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PubMed2005

Meta-analysis: computed tomographic colonography.

BACKGROUND: Computed tomographic (CT) colonography, also called virtual colonoscopy, is an evolving technology under evaluation as a new method of screening for colorectal cancer. However, its performance as a test has varied widely across studies, and the reasons for these discrepancies are poorly defined. PURPOSE: To systematically review the test performance of CT colonography compared to colonoscopy or surgery and to assess variables that may affect test performance. DATA SOURCES: The PubMed, MEDLINE, and EMBASE databases and the Cochrane Controlled Trials Register were searched for English-language articles published between January 1975 and February 2005. STUDY SELECTION: Prospective studies of adults undergoing CT colonography after full bowel preparation, with colonoscopy or surgery as the gold standard, were selected. Studies had to have used state-of-the-art technology, including at least a single-detector CT scanner with supine and prone positioning, insufflation of the colon with air or carbon dioxide, collimation smaller than 5 mm, and both 2-dimensional and 3-dimensional views during scan interpretation. The evaluators of the colonogram had to be unaware of the findings from use of the gold standard test. Data on sensitivity and specificity overall and for detection of polyps less than 6 mm, 6 to 9 mm, and greater than 9 mm in size were abstracted. Sensitivities and specificities weighted by sample size were calculated, and heterogeneity was explored by using stratified analyses and meta-regression. DATA SYNTHESIS: 33 studies provided data on 6393 patients. The sensitivity of CT colonography was heterogeneous but improved as polyp size increased (48% [95% CI, 25% to 70%] for detection of polyps <6 mm, 70% [CI, 55% to 84%] for polyps 6 to 9 mm, and 85% [CI, 79% to 91%] for polyps >9 mm). Characteristics of the CT colonography scanner, including width of collimation, type of detector, and mode of imaging, explained some of this heterogeneity. In contrast, specificity was homogenous (92% [CI, 89% to 96%] for detection of polyps <6 mm, 93% [CI, 91% to 95%] for polyps 6 to 9 mm, and 97% [CI, 96% to 97%] for polyps >9 mm). LIMITATIONS: The studies differed widely, and the extractable variables explained only a small amount of the heterogeneity. In addition, only a few studies examined the newest CT colonography technology. CONCLUSIONS: Computed tomographic colonography is highly specific, but the range of reported sensitivities is wide. Patient or scanner characteristics do not fully account for this variability, but collimation, type of scanner, and mode of imaging explain some of the discrepancy. This heterogeneity raises concerns about consistency of performance and about technical variability. These issues must be resolved before CT colonography can be advocated for generalized screening for colorectal cancer.

Aged↗
PubMed1989

Cleft lip and palate and related disorders: issues for future research of high priority.

On October 14 to 17, 1987, a meeting entitled "State of the Art Conference: Multidisciplinary Management of Cleft Lip and Palate" was held in Iowa City. The major purpose of the conference was to review the available knowledge concerning management of unilateral cleft lip and palate from the perspectives of surgery, speech-language pathology, and orthodontics. The closing feature of the conference was the identification of issues for future research. Participants identified issues of high priority that were then discussed by the entire conference faculty. This paper reports the summary of that discussion and the recommendations of the Conference.

Cleft Lip↗
PubMed2003

A probabilistic model for identifying protein names and their name boundaries.

This paper proposes a method for identifying protein names in biomedical texts with an emphasis on detecting protein name boundaries. We use a probabilistic model which exploits several surface clues characterizing protein names and incorporates word classes for generalization. In contrast to previously proposed methods, our approach does not rely on natural language processing tools such as part-of-speech taggers and syntactic parsers, so as to reduce processing overhead and the potential number of probabilistic parameters to be estimated. A notion of certainty is also proposed to improve precision for identification. We implemented a protein name identification system based on our proposed method, and evaluated the system on real-world biomedical texts in conjunction with the previous work. The results showed that overall our system performs comparably to the state-of-the-art protein name identification system and that higher performance is achieved for compound names. In addition, it is demonstrated that our system can further improve precision by restricting the system output to those names with high certainties.

Artificial Intelligence↗
PubMed2026

Investigating cross-organism prediction of prokaryotic essential proteins using unsupervised language model and ensemble strategy.

