Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “CATALOGING”

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 739 records · Page 41Linked to original sources
PubMed2005

Genetic heterogeneity for autosomal recessive pyridoxine-dependent seizures.

Pyridoxine-dependent seizure (PDS) is a rare autosomal recessive intractable seizure disorder only controlled by a daily supplementation of pharmacological doses of pyridoxine (Vitamin B6). Although glutamate decarboxylase utilizes pyridoxal phosphate as a cofactor during conversion of the excitatory amino acid, glutamate, to the inhibitory neurotransmitter, gamma-amino butyric acid (GABA), several studies have failed to demonstrate a linkage to either of the glutamate-decarboxylase-encoding genes (GAD1 and GAD2) and PDS excluding involvement of this functional candidate. However, in 2000, a locus for PDS was mapped to a 5 cM interval at chromosome 5q31 in four consanguineous and one multisib pedigree (Z(max)=8.43 at theta=0 for marker D5S2017) [Cormier-Daire et al. in Am J Hum Genet 67(4):991-993 2000]. We undertook molecular genetic studies of six nonconsanguineous North American families, using up to ten microsatellite markers to perform haplotype segregation analysis of the 5q31 locus. Assignment to the chromosome 5q PDS locus was excluded in one of the six North American PDS pedigrees, as chromosome 5q31 haplotypes were incompatible with linkage to this locus. The remaining five PDS pedigrees showed haplotype segregation consistent with linkage to 5q31, generating a maximum combined lod score of 1.87 (theta=0) at marker D5S2011. In this study, we establish genetic heterogeneity for PDS, catalog 21 genes within the originally defined PDS interval, and identify additional recombinations that indicate a higher priority interval, containing just 11 genes.

Chromosome Disorders↗
PubMed2004

Analysis of expressed sequence tags from calcifying cells of marine coccolithophorid (Emiliania huxleyi).

An expressed sequence tag (EST) approach was used to investigate gene expression in the unicelluar marine alga Emiliania huxleyi. We randomly selected 3000 EST sequences from a cDNA library of transcripts expressed under conditions promoting coccolithogenesis. Cluster analysis and contig assembly resulted in a unigene set of approximately 1523 ESTs. Only 36% of the unique sequences exhibited significant homology to sequences in GenBank. Of particular interest were the numerous transcripts with homology to sequences associated with sexual reproduction and calcium homeostasis in other unicellular and multicellular organisms. The majority of ESTs (64%) had little or no significant sequence homology to entries in GenBank, suggesting a potential for further novel gene discovery. The catalog of ESTs reported herein represents a significant increase in the limited sequence information currently available for E. huxleyi and should make the coccolithophorid more accessible to powerful genomics and postgenomics technologies.

Base Composition↗
PubMed2002

A listing of skin conditions exhibiting the koebner and pseudo-koebner phenomena with eliciting stimuli.

BACKGROUND: The Koebner phenomenon was first described in 1872. It occurs after a variety of traumatic insults. New examples of koebnerization are reported each decade. OBJECTIVE: We have compiled, for the first time in the dermatologic literature, an extensive list of the cutaneous diseases reported to demonstrate koebnerization, correlated in each case with the precise source of trauma. Cutaneous diseases reported to show a pseudo-Koebner phenomenon and the corresponding mechanism of trauma are also detailed. METHODS: A search and review of the English language literature on MEDLINE was made to identify cutaneous diseases exhibiting the Koebner phenomenon and the correlated mechanism of trauma. RESULTS: Results of our efforts are cataloged in table format. CONCLUSION: We present an extensive list of cutaneous diseases reported to exhibit the Koebner and pseudo-Koebner phenomena, correlating each entry with the mechanism of trauma.

Epidermolysis Bullosa Acquisita↗
PubMed2026

Cancer-associated fusion transcripts: mechanisms, functional roles, and clinical implications.

Fusion transcripts are hybrid RNA molecules generated through genomic rearrangements or RNA-level fusion mechanisms. They represent important molecular features of many cancers and can function as oncogenic drivers, diagnostic biomarkers, prognostic indicators, and therapeutic targets. Since the discovery of the BCR::ABL1 fusion in chronic myeloid leukemia, numerous cancer-associated fusion transcripts have been identified across hematologic malignancies and solid tumors. These fusion events encompass diverse biological mechanisms, including constitutively active kinases, aberrant transcription factors, epigenetic regulators, and non-coding fusion RNAs. This review summarizes current knowledge of the mechanisms underlying fusion transcript formation, including genomic rearrangement-dependent and rearrangement-independent processes, as well as fusion circular RNAs. The functional roles of fusion transcripts in cancer biology and their clinical relevance as diagnostic, prognostic, and predictive biomarkers are discussed. In addition, recent advances in fusion transcript detection and characterization are reviewed, including next-generation sequencing, long-read sequencing, single-cell approaches, artificial intelligence-assisted computational methods, and CRISPR/Cas9-mediated strategies for functional modeling and functional validation of fusion transcripts. Despite the rapid expansion of fusion transcript catalogs, the biological and clinical significance of most identified fusion events remains incompletely understood. Future progress will depend on integrating advanced sequencing technologies, artificial intelligence-assisted computational prioritization, and systematic functional validation to distinguish clinically actionable fusion transcripts from biologically neutral events. Such multidisciplinary approaches will be essential for translating fusion transcript research into precision oncology and improving cancer diagnosis, patient stratification, and targeted therapy.

