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PubMedDate not supplied

Research methodology and applied statistics. Part 2: the literature search.

This paper presents a basic methodology for an effective and efficient retrieval and recording of written materials in a subject area. The purpose of the literature review is examined and the criteria for selection of materials for inclusion are outlined. The methodology then describes the role of the librarian, various types of information resources, how to choose appropriate indexing and abstracting services, and a simple efficient method of recording the items found. The importance and use of Medical Subject Headings for research in physiotherapy is emphasized. A survey of types of book materials and how to locate them is followed by a detailed description of the most useful indexing and abstracting services available, in particular, the publications of the National Library of Medicine, notably Index Medicus, as well as Excerpta Medica and the Science Citation Index. A discussion of on-line search services, their coverage and availability in Canada, concludes the review of information sources. Finally, guidelines for selecting and summarizing the materials located and comments on the literary style for a review are supplied.

Documentation↗
PubMed1999

Inventory management and reagent supply for automated chemistry.

Developments in automated chemistry have kept pace with developments in HTS such that hundreds of thousands of new compounds can be rapidly synthesized in the belief that the greater the number and diversity of compounds that can be screened, the more successful HTS will be. The increasing use of automation for Multiple Parallel Synthesis (MPS) and the move to automated combinatorial library production is placing an overwhelming burden on the management of reagents. Although automation has improved the efficiency of the processes involved in compound synthesis, the bottleneck has shifted to ordering, collating and preparing reagents for automated chemistry resulting in loss of time, materials and momentum. Major efficiencies have already been made in the area of compound management for high throughput screening. Most of these efficiencies have been achieved with sophisticated library management systems using advanced engineering and data handling for the storage, tracking and retrieval of millions of compounds. The Automation Partnership has already provided many of the top pharmaceutical companies with modular automated storage, preparation and retrieval systems to manage compound libraries for high throughput screening. This article describes how these systems may be implemented to solve the specific problems of inventory management and reagent supply for automated chemistry.

Automation↗
PubMed1993

Identification of a tumor marker chromosome by flow sorting, DNA amplification in vitro, and in situ hybridization of the amplified product.

A method combining flow sorting and molecular cytogenetic techniques for the identification of unknown marker chromosomes is described. In this study, the bladder tumor cell line J82 was used, which was known to carry a marker chromosome of the size of chromosome 7 in every cell. From the cytogenetic analysis of Q-banded metaphase cells, it was shown to be composed of approximately 40% presumably the greater part of chromosome 20 and for the rest microscopically unidentifiable material. This marker chromosome was found using flow cytometric analysis to form an independent peak and hence was suitable for isolation using dual-parameter sorting after staining with Hoechst 33258 and chromomycin A3. Subsequently, the marker was isolated by dual-parameter sorting. DNA amplification of 300 isolated chromosomes by polymerase chain reaction (PCR) using the Alu-primer Bk33 and the LINES-primer LH5 was carried out. After purification of the amplified product, a yield of 5 microns of DNA was obtained. The DNA was labelled using Bio-11-dUTP and applied to human lymphocyte metaphase cells in a suppressive in situ hybridization procedure. Fluorescence was visible over chromosome 20 and over the distal one-half of 6p. Together the fluorescent regions accounted for only approximately 60% of the marker length, indicating a possible duplication of chromosome 20 material. This was confirmed by applying bicolor in situ hybridization using chromosome 6- and 20-specific DNA libraries to metaphase cells of the J82 cells.

Aneuploidy↗
PubMed2004

Comparative analysis of prostate-specific membrane antigen (PSMA) versus a prostate-specific membrane antigen-like gene.

BACKGROUND: Currently prostate-specific membrane antigen (PSMA) is showing promise both as an imaging and therapeutic target for occult prostate cancer metastases. First generation antibodies against PSMA are used for the FDA approved Prostascint trade mark monoclonal antibody scan and second generation antibodies are being developed for therapeutic targeting as well as imaging 1. However, there have been reports describing PSMA expression in non-prostatic tissues including kidney, liver, and brain. As we had previously showed the existence of a human PSMA homolog, we set out to determine if this non-prostatic expression was due to expression of the PSMA or another gene. MATERIALS AND METHODS: The PSMA homolog (PSMA-like) cDNA was cloned by screening a liver cDNA library. mRNA expression of the PSMA and PSMA-like genes was determined via Northern blot analysis using two different probes and protein expression confirmed in some tissues via Western blot analysis. Transcriptional regulation of the two genes was examined using reporter constructs driving luciferase expression. RESULTS: The PSMA-like gene possesses 98% identity to the PSMA gene at the nucleotide level and is expressed in kidney and liver under the control of a different promoter to the PSMA gene. The PSMA gene is expressed in several human tissues and is most abundant in the nervous system and the prostate. CONCLUSION: The non-prostatic expression of PSMA should be taken into consideration when designing clinical strategies targeting PSMA.