Cross-organism prediction of essential proteins is a critical task for drug discovery and microbial engineering, yet the generalizability of existing machine learning models across diverse species remains a significant challenge. In this study, we propose DeepPEP, a large language model-based framework designed to reliably transfer essential protein annotations between distantly related organisms. Utilizing 66 curated prokaryotic datasets, we systematically evaluated DeepPEP's cross-organism performance under various conditions. Initial pairwise predictions revealed a correlation between performance and evolutionary distance; however, further investigation demonstrated that integrating training data from multiple organisms yields superior predictive power. In a benchmark scenario designed to simulate real-world applications, DeepPEP outperformed the state-of-the-art tool Geptop 2.0, showcasing a robust ability to identify species-specific essential proteins. Finally, a case study on novel genomes confirmed the model's practical effectiveness. Our results suggest that DeepPEP is a powerful strategy for prokaryotic essential protein prediction, and the rigorous evaluation framework established in this study provides a new benchmark for the field.

Large Language Models↗
PubMed1991

[Medical assimilation processes in the middle ages. From Gundishapur to Toledo].

The medicine of Ancient Greece has had an important impact on world medicine right up to modern times. One of the most interesting lines of development can be followed from about 1000 years after the death of Hippocrates (377 BC). At that time, Greek medicine and philosophy encountered the rising Islamic culture of the Arab world. It went through phases of reception and assimilation in the Middle East where, in addition to Baghdad, the city of Gundishapur is emphasized as an important centre of translation. Some hundred years later Latin Europe benefited from these Arab translations of medical and philosophical texts from Ancient Greece. After the Spanish city of Toledo had been reconquered from the Arabs, European scholars gathered there to translate the Greco-Arab manuscripts into Latin, the language of the learned in medieval Europe. The author tries to describe this course of events.

Asia↗
PubMed2006

A framework for evaluating community-based physical activity promotion programmes in Latin America.

A growing interest in promoting physical activity through multi-sectoral community-based programmes has highlighted the need for effective programme evaluation. Meeting in Rio de Janeiro, an international workgroup of behavioural, medical, public health and other scientists and practitioners endorsed the principle of careful evaluation of all programmes and in a consensus process developed the Rio de Janeiro Recommendations for Evaluation of Physical Activity Interventions". Among these recommendations and principles were that when possible, evaluation should 'built into' the programme from the beginning. The workgroup also called for adequate funding for evaluation, setting a goal of about 10% of programme resources for evaluation. The group also determined that evaluations should be developed in conjunction with and the results shared with all appropriate stakeholders in the programme; evaluations should be guided by ethical standards such as those proposed by the American Evaluation Association and should assess programme processes as well as outcomes; evaluation outcomes should be used to revise and refine ongoing programmes and guide decisions about programme continuation or expansion. It was also recognised that additional training in programme evaluation is needed and the Centers for Disease Control and Prevention's Physical Activity Evaluation Handbook could be easily adapted for use in culturally diverse communities, especially in Latin America. This paper describes a 6-step evaluation process and provides the full set of recommendations from the Rio de Janeiro Workgroup. The handbook has been translated and additional case studies from Colombia and Brazil have been added. Spanish and Portuguese language editions of the Evaluation Handbook are available from the Centers for Disease Control and Prevention, Physical Activity and Health Branch.

Community Networks↗
PubMed2003

"Understanding" medical school curriculum content using KnowledgeMap.

OBJECTIVE: To describe the development and evaluation of computational tools to identify concepts within medical curricular documents, using information derived from the National Library of Medicine's Unified Medical Language System (UMLS). The long-term goal of the KnowledgeMap (KM) project is to provide faculty and students with an improved ability to develop, review, and integrate components of the medical school curriculum. DESIGN: The KM concept identifier uses lexical resources partially derived from the UMLS (SPECIALIST lexicon and Metathesaurus), heuristic language processing techniques, and an empirical scoring algorithm. KM differentiates among potentially matching Metathesaurus concepts within a source document. The authors manually identified important "gold standard" biomedical concepts within selected medical school full-content lecture documents and used these documents to compare KM concept recognition with that of a known state-of-the-art "standard"-the National Library of Medicine's MetaMap program. MEASUREMENTS: The number of "gold standard" concepts in each lecture document identified by either KM or MetaMap, and the cause of each failure or relative success in a random subset of documents. RESULTS: For 4,281 "gold standard" concepts, MetaMap matched 78% and KM 82%. Precision for "gold standard" concepts was 85% for MetaMap and 89% for KM. The heuristics of KM accurately matched acronyms, concepts underspecified in the document, and ambiguous matches. The most frequent cause of matching failures was absence of target concepts from the UMLS Metathesaurus. CONCLUSION: The prototypic KM system provided an encouraging rate of concept extraction for representative medical curricular texts. Future versions of KM should be evaluated for their ability to allow administrators, lecturers, and students to navigate through the medical curriculum to locate redundancies, find interrelated information, and identify omissions. In addition, the ability of KM to meet specific, personal information needs should be assessed.

