gebhart/patrepeval huggingface dataset:
A Metadata Catalog Service for Data Intensive Applications (2003)

Advances in computational, storage and network technologies as well as middle ware such as the Globus Toolkit allow scientists to expand the sophistication and scope of data-intensive applications. These applications produce and analyze terabytes and petabytes of data that are distributed in millions of files or objects. To manage these large data sets efficiently, metadata or descriptive information about the data needs to be managed. There are various types of metadata, and it is likely that a range of metadata services will exist in Grid environments that are specialized for particular types of metadata cataloguing and discovery. In this paper, we present the design of a Metadata Catalog Service (MCS) that provides a mechanism for storing and accessing descriptive metadata and allows users to query for data items based on desired attributes. We describe our experience in using the MCS with several applications and present a scalability study of the service.
Zeta potential of microfluidic substrates: 2. Data for polymers (2004)

Zeta potential data are reviewed for a variety of polymeric microfluidic substrate materials. Many of these materials currently used for microchip fabrication have only recently been employed for generation of electroosmotic flow. Despite their recent history, polymeric microfluidic substrates are currently used extensively for microchip separations and other techniques, and understanding of the surface zeta potential is crucial for experimental design. This paper proposes the use of pC (the negative logarithm of the counterion concentration) as a useful normalization for the zeta potential on polymer substrates in contact with indifferent univalent counterions. Normalizing zeta by pC facilitates comparison of results from many investigators. The sparseness of available data for polymeric substrates prevents complete and rigorous justification for this normalization; however, it is consistent with double layer and adsorption theory. For buffers with indifferent univalent cations, normalization with the logarithm of the counterion concentration in general collapses data onto a single zeta/pC vs. pH curve, and (with the exception of PMMA) the repeatability of the data is quite encouraging. Normalization techniques should allow improved ability to predict zeta potential performance on microfluidic substrates and compare results observed with different parameters.
Enhanced evolutionary PCR using oligonucleotides with inosine at the 3′-terminus (1991)

Journal Article Enhanced evolutionary PCR using oligonucleotides with inosine at the 3′-terminus Get access Mark A. Batzer, Mark A. Batzer 1Department of Biochemistry and Molecular Biology1901 Perdido Street, New Orleans, LA 70112 Search for other works by this author on: Oxford Academic PubMed Google Scholar James E. Carlton, James E. Carlton 2Biotechnology Core Laboratories, Louisiana State University Medical Center1901 Perdido Street, New Orleans, LA 70121 Search for other works by this author on: Oxford Academic PubMed Google Scholar Prescott L. Deininger Prescott L. Deininger 1Department of Biochemistry and Molecular Biology1901 Perdido Street, New Orleans, LA 701123Laboratory of Molecular Genetics, Alton Ochsner Medical FoundationNew Orleans, LA 70121, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 18, 25 September 1991, Page 5081, https://doi.org/10.1093/nar/19.18.5081 Published: 25 September 1991 Article history Received: 12 July 1991 Published: 25 September 1991
Higher levels of prorenin predict development of diabetic retinopathy in patients with type 2 diabetes (2011)

The aim was to determine whether serum prorenin levels affect the development of diabetic retinopathy (DR) in type 2 diabetes. Baseline serum prorenin levels were measured in 196 patients (85 males, 111 females) with type 2 diabetes without DR using the antibody-activating direct prorenin assay. The fundi were checked regularly. The participants were divided into two groups based on the serum prorenin levels (high and low). We used Kaplan—Meyer analysis to detect differences in the development of DR between the two groups within the same gender. Kaplan—Meyer analysis showed that males with a high serum prorenin level tended to develop DR earlier and more frequently than males with a low prorenin level ( p = 0.004 by the log rank test). However, there was no difference in the development of DR between high and low groups in females ( p = 0.58). Serum prorenin levels in males with type 2 diabetes could be a new prognostic indicator of the development of DR.
A new zero-knowledge code based identification scheme with reduced communication (2011)

