gebhart/patrepeval huggingface dataset:
Counting CAG repeats in the Huntington's disease gene by restriction endonuclease EcoP15I cleavage (2002)

Huntington's disease (HD) is a progressive neurodegenerative disorder with autosomal-dominant inheritance. The disease is caused by a CAG trinucleotide repeat expansion located in the first exon of the HD gene. The CAG repeat is highly polymorphic and varies from 6 to 37 repeats on chromosomes of unaffected individuals and from more than 30 to 180 repeats on chromosomes of HD patients. In this study, we show that the number of CAG repeats in the HD gene can be determined by restriction of the DNA with the endonuclease EcoP15I and subsequent analysis of the restriction fragment pattern by electrophoresis through non-denaturing polyacrylamide gels using the ALFexpress DNA Analysis System. CAG repeat numbers in the normal (30 and 35 repeats) as well as in the pathological range (81 repeats) could be accurately counted using this assay. Our results suggest that this high-resolution method can be used for the exact length determination of CAG repeats in HD genes as well as in genes affected in related CAG repeat disorders.
A new route for the synthesis of methacrylic acid from 2-methyl-1,3-propanediol by integrating biotransformation and catalytic dehydration (2012)

Methacrylic acid was produced in high yield by an integrated process involving bioconversion of 2-methyl-1,3-propanediol (2M1,3PD) to 3-hydroxy-2-methylpropionic acid (3H2MPA) via 3-hydroxy-2-methylpropanal (3H2MPAL), and catalytic dehydration of the resulting acid. Whole cells of Gluconobacter oxydans grown on glycerol-based culture medium were used as the catalyst for oxidative biotransformation that involved alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) enzymes in the organism. The effect of several reaction parameters on bioconversion in a batch system was investigated to obtain 95–100% conversion of 2M1,3PD with over 95% selectivity to 3H2MPA. The optimum conditions for bioconversion were pH 6–7.5, 25–30 °C, 5–10 g substrate and 2.6 g cell (dry weight) per liter. Higher substrate concentrations led to enzyme inhibition and incomplete conversion. Loss of catalytic activity was noted during recycling of the cells. The cells were active for a longer period when used for biotransformation of 20 g per L of substrate in a continuous reactor with cell retention. The product of the bio-oxidation, 3H2MPA, was converted using titanium dioxide at 210 °C to give methacrylic acid (MA) with a yield of over 85%. The integrated process provides a new environmentally benign route for production of methacrylic acid from 2-methyl-1,3-propanediol, an industrial by-product, compared with the conventional acetone-cyanohydrin (ACH) process.
Proteomic analysis of injured spinal cord tissue proteins using 2‐DE and MALDI‐TOF MS (2006)

Spinal cord injury (SCI) induces a progressive pathophysiology affecting cell survival and neurological integrity via complex and evolving molecular cascades whose interrelationships are not fully understood. Acute injury to the spinal cord undergoes sequential pathological change including hemorrhage, edema, axonal and neuronal necrosis, and demyelination. In the present study, we aimed to establish the proteomic profiles and characterization of the total protein expressed in traumatic injured spinal cord tissue by using 2-DE and matrix assisted laser desorption/ionization-TOF MS (MALDI-TOF MS). We performed proteomic analysis using 2-DE and MS to describe total proteins and differential proteins expression between normal and traumatic injured spinal cord tissues. The study discovered 947 total proteins and analyzed 219 and 270 proteins from normal and injured tissue, respectively. After 24 h of traumatic damage induction, the injured spinal cord tissue up-regulated over 39 proteins including neurofilament light chain, annexin 5, heat shock protein, tubulin beta, peripherin, glial fibrillary acidic protein delta, peroxiredoxin 2, and apolipoprotein A. Twenty-one proteins showed reduction. The majority of the modulated proteins belonged to the 13 functional categories. Proteins that were identified with neural functional category in injured tissue were considered most likely to be involved in wound healing response coupled with neurogenesis and gliogenesis.
Polycrystalline silicon ion sensitive field effect transistors (2005)

