bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracembler – software for in-silico chromosome walking in unassembled genomes
Authors: Dong Qunfeng , Wilkerson Matthew D , Brendel Volker 
Published: May 2007

Abstract

Background
Whole genome shotgun sequencing produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. We have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user.

Results

Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. We demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus.

Conclusion

Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations.
Advancing translational research with the Semantic Web
Authors: Ruttenberg Alan , Clark Tim , Bug William , Samwald Matthias , Bodenreider Olivier , Chen Helen , Doherty Donald , Forsberg Kerstin , Gao Yong , Kashyap Vipul , Kinoshita June , Luciano Joanne , Marshall M Scott , Ogbuji Chimezie , Rees Jonathan , Stephens Susie , Wong Gwendolyn T , Wu Elizabeth , Zaccagnini Davide , Hongsermeier Tonya , Neumann Eric , Herman Ivan , Cheung Kei-Hoi 
Published: May 2007

AbstractBackgroundA fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthenTranslational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature.ResultsWe present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine.ConclusionSemantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics
Authors: Smith Andrew K , Cheung Kei-Hoi , Yip Kevin Y , Schultz Martin , Gerstein Mark B 
Published: May 2007

AbstractBackgroundA key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among them. These relationships are sometimes simple (e.g. synonyms) but are often more complex (e.g. one-to-many relationships in protein family membership).ResultsWe have built a software system called LinkHub using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. For efficiency, we also provide relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; we have used LinkHub to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as "connecting glue" between different identifier spaces. We demonstrate this with example queries discovering "interologs" of yeast protein interactions in the worm and exploring the relationship between gene essentiality and pseudogene content. We also show how "protein family based" retrieval of documents can be achieved. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code.ConclusionLinkHub leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data.
Discovery and characterization of 91 novel transcripts expressed in cattle placenta
Authors: Kumar Charu G , Larson Joshua H , Band Mark R , Lewin Harris A 
Published: May 2007

Abstract

Background
Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions.

Results
A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions.

Conclusion
The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.
Fibrillary glomerulonephritis with small fibrils in a patient with the antiphospholipid antibody syndrome successfully treated with immunosuppressive therapy
Authors: Javaid Muhammad M , Denley Helen , Tagboto Senyo 
Published: May 2007

Abstract

Background
Fibrillary glomerulonephritis is a rare cause of progressive renal dysfunction, often leading to the need for dialysis within a few years. The role of immunosuppressive treatment is still uncertain although this has been tried with variable success.

Case presentation
A 56 year old woman with the antiphospholipid antibody syndrome (IgM anticardiolipin antibodies) was seen in the nephrology clinic with haematuria, proteinuria, and worsening renal function. A renal biopsy demonstrated a mesangial proliferative glomerulonephritis on light microscopy and smaller fibrils (10.6–13.8 nm in diameter) than is usual for fibrillary glomerulonephritis (typically 18–22 nm) on electron microscopy. Amyloidosis was excluded following detailed evaluation. On account of rapidly worsening renal failure she was started on cyclophosphamide and prednisolone which led to the partial recovery and stabilization of her renal function.

Conclusion
This case highlights the need for routine electron microscopy in native renal biopsies, where the differential diagnosis is wide and varied and the light and immunofluorescence microscopic findings may be non specific.
Exploring the association of dual use of the VHA and Medicare with mortality: separating the contributions of inpatient and outpatient services
Authors: Wolinsky Fredric D , An Hyonggin , Liu Li , Miller Thomas R , Rosenthal Gary E 
Published: May 2007

