gebhart/patrepeval huggingface dataset:
Use of NMR Metabolomics To Analyze the Targets of <scp>d</scp>-Cycloserine in Mycobacteria: Role of <scp>d</scp>-Alanine Racemase (2007)

D-Cycloserine (DCS) is only used with multidrug-resistant strains of tuberculosis because of serious side effects. DCS is known to inhibit cell wall biosynthesis, but the in vivo lethal target is still unknown. We have applied NMR-based metabolomics combined with principal component analysis to monitor the in vivo effect of DCS on Mycobacterium smegmatis. Our analysis suggests DCS functions by inhibiting multiple protein targets.
Energy Harvesting With Microbial Fuel Cell and Power Management System (2010)

This paper presents a system that can harvest energy in the water and use the harvested energy to power electronic devices deployed in the water. The system consists of a microbial fuel cell (MFC) and a power management system. The MFC uses electrochemical reactions and bacteria that exist in the water to harvest energy and generate electricity. The power management system consisting of a charge pump, a super capacitor, two solid-state switches, and a boost converter accumulates the energy harvested by the MFC, stores the energy in the super capacitor, and bursts power to the load. The power management system also boosts the voltage of the MFC to a sufficient level for the electronic devices. The presented energy-harvesting system is self-powered, sustainable, environment friendly, and maintenance-free. The system has been tested and proven through experimental work.
Key Technologies for Developing a 420 kV 50 kA GCB Interrupter Unit (1989)

Polytetrafluoroethylene (PTFE) has been widely used as nozzle material in puffer-type circuit breakers, but the irregular carbonization and under the exposure to interrupted arcs were not fully understood. The addition of a heat-resistant filler has been studied theoretically and experimentally. A model to simulate the wear of the nozzle material is proposed. The model assumes that the radiation energy from the arc is absorbed by the filler particle while the PTFE transmits the energy with negligible absorption. The wear rate reproduced by this model showed good agreement with the experimental results of nozzle wear for a 420 kV, 50 kA interrupter unit. >
Hardware Accelerated Power Estimation (2005)

In this paper, we present power emulation, a novel design paradigm that utilizes hardware acceleration for the purpose of fast power estimation. Power emulation is based on the observation that the functions necessary for power estimation (power model evaluation, aggregation, etc.) can be implemented as hardware circuits. Therefore, we can enhance any given design with "power estimation hardware", map it to a prototyping platform, and exercise it with any given test stimuli to obtain power consumption estimates. Our empirical studies with industrial designs reveal that power emulation can achieve significant speedups (10X to 500X) over state-of-the-art commercial register-transfer level (RTL) power estimation tools.
<i>Staphylococcus aureus</i> Agr and Sar Global Regulators Influence Internalization and Induction of Apoptosis (1998)

Staphylococcus aureus was recently shown to be internalized by and to induce apoptosis in a bovine mammary epithelial cell line, suggesting that these processes could be involved in staphylococcal pathogenesis or persistence. To examine the role of virulence factor regulators during internalization, mutant agr and sar strains of S. aureus were analyzed for their abilities to enter and induce apoptosis in epithelial cells. Like a previously characterized bovine mastitis isolate, the standard laboratory strain, RN6390 (wild type), entered the epithelial cells and subsequently induced apoptosis. In contrast, the mutant strains RN6911 (agr), ALC136 (sar), and ALC135 (agr sar) were internalized by the cultured cells at levels reproducibly greater than that for RN6390 but failed to induce apoptosis. The internalization of S. aureus was affected by growth phase, suggesting a role for agr-regulated surface proteins in this process. Furthermore, the ability to induce apoptosis required metabolically active intracellular bacteria. These data indicate that the ability of S. aureus to enter mammalian cells and induce apoptosis is dependent on factors regulated by Agr and Sar. Since transcriptional control by these global regulators is mediated by quorum-sensing and environmental factors, staphylococci may have the potential to induce several alternative effects on cells from an intracellular environment. A model for the function of the agr locus in the context of internalization, intracellular persistence, and dissemination is proposed.
Analyse Vibrationnelle et Structurale en Série Aliphatique Saturée 4—Spectres de Vibration de I'Acide Diméthylmalonique et de ses Sels Alcalins en Solution Aqueuse (1982)

