gebhart/patrepeval huggingface dataset:
Iterative decoding of non-systematic turbo-codes (2002)

Parallel concatenated convolutional codes (PCCCs) are usually constructed using systematic recursive convolutional codes (SRCCs) as constituent codes. In this paper, we introduce a new version of parallel concatenation that uses nonsystematic recursive convolutional codes (NSRCCs) as constituent codes. A systematic constituent code then becomes a particular case of this general scheme. The use of this larger class of constituent codes enhances the number of possible codes in the search space, thus allowing the possibility of finding better codes. We also introduce a modified iterative decoding method for this more general form of parallel concatenation. The decoding technique is no more complex than the standard iterative decoding algorithm.
Amino acid sequence of the variable region of a human mu chain: location of a possible JH segment. (1980)

The complete amino acid sequence of th variable (V) region of the mu heavy chain of a human IgM immunoglobulin (Cam) has been determined. The strategy for sequence determination involved sequenator analysis of the CNBr cleavage products of the succinylated carboxymethylated Fab mu fragment, and of tryptic peptides of the CNBr polypeptides and thermolytic subpeptides. The variable region of this heavy chain (VH) belongs to the VHIII subgroup; it has greater than 70% homology with other VHIII sequences and contains the VHIII marker peptide, Phe-Thr-Ile-Ser-Arg (residues 67-71). As more sequences have been published, the number of subgroup-specific residues has diminished to the point that no position is absolutely subgroup specific. An analysis of the available human VH sequences in the V/C switch region showed the likelihood of a human JH segment (residues 101-113) analogous to the J segments in mouse light chains. The JH region is highly conserved, has striking homology to proposed mouse JH regions, and has significant homology to known mouse J lambda and J kappa segments.
Comparing the Fundamental Physics and Device Performance of Transparent, Conductive Nanostructured Networks with Conventional Transparent Conducting Oxides (2012)

Abstract Networks made of single‐walled carbon nanotubes (SWNTs) and metallic nanowire networks, graphene, and ultra‐thin metal films have all been proposed as replacements for transparent conducting oxides (TCOs) in photovoltaic and other applications. However, only limited comparisons of nanostructured networks and TCOs are available. Several common figures of merit that are often used to compare the electrical and optical performance of the transparent contacts are evaluated here, and the merits of each method of comparison are discussed. Calculating the current loss due to absorption in the TCO is the most useful metric for evaluating new materials for use in solar cells with well‐defined sheet resistance requirements and known quantum efficiencies. The ‘Haacke’ figure of merit, Φ H , correlates fairly well with current loss and is a good metric for evaluating electro‐optical performance for more general applications. The analyses presented here demonstrate that silver nanowire networks are much closer to achieving optimal electrical and optical properties than carbon‐based networks.
Design considerations for gigabit Ethernet 1000Base-T twisted pair transceivers (2002)

Gigabit Ethernet on Category-5 cable is the next generation high-speed Ethernet LAN for twisted pair copper medium with a minimum required reach of 100 meters. This paper presents a brief overview of the transmission scheme agreed upon by the IEEE 802.3ab task force for 1 Gb/s full-duplex operation over 4 pairs of category-5 cable. Some system level simulation results are presented followed by a discussion of the type of digital and analog circuits required for a single chip mixed-signal CMOS implementation of the transceiver. For reliable operation under worst case cabling conditions, the DSP portion of the transceiver has to perform over 150 Giga operations per second.
Prolonged Treatment of Primary Hepatocytes with Oleate Induces Insulin Resistance through p38 Mitogen-activated Protein Kinase (2007)

