gebhart/patrepeval huggingface dataset:
Ammonificins C and D, Hydroxyethylamine Chromene Derivatives from a Cultured Marine Hydrothermal Vent Bacterium, Thermovibrio ammonificans (2012)

Chemical and biological investigation of the cultured marine hydrothermal vent bacterium, Thermovibrio ammonifican led to the isolation of two hydroxyethylamine chromene derivatives, ammonificins C and D. Their structures were elucidated using combination of NMR and mass spectrometry. Absolute stereochemistry was ascertained by comparison of experimental and calculated CD spectra. Biological evaluation and assessment were determined using the patented ApopScreen cell-based screen for apoptosis-induction. Ammonificins C and D induce apoptosis in micromolar concentrations. To our knowledge, this finding is the first report of chemical compounds that induce apoptosis from the cultured deep-sea marine organism, hydrothermal vent bacterium, Thermovibrio ammonificans.
Model Selection and Accounting for Model Uncertainty in Graphical Models Using Occam's Window (1994)

Abstract We consider the problem of model selection and accounting for model uncertainty in high-dimensional contingency tables, motivated by expert system applications. The approach most used currently is a stepwise strategy guided by tests based on approximate asymptotic P values leading to the selection of a single model; inference is then conditional on the selected model. The sampling properties of such a strategy are complex, and the failure to take account of model uncertainty leads to underestimation of uncertainty about quantities of interest. In principle, a panacea is provided by the standard Bayesian formalism that averages the posterior distributions of the quantity of interest under each of the models, weighted by their posterior model probabilities. Furthermore, this approach is optimal in the sense of maximizing predictive ability. But this has not been used in practice, because computing the posterior model probabilities is hard and the number of models is very large (often greater than 1011). We argue that the standard Bayesian formalism is unsatisfactory and propose an alternative Bayesian approach that, we contend, takes full account of the true model uncertainty by averaging over a much smaller set of models. An efficient search algorithm is developed for finding these models. We consider two classes of graphical models that arise in expert systems: the recursive causal models and the decomposable log-linear models. For each of these, we develop efficient ways of computing exact Bayes factors and hence posterior model probabilities. For the decomposable log-linear models, this is based on properties of chordal graphs and hyper-Markov prior distributions and the resultant calculations can be carried out locally. The end product is an overall strategy for model selection and accounting for model uncertainty that searches efficiently through the very large classes of models involved. Three examples are given. The first two concern data sets that have been analyzed by several authors in the context of model selection. The third addresses a urological diagnostic problem. In each example, our model averaging approach provides better out-of-sample predictive performance than any single model that might reasonably have been selected.
Qualitative and Quantitative Monitoring of Spatio-Temporal Properties with SSTL (2018)

In spatially located, large scale systems, time and space dynamics interact and drives the behaviour. Examples of such systems can be found in many smart city applications and Cyber-Physical Systems. In this paper we present the Signal Spatio-Temporal Logic (SSTL), a modal logic that can be used to specify spatio-temporal properties of linear time and discrete space models. The logic is equipped with a Boolean and a quantitative semantics for which efficient monitoring algorithms have been developed. As such, it is suitable for real-time verification of both white box and black box complex systems. These algorithms can also be combined with stochastic model checking routines. SSTL combines the until temporal modality with two spatial modalities, one expressing that something is true somewhere nearby and the other capturing the notion of being surrounded by a region that satisfies a given spatio-temporal property. The monitoring algorithms are implemented in an open source Java tool. We illustrate the use of SSTL analysing the formation of patterns in a Turing Reaction-Diffusion system and spatio-temporal aspects of a large bike-sharing system.
Freshly isolated mouse 4F7<sup>+</sup> splenic dendritic cells process and present exogenous antigens to T cells (1994)