Humans↗
PubMed2007

Useful plants of the semi-arid northeastern region of Brazil--a look at their conservation and sustainable use.

The use of native plants was examined in three rural communities in the semi-arid of the state of Pernambuco, in northeastern Brazil. The techniques employed in the present study combined a number of different techniques of data-gathering, including semi-structured interviews, guided tour, key-informants, and participating observation, and sampling of the vegetation to evaluate the biodiversity of useful plants. A total of 61 woody species were cataloged, mostly used for construction purposes or fuel. Among the species that stood out for their local importance and multiplicity of uses were: Myracrodruon urundeuva (Engl.) Fr. All., Schinopsis brasiliensis Engl., and Anadenanthera colubrina (Vell.) Brenan. The first two species are included in Brazilian lists of threatened species. Arguments are presented for strategies of management and conservation of plant resources in the semi-arid region that seek alternatives to the use of timber species and the development of alternative non-timber resources.

Biodiversity↗
PubMed2005

A very large diversity space of synthetically accessible compounds for use with drug design programs.

We have constructed a very large virtual diversity space containing more than 10(13) chemical compounds. The diversity space is built from about 400 combinatorial libraries, which have been expanded by choosing sizeable collections of suitable R-groups that can be attached to each link point of their scaffolds. These R-group collections have been created by selecting reagents that have drug-like properties from catalogs of available chemicals. As members of known combinatorial libraries, the compounds in the diversity space are in general synthetically accessible and useful as potential drug leads. Hence, the diversity space can be used as a vast source of compounds by a de novo drug design program. For example, we have used such a program to generate inhibitors of HIV integrase enzyme that exhibited activity in the micromolar range.

Algorithms↗
PubMed2006

Research to practice: efforts to bring effective prevention to every community.

This manuscript describes the pioneering efforts of the Substance Abuse and Mental Health Services Administration's attempts to catalog knowledge, support, and further evaluate the application of evidence-based prevention. The paper begins with a discussion of scientific inquiry, including discussion of cause-and-effect relationships, theory that is useful in explaining those relationships, and suggestion of the opportunities and limitations of research in these and other areas. The authors then describe a system that has been introduced by the Substance Abuse and Mental Health Services Administration's (SAMHSA) Center for Substance Abuse Prevention (CSAP) to systematically access and review applied research efforts in drug abuse prevention and related fields. In addition to identifying the key elements of this National Registry of Effective Prevention Programs (NREPP), the authors provide a brief history of prior efforts that have led us to this point.

Community Mental Health Services↗
PubMed2005

Rice proteome database: a step toward functional analysis of the rice genome.

The technique of proteome analysis using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this study, the proteins of rice were cataloged, a rice proteome database was constructed, and a functional characterization of some of the identified proteins was undertaken. Proteins extracted from various tissues and subcellular compartments in rice were separated by 2D-PAGE and an image analyzer was used to construct a display of the proteins. The Rice Proteome Database contains 23 reference maps based on 2D-PAGE of proteins from various rice tissues and subcellular compartments. These reference maps comprise 13129 identified proteins, and the amino acid sequences of 5092 proteins are entered in the database. Major proteins involved in growth or stress responses were identified using the proteome approach. Some of these proteins, including a beta-tubulin, calreticulin, and ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have unexpected functions. The information obtained from the Rice Proteome Database will aid in cloning the genes for and predicting the function of unknown proteins.

Calreticulin↗
PubMed2006

Features of Arabidopsis genes and genome discovered using full-length cDNAs.

Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5'-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3'-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5'-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper.

Alternative Splicing↗
PubMed2002

Predicting and preventing post-ERCP pancreatitis.

