gebhart/patrepeval huggingface dataset:
In Mouse α-Methylacyl-CoA Racemase, the Same Gene Product Is Simultaneously Located in Mitochondria and Peroxisomes (2000)

alpha-Methylacyl-CoA racemase, an enzyme of the bile acid biosynthesis and branched chain fatty acid degradation pathway, was studied at the protein, cDNA, and genomic levels in mouse liver. Immunoelectron microscopy and subcellular fractionation located racemase to mitochondria and peroxisomes. The enzymes were purified from both organelles with immunoaffinity chromatography. The isolated proteins were of the same size, with identical N-terminal amino acid sequences, and the existence of additional proteins with alpha-methylacyl-CoA racemase activity was excluded. A racemase gene of about 15 kilobases was isolated. Southern blot analysis and chromosomal localization showed that only one racemase gene is present, on chromosome 15, region 15B1. The putative initial ATG in the racemase gene was preceded by a functional promotor as shown with the luciferase reporter gene assay. The corresponding cDNAs were isolated from rat and mouse liver. The recombinant rat protein was overexpressed in active form in Pichia pastoris. The presented data suggest that the polypeptide encoded by the racemase gene can alternatively be targeted to peroxisomes or mitochondria without modifications. It is concluded that the noncleavable N-terminal sequence of the polypeptide acts as a weak mitochondrial and that the C-terminal sequence acts as a peroxisomal targeting signal.
An arginine to glutamine mutation in residue 109 of human ornithine transcarbamylase completely abolishes enzymatic activity in Cos1 cells. (1989)

Ornithine transcarbamylase (OTC) is an important enzyme in the detoxification of ammonia to urea, and its deficiency is the most common inborn error of ureagenesis in humans. Among 24 cases of OTC deficiency previously examined, three unrelated individuals all showed loss of a Taq I site in the OTC gene corresponding to codon 109, suggesting that this Taq I site may be prone to mutation. Two of these patients demonstrated the same C----T transition (in antisense strand) converting Arg109 to Gln. Although these studies implied a strong association between the missense mutation and OTC-deficient phenotype, a causal relationship could not be firmly established. We have investigated this relationship by reconstructing the mutation in vitro. A full-length human OTC cDNA was cloned into an SV40-based expression vector and has been reproducibly expressed at high levels in the cell line Cos1. By site-directed mutagenesis of this wild type sequence, we constructed a missense mutation which contains the C----T transition. Electroporation and transient assay in Cos1 indicated that the specific activity of mutant OTC was 100-fold lower than that of wild type. This result confirms that the Taq I alteration leading to the Gln missense is responsible for the OTC deficiency affecting the above patients.
HER-2 therapy. HER-2/neu diagnostics in breast cancer (2007)

HER-2/neu status of the primary breast cancer (PBC) is determined by immunohistochemistry and fluorescent in situ hybridization. Because of a variety of technical factors, however, the PBC may not accurately reflect the metastatic tumor in terms of HER-2/neu status. Recently published guidelines recommend that tumors be defined as HER-2/neu positive if 30% or more of the cells are 3+. Circulating levels of the HER-2 extracellular domain can be measured in serum using a test cleared by the US Food and Drug Administration, and increased serum HER-2/neu levels to above 15 ng/ml can reflect tumor progression. Studies comparing tissue HER-2/neu status of the PBC and HER-2/neu levels above 15 ng/ml in metastatic breast cancer patients are also reviewed.
Potent Control of Tumor Growth by CEA/CD3-bispecific Single-chain Antibody Constructs That Are Not Competitively Inhibited by Soluble CEA (2009)

