bluuebunny/crossref_metadata_2025_split huggingface dataset:
ShiftDetector: detection of shift mutations
Authors: Seroussi Eyal , Ron Micha , Kedra Darek 
Published: September 2002

Abstract
Motivation: Sequencing of a bi-allelic PCR product, which contains an allele with a deletion/insertion mutation results in a superimposed tracefile following the site of this shift mutation. A trace file of this type hampers the use of current computer programs for base calling. ShiftDetector analyses a sequencing trace file in order to discover if it is a superimposed sequence of two molecules that differ in a shift mutation of 1 to 25 bases. The program calculates a probability score for the existence of such a shift and reconstructs the sequence of the original molecule.
Availability: ShiftDetector is available from http://cowry.agri.huji.ac.il
Contact: seroussi@agri.huji.ac.il
* To whom correspondence should be addressed.
Domain Fishing: a first step in protein comparative modelling
Authors: Contreras-Moreira B. , Bates P.A. 
Published: September 2002

Abstract
Summary: To optimize the search for structural templates in protein comparative modelling, the query sequence is split into domains. The initial list of templates for each domain, extracted from PFAM plus PDB and SCOP, is then ranked according to sequence identity (%ID), coverage and resolution. If %ID is less than 30, secondary structure matching is used to filter out false templates.
Availability: http://www.bmm.icnet.uk/~3djigsaw/dom_fish
Contact: b.contreras-moreira@cancer.org.ukpaul.bates@cancer.org.uk
* To whom correspondence should be addressed.
DiffTool: building, visualizing and querying protein clusters
Authors: Chetouani Farid , Glaser Philippe , Kunst Frank 
Published: September 2002

Abstract
Summary: DiffTool is a resource to build and visualize protein clusters computed from a sequence database. The package provides a clustering tool to construct protein families according to sequence similarities and a web interface to query the corresponding clusters. A subtractive genome analysis tool selects protein families specific for a genome or a group of genomes. For each protein cluster, DiffTool includes access to sequences, coloured multiple alignments and phylogenetic trees.
Availability: A cluster database built from yeast and complete prokaryotic genomes is queryable at http://bioweb.pasteur.fr/seqanal/difftool. All the Perl sources are freely available to non-profit organizations upon request.
Contact: fchetou@infobiogen.fr
* To whom correspondence should be addressed.
The NCTU BioInfo Archive of biological data sets for
bioinformatics research and experimentation
Authors: Hu Yuh-Jyh 
Published: September 2002

Abstract
Most of the current bioinformatics literature lacks an explicit and clear description of the data used in experiments when introducing or evaluating computational tools. Without the exact data set that was fed into computational tools in experiments, any mistaken preparation of the data for later experiments may lead to discrepancy in conclusion. The NCTU BioInfo Archive is a new web-based bioinformatic data archive. It serves as a test bed for evaluating computational tools, as a bridge to link other research communities with bioinformatics, and also as an environment full of motivations and possibilities to encourage more exploratory research in bioinformatics.
Availability: http://bioinfo.cis.nctu.edu.tw
Contact: yhu@cis.nctu.edu.tw
The EBI SRS server—new features
Authors: Zdobnov Evgeny M. , Lopez Rodrigo , Apweiler Rolf , Etzold Thure 
Published: September 2002

Abstract
Motivation: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ‘Nice views’, SRSQuickSearch bookmarklets.
Availability: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.
Contact: EBISRS@ebi.ac.uk
Is posthumous semen retrieval ethically permissible?
Authors: Orr R D , Siegler M 
Published: September 2002

It is possible to retrieve viable sperm from a dying man or from a recently dead body. This sperm can be frozen for later use by his wife or partner to produce his genetic offspring. But the technical feasibility alone does not morally justify such an endeavour. Posthumous semen retrieval raises questions about consent, the respectful treatment of the dead body, and the welfare of the child to be.We present two cases, discuss these three issues, and conclude that such requests should generally not be honoured unless there is convincing evidence that the dead man would want his widow to carry and bear his child. Even with consent, the welfare of the potential child must be considered.
Pushing and pulling in association with low back and shoulder complaints
Authors: Hoozemans M J M , van der Beek A J , Frings-Dresen M H W , van der Woude L H V , van Dijk F J H 
Published: September 2002

