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PubMed2005

Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource.

The Poxvirus Bioinformatics Resource Center (PBRC) has been established to provide informational and analytical resources to the scientific community to aid research directed at providing a better understanding of the Poxviridae family of viruses. The PBRC was specifically established as the result of the concern that variola virus, the causative agent of smallpox, as well as related viruses, might be utilized as biological weapons. In addition, the PBRC supports research on poxviruses that might be considered new and emerging infectious agents such as monkeypox virus. The PBRC consists of a relational database and web application that supports the data storage, annotation, analysis and information exchange goals of the project. The current release consists of over 35 complete genomic sequences of various genera, species and strains of viruses from the Poxviridae family. Sequence and annotation information for these viruses has been obtained from sequences publicly available from GenBank as well as sequences not yet deposited in GenBank that have been obtained from ongoing sequencing projects. In addition to sequence data, the PBRC provides comprehensive annotation and curation of virus genes; analytical tools to aid in the understanding of the available sequence data, including tools for the comparative analysis of different virus isolates; and visualization tools to help better display the results of various analyses. The PBRC represents the initial development of what will become a more comprehensive Viral Bioinformatics Resource Center for Biodefense that will be one of the National Institute of Allergy and Infectious Diseases' 'Bioinformatics Resource Centers for Biodefense and Emerging or Re-Emerging Infectious Diseases'. The PBRC website is available at http://www.poxvirus.org.

Computational Biology↗

PubMed2006

FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum.

The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the F.graminearum genome sequence. A complete manually revised gene set will be completed within the near future. The initial results of systematic manual correction of gene calls are already part of the current gene set. The database can be accessed to retrieve information from bioinformatics analyses and functional classifications of the proteins. The data are also organized in the well established MIPS catalogs and novel query techniques are available to search the data. The comprehensive set of gene calls was also used for the design of an Affymetrix GeneChip. The resource is accessible on http://mips.gsf.de/genre/proj/fusarium/.

Databases, Genetic↗

PubMed2006

CRSD: a comprehensive web server for composite regulatory signature discovery.

Transcription factors (TFs) and microRNAs play important roles in the regulation of human gene expression, and the study of their combinatory regulations of gene expression is a new research field. We constructed a comprehensive web server, the composite regulatory signature database (CRSD), that can be applied in investigating complex regulatory behaviors involving gene expression signatures (GESs), microRNA regulatory signatures (MRSs) and TF regulatory signatures (TRSs). Six well-known and large-scale databases, including the human UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway and Gene Ontology (GO) databases, were integrated to provide the comprehensive analysis in CRSD. Two new genome-wide databases, of MRSs and TRSs, were also constructed and further integrated into CRSD. To accomplish the microarray data analysis at one go, several methods, including microarray data pretreatment, statistical and clustering analysis, iterative enrichment analysis and motif discovery, were closely integrated in the web server, which has not been the case in previous studies. Our implementation showed that the published literature could demonstrate the results of genome-wide enrichment analysis. We conclude that CRSD is a powerful and useful bioinformatic web server and may provide new insights into gene regulation networks. CRSD and the online tutorial are publicly available at http://biochip.nchu.edu.tw/crsd1/.

3' Untranslated Regions↗

PubMed2025

HER2 alterations across solid tumors: implications for comprehensive testing.