The antibody 4F7 was reported to recognize an epitope expressed on dendritic cells (DC) from various tissues. To study the ability of splenic 4F7+ dendritic cells to process antigen for presentation to CD4+ T cells, DC were enriched using a separation procedure avoiding overnight culture which could lead to an altered phenotype. These DC were used as antigen-presenting cells (APC) in stimulation cultures of major histocompatibility complex class II-restricted T cells. It was found that they induce antigen-dependent lymphokine production by T cells and therefore could present exogenous antigens. These processing takes place intracellularly, because fixation abrogates presentation to T cells. Moreover, antigen presentation needs intracellular processing within endo- or lysosomes as chloroquine-treatment prevents T cell activation. Titration of APC numbers revealed that contaminating APC most likely did not account for antigen-specific T cell activation by DC. No evidence was found for release of antigenic peptides or for partial antigen processing possibly done by cell surface located enzymes on DC. In conclusion, these results indicate that freshly enriched DC are able to process antigens similarly to other APC.
Nucleotide excision DNA repair pathway as a therapeutic target in patients with high-risk diffuse large B cell lymphoma (2013)

International audience
Performance Analysis of a Civilian GPS Position Authentication System (2013)

A position authentication method utilizing the white-noise-like GPS spreading codes as tamper proof watermarks is described. In this method a segment of the GPS signal collected by a trusted user (the authenticator) is used as a template. Another user whose position and time report needs to be verified (the supplicant) sends a sample of its signal. The supplicant's sample is compared with the authenticator's template. The absence of a correlation peak between the two signals indicates that the supplicant is using a non-authentic GPS signal. A correlation peak having a delay that is inconsistent with relative range between supplicant and authenticator indicates a falsification of the position or time report. Analysis, simulation and experimental results documenting the system's performance are presented. These results show that this approach can detect a deceptive position report with a resolution of 15 meters (1-sigma) or better. Copyright © 2013 Institute of Navigation.
Prevention of OHSS: Current strategies and new insights (2010)

Ovarian hyperstimulation syndrome (OHSS) is an iatrogenic and potentially life threatening condition that affects young healthy patients. Many strategies have been proposed to prevent this syndrome. However, to avoid OHSS without compromising on IVF outcome is still a challenge. The most important action is to identify patients at risk even before ovarian stimulation is initiated and to give them special attention. Coasting is the most popular method to avoid/minimize OHSS. Cycle cancellation, cryopreservation, GnRH antagonists, GnRH agonists, i.v. albumin are other strategies that can provide some kind of benefit but do not completely avoid both early and late forms of OHSS and/or cannot be applied to every patient. Recent studies demonstrate that dopamine agonists can prevent or minimize OHSS without affecting IVF outcome but clinical protocols are not well established yet.
The Use of Biomarkers in Prostate Cancer Screening and Treatment. (2017)

Prostate cancer screening and diagnosis has been guided by prostate-specific antigen levels for the past 25 years, but with the most recent US Preventive Services Task Force screening recommendations, as well as concerns regarding overdiagnosis and overtreatment, a new wave of prostate cancer biomarkers has recently emerged. These assays allow the testing of urine, serum, or prostate tissue for molecular signs of prostate cancer, and provide information regarding both diagnosis and prognosis. In this review, we discuss 12 commercially available biomarker assays approved for the diagnosis and treatment of prostate cancer. The results of clinical validation studies and clinical decision-making studies are presented. This information is designed to assist urologists in making clinical decisions with respect to ordering and interpreting these tests for different patients. There are numerous fluid and biopsy-based genomic tests available for prostate cancer patients that provide the physician and patient with different information about risk of future disease and treatment outcomes. It is important that providers be able to recommend the appropriate test for each individual patient; this decision is based on tissue availability and prognostic information desired. Future studies will continue to emphasize the important role of genomic biomarkers in making individualized treatment decisions for prostate cancer patients.
A function-based on-chip communication design in the heterogeneous multi-core architecture (2007)

Much emphasis is now placed on chip-multiprocessor (CMP) architecture design for exploiting thread-level parallelism in an application. However, traditional design only satisfies the basic requirements of combining several cores on one single chip, and does not consider different characteristics of cores and their different communication requirements. In this paper, from the abstract of the design principles of Multicore CMP architecture, we propose a novel on-chip communication model called unified-communication which is much suitable for chip multi-processor especially the heterogeneous multi-core processor.
Tandem inverted repeat system for selection of effective transgenic RNAi strains in <i>Chlamydomonas</i> (2004)

