gebhart/patrepeval huggingface dataset:
Toward fully automated genotyping: genotyping microsatellite markers by deconvolution. (1995)

Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA)n repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements.
The Influence of the Proinflammatory Cytokine, Osteopontin, on Autoimmune Demyelinating Disease (2001)

Multiple sclerosis is a demyelinating disease, characterized by inflammation in the brain and spinal cord, possibly due to autoimmunity. Large-scale sequencing of cDNA libraries, derived from plaques dissected from brains of patients with multiple sclerosis (MS), indicated an abundance of transcripts for osteopontin (OPN). Microarray analysis of spinal cords from rats paralyzed by experimental autoimmune encephalomyelitis (EAE), a model of MS, also revealed increased OPN transcripts. Osteopontin-deficient mice were resistant to progressive EAE and had frequent remissions, and myelin-reactive T cells in OPN-/- mice produced more interleukin 10 and less interferon-gamma than in OPN+/+ mice. Osteopontin thus appears to regulate T helper cell-1 (TH1)-mediated demyelinating disease, and it may offer a potential target in blocking development of progressive MS.
Co-purification of p34cdc2/p58cyclin A proline-directed protein kinase and the retinoblastoma tumor susceptibility gene product: interaction of an oncogenic serine/threonine protein kinase with a tumor-suppressor protein. (1992)

Proline-directed protein kinase (PDPK) is characterized as a cytoplasmic oncogenic serine/threonine kinase that is activated by growth factor-mediated mechanisms and is proposed to function in mammalian somatic cells as an S phase promoting factor. The present study was undertaken to assess the hypothesis that p34cdc2/p58cyclinA PDPK is a physiologically relevant form of the p34cdc2 protein kinase that phosphorylates and inactivates the product of the retinoblastoma/osteosarcoma tumor susceptibility gene (Rb protein). In the course of these studies it was determined (fortuitously) that the p34cdc2/p58cyclinA PDPK purified from the cytosol of FM3A mouse mammary carcinoma cells was 'contaminated' by several high molecular weight substrate proteins that essentially co-purified with the protein kinase, one of which was identified as the Rb protein itself (p105Rb). High-resolution fast protein liquid chromatography (FPLC) revealed that the Rb protein co-purified with a particular subset of the PDPK heterodimer, i.e. with a single species of the 58 kDa cyclinA doublet. The subset of PDPK associated with the Rb protein exhibited somewhat lower specific enzyme activity, as judged by in vitro kinase assays and comparative Western blotting. Immunoprecipitation studies confirmed that p105Rb is physically associated with the p34cdc2/p58cyclin A PDPK. Further studies confirmed that the underphosphorylated Rb protein (p105Rb) present in G1 lysates of synchronized human MG63 osteosarcoma cells could be readily phosphorylated by purified PDPK in vitro, resulting in the characteristic shift in the apparent molecular mass (SDS-PAGE) of the Rb protein that is reported to accompany the hyperphosphorylation and functional inactivation of this protein. Moreover, the induction of the cyclin A subunit of PDPK in these synchronized MG63 cells was found to be closely correlated with the cell cycle-dependent phosphorylation of the Rb protein. From these studies it is concluded that the growth factor-sensitive PDPK is a physiological Rb kinase, which may function to inactivate the Rb protein in vivo.
Flexible-foam-based capacitive sensor arrays for object detection at low cost (2008)

Polymer foams are used in the automotive and construction industries for thermal insulation, vibration attenuation, and pressure absorption, due to their lightweight structure, thermal characteristics and low manufacturing costs. These foams have higher elasticity in their cross sections than bulk polymers, which makes them the preferred mount for capacitive sensor arrays. The authors describe a flexible pressure-sensitive surface mounted on packaging foam. The elastic properties of the foam are presented along with the sensor array’s weight sensitivity. The authors illustrate an inventory management application where objects on display can be detected through their weights.
3,4-Diaminopyridine in the treatment of congenital (hereditary) myasthenia. (1991)

Congenital or hereditary myasthenia describes a heterogeneous group of disorders in which the immune system is not implicated. Treatment has previously depended on anticholinesterase medication. The effectiveness of 3,4-diaminopyridine (3,4-DAP), a preparation that enhances acetylcholine release from motor nerve terminals, has been evaluated using a series of standardised strength measures. Sixteen patients (aged seven to 47 years) were studied in an open prospective trial, and four of them in a double blind crossover trial; existing anticholinesterase medication was continued. For the group as a whole, there was a highly significant increase in muscle strength (p less than 0.001; n = 16). In individual paired comparisons, 13 out of 16 showed significant improvement in the open trial and four out of four in the blind crossover trial. In conclusion, 3,4-DAP, either alone or combined with anticholinesterase medication, may be a useful additional treatment in congenital myasthenia.
Cooperative Regulation of Cell Polarity and Growth by Drosophila Tumor Suppressors (2000)