We report the operation of polycrystalline silicon ion sensitive field effect transistors. These devices can be fabricated on inexpensive disposable substrates such as glass or plastics and are, therefore, promising candidates for low cost single-use intelligent multisensors. In this work we have developed an extended gate structure with a Si3N4 sensing layer. Nearly ideal pH sensitivity (54mV∕pH) and stable operation have been achieved. Temperature effects have been characterized. A penicillin sensor has been fabricated by functionalizing the sensing area with penicillinase. The sensitivity to penicillin G is about 10mV∕mM, in solutions with concentration lower than the saturation value, which is about 7 mM.
Optical phase-shifted array resonator used in radio-frequency-excited slab waveguide <inline-formula><roman>CO</roman><sub><roman>2</roman></sub></inline-formula> lasers (1998)

An optical resonator with a phase-shifting array end mirror is presented to obtain an output beam of spatially suppressed far-field intensity distribution from a CO2 laser with a slab waveguide gain medium. A highly spatially suppressed single-peak intensity distribution in the far field and a power of 46 W have been obtained from a 200-mm-gainlength device.
Anti-CD3 antibody induces unresponsiveness to IL-2 in Th1 clones but not in Th2 clones. (1990)

Abstract Culture of murine T cells with immobilized (platebound) anti-CD3 antibody results in autocrine growth factor secretion in both Th1 (IL-2 producing) and Th2 (IL-4 producing) cells. Using a panel of murine T cell clones, we demonstrate that the IL-2-induced proliferation of Th1 clones is dramatically inhibited by immobilized anti-CD3 antibody, whereas that of Th2 clones is not. This unresponsiveness of Th1 clones to IL-2 is not due to decreases in IL-2R expression. Supernatants from Th1 or Th2 cell cultures fail to alter the effects of anti-CD3 on the two types of clones, suggesting that unresponsiveness induced in Th1 clones or the lack thereof in Th2 clones is not mediated by a stable cytokine(s). Accessory cells enhance the proliferation of Th1 cells exposed to low concentrations of anti-CD3, but the unresponsiveness induced by high concentrations of anti-CD3 is not prevented by accessory cells. Finally, soluble anti-CD4 antibody prevents the induction of the unresponsive state even at high concentrations of anti-CD3. These experiments demonstrate that two subsets of cloned CD4+ T cells differ in their responses to anti-CD3, and that CD4 molecules may play a critical role in regulating the outcome of receptor-mediated stimulation.
249: Comparison of Genomic Alterations of Disseminated Tumor Cells and the Primary Tumor From Prostate Carcinoma Patients (2006)

You have accessJournal of UrologyDiscussed Poster, Sunday, May 21, 2006, 9:00 am - 12:00 pm1 Apr 2006249: Comparison of Genomic Alterations of Disseminated Tumor Cells and the Primary Tumor From Prostate Carcinoma Patients Karen Blümke, Christina Karzek, Udo Bilkenroth, Helge Taubert, Andres Melchior, Hans Heynemann, and Paolo Fomara Karen BlümkeKaren Blümke More articles by this author , Christina KarzekChristina Karzek More articles by this author , Udo BilkenrothUdo Bilkenroth More articles by this author , Helge TaubertHelge Taubert More articles by this author , Andres MelchiorAndres Melchior More articles by this author , Hans HeynemannHans Heynemann More articles by this author , and Paolo FomaraPaolo Fomara More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)32516-3AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "249: Comparison of Genomic Alterations of Disseminated Tumor Cells and the Primary Tumor From Prostate Carcinoma Patients." The Journal of Urology, 175(4S), p. 83 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 175Issue 4SApril 2006Page: 83 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Karen Blümke More articles by this author Christina Karzek More articles by this author Udo Bilkenroth More articles by this author Helge Taubert More articles by this author Andres Melchior More articles by this author Hans Heynemann More articles by this author Paolo Fomara More articles by this author Expand All Advertisement PDF downloadLoading ...
Disease Progression in Hemodynamically Stable Patients Presenting to the Emergency Department With Sepsis (2010)