Aims:To examine the association between exposure to pushing/pulling at work and low back and shoulder complaints.Methods:A cross sectional questionnaire survey was carried out among 434 workers from several companies with mainly pushing/pulling tasks. From the same companies 188 workers without physically demanding tasks served as reference. The questionnaire was used to assess the exposure to pushing/pulling and other physical risk factors for low back and shoulder complaints. Mean scores at company level were used to classify groups into medium and high exposed to pushing/pulling and a reference group. Psychosocial factors at work were also assessed. Several pain related questionnaires were used to assess the 12 month prevalence of low back and shoulder complaints in three dimensions: trouble (ache, pain, discomfort), pain intensity, and disability. Prevalence rate ratios (PRs) were calculated using Cox’s proportional hazards regression analysis.Results:The 12 month prevalence of low back complaints was almost equal for all three groups. The prevalence of shoulder complaints increased with an increase in exposure level. Adjusted PRs showed that the high exposed group had an increased risk for low back complaints compared to the reference group. For all dimensions of shoulder complaints a clear tendency towards a dose–response relation was observed. The high exposed group had significant PRs for shoulder complaints, ranging from 2.09 to 6.37. Generally, psychosocial factors had a confounding effect for pain intensity and disability, but not for trouble.Conclusions:For shoulder complaints a dose–response relation was observed for exposure to pushing/pulling. Low back complaints were less consistently associated with pushing/pulling. Stronger associations were observed for more severe cases of low back and shoulder complaints. It is hypothesised that work related psychosocial factors affect these associations.
HIV associated thrombotic microangiopathy
Authors: Ahmed S , Siddiqui R K , Siddiqui A K , Zaidi S A , Cervia J 
Published: September 2002

Abstract
Thrombotic microangiopathy (TMA) is a known complication of HIV infection. Endothelial cell injury appears to be the primary event causing platelet activation and deposition in the microvasculature. Direct cytopathic roles of HIV as well as other factors such as malignancy, drugs, and infectious agents have been implicated in the pathogenesis of HIV-TMA. Although the the majority of patients present in a more advanced stage of HIV disease, TMA can be the initial presenting symptom of HIV infection. Clinical features are those of idiopathic TMA, and the diagnosis should be suspected in any patient with new onset thrombocytopenia and microangiopathic haemolytic anaemia. Therapy with plasma exchange or infusion appears to be efficacious. A rapid diagnosis and institution of plasmapheresis is crucial for a favourable outcome. The long term prognosis of HIV-TMA is unfavourable and may depend on the stage of HIV infection. The recent data after the use of highly active retroviral treatment, however, are unavailable and current prognosis is therefore uncertain.
Early recognition of diabetic neuropathy: evaluation of a simple outpatient procedure using thermal perception
Authors: Viswanathan V , Snehalatha C , Seena R , Ramachandran A 
Published: September 2002

Abstract

Objective
To determine the effectiveness of Tip-therm, a temperature discriminator, in making an early diagnosis of distal symmetrical polyneuropathy in diabetic patients and to compare its effectiveness with the Semmes-Weinstein monofilament and biothesiometry, which are established methods of diagnosing neuropathy in diabetic patients.

Patients and methods
From the diabetic subjects who came to the hospital for review, 910 consecutive cases were selected. All were tested with the Semmes-Weinstein monofilament (10 g monofilament) and biothesiometry and also by using the Tip-therm for comparison.

Results
Out of the 241 patients who had no sensation to the monofilament only four (1.7%) felt Tip-therm whereas 237 (98.3%) patients could not feel Tip-therm. Among 298 patients diagnosed as having neuropathy by biothesiometry, only eight (2.7%) patients exhibited sensation with Tip-therm while 290 (97.3%) patients could not feel it.

Conclusion
A simple device, Tip-therm, which tests for temperature discrimination, was compared with two validated methods for detection of neuropathy—a monofilament and biothesiometry. Tip-therm appears to be an inexpensive, highly sensitive, and specific device for detection of diabetic neuropathy when compared with biothesiometry and a monofilament.
National audit of the management of peritonsillar abscess
Authors: Mehanna H M , Al-Bahnasawi L , White A 
Published: September 2002

AbstractAn anonymous postal survey of 200 consultants was used to audit the current prevalent practices in the management of quinsy in the UK; 101 responded. The findings reveal that on average an otolaryngology department treats 29 cases per year, the vast majority (94%) on an inpatient basis. The main initial treatment was needle aspiration combined with intravenous antibiotics. Interestingly, those departments treating more than 20 cases a year are more likely to use needle aspiration, while departments in England and Wales use significantly more incision and drainage than those in Scotland. Incision and drainage (52%) was the most common form of treatment of non-resolving patients. The median hospital stay was two days.
Randomised controlled trials investigating pharmacological and psychological interventions for treatment-refractory depression
Authors: Stimpson Nicola , Agrawal Niruj , Lewis Glyn 
Published: September 2002