Loss of cell polarity and tissue architecture are characteristics of malignant cancers derived from epithelial tissues. We provide evidence from Drosophila that a group of membrane-associated proteins act in concert to regulate both epithelial structure and cell proliferation. Scribble (Scrib) is a cell junction-localized protein required for polarization of embryonic and, as demonstrated here, imaginal disc and follicular epithelia. We show that the tumor suppressors lethal giant larvae (lgl) and discs-large (dlg) have identical effects on all three epithelia, and that scrib also acts as a tumor suppressor. Scrib and Dlg colocalize and overlap with Lgl in epithelia; activity of all three genes is required for cortical localization of Lgl and junctional localization of Scrib and Dlg. scrib, dlg, and lgl show strong genetic interactions. Our data indicate that the three tumor suppressors act together in a common pathway to regulate cell polarity and growth control.
Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis (2017)

Incidences of invasive pulmonary aspergillosis, an infection caused predominantly by Aspergillus fumigatus, have increased due to the growing number of immunocompromised individuals. While A. fumigatus is reliant upon deficiencies in the host to facilitate invasive disease, the distinct mechanisms that govern the host-pathogen interaction remain enigmatic, particularly in the context of distinct immune modulating therapies. To gain insights into these mechanisms, RNA-Seq technology was utilized to sequence RNA derived from lungs of 2 clinically relevant, but immunologically distinct murine models of IPA on days 2 and 3 post inoculation when infection is established and active disease present. Our findings identify notable differences in host gene expression between the chemotherapeutic and steroid models at the interface of immunity and metabolism. RT-qPCR verified model specific and nonspecific expression of 23 immune-associated genes. Deep sequencing facilitated identification of highly expressed fungal genes. We utilized sequence similarity and gene expression to categorize the A. fumigatus putative in vivo secretome. RT-qPCR suggests model specific gene expression for nine putative fungal secreted proteins. Our analysis identifies contrasting responses by the host and fungus from day 2 to 3 between the two models. These differences may help tailor the identification, development, and deployment of host- and/or fungal-targeted therapeutics.
Synthesis of some novel 1,3-dihydro-2H-benzimidazol-2-ylidenes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleSynthesis of some novel 1,3-dihydro-2H-benzimidazol-2-ylidenesRobert A. Mack, Vassil St. Georgiev, Edwin S. C. Wu, and James R. MatzCite this: J. Org. Chem. 1993, 58, 22, 6158–6162Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/jo00074a059https://doi.org/10.1021/jo00074a059research-articleACS PublicationsRequest reuse permissionsArticle Views222Altmetric-Citations7LEARN 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
Dietary Antioxidant Vitamins and Death from Coronary Heart Disease in Postmenopausal Women (1996)

These results suggest that in postmenopausal women the intake of vitamin E from food is inversely associated with the risk of death from coronary heart disease and that such women can lower their risk without using vitamin supplements. By contrast, the intake of vitamins A and C was not associated with lower risks of dying from coronary disease.
A functional role of prostate-specific membrane antigen in prostate cancer metastasis (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

4373 

Despite the consistent finding of upregulated prostate specific membrane antigen (PSMA) with increased prostate cancer (PCa) aggressiveness, the functional role of PSMA in PCa is unknown. Recently, it was reported that suppression of PSMA expression increases invasiveness, and expression of inactivating PSMA mutants reduces invasiveness. In this study, using in vitro cell model systems and live-cell imaging methods, we characterized the role of PSMA in cell motility and adhesion. We demonstrated, using wound-healing assay, that PSMA expression reduces cell motility when compared with control PSMA-negative PCa cells. Six hours after wounding, significant numbers of PSMA-negative cells migrating into the wounded area could be observed. In contrast, limited migration was observed in cells expressing PSMA. We also found enhanced PCa cell motility in cells when the PSMA enzymatic activity was inhibited by a specific anti-PSMA antibody. When live cell motility was recorded, the number of PSMA-positive LNCaP cells migrating into the wounded area was almost 2-fold higher in the presence of the inhibitory antibody than control LNCaP cells in the absence of the antibody. No difference in the number of the PSMA-negative PC3 cell migration was observed with or without the application of the inhibitory antibody. More interestingly, we found that expression of PSMA results in morphologically better-spreading PCa cells with redistributed F-actin filaments that regulate cell adhesion and motility. Since the progression of PCa is a multi-stage process that requires repeated adhesion to and detachment from the extracellular matrix microenvironment, our results suggest that PSMA may play a role in PCa adhesion and migration during PCa metastasis.
Advantages of the Parent Nucleoside GS-441524 over Remdesivir for Covid-19 Treatment (2020)