RNA interference (RNAi), the double-stranded RNA (dsRNA) triggered post-transcriptional gene silencing, is becoming a powerful tool for reverse genetics studies. Stable RNAi, induced by the expression of inverted repeat (IR) transgenes, has been achieved in protozoa, algae, fungi, plants, and metazoans. However, the level of gene silencing is often quite variable, depending on the type of construct, transgene copy number, site of integration, and target gene. This is a hindrance in functional genomics studies, where it is desirable to suppress target genes reliably to analyze unknown phenotypes. Consequently, we explored strategies for direct selection of effective transgenic RNAi lines in Chlamydomonas reinhardtii. We initially attempted to suppress expression of the Rubisco small subunit multigene family by placing an IR, homologous to the conserved coding sequence, in the 3'UTR of a transgene conferring resistance to bleomycin. However, this approach was fairly inefficient at inducing RNAi as many strains displayed defective transgene integration, resulting in partial or complete deletion of the IR, or low levels of dsRNA expression, presumably due to transcriptional silencing of the integrated IR transgenes. To overcome these problems we designed a system consisting of tandem IR transgenes that consistently triggered co-silencing of a gene with a selectable RNAi-induced phenotype (encoding tryptophan synthase beta subunit) and another gene of interest (encoding either Ku80, an RNA-binding protein, or a thioredoxin isoform). We anticipate that this approach will be useful for generating stable hypomorphic epi-mutants in high-throughput phenotypic screens.
Point mutations within a dimer interface homology domain of c-Mpl induce constitutive receptor activity and tumorigenicity. (1995)

c-Mpl, a receptor for thrombopoietin (TPO), belongs to the haemopoietin/cytokine receptor superfamily, a group of cell surface molecules characterized by conserved sequence motifs within their ligand binding domains. A recurring mechanism for the activation of haemopoietin receptors is the formation of functional complexes by receptor subunit oligomerization. Within the growth hormone receptor, a cluster of extracellular amino acids forms a dimer interface domain that stabilizes ligand-induced homodimers. This domain appears to be functionally conserved in the erythropoietin (EPO) receptor because substitution of cysteines for residues in the analogous region causes EPO-independent receptor activation via disulfide-linked homodimerization. This report identifies an homologous domain within the c-Mpl receptor. The substitution of cysteine residues for specific amino acids in the dimer interface homology regions of c-Mpl induced constitutive receptor activity. Factor-dependent FDC-P1 and Ba/F3 cells expressing the active receptor mutants no longer required exogenous factors and proliferated autonomously. The results imply that the normal process of TPO-stimulated Mpl activation occurs through receptor homodimerization and is mediated by a conserved haemopoietin receptor dimer interface domain. Moreover, cells expressing activated mutant Mpl receptors were tumorigenic in transplanted mice. Thus, like v-mpl, its viral counterpart, mutated forms of the cellular mpl gene also have oncogenic potential.
OPU: An FPGA-Based Overlay Processor for Convolutional Neural Networks (2019)

Field-programmable gate array (FPGA) provides rich parallel computing resources with high energy efficiency, making it ideal for deep convolutional neural network (CNN) acceleration. In recent years, automatic compilers have been developed to generate network-specific FPGA accelerators. However, with more cascading deep CNN algorithms adapted by various complicated tasks, reconfiguration of FPGA devices during runtime becomes unavoidable when network-specific accelerators are employed. Such reconfiguration can be difficult for edge devices. Moreover, network-specific accelerator means regeneration of RTL code and physical implementation whenever the network is updated. This is not easy for CNN end users. In this article, we propose a domain-specific FPGA overlay processor, named OPU to accelerate CNN networks. It offers software-like programmability for CNN end users, as CNN algorithms are automatically compiled into executable codes, which are loaded and executed by OPU without reconfiguration of FPGA for switch or update of CNN networks. Our OPU instructions have complicated functions with variable runtimes but a uniform length. The granularity of instruction is optimized to provide good performance and sufficient flexibility, while reducing complexity to develop microarchitecture and compiler. Experiments show that OPU can achieve an average of 91% runtime multiplication and accumulation unit (MAC) efficiency (RME) among nine different networks. Moreover, for VGG and YOLO networks, OPU outperforms automatically compiled network-specific accelerators in the literature. In addition, OPU shows 5.35× better power efficiency compared with Titan Xp. For a real-time cascaded CNN networks scenario, OPU is 2.9× faster compared with edge computing GPU Jetson Tx2, which has a similar amount of computing resources.
Design and implementation of a high speed CMOS imaging system (2010)

