evidence on the place of human papilloma virus testing in three clinical settings, as a primary screening tool, in triage and as a test of cure. It also reviews the current understanding of the psychological impact of a positive human papilloma virus test.

Female↗

New methods and techniques in anthropology.

Since the discovery of the Tyrolean Iceman in 1991, advanced imaging and post-processing techniques have been successfully applied to anthropological research. Among the specific techniques are spiral computed tomography and 3-dimensional reconstructions, which include stereolithographic and fused deposition modeling of volume data sets. The Iceman's skull was the first to be produced using stereolithography; subsequently, it has been successfully applied in preoperative planning. With the advent of high-end performance graphics workstations and biomedical image processing software packages, 3-dimensional reconstructions have become established as routine tools for analyzing volume data sets. These techniques enabled dramatically new insights to be gained in the field of physical anthropology. Computed tomography became the ideal research tool to access the internal structures of various precious fossils without even touching--let alone damaging--them. Among the most precious are specimens from the genus Australopithecus (1.8 Myr-3.5 Myr), as well as representatives of Homo heidelbergensis (200 kyr-600 kyr) and Homo neanderthalensis (40 kyr-100 kyr); such fossils have been CT-scanned during the last five years. The fossils often are filled with a stone matrix or other encrustations. During the post-processing routines, highly advanced algorithms were used to remove these encrustations virtually (the concrete fossils remain untouched). Thus it has been possible to visualize the morphological structures that are hidden by the matrix layer. Some specimens have been partially destroyed, but it has been possible for the missing parts were reconstructed on the computer screen in order to get estimations of brain volume and endocranial morphology, both major fields of interest in physical anthropology. Moreover, the data in computerized form allows new descriptions of morphological structures using geometric morphometrics. Some of the results may change aspects and interpretations in human evolution and approaches to long-standing questions in this field. We subsume the introduction of these new imaging and post-processing techniques into a new field of research: Virtual Anthropology.

Animals↗

In silico panning for a non-competitive peptide inhibitor.

BACKGROUND: Peptide ligands have tremendous therapeutic potential as efficacious drugs. Currently, more than 40 peptides are available in the market for a drug. However, since costly and time-consuming synthesis procedures represent a problem for high-throughput screening, novel procedures to reduce the time and labor involved in screening peptide ligands are required. We propose the novel approach of 'in silico panning' which consists of a two-stage screening, involving affinity selection by docking simulation and evolution of the peptide ligand using genetic algorithms (GAs). In silico panning was successfully applied to the selection of peptide inhibitor for water-soluble quinoprotein glucose dehydrogenase (PQQGDH). RESULTS: The evolution of peptide ligands for a target enzyme was achieved by combining a docking simulation with evolution of the peptide ligand using genetic algorithms (GAs), which mimic Darwinian evolution. Designation of the target area as next to the substrate-binding site of the enzyme in the docking simulation enabled the selection of a non-competitive inhibitor. In all, four rounds of selection were carried out on the computer; the distribution of the docking energy decreased gradually for each generation and improvements in the docking energy were observed over the four rounds of selection. One of the top three selected peptides with the lowest docking energy, 'SERG' showed an inhibitory effect with Ki value of 20 microM. PQQGDH activity, in terms of the Vmax value, was 3-fold lower than that of the wild-type enzyme in the presence of this peptide. The mechanism of the SERG blockage of the enzyme was identified as non-competitive inhibition. We confirmed the specific binding of the peptide, and its equilibrium dissociation constant (KD) value was calculated as 60 microM by surface plasmon resonance (SPR) analysis. CONCLUSION: We demonstrate an effective methodology of in silico panning for the selection of a non-competitive peptide inhibitor from small virtual peptide library. This study is the first to demonstrate the usefulness of in silico evolution using experimental data. Our study highlights the usefulness of this strategy for structure-based screening of enzyme inhibitors.

Acinetobacter calcoaceticus↗

Recombinant antigen-based enzyme immunoassay for screening of Treponema pallidum antibodies in blood bank routine.