Antibodies, Monoclonal↗
PubMed2002

Increased expression of the acid sphingomyelinase-like protein ASML3a in bladder tumors.

PURPOSE: The function of the tumor suppressor gene DBCCR1 (deleted in bladder cancer chromosome region 1) is unknown despite data supporting an important role for DBCCR1 in bladder tumorigenesis. DBCCR1 has not yet been placed in a protein family or functional pathway. Protein-protein interactions are crucial for almost every aspect of cellular function. We hypothesized that the discovery of DBCCR1 protein binding partners would yield important clues for solving the mystery of DBCCR1 function. MATERIALS AND METHODS: We used the yeast 2-hybrid system to screen an adult human bladder cDNA library for DBCCR1 interacting proteins. RESULTS: In the screen ASML3a (acid sphingomyelinase-like phosphodiesterase 3a) was identified as a novel DBCCR1 binding partner. Transient transfection of bladder tumor cell lines showed that DBCCR1 over expression in human bladder tumor cells results in the up-regulation of ASML3a RNA and protein expression. ASML3a protein was also differentially expressed in 8 of 12 bladder tumors relative to corresponding normal urothelial tissue. CONCLUSIONS: It appears that DBCCR1 and ASML3a are involved in the process of bladder tumorigenesis. Their interaction may provide clues to discern their functions.

3T3 Cells↗
PubMed2005

Solid-phase synthesis of N-formylhydroxylamines (reverse/retro-hydroxamates).

N-Formylhydroxylamines, also known as reverse- or retro-hydroxamates, have become of significant interest in the recent past as inhibitors of metalloenzymes. Although solution-phase synthetic routes to such compounds have been reported, these are often lengthy and involve purification at each stage. Herein, novel three-step solid-phase synthetic approaches are described that enable libraries of such compounds to be produced in a convergent and efficient manner using commercially available starting materials. [reaction: see text]

Combinatorial Chemistry Techniques↗
PubMed2026

A systematic approach to standardizing the visual appearance of endometriotic lesions for artificial intelligence recognition.

INTRODUCTION: Numerous studies have shown that the diagnostic performance and reproducibility of visual recognition of endometriosis during laparoscopy are poor. The use of artificial intelligence (AI) seems relevant for exhaustive lesion recognition. Standardization of the visual classification of lesions, in the form of an ontology, is an essential prerequisite to enable medical experts to annotate surgical data consistently and subsequently allow engineers to train and build an artificial intelligence tool for endometriosis recognition. MATERIAL AND METHODS: A systematic search was conducted in the MEDLINE (via PubMed), EMBASE, and the Cochrane Library databases up to May 2022, aiming to identify studies describing the laparoscopic visual appearance of superficial endometriosis, endometriomas, and deep infiltrating endometriosis. The accumulated data in the literature concerning the visual appearance of the different forms of endometriosis were used to create an ontology that could be used for artificial intelligence applications. RESULTS: Out of 932 articles screened, 35 studies were selected based on the inclusion criteria of human subjects with histologically confirmed endometriosis lesions visualized via laparoscopy. The selected studies were reviewed to develop a visual ontology of endometriosis lesions observed via laparoscopy. The lesions were categorized into 4 classes and further subdivided into 11 subclasses: superficial (black, red, white, or subtle), adhesions (dense or filmy), deep (obliteration, retraction, or deformation), and ovarian (endometrioma or chocolate fluid). The positive predictive value (PPV) varied across lesion types: black lesions (PPV 47%-97%), red lesions (PPV 33%-100%), white lesions (PPV 20%-81%), and ovarian endometriosis (PPV 42%-98%). Nonspecific lesions such as adhesions (PPV 16%-50%) and subtle superficial lesions (PPV 0%-67%) presented lower PPVs. Deep endometriosis lesions, often buried within organs, required indirect signs (obliteration, retraction, deformation) for identification. CONCLUSIONS: The visual ontology proposed in this systematic search could facilitate the detection and classification of endometriosis lesions using artificial intelligence. This study highlights the challenges of reaching a consensus on lesion recognition and classification in AI projects due to the diverse visual presentations of endometriosis.

