gebhart/patrepeval huggingface dataset:
Cluster analysis for gene expression data: a survey (2004)

DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increases the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. Cluster analysis seeks to partition a given data set into groups based on specified features so that the data points within a group are more similar to each other than the points in different groups. A very rich literature on cluster analysis has developed over the past three decades. Many conventional clustering algorithms have been adapted or directly applied to gene expression data, and also new algorithms have recently been proposed specifically aiming at gene expression data. These clustering algorithms have been proven useful for identifying biologically relevant groups of genes and samples. In this paper, we first briefly introduce the concepts of microarray technology and discuss the basic elements of clustering on gene expression data. In particular, we divide cluster analysis for gene expression data into three categories. Then, we present specific challenges pertinent to each clustering category and introduce several representative approaches. We also discuss the problem of cluster validation in three aspects and review various methods to assess the quality and reliability of clustering results. Finally, we conclude this paper and suggest the promising trends in this field.
Cognitive Development of Children with Craniosynostosis (2015)

Investigators from University of Washington, Seattle, WA; Harvard U, MA; St Louis, MO; Atlanta, GA; Northwestern U, and Shriner's Hospital, Chicago, compared the development of school-aged children with single-suture craniosynostosis (sagittal, metopic, unicoronal, lambdoid) and unaffected children.
Capsule measuring ring to predict capsular bag diameter and follow its course after foldable intraocular lens implantation (2003)

A correlation was found between capsular bag shrinkage and AL. Using preoperative biometric data, a regression formula of moderate validity was determined to predict capsular bag shrinkage.
Synthesis and Characterization of Vanadium(V)−Phosphinimide Complexes (2003)

Synthetic routes to vanadium(V)-phosphinimide derivatives are addressed. Initial synthetic efforts afforded the known compound formulated as VCl(2)(NPPh(3))(3) which was crystallographically determined to be the salt [VCl(NPPh(3))(3)]Cl (1). Reactions of the vanadium-imide precursors VCl(3)(NAr) (Ar = Ph, C(6)H(3)-2,6-iPr(2)) with R(3)PNSiMe(3) (R = Ph, iPr, tBu) afforded VCl(2)(NPh)(NPPh(3)) (4), VCl(2)(NPh)(NPiPr(3)) (5), VCl(2)(NPh)(NPtBu(3)) (6), VCl(2)(NC(6)H(3)-2,6-iPr(2))(NPPh(3)) (7), VCl(2)(NC(6)H(3)-2,6-iPr(2))(NPiPr(3)) (8), and VCl(2)(NC(6)H(3)-2,6-iPr(2))(NPtBu(3)) (9) in yields ranging from 72% to 84%. Subsequent alkylation or arylation reactions resulted in VMe(2)(NC(6)H(3)-2,6-iPr(2))(NPtBu(3)) (10), VPh(2)(NPh)(NPtBu(3)) (11), VPh(2)(NC(6)H(3)-2,6-iPr(2))(NPiPr(3)) (12), and VPh(2)(NC(6)H(3)-2,6-iPr(2))(NPtBu(3)) (13) while substitution reactions with Li[N(SiMe(3))(2)] and Li[SBn] gave VCl(N(SiMe(3))(2))(NPh)(NPtBu(3)) (14) and V(SBn)(2)(NC(6)H(3)-2,6-iPr(2))(NPtBu(3)) (15) in yields ranging from 40% to 49% yield. Polarization of the N-P phosphinimide bond and V-N multiple bond character are evidenced by crystallographic data.
Porous collagen sponge for esophageal replacement (1993)

