gebhart/patrepeval huggingface dataset:
Potent Neutralization of Hendra and Nipah Viruses by Human Monoclonal Antibodies (2005)

Hendra virus (HeV) and Nipah virus (NiV) are closely related emerging viruses comprising the Henipavirus genus of the Paramyxovirinae. Each has a broad species tropism and can cause disease with high mortality in both animal and human hosts. These viruses infect cells by a pH-independent membrane fusion event mediated by their attachment (G) and fusion (F) envelope glycoproteins (Envs). Seven Fabs, m101 to -7, were selected for their significant binding to a soluble form of Hendra G (sG) which was used as the antigen for panning of a large naïve human antibody library. The selected Fabs inhibited, to various degrees, cell fusion mediated by the HeV or NiV Envs and virus infection. The conversion of the most potent neutralizer of infectious HeV, Fab m101, to immunoglobulin G1 (IgG1) significantly increased its cell fusion inhibitory activity: the 50% inhibitory concentration was decreased more than 10-fold to approximately 1 microg/ml. The IgG1 m101 was also exceptionally potent in neutralizing infectious HeV; complete (100%) neutralization was achieved with 12.5 microg/ml, and 98% neutralization required only 1.6 microg/ml. The inhibition of fusion and infection correlated with binding of the Fabs to full-length G as measured by immunoprecipitation and less with binding to sG as measured by enzyme-linked immunosorbent assay and Biacore. m101 and m102 competed with the ephrin-B2, which we recently identified as a functional receptor for both HeV and NiV, indicating a possible mechanism of neutralization by these antibodies. The m101, m102, and m103 antibodies competed with each other, suggesting that they bind to overlapping epitopes which are distinct from the epitopes of m106 and m107. In an initial attempt to localize the epitopes of m101 and m102, we measured their binding to a panel of 11 G alanine-scanning mutants and identified two mutants, P185A and Q191 K192A, which significantly decreased binding to m101 and one, G183, which decreased binding of m102 to G. These results suggest that m101 to -7 are specific for HeV or NiV or both and exhibit various neutralizing activities; they are the first human monoclonal antibodies identified against these viruses and could be used for treatment, prophylaxis, and diagnosis and as research reagents and could aid in the development of vaccines.
Ubiquilin 1 Modulates Amyloid Precursor Protein Trafficking and Aβ Secretion (2006)

Ubiquilin 1 (UBQLN1) is a ubiquitin-like protein, which has been shown to play a central role in regulating the proteasomal degradation of various proteins, including the presenilins. We recently reported that DNA variants in UBQLN1 increase the risk for Alzheimer disease, by influencing expression of this gene in brain. Here we present the first assessment of the effects of UBQLN1 on the metabolism of the amyloid precursor protein (APP). For this purpose, we employed RNA interference to down-regulate UBQLN1 in a variety of neuronal and non-neuronal cell lines. We demonstrate that down-regulation of UBQLN1 accelerates the maturation and intracellular trafficking of APP, while not interfering with alpha-, beta-, or gamma-secretase levels or activity. UBQLN1 knockdown increased the ratio of APP mature/immature, increased levels of full-length APP on the cell surface, and enhanced the secretion of sAPP (alpha- and beta-forms). Moreover, UBQLN1 knockdown increased levels of secreted Abeta40 and Abeta42. Finally, employing a fluorescence resonance energy transfer-based assay, we show that UBQLN1 and APP come into close proximity in intact cells, independently of the presence of the presenilins. Collectively, our findings suggest that UBQLN1 may normally serve as a cytoplasmic "gatekeeper" that may control APP trafficking from intracellular compartments to the cell surface. These findings suggest that changes in UBQLN1 steady-state levels affect APP trafficking and processing, thereby influencing the generation of Abeta.
A bed temperature monitoring system for assessing body movement during sleep (1988)

A method of monitoring and analysing temperature distribution in a patient's bed during bed rest and sleep is described. The system consists of 16 temperature sensors, a solid-state recorder and a personal computer. The temperature sensors are attached on the surface of a bed mat. The temperature of the 16 measurement points are recorded and stored on a multichannel solid-state recorder, where a programmable read-only memory (PROM) is used as the memory device. The PROM is detachable from the recorder, and the temperature data is read by a computer. A two-dimensional temperature distribution pattern is obtained by interpolating the temperature between measured points. The system was effective for long-term temperature monitoring without patient discomfort, and it proved reliable and easy to use. The temperature distribution and changes in the distribution indicated body movement and hence periods of sleep.
A simple assay for frequency of chromosome breaks and loss (micronuclei) by flow cytometry of human reticulocytes (2004)

