gebhart/patrepeval huggingface dataset:
Cloning and Expression of Bovine BRCA1 (2001)

Breast ovarian cancer susceptibility (BRCA) proteins appear to be involved in cell cycle regulation, DNA repair or genome integrity and induction of apoptosis in a variety of cells from humans and laboratory animals. The BRCA gene and protein have not been identified in cattle. The pattern of BRCA1 gene expression during normal mammary gland development and involution has not been examined in detail in any mammalian species. Therefore, the purpose of the present study was to clone the BRCA1 gene in Holstein dairy cattle and determine if the BRCA1 gene is differentially expressed through various stages of mammary gland development. We also localized immunoreactive BRCA1 protein in bovine mammary cells and milk fat globule membrane. Bovine BRCA1 cDNA was highly conserved to the human. Five hundred base pairs of exon 11 (+3384/ + 3866, human BRCA1 cDNA position) and the C-terminus 1 kb were identical to the human. Seven hundred base pairs of the N-terminus, which contain two ring domains, showed 90 % homology to human BRCA1. In bovine tissues, the degree of BRCA1 gene expression, from highest to lowest , was as follows: liver, spleen, mammary tissues and kidney. The mammary tissues of early pregnancy heifers (3 months) showed much higher mammary gland BRCA1 mRNA expression than other mammary developmental stages. BRCA1 expression declined during the remainder of pregnancy and remained low for lactating cows. However, its expression increased when involution proceeded. Immunohistochemical studies showed that immunoreactive BRCA1 was localized in the nucleus and cytoplasm of mammary epithelial cells from lactating cows. It was not present in myoepithelial cells. The protein was also localized in the milk fat globule membranes. Our data suggest that BRCA1 is involved in bovine mammary gland development and/or differentiation, is specifically localized in secretary epithelial cells and is likely a secreted protein during normal lactation.
A new multi-position calibration method for MEMS inertial navigation systems (2007)

The Global Positioning System (GPS) is a worldwide navigation system that requires a clear line of sight to the orbiting satellites. For land vehicle navigation, a clear line of sight cannot be maintained all the time as the vehicle can travel through tunnels, under bridges, forest canopies or within urban canyons. In such situations, the augmentation of GPS with other systems is necessary for continuous navigation. Inertial sensors can determine the motion of a body with respect to an inertial frame of reference. Traditionally, inertial systems are bulky, expensive and controlled by government regulations. Micro-electro mechanical systems (MEMS) inertial sensors are compact, small, inexpensive and most importantly, not controlled by governmental agencies due to their large error characteristics. Consequently, these sensors are the perfect candidate for integrated civilian navigation applications with GPS. However, these sensors need to be calibrated to remove the major part of the deterministic sensor errors before they can be used to accurately and reliably bridge GPS signal gaps. A new multi-position calibration method was designed for MEMS of high to medium quality. The method does not require special aligned mounting and has been adapted to compensate for the primary sensor errors, including the important scale factor and non-orthogonality errors of the gyroscopes. A turntable was used to provide a strong rotation rate signal as reference for the estimation of these errors. Two different quality MEMS IMUs were tested in the study. The calibration results were first compared directly to those from traditional calibration methods, e.g. six-position and rate test. Then the calibrated parameters were applied in three datasets of GPS/INS field tests to evaluate their accuracy indirectly by comparing the position drifts during short-term GPS signal outages.
Compact Low-Loss Planar Magic-T (2008)