BackgroundAbout 30% of people with depression do not respond to an antidepressant at the recommended dose and can be described as having treatment-refractory depression.AimsTo summarise the findings from all randomised controlled trials (RCTs) that have assessed the efficacy of a pharmacological or psychological intervention for treatment-refractory depression.MethodWe used a systematic search strategy to identify RCTs that included adults aged 18–75 years with a diagnosis of unipolar depression that had not responded to a 4-week course of a recommended dose of an antidepressant.ResultsWe identified 16 RCTs. None of the included trials assessed the efficacy of psychotherapy. All the trials were too small to detect an important clinical response. We found only two trials on lithium augmentation, which randomised 50 subjects in total.ConclusionsThere is little evidence to guide the management of depression that has not responded to a course of antidepressants. Treatment-refractory depression is an important public health problem and large pragmatic trials are needed to inform clinical practice.
Getting the point: electrophysiological correlates of protodeclarative pointing
Authors: Henderson Lynnette M. , Yoder Paul J. , Yale Marygrace E. , McDuffie Andrea 
Published: September 2002

AbstractWe examined the longitudinal relationships between power data in two bands (i.e. 4–6 and 6–9 Hz) of electrical activity in the brain at 14 months, as measured by background electroencephalograms (EEG), with protodeclarative and protoimperative pointing at 18 months, as measured by the Early Social Communication Scales (ESCS), [Mundy et al., ESCS: A Preliminary Manual for the Abridged Early Social Communication Scales, 1996, unpublished manual] (n=27). EEGs were recorded from 64 sensors using the Electrical Geodesics (EGI) system's dense array sensor nets. Multivariate permutation testing (MPT), which controlled for experiment‐wise error due to multiple significance tests, revealed significant correlations between log‐transformed power in the frontal region at 14 months and protodeclarative, but not protoimperative, pointing at 18 months.
Language transactions during development and intervention: theoretical implications for developmental neuroscience
Authors: Camarata Stephen , Yoder Paul 
Published: September 2002

AbstractRecent modeling of language development and intervention for children with disabilities has increasingly focused on the interactions between adults and children. These models have resulted in a number of recent advances in the behavioral treatment of language abilities in children with disabilities. Because these interventions are associated with substantial growth in a number of skills including speech, grammar and vocabulary, these paradigms may provide a useful model for studying neurological development of these aspects of language. The purpose of this paper is to discuss the potential neurodevelopmental ramifications of this type of theoretical model for facilitating language growth in children with and without disabilities. Indeed, because intervention can sometimes trigger rapid advances in language skills and presumably, associated neurological organization, this may prove to be a very useful paradigm for understanding the neurological correlates of language growth.
Alexander disease: a review and the gene
Authors: Johnson Anne B. 
Published: September 2002

AbstractThis review presents historical and clinical information on the rare human brain disorder known as Alexander disease (ALX), and reports on the recent discovery of the gene that appears to be causative. The disease is a fatal, white matter disorder (leukodystrophy) of childhood. Adult onset cases also have been described, but it has not been clear whether they represent the same disease. Until recently the diagnosis was made by the pathological examination of brain tissue, in which abundant Rosenthal fibers were found. These abnormal structures occurred within astrocytes, but their composition was unclear. In 1985, a child underwent a diagnostic brain biopsy at this institution, which established the diagnosis of ALX. Ultrastructural immunocytochemistry revealed that the Rosenthal fibers contained abundant amounts of glial fibrillary acidic protein (GFAP), a normal component of astocytic intermediate filaments. Thus, the gene for this filament protein was considered a candidate gene for the cause of ALX, and DNA samples from children presumed or proven to have this disorder were banked for future study. Other work on the same brain biopsy showed that Rosenthal fibers also contained abundant αB‐crystallin, a heat shock protein, but no defect was found in its gene. A decade after the biopsy, a transgenic mouse with an extra copy of the gene for GFAP was produced. These mice died early and their brains contained Rosenthal fibers. Although not an exact model for ALX, this also suggested that the gene for GFAP should be considered a candidate gene for ALX. Subsequent research has demonstrated that the great majority of childhood ALX cases contain mutations in the gene for GFAP. This work is now being extended as a diagnostic test, as well as to seek understanding of the pathogenesis of ALX and possible approaches for treatment.
Gene structure and genetic localization of the PCLO gene encoding the presynaptic active zone protein Piccolo
Authors: Fenster Steven D. , Garner Craig C. 
Published: September 2002

AbstractPiccolo belongs to a family of presynaptic cytoskeletal proteins likely to be involved in the assembly and function of presynaptic active zones as sites of neurotransmitter release. Given that abnormalities in the formation of synaptic junctions are thought to contribute to cognitive dysfunction during brain development, we have analyzed and compared the gene structure of the Piccolo gene, PCLO, from humans and mice and determined their chromosomal localization. A comparison of the deduced amino acid sequence of cDNA clones encoding Piccolo from human, mouse, rat and chicken reveals the presence of distinct homology domains. Only subsets of these are also present in the structurally related active zone protein Bassoon indicating that Piccolo and Bassoon perform related but distinct functions at active zones. Characterization of the PCLO gene reveals the presence of 25 coding exons spread over 380 kb of genomic DNA. The human PCLO gene maps to 7q11.23‐q21.3, a region of chromosome 7 implicated as a linkage site for autism and Williams Syndrome suggesting that alterations in the expression of Piccolo or the PCLO gene could contribute to developmental disabilities and mental retardation.
Functions of PI 3‐kinase in development of the nervous system
Authors: Rodgers Erin E. , Theibert Anne B. 
Published: September 2002