In this paper we present a new 5-pass identification scheme with asymptotic cheating probability ½ based on the syndrome decoding problem. Our protocol is related to the Stern identification scheme but has a reduced communication cost compared to previous code-based zero-knowledge schemes, moreover our scheme permits to obtain a very low size of public key and secret key. The contribution of this paper is twofold, first we propose a variation on the Stern authentication scheme which permits to decrease asymptotically the cheating probability to 1/2 rather than 2/3 (and very close to 1/2 in practice) but with less communication. Our solution is based on deriving new challenges from the secret key through cyclic shifts of the initial public key syndrome; a new proof of soundness for this case is given Secondly we propose a new way to deal with hashed commitments in zero-knowledge schemes based on Stern's scheme, so that in terms of communication, on the average, only one hash value is sent rather than two or three. Overall our new scheme has the good features of having a zero-knowledge security proof based on well known hard problem of coding theory, a small size of secret and public key (a few hundred bits), a small calculation complexity, for an overall communication cost of 19kb for authentication (for a 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">16</sup> security) and a signature of size of 93kb (11.5kB) (for security 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">80</sup> ), an improvement of 40% compared to previous schemes based on coding theory.
Orientation Imaging Microscopy: New Possibilities for Microstructural Investigations Using Automated BKD Analysis (1994)

A new microscopy, called Orientation Imaging Microscopy, is described. Imaging results from precise measurements of local lattice orientation rapidly obtained by Backscattered Kikuchi Diffraction. The hardware configuration of the microscope is described and a description of image formation presented. Applications to several materials of differing lattice structure are described. Connections of the microscopy with various aspects of modern texture analysis are emphasized.
An Innovative Technique of Vertebral Body Stapling for the Treatment of Patients With Adolescent Idiopathic Scoliosis: A Feasibility, Safety, and Utility Study (2003)

The data demonstrate that vertebral body stapling for the treatment of scoliosis in the adolescent was feasible and safe in this group of 21 patients. In the short-term, stapling appears to have utility in stabilizing curves of progressive adolescent idiopathic scoliosis.
Stability and Performance of a Population Pharmacokinetic Model (1997)

This study aimed to determine the stability (in terms of covariate selection) of a population pharmacokinetic model and evaluate its performance in the absence of a test data set. Data from 88 full‐term infants, 11 of whom were human immunodeficiency virus (HIV)–seropositive, taking an antiinfective agent were analyzed using exploratory data analysis methods and the nonlinear mixed‐effects modeling (NONMEM) program to obtain the final population pharmacokinetic model. The stability of the population pharmacokinetic model was tested using the nonparametric bootstrap approach in four steps: 1) with the base pharmacokinetic model, 100 bootstrap replicates of the original data were generated by sampling with replacement; 2) ascertainment that each bootstrap data replicate was described by the basic structural model using the NONMEM objective function; 3) generalized additive modeling (GAM) applied to empiric Bayesian estimates for covariate selection at α = 0.05 and a frequency (f) cutoff value of 0.50; and 4) NONMEM population model building using covariates selected in the third step with α = 0.005. Performance of the population pharmacokinetic model was evaluated using 200 additional bootstrap replicates of the data by fitting the model obtained in step 4 to them. Parameters obtained were compared with those obtained in the model stability step, and improved prediction error, a measure of predictive accuracy as an index of internal validation, was computed. The reciprocal of serum creatinine (RSC; f = 0.73) and HIV (f = 0.70) were selected by GAM as predictors of clearance (Cl). The population pharmacokinetic model obtained without the determination of model stability included RSC as a predictor of Cl, but the final model from the model stability step included both HIV and RSC as predictors of Cl. Final population pharmacokinetic parameters were obtained with this model fitted to the original data; however, the 95% confidence interval on the HIV status regression coefficient included zero, indicating no significance. The mean parameter estimates obtained with the additional 200 bootstrap replicates of data were within 15% of those obtained with the final model at the regression stability step. Bootstrap resampling procedure is useful for evaluating the stability and performance of a population model by repeatedly fitting it to the bootstrap samples when there is no test data set.
Posterior Reversible Encephalopathy Syndrome (2011)

