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PubMed1991

Communication problems associated with cleft palate and related disorders. Annotated bibliography.

The books in this annotated bibliography were selected because of the general nature of the information that they provide. Most of these books contain bibliographies that include references of a more technical nature should the reader desire such information. These books are available at most university libraries. Additional information can be obtained from brochures and fact sheets published by the Cleft Palate Foundation (1218 Grandview Avenue, Pittsburgh, PA 15211). These publications were prepared primarily for patients and parents, but can provide useful information to professionals who typically do not work with patients with cleft palate and craniofacial anomalies.

Child↗
PubMed1982

Evaluation of nutrition interventions. An annotated bibliography and review of methodologies and results. Food and Agriculture Organization of the United Nations.

1. This is the second edition of an annotated bibliography covering evaluation methodology and evaluations of nutrition interventions. It contains more than 110 items on methodology and around 300 reports describing the results from evaluation studies. Included are most of the 250 items listed in the first edition, which was compiled in 1980, by G.P. Sevenhuysen and Ann Burgess. Almost all the items are available in the FAO libraries in Rome. 2. The most useful of the items are starred and also indexed in Tables 1, 2 or 3. Evaluation methodology 3. There was general agreement in the guidelines on evaluation methodology on the following points: Evaluation should be an integral routine programme activity wherever possible; Field staff must be involved at all stages of the evaluation including interpretation; Results should be rapidly 'fed-back' to allow adaptations to be made to the programme if necessary. 4. Many of the guidelines did not adequately cover the following points: How to conduct both 'operational' and 'impact' evaluation; The importance of taking into account, when designing the evaluation, the needs of the people who will use the results; How to select a representative sample; How to overcome the problem of 'drop-outs'; How to measure 'leakage' of programme inputs; How to control for non-programme variables; How to distinguish among the effects of multiple inputs; How to measure costs and cost-effectiveness; How to ensure data reliability. A review of reports of evaluation studies confirmed that better guidelines are needed in these areas. Evaluation reports 5. In only about one third of the studies examined were sufficient details available for a good assessment to be made of the reliability of the results. 6. Among the problems that made it difficult to assess the value of some of the results were: A lack of specific programme objectives and of baseline data; Inadequate statistical testing of the results; Conclusions based mainly on subjective opinion rather than objective information; A weak data base, due to an unrepresentative sample, a high 'drop-out' rate among the selected sample, or insufficient data collected; A lack of information on the 'dosage' of the input actually reaching the recipients; A lack of information on possible differences in age distribution, and other variables, in the test and control groups; No control of non-programme variables; An evaluation design that did not allow the different contributions of multiple programme inputs to be assessed; No data on costs; Lack of information on which to judge data reliability.

Evaluation Studies as Topic↗
PubMed2025

A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization.

Next-Generation Sequencing (NGS), also known as high-throughput sequencing technologies, has enabled rapid and efficient sequencing of large amounts of DNA and RNA. These technologies have revolutionized the field of genomics, transcriptomics, and proteomics and have been widely used in cancer research, leading to advances in clinical diagnosis and treatment. Improvements in the NGS technologies enabled millions of fragments to be sequenced simultaneously in a time- and cost-effective manner and resulted in large amount of genomic data which require efficient analysis methods. Analysis of the genomic data requires both efficient computer resources and bioinformatics approaches. This chapter details a comprehensive computational approach and analysis steps for genomic data analysis.

Computational Biology↗
PubMed2025

Improved diagnosis of patients with rare diseases through the application of constrained coding region annotation and de novo status.