This work reports a comparison of an enzyme immunoassay (EIA) using two major Treponema pallidum recombinant antigens with a T. pallidum hemagglutination (TPHA) assay and a nontreponemal Venereal Disease Reference Laboratory (VDRL) test. A total of 1,822 normal donor serum samples was tested for cardiolipin and T. pallidum antibodies, respectively, by the VDRL assay and EIA. Among these samples, 440 were further tested by TPHA technology. Four samples were found positive by EIA, while all were reported to be negative by both TPHA and VDRL routine assays. Subsequent testing of EIA-positive samples confirmed 100% (four of four samples) and 25% (one of four samples) positive results, respectively, by immunofluorescence assay and a Western blot (immunoblot) syphilis kit. The sensitivity of the recombinant EIA was estimated at virtually 100% with a reference panel of 50 syphilitic samples. According to this study, the newly developed EIA kit shows 100% sensitivity combined to a specificity greater than 99.8% for detecting treponemal immunoglobulin G antibodies in blood bank syphilis screening.

Antibodies, Bacterial↗

Sorbitol dehydrogenase deficiency in several pig tissues: potential implications for studies of experimental diabetes.

Screening for red blood cell sorbitol dehydrogenase deficiency in 12 different mammalian species was performed. A wide inter-species variability in red cell sorbitol dehydrogenase with a virtually complete deficiency in pigs was observed. Aldose reductase and sorbitol dehydrogenase activities in 12 different pig tissues also were measured. Aldose reductase activity was present in all the tissues studied, whereas organ specificity for sorbitol dehydrogenase was observed. Sorbitol dehydrogenase activity was not detectable in lenses, among other tissues, making the pig a potential model for studies in experimental diabetes, particularly for the investigation of sorbitol dehydrogenase deficiency as a risk factor in the development of cataracts.

Aldehyde Reductase↗

Minimal access surgery (MAS)-related surgeon morbidity syndromes.

The benefits of minimal access surgery (MAS) in terms of accelerated recovery, reduced period of short-term disability, and patient outcome account for the widespread use of the laparoscopic approach by the majority of general surgeons. In adopting this approach with its current limitations and poor ergonomics, surgeons have been known to sustain surgery-related injuries encompassed by a spectrum best described as MAS-related surgeon morbidity syndromes, some of which are currently overlooked and poorly researched. Equivalent morbidities including the overuse syndrome (from overuse of certain muscle groups during long operations) have been documented in open surgery but are nowadays rare occurrences. As more advanced MAS operations are performed with long execution times, new patterns of neuromusculoskeletal injuries are being recognized. The surgical fatigue syndrome has also been described, though its complex nature is not fully understood. Virtually little is known on other long-term adverse effects on the surgeon following many years of operating from images displayed on a television monitor or LCD screen, and these include deterioration of visual acuity and function of the ocular muscles responsible for fixation-refixation of the eyeballs. The limited reported literature on the MAS-related surgeon morbidity syndromes identifies certain risk factors for these injuries pertaining to central and peripheral domains. Only improved knowledge of the etiology and underlying ergonomic factors based on investigative studies followed by improved instrumentation and operating room (OR) ergonomics will provide near- and long-term solutions.

Cumulative Trauma Disorders↗

Two-dimensional separation of human body fluid proteins.

High resolution protein patterns of various human body fluids are compared. They were obtained by non-restrictive agarose electrophoresis in the first and exclusion electrophoresis on polyacrylamide pore gradients in the second dimension. The majority of serum proteins above 10 mg/dl have been identified and the heterogeneities of high density lipoproteins, immunoglobulins and haptoglobins become visible within the charge/size grid of the two-dimensional pattern. Since secretory and serum-derived components can be differentiated, the contribution of protein synthesis and filtration to the formation of the finally released fluid can be assessed. The technique may be used to screen complex soluble protein mixtures for pathological components. There is a wide range of variations in composition from the secretory fluids (e.g. tears, colostrum, milk, seminal fluid) to virtually "pure" filtrates (pleural effusions, osteoarthritic synovial fluid, cyst puncture fluid, and amniotic fluid). It is evident that the composition of the serum-derived fraction depends primarily upon the selectivity of the respective blood/body fluid barriers. The resolution capacity of the technique is compared with that obtained by two-dimensional gel-focusing/SDS electrophoresis of the constituent serum protein subunits.