Posterior reversible encephalopathy syndrome (PRES) is characterized by headache, altered mental status, visual disturbances, and seizures. Radiological features typically include edema of the posterior cerebral regions, especially of the parietooccipital lobes. Atypical imaging features, such as involvement of anterior cerebral regions, deep white matter, and the brain stem are also frequently seen. Vasoconstriction is common in vascular imaging. Different conditions have been associated with PRES, but toxemia of pregnancy, solid organ or bone marrow transplantation, immunosuppressive treatment, cancer chemotherapy, autoimmune diseases, and hypertension are most commonly described. The pathophysiology of PRES is unclear and different hypotheses are being discussed. Posterior reversible encephalopathy syndrome is best managed by monitoring and treatment in the setting of a neurointensive care unit. The prognosis is usually benign with complete reversal of clinical symptoms within several days, when adequate treatment is immediately initiated. Treatment of severe hypertension, seizures, and withdrawal of causative agents represent the hallmarks of specific therapy in PRES. Delay in diagnosis and treatment may lead to permanent neurological sequelae. Therefore, awareness of PRES is of crucial importance for the intensivist.
The hypoxic cell: a target for selective cancer therapy--eighteenth Bruce F. Cain Memorial Award lecture. (1999)

It has been appreciated for more than 50 years that very low levels of oxygenation, or hypoxia, both protect cells from killing by X-irradiation and are present in solid tumors but not in normal tissues. Until recently, however, there has been no definitive proof that hypoxia in human tumors contributes to radiotherapy treatment failure. We now know that hypoxia in solid tumors is not only a major problem for radiation therapy but also leads to resistance to most anticancer drugs and, importantly, appears to accelerate malignant progression and increase metastasis. To date, efforts to overcome the problem of hypoxia have had only limited success. However, the recent development of new drugs that are nontoxic until they are activated in the hypoxic cell opens a new era. The first of these new drugs to be tested clinically, tirapazamine, a drug that is highly toxic to hypoxic but not aerobic cells, has already demonstrated efficacy in selective potentiation of cisplatin in randomized Phase III trials with non-small cell lung cancer. The unique presence of hypoxic cells in human tumors provides an important target for selective cancer therapy.
Discovery and Optimization of Imidazopyridine-Based Inhibitors of Diacylglycerol Acyltransferase 2 (DGAT2) (2015)

The medicinal chemistry and preclinical biology of imidazopyridine-based inhibitors of diacylglycerol acyltransferase 2 (DGAT2) is described. A screening hit 1 with low lipophilic efficiency (LipE) was optimized through two key structural modifications: (1) identification of the pyrrolidine amide group for a significant LipE improvement, and (2) insertion of a sp(3)-hybridized carbon center in the core of the molecule for simultaneous improvement of N-glucuronidation metabolic liability and off-target pharmacology. The preclinical candidate 9 (PF-06424439) demonstrated excellent ADMET properties and decreased circulating and hepatic lipids when orally administered to dyslipidemic rodent models.
Percutaneous peptide immunization via corneum barrier-disrupted murine skin for experimental tumor immunoprophylaxis (2000)

H-2K(b)-restricted tumor epitope peptides, including tyrosinase-related protein 2 residues 181-188 (TRP-2) and connexin 37 residues 52-59 (MUT1), were applied to permeability barrier-disrupted C57BL/6 (B6) mouse skin from which the stratum corneum of the epidermis had been removed by tape-stripping. This procedure primed tumor-specific cytotoxic T lymphocytes (CTLs) in the lymph nodes and spleen, protected mice against subsequent challenge with corresponding tumor cells, and suppressed the growth of established tumors. Preventive and therapeutic effectiveness was correlated with the frequency of tumor-specific CTL precursors. MHC class II Ia(b+) cells separated from tape-stripped skin, compared with those from intact skin, exhibited a strong antigen-presenting capacity for CTL, suggesting that CTL expansion after peptide application is primarily mediated by epidermal Langerhans cells. Thus, percutaneous peptide immunization via barrier-disrupted skin provides a simple and noninvasive means of inducing potent anti-tumor immunity which may be exploited for cancer immunotherapy.
Distinct ongoing Ig heavy chain rearrangement processes in childhood B- precursor acute lymphoblastic leukemia (1993)