AbstractIn the nervous system, receptor regulated phosphoinositide (PI) 3‐kinases (PI 3‐kinases) participate in fundamental cellular activities that underlie development. Activated by trophic factors, growth factors, neuregulins, cytokines, or neurotransmitters, PI 3‐kinases have been implicated in neuronal and glial survival and differentiation. PI 3‐kinases produce inositol lipid second messengers that bind to pleckstrin homology (PH) domains in diverse groups of signal transduction proteins, and control their enzymatic activities, subcellular membrane localization, or both. Downstream targets of the inositol lipid messengers include protein kinases and regulators of small GTPases. The kinase Akt/PKB functions as a key component of the PI 3‐kinase dependent survival pathway through its phosphorylation and regulation of apoptotic proteins and transcription factors. Furthermore, since members of the Rho GTPase and Arf GTPase families have been implicated in regulation of the actin cytoskeleton, vesicular trafficking, and transcription, the downstream targets of PI 3‐kinase that control these GTPases are excellent candidates to mediate aspects of PI 3‐kinase dependent neuronal and glial differentiation.
Modulation of glial glutamate transport through cell interactions with the extracellular matrix
Authors: Ye Zu‐Cheng , Sontheimer Harald 
Published: September 2002

AbstractGlial glutamate transport plays a pivotal role in maintaining glutamate homeostasis in the central nervous system. Expression of glutamate transporters is highly regulated during brain development, and a number of pathological conditions are associated with deficits in expression and/or function of glutamate transports. While several soluble factors have been shown to regulate the expression of glutamate transporter, the contribution of cell–cell interaction and cell–environmental interaction in the regulation of glutamate transport is unknown. Extracellular matrix (ECM) molecules are essential components in cell–cell and cell–environmental interactions, and the ECM has been shown to play critical role in normal development and during brain pathogenesis. We, therefore, investigated the possibility that ECM molecules may regulate astrocytic glutamate transport. Therefore, we cultured rat cortical astrocytes with different ECMs and determined expression levels of the two astrocytic glutamate transporters GLT‐1 and GLAST by Western Blot and determined transporter activity through measurements of 3H‐d‐aspartate uptake. Astrocytes grown on poly‐ornithine or poly‐d/l‐lysine showed approximately two‐fold higher GLT‐1 expression than sister cells grown on plastic dishes without ECM. Naturally occurring ECM's, including laminin and collagen, showed a dose‐dependent regulation of GLT‐1 protein expression. These effects were specific for GLT‐1 as GLAST expression was unaffected by different ECMs. Surprisingly, however, none of the examined ECMs altered the apparent glutamate uptake activity. In probing blots side‐by‐side for expression of Na+/K+‐ATPase, we found that ECMs affected expression of Na+/K+‐ATPase and GLT‐1 in a reciprocal fashion. Poly‐ornithine, for example, enhanced GLT‐1 expression, but reduced expression of Na+/K+‐ATPase. Na+ transport may, thus, be a limiting factor for glutamate uptake.
22q11 DS: genomic mechanisms and gene function in DiGeorge/velocardiofacial syndrome
Authors: Maynard Thomas M. , Haskell Gloria T. , Lieberman Jeffrey A. , LaMantia Anthony‐Samuel 
Published: September 2002

Abstract22q11 deletion syndrome (22qDS), also known as DiGeorge or velocardiofacial syndrome (DGS/VCFS), is a relatively common genetic anomaly that results in malformations of the heart, face and limbs. In addition, patients with 22qDS are at significant risk for psychiatric disorders as well, with one in four developing schizophrenia, and one in six developing major depressive disorders. Like several other deletion syndromes associated with psychiatric or cognitive problems, it has been difficult to determine which of the specific genes in this genomic region may mediate the syndrome. For example, patients with different genomic deletions within the 22q11 region have been found that have similar phenotypes, even though their deletions do not compromise the same set of genes. In this review, we discuss the individual genes found in the region of 22q11 that is commonly deleted in 22qDS patients, and the potential roles each of these genes may play in the syndrome. Although many of these genes are interesting candidates by themselves, we hypothesize that the full spectrum of anomalies associated with 22qDS may result from the combined result of disruptions to numerous genes within the region that are involved in similar developmental or cellular processes.