Blood Proteins↗

BNP as a marker of diastolic dysfunction in the general population: Importance of left ventricular hypertrophy.

BNP is a marker of systolic left ventricular dysfunction (LVSD) and heart failure. To assess BNP for the detection of diastolic dysfunction in the general population, we examined 1678 subjects within an age- and sex-stratified survey (MONICA Augsburg). BNP was measured using a commercially available RIA (Shionogi). BNP increased in subjects with diastolic dysfunction (mean 20.3+/-4.7 pg/ml vs. control 9.6+/-0.5 pg/ml, p<0.001), but to a lesser extent than in subjects with LV hypertrophy (LVH, mean 37.3+/-49.1 pg/ml, p<0.001 vs. control) or LVSD (mean 76.2+/-23.2 pg/ml, p<0.001 vs. control). Individuals with sole diastolic abnormality displayed BNP concentrations at the control level (mean 9.7+/-1.7 pg/ml). In univariate analysis, age, BMI, systolic blood pressure, left atrial size, LV mass index, diastolic dysfunction and EF displayed a significant correlation with BNP (p<0.001). However, LV mass index displaced diastolic dysfunction as a significant predictor of BNP in multivariate analysis. Upon ROC analysis, sensitivity and specificity for the detection of diastolic dysfunction by BNP were only 61% and 55%, respectively. Nevertheless, a normal BNP test virtually excluded the presence of diastolic dysfunction and concomitant LVH (NPV 99.9%). Increased BNP concentrations in subjects with diastolic dysfunction are strongly related to LVH. Population-wide screening for diastolic dysfunction with BNP cannot be recommended although a normal BNP test usually excludes diastolic dysfunction and LV hypertrophy.

Adult↗

Interactive computer-training as a therapeutic tool in Alzheimer's disease.

The current study sought to evaluate a novel kind of interactive computer-based cognitive training (ICT) in Alzheimer's disease (AD). AD patients (N = 9), age- and gender-matched patients with a major depressive episode (N = 9), and healthy control subjects (N = 10) were trained to use an ICT program that relates to activities of daily living (ADL). Digital photographs of a shopping route were implemented in a close-to-reality simulation on a computer touch-screen. The task was to find a predefined shopping route, to buy three items, and to answer correctly 10 multiple-choice questions addressing knowledge related to the virtual tasks. Training performance was rated using the number of mistakes (wrong way), time needed for the tasks, number of correct multiple-choice answers, and of repeat of instruction. Compared to normal controls and depressed patients, AD patients performed significantly worse with regard to all variables. Within a 4-week training period including 12 sessions, however, substantial training gains were observed, including a significant reduction of mistakes. Training effects were sustained until follow-up 3 weeks later. The performance of the depressed patients and the normal controls improved as well, with no difference between the two groups. Self-reported effects revealed that the training was well perceived. Thus, the task performance of AD patients improved substantially and subjects appeared to have liked this approach to ICT. New interactive media, therefore, may yield interesting opportunities for rehabilitation and (psycho)therapeutic interventions.

Activities of Daily Living↗

Characterization of an alternatively spliced AATYK mRNA: expression pattern of AATYK in the brain and neuronal cells.