Exposure to environmental stress, such as radiation, poor nutrition, or smoking, can cause hazardous lesions in DNA, including double-strand breaks. In red blood cells, a DNA fragment or lagging chromosome forms a micronucleus when left behind after the main nucleus is extruded to form the mature reticulocyte during erythropoiesis. Reticulocytes with micronuclei in human peripheral blood are not generally available for analysis because the spleen removes aberrant cells. We have developed a simple and rapid method to isolate and analyze immature reticulocytes in the peripheral blood for the presence of micronuclei before these cells are removed by the spleen. This method applies single-laser flow-cytometry to measure micronuclei in an enriched transferrin-positive reticulocyte population. Abramsson-Zetterberg et al. (Abramsson-Zetterberg, L., Zetterberg, G., Bergqvist, M., and Grawe, J. Environ. Mol. Mutagen. 36, 22-31, 2000) have described a method to measure micronuclei in an enriched reticulocyte population using a dual-laser flow cytometry. Unlike the beads used in their magnetic-immunoseparation procedures, the beads used in this study do not require a prelabeling step and are compatible with the flow cell, sparing the need to release the cells from the beads and avoiding the potentially confounding DNase-treatment step. Dertinger et al. (Dertinger, S. D., Torous, D. K., Hall, N. E., Murante, F. G., Gleason, S. E., Miller, R. K., and Tometsko, C. R. Mutat. Res. 515, 3-14, 2002; Dertinger, S. D., Chen, Y., Miller, R. K., Brewer, K. J., Smudzin, T., Torous, D. K., Hall, N. E., Olvany, K. A., Murante, F. G., and Tometsko, C. R. (2003) Mutat. Res. 542, 77-87, 2003) further improved the scoring of micronuclei to enable the use of bench-top instruments in analyzing samples of unenriched reticulocyte-populations. The present method is distinct from flow cytometric assays, such as reported by Dertinger et al., which enable scoring of limited numbers of reticulocytes per sample and require lengthy data acquisition times. We assessed DNA damage in smokers using this novel flow-cytometry based micronuclei-assay. The results show that this assay can effectively detect micronuclei in human blood samples. This method, unlike available micronuclei assays, allows rapid evaluation of a large number of cells and therefore should prove to be useful in monitoring of human populations for genetic damage.
Ketamine-Induced Neuronal Cell Death in the Perinatal Rhesus Monkey (2007)

Ketamine is widely used as a pediatric anesthetic. Studies in developing rodents have indicated that ketamine-induced anesthesia results in brain cell death. Additional studies are needed to determine if ketamine anesthesia results in brain cell death in the nonhuman primate and if so, to begin to define the stage of development and the duration of ketamine anesthesia necessary to produce brain cell death. Rhesus monkeys (N = 3 for each treatment and control group) at three stages of development (122 days of gestation and 5 and 35 postnatal days [PNDs]) were administered ketamine intravenously for 24 h to maintain a surgical anesthetic plane, followed by a 6-h withdrawal period. Similar studies were performed in PND 5 animals with 3 h of ketamine anesthesia. Animals were subsequently perfused and brain tissue processed for analyses. Ketamine (24-h infusion) produced a significant increase in the number of caspase 3-, Fluoro-Jade C- and silver stain-positive cells in the cortex of gestational and PND 5 animals but not in PND 35 animals. Electron microscopy indicated typical nuclear condensation and fragmentation in some neuronal cells, and cell body swelling was observed in others indicating that ketamine-induced neuronal cell death is most likely both apoptotic and necrotic in nature. Ketamine increased N-methyl-D-aspartate (NMDA) receptor NR1 subunit messenger RNA in the frontal cortex where enhanced cell death was apparent. Earlier developmental stages (122 days of gestation and 5 PNDs) appear more sensitive to ketamine-induced neuronal cell death than later in development (35 PNDs). However, a shorter duration of ketamine anesthesia (3 h) did not result in neuronal cell death in the 5-day-old monkey.
Design and Applications for Embedded Networks-on-Chip on FPGAs (2016)