While remdesivir has garnered much hope for its moderate anti-Covid-19 effects, its parent nucleoside, GS-441524, has been overlooked. Pharmacokinetic analysis of remdesivir evidences premature serum hydrolysis to GS-441524; GS-441524 is the predominant metabolite reaching the lungs. With its synthetic simplicity and <i>in vivo</i> efficacy in the veterinary setting, we contend that GS-441524 is superior to remdesivir for Covid-19 treatment.
Outcome of Respiratory Symptoms After Antireflux Surgery on Patients With Gastroesophageal Reflux Disease (1996)

Respiratory symptoms are common in patients with GERD. Unlike classic reflux symptoms, the beneficial effects of antireflux surgery on respiratory symptoms are less predictable. The probability of relief of these respiratory symptoms with antireflux surgery is directly dependent on esophageal motor function.
The International Workshop on Meibomian Gland Dysfunction: Report of the Diagnosis Subcommittee (2011)

Diagnostic tests of meibomian gland dysfunction (MGD) and of MGD-related disorders are based on the demonstration of abnormal anatomy and physiology of the glands and the detection of specific pathologic events. For this reason, this subcommittee report is divided into two sections. In part I, those aspects of meibomian anatomy and physiology that are relevant to currently available tests are described; a fuller account of the anatomy and physiology is provided in the report of the Anatomy Subcommittee of this workshop. In part II, each test and its performance is described in detail. In part III, the practical application of selected tests is summarized and recommendations for future approaches are made.
Growth Hormone Administration and Exercise Effects on Muscle Fiber Type and Diameter in Moderately Frail Older People (2001)

Our results are encouraging in that they suggest an effect of growth hormone on a specific aging-correlated deficit. IGF-I was increased by administrating rhGH and muscle strength was increased by exercise. The administration of rhGH to frail older individuals in this study resulted in significant changes in the proportions of fiber types. Whether changes in fiber cross-sectional area or absolute number occur with long-term growth hormone administration requires further study.
Specific developmental disruption of disrupted-in-schizophrenia-1 function results in schizophrenia-related phenotypes in mice (2007)

Disrupted-in-schizophrenia 1 (DISC1) was initially discovered through a balanced translocation (1;11)(q42.1;q14.3) that results in loss of the C terminus of the DISC1 protein, a region that is thought to play an important role in brain development. Here, we use an inducible and reversible transgenic system to demonstrate that early postnatal, but not adult induction, of a C-terminal portion of DISC1 in mice results in a cluster of schizophrenia-related phenotypes, including reduced hippocampal dendritic complexity, depressive-like traits, abnormal spatial working memory, and reduced sociability. Accordingly, we report that individuals in a discordant twin sample with a DISC1 haplotype, associating with schizophrenia as well as working memory impairments and reduced gray matter density, were more likely to show deficits in sociability than those without the haplotype. Our findings demonstrate that alterations in DISC1 function during brain development contribute to schizophrenia pathogenesis.
CD38-targeting antibodies in multiple myeloma: mechanisms of action and clinical experience (2018)

Multiple myeloma (MM) is generally an incurable hematological malignancy with heterogeneous overall survival rates ranging from a few months to more than 10 years. Survival is especially poor for patients who developed disease that is refractory to immunomodulatory drugs and proteasome inhibitors. Areas covered: This review will discuss the importance of CD38-targeting antibodies for the treatment of MM patients to improve their outcome. Expert commentary: Intense immuno-oncological laboratory research has resulted in the development of functionally active monoclonal antibodies against cell surface markers present on MM cells. In this respect, CD38-targeting antibodies such as daratumumab, MOR202, and isatuximab, have high single agent activity in heavily pretreated MM patients by virtue of their pleiotropic mechanisms of action including Fc-dependent effector mechanisms and immunomodulatory activities. Importantly, CD38-targeting antibodies are well tolerated, with infusion reactions as most frequent adverse event. Altogether, this makes them attractive combination partners with other anti-MM agents. Daratumumab is already approved as monotherapy and in combination with lenalidomide-dexamethasone as well as bortezomib-dexamethasone in pretreated MM patients. Furthermore, results from studies evaluating CD38-targeting antibodies in newly diagnosed MM patients are also promising, indicating that CD38-targeting antibodies will be broadly used in MM, resulting in further improvements in survival.
An on-line communication print service for the demanding client (1993)