The AATYK gene encodes a tyrosine kinase whose expression is up-regulated during the apoptosis and differentiation of 32Dcl3 myeloblastic cells. Because high levels of AATYK mRNA have also been detected in the brain, and because these transcripts differ in size from that observed in the 32Dcl3 cell line, it was of interest to determine whether this gene encodes mRNAs that are alternatively spliced and whether these mRNAs are expressed in a tissue-specific manner. We have isolated a novel, alternatively spliced AATYK mRNA using cDNA library screening and RT-PCR, whose expression is readily detected in the brain but not myeloid cells. Western blot analysis revealed that the AATYK protein was expressed in virtually all regions of the adult rat brain in which neurons are present, including olfactory bulb, forebrain, cortex, midbrain, cerebellum and pons. Immunohistochemical labeling of adult brain sections showed the highest levels of AATYK expression in the cerebellum and olfactory bulb. Expression of AATYK was also up-regulated as a function of RA-induced neuronal differentiation of p19 embryonal carcinoma cells, supporting a role for this protein in mature neurons and neuronal differentiation.

Alternative Splicing↗

Human medulloblastomas lack point mutations and homozygous deletions of the hSNF5/INI1 tumour suppressor gene.

Medulloblastomas (MBs) are malignant primitive neuroectodermal tumours (PNETs) of the cerebellum occurring predominantly in childhood. The association of monosomy of chromosome 22 with MB is controversial. Atypical teratoid/rhabdoid tumours (AT/RTs) of the brain share clinical and histological features with MBs and supratentorial PNETs (sPNETs). In particular, AT/RTs can be misdiagnosed as MBs and sPNETs because AT/RTs frequently contain areas of primitive neuroepithelial cells similar to PNETs. Recently, mutations of the tumour suppressor gene hSNF5/INI1, located on 22q11.23, have been described in AT/RTs, MBs and sPNETs, with conflicting data on the prevalence of hSNF5/INI1 mutations in the latter entities. Therefore, we screened MBs for point mutations and homozygous deletions of the hSNF5/INI1 tumour suppressor gene. In 90 MBs, no mutations of the hSNF5/INI1 gene were identified. Thus, our study virtually rules out hSNF5/INI1 as a tumour suppressor gene involved in the pathogenesis of medulloblastoma.

Adolescent↗

PipeOnline 2.0: automated EST processing and functional data sorting.

Expressed sequence tags (ESTs) are generated and deposited in the public domain, as redundant, unannotated, single-pass reactions, with virtually no biological content. PipeOnline automatically analyses and transforms large collections of raw DNA-sequence data from chromatograms or FASTA files by calling the quality of bases, screening and removing vector sequences, assembling and rewriting consensus sequences of redundant input files into a unigene EST data set and finally through translation, amino acid sequence similarity searches, annotation of public databases and functional data. PipeOnline generates an annotated database, retaining the processed unigene sequence, clone/file history, alignments with similar sequences, and proposed functional classification, if available. Functional annotation is automatic and based on a novel method that relies on homology of amino acid sequence multiplicity within GenBank records. Records are examined through a function ordered browser or keyword queries with automated export of results. PipeOnline offers customization for individual projects (MyPipeOnline), automated updating and alert service. PipeOnline is available at http://stress-genomics.org.

Automation↗

Generation and validation of rapid computational filters for cyp2d6 and cyp3a4.

CYP2D6 and CYP3A4 represent two particularly important members of the cytochrome p450 enzyme family due to their involvement in the metabolism of many commercially available drugs. Avoiding potent inhibitory interactions with both of these enzymes is highly desirable in early drug discovery, long before entering clinical trials. Computational prediction of this liability as early as possible is desired. Using a commercially available data set of over 1750 molecules to train computer models that were generated with commercially available software enabled predictions of inhibition for CYP2D6 and CYP3A4, which were compared with empirical data. The results suggest that using a recursive partitioning (tree) technique with augmented atom descriptors enables a statistically significant rank ordering of test-set molecules (Spearman's rho of 0.61 and 0.48 for CYP2D6 and CYP3A4, respectively), which represents an increased rate of identifying the best compounds when compared with the random rate. This approach represents a valuable computational filter in early drug discovery to identify compounds that may have p450 inhibition liabilities prior to molecule synthesis. Such computational filters offer a new approach in which lead optimization in silico can occur with virtual molecules simultaneously tested against multiple enzymes implicated in drug-drug interactions, with a resultant cost savings from a decreased level of molecule synthesis and in vitro screening.

Computational Biology↗

The use of virtual reality in the assessment of driving performance in persons with brain injury.