Humans↗
PubMed1997

A novel case of unilateral blepharophimosis syndrome and mental retardation associated with de novo trisomy for chromosome 3q.

We have evaluated a 3 2/12 year old girl who presented with unilateral blepharophimosis, ptosis of the eyelid, and mental retardation. Additional dysmorphic features include microcephaly, high, narrow forehead, short stubby fingers, and adduction of the right first toe. Cytogenetic analysis showed an unbalanced karyotype consisting of 46,XX,add(7)(q+) that was de novo in origin. Fluorescence in situ hybridisation (FISH) using microdissected library probe pools from chromosomes 1,2,3,7, and 3q26-qter showed that the additional material on 7q was derived from the distal end of the long arm of chromosome 3. Our results indicate that the patient had an unbalanced translocation, 46,XX,der(7)t(3;7)(q26-qter;q+) which resulted in trisomy for distal 3q. All currently reported cases of BPES (blepharophimosis-ptosis-epicanthus inversus syndrome) with associated cytogenetic abnormalities show interstitial deletions or balanced translocations involving 3q22-q23 or 3p25.3. Our patient shares similar features to BPES, except for the unilateral ptosis and absence of epicanthus inversus. It is possible that our patient has a contiguous gene defect including at least one locus for a type of blepharophimosis, further suggesting that multiple loci exist for eyelid development.

Adult↗
PubMed1996

Satellite-delivered medical education and training for central Europe: a TEMPUS project. Trans-European Mobility Programme for University Students.

This paper reports the experience gained in delivering continuing and postgraduate medical education by satellite to update medical teachers in Central Europe. An infrastructure of receiving sites was established in the Czech Republic, Slovakia, Poland and Hungary. The sites participated in regular, live interactive broadcasts on a range of medical education topics. Over three years a network of sites was established incrementally and a national coordinator identified for each country, who fed back from national coordinating committees to an overall steering body. In the final year a formal evaluation revealed high satisfaction levels and maintenance of activity during the grant period. The major problems related to a lack of telephone lines to facilitate interactivity, the timing of the programmes, and the need for training in medical English language. Video libraries were established, and the majority continued to be active at the end of the project grant. Material was incorporated into both undergraduate and postgraduate education. It is calculated that continuing professional development can be delivered at less than 18 ECU per participant per country.

Curriculum↗
PubMed2003

[Acute and chronic injuries after electrical accidents].

BACKGROUND: Electrical accidents are potentially fatal incidents with effect on the cardiovascular, nerve and musculoskeletal systems and on the skin (burns). The electrical engineering industry points out that the follow-up of injured persons from site of accident to hospital is quite random. This paper gives a review of the current literature and proposes guidelines for the follow-up of victims of electrical accidents. MATERIAL AND METHOD: A search of the literature was conducted on Medline, Embase, Biosis, Healthline, the Cochrane Library, the ISI citation databases, and on several other search engines. The revised guidelines were developed in consultation with 23 medical and industry institutions. RESULTS AND INTERPRETATION: Serious acute effects of electrical accidents include cardiac arrest, respiration failure, burns (also (internal burns) with necrosis of e.g. muscle tissue), injuries to the nerve system, and renal failure. Traumas caused by falls are also frequent. Possible chronic effects are mostly seen in the nerve system as encephalopathy and psychological sequelae or as spinal cord and peripheral nerve injury. Most importantly, long latent periods are possible for some chronic nerve injuries. This paper suggest guidelines for acute (on the spot) action and criteria for referral to hospital, observation in hospital and further follow-up.

Accidents↗
PubMed1996

Molecular cloning, chromosomal mapping, and characterization of the human cardiac-specific homeobox gene hCsx.