Acute lymphoblastic leukemia (ALL) is thought to arise from the clonal expansion of a single transformed precursor cell. However, an oligoclonal Ig heavy chain (IgH) rearrangement pattern has been observed in 30% of ALL patients and was shown to be the result of ongoing rearrangement events. The extent and nature of these ongoing rearrangement processes in individual patients has so far remained obscure. We performed a detailed analysis of leukemic VHDJH rearrangements in three children with B-precursor ALL at diagnosis and one B-lymphoid blast crisis of a child with Ph+ chronic myeloid leukemia at diagnosis and relapse. The children were selected because they presented with multiple IgH rearrangements on Southern blot analysis. Polymerase chain reaction analysis of leukemic cells from two B-precursor ALL patients showed exclusively two groups of related sequences resulting from VH gene replacement events. Most VH gene replacements involved 3′ located acceptor VH genes. Analysis of cells from the other B-precursor ALL patient showed exclusively related sequences as a result of VH gene joinings to a pre-existing DJH rearrangement. In the B-lymphoid blast crisis, a single germline precursor cell had generated multiple unrelated rearrangements and additional groups of related rearrangements resulting from VH to DJH joinings. Direct proof for the VH to DJH joining mechanism was obtained by amplification of the expected preexisting DJH rearrangements. Our findings suggest that the pattern of ongoing rearrangements in an individual patient reflects the IgH rearrangement status of the precursor cell at the time of malignant transformation. Sequence analysis of VHDJH rearrangements at diagnosis may therefore allow a prediction of the reliability of complementarity determining region 3 probes for the detection of minimal residual disease.
Antigen presentation by B lymphocytes: mechanisms and functional significance. (1989)

B lymphocytes are remarkably efficient at presenting protein antigens that bind to their immunoglobulin (Ig) receptors to class II MHC-restricted CD4+ helper T cells. Ig molecules function as high-affinity binding sites for capturing antigens at limiting concentrations. In addition, Ig receptor-mediated endocytosis leads to an intracellular pathway of protein traffic that favors recycling of antigens and optimizes the processing of these antigens. As a result, small amounts of endocytosed antigens are capable of associating with MHC molecules and being presented in a form that can be specifically recognized by T lymphocytes. The antigen presenting function of B cells is particularly important in secondary antibody responses, which require low concentrations of antigens and MHC-restricted T-B cell cooperation.
Harnessing Plasticity to Reset Dysfunctional Neurons (2011)

For a long time, it was thought that the adult mammalian brain was hard-wired and that once circuits were laid down and their functions assigned, little change was possible. This notion is no longer tenable. The brain has a lifelong inherent ability to change and adapt: individual neurons and neural circuits can change their “job descriptions” and their allegiance in response to demands. The mechanisms underlying this process are complex, have varying time courses (from milliseconds to months), and are incompletely understood. They include changes in synaptic strength, the pruning and growth of neuronal connections, and even the introduction of . . .
Microwave ZnO Thin-Film Transistors (2008)

We have developed ZnO thin-film transistor design and fabrication techniques to demonstrate microwave frequency operation with 2-mum gate length devices produced on GaAs substrates. Using SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gate insulator and pulsed laser deposited ZnO active layers, a drain-current ON/OFF ratio of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> , a drain-current density of 400 mA/mm, a field-effect mobility of 110 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V ldr s, and a subthreshold gate voltage swing of 109 m\/dec were achieved. Devices with Ti-gate metal had current and power gain cutoff frequencies of 500 and 400 MHz, respectively.
GMR in DC magnetron sputtered Ni/sub 81/Fe/sub 19//Cu multilayers (1998)