Free fatty acid (FFA) is believed to be a major environmental factor linking obesity to Type II diabetes. We have recently reported that FFA can induce gluconeogenesis in hepatocytes through p38 mitogen-activated protein kinase (p38). In this study, we have investigated the role of p38 in oleate-induced hepatic insulin resistance. Our results show that a prolonged treatment of primary hepatocytes with oleate blunted insulin suppression of hepatic gluconeogenesis, and decreased insulin-induced phosphorylation of Akt in a p38-dependent manner. Reduction of the insulin-induced Akt phosphorylation by oleate correlated with activation of p38. In the presence of p38 inhibition, prolonged exposure of hepatocytes to oleate failed to reduce insulin-stimulated phosphorylation of Akt. An siRNA against p38alpha prevented oleate suppression of the insulin-induced phosphorylation of Akt. Furthermore, a prolonged exposure of hepatocytes to oleate decreased insulin-induced tyrosine phosphorylation of IRS1/2, while slightly increasing serine phosphorylation of IRS. The decrease of insulin-stimulated tyrosine phosphorylation of IRS1/2 in hepatocytes by oleate was reversed by the inhibition of p38. We further show that a prolonged exposure of primary hepatocytes to oleate elevated the protein level of the phosphatase and tensin homolog deleted on chromosome 10 (PTEN) gene in a p38-dependent manner, but had no effect on the mRNA level of PTEN. Knocking down the PTEN gene prevented oleate to inhibit insulin activation of Akt and insulin suppression of gluconeogenesis. Together, results from this study demonstrate a critical role for p38 in oleate-induced hepatic insulin resistance.
Modeling sonic logs in oil wells: a comparison of neural networks ensembles and kernel methods (2001)

Oil well logs are frequently used to determine the mineralogy and physical properties of potential reservoir rocks, and the nature of the fluids they contain. Recently we reported an exploratory use of neural network ensembles for modeling these records. We showed that ensembles are clearly superior to linear multivariate regression as modeling technique, revealing an underlying nonlinear functional dependency between the correlated variables. In this work we use kernel methods to develop nonlinear local models relating Sonic logs (transit time of compressional waves) with other commonly measured properties (Resistivity and Natural Formation Radioactivity Level or Gamma Ray log). The kernel considered is conceptually simple and numerically robust, and allows to obtain the same performance as neural networks ensembles on this task.
LAN (Local Area Network) Interoperability Study of Protocols Needed for Distributed Command and Control (1985)

The study examined distributed processing requirements for strategic and tactical C3I systems, reviewed the characteristics and architectural issues for distributed processing global operating systems, compared the DoD and ISO networking protocol architecture models, the protocols for LAN's developed by the IEEE and ANSI, reviewed and conducted performance evaluation of Ethernet, DoD's Internet Protocal and Transmission Control Protocol and reported characteristics of CSMA/CD, Token Bus and Token Ring LAN's, reviewed three alternatives to using TCP for an intra-LAN protocol and examined the methods for employing gateway elements to interconnect LAN-based system elements. A comprehensive discussion of the results is given followed by a set of concise conclusions. Ten recommendations are given, providing a roadmap to guide the Air Force in developing C3I systems and LAN-based protocols. Three major areas are identified where future work is needed. A set of protocols and design approaches for internetworking is contained in a set of appendices. Keywords include; Local area network protocols, Distributed systems, and Computer networks.
2-Alkenyldiphenylphosphine Oxides and PO-Ylids Derived Thereof in trans Selective Horner-Wittig Olefination Reactions (1996)

Allylic PO-ylides generated by deprotonation of 2-alkenyldiphenylphosphine oxides with BuLi were used to prep. 1,3-dienes trans-selectively. The (Z/E) ratios of the newly formed double bond are 1:99 when straight-chain, while they were 2:98 to 4:96 when b-branched aliph., and 4:96 to 6:94 when arom. aldehydes were employed. [on SciFinder (R)]
Co-Design of a CMOS Rectifier and Small Loop Antenna for Highly Sensitive RF Energy Harvesters (2014)

In this paper, a design method for the co-design and integration of a CMOS rectifier and small loop antenna is described. In order to improve the sensitivity, the antenna-rectifier interface is analyzed as it plays a crucial role in the co-design optimization. Subsequently, a 5-stage cross-connected differential rectifier with a 7-bit binary-weighted capacitor bank is designed and fabricated in standard 90 nm CMOS technology. The rectifier is brought at resonance with a high-Q loop antenna by means of a control loop that compensates for any variation at the antenna-rectifier interface and passively boosts the antenna voltage to enhance the sensitivity. A complementary MOS diode is proposed to improve the harvester's ability to store and hold energy over a long period of time during which there is insufficient power for rectification. The chip is ESD protected and integrated on a compact loop antenna. Measurements in an anechoic chamber at 868 MHz demonstrate a -27 dBm sensitivity for 1 V output across a capacitive load and 27 meter range for a 1.78 W RF source in an office corridor. The end-to-end power conversion efficiency equals 40% at -17 dBm.
The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity (2015)

Prioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and Mendelian diseases. A large number of in silico tools have been employed for the task of pathogenicity prediction, including PolyPhen-2, SIFT, FatHMM, MutationTaster-2, MutationAssessor, Combined Annotation Dependent Depletion, LRT, phyloP, and GERP++, as well as optimized methods of combining tool scores, such as Condel and Logit. Due to the wealth of these methods, an important practical question to answer is which of these tools generalize best, that is, correctly predict the pathogenic character of new variants. We here demonstrate in a study of 10 tools on five datasets that such a comparative evaluation of these tools is hindered by two types of circularity: they arise due to (1) the same variants or (2) different variants from the same protein occurring both in the datasets used for training and for evaluation of these tools, which may lead to overly optimistic results. We show that comparative evaluations of predictors that do not address these types of circularity may erroneously conclude that circularity confounded tools are most accurate among all tools, and may even outperform optimized combinations of tools.
Carbon nanotube sensor for vibrating molecules (2013)

The transport properties of a carbon nanotube (CNT) capacitively coupled to a molecule vibrating along one of its librational modes are studied and its transport properties analyzed in the presence of a scanning tunnel microscope tip. We evaluate the linear charge and thermal conductances of the system and its thermopower. They are dominated by position-dependent Franck-Condon factors, governed by a position-dependent effective coupling constant peaked at the molecule position. Both conductance and thermopower allow us to extract some information on the position of the molecule along the CNT. Crucially, however, thermopower also sheds light on the vibrational level spacing, allowing a more complete characterization of the molecule to be obtained, even in the linear regime.
Influence of polymer microstructure on the performance of post‐treated latex‐based pressure sensitive adhesives (2011)

Abstract Latex‐based butyl acrylate (BA)/acrylic acid (AA)/2‐hydroxyethyl methacrylate (HEMA) pressure sensitive adhesive (PSA) films with various microstructures were heated to improve their performance. The treated PSA films showed significantly better performance than original latex‐based PSA films with similar polymer microstructures. The effect of the heat treatment depended on the polymer microstructure of the untreated PSA films (or corresponding latices). Decreasing the amount of very small sol polymers (i.e., M x &lt; 2 M e ) in gel‐free untreated PSA films, or both very small (i.e., M x &lt; 2 M e ) and very large sol polymers (i.e., M x &gt; 20 M e ) in gel‐containing untreated PSA films led to treated PSA films with significantly better performance. (Note: M e is the molecular weight between two adjacent entanglement points in a polymer material.) In addition, simultaneously increasing the sol polymer molecular weight ( M w ) as well as the size of the chain segments between two adjacent cross‐linking points ( M c ) of the gel polymer in the original PSAs resulted in treated PSA films with better performance. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Biological Effects of C-type Natriuretic Peptide in Human Myofibroblastic Hepatic Stellate Cells (1999)

During chronic liver diseases, hepatic stellate cells (HSC) acquire a myofibroblastic phenotype, proliferate, and synthetize fibrosis components. Myofibroblastic HSC (mHSC) also participate to the regulation of intrahepatic blood flow, because of their contractile properties. Here, we examined whether human mHSC express natriuretic peptide receptors (NPR). Only NPR-B mRNA was identified, which was functional as demonstrated in binding studies and by increased cGMP levels in response to C-type natriuretic peptide (CNP). CNP inhibited mHSC proliferation, an effect blocked by the protein kinase G inhibitor 8-(4 chlorophenylthio)-cGMP and by the NPR antagonist HS-142-1 and reproduced by analogs of cGMP. Growth inhibition was associated with a reduction of extracellular signal-regulated kinase and c-Jun N-terminal kinase and with a blockade of AP-1 DNA binding. CNP and cGMP analogs also blunted mHSC contraction elicited by thrombin, by suppressing calcium influx. The relaxing properties of CNP were mediated by a blockade of store-operated calcium channels, as demonstrated using a calcium-free/calcium readdition protocol. These results constitute the first evidence for a hepatic effect of CNP and identify mHSC as a target cell. Activation of NPR-B by CNP in human mHSC leads to inhibition of both growth and contraction. These data suggest that during chronic liver diseases, CNP may counteract both liver fibrogenesis and associated portal hypertension.
Multiparty Turn Taking in Situated Dialog: Study, Lessons, and Directions (2011)

We report on an empirical study of a multiparty turn-taking model for physically situated spoken dialog systems. We present subjective and objective performance measures that show how the model, supported with a basic set of sensory competencies and turn-taking policies, can enable interactions with multiple participants in a collaborative task setting. The analysis brings to the fore several phenomena and frames challenges for managing multiparty turn taking in physically situated interaction. 1.
Visualisation and Quantitative Analysis of the Rodent Malaria Liver Stage by Real Time Imaging (2009)

The quantitative analysis of Plasmodium development in the liver in laboratory animals in cultured cells is hampered by low parasite infection rates and the complicated methods required to monitor intracellular development. As a consequence, this important phase of the parasite's life cycle has been poorly studied compared to blood stages, for example in screening anti-malarial drugs. Here we report the use of a transgenic P. berghei parasite, PbGFP-Luc(con), expressing the bioluminescent reporter protein luciferase to visualize and quantify parasite development in liver cells both in culture and in live mice using real-time luminescence imaging. The reporter-parasite based quantification in cultured hepatocytes by real-time imaging or using a microplate reader correlates very well with established quantitative RT-PCR methods. For the first time the liver stage of Plasmodium is visualized in whole bodies of live mice and we were able to discriminate as few as 1-5 infected hepatocytes per liver in mice using 2D-imaging and to identify individual infected hepatocytes by 3D-imaging. The analysis of liver infections by whole body imaging shows a good correlation with quantitative RT-PCR analysis of extracted livers. The luminescence-based analysis of the effects of various drugs on in vitro hepatocyte infection shows that this method can effectively be used for in vitro screening of compounds targeting Plasmodium liver stages. Furthermore, by analysing the effect of primaquine and tafenoquine in vivo we demonstrate the applicability of real time imaging to assess parasite drug sensitivity in the liver. The simplicity and speed of quantitative analysis of liver-stage development by real-time imaging compared to the PCR methodologies, as well as the possibility to analyse liver development in live mice without surgery, opens up new possibilities for research on Plasmodium liver infections and for validating the effect of drugs and vaccines on the liver stage of Plasmodium.
Shared Memory Consistency Models: A Tutorial (1995)

Parallel systems that support the shared memory abstraction are becoming widely accepted in many areas of computing. Writing correct and efficient programs for such systems requires a formal specification of memory semantics, called a memory consistency model. The most intuitive model—sequential consistency—greatly restricts the use of many performance optimizations commonly used by uniprocessor hardware and compiler designers, thereby reducing the benefit of using a multiprocessor. To alleviate this problem, many current multiprocessors support more relaxed consistency models. Unfortunately, the models supported by various systems differ from each other in subtle yet important ways. Furthermore, precisely defining the semantics of each model often leads to complex specifications that are difficult to understand for typical users and builders of computer systems. The purpose of this tutorial paper is to describe issues related to memory consistency models in a way that would be understandable to most computer professionals. We focus on consistency models proposed for hardware-based shared-memory systems. Many of these models are originally specified with an emphasis on the system optimizations they allow. We retain the system-centric emphasis, but use uniform and simple terminology to describe the different models. We also briefly discuss an alternate programmer-centric view that describes the models in terms of program behavior rather than specific system optimizations.1
The Tree-to-Tree Correction Problem (1979)

The tree-to-tree correctmn problem Is to determine, for two labeled ordered trees T and T', the distance from T to T' as measured by the mlmmum cost sequence of edit operaUons needed to transform T into T' The edit operations investigated allow changing one node of a tree into another node, deleting one node from a tree, or inserting a node into a tree An algorithm Is presented which solves this problem m time O(V* V'*LZ* L'2), where V and V' are the numbers of nodes respectively of T and T', and L and L' are the maximum depths respectively of T and T' Possible apphcatmns are to the problems of measuring the similarity between trees, automatic error recovery and correction for programming languages, and determining the largest common substructure of two trees KEY WORDS AND PHRASES tree correction, tree modification, tree similarity CR CATEGORIES 3 79, 4A2, 4 22, 5 23, 5 25
HIV-specific T-helper activity in seronegative health care workers exposed to contaminated blood (1994)

<h3>Objective.</h3> —To evaluate human immunodeficiency virus (HIV) type 1—specific cellular immune responses in HIV-seronegative health care workers with occupational high-risk exposures to HIV-infected (HIV-positive) patients. <h3>Design.</h3> —Peripheral blood mononuclear cells (PBMCs) were obtained after occupational exposures to HIV, and PBMCs from health care workers exposed to HIV-negative patients served as controls. The PBMCs were stimulated in vitro with HIV envelope synthetic peptides. Interleukin 2 (IL-2) production was measured in a bioassay. The HIV antibody status was determined by standard enzyme-linked immunosorbent assays. Exposed individuals were also evaluated for HIV proviral DNA by polymerase chain reaction techniques. <h3>Participants.</h3> —The PBMCs from eight health care workers with high-risk exposures and nine control health care workers were studied. <h3>Results.</h3> —The PBMCs from all individuals showed strong IL-2 production to control antigens, indicating intact T-helper function. Interleukin 2 production to HIV peptides was detected in PBMCs from six of eight HIV-exposed individuals, but in only one of the nine health care workers exposed to HIV-negative body fluids (<i>P</i>&lt;.008). None of the HIV-exposed health care workers became infected as determined by negative HIV antibody and polymerase chain reaction analysis after follow-up evaluation that ranged from 8 to 64 weeks. <h3>Conclusion.</h3> —Human immunodeficiency virus—specific T-helper activity was detected in six (75%) of eight HIV-negative health care workers with exposure to HIV-positive body fluids. Potent HIV-specific T-helper activity was detectable 4 to 8 weeks after the exposure and was lost in individuals followed up for 8 to 64 weeks. Three health care workers remained responsive at 8,19, and 24 weeks. Exposure to HIV without evidence of subsequent infection appears to result in activation of cellular immunity without activation of antibody production. (<i>JAMA</i>. 1994;271:42-46)
Repeated 0.5-Gy Gamma Irradiation Attenuates Autoimmune Disease in MRL-lpr/lprMice with Suppression of CD3+CD4−CD8−B220+T-Cell Proliferation and with Up-regulation of CD4+CD25+Foxp3+Regulatory T Cells (2007)

Tago, F., Tsukimoto, M., Nakatsukasa, H. and Kojima. S. Repeated 0.5 Gy Gamma Irradiation Attenuates Autoimmune Disease in MRL-lpr/lpr Mice with Suppression of CD3(+)CD4(-)CD8(-)B220(+) T-Cell Proliferation and with Up-regulation of CD4(+)CD25(+)Foxp3(+) Regulatory T Cells. Radiat. Res. 169, 59-66 (2008). MRL-lpr/lpr mice are used as a model of systemic lupus erythematosus. We previously reported attenuation of autoimmune disease in MRL-lpr/lpr mice by repeated gamma irradiation (0.5 Gy each time). In this study, we investigated the mechanisms of this attenuation by measuring the weight of the spleen and the population of highly activated CD3(+)CD4(-)CD8(-)B220(+) T cells, which are characteristically involved in autoimmune pathology in these mice. Splenomegaly and an increase in the percentage of CD3(+)CD4(-)CD8(-)B220(+) T cells, which occur with aging in nonirradiated mice, were suppressed in irradiated mice. The high proliferation rate of CD3(+)CD4(-)CD8(-)B220(+) T cells was suppressed in the irradiated animals. The production of autoantibodies and the level of IL6, which activates B cells, were also lowered by radiation exposure. These results indicate that progression of pathology is suppressed by repeated 0.5-Gy gamma irradiation. To uncover the mechanism of the immune suppression, we measured the regulatory T cells, which suppress activated T cells and excessive autoimmune responses. We found that regulatory T cells were significantly increased in irradiated mice. We therefore conclude that repeated 0.5-Gy gamma irradiation suppresses the proliferation rate of CD3(+)CD4(-)CD8(-)B220(+) T cells and the production of IL6 and autoantibodies and up-regulates regulatory T cells.