PURPOSE: ERBB2 (HER2) alterations (eg, overexpression, amplification, and mutations) are known to drive tumor progression. These changes, particularly in non-breast and gastric/gastroesophageal cancers, remain poorly characterized. With pan-tumor approval of HER2-targeted therapies like Trastuzumab deruxetecan (T-DXd), understanding ERBB2 alterations across diverse cancers is crucial. METHODS: HER2 analysis was conducted on 653 solid tumor specimens at the University of Alabama, using immunohistochemistry (IHC), copy number (CN) variation (CNV) assessment, and mutational profiling. The correlation between CN amplification and IHC expression was evaluated using Somers' D ordinal association. RESULTS: Of the 653 cases, HER2 IHC scores were distributed as 3+ (3.1%), 2+ (13.2%), and 1+ (19.8%), with 63.9% being IHC-negative. ERBB2 CN amplification was observed in 3.1%, with 75% exhibiting IHC3+. Pathogenic mutations were found in 3.1%, with low IHC3+ rates (5%). Among samples with ERBB2 mutations, only 3 had CN amplifications (1-positive, 2-intermediate). Somers'-D analysis revealed a strong association between CNV and IHC expression (D = 0.73, P < .001). CONCLUSION: This study highlights ERBB2 alterations across diverse cancers, demonstrating their heterogeneity and clinical significance. ERBB2 mutation-carrying tumors are less likely to have HER2 protein 3+ expression or CN amplification, indicating the need for comprehensive genomic analysis to identify those patients. In the context of pan-tumor approval of T-DXd for HER2, findings support integrating genomic and phenotypic data to enhance diagnostic precision and inform therapeutic decision-making. Comprehensive ERBB2 (HER2) testing across tumor types is essential to expand access to HER2-targeted therapies.

Humans↗

PubMed1997

Prior knowledge and reading comprehension ability of deaf adolescents.

Fifty-one severely to profoundly deaf students (mean dB hearing loss = 89) were randomly assigned to two groups that differed by the type of probes (short or long) used to elicit prior knowledge (PK). PK scores were used to predict reading comprehension (RC), which was assessed by students' responses to three types of questions: test-explicit (TE), text-implicit (TI), and script-implicit (SI). Multiple regression models with PK scores and scores from a standardized achievement test (Stanford Achievement Test - Hearing Impaired Version, reading subtest) were also used to predict RC. The regression model showed that, for the group pretested with an in-depth, or long, probe of PK, the best predictor of RC was the ability to answer TE and SI questions. We present discussions of the observed differences in comprehension as a function of long and short knowledge probes and the use of three question types, together with implications for instruction.

Journal Article↗

PubMed1987

5-year results of a comprehensive rehabilitation programme after myocardial infarction.

A comprehensive cardiac rehabilitation programme has been offered to a non-selected consecutive group of patients who have survived an acute myocardial infarction (MI). The programme includes follow-up at a post-MI clinic, physical training in outpatient groups, the provision of information on smoking and diet, and psychological support to patients and their families. The intervention group, consisting of the 147 patients participating in the programme has been compared with a nonselected consecutive reference group of 158 patients receiving standard care. During the five-year follow-up there was no difference in cardiac mortality between the groups, but the recurrence rate of non-fatal MI (17.3 vs 33.3%. P = 0.02) and the rate of total cardiac events was lower in the intervention group (39.5 vs 53.2%, P = 0.05). There was an alteration of risk factors, as there were fewer smokers and uncontrolled hypertensives in the intervention group. Patients in the reference group used more sedatives and long-acting nitroglycerine and had a lower return-to-work rate during the study period. The programme proved to be particularly effective in the age group below 55 years, where a significantly lower rate of total cardiac events was observed and more patients returned to work than in the reference group. It is concluded that the combined effect of the comprehensive programme has contributed to the long-term results, and that the programme offers an effective and safe method of secondary prevention after MI.

Diet↗

PubMed1995

Implementing comprehensive quality control in the andrology laboratory.

Comprehensive quality control procedures were integrated into the routine semen analysis workload of a large university-based andrology laboratory. Methods were chosen to match as far as possible those which have been used successfully for many years in disciplines such as clinical chemistry. Levey-Jennings and cusum charts were plotted in order to monitor the immunobead-binding test for antisperm antibodies and a video-taped control sample for computerized semen analysis. A cryopreserved semen control was also charted. Daily manual sperm counts were plotted against the corresponding computer-assisted semen analysis (CASA) value. Multiple readings of 30 slides were used to monitor morphology assessments. Monthly means for morphology were also calculated regularly. Coefficients of variation were calculated for all variables and were found to be more appropriate for some aspects, such as CASA, than for others, such as morphology, when difference from the previous reading of the same slide was found to be more useful. These integrated quality control procedures had a direct influence on the production of results from the laboratory. Together with a high standard of technician training, comprehensive routine quality control based on repeated analyses of control samples is an effective way of assuring the validity of semen analysis results.

Antibodies↗

PubMed2002

A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes.

