gebhart/patrepeval huggingface dataset:
The emerging genomics and systems biology research lead to systems genomics studies (2014)

Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathway-based biomarker and drug target identification. With the advent of high-throughput next-generation sequencing technologies, sequencing both DNA and RNA has generated multi-layer genomic data that can provide DNA polymorphism, non-coding RNA, messenger RNA, gene expression, isoform and alternative splicing information. Systems biology on the other hand studies complex biological systems, particularly systematic study of complex molecular interactions within specific cells or organisms. Genomics and molecular systems biology can be merged into the study of genomic profiles and implicated biological functions at cellular or organism level. The prospectively emerging field can be referred to as systems genomics or genomic systems biology. The Mid-South Bioinformatics Centre (MBC) and Joint Bioinformatics Ph.D. Program of University of Arkansas at Little Rock and University of Arkansas for Medical Sciences are particularly interested in promoting education and research advancement in this prospectively emerging field. Based on past investigations and research outcomes, MBC is further utilizing differential gene and isoform/exon expression from RNA-seq and co-regulation from the ChiP-seq specific for different phenotypes in combination with protein-protein interactions, and protein-DNA interactions to construct high-level gene networks for an integrative genome-phoneme investigation at systems biology level.
Cell surface glycoprotein of reactive stromal fibroblasts as a potential antibody target in human epithelial cancers. (1990)

The F19 antigen is a cell surface glycoprotein (Mr, 95,000) of human sarcomas and proliferating, cultured fibroblasts that is absent from resting fibroblasts in normal adult tissues. Normal and malignant epithelial cells are also F19-. The present immunohistochemical study describes induction of F19 in the reactive mesenchyme of epithelial tumors. F19+ fibroblasts were found in primary and metastatic carcinomas, including colorectal (18 of 18 cases studied), breast (14/14), ovarian (21/21), bladder (9/10), and lung carcinomas (13/13). In contrast, the stroma of benign colorectal adenomas, fibrocystic disease and fibroadenomas of breast, benign prostate hyperplasia, in situ bladder carcinomas, and benign ovarian tumors showed no or only moderate numbers of F19+ fibroblasts. Analysis of dermal incision wounds revealed that F19 is strongly induced during scar formation. Comparison of F19 with the extracellular matrix protein tenascin, a putative marker of tumor mesenchyme, showed a cellular staining pattern for F19 vs. the extracellular matrix pattern for tenascin and widespread expression of tenascin in F19- normal tissues and benign tumors. Our results suggest that the F19+ phenotype correlates with specialized fibroblast functions in wound healing and malignant tumor growth. Because of its abundance in tumor mesenchyme, F19 may serve as a target for antibodies labeled with radioisotopes or toxic agents, or inflammatogenic antibodies, in carcinoma patients.
A Preliminary Evaluation of Alternative Telecommunication Systems for the Delivery of Primary Health Care to Remote Areas (1975)

Adequate health-care facilities are seldom available to persons physically remote from population centers. One method of relieving part of the problem is to provide facilities for diagnosing medical problems remotely via some form of communications technology. With this in mind, an experiment was conducted to compare the efficiency and effectiveness of two-way communication systemscolor television, black-and-white television, and hands-free telephone-as an alternative to physical presence consultation. Our results indicate that the taken to complete the diagnostic consultation was essentially the same across all four modes. Furthermore, no significant differences were found among the three remote modes for accuracy of diagnosis and patient management effectiveness, and physical presence consultations were found superior only in discovering secondary medical problems. Nevertheless, the attitudes of both patients and doctors showed a preference for color television over black-and-white television over hands-free telephone.
Bifunctional chiral synthons via biochemical methods. III. Optical purity enhancement in enzymic asymmetric catalysis (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBifunctional chiral synthons via biochemical methods. III. Optical purity enhancement in enzymic asymmetric catalysisYi Fong Wang, Ching Shih Chen, Gary Girdaukas, and Charles J. SihCite this: J. Am. Chem. Soc. 1984, 106, 12, 3695–3696Publication Date (Print):June 1, 1984Publication History Published online1 May 2002Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/ja00324a062https://doi.org/10.1021/ja00324a062research-articleACS PublicationsRequest reuse permissionsArticle Views722Altmetric-Citations185LEARN 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
<sup>133</sup>Cs Chemical Shielding Anisotropies and Quadrupole Couplings from Magic-Angle Spinning NMR of Cesium Salts (1996)