Field-programmable gate-arrays (FPGAs) have evolved to include embedded memory, high-speed I/O interfaces and processors, making them both more efficient and easier-to-use for compute acceleration and networking applications. However, implementing on-chip communication is still a designer's burden wherein custom system-level buses are implemented using the fine-grained FPGA logic and interconnect fabric. Instead, we propose augmenting FPGAs with an embedded network-on-chip (NoC) to implement system-level communication. We design custom interfaces to connect a packet-switched NoC to the FPGA fabric and I/Os in a configurable and efficient way and then define the necessary conditions to implement common FPGA design styles with an embedded NoC. Four application case studies highlight the advantages of using an embedded NoC. We show that access latency to external memory can be ~1.5× lower. Our application case study with image compression shows that an embedded NoC improves frequency by 10-80%, reduces utilization of scarce long wires by 40% and makes design easier and more predictable. Additionally, we leverage the embedded NoC in creating a programmable Ethernet switch that can support up to 819 Gb/s-5× more switching bandwidth and 3× lower area compared to previous work. Finally, we design a 400 Gb/s NoC-based packet processor that is very flexible and more efficient than other FPGA-based packet processors.
Diversifying Carotenoid Biosynthetic Pathways by Directed Evolution (2005)

Microorganisms and plants synthesize a diverse array of natural products, many of which have proven indispensable to human health and well-being. Although many thousands of these have been characterized, the space of possible natural products--those that could be made biosynthetically--remains largely unexplored. For decades, this space has largely been the domain of chemists, who have synthesized scores of natural product analogs and have found many with improved or novel functions. New natural products have also been made in recombinant organisms, via engineered biosynthetic pathways. Recently, methods inspired by natural evolution have begun to be applied to the search for new natural products. These methods force pathways to evolve in convenient laboratory organisms, where the products of new pathways can be identified and characterized in high-throughput screening programs. Carotenoid biosynthetic pathways have served as a convenient experimental system with which to demonstrate these ideas. Researchers have mixed, matched, and mutated carotenoid biosynthetic enzymes and screened libraries of these "evolved" pathways for the emergence of new carotenoid products. This has led to dozens of new pathway products not previously known to be made by the assembled enzymes. These new products include whole families of carotenoids built from backbones not found in nature. This review details the strategies and specific methods that have been employed to generate new carotenoid biosynthetic pathways in the laboratory. The potential application of laboratory evolution to other biosynthetic pathways is also discussed.
General cost functions for support vector regression. (1998)

The concept of Support Vector Regression is extended to a more general class of convex cost functions. Moreover it is shown how the resulting convex constrained optimization problems can be efficiently solved by a Primal-Dual Interior Point path following method. Both computational feasibility and improvement of estimation is demonstrated in the experiments.
Snapshot Mueller matrix spectropolarimeter (2007)

We present a new snapshot technique for performing spectrally resolved Mueller matrix polarimetry. The basic approach is an extension of the channeled spectropolarimetry technique, employing frequency-domain interferometry to encode polarization information into modulation of the spectrum.
Myocardial protective effect of FR167653; a novel cytokine inhibitor in ischemic-reperfused rat heart (2004)

These data demonstrated positive inotropic and antiapoptotic effects of a newly synthesized compound (FR167653) of cytokine inhibitors and its inhibitory effect on myocardial TNFalpha production and p38 MAPK activation in ischemic-reperfused rat heart. This suggested that cytokine inhibition is significant as a method for myocardial protection against ischemia-reperfusion injury.
Mutation in the NDUFS4 gene of complex I abolishes cAMP‐dependent activation of the complex in a child with fatal neurological syndrome (2001)

Evidence is presented showing that in a patient with fatal neurological syndrome, the homozygous 5 bp duplication in the cDNA of the NDUFS4 18 kDa subunit of complex I abolishes cAMP-dependent phosphorylation of this protein and activation of the complex. These findings show for the first time that human complex I is regulated via phosphorylation of the subunit encoded by the NDUFS4 gene.
TaBERT: Pretraining for Joint Understanding of Textual and Tabular Data (2020)