A new artificial esophagus with a bilayered structure made of porous collagen sponge and silicone was studied. The concept of this study was not to replace an esophageal defect permanently with prosthesis but to promote tissue regeneration by collagen. Five centimeters of cervical esophagus were replaced by this artificial esophagus in 19 adult mongrel dogs. Two weeks after implantation, the collagen sponge was replaced by autologous tissue and regeneration of the "neoesophagus" was observed in all animals. The inner surface of the neoesophagus was covered with mature mucosal epithelium similar to the intact esophagus 4-5 weeks after implantation. The replacement site was not complicated by infection, anastomotic leakage, or exuberant granulation tissue development on the luminal surface. In a long-term survival study, animals showed moderate-grade stenosis but could take normal feed orally and with no clinical problems observed.
Intracellular Localization of Human Cytidine Deaminase (1999)

The cytidine deaminases belong to the family of multisubunit enzymes that catalyze the hydrolytic deamination of their substrate to a corresponding uracil product. They play a major role in pyrimidine nucleoside and nucleotide salvage. The intracellular distribution of cytidine deaminase and related enzymes has previously been considered to be cytosolic. Here we show that human cytidine deaminase (HCDA) is present in the nucleus. A highly specific, affinity purified polyclonal antibody against HCDA was used to analyze the intracellular localization of native HCDA in a variety of mammalian cells by in situ immunochemistry. Native HCDA was found to be present in the nucleus as well as the cytoplasm in several cell types. Indirect immunofluorescence microscopy indicated a predominantly nuclear localization of FLAG-tagged HCDA overexpressed in these cells. We have identified an amino-terminal bipartite nuclear localization signal that is both necessary and sufficient to direct HCDA and a non-nuclear reporter protein to the nucleus. We also show HCDA binding to the nuclear import receptor, importin alpha. Similar putative bipartite nuclear localization sequences are found in other cytidine/deoxycytidylate deaminases. The results presented here suggest that the pyrimidine nucleotide salvage pathway may operate in the nucleus. This localization may have implications in the regulation of nucleoside and nucleotide metabolism and nucleic acid biosynthesis.
Microfluidic Paper-Based Analytical Devices (μPADs) and Micro Total Analysis Systems (μTAS): Development, Applications and Future Trends (2013)

Microfluidic paper-based analytical devices and micro total analysis systems are relatively new group of analytical tools, capable of analyzing complex biochemical samples containing macromolecules, proteins, nucleic acids, toxins, cells or pathogens. Within one analytical run, fluidic manipulations like transportation, sorting, mixing or separation are available. Recently, microfluidic devices are a subject of extensive research, mostly for fast and non-expensive biochemical analysis but also for screening of medical samples and forensic diagnostics. They are used for neurotransmitter detection, cancer diagnosis and treatment, cell and tissue culture growth and amplification, drug discovery and determination, detection and identification of microorganisms. This review summarizes development history, basic fabrication methods, applications and also future development trends for production of such devices.
CD200 and its receptors as targets for immunoregulation. (2005)

A diverse array of cell surface receptors is known to control immune function, reflecting the integration of positive and negative signaling. Many receptors with opposing functions are isoforms of molecules with similar extracellular domains and different intracellular signaling cytoplasmic domains. The receptor(s) for the relatively ubiquitously expressed cell-surface molecule CD200 (previously referred to as OX2), CD200R(s) is one example of such paired receptors, a feature confirmed by structural and functional analysis. Expression of CD200Rs is most apparent in tissues of myeloid/macrophage origin, although some expression on lymphoid cells has also been documented. This review discusses new data in the field, and the evidence that agonists/antagonists of CD200 or the different CD200Rs might contribute to the treatment of numerous diseases, including allergy, autoimmunity, transplantation and cancer.
Innovation from reduction: gene loss, domain loss and sequence divergence in genome evolution. (2003)