Pancreatitis is rightly the most feared complication of endoscopic retrograde cholangiopancreatography (ERCP). Ten percent to 15% of cases of post-ERCP pancreatitis (PEP) are severe by clinical and radiologic criteria. Such cases carry significant morbidity and mortality and are responsible for the vast majority of ERCP-related deaths. The prediction and prevention of PEP have been of great interest to endoscopists since the introduction of ERCP 30 years ago. Prediction and diagnosis of PEP have become more accurate with the widespread availability of serum amylase estimation. A variety of cytokines (eg, interleukin -1, IL-6, and IL-8) and acute phase reactants (eg, C-reactive protein) are also elevated in the serum in acute pancreatitis, and these form the basis of evolving tests for PEP. Urine testing (for amylase) in acute pancreatitis is obsolete, but it may soon undergo a revival in the form of a rapid (3-minute) dipstick test for trypsinogen-2, a sensitive and specific test for this disease. The prevention of PEP takes multiple forms. The following steps are recommended for clinicians: 1) avoid ERCP when other, less invasive or noninvasive imaging tests can do the job (eg, CT or magnetic resonance imaging); 2) avoid high-risk (of PEP) procedures, such as needle-knife papillotomy, balloon dilation of the biliary sphincter, and pancreatic sphincterotomy, and take steps to reduce risk when these procedures are unavoidable; 3) ensure that those who perform ERCP have adequate training and experience; and 4) consider pharmacologic intervention. Despite a depressing catalog of drug interventions that have failed over the years (eg, antihistamines, anticholinergics, and corticosteroids), three agents have recently shown promise: somatostatin; its octapeptide analogue, octreotide; and gabexate mesylate, a protease inhibitor.

Acute Disease↗
PubMed2000

The promise of transcription profiling for understanding the pathogenesis of scleroderma.

Transcription profiling, expression fingerprinting, and microarray analysis are terms that describe the cataloging of mRNA levels in a given tissue. Recent profiling technologies allow the determination of thousands of mRNA transcript levels simultaneously. The application of this technology to scleroderma has already offered insights into the disease. This article reviews these recent findings and also describes the technology itself in its several variations, along with cost comparisons. Finally, the types of information we might derive from transcription profiling are reviewed and it is asked whether this technology will significantly advance our understanding of scleroderma.

DNA Fingerprinting↗
PubMed2004

The use of graft materials in anterior compartment pelvic reconstruction.

Since 1996, the number of reports in the urologic and gynecologic literature using synthetic and allograph prosthetics to enhance the durability of anterior compartment repairs have increased significantly. Central to the use of these prosthetics is long-term follow-up to demonstrate that their use actually confers a benefit to patients and surgeons alike. This review attempts to catalog those reports and the outcomes, with an emphasis on the cadaveric prolapse repair with sling, which is used by the authors for repair of anterior compartment prolapse with overt or occult genuine stress urinary incontinence.

Cadaver↗
PubMed2025

Glutaryl-CoA dehydrogenase (GCDH) enhances renal malignancy risk via modulating glutarylcarnitine levels.

BACKGROUND: Crotonylation, a recently identified lysine acylation, plays a critical role in post-translational modifications [1]. It has been implicated in tumorigenesis by modulating metabolic reprogramming [2], DNA repair, immune evasion [3], and oncogenic signaling pathways, including PKA-FAK-AKT and androgen receptor signaling [4]. The specific role of crotonylation in renal malignancy (RM) remains poorly understood, especially in interaction with gene expression and metabolic pathway interactions. METHODS: This study integrates genome-wide association study (GWAS) summary statistics for RM from the FinnGen database, data on crotonylation-associated gene expression obtained from the eQTLGen consortium, and metabolite GWAS data obtained from the GWAS Catalog. A combined two-sample Mendelian randomization (MR), summary data-based Mendelian randomization (SMR), and mediation analyses were performed to investigate the causal link between Glutaryl-CoA dehydrogenase (GCDH) and RM, with a specific focus on glutarylcarnitine metabolism. RESULTS: MR analysis demonstrated a significant association; increased expression of GCDH is likely to increase the risk of RM (OR = 1.25, P = 0.0045). Mediation analysis revealed that elevated GCDH expression significantly reduced glutarylcarnitine (C5-DC) levels, which in turn was inversely associated with RM risk. A three-step MR-based mediation confirmed a significant mediating effect of glutarylcarnitine (β₁₂ = 0.0680, P = 0.002), with 30.25% of the total effect attributable to it. The robustness of these findings was further demonstrated by sensitivity analyses and SMR results. CONCLUSION: This study represents the first evidence that GCDH might exert an indirect pro-RM effect via the downregulation of glutarylcarnitine, thus providing new insights into tumor metabolic pathways and positioning glutarylcarnitine as a potentially diagnostic biomarker and therapeutic target for RM.

GCDH↗
PubMed1987

Revisiting the recurrent groin hernia.