Carcinoembryonic antigen (CEA, CD66e) is a well-characterized tumor-associated antigen that is frequently overexpressed in tumors. Phospholipases release CEA from tumor cells resulting in high circulating serum levels of soluble CEA (sCEA) that has been validated as marker for progression of colorectal, breast, and lung cancers. sCEA also acts as a competitive inhibitor for anticancer strategies targeting membrane-bound CEA. As a novel therapeutic approach for treatment of tumors expressing CEA on their cell surface, we constructed a series of bispecific single-chain antibodies (bscAb) combining various single-chain variable fragments recognizing human CEA with a deimmunized single-chain variable fragments recognizing human CD3. CEA/CD3-bscAbs redirected human T cells to lyse CEA-expressing tumor cells in vitro and in vivo. Efficient tumor cell lysis was achieved in vitro at bscAb concentrations from 1 pg/mL (19 fM) to 8.9 pg/mL with preactivated CD8 T cells, and 200 to 500 pg/mL with unstimulated peripheral blood mononuclear cell. The cytotoxic activity of a subset of CEA/CD3-bscAbs was not competitively inhibited by sCEA at concentrations that exceeded levels found in the serum of most cancer patients. Treatment with CEA/CD3-bscAbs prevented the growth of human colorectal cancer lines in a severe combined immunodeficiency mouse model modified to show human T cell killing of tumors. A murine surrogate CEA/CD3-bscAb capable of recruiting murine T cells for redirected tumor lysis in immunocompetent mice prevented the growth of lung tumors expressing human CEA. Together, our results reveal a unique opportunity for targeting cytotoxic T cells toward CEA-expressing tumors without being competitively inhibited by sCEA and establish CEA/CD3-bscAb as a promising and potent therapeutic approach.
Sweet delivery – sugar translocators as ports of entry for antisense oligodeoxynucleotides in plant cells (2007)

Antisense oligodeoxynucleotides (ODNs) are short (12-25 nt long) stretches of single-stranded DNA that may be delivered to a cell, where they hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. Here we used confocal microscopy to monitor the uptake and trafficking of ODNs in barley tissues. We conclude that uptake of ODNs across the plant plasma membrane is mediated by active transport of mono- or disaccharides through sugar translocators. We demonstrate that sugar transport can deliver ODNs to barley seeds, and that this strategy may be employed to suppress gene activity in endosperm cells by antisense ODN inhibition. We further found that sucrose compared favorably with oligofectamine as a vehicle for ODN delivery to human cells in a low-serum environment.
Contribution of Each Amino Acid Residue in Polymyxin B3 to Antimicrobial and Lipopolysaccharide Binding Activity (2009)

This study on the structure-activity relationship of polymyxin B, a cyclic peptide antibiotic, used sixteen synthetic polymyxin B(3) analogs including alanine scanning analogs to elucidate the contribution of the side chains to antimicrobial activity and lipopolysaccharide (LPS) binding. Of these analogs, [Ala(5)]-polymyxin B(3) showed greatly reduced antimicrobial activity against Escherichia coli (E. coli), Salmonella Typhimurium (S. Typhimurium) and Pseudomonas aeruginosa (P. aeruginosa) with MIC values of 4-16 nmol/ml, suggesting that the Dab (alpha,gamma-diaminobutyric acid) residue at position 5 is the most important residue contributing to bactericidal activity. The antibacterial contribution of Dab when located within the lactam ring (positions 5, 8 and 9) was greater than when located outside the ring (positions 1 and 3). [D-Ala(6)]-, [L-Phe(6)]-, [Ala(7)]-, and [Gly(7)]-polymyxin B(3) analogs retained potent antimicrobial activity, indicating that neither the reduction of hydrophobic character of the D-Phe(6)-Leu(7) region nor the D-configuration at position 6 is indispensable for antimicrobial activity. LPS binding studies showed that decreased hydrophobicity of the lactam ring had little effect, but the N(gamma)-amino function of the Dab residues at position 1, 3, 5, 8 and 9 greatly affected LPS binding, with the contribution of Dab(5) being the most significant.
Scalable storage servers for digital audio and video (1994)