Abstracting and Indexing↗
PubMed2005

Probabilistic finite-state machines--part I.

Probabilistic finite-state machines are used today in a variety of areas in pattern recognition, or in fields to which pattern recognition is linked: computational linguistics, machine learning, time series analysis, circuit testing, computational biology, speech recognition, and machine translation are some of them. In Part I of this paper, we survey these generative objects and study their definitions and properties. In Part II, we will study the relation of probabilistic finite-state automata with other well-known devices that generate strings as hidden Markov models and n-grams and provide theorems, algorithms, and properties that represent a current state of the art of these objects.

Algorithms↗
PubMed2005

Probabilistic finite-state machines--part II.

Probabilistic finite-state machines are used today in a variety of areas in pattern recognition or in fields to which pattern recognition is linked. In Part I of this paper, we surveyed these objects and studied their properties. In this Part II, we study the relations between probabilistic finite-state automata and other well-known devices that generate strings like hidden Markov models and n-grams and provide theorems, algorithms, and properties that represent a current state of the art of these objects.

Algorithms↗
PubMed2006

Gonadotrophins for idiopathic male factor subfertility.

BACKGROUND: Male factor infertility accounts for 50% of infertility. The treatment of idiopathic male infertility is empirical. Urinary, purified, and recombinant gonadotrophins have been used to improve sperm parameters in idiopathic male infertility with the goal of increasing pregnancy rates. Research addressing pregnancy rates in partners of men treated with gonadotrophins has had conflicting results and needs to be analysed. OBJECTIVES: To determine the effectiveness of gonadotrophin administration to men with idiopathic subfertility on spontaneous pregnancy rate and in assisted reproductive techniques (ARTs). SEARCH STRATEGY: We searched the Cochrane Menstrual Disorders and Subfertility Group trials register (19 November 2004), the Cochrane Central Register of Controlled Trials (The Cochrane Library, issue 4, 2004), MEDLINE (1966 to April 2005), EMBASE and Biological Abstracts (1980 to November 2004). Searches were not limited by language. The bibliographies of included, excluded trials and abstracts of major meetings were searched for additional trials. Authors and pharmaceutical companies were contacted for missing and unpublished data. SELECTION CRITERIA: Truly randomised controlled trials where gonadotrophins were administered for the treatment of idiopathic male subfertility with reporting of pregnancy rates were included in the review. DATA COLLECTION AND ANALYSIS: Two reviewers independently assessed trial quality and extracted data. Study authors were contacted for additional information. Adverse effects information was collected from the trials. We analysed data regarding pregnancy occurring within 3 months after gonadotrophin therapy. MAIN RESULTS: Four RCTs with 278 participant were included in the analysis. None of the studies had an adequate sample size and they had variable follow-up periods. None of the studies reported live birth or miscarriage rates. Compared to placebo or no treatment, gonadotrophins showed a significantly higher pregnancy rate per couple randomized within 3 months of completing therapy (OR 3.03, 95% CI 1.30 to 7.09). Pregnancy rate was 13.4% (19/142) in the gonadotrophin group and 4.4% (6/136) in the control group. AUTHORS' CONCLUSIONS: The number of trials and participants is insufficient to draw final conclusions. A large multicenter study with adequate power is needed.

Follicle Stimulating Hormone↗
PubMed2005

[Linguistic adaptation into Spanish and validation of the Arthritis Treatment Satisfaction Questionnaire].