A significant portion of ED patients with less severe sepsis progress to severe sepsis or shock within 72 hours. Additional diagnostic approaches are needed to risk stratify and more effectively treat ED patients with sepsis.
Real-time observations of lithium battery reactions—operando neutron diffraction analysis during practical operation (2016)

Among the energy storage devices for applications in electric vehicles and stationary uses, lithium batteries typically deliver high performance. However, there is still a missing link between the engineering developments for large-scale batteries and the fundamental science of each battery component. Elucidating reaction mechanisms under practical operation is crucial for future battery technology. Here, we report an operando diffraction technique that uses high-intensity neutrons to detect reactions in non-equilibrium states driven by high-current operation in commercial 18650 cells. The experimental system comprising a time-of-flight diffractometer with automated Rietveld analysis was developed to collect and analyse diffraction data produced by sequential charge and discharge processes. Furthermore, observations under high current drain revealed inhomogeneous reactions, a structural relaxation after discharge, and a shift in the lithium concentration ranges with cycling in the electrode matrix. The technique provides valuable information required for the development of advanced batteries.
Characterizing user behavior in online social networks (2009)

Understanding how users behave when they connect to social networking sites creates opportunities for better interface design, richer studies of social interactions, and improved design of content distribution systems. In this paper, we present a first of a kind analysis of user workloads in online social networks. Our study is based on detailed clickstream data, collected over a 12-day period, summarizing HTTP sessions of 37,024 users who accessed four popular social networks: Orkut, MySpace, Hi5, and LinkedIn. The data were collected from a social network aggregator website in Brazil, which enables users to connect to multiple social networks with a single authentication. Our analysis of the clickstream data reveals key features of the social network workloads, such as how frequently people connect to social networks and for how long, as well as the types and sequences of activities that users conduct on these sites. Additionally, we crawled the social network topology of Orkut, so that we could analyze user interaction data in light of the social graph. Our data analysis suggests insights into how users interact with friends in Orkut, such as how frequently users visit their friends' or non-immediate friends' pages. In summary, our analysis demonstrates the power of using clickstream data in identifying patterns in social network workloads and social interactions. Our analysis shows that browsing, which cannot be inferred from crawling publicly available data, accounts for 92% of all user activities. Consequently, compared to using only crawled data, considering silent interactions like browsing friends' pages increases the measured level of interaction among users.
Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities (2003)

Prokaryotic chromosomes often contain islands, such as temperate phages or pathogenicity islands, delivered by site-specific integrases. Integration usually occurs within a tRNA or tmRNA gene, splitting the gene, yet sequences within the island restore the disrupted gene. The regenerated RNA gene and the displaced fragment of that gene thus mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm generates a list of tRNA and tmRNA genes, uses each as the query for a BLAST search of the starting DNA and removes unlikely hits through a series of filters. A search for islands in 106 whole bacterial genomes produced 143 candidates, with the search itself providing an estimate of three false candidates among these. Preliminary phylogenetic analysis of the associated integrases reduced this set to 89 cases of independently evolved site specificity, which showed strong bias for the tmRNA gene. The website Islander (http://www.indiana.edu/ approximately islander) presents the candidate islands in GenBank-style files and correlates integrase phylogeny with site specificity.
A Method for Efficient Broadband Marine Acquisition and Processing (2009)

We present a new method for broadband marine acquisition and processing. A 3D shallow towed-streamer spread is deployed, designed to optimize the mid- and high-frequency parts of the bandwidth. In addition, data are simultaneously acquired from a small nu
Simulated moving bed under linear conditions: Experimental vs. calculated results (1997)