In order to meet the needs of measurement of high-speed target, the timing sequence of LUPA300, an array CMOS image sensor of CYPRESS, is analyzed. The driving timing and control software is designed for the array CMOS sensor. High speed CMOS imaging system, whose hardware platform is FPGA, is emphasized. Real-time non-uniformity correction for CMOS sensor is implemented in the output stage. The experimental result shows that the system could control the CMOS sensor flexibly. The image is clear and stable. The maximum resolution of the image is 640H×480V pixels and the system can operate up to 250 frames per second in full resolution.
Prevalence of and interventions for sarcopenia in ageing adults: a systematic review. Report of the International Sarcopenia Initiative (EWGSOP and IWGS) (2014)

prevalence of sarcopenia is substantial in most geriatric settings. Well-designed, standardised studies evaluating exercise or nutrition interventions are needed before treatment guidelines can be developed. Physicians should screen for sarcopenia in both community and geriatric settings, with diagnosis based on muscle mass and function. Supervised resistance exercise is recommended for individuals with sarcopenia. EAA (with leucine) and HMB may improve muscle outcomes.
Activation of human B lymphocytes. I. Direct plaque-forming cell assay for the measurement of polyclonal activation and antigenic stimulation of human B lymphocytes. (1976)

A model for the detection of single cell antibody production by human tonsillar lymphocytes after stimulation with either sheep red blood cells (SRBC) or polyclonal B-cell activators has been described. The culture system is a modified Mishell-Dutton technique with certain critical factors identified. The assay is a sensitive and resproducible hemolysis-in-gel system employing an ultra-thin layer gel technique measuring plaque-forming cells (PFC) against SRBC targets. Several factors essential for optimal responses are described, but the critical feature of the culture system is the use of selected lots of human AB serum supplements which are extensively absorbed with SRBC. This removes a blocking factor present in most human serum which suppresses the B-cell response to SRBC targets after stimulation with either SRBC or several polyclonal B-cell activators. In addition, absorption of serum with SRBC eliminates the presence of artifactual plaques. Background PFC are extremely low and stimulated cultures show significant and reproducible responses. These studies provide a simple, sensitive, and reproducible model for probing the complex events associated with activation of human B lymphocytes.
Performance improvement of visible light communications using optical beamforming (2013)

We propose and demonstrate a new visible light communication technology using optical beamforming. Optical beamforming is a technology to focus LED light on a desired target. Our experimental results show that the signal-to-noise ratio of the visible light communication can be improved by 13.4 dB using the proposed optical beamforming technology. We also propose an algorithm to detect the location of the target device based on the optical beamforming. We use a concept of direction code in the proposed automatic location-detecting algorithm.
Incorporating Supervised Learning in the Domains Account of Categorization (1992)

This note presents an extension to the ‘domains’ account of cognitive categorization described by Robins. Current connectionist models of various aspects of categorization are based on either ‘supervised learning’ (the use of explicit categorizing information) or ‘unsupervised learning’ (using just the observable structure of a population). The domains account is an example of an unsupervised account. It seems clear, however, that humans employ both supervised and unsupervised methods of category learning. This note describes an extension to the domains approach which incorporates supervised learning, thereby providing an account of both mechanisms in the same unifying framework.
Video content dependent directional transform for intra frame coding (2012)