Abstract Les spectres de vibration (Raman et infrarouge) de l'acide dimétyhlmalonique et de ses sels alcalins en solution aqueuse (H 2 O et D 2 O) ont été anregistrés de 250 à 4000 cm −1 . L' ananlyse de l'état de polaristion des raies Raman observées permet de conclure que l'acide diméthylmalonique et le sel neutre appartiennent au groupe C 2 tandis que le sel acide répond au groupoe C s , le plan de symétrie étant bissectrur du groupe COO − . Une attribution des raies observées aux vibrations fondamentales est proposée.
Implications of radio fingerprinting on the security of sensor networks (2007)

We demonstrate the feasibility of finger-printing the radio of wireless sensor nodes (Chipcon 1000 radio, 433MHz). We show that, with this type of devices, a receiver can create device radio finger-prints and subsequently identify origins of messages exchanged between the devices, even if message contents and device identifiers are hidden. We further analyze the implications of device fingerprinting on the security of sensor networking protocols, specifically, we propose two new mechanisms for the detection of wormholes in sensor networks.
Reversed-Phase and Hydrophobic Interaction Chromatography of Peptides and Proteins (2020)

Hydrophobic interaction chromatography was first developed in the early 1970s for the separation of proteins by using columns packed with appropriately modified agarose beads. The hydrophobic interaction parameter was found to be a linear function of the protein surface area and the molal surface tension increment of the salt in the eluant, in accordance to the theory. The silanol groups at the surface of silica serve as convenient anchor groups for covalent binding of almost any desired functional groups via siloxane bridges by using appropriate silanizing agents. The mobile phases in Reversed-phase chromatography are typically hydro-organic mixtures containing methanol, isopropanol, acetonitrile, or tetrahydrofuran as the organic “modifier.” The influence of residence time on bovine and human growth hormone conformation in reversed-phase gradient elution was studied by online spectroscopic analysis and significant time-dependent changes were observed in the spectroscopic properties of the protein.
WHO Declares COVID-19 a Pandemic. (2020)

The World Health Organization (WHO) on March 11, 2020, has declared the novel coronavirus (COVID-19) outbreak a global pandemic (1). At a news briefing , WHO Director-General, Dr. Tedros Adhanom Ghebreyesus, noted that over the past 2 weeks, the number of cases outside China increased 13-fold and the number of countries with cases increased threefold. Further increases are expected. He said that the WHO is "deeply concerned both by the alarming levels of spread and severity and by the alarming levels of inaction," and he called on countries to take action now to contain the virus. "We should double down," he said. "We should be more aggressive." [...].
A Light CNN for Deep Face Representation With Noisy Labels (2018)

The volume of convolutional neural network (CNN) models proposed for face recognition has been continuously growing larger to better fit the large amount of training data. When training data are obtained from the Internet, the labels are likely to be ambiguous and inaccurate. This paper presents a Light CNN framework to learn a compact embedding on the large-scale face data with massive noisy labels. First, we introduce a variation of maxout activation, called max-feature-map (MFM), into each convolutional layer of CNN. Different from maxout activation that uses many feature maps to linearly approximate an arbitrary convex activation function, MFM does so via a competitive relationship. MFM can not only separate noisy and informative signals but also play the role of feature selection between two feature maps. Second, three networks are carefully designed to obtain better performance, meanwhile, reducing the number of parameters and computational costs. Finally, a semantic bootstrapping method is proposed to make the prediction of the networks more consistent with noisy labels. Experimental results show that the proposed framework can utilize large-scale noisy data to learn a Light model that is efficient in computational costs and storage spaces. The learned single network with a 256-D representation achieves state-of-the-art results on various face benchmarks without fine-tuning.
A 3-D packaging concept for cost effective packaging of MEMS and ASIC on wafer level (2009)