Analyses of genome sequences have revealed a surprisingly variable distribution of genes, reflecting the generation of novel genes, lateral gene transfer and gene loss. The impact of gene loss on organisms has been difficult to examine, but the loss of protein coding genes, the loss of domains within proteins and the divergence of genes have made surprising contributions to the differences among organisms. This paper reviews surveys of gene loss and divergence in fungal and archaeal genomes that indicate suites of functionally related genes tend to undergo loss and divergence. Instances of fungal gene loss highlighted here suggest that specific cellular systems have changed, such as Ca 2+ biology in Saccharomyces cerevisiae and peroxisome function in Schizosaccharomyces pombe. Analyses of loss and divergence can provide specific predictions regarding protein-protein interactions, and the relationship between networks of protein interactions and loss may form a part of a parametric model of genome evolution.
Aminopyridine-Based c-Jun N-Terminal Kinase Inhibitors with Cellular Activity and Minimal Cross-Kinase Activity (2006)

The c-Jun N-terminal kinases (JNK-1, -2, and -3) are members of the mitogen activated protein (MAP) kinase family of enzymes. They are activated in response to certain cytokines, as well as by cellular stresses including chemotoxins, peroxides, and irradiation. They have been implicated in the pathology of a variety of different diseases with an inflammatory component including asthma, stroke, Alzheimer's disease, and type 2 diabetes mellitus. In this work, high-throughput screening identified a JNK inhibitor with an excellent kinase selectivity profile. Using X-ray crystallography and biochemical screening to guide our lead optimization, we prepared compounds with inhibitory potencies in the low-double-digit nanomolar range, activity in whole cells, and pharmacokinetics suitable for in vivo use. The new compounds were over 1,000-fold selective for JNK-1 and -2 over other MAP kinases including ERK2, p38alpha, and p38delta and showed little inhibitory activity against a panel of 74 kinases.
Inhibition of interleukin 8 attenuates angiogenesis in bronchogenic carcinoma. (1994)

We investigated the role of interleukin 8 (IL-8) in mediating angiogenesis in human bronchogenic carcinoma. Increased quantities of IL-8 were detected in tumor tissue as compared with normal lung tissue. Immunohistochemical staining of tumors revealed primary localization of IL-8 to individual tumor cells and demonstrated the capacity of tumor to elaborate IL-8. Functional studies that used tissue homogenates of tumors demonstrated the induction of both in vitro endothelial cell chemotaxis and in vivo corneal neovascularization. It is important to note that the addition of neutralizing antisera to IL-8 to these assays resulted in the marked and specific attenuation of these responses. Our observations definitively establish IL-8 as a primary mediator of angiogenesis in bronchogenic carcinoma and offer a potential target for immunotherapies against solid malignancies.
A phenotypic host range alteration determines RD114 virus restriction in feline embryonic cells (1993)

We have characterized the restriction mechanism for RD114 virus replication in embryonic feline cells (FeF). By comparing growth properties of the virus in FeF cells with its behavior in a fetal feline glial cell line (G355) permissive for RD114, we showed that both cell lines were readily infectible by virus grown in permissive cells and that no significant differences in viral integration or viral RNA expression could be detected. However, analysis of viral protein expression revealed differences in viral env gene processing in the two cell types. Envelope precursor pR85 was produced, but the expected processed gp70 product was detectable only in permissive (G355) cells. An envelope product of 85 kDa was packaged into virions produced by FeF cells, while virions produced by G355 cells contained the expected RD114 gp70. While the gp85 env-containing virions were infectious for permissive G355 cells, they were unable to infect FeF cells. The block to infection by the gp85-containing particles in FeF cells could be abrogated by treatment with the glycosylation inhibitor tunicamycin. Our results indicate that restriction of RD114 virus involves a novel mechanism dependent on two factors: altered glycosylation of the envelope to a gp85 form and an altered RD114 receptor in FeF cells.
Tissue response during Piezocision-assisted tooth movement: a histological study in rats (2013)

Within the limitations of our study (number of animals, duration in time, and limited data on the anabolic activity), our preliminary results suggest that Piezocision-facilitated orthodontic tooth movement increases the rate of movement of the teeth undergoing orthodontic treatment through the coupled remodelling of the alveolar bone. This process is initiated by the osteoclastic activity following surgery and extended via the synergistic relationship between Piezocision and tooth movement.
Antibiotic action of pyocyanin (1981)