Abstract A simulated moving bed (SMB) was operated for the separation of mixtures of 2‐phenyl ethanol and 3‐phenyl‐1‐propanol on columns packed with Zorbax C18 bonded silica, using a 60:40 (v/v) solution of methanol and water as the mobile phase. Series of four or eight columns were used. The experiments were carried out with low concentration mixtures, that is, under linear conditions. Band profiles of both compounds eluted from one of the columns during successive periods after steady state had been reached were recorded, as were the concentration histories at the extract and raffinate ports. These experimental results are compared to those predicted by two models: the linear ideal and the linear equilibrium‐dispersive models of chromatography, applied to the SMB separator. These two models give excellent agreement between the experimental profiles and those calculated with the model. As expected, the profiles predicted by the ideal and the equilibrium‐dispersive models differ only by the lack of dispersion in the profiles given by the former. The latter model is demonstrated to be a solid, reliable tool for further studies of the SMB design and optimization.
Signal Requirement for Memory Cytotoxic T Lymphocytes. (1993)

Generation of an optimal immune response against a pathogen leads to protection from disease. Cytokines orchestrate a complex but well coordinated interaction between the cells of the immune system. Precise and sequential signals are required for the induction of a particular cellular function. In this study, I have analyzed the minimal signal requirement for memory cytotoxic T lymphocyte (mCTL) effector function. I have used human peripheral blood T cells as the source of influenza virus specific mCTL precursors, and influenza virus infected and formaldehyde fixed cells as antigen presenters in our assay system. Using this model, we have identified an essential requirement for antigenic restimulation in influenza virus specific mCTL induction. Further I show here, using known recombinant cytokines, that IL-4, IL-7, IL-10 and IL-12 can function as CTL differentiation factors. Unlike many previous reports, in our assay system, we did not find any direct cytotoxicity induction by IL-2, but it has modulatory role on IL-7, IL-10 and IL-12 mediated induction of cytotoxicity. In contrast to IL-2, IL-4 has both positive and negative regulatory effects on cytotoxicity induction and depends critically on the time of addition of cytokines after antigen encounter.
A formal study of distributed meeting scheduling (1991)

article Free Access Share on A formal study of distributed meeting scheduling: preliminary results Authors: Sandip Sen Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MIView Profile , Edmund H. Durfee Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MIView Profile Authors Info & Claims ACM SIGOIS BulletinVolume 12Issue 2-3Nov. 1991 pp 55–68https://doi.org/10.1145/127769.122837Online:01 October 1991Publication History 21citation525DownloadsMetricsTotal Citations21Total Downloads525Last 12 Months13Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Spongialization (1979)

Spongialization is an extension of the concept of Pridie for resurfacing damaged joints. The diseased cartilage is excised and the subchondral plate completely removed exposing the cancellous bone or "spongiosa" from which a new fibrous tissue surface can grow. The technique is particularly applicable to a localized lesion of the patella. Eighty-five patients who had patellar spongialization and were followed from 6--36 months (average 15 months) are reported, with 79% reporting good or excellent results. Provided that there was severe cartilage damage in each case, the early results are better than with either patellectomy or "shaving" of the diseased cartilage.
Evaluation of a Rapid Bedside Assay for Detection of Serum Cardiac Troponin T (1995)

The rapid cTnT assay is a simple, efficient test that for the first time provides clinicians with a useful laboratory tool for point-of-care evaluation of patients with chest pain.
Towards a semantic-based approach for software reusable component classification and retrieval (2004)

In this paper, we propose a semantic-based approach to improve software component reuse. The whole approach extends the software reusable library to the World Wide Web; overcomes the keyword-based barrier by allowing user queries in natural language; treats a software component as a service described by semantic service representation format; enhances the retrieval by semantically matching between a user query semantic representation and software component semantic descriptions against a domain ontology; and finally stores the relevant software components into a reusable repository based UDDI infrastructure. The technologies applied to achieve the goal include: Natural Language Processing, Web services, Semantic Web, Conceptual Graph, domain ontology. The research in the first phase will focus on the classification and retrieval for software reusable components. In the classification process, natural language processing and domain knowledge technologies are employed for program understanding down to code level, and Web services and Semantic Web technologies as well as Conceptual Graph are used to semantically describe/represent a component. In the retrieval process, a user query in natural language is translate into semantic representation formats in order to augment retrieval recall and precision by deploying the same semantic representation technologies on both the user query side and the component side.
Automatic Personal Identification System for Security in Critical Services: Two Case Studies based on a Wireless Biometric Badge (2011)