Recent years have witnessed the burgeoning of pretrained language models (LMs) for text-based natural language (NL) understanding tasks. Such models are typically trained on free-form NL text, hence may not be suitable for tasks like semantic parsing over structured data, which require reasoning over both free-form NL questions and structured tabular data (e.g., database tables). In this paper we present TaBERT, a pretrained LM that jointly learns representations for NL sentences and (semi-)structured tables. TaBERT is trained on a large corpus of 26 million tables and their English contexts. In experiments, neural semantic parsers using TaBERT as feature representation layers achieve new best results on the challenging weakly-supervised semantic parsing benchmark WikiTableQuestions, while performing competitively on the text-to-SQL dataset Spider. Implementation of the model will be available at http://fburl.com/TaBERT .
Presqualene Alcohol (1971)

Abstract An optically active (+) C30 alcohol has been isolated after hydrolysis of presqualene pyrophosphate by yeast microsomes. This alcohol can be prepared on a relatively large scale directly from farnesyl pyrophosphate in incubations with yeast microsomes from which inhibitors of phosphatase are omitted. The alcohol is named presqualene alcohol as its pyrophosphorylated form appears to be identical with natural presqualene pyrophosphate and is converted into squalene by microsomes in the presence of NADPH. The elemental compositions of presqualene alcohols biosynthesized from protio-farnesyl pyrophosphate and from [1-D2]-farnesyl pyrophosphate were found by high resolution mass spectrometry to be C30H49OH and C30H46D3OH, respectively. Presqualene alcohol contains five double bonds and one carbocycle. Mass spectral, nuclear magnetic resonance, and infrared spectroscopic studies as well as chemical degradation of presqualene alcohol indicate that its structure is that of a tetrasubstituted cyclopropane: cis-(1,2-anti-1,3-anti)-3-(2',6',10'-trimethylundeca-2',6'-10'-trienyl)-2-(2'',6''-dimethylnona-2'',6''-dienyl)-2-methyl-1-hydroxymethylcyclopropane. The data limit the absolute configuration around the three asymmetrical centers of the ring to either 1R, 2R, 3R or 1S, 2S, 3S out of the eight possible isomers.
BOOTP Vendor Information Extensions (1993)

This RFC is a slight revision and extension of RFC-1048 by Philip
Prindeville, who should be credited with the original work in this
memo. This memo will be updated as additional tags are defined. This
edition introduces Tag 14 for Merit Dump File, Tag 15 for Domain Name,
Tag 16 for Swap Server and Tag 17 for Root Path. This memo is a status
report on the vendor information extensions used int the Bootstrap
Protocol (BOOTP).
Control of Macrophage Activation and Function by PPARs (2010)

Abstract: Macrophages, a key component of the innate defense against pathogens, participate in the initiation and resolution of inflammation, and in the maintenance of tissues. These diverse and at times antithetical functions of macrophages are executed via distinct activation states, ranging from classical to alternative to deactivation. Because the dysregulation of macrophage activation is pathogenically linked to various metabolic, inflammatory and immune disorders, regulatory proteins controlling macrophage activation have emerged as important new therapeutic targets. Here, the mechanisms by which peroxisome proliferator-activated receptors (PPARs) transcriptionally regulate macrophage activation in health and disease states, including obesity, insulin resistance and cardiovascular disease, are reviewed.
Demonstration of fully functional 8Mb perpendicular STT-MRAM chips with sub-5ns writing for non-volatile embedded memories (2014)

We present major breakthroughs in MTJ design for STT-MRAM applications allowing reliable write for pulse lengths down to 1.5ns, data retention up to 125°C for 10 years and full compatibility with BEOL process up to 400°C for 1 hour. We have successfully integrated the novel structure onto an 8Mbit test chip. We demonstrate writing of every single cell in the array using sub-5ns pulses over a wide temperature range without using any error correction. We also show that sensing times of 4ns are sufficient to read every data cell. The inherent scalability of the design makes it a prime candidate for universal embedded non-volatile memories down to the 28nm node and beyond.
Biocompatibility of Polyvinylalcohol Gel as a Vitreous Substitute (2006)