The mode-dependent directional transform (MDDT) employed Karhunen-Loève Transform (KLT) for compressing directional residue signal of intra prediction along its direction. The transform bases were derived from the singular value decomposition (SVD) of residue signals coming from all kinds of video sequences, which were expected to be efficient for most of video sequences. However, the advantage of KLT comes from the concept of a “signal content dependent transform”. MDDT and its variants failed to exploit such a concept, so they did not fully exploit the efficiency of KLT. In this paper, a video content feature is firstly defined as the histogram of the residue produced by intra prediction. Secondly, one KLT basis is computed for each feature of each mode from off-line experiments. Thus, multiple KLT bases identified by their features are provided to each mode instead of only one basis in MDDT. One of them is selected during encoding process by matching the feature of signal being processed to the predefined features. The experiments show that the average improvement of 0.17dB PSNR and 2.23% bits saving can be achieved by the proposed video content dependent directional transform (CDDT) comparing to the state-of-the-art MDDT.
Analysis of the trace water in anhydrous hydrofluoric acid by the conductivity (1980)

無水フッ化水素酸中の微量水分と伝導率の関係を,密閉系添加方式により調査した.高純度フッ化水素酸に既知量の水その他の成分を添加したときの伝導率変化の挙動を解析することによって,100ppm以下の微量水分(カールフィッシャー法の適用困難な領域)と伝導率の関係を明らかにし,フルオロ硫酸,ヘキサフルオロケイ酸及び亜硫酸のそれぞれ数百ppmの存在は伝導率に影響しないことを確かめた.又,貯そう及び流送管中で伝導率を直接測定する,バイパス型及びオンストリーム型のフローセルを開発した.以上により伝導率10-5Ω-1cm-1けたの無水フッ化水素酸中のppmけたの微量水分の連続測定が可能となった.
A medium-voltage motor drive based on diode-clamped modular multilevel converters (2017)

Modular multilevel converters (MMC) have shown a great potential in the area of medium-voltage drives, for it can produce excellent output waveform with low average switching frequencies. A key issue of MMC is that it requires a complex voltage balancing method to balance the capacitor voltage of each submodule (SM). In this paper, a medium-voltage motor drive based on diode-clamped modular multilevel converter (DCM2C) is proposed. This topology is prominent in reducing voltage balancing control complexity by using a balancing branch between each SM to clamp the capacitor voltage.
The effect of dissolved oxygen (DO) concentration on the glycosylation of recombinant protein produced by the insect cell–baculovirus expression system (2001)

The effect of dissolved oxygen concentration on human secreted alkaline phosphatase (SEAP) glycosylation by the insect cell-baculovirus expression system was investigated in a well-controlled bioreactor. Oligomannose-type N-linked glycans (i.e., Man2 to Man6 and Man3F) were present in SEAP produced by Spodoptera frusiperda Sf-9 (Sf-9) and Trichoplusia ni BTI-Tn-5B1-4 (Tn-5B1-4) insect cell lines. The relative amounts of the most highly processed glycans (i.e., Man3F and Man2 in the SEAP from Sf-9 and Tn-5B1-4 cells, respectively) were significantly higher at 50% of air saturation than at either 10% or 190% of air saturation. That is, glycan processing was inhibited at both low and high dissolved oxygen concentrations.
Phages specific for mycobacterial lipoarabinomannan help serodiagnosis of tuberculosis. (2009)

This study evaluated the possibility to use six phages specific to the Mycobacterium tuberculosis lipoarabinomannan (LAM) as tools for tubercular serodiagnosis. We analysed sera samples from 30 subjects with active tuberculosis (TB+), 30 with latent tubercular infection (LTBI) and 60 healthy subjects as controls (K). Our data indicated a good antibody response of the TB+ and LTBI patients against the phage Ri(7)17; the optical density (OD) values obtained from sera patients was statistically significant when compared to the control samples. Our results confirm that phage display technology might be useful to develop new tools for diagnosis of tuberculosis.
A system architecture for autonomous visual road vehicle guidance (2002)

A hierarchical system architecture for autonomous visual road vehicle guidance is presented, which consists of four levels: a vehicle level, a 4D-level, a rule-based level, and a knowledge-based level. The system architecture is applied to VaMP, a Mercedes passenger car which autonomously performs missions on German freeways. VaMP perceives the environment with its sense of vision and conventional sensors. It controls its actuators for locomotion and attention focussing.