In this article, we present the results of a pilot study that examined the driving performance of persons with brain injury using a virtual reality environment, known as the DriVR. Virtual driving performance was examined and compared to on-road, cognitive, visual-perceptual, and driving video test results. The DriVR appeared to be a useful adjunctive screening tool for assessing driving performance. However as with any new assessment tool, will need to undergo further empirical validation.

Automobile Driver Examination↗

Identifying JAK2 and ANXA5 as Key Genes Linking Obstructive Sleep Apnea and Oxidative Stress via Machine Learning and Multilayer Transcriptomic Integration With Functional Validation.

Obstructive sleep apnea (OSA) is a common and severe sleep disorder closely associated with oxidative stress (OS). This study aims to identify and validate potential OS-related genes associated with OSA through bioinformatics methods. We successfully identified OS-related differentially expressed genes (OS-DEGs) by combining the limma test, weighted correlation network analysis (WGCNA), and OS-related genes from the GeneCards database. Key genes and potential biological roles were further identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), enrichment analysis, protein-protein interaction (PPI) network analysis, Lasso regression analysis, random forest algorithm, and support vector machine recursive feature elimination (SVM-RFE) method. Evaluate and validate the accuracy of key genes through receiver operating characteristic (ROC) curve analysis. The human single-cell RNA sequencing (scRNA-seq) dataset is used for cell classification annotation, analysis of key gene single-cell expression profiles, and virtual gene knockout experiments based on the scTenifoldKnk algorithm. Integrating scRNA-seq sequencing, pseudotime trajectory inference, cell-cell communication analysis, and bulk immune infiltration deconvolution reveals monocyte subtype remodeling in OSA. Finally, the expression levels of key genes in clinical samples were validated using real-time quantitative PCR (RT-qPCR) and Western blotting. A total of 57 common DEGs, indicating significant enrichment in OS, inflammation, and tumor pathways, particularly prominent in the immunometabolism pathway. By integrating DEGs, WGCNA, PPI results, and machine learning methods, key genes Janus kinase 2 (JAK2) and ANXA5 were screened out. JAK2 was significantly upregulated under disease conditions, while ANXA5 was significantly downregulated. ROC curve exhibited high accuracy (area under the curve [AUC] >&#x2009;0.85). Human scRNA-seq analysis revealed that key genes were predominantly highly expressed in monocytes. Virtual knockout experiments demonstrated that these key genes play a crucial role in regulating immune responses and inflammatory reactions. PPI networks and enrichment analysis verified that downstream genes S100P, ALOX5AP, PROK2, and PADI4 may collaboratively participate in immune response and inflammation regulation. Finally, clinical sample experiment further validated the results of bioinformatics analysis. This study provides new research insights for the diagnosis, mechanism research, and treatment development of OSA in the future by integrating multilayer transcriptomic and machine learning techniques.

Humans↗

Identification of a light-regulated MYB gene from an Arabidopsis transcription factor gene collection.

Seven different MYB-related genes have been isolated from a genomic Arabidopsis library with probes based on MYB DNA-binding motifs. The predicted amino acid sequence of these genes showed high similarity in the MYB domain but outside this region virtually no similarities were found. The set of MYB-related genes was used to identify differentially expressed genes following the transfer of etiolated seedlings to light. This differential screen resulted in the selection of the ATM4 gene which is induced by light within one hour of exposure of etiolated or dark-adapted seedlings.

Amino Acid Sequence↗

[Electroencephalographic demonstration of central nervous system effects of different premedication regimens].