This design allows broadband power combining with high isolation between the H port and E port, and achieves a lower insertion loss than any other broadband planar magic-T. Passive micro wave/millimeter-wave signal power is combined both in-phase and out-of-phase at the ports, with the phase error being less than 1 , which is limited by port impedance. The in-phase signal combiner consists of two quarter-wavelength-long transmission lines combined at the microstrip line junction. The out-of-phase signal combiner consists of two half-wavelength-long transmission lines combined in series. Structural symmetry creates a virtual ground plane at the combining junction, and the combined signal is converted from microstrip line to slotline. Optimum realizable characteristic impedances are used so that the magic-T provides broadband response with low return loss. The magic-T is used in microwave and millimeter-wave frequencies, with the operating bandwidth being approximately 100 percent. The minimum isolation obtainable is 32 dB from port E to port H. The magic-T VSWR is less than 1.1 in the operating band. Operating temperature is mainly dependent on the variation in the dielectric constant of the substrate. Using crystallized substrate, the invention can operate in an extremely broad range of temperatures (from 0 to 400 K). It has a very high reliability because it has no moving parts and requires no maintenance, though it is desirable that the magic-T operate in a low-humidity environment. Fabrication of this design is very simple, using only two metallized layers. No bond wires, via holes, or air bridges are required. Additionally, this magic-T can operate as an individual component without auxiliary components.
Production of knockout mice by random or targeted mutagenesis in spermatogonial stem cells (2006)

Stem cells represent a unique population of cells with self-renewal capacity. Although they are important therapeutic targets, the genetic manipulation of tissue-specific stem cells has been limited, which complicates the study and practical application of these cells. Here, we demonstrate successful gene trapping and homologous recombination in spermatogonial stem cells. Cultured spermatogonial stem cells were transfected with gene trap or gene targeting vectors. Mutagenized stem cells were expanded clonally by drug selection. These cells underwent spermatogenesis and produced heterozygous offspring after transplantation into the seminiferous tubules of infertile mouse testes. Heterozygous mutant mice were intercrossed to produce homozygous gene knockouts. Using this strategy, the efficiency of homologous recombination for the occludin gene locus was 1.7% using a nonisogenic DNA construct. These results demonstrate the feasibility of altering genes in tissue-specific stem cells in a manner similar to embryonic stem cells and have important implications for gene therapy and animal transgenesis.
Monocyclic Endothelins (1991)

Monocyclic fragment analogues of endothelin-1 (ET-1) were prepared by standard solid-phase peptide synthetic methods. The analogues were designed to determine the importance of the unique bicyclic structure of the endothelins, vasoactive intestinal contractor, and the sarafotoxins to their binding affinity and functional activity. The binding affinity of the monocyclic analogues to the endothelin receptor was examined in three tissue preparations: (a) rabbit pulmonary artery, (b) rabbit aorta, and (c) rat heart ventricle. Functional activity was assessed in two tissues: (a) rabbit pulmonary artery and (b) rat left atria. Binding was not observed for the disulfide bridged cyclic 3-11 loop of ET-1 at concentrations of up to 100 microM. Attachment of the weakly binding 16-21 C-terminal hexapeptide of ET-1 to the cyclic 3-11 loop did not significantly enhance the observed receptor binding over that of the hexapeptide. Monocyclic Cys-Ser-Aoc-Val-Tyr-Phe-Cys-His-Leu-Asp-Ile-Ile-Trp (Aoc = 8-aminooctanoic acid) exhibited the greatest binding affinity (1.0 to 1.6 microM) in all three tissues, but was still approximately 1,000-fold less effective than ET-1. At concentrations of up to 30 microM, none of the analogues exhibited any functional activity.
Automatic request categorization in internet services (2008)

Modeling system performance and workload characteristics has become essential for efficiently provisioning Internet services and for accurately predicting future resource requirements on anticipated workloads. The accuracy of these models benefits substantially by differentiating among categories of requests based on their resource usage characteristics. However, categorizing requests and their resource demands often requires significantly more monitoring infrastructure. In this paper, we describe a method to automatically differentiate and categorize requests without requiring sophisticated monitoring techniques. Using machine learning, our method requires only aggregate measures such as total number of requests and the total CPU and network demands, and does not assume prior knowledge of request categories or their individual resource demands. We explore the feasibility of our method on the .Net PetShop 4.0 benchmark application, and show that it works well while being lightweight, generic, and easily deployable.
Combination of Modified NS1 and NS3 as a Novel Vaccine Strategy against Dengue Virus Infection (2019)