Magnitudes and relative orientations of 133Cs quadrupole coupling and chemical shielding tensors have been accurately determined from 133Cs magic-angle spinning (MAS) NMR spectra of the central and satellite transitions for four powdered cesium salts. Effects of small 133Cs chemical shielding anisotropies on the spectral appearance are observed in highly stabilized low-speed 133Cs MAS NMR spectra and analyzed by iterative fitting and numerical error analysis of the complete manifolds of spinning sidebands. 133Cs MAS NMR spectra of the single Cs site for CsVO3 and CsClO4, recorded at different spinning speeds, give consistent values for the parameters describing the two tensor interactions, while numerical error analysis of the spectra demonstrates that high levels of accuracy can be obtained for all parameters employing low-speed MAS NMR. The performance of the method for powders containing multiple sites is demonstrated by the 133Cs MAS spectra of Cs2CrO4 and Cs2SO4. The error limits for the 133Cs MAS NMR data for Cs2CrO4 are similar to those reported in a recent single-crystal NMR study. Quadrupole coupling parameters and isotropic chemical shifts are reported for Cs2CO3 from a high-speed 133Cs MAS spectrum. A linear correlation between 133Cs quadrupole tensor elements and estimated EFG tensor elements from point-charge calculations, employing effective oxygen charges, is reported and used to assign the NMR parameters for the two different crystallographic sites in Cs2CrO4, Cs2SO4, and Cs2CO3.
JPred4: a protein secondary structure prediction server (2015)

JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.
Early induction of ribonucleotide reductase gene expression by transforming growth factor beta 1 in malignant H-ras transformed cell lines. (1991)

Previous investigations have indicated that the suppression of proliferation by transforming growth factor (TGF) beta 1 is often lost upon cellular transformation, and that proliferation of some tumors is stimulated by TGF-beta. The present study provides the first observation of a link between TGF-beta 1 regulation of this process and alterations in the expression of ribonucleotide reductase, a highly controlled rate-limiting step in DNA synthesis. A series of radiation and T24-H-ras-transformed mouse 10T1/2 cell lines exhibiting increasing malignant potential was evaluated for TGF-beta 1 induced alterations in ribonucleotide reductase M1 and M2 gene expression. Early increases in M1 and/or M2 message and protein levels were observed only in malignant cell lines. The TGF-beta 1 induced changes in M1 and/or M2 gene expression occurred prior to any detectable changes in the rates of DNA synthesis, supporting the novel concept that ribonucleotide reductase gene expression can be elevated by TGF-beta 1 without altering the proportion of cells in S phase. T24-H-ras-transformed 10T1/2 cells were transfected with a plasmid containing the coding region of TGF-beta 1 under the control of a zinc-sensitive metallothionein promoter. When these cells were cultured in the presence of zinc, a large induction of TGF-beta 1 message was observed within 1 h. Both M1 and M2 genes were also induced, with increased mRNA levels appearing 2 h after zinc treatment, or 1 h after TGF-beta 1 message levels were clearly elevated. In total, the data suggests a mechanism of autocrine stimulation of malignant cells by TGF-beta 1, in which early alterations in the regulation of ribonucleotide reductase may play an important role.
Two-dimensional temperature mapping using thermographic phosphors (1990)

We have demonstrated the feasibility of extending a point-temperature measurement method to two-dimensional mapping of temperature distributions on surfaces. The point-measurement method used the temperature-dependant characteristics of sharp emission lines from thermographic phosphors to measure temperature. The two-dimensional extrusion uses an ultraviolet light source to illuminate the phosphor-coated surface and a high-grain video camera filtered to select the desired emission line. By changing filters, we acquire video data that are over-laid and analyzed by a video processor, then displayed in contour or pseudocolor maps of the temperature distribution. 13 refs., 14 figs., 1 tabs.
Making business sense of the Internet. (1998)

For managers in large, well-established businesses, the Internet is a tough nut to crack. It is very simple to set up a Web presence and very difficult to create a Web-based business model. Established businesses that over decades have carefully built brands and physical distribution relationships risk damaging all they have created when they pursue commerce through the Net. Still, managers can't avoid the impact of electronic commerce on their businesses. They need to understand the opportunities available to them and recognize how their companies may be vulnerable if rivals seize those opportunities first. Broadly speaking, the Internet presents four distinct types of opportunities. First, it links companies directly to customers, suppliers, and other interested parties. Second, it lets companies bypass other players in an industry's value chain. Third, it is a tool for developing and delivering new products and services to new customers. Fourth, it will enable certain companies to dominate the electronic channel of an entire industry or segment, control access to customers, and set business rules. As he elaborates on these four points, the author gives established companies a systematic way to sort through the risks and rewards of doing business in cyberspace.
ipShield: a framework for enforcing context-aware privacy (2014)