We recently developed a method for producing comprehensive gene and species phylogenies from unaligned whole genome data using singular value decomposition (SVD) to analyze character string frequencies. This work provides an integrated gene and species phylogeny for 64 vertebrate mitochondrial genomes composed of 832 total proteins. In addition, to provide a theoretical basis for the method, we present a graphical interpretation of both the original frequency matrix and the SVD-derived matrix. These large matrices describe high-dimensional Euclidean spaces within which biomolecular sequences can be uniquely represented as vectors. In particular, the SVD-derived vector space describes each protein relative to a restricted set of newly defined, independent axes, each of which represents a novel form of conserved motif, termed a correlated peptide motif. A quantitative comparison of the relative orientations of protein vectors in this space provides accurate and straightforward estimates of sequence similarity, which can in turn be used to produce comprehensive gene trees. Alternatively, the vector representations of genes from individual species can be summed, allowing species trees to be produced.

Algorithms↗

PubMed2004

A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches.

The Arabidopsis proline-rich extensin-like receptor kinase (PERK) family consists of 15 predicted receptor kinases. A comprehensive expression analysis was undertaken to identify overlapping and unique expression patterns within this family relative to their phylogeny. Three different approaches were used to study AtPERK gene family expression, and included analyses of the EST, MPSS and NASCArrays databases as well as experimental RNA blot analyses. Some of the AtPERK members were identified as tissue-specific genes while others were more broadly expressed. While in some cases there was a good association between these different expression patterns and the position of the AtPERK members in the kinase phylogeny, in other cases divergence of expression patterns was seen. The PERK expression data identified by the bioinformatics and experimental approaches were found generally to show similar trends and supported the use of data from large-scale expression studies for obtaining preliminary expression data. Thus, the bioinformatics survey for ESTs and microarrays is a powerful comprehensive approach for obtaining a genome-wide view of genes in a multigene family.

Arabidopsis↗

PubMed1997

A comprehensive treatment approach for patellofemoral pain syndrome in young women.

BACKGROUND AND PURPOSE: The purposes of this study were (1) to evaluate a comprehensive treatment approach for patients with patellofemoral pain syndrome and (2) to compare a training program using isometric muscle contractions with a training program using eccentric muscle contractions. SUBJECTS: Forty female patients with patellofemoral pain syndrome, aged 15 to 28 years (mean = 20.2, SD = 3.2), were randomly assigned to either a group using isometric muscle contractions or a group using eccentric muscle contractions. METHODS: The effects of 12 weeks of treatment, consisting of an educational component and a training program, on physical activity, pain, and muscle function were evaluated after 3 and 12 months. RESULTS: No differences were found between the two groups, except in one of the torque measurements. A reduction in pain and improvements in torque, vertical jumping ability, and physical activity level were seen in both groups after treatment. At the 12-month follow-up, 85% of the subjects were participating in sports without pain and 37 subjects rated their overall knee function as excellent or good. CONCLUSION AND DISCUSSION: The results indicate that the improvements shown in this study may be due to spontaneous recovery over time, the education given to the subjects, the pain monitoring system, the gradually progressing training program, and the adjusted physical activity. [Thomeé R. A. Comprehensive treatment approach for patellofemoral pain syndrome in young women.

Adolescent↗

PubMed2006

The ICF comprehensively covers the spectrum of health problems encountered by health professionals in patients with musculoskeletal conditions.

OBJECTIVES: The objective of this study was to investigate, whether the International Classification of Functioning, Disablity and Health (ICF) comprehensively covers the spectrum of health problems encountered by medical doctors and physiotherapists in patients with musculoskeletal conditions. METHODS: A worldwide e-mail survey with questionnaires that requested lists of relevant areas in the ICF components-body functions, body structures, activities and participation, and environmental factors-in patients with rheumatoid arthritis, osteoarthritis, low back pain and osteoporosis was conducted. The suitability of linking the named concepts to the ICF as well as the precision of the linking was characterized by assigning the concepts to six groups. RESULTS: All concepts that were named by the experts could be linked to the ICF, with the exception of personal factors. Between 32% (environmental factors) and 51% (activities and participation) of the named concepts were linked to an ICF category with an identical meaning and the same grade of precision. All other named concepts were linked to ICF categories with a lower level of precision, or encompassed more than one ICF category, or were linked to an ICF category with a related, but not identical meaning. CONCLUSIONS: The ICF covers comprehensively the spectrum of problems encountered in patients with musculoskeletal conditions by clinical experts throughout the world. This strengthens the validity of the ICF in the view of the users and will encourage the use of ICF-based applications such as the ICF checklist and the now-developed ICF Core Sets.