AbstractBackgroundOlder veterans may use both the Veterans Health Administration (VHA) and Medicare, but the association of dual use with health outcomes is unclear. We examined the association of indirect measures of dual use with mortality.MethodsOur secondary analysis used survey, claims, and National Death Index data from the Survey on Assets and Health Dynamics among the Oldest Old. The analytic sample included 1,521 men who were Medicare beneficiaries. Veterans were classified as dual users when their self-reported number of hospital episodes or physician visits exceeded that in their Medicare claims. Veterans reporting inpatient or outpatient visits but having no Medicare claims were classified as VHA-only users. Proportional hazards regression was used.Results897 (59%) of the men were veterans, of whom 134 (15%) were dual users. Among dual users, 60 (45%) met the criterion based on inpatient services, 54 (40%) based on outpatient services, and 20 (15%) based on both. 766 men (50%) died. Adjusting for covariates, the independent effect of any dual use was a 38% increased mortality risk (AHR = 1.38; p = .02). Dual use based on outpatient services marginally increased mortality risk by 45% (AHR = 1.45; p = .06), and dual use based on both inpatient and outpatient services increased the risk by 98% (AHR = 1.98; p = .02).ConclusionIndirect measures of dual use were associated with increased mortality risk. New strategies to better coordinate care, such as shared medical records, should be considered.
Rosiglitazone decreases postprandial production of acylation stimulating protein in type 2 diabetics
Authors: Tahiri Youssef , Karpe Fredrik , Tan Garry D , Cianflone Katherine 
Published: May 2007

Abstract

Background
We evaluated plasma ASP and its precursor C3 in type 2 diabetic men with/without rosiglitazone (ROSI) treatment compared to healthy non-obese men. We tested (1) whether plasma ASP or C3 are altered postprandially in subcutaneous adipose tissue or forearm muscle effluent assessed by arteriovenous (A-V) differences in healthy lean men and older obese diabetic men and (2) whether treatment with ROSI changes the arteriovenous gradient of ASP and/or C3.

Methods
In this ongoing placebo-controlled, crossover, double-blinded study, AV differences following a mixed meal were measured in diabetic men (n = 6) as compared to healthy men (n = 9).

Results
Postprandial arterial and adipose venous TG and venous NEFA were increased in diabetics vs. controls (p < 0.05–0.0001). ROSI treatment decreased postprandial arterial TG (p < 0.001), adipose venous NEFA (p < 0.005), reduced postprandial glucose (p < 0.0001) and insulin concentrations (p < 0.006). In healthy men, there was no change in postprandial C3, but an increase in adipose venous ASP vs. arterial ASP (p < 0.02), suggesting ASP production, with no change in forearm muscle. In older, obese diabetic subjects, arterial C3 was greater than in controls (p < 0.001). Arterial C3 was greater than venous C3 (p < 0.05), an effect that was lost with ROSI treatment. In diabetics, postprandial venous ASP was greater than arterial (p < 0.05), indicating ASP production, an effect that was lost with ROSI treatment (p < 0.01).

Conclusion
Increased postprandial venous production of ASP is specific for adipose tissue (absent in forearm muscle). Increased postprandial C3 and ASP in diabetic subjects is consistent with an ASP resistant state, this state is partially normalized by treatment with ROSI.
Vitamin D 1α-Hydroxylase Gene Mutations in Patients with 1α-Hydroxylase Deficiency
Authors: Kim Chan Jong , Kaplan Larry E. , Perwad Farzana , Huang Ningwu , Sharma Amita , Choi Yong , Miller Walter L. , Portale Anthony A. 
Published: May 2007