Smart phones are used to collect and share personal data with untrustworthy third-party apps, often leading to data misuse and privacy violations. Unfortunately, state-of-the-art privacy mechanisms on Android provide inadequate access control and do not address the vulnerabilities that arise due to unmediated access to so-called innocuous sensors on these phones. We present ipShield, a framework that provides users with greater control over their resources at runtime. ipShield performs monitoring of every sensor accessed by an app and uses this information to perform privacy risk assessment. The risks are conveyed to the user as a list of possible inferences that can be drawn using the shared sensor data. Based on user-configured lists of allowed and private inferences, a recommendation consisting of binary privacy actions on individual sensors is generated. Finally, users are provided with options to override the recommended actions and manually configure context-aware fine-grained privacy rules. We implemented ipShield by modifying the AOSP on a Nexus 4 phone. Our evaluation indicates that running ipShield incurs negligible CPU and memory overhead and only a small reduction in battery life.
The dielectric properties of biological tissues: II. Measurements in the frequency range 10 Hz to 20 GHz (1996)

Three experimental techniques based on automatic swept-frequency network and impedance analysers were used to measure the dielectric properties of tissue in the frequency range 10 Hz to 20 GHz. The technique used in conjunction with the impedance analyser is described. Results are given for a number of human and animal tissues, at body temperature, across the frequency range, demonstrating that good agreement was achieved between measurements using the three pieces of equipment. Moreover, the measured values fall well within the body of corresponding literature data.
Formation of 50 kbp chromatin fragments in isolated liver nuclei is mediated by protease and endonuclease activation (1994)

Isolated rat liver nuclei were incubated in the presence of divalent cations, and the mechanisms underlying the subsequent chromatin fragmentation were investigated. Either of the two cations, Ca2+ or Mg2+ was sufficient to produce chromatin fragments with sizes between 700 and 300 kbp. The formation of chromatin fragments of 50 kbp as well as the following internucleosomal DNA cleavage--which are characteristic of apoptosis--were markedly stimulated in the presence of Ca2+. Chromatin degradation to 50 kbp and smaller (oligonucleosome-size) fragments was prevented by inhibitors of endonucleases and serine proteases. We suggest a mechanism whereby the concerted activity of both proteases and endonucleases results in the widespread chromatin cleavage observed in cells undergoing apoptosis.
Nanopore-facilitated single molecule detection of circulating microRNAs in cancer patients (2010)

Developing new technologies for cancer screening and early diagnosis is a critical issue for saving cancer patients' lives. MicroRNAs (miRNAs) are a class of short (~18-24-nt) non-coding RNAs molecules that regulate gene expression at the post-transcriptional level. Aberrant expression of miRNAs has been found in all types of tumors. Thus miRNAs have been recognized as potential cancer biomarkers. Most notably, specific miRNAs are released from the primary tumor into blood circulation, making the detection of circulating miRNAs profile a powerful tool for noninvasive cancer detection, diagnosis, staging, and monitoring. We developed a robust nanopore sensor that selectively detects single molecules of circulating miRNAs derived from primary cancer. The nanopore is a fabricated 2-nm molecular pore. Such a tiny pore can generate a signature current signal when a miRNA molecule is specifically captured in it. These signals function as fingerprints that enable us to identify a specific miRNA and quantify its concentration. The prototype of nanopore sensor has demonstrated the capability to discriminate single nucleotide difference between miRNAs (single nucleotide polymorphisms, SNPs). In clinical tests, the nanopore has shown the power to differentiate miRNA levels in blood from lung cancer patients and healthy people. Due to the label-free single molecule detection without nucleic acids amplification, the nanopore sensor is higher selective, precise and accurate over the gold standard RT-PCR and microarray. This noninvasive clinical test requires a mere 5 ml of peripheral blood, with a reduced cost from several hundred dollars today to less than 20 dollars per sample. The developing nanopore array would give a high throughput capability for detecting miRNA profile. If validated in clinical trial, the nanopore sensor will become a system available to monitor cancer patients and to screen high risk populations for early diagnosis of cancers which will potentially save the lives of millions. Potential Areas of Applications: * Detection of microRNAs, study of DNA, RNA, DNA/RNA hybrid unzipping kinetics * Study of miRNA mechanism and principle of regulation * Drug discovery and development * Biomarker characterization * Diagnostics and prognostics.
Aminopeptidases: structure and function (1993)