Dengue virus (DENV) causes a range of illness, including dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. DENV nonstructural protein (NS) 1 has been considered to be a desirable vaccine candidate for its ability to induce Ab and complement-dependent cytolysis of DENV-infected cells as well as to block the pathogenic effects of NS1. However a potential drawback of NS1 as a vaccine is that anti-DENV NS1 Abs can lead to endothelial cell damage and platelet dysfunction by antigenic cross-reactivity. Therefore, we modified the DENV NS1 by replacing the C-terminal cross-reactive epitopes with the corresponding region of Japanese encephalitis virus NS1 to generate a chimeric DJ NS1 protein. Active immunization with DJ NS1 induced a strong Ab response. To enhance cellular immunity, we further combined DJ NS1 with DENV NS3 to immunize mice and showed activation of Ag-specific CD4<sup>+</sup> and CD8<sup>+</sup> T cells in addition to Ab responses. We further detected NS3-specific CTL activities as well as CD107a expression of effector cells. Importantly, the protective effects attributed by DJ NS1 and NS3 immunization were demonstrated in a DENV-infected mouse model by reduced viral titers, soluble NS1 levels, mouse tail bleeding time, and vascular leakage at skin injection sites. Collectively, the results from this study reveal the humoral and cellular immune responses and the protective effects conferred by DJ NS1 and NS3 immunization in the mouse model of DENV infection and provide a potential strategy for dengue vaccine design.
Anti‐JC virus antibodies: Implications for PML Risk Stratification (2010)

This 2-step assay provides a means to classify MS patients as having detectable or not detectable levels of anti-JCV antibodies. The finding that all 17 of the pre-PML samples that were available tested seropositive, and none tested seronegative, warrants further research on the clinical utility of the anti-JCV antibody assay as a potential tool for stratifying MS patients for higher or lower risk of developing PML.
Energy-efficient cache design using variable-strength error-correcting codes (2011)

Voltage scaling is one of the most effective mechanisms to improve microprocessors' energy efficiency. However, processors cannot operate reliably below a minimum voltage, Vccmin, since hardware structures may fail. Cell failures in large memory arrays (e.g., caches) typically determine Vccmin for the whole processor. We observe that most cache lines exhibit zero or one failures at low voltages. However, a few lines, especially in large caches, exhibit multi-bit failures and increase Vccmin. Previous solutions either significantly reduce cache capacity to enable uniform error correction across all lines, or significantly increase latency and bandwidth overheads when amortizing the cost of error-correcting codes (ECC) over large lines. In this paper, we propose a novel cache architecture that uses variable-strength error-correcting codes (VS-ECC). In the common case, lines with zero or one failures use a simple and fast ECC. A small number of lines with multi-bit failures use a strong multi-bit ECC that requires some additional area and latency. We present a novel dynamic cache characterization mechanism to determine which lines will exhibit multi-bit failures. In particular, we use multi-bit correction to protect a fraction of the cache after switching to low voltage, while dynamically testing the remaining lines for multi-bit failures. Compared to prior multi-bit-correcting proposals, VS-ECC significantly reduces power and energy, avoids significant reductions in cache capacity, incurs little area overhead, and avoids large increases in latency and bandwidth.
Overexpression of Cytochrome<i>c</i>by a Recombinant Rabies Virus Attenuates Pathogenicity and Enhances Antiviral Immunity (2001)

The pathogenicity of individual rabies virus strains appears to correlate inversely with the extent of apoptotic cell death they induce and with the expression of rabies virus glycoprotein, a major inducer of an antiviral immune response. To determine whether the induction of apoptosis by rabies virus contributes to a decreased pathogenicity by stimulating antiviral immunity, we have analyzed these parameters in tissue cultures and in mice infected with a recombinant rabies virus construct that expresses the proapoptotic protein cytochrome c. The extent of apoptosis was strongly increased in primary neuron cultures infected with the recombinant virus carrying the active cytochrome c gene [SPBN-Cyto c(+)], compared with cells infected with the recombinant virus containing the inactive cytochrome c gene [SPBN-Cyto c(-)]. Mortality in mice infected intranasally with SPBN-Cyto c(+) was substantially lower than in SPBN-Cyto c(-)-infected mice. Furthermore, virus-neutralizing antibody (VNA) titers were significantly higher in mice immunized with SPBN-Cyto c(+) at the same dose. The VNA titers induced by these recombinant viruses paralleled their protective activities against a lethal rabies virus challenge infection, with SPBN-Cyto c(+) revealing an effective dose 20 times lower than that of SPBN-Cyto c(-). The strong increase in immunogenicity, coupled with the marked reduction in pathogenicity, identifies the SPBN-Cyto c(+) construct as a candidate for a live rabies virus vaccine.
Multivariate Statistical Monitoring of Sensor Faults of A Multivariable Artificial Pancreas (2017)