The increased interest in on-line documentation is htinga~mado~ti~donm~dprintas as volumes decrease but quality requirements increase. Not only are printers m-evaluating theft futures,but they are consultingwithcustorners on how a new service offering would enhance the on-line document. This new service would allow users to submit files toanoff-siteprinteras easily as using the desktop icon. The explanation of this solution will encompaw Wt only the communication meditnn, butalso the hardware and software available for any type of platform or network. This paper will describe working solutions for on-line/offsite network connections and the level of quality and expertise which should keexpected. We will try to evaluate the future forprintersin a global, international market place.
Compliant motion control for continuum robots with intrinsic actuation sensing (2011)

Novel minimally invasive surgical paradigms accessing deep surgical sites present a new challenge of safe instrument insertion and navigation. This paper addresses this challenge by presenting a new framework for compliant motion control of multi-backbone continuum robots subject to whole-arm contacts. This control framework does not rely on knowledge of contact locations along the length of a continuum robot. Instead, the forces at joint level are applied as controller inputs to generate compliant motion. The paper first presents a new mapping of the external wrenches to a generalized force in the configuration space of a single-stage multi-backbone continuum robot. A closed-form analytic expression for the passive stiffness of a multi-backbone continuum robot segment is also presented. A controller, robust to uncertainties of the system model, is proposed to provide compliant motion of the continuum robot segment by using the generalized force and stiffness definitions. Stability, convergence, and controller properties are shown through experimental validation. The presented framework defines a method for providing compliant motion to continuum robots without explicit knowledge of the environment. We believe this work enables new control algorithms for rapidly deployable surgical robots and supports novel surgical paradigms by increasing safety during unstructured interaction with flexible anatomy.
The synthesis and configurational stability of differentially protected .beta.-hydroxy-.alpha.-amino aldehydes (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe synthesis and configurational stability of differentially protected .beta.-hydroxy-.alpha.-amino aldehydesPhilip Garner and Jung Min ParkCite this: J. Org. Chem. 1987, 52, 12, 2361–2364Publication Date (Print):June 1, 1987Publication History Published online1 May 2002Published inissue 1 June 1987https://pubs.acs.org/doi/10.1021/jo00388a004https://doi.org/10.1021/jo00388a004research-articleACS PublicationsRequest reuse permissionsArticle Views5084Altmetric-Citations369LEARN 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
Orthogonal Color-Mixture Functions* (1954)

Spectre-photometric curves uniquely determined by every set of color specifications can be based on a Fourier-type analysis, using normal and orthogonal color-mixture functions. Normal and orthogonal color-mixture functions are convenient for the investigation of the propagation of errors in spectrophotometric colorimetry. The space based on normal and orthogonal color-mixture functions serves as a suggestive model for the as yet unavailable visually homogeneous color space, in which visual thresholds of color shall be represented by equal-size spheres, at least for some fixed conditions of adaptation. Recent puzzling results of investigations of color discrimination and heterochromatic photometry can be explained in a straightforward manner in terms of general properties of visually homogeneous color space. Those properties are independent of the detailed structure of that space and are exemplified, though probably in a simplified manner, by the color space based on normal and orthogonal color-mixture functions.
Compiler-assisted Hybrid Operand Communication (2009)

Communication of operands among in-flight instructions can be power intensive, especially in superscalar processors where all result tags are broadcast to a small number of consumers through a multi-entry CAM. Token-based point-to-point communication of operands in dataflow architectures is highly efficient when each produced token has only one consumer, but inefficient when there are many consumers due to the construction of software fanout trees. Placing operands in registers is efficient for broadcasting the values which have consumers spread over a long lifetime, but inefficient for shorter-lived operations. This paper evaluates a compilerassisted hybrid instruction communication model that combine tokens instruction communication with statically assigned broadcast tags. Each fixed-size block of code is given a small number of architectural broadcast identifiers, which the compiler can assign