PURPOSE: Identifying the pathogenic variant in a patient with rare disease (RD) is the first step in ending their diagnostic odyssey. De novo (Dn) variants affecting protein-coding DNA are a well-established cause of Mendelian disorders in patients with RD. Constrained coding regions (CCRs) are specific segments of coding DNA that are devoid of functional variants in healthy individuals. METHODS: We evaluated the diagnostic utility of incorporating combined Dn/CCR status into the variant prioritization cascade for patients with RD that have undergone genomic sequencing. Using the Genomics England 100,000 Genomes Project v12, we selected 3090 trios that have undergone diagnostic evaluation and been analyzed with an advanced Dn identification pipeline. RESULTS: Our analysis shows that the diagnostic rate increased from 71% in the full cohort to 87% for Dn/CCR variants. Of note, manual evaluation of the Dn/CCR variants from undiagnosed patients with clinical follow-up revealed a diagnosis for 13 further patients. This outcome increases the diagnostic rate for Dn/CCR variants to 91% and suggests that the application of this metric can prioritize diagnostic variants in undiagnosed patients. CONCLUSION: We demonstrate the potential clinical utility of performing bespoke Dn analyses of patients with RD and for incorporating CCR information into the filtering cascade to prioritize pathogenic variants.

Humans↗
PubMed2025

Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings.

MOTIVATION: Rare diseases collectively affect 5% of the population. However, fewer than 50% of rare disease patients receive a molecular diagnosis after whole genome sequencing. Supervised machine learning is a valuable approach for the pathogenicity scoring of human genetic variants. However, existing methods are often trained on curated but limited central repositories, resulting in poor accuracy when tested on external cohorts. Yet, large collections of variants generated at hospitals and research institutions remain inaccessible to machine-learning purposes because of privacy and legal constraints. Federated learning (FL) algorithms have been recently developed enabling institutions to collaboratively train models without sharing their local datasets. RESULTS: Here, we present a proof-of-concept study evaluating the effectiveness of FL for the clinical classification of genetic variants. A comprehensive array of diverse FL strategies was assessed for coding and non-coding Single Nucleotide Variants as well as Copy Number Variants. Our results showed that federated models generally achieved comparable or superior performance to traditional centralized learning. In addition, federated models reached a robust generalization to independent sets with smaller data fractions as compared to their centralized model counterparts. Our findings support the adoption of FL to establish secure multi-institutional collaborations in human variant interpretation. AVAILABILITY AND IMPLEMENTATION: All source code required to reproduce the results presented in this article, implemented in Python, is available under the GNU General Public License v3 at https://github.com/RausellLab/FedLearnVar.

Humans↗
PubMed2026

The complete and annotated mitochondrial genome of Hemileia vastatrix Race I, causal agent of coffee leaf rust.

Hemileia vastatrix is the fungal pathogen responsible for coffee leaf rust (CLR), the most economically important disease of Coffea arabica worldwide. Recently, the nuclear genome of this fungus was completely deciphered. However, the mitochondrial genome of H. vastatrix has remained undercharacterized. Here, we present the complete, circularized mitochondrial genome of H. vastatrix Race I (isolate HvRI), assembled using a hybrid approach combining PacBio HiFi long reads and BGIseq short reads. The genome is 173,525 bp in length with a GC content of 33.1% and encodes 41 functional genes, including 15 protein-coding genes, 2 rRNAs, and 24 tRNAs. The assembly reveals significant structural complexity, driven by intron expansion in the cox1 and cob genes. Notably, the atp8 gene contains a group II intron, rare for this locus, whose internal open reading frame displays evidence of pseudogenization via internal stop codons.. We also characterized a putative replication initiation zone (~1.2 kb) defined by a poly-G homopolymer and conserved regulatory motifs. The mitogenome of the HvRI isolate does not contain cob mutations that lead to amino acid substitutions G143A and F129L associated with the quinone outside inhibitor (QoI) fungicide resistance. This high-quality mitogenome is an important resource for comparative mitogenomics, population diversity studies, and the molecular surveillance of QoI fungicide resistance.

Genome, Mitochondrial↗
PubMed1969

Annotations.

Explore the source record for details and available documents.

Child, Preschool↗
PubMed1979

An annotation on the pulse in aortic regurgitation: Thomas Cuming, 1822.

The classic bounding pulse of aortic regurgitation was described by several authors before Corrigan made his comprehensive study of the disorder in 1832. The case report of Thomas Cuming, published 10 years earlier, is worthy of review. This Dublin practitioner not only presented signs and symptoms of aortic regurgitation proved at autopsy, but also attempted with considerable success to relate the signs to circulatory dynamics.

Adult↗