BACKGROUND: Csx/Nkx2.5, a murine nonclustered homeobox gene expressed primarily in the heart, has significant sequence similarity to the Drosophila tinman gene. Tinman is essential for heart and gut formation in Drosophila. Targeted mutation in the mouse gene, Csx/Nkx2.5, arrests cardiac development during early embryonic stages, suggesting an evolutionary conservation in cardiogenesis. MATERIALS AND METHODS: We have isolated and characterized a human homolog, hCsx, from an adult cardiac cDNA library. Northern blotting and ribonuclease protection was used to define the pattern of expression during normal development and in disease states. Chromosomal localization of the gene was determined by somatic cell hybrid analysis and fluorescent in situ hybridization. RESULTS: The predicted amino acid sequence of hCsx has 87% overall homology to the murine gene with 100% identity in the homeodomain. The homeodomain sequence of hCsx is 95% identical to its Xenopus homolog, and 65% to tinman. hCsx mRNA was detected exclusively in the heart. hCsx transcript was detected at 12 weeks in human embryonic heart, the earliest time point examined, and was up-regulated 5-fold between 12 and 19 weeks. There was no significant alteration of hCsx message level in the myocardium of 14 patients with end stage heart failure compared to a normal control. The human gene mapped to the distal portion of chromosome 5, the 5q34-q35 region. This defines a new synteny region between human chromosome 5q and the t-locus of mouse chromosome 17, where the mouse Csx gene is located. CONCLUSIONS: hCsx, the human homolog of Drosophila tinman, is expressed in heart in a tissue restricted manner. Distal 5q trisomies produce several phenotypic abnormalities, including a high incidence of congenital heart disease. Isolation of the hCsx gene will allow further studies of mutations in this gene and their potential associations with some forms of congenital heart disease in humans.

Amino Acid Sequence↗
PubMed2006

Antibody molecules discriminate between crystalline facets of a gallium arsenide semiconductor.

Seamless integration of biomolecules with manmade materials will most likely rely on molecular recognition and specific binding. In the following we show that combinatorial antibody libraries, based on the vast repertoire of the human immune system, can be harnessed to generate such binders. As a demonstration, we isolate antibody fragments that discriminate and bind selectively GaAs (111A) facets as opposed to GaAs (100). The isolated antibodies are utilized for exclusive localization of a fluorescent dye on (111A) surfaces in a structure comprising a mixture of (100) and (111A) surfaces. The potential importance of structure rigidity to facet recognition is suggested vis-a-vis published experiments with short and longer peptides.

Antibodies↗
PubMed2004

Mimotopes for lupus-derived anti-DNA and nucleosome-specific autoantibodies selected from random peptide phage display libraries: facts and follies.

Autoantibodies against chromatin are the most characteristic serological feature in SLE patients. Anti-dsDNA and nucleosome-specific antibodies are associated with glomerulonephritis, the most serious manifestation of SLE. Identification of peptides mimicking conformational epitopes (so-called mimotopes) on the nucleosome recognized by these antibodies is of considerable interest. Using an approach similar to that used previously to characterize mimotopes for anti-DNA autoantibodies, we have selected and identified a mimotope for a nucleosome-specific autoantibody (#32) by screening a random peptide phage display library. However, the reactivity of monoclonal antibody (mAb) #32 with the selected mimotope (MIMO#0) in ELISA was dependent on the blocking reagents used. Using nonfat dry milk (5%), mAb #32 clearly bound to MIMO#0, but using fetal bovine calf serum (FCS) (5%), there was no binding. Furthermore, again dependent on the blocking reagent used in ELISA, the selected mimotope MIMO#0 was not only recognized by the selecting antibody mAb #32, but also by a large number of other monoclonal anti-DNA, anti-histone and nucleosome-specific autoantibodies (NSA). We could demonstrate that the selected mimotope was able to bind directly to nucleosomal material (DNA/histone complexes) and labeled DNA. This finding was extended to other previously identified mimotopes for anti-DNA autoantibodies. We conclude that nucleosomal material (DNA/histone complexes), derived from reagents used during the mimotope selection procedure, resulted in the selection of DNA-binding peptides from the phage display library, rather than mimotopes. In addition, we could demonstrate that blocking reagents greatly influence the reactivity of anti-DNA, anti-histone and nucleosome-specific autoantibodies in ELISA. Development of blocking reagents devoid of nucleosomal material (DNA/histone complexes) is urgently needed for assay systems in which anti-nuclear autoantibodies are tested.

Amino Acid Motifs↗
PubMed1999

The analysis of peculiar urinary (and other) calculi: an endless source of challenge.