The paper describes an architecture designed to allow distributed hierarchies to be modelled and controlled. The use of node and network link capabilities and file importance gradings is used to model and control the resultant highly distributed server hierarchy. These gradings together are used to form file interests which, in the case of file replication, determine how files and updates are propagated throughout the distributed hierarchy, and how often updates are performed. These gradings encapsulate most of the behaviour required in a distributed storage server architecture. The paper discusses the load balancing techniques used in the system, and the distribution of the hierarchy and its formation. The use of the previously described capabilities in the modelling and control of the hierarchy is then discussed, followed by a description of the design of the individual storage nodes.
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database (2003)

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.
Peptidylproline cis‐trans‐isomerases: immunophilins (1993)

Two sequence-unrelated families of proteins possess peptidylproline cis-trans-isomerase activities (PPIase). PPIases are highly sequence conserved and multifunctional proteins which are present in many types of cells with a considerably divergent phylogenetic distribution. On the cellular level, PPIases occur in every compartment, both as free species and anchored to membranes. Diverse posttranslational modifications such as glycosylation, N-terminal modifications and phosphorylation constitute the additional functional features of PPIases. Folding, assembly and trafficking of proteins in the cellular milieu are regulated by PPIases. These enzymes accelerate the rate of in-vitro protein folding and they have the ability to bind proteins and act as chaperones. Some PPIases are coregulatory subunits of molecular complexes including heat-shock proteins, glucocorticoid receptors and ion channels. Secreted forms of PPIases are inflammatory and chemotactic agents for monocytes, eosinophils and basophils. The potent and clinically useful immunosuppressants CsA, FK506 or rapamycin bind with high affinities to PPIases (immunophilins). The binding criterion allows us to sort the PPIases for the following two superfamilies of proteins: the cyclophilins (CsA-binding proteins) and the FKBP (FK506/rapamycin-binding proteins). Although none of PPIases appeared to be essential for the viability of haploid yeast cells some of the immunophilin/immunosuppressant complexes are toxic both for yeast and mammalian cells. At least seven unlinked genes of cyclophilins and four unlinked genes of FKBP exist in human genomic DNA. Selected immunophilins regulate two different signalling pathways in lymphoid cells, namely the secretion of growth factors by stimulated T-cells and interleukin-2-induced T-cell proliferation. Moreover, selected FKBP mediate the cytotoxic effects of rapamycin in non-lymphoid cells. Accounts of the discovery of PPIases (immunophilins) and their functions are given in this review. A larger spectrum of proteins is analysed in relation to various signal-transduction pathways in lymphoid cells which involve immunophilins or their complexes with the immunosuppressants CsA, FK506 or rapamycin.
Oxidative Stress in the Newborn – A 30-Year Perspective (2005)

In this review the development of the concept 'hypoxia-reoxygenation injury' is outlined. An update of some important factors and mechanisms related to oxidative stress injury in newborn infants is presented, including the metabolism of glutathione, the role of antioxidants, iron and nitric oxide, and how these may influence health and disease in the newborn and contribute to 'oxygen radical disease of the newborn'. New insight into how hyperoxia and hypoxia may induce changes leading to retinopathy of prematurity by vascular endothelial growth factor acting in concert with insulin-like growth factor is briefly summarized. Inflammation and oxidative stress seem to be two sides of the same coin in newborn babies both contributing to injury partly through similar mechanisms.
Identification of Genes Involved in Decolorization of Crystal Violet and Malachite Green in Citrobacter sp. (2004)