Activities of Daily Living↗

PubMed2004

Comprehensive community initiatives: a rural perspective.

This article challenges the notion that the comprehensive community initiative (CCI) is a singularly urban intervention strategy by comparing a rural comprehensive initiative with the literature on urban CCIs. Characteristics of CCIs in urban settings are discussed and compared with Warren Family Institute (WFI), a demonstration project in rural North Carolina. Findings support the thesis that the CCI has been implemented and found effective in rural settings. The author presents a comparison of the common complications faced by urban CCIs with those encountered during the planning, implementation, and evaluation of WFI. Differences between these two CCIs were rooted in demographic, geographic, and sociohistoric distinctions between rural and urban settings. Substantial similarities were seen between rural and urban CCIs, which suggests the need to broaden the discussion on CCIs to include research on rural initiatives in the CCI literature.

Community-Institutional Relations↗

PubMed1996

Comprehensive long-term management program for asthma: effect on outcomes in adult African-Americans.

To determine if a comprehensive long-term management program, emphasizing inhaled corticosteroids and patient education, would improve outcomes in adult African-American asthmatics a nonrandomized control trial with a 2-year intervention was performed in a university-based clinic. Inclusion criteria consisted of (> or = 5) emergency department (ED) visits or hospitalizations (> or = 2) during the previous 2 years. Intervention patients were volunteers; a comparable control group was identified via chart review at hospitals within the same area and time period as the intervention patients. Individualized doses of beclomethasone with a spacer, inhaled albuterol "as needed," and crisis prednisone were the primary therapies. Environmental control, peak flow monitoring, and a partnership with the patient were emphasized. Detailed patient education was an integral part of management. Control patients received usual care from local physicians. ED visits and hospitalizations for 2 years before and 2 years during the intervention period were compared. Quality of life (QOL) measurements were made at baseline and every 6 months in the intervention group. Study group (n = 21) had a significant reduction in ED visits (2.3 +/- 0.2 pre-intervention versus 0.6 +/- 0.2 post-intervention; P = 0.0001). Control group (n = 18) did not have a significant change in ED visits during the 2-year post-intervention period (2.6 +/- 0.2 pre-intervention versus 2.0 +/- 0.2 post-intervention; P = 0.11). Both groups had significant reductions in hospitalizations, but the study group had a greater reduction. Sixty-two percent of study patients had complete elimination of ED visits and hospitalizations, whereas no control patients had total elimination of the need for institutional acute care. QOL in the study patients revealed significant improvements for most parameters. A comprehensive long-term management program emphasizing inhaled corticosteroids combined with other state-of-the-art management, including intensive patient education, improves outcomes in adult African-American asthmatics.

Adrenal Cortex Hormones↗

PubMed2001

Role of anterior temporal cortex in auditory sentence comprehension: an fMRI study.

Recent neuropsychological and functional imaging evidence has suggested a role for anterior temporal cortex in sentence-level comprehension. We explored this hypothesis using event-related fMRI. Subjects were scanned while they listened to either a sequence of environmental sounds describing an event or a corresponding sentence matched as closely as possible in meaning. Both types of stimuli required subjects to integrate auditory information over time to derive a similar meaning, but differ in the processing mechanisms leading to the integration of that information, with speech input requiring syntactic mechanisms and environmental sounds utilizing non-linguistic mechanisms. Consistent with recent claims, sentences produced greater activation than environmental sounds in anterior superior temporal lobe bilaterally. A similar speech > sound activation pattern was noted also in posterior superior temporal regions in the left. Envirornmental sounds produced greater activation than sentences in right inferior frontal gyrus. The results provide support for the view that anterior temporal cortex plays an important role in sentence-level comprehension.