Aminopeptidases catalyze the cleavage of amino acids from the amino terminus of protein or peptide substrates. They are widely distributed throughout the animal and plant kingdoms and are found in many subcellular organelles, in cytoplasm, and as membrane components. Several aminopeptidases perform essential cellular functions. Many, but not all, of these peptidases are zinc metalloenzymes and are inhibited by the transition-state analog bestatin. Some are monomeric, and others are assemblies of relatively high mass (50 kDa) subunits. cDNA sequences are available for several aminopeptidases, and a 3-dimensional structure is available for the bovine lens enzyme. Crystallographic, electron micrographic, NMR, and photoaffinity labeling studies indicate that lens leucine aminopeptidase protomers are bilobal and that bestatin and substrates are bound in an active site, which is found in the larger lobe on each protomer. Zn2+ is involved in substrate liganding in most aminopeptidases. There is no evidence of an acyl-enzyme intermediate in hydrolysis. Amino acid sequences determined directly or deduced from cDNAs indicate some amino acid sequence homologies in organisms as diverse as Escherichia coli and mammals, particularly in catalytically important residues or in residues involved in metal ion binding.
Controlling water in producing operations (1984)

Remedial cementing is the means most frequently used to inhibit water production. However, plugback and squeeze treatments are effective only if water-producing (or thieving) intervals can be identified and isolated, and if the formation prevents water from bypassing the treated interval. Cementing operations are detailed and sample calculations are provided, together with discussion of widely held misconceptions that surround this subject.
IFN-γ and TNF Regulate Macrophage Expression of the Chemotactic S100 Protein S100A8 (2000)

The murine calcium-binding protein S100A8 is a potent chemoattractant for neutrophils and monocytes in vivo and in vitro but may also play a protective role. We show that the kinetics of induction of S100A8 mRNA in elicited murine macrophages (Mac) by LPS, IFN-gamma, and TNF were distinct from the C-C chemokines monocyte chemoattractant protein-1 (MCP-1), macrophage-inflammatory protein-1alpha (MIP-1alpha), and RANTES. Monomeric S100A8 was predominantly secreted. IFN substantially increased S100A8 mRNA levels after 1 h with optimal induction after 12 h; induction by TNF was slower and more sustained. TNF did not up-regulate MCP-1 and MIP-1alpha mRNA in these cells. Luciferase reporter assays confirmed that LPS and IFN induce S100A8 gene transcription and mRNA in LPS-treated Mac showed little decay over 16 h, whereas transcripts induced by IFN and TNF were markedly less stable. Newly synthesized proteins may be required for mRNA transcription and stabilization in response to LPS. S100A9 associates with A8 in neutrophils, but was not coinduced with S100A8. S100A8 gene induction in Mac stimulated with LPS and IFN may be modulated by mobilization of intracellular Ca2+ concentration from distinct intracellular stores and/or the extracellular compartment and by distinct pathways involving protein kinase C and leading to activation of mitogen-activated protein kinase.
Contemporary issues: diseases with a food vector. (1988)

Foodborne disease has become a contemporary issue. Several large, well-publicized outbreaks of foodborne disease have heightened public awareness that harmful microorganisms may be present in food and that chronic as well as acute disease may be caused by foodborne microbes. The field of food microbiology has likewise experienced a resurgence of interest. New tools, such as recombinant deoxyribonucleic acid technology and monoclonal antibody production, used to elucidate microbial virulence factors have facilitated identification of disease-causing microbes once thought to be harmless and demonstrated the complexity of individual virulence mechanisms previously considered to be well understood. Foodborne pathogens are also causing disease via some surprising food vectors, such as chopped, bottled garlic and sauteed onions. In addition to acute gastrointestinal disturbances, certain microorganisms may, through complex interactions with the human immune response, cause chronic diseases that affect several major organ systems. These microbes are serving as models in studies of molecular mimicry and genetic interrelatedness of procaryotes and eucaryotes. Other recently recognized attributes of foodborne microorganisms, such as the heat shock phenomenon and the possible nonculturability of some bacteria, may affect their ability to cause disease in humans. Because foodborne disease is a major cause of morbidity and mortality, the study of these diseases and their causative microorganisms presents a unique challenge to many professionals in the subdisciplines of microbiology, epidemiology, and clinical medicine.
Copper-Catalyzed One-Pot Multicomponent Coupling Reaction of Phenols, Amides, and 4-Bromphenyl Iodide (2008)

An efficient copper-catalyzed multicomponent reaction of phenols, amides, and 4-bromphenyl iodide was developed that uses commercially available N,N-dimethylglycine as the ligand. This multicomponent reaction proceeds in moderate to good yields for a range of phenols and amides. The simple experimental procedure and high levels of functional group compatibility make this method attractive for applications on pesticides.