The anatomic defects of recurrent groin hernia in 413 patients treated consecutively using the preperitoneal approach have been cataloged and the results of the repair evaluated. No specific predicting factors could be identified for most of the patients. Defects are highly variable and not at all predictable. Pure direct defects predominated (58 percent), tended to be at the tubercle (41.9 percent), and were relatively small (less than 4 cm in 77 percent of the patients). Recurrence was associated with a number of previous repairs but the rate was only 4.3 percent for the series with 11 of 18 patients having at least three repairs. The recurrence rate for first rerepair using this approach was 1.6 percent (4 of 248 patients) within 5 years for 80 percent of the patients followed. The preperitoneal approach is a useful, safe, and effective technique for the treatment of recurrent groin hernia and should be widely implemented.

Aged↗
PubMed1989

Identification of Dictyostelium discoideum plasma membrane proteins by cell surface labeling and quantitative two-dimensional gel electrophoresis.

Plasma membrane proteins of the cellular slime mold Dictyostelium discoideum were characterized by two-dimensional polyacrylamide gel electrophoresis using a variety of labeling techniques and a microcomputer-based videodensitometer. Algorithms for the determination of molecular weights and isoelectric points were developed to aid in the comparison of polypeptides from different autoradiographs, Coomassie blue-stained gels, and Western blots. Cell homogenates were compared to plasma membranes isolated by a silica density perturbation technique and to cytoskeletons obtained by nonionic detergent extraction. Plasma membrane proteins were distinguished from subcellular contaminants by lactoperoxidase-catalyzed radioiodination, by selective labeling with N-hydroxysuccinimidyl-2-iminobiotin, and by quantitatively determining the enrichments of individual polypeptides from gels of plasma membrane proteins relative to their counterparts in gels of total cell lysate proteins. In contrast to defining plasma membrane purity by measuring a representative marker enzyme activity, the quantitative two-dimensional gel analysis strategy presented allowed for a rigorous evaluation of the enrichments of all detectable polypeptides in the subcellular fraction. Quantitative two-dimensional gel analysis avoided problems encountered with marker enzyme activation or inhibition during subcellular fractionation as enrichments were based solely on polypeptide amounts. It was also capable of identifying a wider spectrum of plasma membrane proteins than any of the labeling techniques employed in this study. A high resolution two-dimensional gel catalog was generated containing information about plasma membrane protein orientation in the bilayer, association with the cytoskeleton, phosphorylation state, glycosylation state, copy number, isoelectric point, and molecular weight.

Cytoskeleton↗
PubMed1993

Management of pediatric postoperative chylothorax.

Questions persist about the management of postoperative chylothorax in infants and children. Our experience with postoperative chylothorax over the most recent decade (1980 to 1990) has been reviewed. The type and amount of drainage, data from cardiac catheterization and echocardiography, operative decisions and details, and eventual outcomes have been cataloged. All patients were initially treated with total gut rest, with operation reserved for unabated drainage. Chylothorax developed postoperatively in 15 infants and 11 children (18 with a cardiac procedure and 8 with a noncardiac procedure). The average age was 3.1 years. Spontaneous cessation and cure occurred in 19 (73.1%) of these 26 patients, with an average drainage duration of 11.9 days (range, 4 to 30 days). Those for whom operation was chosen drained preoperatively for an average of 29.2 days (range, 25 to 40 days). There were no deaths in either group. Complications were lymphopenia (2 patients) and fungal sepsis (1 patient). The amount of drainage per day was not significantly different between patients treated operatively and those treated nonoperatively. Failure of nonoperative management was associated with venous hypertension from increased right-sided cardiac pressures or central venous thrombosis (p < 0.05, Fisher's exact test). Presumably this increased pressure is transmitted to the lymphatic system. These patients should be identified early and considered for thoracic duct suture or pleuroperitoneal shunting.

Cardiac Surgical Procedures↗
PubMed1975

Nerve-impulse patterns: a quantitative display technique for three neurons.

A scatter diagram is described that displays the relative timings of nerve impulses in 3 simultaneously monitored neurons. The technique is a generalization of the cross-correlation histogram for two impulse trains. The time intervals between impulses in different neurons are plotted on triangular coordinates to yield a Joint Impulse Configuration Scatter Diagram. The resulting 'snowflake' plot shows a pattern of spots and lines, which is interpretable in terms of the functional circuitry among teh neurons. Illustrations are given of the snowflakes produced by a variety of three-neuron circuits, which may serve as a preliminary catalog of snowflake types for interpretation of experimental data.

Computers↗
PubMed1988

An image filing system for the implementation of image processing algorithms in a research environment.

An image filing system (IFS) has been written to facilitate the implementation and testing of image processing algorithms in a research environment. A programming substrate has been developed to provide applications with routines for acquiring, displaying, and manipulating images without regard for the underlying information format. Images of diverse modalities are cataloged and tracked through a series of image operations with descriptive pointers to all antecedents. This paper presents the design and implementation of the image filing system and describes one of the major image processing applications developed in the IFS environment.

Algorithms↗