BACKGROUND AND OBJECTIVE: Linguistic adaptation and validation into Spanish of the ARTS questionnaire, a self reported instrument designed to measure four osteoarthritis treatment satisfaction dimensions: treatment advantages, treatment convenience, apprehension about treatment and satisfaction with medical care. MATERIAL AND METHOD: Adaptation was performed using conceptual equivalence, supervised by a panel of 6 experts and 4 independent translators, who were in charge of performing translation and back-translation of the items. A sample of patients suffering from knee, hip or column osteoarthritis was used to estimate the psychometric properties of feasibility, reliability, validity and sensitivity to change. Three groups were identified: adequate analgesic effect and tolerability, treatment-switch because of a weak analgesic effect, and treatment- switch due to poor tolerability. The ARTS was administered at baseline, 1 week later for retest, and after 4 weeks of treatment with NSAIDs or Cox II-inhibitors. RESULTS: A sample of 163 patients was formed (67.7 [9.2] years old). No floor or ceiling effects were found, items were well understood and non- response rates were below 1%. Cronbach's alpha for the total scales was 0.85, and the intraclass correlation coefficient was 0.81. Exploratory factor analysis yielded 4 dimensions which were coherent with those proposed by the original authors. Concurrent validity was measured with SF-36, a pain VAS instrument, a treatment compliance VAS, and the Morisky-Green compliance questionnaire. The adapted instrument showed a good discriminatory validity, and it was able to distinguish between patients needing a change in treatment and those who did not need it. It was also sensitive to changes in patients' treatment effectiveness after a 30 days follow up. CONCLUSIONS: A psychometrically valid and conceptually equivalent ARTS questionnaire has been produced to explore satisfaction with treatment in patients with osteoarthritis in Spanish speaking countries.

Humans↗
PubMed2004

Linguistic and cognitive functioning and autism symptoms in young children with fragile X syndrome.

Linguistic and cognitive profiles were examined in 18 children with autism and 18 children with fragile X syndrome (mean ages = 34 months). State-of-the-art diagnostic procedures for autism symptom identification were administered. Eight children with fragile X met criteria for autism. Comparison of linguistic and cognitive profiles (autism, fragile X without autism, fragile X with autism) revealed that children with fragile X (with autism) were more impaired in nonverbal cognition and expressive language. Receptive language was a relative strength for children with fragile X (without autism). There were no differences in receptive language in children with autism, regardless of fragile X status. Low receptive language may be a marker for autism symptoms in young children with fragile X.

Autistic Disorder↗
PubMedDate not supplied

Hypothalamic-pituitary-adrenal axis suppression and inhaled corticosteroid therapy. 2. Review of the literature.

In the first part of this two-part review it was noted that inhaled corticosteroids had become the mainstay of treatment for chronic asthma and yet the effects of long-term use of these compounds on the hypothalamic-adrenal-pituitary (HPA) axis were largely being determined by testing methods of limited reliability, especially by morning plasma cortisol measurements. It was established in our examination of the published literature and in our presentation of current knowledge of the structure and function of the HPA axis that safe, accurate and discriminating techniques to assess the functional status of the HPA axis were available. It was concluded that two state-of-the-art tests that have been insufficiently used were the ACTH stimulation test and measurement of the 24-hour integrated serial plasma cortisol concentrations. These two tests can detect adrenal suppression before the appearance of clinical effects. For part 2 of this review we conducted an exhaustive search of the English language clinical and pharmacological literature on the use of inhaled corticosteroids from 1988 until the present time to identify studies in which one or both of these testing methods have been used. We present our analysis of this limited number of studies to determine what accurately can be known of the HPA axis safety profile of three of the most commonly used and investigated inhaled corticosteroids - beclomethasone dipropionate, budesonide and fluticasone propionate. The first finding of significance was that only 50 reports were identified in which information on the HPA axis safety effects of orally inhaled steroids in asthma patients or in clinical pharmacological studies met our inclusion requirements. By analysis of the data presented in these reports we were able to reach the following conclusions: (1) inhaled corticosteroids administered chronically, and prudently, within recommended dose ranges do not endanger the functioning of the HPA axis, (2) the increasing tendency to use higher doses of inhaled corticosteroids on the assumption that there are clear dose-response benefits and no adverse HPA axis effects from long-term high-dose regimens is misguided and not supported by reliable published information, (3) the corollary - that higher corticosteroid potencies (as measured, for example, by skin-blanching activity) can have greater therapeutic effect in lung tissue without greater concomitant systemic activity - is a flawed concept, and (4) the limited clinical and pharmacological data support our part 1 conclusions that discriminating techniques to assess the functional HPA axis status should be an integral part of the drug development process and that further HPA axis function studies are required on existing inhaled corticosteroids - if they lack a rigorous testing history or long-term record of clinical safety.

Adrenal Cortex Hormones↗
PubMed1991

On drawing impairment in Alzheimer's disease.