Polyvinylalcohol (PVA) hydrogel cross-linked by gamma irradiation was assessed as a possible vitreous substitute. From a series of experiments, rise of intraocular pressure and inflammatory changes in the vitreous cavity after operation were observed in some cases. Crab-eating macaques were used for this experiment. PVA gels were injected into vitreous cavity after vitrectomy and followed clinically by opthalmoscopy, tonometry, fundus photography, electroretinogram (ERG), chemotaxis, and flare cell meter. Histopathologic examination by light and electron microscopy was performed after 3 months. As a result, there were no significant changes in ophthalmoscopic findings. No abnormal rising of intraocular pressure (IOP) was recognized. ERG did not show meaningful amplitude weakness. From the photon counting of flare cell meter, significant break of blood-aqueous barrier and blood-retinal barrier was not observed. Histopathologic examination revealed that all layers of the retina were intact and no loss of tissue was evident. However, in PVA gel-injected eyes, some vacuolations of the inner retina were found in some specimens. To conclude, PVA gel was well tolerated in these experiments. The gel with a network similar to the vitreous body showed the best biocompatibility, though it is necessary to investigate the biocompatibility for the long-term. PVA gel is a good candidate for a vitreous substitute.
Wireless Data Network Infrastructure at Carnegie Mellon University (1996)

This article describes the Wireless Andrew infrastructure we are building. We begin with an overview of the infrastructure and the characteristics of the two types of wireless networks we are using. Next, we describe in more detail each of these networks. We discuss the technology used, our implementation of it in our wireless network infrastructure, and our current deployment experience. Finally, we summarize the lessons we have learned and present conclusions. Overview of Infrastructure
A New Route to Spiropyrrolidinyl-oxindole Alkaloids via Iodide Ion Induced Rearrangement of [(N-Aziridinomethylthio)methylene]-2-oxindoles (2001)

A new approach for the synthesis of spiropyrrolidinyloxindole alkaloids, i.e. coerulescine (4) and horsfiline (5) has been developed via iodide ion induced rearrangement of [(N-aziridinomethylthio)methylene]oxindoles 2 to the respective spiropyrroline-2-oxindole derivatives 3 and their subsequent one-pot reductive dethiomethylation-N-methylation. [reaction: see text]
Iterative transmission of media streams (1997)

Multimedia streams are difficult to transmit in full quality and real-time due to their size and constraints imposed by their timely presentation, Especially in slow channels with variable throughput such as typical Internet connections -media streaming is extremely hard, We introduce a new iterative method for the transmission of media streams. The idea is to match each iteration of the transmission process exactly to the play-out time of the respective media stream, thus allowing synchronous presentation of the stream's contents during the transmission. The quality of the playback improves with the number of completed iterations, from rough during the first pass to full quality at the end. The WebMovie system implements this iterative streaming scheme for video data. After the introduction of the system, performance measurements are discussed and compared to conventional methods of movie transmission.
Enabling datacenter servers to scale out economically and sustainably (2013)

As cloud applications proliferate and data-processing demands increase, server resources must grow to unleash the performance of emerging workloads that scale well with large number of compute nodes. Nevertheless, power has become a crucial bottleneck that restricts horizontal scaling (scale out) of server systems, especially in datacenters that employ power over-subscription. When a datacenter hits the maximum capacity of its power provisioning equipment, the owner has to either build another facility or upgrade existing utility power infrastructure -- both approaches add huge capital expenditure, require significant construction lead time, and can further increase the owner's carbon footprint.
Identification of Ligands for Two Human Bitter T2R Receptors (2004)

Earlier, a family of G protein-coupled receptors, termed T2Rs, was identified in the rodent and human genomes through data mining. It was suggested that these receptors mediate bitter taste perception. Analysis of the human genome revealed that the hT2R family is composed of 25 members. However, bitter ligands have been identified for only three human receptors so far. Here we report identification of two novel ligand-receptor pairs. hT2R61 is activated by 6-nitrosaccharin, a bitter derivative of saccharin. hT2R44 is activated by denatonium and 6-nitrosaccharin. Activation profiles for these receptors correlate with psychophysical data determined for the bitter compounds in human studies. Functional analysis of hT2R chimeras allowed us to identify residues in extracellular loops critical for receptor activation by ligands. The discovery of two novel bitter ligand-receptor pairs provides additional support for the hypothesis that hT2Rs mediate a bitter taste response in humans.