Crystal violet와 malachite green색소 분해에 관여하는 유전자들을 규명하기 위하여 색소분해능을 가진 Citrobacter sp.의 염색체 DNA속에의 transposon 도입에 의해 생성된 무작위 변이주들이 분리되었다. 이들 변이 주들로부터 두가지 색소분해능을 소실한 14개의 변이주들이 선별되었고, 이들로부터 염색체 DNA를 분리하여 EcoRl으로 절단한 후 Tn5 단편을 probe로하여 Southern hybridization을 행한 결과, 염색체 DNA상의 각각 다른 부위에 Transposon이 Single 삽입된 5개의 변이주 (Cmg2, Cmg6, Cmg8, Cmgll, Cmg12)가 최종적으로 분리되었다. 이들 변이주들의 Transposon 삽입부위 주위의 염기서열과 이로부터 유추되는 아미노산서열을 database상에 등록되어 있는 유전자의 염기서열과 단백질의 아미노산 서열에 대한 상동성을 비교한 결과, Cmg2는 대장균 maltose trnasporter (Mal C)이고, Cmg6은 LysR-type 전사조절 단백질이며, Cmg12는 산화환원효소를 코드하는 유전자인 것으로 알려졌고, 나머지 Cmg8과 Cmg11은 아직까지 기능이 알려져 있지 않은 단백질을 코드하는 유전자인 것으로임이 판명되었다. To identify genes involved in the decolorization of both crystal violet and malachite green, we isolated random mutants generated by transposon insertion in triphenylmethane-decolorizing bacterium, Citrobacter sp. The resulting mutant bank yielded 14 mutants with complete defect in color removal capability of both crystal violet and malachite green. Southern hybridization with a Tn5 fragment as a probe showed a single hybridized band in 5 mutants and these mutants appeared to have insertions at different sites of the chromosome. Tn5-inserted genes were isolated and the DNA sequence flanking Tn5 was determined. From comparison with a sequence database, putative protein products encoded by cmg genes were identified as follows. cmg 2 is MaIC protein in maltose transport system; cmg 6 is transcriptional regulator (LysR-type): cmg 12 is a putative oxidoreductase. The sequences deduced from two cmg genes, cmg 8 and cmg 11, showed no significant similarity to any protein with a known function. Therefore, these results indicate that these two cmg genes encode unidentified proteins responsible for decolorization of both crystal violet and malachite green.
Role of matrix metalloproteinases in skeletal muscle (2009)

Matrix metalloproteases (MMPs) are key regulatory molecules in the formation, remodeling and degradation of extracellular matrix (ECM) components in both physiological and pathological processes in many tissues. In skeletal muscle, MMPs play an important role in the homeostasis and maintenance of myofiber functional integrity by breaking down ECM and regulating skeletal muscle cell migration, differentiation and regeneration. Skeletal muscle satellite cells, a group of quiescent stem cells located between the basement membrane and the plasmalemma of myofibers, are responsible for lifelong maintenance and repairing, which can be activated and as a result migrate underneath the basement membrane to promote regeneration at the injured site. MMPs are able to degrade ECM components, thereby facilitating satellite cell migration and differentiation. This current review will focus on the critical roles of MMPs in skeletal muscle injury and repair, which include satellite cell activation with migration and differentiation. The effect of MMPs on muscle regeneration and fibrous scar tissue formation, as well as therapeutic insights for the future will be explored.
Negative Deceptive Opinion Spam (2013)

The rising influence of user-generated online reviews (Cone, 2011) has led to growing in-centive for businesses to solicit and manufac-ture DECEPTIVE OPINION SPAM—fictitious reviews that have been deliberately written to sound authentic and deceive the reader. Re-cently, Ott et al. (2011) have introduced an opinion spam dataset containing gold standard deceptive positive hotel reviews. However, the complementary problem of negative deceptive opinion spam, intended to slander competitive offerings, remains largely unstudied. Follow-ing an approach similar to Ott et al. (2011), in this work we create and study the first dataset of deceptive opinion spam with negative sen-timent reviews. Based on this dataset, we find that standard n-gram text categorization tech-niques can detect negative deceptive opinion spam with performance far surpassing that of human judges. Finally, in conjunction with the aforementioned positive review dataset, we consider the possible interactions between sentiment and deception, and present initial results that encourage further exploration of this relationship. 1
Inspection of intrinsic critical currents for spin-transfer magnetization switching (2005)