Biologically produced pyocyanin was purified, and the nature of its antibacterial action was determined for several bacteria. The pigment was shown to be bactericidal for all susceptible organisms. The bactericidal effect was dependent upon pyocyanin concentration and resulted in decreases in viability ranging from 1 to 8 log viable cells ml-1. The gram-positive bacteria were more susceptible as a group to the antibiotic action than were the gram-negative bacteria. All apyocyanogenic pseudomonads tested were totally resistant to the pigment, suggesting that resistance may be a characteristic of the genus. Pseudomonas aeruginosa, the producer organism, was also essentially unaffected by high concentrations of pyocyanin. Facultative anaerobes were twofold or more times resistant to the action of the pigment under fermentative conditions; however, the antibiotic action did not require oxygen since denitrifying bacteria were more susceptible during anaerobic respiration than during aerobic respiration.
‘Click labelling’ in PET radiochemistry (2009)

Abstract The copper(I)‐catalysed 1,3‐dipolar cylcoaddition of terminal alkynes with substituted azides has seen a rapidly growing popularity in a wide range of applications. This versatile coupling reaction has been also recognised as an invaluable tool to meet the high radiosynthetic demands of tracers for Positron Emission Tomography (PET). Here, we are reviewing publications from 2006 to March 2009. Copyright © 2009 John Wiley &amp; Sons, Ltd.
The immune response to osteochondral allografts in dogs. (1987)

Dog leukocyte antigen (DLA)-matched and mismatched, fresh and frozen (cryopreserved) osteochondral allografts of the proximal part of the radius were implanted orthotopically in beagles. The systemic and local (intra-articular) immune responses were monitored for eleven months using a 51chromium release assay with donor peripheral-blood lymphocytes as target cells. DLA-mismatched fresh grafts markedly and persistently stimulated the formation of antibody directed against donor cell-surface antigens, while DLA-matched grafts did not elicit systemically detectable antibody. The same general pattern was noted when antibody-dependent cell-mediated cytotoxicity was assayed. There was measurable cell-mediated immunity to donor cells from six weeks after surgery onward, although no distinct pattern or differences between experimental groups were noted. Higher titers of anti-DLA antibody were found in synovial fluid than in serum; in fact, synovial antibody was detectable when systemic antibody was not. Joints that received DLA-mismatched grafts had the highest titer of antibody and the intra-articular response was significantly reduced when the graft had been frozen.
Lens Proteins and Aging (1983)

Aging of the eye lens is reflected by pronounced changes on the molecular level. So far, these alterations have been investigated in particular with respect to the structural lens proteins or crystallins, which comprise approximately 95% of the dry weight. It seems that virtually postsynthetic modifications are involved, although errors on the translational level cannot be excluded. A variety of chemically or physically defined processes have been observed with aging. These include formation of high-molecular-weight, eventually insoluble aggregates; formation of disulfide bridges and other covalent crosslinks; deamidation of asparaginyl and glutaminyl residues; partial degradation of polypeptides at characteristic sites; racemization of aspartyl residues; nonenzymatic glycosylation; and photooxidation of tryptophanyl residues.
Shield as Signal: Lipopolysaccharides and the Evolution of Immunity to Gram-Negative Bacteria (2006)

ccording to the innate immunity concept [1], animals defend themselves from microbes by recognizing pathogen-associated molecular patterns. To detect many Gram-negative bacteria, animals use the CD14-MD-2-TLR4 receptor mechanism to recognize the lipid A moiety of the cell wall lipopolysaccharide (LPS). Lipid A is a glucosamine disaccharide that carries phosphates at positions 1 and 49 and usually has four primary (glucosamine-linked) hydroxyacyl chains and one or more secondary acyl chains. Gram-negative bacteria produce numerous variations on this basic structure, yet sensitive LPS recognition and proinflammatory signaling by human TLR4 occur only when lipid A has both phosphates and is hexaacyl, with two secondary acyl chains.
Introns increase gene expression in cultured maize cells. (1987)