Automatic Personal Identification System for Security in Critical Services: Two Case Studies based on a Wireless Biometric Badge
Active Flow Control via Discrete Sweeping and Steady Jets on a Simple-Hinged Flap (2018)

Active flow control (AFC) in the form of sweeping jet (SWJ) excitation and discrete steady jet excitation is used to control the flow separation on a National Advisory Council for Aeronautics (NACA) 0015 semispan wing with a deflected, simple-hinged, trailing edge flap. This geometry has been the focus of several recent publications that investigated methods to improve the efficiency of SWJ actuators. In the current study, the interaction of the AFC excitation with the separated flowfields of several flap deflection angles was examined. Previous studies with this model have been limited to a maximum flap deflection angle of 40 deg. The flap deflection range was extended to 60 deg because systems studies have indicated that a high-lift system with simple-hinged flaps may require larger flap deflections than the Fowler flaps found on most high-lift systems. The results obtained at flap deflection angles of 20, 40, and 60 deg are presented and compared. Force and moment data, particle image velocimetry (PIV) data, and steady and unsteady surface pressure data are used to describe the flowfield with and without AFC. With a flap deflection of 60 deg, increasing the SWJ actuator momentum at the flap shoulder increased lift due to an increase in circulation but did not completely eliminate the recirculation region above the flap surface. AFC using the discrete steady jet actuators of this study increased lift as well but required more mass flow than the SWJ actuators and had a detrimental effect on lift at the highest mass flow level tested. PIV results showed that the angle between the excitation and the flap surface was not optimal for attaching the separated shear layer.
Taking advantage of neural development to treat glioblastoma (2014)

Glioblastoma (GBM) is by far the most common and most malignant primary adult brain tumor (World Health Organization grade IV), containing a fraction of stem-like cells that are highly tumorigenic and multipotent. Recent research has revealed that GBM stem-like cells play important roles in GBM pathogenesis. GBM is thought to arise from genetic anomalies in glial development. Over the past decade, a wide range of studies have shown that several signaling pathways involved in neural development, including basic helix-loop-helix, Wnt-β-catenin, bone morphogenetic proteins-Smads, epidermal growth factor-epidermal growth factor receptor, and Notch, play important roles in GBM pathogenesis. In this review, we highlight the significance of these pathways in the context of developing treatments for GBM. Extrapolating knowledge and concepts from neural development will have significant implications for designing better strategies with which to treat GBM.
Lifespan Extension and Rescue of Spongiform Encephalopathy in Superoxide Dismutase 2 Nullizygous Mice Treated with Superoxide Dismutase–Catalase Mimetics (2001)

Superoxide is produced as a result of normal energy metabolism within the mitochondria and is scavenged by the mitochondrial form of superoxide dismutase (sod2). Mice with inactivated SOD2 (sod2 nullizygous mice) die prematurely, exhibiting several metabolic and mitochondrial defects and severe tissue pathologies, including a lethal spongiform neurodegenerative disorder (Li et al., 1995; Melov et al., 1998, 1999). We show that treatment of sod2 nullizygous mice with synthetic superoxide dismutase (SOD)-catalase mimetics extends their lifespan by threefold, rescues the spongiform encephalopathy, and attenuates mitochondrial defects. This class of antioxidant compounds has been shown previously to extend lifespan in the nematode Caenorhabditis elegans (Melov et al., 2000). These new findings in mice suggest novel therapeutic approaches to neurodegenerative diseases associated with oxidative stress such as Friedreich ataxia, spongiform encephalopathies, and Alzheimer's and Parkinson's diseases, in which chronic oxidative damage to the brain has been implicated.