Sensor faults in an artificial pancreas (AP) system for people with type 1 diabetes (T1D) can yield insulin infusion rates that may cause hypoglycemia or hyperglycemia. New statistical process monitoring methods are proposed for real-time detection of sensor-related faults in AP systems to mitigate their effects. Remodulated dynamic time warping for synchronization of signal trajectories and Savitzky-Golay filter for calculation of real-time numerical derivatives are integrated with multiway principal component analysis. Data from 14 subjects that participated in 60 hours of closed-loop AP experiments with variations in meals and physical activity levels and times are used. Glucose measurements from a continuous glucose monitoring sensor are monitored for fault detection. The results illustrate that the proposed method is able to detect various types of unexpected dynamical changes or faults, and label them correctly. There were no missed faults in any tested cases. The algorithm can inform AP users about sensor faults and unexpected changes, and provides valuable information to an AP for prevention hypoglycemia or hyperglycemia that may be caused by sensor faults.
Improved Manifold Coordinate Representations of Large-Scale Hyperspectral Scenes (2006)

In recent publications, we have presented a data-driven approach to representing the nonlinear structure of hyperspectral imagery using manifold coordinates. The approach relies on graph methods to derive geodesic distances on the high-dimensional hyperspectral data manifold. From these distances, a set of intrinsic manifold coordinates that parameterizes the data manifold is derived. Scaling the solution relied on divide-conquer-and-merge strategies for the manifold coordinates because of the computational and memory scaling of the geodesic coordinate calculations. In this paper, we improve the scaling performance of isometric mapping (ISOMAP) and achieve full-scene global manifold coordinates while removing artifacts generated by the original methods. The CPU time of the enhanced ISOMAP approach scales as <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$O(N log^2(N))$</tex> , where <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$N$</tex> is the number of samples, while the memory requirement is bounded by <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$O(Nlog(N))$</tex> . Full hyperspectral scenes of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$O(10^6)$</tex> samples or greater are obtained via a reconstruction algorithm, which allows insertion of large numbers of samples into a representative “backbone” manifold obtained for a smaller but representative set of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$O(10^5)$</tex> samples. We provide a classification example using a coastal hyperspectral scene to illustrate the approach.
Factor VII-Deficient Substrate Plasmas Depleted of Protein C Raise the Sensitivity of the Factor VII Bio-Assay to Activated Factor VII: an International Study (1994)

Plasma from healthy individuals, pregnant women and patients on warfarin were distributed to 3 laboratories supporting major cardiovascular surveys (Northwick Park, Muenster and Houston) for assay of factor VII coagulant activity (VIIc) with their own bio-assays. The mean VIIc in 147 samples agreed to within 1% of standard in Northwick Park and Houston, but was 14% of standard lower in Muenster owing to its more potent standard. In samples with an increased VIIc the Northwick Park assay gave a higher result than the other assays owing to its increased responsiveness to activated factor VII (VIIa). Thus when VIIa concentrations were determined directly with a clotting assay which utilises a soluble recombinant tissue factor, the increase in VIIc with increase in VIIa was considerably greater with the Northwick Park assay than the Muenster assay. This feature of the Northwick Park assay was traced to the virtual absence of protein C in its substrate plasma. Factor Va appears rate-limiting for the coagulant expression of VIIa in test plasma. If the thrombotic response to release of tissue factor is determined by the circulating concentration of VIIa, then the Northwick Park factor VII bio-assay may be preferable to other bio-assays currently employed to estimate risk of acute coronary events.
Protein identification and immunoassay evaluation of a panel of biomarkers discovered through proteomic profiling for the detection of ovarian cancer (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