In this paper, we present results of a study on Ni/sub 81/Fe/sub 19/Cu MLs deposited using a four-source DC magnetron sputtering system operated in planetary mode. A significant change of GMR value with deposition conditions, especially base pressure and deposition pressure, has been observed for Ni/sub 18/Fe/sub 19//Cu MLs. With an optimized process, we have obtained a GMR response of 9.5% with a field sensitivity of 0.44%/Oe for Si/[(Ni/sub 81/Fe/sub 19/)17 /spl Aring//Cu20 /spl Aring/]/sub 20/ MLs without an Fe buffer layer. The insertion of a very thin layer of a second magnetic species at nonmagnetic/magnetic interfaces in the ML stack makes GMR response either sensitive or less sensitive to deposition conditions depending on the species selected. We believe that the key to obtaining large GMR values in Ni/sub 81/Fe/sub 19//Cu MLs lies in the control of layered structure and interfacial chemistry. In addition, these Ni/sub 81/Fe/sub 19//Cu MLs survive high temperature annealing up to 250/spl deg/C, retaining a GMR value of 8.5%. The thermal stability exhibited by these MLs over the temperature range for device fabrication makes them valuable for high density recording head sensor applications.
TCR Mimic Monoclonal Antibodies Induce Apoptosis of Tumor Cells via Immune Effector-Independent Mechanisms (2011)

mAbs that recognize peptides presented on the cell surface by MHC class I molecules are potential therapeutic agents for cancer therapy. We have previously demonstrated that these Abs, which we termed TCR mimic mAbs (TCRm), reduce tumor growth in models of breast carcinoma. However, mechanisms of TCRm-mediated tumor growth reduction remain largely unknown. In this study, we report that these Abs, in contrast to several mAbs used currently in the clinic, destroy tumor cells independently of immune effector mechanisms such as Ab-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). We found that TCRm-mediated apoptosis of tumor cells was associated with selective and specific binding of these Abs to peptide/HLA class I complexes, which triggered the activation of JNK and intrinsic caspase pathways. This signaling was accompanied by the release of mitochondrial cytochrome c and apoptosis-inducing factor. TCRm-induced apoptosis in tumor cells was completely inhibited by soluble MHC tetramers loaded with relevant peptide as well as with inhibitors for JNK and caspases. Furthermore, mAbs targeting MHC class I, independent of the peptide bound by HLA, did not stimulate apoptosis, suggesting that the Ab-binding site on the MHC/peptide complex determines cytotoxicity. This study suggests the existence of mechanisms, in addition to ADCC and CDC, through which these therapeutic Abs destroy tumor cells. These mechanisms would appear to be of particular importance in severely immunocompromised patients with advanced neoplastic disease, since immune cell-mediated killing of tumor cells through ADCC and CDC is substantially limited in these individuals.
Molecular structure and assembly of the tight junction (1998)

Polarized epithelial cells separate two extremely different cellular milieus. The tight junction (TJ) is the most apical component of the junctional complex and serves as the permeability barrier between these environments. The tight junctional complex appears to be a dynamic and regulated structure. Some of its protein components have been identified and include the transmembrane protein occludin. Nontransmembrane proteins on the cytosolic leaflet including ZO-1, ZO-2, cingulin, 7H6, and several unidentified phosphoproteins are also believed to be part of the TJ. Interactions of some of these proteins with the actin cytoskeleton are a major determinant of TJ structure and may also play a role in the regulation of TJ assembly. Recent progress using the "calcium switch" and the "ATP depletion-repletion" model of TJ formation offers new insight regarding how these structures form. TJ biogenesis appears to be regulated, in part, by classic signal transduction pathways involving heterotrimeric G proteins, release of intracellular Ca2+, and activation of protein kinase C. Although many of the details of the signaling pathways have yet to be defined, these observations may provide insight into how TJs form during tubular development. Furthermore, it may be possible to suggest potential therapeutic targets for intervention in a variety of diseases (e.g., ischemia, toxic injury to the kidney and other epithelial tissue) where TJ integrity has been compromised and reassembly is required.