We examined the relationships between critical current, I/sub c/, and switching time, /spl tau//sub p/, for spin-transfer switching in two regions: (region I) /spl tau//sub p//spl Gt//spl tau//sub 0/, where thermal switching is accompanied and (region II) /spl tau//sub p/< several tens times /spl tau//sub 0/, where /spl tau//sub 0/ is the attempt time for thermal switching (/spl ap/1 ns). We estimated I/sub c0/, defined as the intrinsic I/sub c/ at 0 K, for both regions and confirmed experimentally that those I/sub c0/ coincided with each other at room temperature (RT). The value of I/sub c/ at /spl tau//sub p/=1 ns, measured with microwaves, was approximately 1.6 times the I/sub c0/. This suggested that we use at least two times I/sub c0/ as the writing currents of magnetic memory devices for nsec spin-transfer switching at RT. Although I/sub c0/ for both regions were defined as I/sub c/ at 0 K (I/sub c//sup 0K/) in theory, they showed temperature dependence at low temperatures; |I/sub c0/| for region I increased with decreasing temperature, and the estimated I/sub c//sup 0K/ was approximately three times I/sub c0/ for RT. This temperature dependence was quite different from that for region II.
The Chemistry of Carbonyl Fluoride. I. The Fluorination of Organic Compounds (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Chemistry of Carbonyl Fluoride. I. The Fluorination of Organic CompoundsF. S. Fawcett, C. W. Tullock, and D. D. CoffmanCite this: J. Am. Chem. Soc. 1962, 84, 22, 4275–4285Publication Date (Print):November 1, 1962Publication History Published online1 May 2002Published inissue 1 November 1962https://pubs.acs.org/doi/10.1021/ja00881a017https://doi.org/10.1021/ja00881a017research-articleACS PublicationsRequest reuse permissionsArticle Views2097Altmetric-Citations128LEARN 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-Alertsclose Get e-Alerts
Sampling-based contact-rich motion control (2010)

Human motions are the product of internal and external forces, but these forces are very difficult to measure in a general setting. Given a motion capture trajectory, we propose a method to reconstruct its open-loop control and the implicit contact forces. The method employs a strategy based on randomized sampling of the control within user-specified bounds, coupled with forward dynamics simulation. Sampling-based techniques are well suited to this task because of their lack of dependence on derivatives, which are difficult to estimate in contact-rich scenarios. They are also easy to parallelize, which we exploit in our implementation on a compute cluster. We demonstrate reconstruction of a diverse set of captured motions, including walking, running, and contact rich tasks such as rolls and kip-up jumps. We further show how the method can be applied to physically based motion transformation and retargeting, physically plausible motion variations, and reference-trajectory-free idling motions. Alongside the successes, we point out a number of limitations and directions for future work.
Prohormone Thiol Protease and Enkephalin Precursor Processing: Cleavage at Dibasic and Monobasic Sites (1992)

Production of active enkephalin peptides requires proteolytic processing of proenkephalin at dibasic Lys-Arg, Arg-Arg, and Lys-Lys sites, as well as cleavage at a monobasic arginine site. A novel "prohormone thiol protease" (PTP) has been demonstrated to be involved in enkephalin precursor processing. To find if PTP is capable of cleaving all the putative cleavage sites needed for proenkephalin processing, its ability to cleave the dibasic and the monobasic sites within the enkephalin-containing peptides, peptide E and BAM-22P (bovine adrenal medulla docosapeptide), was examined in this study. Cleavage products were separated by HPLC and subjected to microsequencing to determine their identity. PTP cleaved BAM-22P at the Lys-Arg site between the two basic residues. The Arg-Arg site of both peptide E and BAM-22P was cleaved at the NH2-terminal side of the paired basic residues to generate [Met]-enkephalin. Furthermore, the monobasic arginine site was cleaved at its NH2-terminal side by PTP. These findings, together with previous results showing PTP cleavage at the Lys-Lys site of peptide F, demonstrate that PTP possesses the necessary specificity for all the dibasic and monobasic cleavage sites required for proenkephalin processing. In addition, the unique specificity of PTP for cleavage at the NH2-terminal side of arginine at dibasic or monobasic sites distinguishes it from many other putative prohormone processing enzymes, providing further evidence that PTP appears to be a novel prohormone processing enzyme.