Abstract
Context: Vitamin D 1α-hydroxylase deficiency, also known as vitamin D-dependent rickets type 1, is an autosomal recessive disorder characterized by the early onset of rickets with hypocalcemia and is caused by mutations of the 25-hydroxyvitamin D 1α-hydroxylase (1α-hydroxylase, CYP27B1) gene. The human gene encoding the 1α-hydroxylase is 5 kb in length, located on chromosome 12, and comprises nine exons and eight introns. We previously isolated the human 1α-hydroxylase cDNA and gene and identified 19 different mutations in 25 patients with 1α-hydroxylase deficiency.
Objectives, Patients, and Methods: We analyzed the 1α-hydroxylase gene of 10 patients, five from Korea, two from the United States, and one each from Argentina, Denmark, and Morocco, all from nonconsanguineous families. Each had clinical and radiographic features of rickets, hypocalcemia, and low serum concentrations of 1,25-dihydroxyvitamin D3.
Results: Direct sequencing identified the responsible 1α-hydroxylase gene mutations in 19 of 20 alleles. Four novel and four known mutations were identified. The new mutations included a nonsense mutation in exon 6, substitution of adenine for guanine (2561G→A) creating a stop signal at codon 328; deletion of adenine in exon 9 (3922delA) causing a frameshift; substitution of thymine for cytosine in exon 2 (1031C→T) causing the amino acid change P112L; and a splice site mutation, substitution of adenine for guanine in the first nucleotide of intron 7 (IVS7+1 G→A) causing a frameshift.
Conclusions: Mutations in the 1α-hydroxylase gene previously were identified in 44 patients, to which we add 10 more. The studies show a strong correlation between 1α-hydroxylase mutations and the clinical findings of 1α-hydroxylase deficiency.
Hypertrophy and Increased Kisspeptin Gene Expression in the Hypothalamic Infundibular Nucleus of Postmenopausal Women and Ovariectomized Monkeys
Authors: Rometo Adonna M. , Krajewski Sally J. , Lou Voytko Mary , Rance Naomi E. 
Published: May 2007

Abstract
Context: Human menopause is characterized by ovarian failure, gonadotropin hypersecretion, and neuronal hypertrophy in the hypothalamic infundibular (arcuate) nucleus. Recent studies have demonstrated a critical role for kisspeptins in reproductive regulation, but it is not known whether menopause is accompanied by changes in hypothalamic kisspeptin neurons.
Objectives: Our objective was to map the location of neurons expressing kisspeptin gene (KiSS-1) transcripts in the human hypothalamus and determine whether menopause is associated with changes in the size and gene expression of kisspeptin neurons. In monkeys, our objective was to evaluate the effects of ovariectomy and hormone replacement on neurons expressing KiSS-1 mRNA in the infundibular nucleus.
Subjects: Hypothalamic tissues were collected at autopsy from eight premenopausal and nine postmenopausal women and from 42 young cynomolgus monkeys in various endocrine states.
Methods: We used hybridization histochemistry, quantitative autoradiography, and computer-assisted microscopy.
Results: Examination of human hypothalamic sections revealed that KiSS-1 neurons were located predominantly in the infundibular nucleus. In the infundibular nucleus of postmenopausal women, there was a significant increase in the size of neurons expressing KiSS-1 mRNA and the number of labeled cells and autoradiographic grains per neuron. Similar to postmenopausal women, ovariectomy induced neuronal hypertrophy and increased KiSS-1 gene expression in the monkey infundibular nucleus. Conversely, in ovariectomized monkeys, estrogen replacement markedly reduced KiSS-1 gene expression.
Conclusions: The cynomolgus monkey experiments provide strong evidence that the increase in KiSS-1 neuronal size and gene expression in postmenopausal women is secondary to ovarian failure. These studies suggest that kisspeptin neurons regulate estrogen negative feedback in the human.
The Molecular Mechanisms Underlying the Proinflammatory Actions of Thiazolidinediones in Human Macrophages
Authors: Hall Julie M. , McDonnell Donald P. 
Published: May 2007