Spontaneous drawings of 38 patients, diagnosed by the National Institute of Neurological Disorders and Stroke-Alzheimer's Disease and Related Disorders Association criteria as "probable Alzheimer's disease," and of 39 normal control subjects were analyzed by two independent observers using a standardized scoring system. Drawings of patients with Alzheimer's disease displayed fewer angles, impaired perspective and spatial relations, simplification, and overall impairment compared with those of the control subjects. This represents a combination of the deficits seen following right- and left-hemisphere lesions. Neglect, tremor, and perseveration were not prominent. Drawing impairment was relatively independent of language or memory impairment, but drawing performance was related to perceptual and executive dysfunction in the visuospatial domain. Deterioration was followed up for up to 3 years.

Aged↗
PubMed1996

Prostate cancer, race, and socioeconomic status: inadequate adjustment for social factors in assessing racial differences.

BACKGROUND: This paper reviews the state of the art in analyzing race, social factors, and economic factors in cancer research, with an emphasis on prostate cancer and the role of socioeconomic status (SES) in racial differences in mortality. It analyzes the quality of articles in the literature that assess the role of SES in cancer mortality. METHODS: English-language titles were identified using MEDLINE with publication dates from mid-1985 through July 1994. Articles in the references of these articles were also included in the final selection, based originally on title and ultimately on content, dating back to 1978. Articles that included SES information and distinguished between whites and African-Americans were chosen, resulting in a final selection of 21 articles. Articles are summarized with consideration of five criteria considered minimal requirements of a well-designed study of the role of race in cancer mortality: (1) SES measure(s) should be on an individual level, not census level; (2) SES should be controlled for when making comparisons between whites and blacks; (3) SES should include at least (individual level) measures of income and education; (4) sample sizes are sufficient for the relevant populations; and (5) specific cancer sites should be studied separately. RESULTS: Of the articles reviewed, only two meet the minimum standards, neither of which studied prostate cancer. It is not clear whether observed racial differences in prostate cancer are directly attributable to race or reflect underlying social factor differences between whites and African-Americans. CONCLUSIONS: In the future, specific characteristics of SES should be measured at the individual level; there is a need for expansion and standardization of data in terms of social and economic content; other methodological advances are needed in modeling to take into consideration the influence of SES in outcome research related to cancer.

Humans↗
PubMed2000

Toward a psychology of positive youth development.

This article analyzes the development of initiative as an exemplar of one of many learning experiences that should be studied as part of positive youth development. The capacity for initiative is essential for adults in our society and will become more important in the 21st century, yet adolescents have few opportunities to learn it. Their typical experiences during schoolwork and unstructured leisure do not reflect conditions for learning initiative. The context best suited to the development of initiative appears to be that of structured voluntary activities, such as sports, arts, and participation in organizations, in which youths experience the rare combination of intrinsic motivation in combination with deep attention. An incomplete body of outcome research suggests that such activities are associated with positive development, but the developmental processes involved are only beginning to be understood. One promising approach has recorded language use and has found that adolescents participating in effective organizations acquire a new operating language that appears to correspond to the development of initiative.

Adolescent↗
PubMed2026

Fast, accurate construction of multiple sequence alignments from protein language embeddings.

Multiple sequence alignment (MSA) is a foundational task in computational biology, underpinning protein structure prediction, evolutionary analysis, and domain annotation. Traditional MSA algorithms rely on pairwise amino acid substitution matrices derived from conserved protein families. While effective for aligning closely related sequences, these scoring schemes struggle in the low-identity "twilight zone." Here, we present a new approach for constructing MSAs leveraging amino acid embeddings generated by protein language models (PLMs), which capture rich evolutionary and contextual information from massive and diverse sequence datasets. We introduce a windowed reciprocal-weighted embedding similarity metric that is surprisingly effective in identifying corresponding amino acids across sequences. Building on this metric, we develop ARIES (Alignment via RecIprocal Embedding Similarity), an algorithm that constructs a PLM-generated template embedding and aligns each sequence to this template via dynamic time warping in order to build a global MSA. Across diverse benchmark datasets, ARIES achieves higher accuracies than existing state-of-the-art approaches, especially in low-identity regimes where traditional methods degrade, while scaling almost linearly with the number of sequences to be aligned. Together, these results provide the first large-scale demonstration of the power of PLMs for accurate and scalable MSA construction across protein families of varying sizes and levels of similarity, highlighting the potential of PLMs to transform comparative sequence analysis.

Deep Learning↗