Using electroporation-mediated gene transfer, the gene encoding the Slow (S) migrating polypeptide of the maize (Zea mays L.) alcohol dehydrogenase-1 (Adh1) enzyme has been introduced stably and transiently into maize cells containing an endogenous Fast (F) ADH1 electromorph. In stable transformants an 11.5-kb fragment was sufficient to program normal S expression relative to the endogenous F allele. In transient assays, Adh1-S gene constructs lacking the 9 Adh1-S intervening sequences (introns) were expressed at levels 50- to 100-fold less than the intact gene; the presence of intron 1 alone restored levels of gene expression to those found with the intact gene. The last two introns also stimulate Adh1-S expression, but the level is threefold below that of the intact gene. The expression of a chimeric chloramphenicol acetyltransferase (CAT) gene utilizing the 5' promoter and 3' polyadenylation regions of the Adh1 gene was increased 100-fold by the addition of sequences containing the Adh1 intron 1. The Adh1 intron 1 sequences did not stimulate CAT expression when located outside the transcribed region. When located within the transcribed region, the Adh1 intron 1 region efficiently stimulated CAT expression only when located between the promoter and the CAT coding region. A construct containing the Adh1 intron 1 fragment produced 40-fold more mRNA than a construct containing an equivalent cDNA fragment. Both the Adh1 intron 1 and the intron from a second maize gene, Bronze1, stimulated expression from other promoters (cauliflower mosaic virus 35S and nopaline synthase) and of other coding regions (luciferase and neomycin phosphotransferase II) as well. These results indicated that introns increase both Adh1 and chimeric gene expression in maize and the optimal location for such an intron is near the 5' end of the mRNA.
Evaluating β-turn mimics as β-sheet folding nucleators (2009)

Beta-turns are common conformations that enable proteins to adopt globular structures, and their formation is often rate limiting for folding. Beta-turn mimics, molecules that replace the i + 1 and i + 2 amino acid residues of a beta-turn, are envisioned to act as folding nucleators by preorganizing the pendant polypeptide chains, thereby lowering the activation barrier for beta-sheet formation. However, the crucial kinetic experiments to demonstrate that beta-turn mimics can act as strong nucleators in the context of a cooperatively folding protein have not been reported. We have incorporated 6 beta-turn mimics simulating varied beta-turn types in place of 2 residues in an engineered beta-turn 1 or beta-bulge turn 1 of the Pin 1 WW domain, a three-stranded beta-sheet protein. We present 2 lines of kinetic evidence that the inclusion of beta-turn mimics alters beta-sheet folding rates, enabling us to classify beta-turn mimics into 3 categories: those that are weak nucleators but permit Pin WW folding, native-like nucleators, and strong nucleators. Strong nucleators accelerate folding relative to WW domains incorporating all alpha-amino acid sequences. A solution NMR structure reveals that the native Pin WW beta-sheet structure is retained upon incorporating a strong E-olefin nucleator. These beta-turn mimics can now be used to interrogate protein folding transition state structures and the 2 kinetic analyses presented can be used to assess the nucleation capacity of other beta-turn mimics.
Further studies of imido alkylidene complexes of tungsten, well-characterized olefin metathesis catalysts with controllable activity (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFurther studies of imido alkylidene complexes of tungsten, well-characterized olefin metathesis catalysts with controllable activityRichard R. Schrock, R. T. DePue, J. Feldman, K. B. Yap, D. C. Yang, W. M. Davis, L. Park, M. DiMare, M. Schofield, and Cite this: Organometallics 1990, 9, 8, 2262–2275Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/om00158a025https://doi.org/10.1021/om00158a025research-articleACS PublicationsRequest reuse permissionsArticle Views1663Altmetric-Citations254LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts