gebhart/patrepeval huggingface dataset:
PD‐L2 expression extends beyond dendritic cells/macrophages to B1 cells enriched for VH11/VH12 and phosphatidylcholine binding (2007)

B1 B cells are the major source of natural antibody that is essential for innate immunity. The B1 repertoire is skewed toward production of phosphatidylcholine (PtC)-binding V(H)11 and V(H)12 immunoglobulin that plays a key role in immune defense against bacterial infection. Programmed death-ligand 2 (PD-L2) is a ligand for the immunosuppressive receptor programmed death-1 (PD-1). It has been reported that expression of PD-L2 is restricted to dendritic cells and macrophages in mice. Here we show that 50-70% of resting peritoneal B1 cells express PD-L2, which is not present or inducible on conventional B2 B cells or PD-L2(-) B1 cells. Although PD-L2(+) and PD-L2(-) B1 cells are similar in proliferative responses and spontaneous immunoglobulin secretion, PD-L2(+) B1 cells are highly enriched for expression of V(H)11 and V(H)12 genes and encompass the bulk of PtC-binding B1 cells. These findings extend the range of known PD-L2 expression to B cells and show that B1 cells identified by this marker express a specific repertoire associated with anti-bacterial immunity.
Anomalous dynamics of translocation (2001)

We study the dynamics of the passage of a polymer through a membrane pore (translocation), focusing on the scaling properties with the number of monomers N. The natural coordinate for translocation is the number of monomers on one side of the hole at a given time. Commonly used models that assume Brownian dynamics for this variable predict a mean (unforced) passage time tau that scales as N2, even in the presence of an entropic barrier. In particular, however, the time it takes for a free polymer to diffuse a distance of the order of its radius by Rouse dynamics scales with an exponent larger than two, and this should provide a lower bound to the translocation time. To resolve this discrepancy, we perform numerical simulations with Rouse dynamics for both phantom (in space dimensions d=1 and 2), and self-avoiding (in d=2) chains. The results indicate that for large N, translocation times scale in the same manner as diffusion times, but with a larger prefactor that depends on the size of the hole. Such scaling implies anomalous dynamics for the translocation process. In particular, the fluctuations in the monomer number at the hole are predicted to be nondiffusive at short times, while the average pulling velocity of the polymer in the presence of a chemical-potential difference is predicted to depend on N.
Cloning and Gene Replacement Mutagenesis of a Pseudomonas atlantica Agarase Gene (1988)

An agarase gene (agrA) was isolated by cloning genomic DNA prepared from Pseudomonas atlantica. The agarase activity in recombinant Escherichia coli was found in cell-free culture supernatants and could pass through a 0.45-mum-pore-size membrane separating cells from agar, suggesting that the gene product was exported in E. coli. The enzyme was specific for agar and agarose and did not digest alginate or carrageenan. Mutations generated by transposon mini-Mu d1(lacZ Km) were used to define the agrA coding region, as well as the direction of transcription of the gene. A procedure was developed to produce a P. atlantica agrA mutant. This required construction of an agrA::kan insertion mutation in vitro and subsequent introduction of the defect into the chromosome of P. atlantica by recombinational exchange. Transformation of P. atlantica with plasmids containing agrA::kan utilized a Tris-polyethylene glycol 6000-CaCl(2) treatment for making competent cells. Replacement of wild-type agrA with agrA::kan resulted in loss of agarase activity. Uses of the agrA gene probe and an Agr mutant for environmental studies are discussed.
Performance evaluation of a recursive LA/IR protocol for MC-CDMA power line communications (2003)

The performance evaluation of a recursive link adaptation/incremental redundancy (LA/IR) protocol is made on a power line channel for communication purposes. The recursive LA/IR protocol has been tested for a wireless channel and proved to have an improved performance compared to other pure IR protocols or hybrid non-recursive LA/IR. The communication medium is the power line in buildings grid where users are plugged on/off randomly. The transmission scheme is a MC-CDMA where information bits are coded using rate compatible punctured convolutional codes (RCPC) codes. The performance measures are: (a) the number of users versus delay due to retransmissions, and (b) the effective code rate that gives an indication of the system throughput.
Validation of a new scoring system for the assessment of clinical trial research of oral mucositis induced by radiation or chemotherapy (1999)

The scoring system evaluated was easily used, showed high interobserver reproducibility, was responsive over time, and measured those elements deemed to be associated with mucositis. The use of concomitant symptomatic measurements appeared to be unnecessary.
PointPillars: Fast Encoders for Object Detection From Point Clouds (2019)

Object detection in point clouds is an important aspect of many robotics applications such as autonomous driving. In this paper, we consider the problem of encoding a point cloud into a format appropriate for a downstream detection pipeline. Recent literature suggests two types of encoders; fixed encoders tend to be fast but sacrifice accuracy, while encoders that are learned from data are more accurate, but slower. In this work, we propose PointPillars, a novel encoder which utilizes PointNets to learn a representation of point clouds organized in vertical columns (pillars). While the encoded features can be used with any standard 2D convolutional detection architecture, we further propose a lean downstream network. Extensive experimentation shows that PointPillars outperforms previous encoders with respect to both speed and accuracy by a large margin. Despite only using lidar, our full detection pipeline significantly outperforms the state of the art, even among fusion methods, with respect to both the 3D and bird’s eye view KITTI benchmarks. This detection performance is achieved while running at 62 Hz: a 2 - 4 fold runtime improvement. A faster version of our method matches the state of the art at 105 Hz. These benchmarks suggest that PointPillars is an appropriate encoding for object detection in point clouds.
Fiber Optic Networks (1992)

Fibre optic networks applications and their requirements fibres, couplers and taps tunable filters laser diodes lightwave amplifiers modulation and remodulation techniques detection and demodulation of optical signals subcarrier (wavelength x frequency) techniques frequency stability and its control organizing the system topologically layered architectures in lightwave networks multiaccess, switching and performance operating third generation links operating third generation multipoints operating third generation networks.
Hepatocyte Ploidy Is a Diversity Factor for Liver Homeostasis (2017)

Polyploidy, the existence of cells containing more than one pair of chromosomes, is a well-known feature of mammalian hepatocytes. Polyploid hepatocytes are found either as cells with a single polyploid nucleus or as multinucleated cells with diploid or even polyploid nuclei. In this study, we evaluate the degree of polyploidy in the murine liver by accounting both DNA content and number of nuclei per cell. We demonstrate that mouse hepatocytes with diploid nuclei have distinct metabolic characteristics compared to cells with polyploid nuclei. In addition to strong differential gene expression, comprising metabolic as well as signaling compounds, we found a strongly decreased insulin binding of nuclear polyploid cells. Our observations were associated with nuclear ploidy but not with total ploidy within a cell. We therefore suggest ploidy of the nuclei as an new diversity factor of hepatocytes and hypothesize that hepatocytes with polyploid nuclei may have distinct biological functions than mono-nuclear ones. This diversity is independent from the well-known heterogeneity related to the cells' position along the porto-central liver-axis.
Phoneme recognition using time-delay neural networks (1989)

The authors present a time-delay neural network (TDNN) approach to phoneme recognition which is characterized by two important properties: (1) using a three-layer arrangement of simple computing units, a hierarchy can be constructed that allows for the formation of arbitrary nonlinear decision surfaces, which the TDNN learns automatically using error backpropagation; and (2) the time-delay arrangement enables the network to discover acoustic-phonetic features and the temporal relationships between them independently of position in time and therefore not blurred by temporal shifts in the input. As a recognition task, the speaker-dependent recognition of the phonemes B, D, and G in varying phonetic contexts was chosen. For comparison, several discrete hidden Markov models (HMM) were trained to perform the same task. Performance evaluation over 1946 testing tokens from three speakers showed that the TDNN achieves a recognition rate of 98.5% correct while the rate obtained by the best of the HMMs was only 93.7%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Circadian Modulation of GABA-Mediated Cortical Inhibition (2011)

Circadian rhythms exert powerful influence on various aspects of human physiology and behavior. Here, we tested changes of human cerebral cortex excitability over the course of the day with transcranial magnetic stimulation (TMS). At different times of the day, intracortical and corticospinal excitability of the primary motor cortex (M1) was evaluated in 15 healthy subjects by TMS of left M1. While motor thresholds, short-interval intracortical inhibition and facilitation and input/output curves remained unchanged, we found that a specific form of γ-aminobutyric acid (GABA)-mediated intracortical inhibition, revealed by long-interval intracortical inhibition and cortical silent periods, progressively decreased during the course of the day. Additional experiments demonstrated that morning inhibition persisted irrespective of previous sleep or sleep deprivation. Corticotropin-releasing hormone (CRH) infusions in the evening lead to morning cortisol levels but did not restore levels of morning inhibition, whereas suppression of endogenous CRH release by repeated oral dexamethasone intake over 24 h prevented morning inhibition. The findings suggest a specific modulation of GABAergic motor cortex inhibition within the circadian cycle, possibly linked to the CRH system, and may indicate a neurobiological basis for variable neuroplasticity over the course of the day.
Cell Death Regulation in Drosophila (2000)

Programmed cell death, or apoptosis, is a genetically encoded form of cell suicide that results in the orderly death and phagocytic removal of excess, damaged, or dangerous cells during normal development and in the adult. The cellular machinery required to carry out apoptosis is present in most, if not all cells, but is only activated in cells instructed to die (for review see Jacobson et al. 1997). Here, we review cell death regulation in the fly in the context of a first pass look at the complete Drosophila genome and what is known about death regulation in other organisms, particularly worms and vertebrates.
A distinct pattern of cytokine gene expression by human CD83+ blood dendritic cells (1995)

Dendritic cells are the most potent antigen-presenting cells of the immune system. Although dendritic cells are likely to secrete selective cytokines that facilitate antigen presentation, the difficulty in isolating pure dendritic cells in sufficient numbers has made assessment of this function imprecise. In this study, pure populations of CD83+ human blood dendritic cells were isolated by previously established enrichment procedures and subsequent cell sorting. Cytokine gene expression was assessed by reverse transcription-polymerase chain reaction (RT-PCR) amplification of mRNA. Resting CD83+ dendritic cells expressed interleukin-6 (IL-6), IL-8, IL-10, tumor necrosis factor-alpha (TNF-alpha), and transforming growth factor-beta 1 (TGF-beta 1) mRNA, while activation of cells with phorbol myristate acetate induced IL-1 alpha and beta, IL-9, TNF-beta, interferon-gamma, granulocyte-macrophage colony-stimulating factor (GM-CSF), M-CSF, and G-CSF mRNA expression. Resting CD83+ cells also expressed the Rantes, MCP-1, MIP-1 alpha, and MIP-1 beta chemokines, with 1-309 expression induced upon activation. Resting and activated CD83+ dendritic cells also expressed receptors for IL-2 (CD25), TGF-beta 1 and -beta 3, and GM-CSF as determined by indirect immunofluorescence staining. These results indicate that dendritic cells have the ability to produce a variety of soluble factors which are likely to contribute substantially to the potent allostimulatory activity of these cells.
Three-Year Safety and Efficacy of Vicriviroc, a CCR5 Antagonist, in HIV-1–Infected Treatment-Experienced Patients (2010)

Vicriviroc seems safe and demonstrates sustained virologic suppression through 3 years of follow-up. Further trials of vicriviroc will establish its clinical utility for the treatment of HIV-1 infection.
Conditional Image Generation with PixelCNN Decoders (2016)

This work explores conditional image generation with a new image density model based on the PixelCNN architecture. The model can be conditioned on any vector, including descriptive labels or tags, or latent embeddings created by other networks. When conditioned on class labels from the ImageNet database, the model is able to generate diverse, realistic scenes representing distinct animals, objects, landscapes and structures. When conditioned on an embedding produced by a convolutional network given a single image of an unseen face, it generates a variety of new portraits of the same person with different facial expressions, poses and lighting conditions. We also show that conditional PixelCNN can serve as a powerful decoder in an image autoencoder. Additionally, the gated convolutional layers in the proposed model improve the log-likelihood of PixelCNN to match the state-of-the-art performance of PixelRNN on ImageNet, with greatly reduced computational cost.
Derivative Dynamic Time Warping (2001)

1 Introduction Time series are a ubiquitous form of data occurring in virtually every scientific discipline. A common task with time series data is comparing one sequence with another. In some domains a very simple distance measure, such as Euclidean distance will suffice. However, it is often the case that two sequences have the approximately the same overall component shapes, but these shapes do not line up in X-axis. Figure 1 shows this with a simple example. In order to find the similarity between such sequences, or as a preprocessing step before averaging them, we must “warp” the time axis of one (or both) sequences to achieve a better alignment. Dynamic time warping (DTW), is a technique for efficiently achieving this warping. In addition to data mining (Keogh & Pazzani 2000, Yi et. al. 1998, Berndt & Clifford 1994), DTW has been used in gesture recognition (Gavrila & Davis 1995), robotics (Schmill et. al 1999), speech processing (Rabiner & Juang 1993), manufacturing (Gollmer & Posten 1995) and medicine (Caiani et. al 1998).
Biodegradation of Nitro-Substituted Explosives 2,4,6-Trinitrotoluene, Hexahydro-1,3,5-Trinitro-1,3,5-Triazine, and Octahydro-1,3,5,7-Tetranitro-1,3,5-Tetrazocine by a Phytosymbiotic Methylobacterium sp. Associated with Poplar Tissues ( Populus deltoides × nigra DN34) (2004)

A pink-pigmented symbiotic bacterium was isolated from hybrid poplar tissues (Populus deltoides x nigra DN34). The bacterium was identified by 16S and 16S-23S intergenic spacer ribosomal DNA analysis as a Methylobacterium sp. (strain BJ001). The isolated bacterium was able to use methanol as the sole source of carbon and energy, which is a specific attribute of the genus Methylobacterium. The bacterium in pure culture was shown to degrade the toxic explosives 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazene (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine (HMX). [U-ring-(14)C]TNT (25 mg liter(-1)) was fully transformed in less than 10 days. Metabolites included the reduction derivatives amino-dinitrotoluenes and diamino-nitrotoluenes. No significant release of (14)CO(2) was recorded from [(14)C]TNT. In addition, the isolated methylotroph was shown to transform [U-(14)C]RDX (20 mg liter(-1)) and [U-(14)C]HMX (2.5 mg liter(-1)) in less than 40 days. After 55 days of incubation, 58.0% of initial [(14)C]RDX and 61.4% of initial [(14)C]HMX were mineralized into (14)CO(2). The radioactivity remaining in solution accounted for 12.8 and 12.7% of initial [(14)C]RDX and [(14)C]HMX, respectively. Metabolites detected from RDX transformation included a mononitroso RDX derivative and a polar compound tentatively identified as methylenedinitramine. Since members of the genus Methylobacterium are distributed in a wide diversity of natural environments and are very often associated with plants, Methylobacterium sp. strain BJ001 may be involved in natural attenuation or in situ biodegradation (including phytoremediation) of explosive-contaminated sites.
Regulation of gonadotropin-releasing hormone gene expression in the rat during the luteinizing hormone surge. (1995)

In the present study we characterized GnRH gene expression in intact female rats across the estrous cycle and during a steroid-induced LH surge in ovariectomized (OVX) rats, using the quantitative ribonuclease protection assay. We measured cytoplasmic messenger RNA (mRNA) levels and nuclear primary transcript levels as an index of transcription. In Exp I, cycling rats were killed at 1100 or 1800 h on estrus, diestrus day 1, or diestrus day 2 (D2) or at 1100, 1500, 1800, or 2100 h on proestrus (P). In Exp II, proestrous rats were killed at the same time points or injected with pentobarbital (Pb) at the onset of the LH surge and killed on that day or the following day. In Exp III, a LH surge was induced in OVX rats treated with estradiol benzoate plus progesterone. Rats were killed at 1200, 1500, 1600, 1700, or 2100 h on the day of the surge. For all experiments, blood samples were collected and frozen for quantitation of LH by RIA. The preoptic area-anterior hypothalamus was dissected, and cytoplasmic and nuclear RNA were extracted and assayed separately by ribonuclease protection assay. In Exp I, cytoplasmic mRNA levels exhibited two significant peaks, one on D2 and another at 1500h on P. Primary transcript levels were significantly elevated only at 1500 h on P. In Exp II, proestrous rats and rats given Pb and killed the next day had a peak in cytoplasmic mRNA levels at 1500 h, which was blocked in rats given Pb and killed the same day. In Exp III with OVX rats, no significant changes in mRNA or primary transcript levels were observed between steroid or control groups. We hypothesize that the increase in cytoplasmic mRNA levels in cycling rats on D2 is probably due to a posttranscriptional mechanism, because it was not paralleled by changes in primary transcript levels, which would be expected if a transcriptional mechanism were involved. On P, both cytoplasmic mRNA and primary transcript levels changed, suggesting a transcriptional mechanism at this time.
Regulation of herpesvirus macromolecular synthesis: sequential transition of polypeptide synthesis requires functional viral polypeptides. (1975)

It was previously shown that virus-specific polypeptides made in HEp-2 cells infected with herpes simplex 1 form three groups designated alpha, beta, and gamma whose synthesis is coordinately regulated and sequentially ordered. This report shows that one or more functional alpha polypeptides are necessary to turn on the synthesis of beta and gamma groups, and conversely, one or more polypeptides in the latter groups turn off the synthesis of alpha polypeptides. Specifically, infected cells maintained in medium containing either canavanine, an analogue of arginine, or azetidine-2-carboxylic acid an analogue of proline and hydroxyproline, synthesized alpha polypeptide at rates comparable to maximal rates in untreated infected cells but did not undergo the normal transition to beta and gamma polypeptide synthesis. The transition to gamma polypeptide synthesis and shut-off of synthesis of earlier polypeptide groups proceeded normally if addition of canavanine was delayed until at least 4-5 hr after infection. Addition of canavanine after the onset of beta and gamma polypeptide synthesis, i.e., between 2 and 3.5 hr after infection, resulted in sustained, simultaneous synthesis of all three polypeptide groups, a phenomenon not seen in untreated infected cells. Canavanine-treated infected cells, synthesizing alpha polypeptides, recovered the capacity to make beta and gamma polypeptides after removal of the analogue, but only after a 1-to 2-hr delay compared with infected untreated cells. The data indicate that the on and off controls inherent in the cascade regulation of viral polypeptide synthesis are mediated by one or more polypeptides in each group at transcriptional or post-transcriptional levels.
Concept indexing (1999)

Marking text in a document is a convenient way of identifying bits of knowledge that are relevant for the reader, a colleague or a larger group. Based on such markings, networks of concepts with hyperlinks to their occurrences in a collection of documents can be developed. On the Internet, marked documents can easily be shared, concepts can be constructed collaboratively and the concept-document network can be used for navigation and direct access. Text marking, grounded concepts and the Internet as base technology are characteristics of our tool for managing so called “concept indexes”. We describe the current and the new design and outline some application scenarios: electronic help desks, information digests on the Web, teaching design in virtual classes and planning under quality control in distributed teams.
Low-Temperature Solution-Processed Perovskite Solar Cells with High Efficiency and Flexibility (2014)

Perovskite compounds have attracted recently great attention in photovoltaic research. The devices are typically fabricated using condensed or mesoporous TiO2 as the electron transport layer and 2,2'7,7'-tetrakis-(N,N-dip-methoxyphenylamine)9,9'-spirobifluorene as the hole transport layer. However, the high-temperature processing (450 °C) requirement of the TiO2 layer could hinder the widespread adoption of the technology. In this report, we adopted a low-temperature processing technique to attain high-efficiency devices in both rigid and flexible substrates, using device structure substrate/ITO/PEDOT:PSS/CH(3)NH(3)PbI(3-x)Cl(x)/PCBM/Al, where PEDOT:PSS and PCBM are used as hole and electron transport layers, respectively. Mixed halide perovskite, CH(3)NH(3)PbI(3-x)Cl(x), was used due to its long carrier lifetime and good electrical properties. All of these layers are solution-processed under 120 °C. Based on the proposed device structure, power conversion efficiency (PCE) of 11.5% is obtained in rigid substrates (glass/ITO), and a 9.2% PCE is achieved for a polyethylene terephthalate/ITO flexible substrate.