Heterogeneous integration bridges the gap between nanoelectronics and its derived applications. Currently MEMS and their signal conditioning ASICs are produced and packaged at different industry sectors (different jabs). To reduce costs and enhance Yield and performance at the same time this quite expensive way of packaging has to be modified. This paper presents a different pack-aging concept. It uses standard redistribution layer technology (RDL) to package thinned chips on a full wafer substrate e.g. thinned ASIC chips on a MEMS wafer. For this approach no Through Silicon Vias (TSV) are needed Standard chips can be used without redesign. Only Known Good Dies (KGDs) are packaged with the cost benefit of wafer level technology. At the starting point for this type of packaging both ASIC and MEMS chips are still parts of full wafers. The wafer with the larger sized chips (e.g. MEMS chips) is used as a substrate for the further process steps. The wafer with the smaller sized chips (e.g. ASIC chips) is thinned down on wafer level to a thickness of 10 mu m to 40 mu m and diced. These thinned chips are glued onto the base wafer with a polymer layer (BCB from Dow Chemical). The polymer has been deposited and structured before gluing the next chip on top. After placement of the thinned chips the wafer is again coated with BCB to embed the chips. This polymer layer is photostructured to open contact pads on the base chips as well as on the embedded chips. The next step is the built-up of metal routing. Here a semi-additive process is used, which means electroplating on a sputter seed layer of TiW/Cu. This metal layer is followed by another polymer layer for passivation and acting as a solder mask. Then Under Bump Metallization (UBM) is applied again by electroplating. Finally Balling is done either by Ball Placement or by Solder Paste Printing. Now the wafer is diced and the full ASIC-MEMS package can be flip chiped onto a Printed Circuit Board (PCB). The technology will be demonstrated by the project RESTLES (Reliable System Level Integration of Stacked Chips on MEMS). RESTLES will integrate technologies like silicon MEMS, ASIC, wafer thinning, chip stacking and flip chip to one pack-aged chip stack at die scale. The influence of the heterogeneous stack on performance and control mechanisms to eliminate parasitic effects will be investigated.
Serum Total Gangliosides and TA90-IC Levels (2002)

We speculate that a multiple-marker analysis that combines CEA values with serum ganglioside and TA90-IC values may be more sensitive than CEA value alone for detecting colorectal cancer. The potential prognostic significance of TA90-IC status in advanced disease warrants further investigation.
Preparation of Tetragonal Perovskite Single Phase PbTiO<sub>3</sub> Film Using an Improved Metal-Organic Chemical Vapor Deposition Method Alternately Introducing Pb and Ti Precursors (1993)

Perovskite single-phase PbTiO 3 films consisting of both a - and c -axis-oriented grains were prepared on a single-crystalline MgO substrate at a low substrate temperature of 510°C with an improved MOCVD (metal-organic chemical vapor deposition) method using tetra-ethyl-lead, titanium-iso-propoxide and ozone oxidant. Pb and Ti precursor vapors are alternately introduced into the reactor through different inlets, so that complicated vapor-phase reactions between the precursors and the reactions of which were unavoidable in conventional MOCVD, can be significantly inhibited in the inlet manifold. It is probable that this inhibition contributed to the present accomplishment of low-temperature epitaxial growth since it suppresses the vapor-phase generation of various Ti-Pb intermediates and oxides which are considered to greatly impede the flexibility in epitaxy.
Protocol Matters: Which Methylome are You Actually Studying? (2010)