The exact composition of calculi is clinically important, but many specimens are not examined, with resultant loss of important information. We describe the incidence and nature of false stones, peculiar calculi and crystals growing on surprising materials. We studied 3100 calculi (97% urinary, 2% digestive and 1% others). Fourier transform infrared spectroscopy was used to identify calculi by detailed comparison with libraries of reference spectra. We also used UV-visible spectroscopy, nuclear magnetic resonance and gas chromatography-mass spectrometry for specific situations. Among 3100 calculi, 154 (5%) had an unusual composition; 101 specimens (3.3%) were false calculi or artifacts, 31 (1%) contained drugs or metabolites and 22 (0.7%) corresponded to crystallizations around other materials. The findings contribute to immediate patient management and to advances in scientific and medical knowledge. We conclude that the analysis of all calculi must be carried out, to determine their composition, and an efficient strategy must be used.

Calculi↗
PubMed2002

[Cloning a gene related to resistance to TuMV in cabbage].

A cDNA library was constructed from cabbage 84075 which resists TuMV. The degenerate primers was designed with the disease resistance gene conservative domain (NBS-LRR). The fragments of 513 bp were amplified by RT-PCR and genomic DNA PCR from resistant material 84075, then cloned and sequenced. Two recombinants which are highly homologous with the resistance genes cloned in other plants were used as probes, (named as Bor1, Bor2), the cDNA library was screened. A positive clone was obtained, named as TuR2, whose length was 762 bp, which encodes 226 amino acids, contains a long 681 bp open reading frame (ORF), and has different homology score of amino acid compared with the cloned resistance disease genes of other plants. TuR2 was used as probe. Southern blotting hybridization with genomic DNA shows that TuR2 is probably present in single copy; No. rthern blotting hybridization with RNA shows that the gene expression is constitutive and not differential in every part of the resistance plant 84075, the result of separating detection in F2 population shows that TuR2 gene is probably related to resistance to TuMV in cabbage.

Amino Acid Sequence↗
PubMed2025

Whole-Genome Bisulfite Sequencing with a Small Amount of DNA.

Whole-genome bisulfite sequencing (WGBS) is the most widely used method to study DNA methylation profiles across the genome. Since the bisulfite reaction causes DNA degradation, a new approach called post-bisulfite adapter tagging (PBAT) was developed to overcome this problem by adding adapters after bisulfite treatment. In mammals, the PBAT method is used for single-cell bisulfite sequencing (scBS-seq), which enables DNA methylation analysis using a very small amount of DNA from only a few cells, including single-cell input. This protocol involves bisulfite conversion, followed by preamplification and tagging with random hexamer primers prior to Illumina library preparation. Since many procedures are completed in one single test tube, the loss of DNA can be minimized, enabling highly sensitive experiments to study DNA methylation profiles from a very small amount of input material.

Sulfites↗
PubMed1987

Ethics in health sciences librarianship.

Against a background of discussion about drafting of an ethical code for librarians and a review of articles confronting ethical issues in librarianship, the authors surveyed the 150 institutional members of the Health Science Librarians of Illinois (HSLI) regarding their perceptions of ethical concerns. Among the issues addressed in the survey are library organization, personnel policies, and professional competency, along with the traditional concerns of professional versus personal values, privacy and confidentiality, access to materials, and materials selection criteria in a health sciences context. Based on a 60% response rate, survey results indicate widespread agreement on some issues and a conspicuous lack of consensus on others. Further research is suggested in order to assess the need for a separate ethical code for health sciences librarians.

Attitude↗
PubMed1982

The use of learning resource centers in the teaching of pulmonary medicine.

Learning resource centers (LRC) are areas designed for individual study which contain a variety of self-instructional materials. To evaluate the use of LRC in teaching pulmonary medicine, a survey was conducted of medical school pulmonary sections; responses were obtained from 30 sections with an NHLBI pulmonary Academic Award (PAA groups), and 21 sections without PAA (non-PAA group). LRC were established in 77 percent of the PAA group but only 14 percent of the non-PAA group. A higher percentage of pulmonary fellows than students used the resource center and student use was higher when the LRC was formally integrated into the curriculum. Textbooks and journals were more heavily used than materials utilizing audiovisual educational techniques. The results of this study suggest that pulmonary LRC use is modest, LRC cost is high, and LRC educational value may not be superior to general medical libraries.

Academic Medical Centers↗