Adult↗

PubMed2002

Segregating early physical and syntactic processes in auditory sentence comprehension.

Auditory language comprehension involves physical as well as syntactic processing. The present study examined whether early physical and syntactic processes in spoken sentence comprehension can be segregated using event-related brain potentials (ERPs). In the physical manipulation condition, the terminal word of the sentence was presented either from the same or from a different location to the preceding sentence fragment. In the syntactic manipulation condition, the terminal word was either a syntactically correct continuation of the preceding sentence fragment or violated syntactic constraints. These two factors were completely crossed. Physical deviances elicited the mismatch negativity (MMN) and syntactic deviances the early syntax-related negativity, both deviance-related components of the ERP. Sentences which violated physical as well as syntactic constraints elicited a negativity which was larger than that elicited by only a physical or only a syntactic deviance. The elicitation of the MMN in connected speech demonstrates that this component can be used as a probe for auditory change-detection even in ecologically highly valid situations. The increase of deviance-related effects with double deviants suggests that the early physical and syntactic processing systems act, to a high degree, in parallel and independently of each other.

Adolescent↗

PubMed1981

When to use a comprehensive final examination.

In summary, comprehensive testing should be discouraged when it involves simply repeating earlier content by means of new or reused test items designed to assess the same knowledge previously measured. A more advanced approach to comprehensive testing should be encouraged. This approach would challenge the student to integrate earlier concepts and principles as he undertakes more sophisticated tasks such as application of knowledge and problem-solving.

Education, Medical, Undergraduate↗

PubMed1992

Six years of comprehensive, clinical, performance-based assessment using standardized patients at the Southern Illinois University School of Medicine.

By the end of 1990-91, the Southern Illinois University School of Medicine had had six years of experience with comprehensive, performance-based examinations of senior medical students' levels of clinical competence; this report assesses the psychometric aspects of the six examinations given during that period. The examinations were aimed at determining the students' readiness for postgraduate training. Compared with other clinical performance-based assessments that use standardized patients (SPs), these examinations had two important and unique features: (1) the examinations assessed a comprehensive range of clinical skills and reasoning; and (2) they approximated the challenges of real clinical practice wherein a practitioner's skills need to be orchestrated and prioritized in order to meet the challenges of the case encountered. Each year, the performance-based assessment given was an intensive clinical examination requiring each student to work up 13 to 18 SP problems over a three-day period. To administer an examination to an entire class of students took three weeks. Because all students after the first year of administration (1986) were required to pass these examinations, the fairness of test design and scoring and the setting of performance standards for the examinations became important issues for the faculty. The results, accumulated over six years and based on a total of 6,804 student-patient encounters involving 405 students, indicate that this kind of clinical performance-based examination can discriminate a wide range of students' clinical performances. The results provide evidence for the examinations' test security, content validity, construct validity, and reliability.

Clinical Clerkship↗

PubMed1997

Implementing a comprehensive approach to managing faculty roles, rewards, and development in an era of change.

The current environment in which medicine is taught and practiced requires that medical schools pay increased attention to the faculty member's roles, rewards, career development, and productivity. Medical schools must make strategic decisions about the allocation of resources that can nurture their faculties and support the activities in academic and community settings in which faculty are involved. From 1993 to 1995 Allegheny University of the Health Sciences (formerly Medical College of Pennsylvania and Hahnemann University) designed a comprehensive system for the professional development of faculty. This system is based upon expanded categories of faculty academic activity and scholarship. New programs were implemented to reorient faculty toward conducting and documenting the expanded array of scholarly activities. The main characteristics of the new system are the establishment of formally defined performance expectations, the vertical alignment of the individual faculty member's objectives with the department's mission and the school's mission, and an increasing emphasis upon faculty interdependence, accountability, and use of sound business practices. The authors describe these and other aspects of the design of the new system in detail and report initial results and lessons learned from the system's implementation, evaluation, and dissemination throughout the university. The long-term success of this comprehensive professional development program will be assessed over time by observing how this institution advances its mission in a well-planned and cost-effective manner that retains talented, productive, and professionally fulfilled faculty.

Academic Medical Centers↗