Abstract
It is hypothesized that the antiinflammatory actions of peroxisome proliferator-activated receptors (PPARs) may explain the protective effect of these receptors in diabetes, atherosclerosis, cancer, and other inflammatory diseases. However, emerging evidence for proinflammatory activities of activated PPARs is concerning in light of new studies that associate PPAR modulators with an increased incidence of both cardiovascular events in humans and the sporadic formation of tumors in rodents. In an attempt to define the role of each PPAR subtype in inflammation, we made the unexpected observation that human PPARδ is a positive regulator of inflammatory responses in both monocytes and macrophages. Notably, TNFα-stimulated cells administered PPARδ agonists express and secrete elevated levels of inflammatory cytokines. Most surprising, however, was the finding that thiazolidinediones (TZDs) and other known PPARγ ligands display different degrees of proinflammatory activities in a PPARγ- and PPARα-independent manner via their ability to augment PPARδ signaling. A series of mechanistic studies revealed that TZDs, at clinically relevant concentrations, bind and activate the transcriptional activity of PPARδ. Collectively, these studies suggest that the observed proinflammatory and potentially deleterious effects of PPARγ ligands may be mediated through an off-target effect on PPARδ. These studies highlight the need for PPAR modulators with increased receptor subtype specificity. Furthermore, they suggest that differences in systemic exposure and consequently in the activation of PPARγ and PPARδ may explain why TZDs can exhibit both inflammatory and antiinflammatory activities in humans.
Newly Designed Catalysts for the Enantioselective Borohydride Reduction: Prediction from the Theoretical Analysis
Authors: Ikeno Taketo , Iwakura Izumi , Shibahara Atsushi , Hatanaka Miho , Kokura Ai , Tanaka Saiko , Nagata Takushi , Yamada Tohru 
Published: May 2007

Abstract
For the catalytic enantioselective borohydride reduction, the theoretical simulation of various axial groups in Co complex catalysts predicted that the Co–carbene complexes could be employed as efficient catalysts. The newly designed complexes generated from the Co complex and methyl diazoacetate made it possible to catalyze the enantioselective borohydride reduction in a halogen-free solvent.
Experiential Learning as Part of Pharmacist Supplementary Prescribing Training: Feedback from Trainees and Their Mentors
Authors: George Johnson , Bond Christine M , McCaig Dorothy J , Cleland Jennifer , Cunningham IT Scott , Diack H Lesley , Stewart Derek C 
Published: May 2007

BACKGROUND: A period of learning in practice (PLP) is an integral part of supplementary prescribing training for pharmacists in Great Britain. During the PLP, a designated medical practitioner (DMP) supervises and supports the trainee to develop competence in prescribing. OBJECTIVE: To evaluate the views and experiences of supplementary prescribing pharmacists and DMPs regarding the PLP and identify their perceived support needs during the PLP. METHODS: Prepiloted questionnaires were mailed in September 2006 to all pharmacists who had started their supplementary prescribing training at The Robert Gordon University, Aberdeen, Scotland (n = 242) and their DMPs (n = 232). Nonrespondents were sent up to 2 reminders. Responses were analyzed using descriptive and comparative statistics; responses to open questions were analyzed thematically. RESULTS: Responses were received from 186 (76.9%) pharmacists and 144 (62.1%) DMPs. Just over half of the pharmacists agreed/strongly agreed that they knew what was expected of them and their DMPs during the PLP, but less than half agreed/strongly agreed that it was important to communicate with pharmacist colleagues in the prescribing course. One hundred twelve (60.2%) pharmacists had their consultation skills reviewed by their DMPs during the PLP. Opportunities for professional development and teamwork were regarded as major positive experiences by both pharmacists and DMPs. Organizational, attitudinal, and time barriers were also reported. There was considerable interest among both pharmacists and DMPs for an Internet-based support network during the PLP. CONCLUSIONS: Information on the roles and responsibilities of pharmacists and DMPs during the PLP should be enhanced. The Internet could be a useful medium for communication during the PLP. Input from a multidisciplinary team of healthcare professionals and review of consultation videos could further enhance the PLP experience. TRASFONDO: Un período de aprendizaje en la práctica (PAP) es parte integral del adiestramiento de prescripción suplementaria (PS) para farmacéuticos en Gran Bretaña. Durante el PAP, un profesional médico designado (PMD) supervisa y ofrece apoyo a la persona que se adiestra para desarrollar la facultad de prescribir.