INTRODUCTION: For many years, the main goal of premedication was prevention of the dangerous side effects sometimes encountered in anesthetics with anticholinergics, antiemetic antihistaminics, and opioids. Because the rules were always preoperative fasting, premedication was administered i.m. Thus, the onset of action was within 15-30 min from administration. In recent years, with the introduction of newer anesthetics with fewer side effects, anxiolysis became the main aim in premedication. Moreover, the oral route became popular since it obviously did not increase the acidity or volume of the gastric content. However, the uptake and thus onset of action of orally administered drugs may take longer and can differ considerably between individual patients. Therefore, the optimum interval between administration and induction of anesthesia remains controversial. The present study was carried out to examine the time course of drug action and the effects of different premedication regimens on the electroencephalogram (EEG). PATIENTS AND METHODS: After obtaining informed consent, in 38 unselected adult patients (ASA I and II, < 65 years) scheduled for elective surgery, the EEG was recorded continuously before and after premedication. The patients were randomly assigned to four groups: M: midazolam, 0.2 mg/kg BW orally; N: nordazepam, 0.2 mg/kg BW orally; AP: atropine, 0.5 mg, plus promethazine, 50 mg i.m.; APP: atropine, 0.5 mg, plus promethazine, 50 mg, plus pethidine, 0.7 mg/kg BW i.m. The EEG was recorded for a reference period of 10 min before and a study period of 30 min after premedication. Automated EEG processing was performed with CATEEM (computer-aided topographical electroencephalometry). Surface electrodes were placed according to the 10-20 system. Date were collected via an amplifier (resistance 10 M omega) and a digitalization unit (filter 0.2-35 Hz, sampling rate 512 Hz, 12 bit A/D convertor). The original EEG signals were used in an interpolation algorythm to produce an additional 82 virtual recording points, allowing for high topographical resolution. After spectral analysis (fast Fourier transformation), the different frequency ranges of the EEG power spectrum are displayed in different colors. The screen displays the on-line map with color-based topographical power distribution. In order to achieve a pharmacodynamic time profile, the study period was subdivided into three periods of 10 min each. For clinical evaluation of vigilance, a 6-grade scoring system was used 1 = awake, 6 = not arousable). RESULTS: All data are presented with respect to reference period. The power density of each frequency range for each electrode is integrated over the selected period and mean values are shown. Changes in power density with time are expressed as percentage change from reference period. Biometrical data showed no significant differences between groups. The median vigilance score 30 min after premedication (end of study period) was 4 in groups M, AP, and APP, and 3 in group N. In both benzodiazepine groups, a distinct increase in power density was found in the beta-bands, while in groups AP and APP the increase was most pronounced in the delta and theta bands. In group M, there was a linear increase in beta 1 power up to 310%, while in the beta 2 range there was a 170% maximum within the second period of 10 min. In group N, there was a similar course with a lower increase in beta 1 (220%) and beta 2 (130%). Increases in both beta-bands were most pronounced with frontal electrodes. While group M showed an increase in delta power (150%), together with moderate suppression in alpha (alpha 1 50%, alpha 2 40%), nordazepam caused only a slight increase in delta (124%) and a distinct increase in alpha 2 to 150%, predominantly in the frontal areas. Group APP showed a linear increase in both delta up to 210% and theta power to 190%. (ABSTRACT TRUNCATED)

Adult↗

Molecular cloning of rat cerebellin-like protein cDNA which encodes a novel membrane-associated glycoprotein.

Rat cerebellin and an apparent metabolite des-Ser1-cerebellin have been shown to be located in cerebellar Purkinje cells and the dorsal cochlear nucleus. A cDNA clone was isolated by screening a rat brain cDNA library using an oligonucleotide corresponding to rat cerebellins. The clone encodes 224 amino acid residues of a glycoprotein a part of whose sequence is virtually the same as that of cerebellins and which contains one putative transmembrane spanning domain. Neither an N-terminal cleavable signal peptide nor dibasic pair specific endopeptidase directly precedes or follows the cerebellin-like sequence. Expression of the cerebellin-like protein gene is developmentally regulated in rat cerebellum and shows tissue specific alternative splicing in the brain, adrenal gland and spleen of the rat. The results of Southern blot indicated the gene to possibly be a member of some gene family. Rat cerebellin-like protein, possibly a precursor of cerebellins, is a novel membrane-associated glycoprotein expressed in nervous, adrenal and immune systems and appears to synaptic functions in the central nervous system.

Amino Acid Sequence↗