1063 

In a previously reported multi-center study, we analyzed serum protein profiles of 503 samples from women with ovarian cancer or benign pelvic masses, and from healthy controls using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF/MS). Three biomarkers at mass charge ratios (m/z) of 28kD, 12.8kD, and 3272D were discovered and independently validated for their ability to detect early stage ovarian cancer from healthy controls and their complementary value to the existing tumor marker CA125. To facilitate further evaluation, we have since identified the protein identities of these markers to be (1) apolipoprotein A1 (m/z 28kD, down-regulated in cancer), (2) a truncated form of transthyretin (m/z 12.8kD, down-regulated in cancer), and (3) a cleavage fragment of inter-alpha-trypsin inhibitor heavy chain H4 (m/z 3272, up-regulated in cancer). With protein identification, we were able to further evaluate two of the markers using commercially available immunoassays on archived serum samples from healthy women (n=41) and patients with ovarian (n=41), breast (n=20), colon (n=20), and prostate (n=20) cancers collected at the Johns Hopkins Medical Institutions. As shown in the figure, serum levels of apolipoprotein A1 and transthyretin were both down-regulated among the patients with late stage ovarian cancer compared to the healthy controls (P < 0.002, 0.0002, and 0.00001, respectively). The mean serum apolipoprotein A1 level among the healthy controls was not significantly different from that of patients with breast or colorectal cancer (P = 0.844, 0.330, respectively) and only marginally different from that of patients with prostate cancer (P < 0.05). The mean serum transthryetin level was down-regulated among patients with colorectal cancer (P < 0.01) albeit to a lesser degree than that in patients with ovarian cancer. There were no significant differences in mean serum transthyretin levels between the healthy controls and patients with breast or prostate cancer (P = 0.929, 0.547, respectively). It needs to be noted that the transthyretin immunoassay was not specific to the particular truncated form that we had identified. However, in a separate analysis, we were able to show that several transthyretin variants as well as the relative proportions among them were also informative for the detection of early stage ovarian cancer. The current results demonstrated a fairly high level of site specificity of two of the identified biomarkers for ovarian cancer.



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Bacteriostatic and Bactericidal Activities of Selected Beta-Lactam Antibiotics Studied on Agar Plates (1977)

A novel and time-saving method for assessing bactericidal activities of beta-lactam antibiotics on agar plates is described. Minimal inhibitory concentrations (MICs) were determined by the agar dilution method. A potent beta-lactamase solution was sprayed onto the plates to inactivate the antibiotic. After further incubation at 37 degrees C overnight, the minimal concentration at which no visible growth occurred on the plates was defined as minimal bactericidal concentration (MBC). With undiluted culture as the inoculum, strains of Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae showed a marked increase in MBC values compared with the values of MIC. There was a marked decrease in both the MICs and MBCs with diminution of inoculum size. The two concentrations were almost the same when the inoculum size was decreased to a 10(-4) dilution. In contrast, MIC and MBC for enterococci showed no marked decrease with decrease in inoculum size. Although the present study was performed with beta-lactamase-unstable penicillins and cephalosporins, the method can be applicable with any beta-lactam antibiotic if optimal and potent enzymes are available.
Mechanical Performance of Transverse Flux Machines (2019)

This research examines the structural and vibrational characteristics of double-sided flux-concentrating transverse flux machines (TFMs), designed for direct-drive application. Two prototypes of TFM with different stator cores, one with Quasi U-Core and the other with E-Core, have been used for this study. Three-dimensional finite element analysis has been carried out to determine the no-load and with-load performances of the TFMs along with their fluctuating axial electromagnetic force densities acting on the stator teeth. The deformation response of the stator cores was observed in the static structural analysis. Acceleration and noise measurements were experimentally obtained to characterize the vibrational performance of the prototypes.