The field of epigenetics is now capitalizing on the vast number of emerging technologies, largely based on second-generation sequencing, which interrogate DNA methylation status and histone modifications genome-wide. However, getting an exhaustive and unbiased view of a methylome at a reasonable cost is proving to be a significant challenge. In this article, we take a closer look at the impact of the DNA sequence and bias effects introduced to datasets by genome-wide DNA methylation technologies and where possible, explore the bioinformatics tools that deconvolve them. There remains much to be learned about the performance of genome-wide technologies, the data we mine from these assays and how it reflects the actual biology. While there are several methods to interrogate the DNA methylation status genome-wide, our opinion is that no single technique suitably covers the minimum criteria of high coverage and, high resolution at a reasonable cost. In fact, the fraction of the methylome that is studied currently depends entirely on the inherent biases of the protocol employed. There is promise for this to change, as the third generation of sequencing technologies is expected to again 'revolutionize' the way that we study genomes and epigenomes.
An erasure-resilient encoding system for flexible reading and writing in storage networks (2012)

We introduce the Read-Write-Coding-System (RWC), a very flexible class of linear block codes that generate efficient and flexible erasure codes for storage networks. In particular, given a message x of k symbols and a codeword y of n symbols, an RW code defines additional parameters k≤ r,w≤ n that offer enhanced possibilities to adjust the fault-tolerance capability of the code. More precisely, an RWC provides linear (n,r,d) -codes that have: (a) minimum (Hamming) distance d = n-r+1 for any two codewords, and (b) for any codeword y 1 there exists a codeword y 2 with distance of at most w . Furthermore, depending on the values r,w and the code alphabet, different block codes such as parity codes (e.g., RAID 4/5) or Reed-Solomon (RS) codes (if r = k and thus, w = n ) can be generated. In storage networks in which I/O accesses are very costly and redundancy is crucial, this flexibility has considerable advantages as r and w can optimally be adapted to read or write intensive applications; only w symbols must be updated if the message x changes completely, which is different from other codes that always need to rewrite y completely as x changes. In this article, we first state a tight lower bound and basic conditions for all RW codes. Furthermore, we introduce special RW codes in which all mentioned parameters are adjustable even online, that is, RW codes which are adaptive to changing demands. At last, we investigate the question for which choices of (k,r,w,n) a coding system exists over the binary alphabet F 2 = {0,1} and discuss how RW codes can be combined.
A COL1A1 Sp1 binding site polymorphism predisposes to osteoporotic fracture by affecting bone density and quality (2001)

Osteoporosis is a common disease with a strong genetic component. We previously described a polymorphic Sp1 binding site in the COL1A1 gene that has been associated with osteoporosis in several populations. Here we explore the molecular mechanisms underlying this association. A meta-analysis showed significant associations between COL1A1 "s" alleles and bone mineral density (BMD), body mass index (BMI), and osteoporotic fractures. The association with fracture was stronger than expected on the basis of the observed differences in BMD and BMI, suggesting an additional effect on bone strength. Gel shift assays showed increased binding affinity of the "s" allele for Sp1 protein, and primary RNA transcripts derived from the "s" allele were approximately three times more abundant than "S" allele--derived transcripts in "Ss" heterozygotes. Collagen produced from osteoblasts cultured from "Ss" heterozygotes had an increased ratio of alpha 1(I) protein relative to alpha 2(I), and this was accompanied by an increased ratio of COL1A1 mRNA relative to COL1A2. Finally, the yield strength of bone derived from "Ss" individuals was reduced when compared with bone derived from "SS" subjects. We conclude that the COL1A1 Sp1 polymorphism is a functional genetic variant that predisposes to osteoporosis by complex mechanisms involving changes in bone mass and bone quality.
From Footprints to Beliefprints: Motion Planning under Uncertainty for Maneuvering Automated Vehicles in Dense Scenarios (2018)

Motion planning for car-like robots is one of the major challenges in automated driving. It requires to solve a two-point boundary value problem that connects a start and a goal configuration with a collision-free trajectory. This paper introduces a novel approach for motion planning under uncertainty resulting in motion plans with higher robustness due to a bounded risk of collision. To that end, the state of the art G <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> and G <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> continuous steering functions, namely Dubins, Reeds-Shepp, Hybrid Curvature, and Continuous Curvature Steer, are extended to belief space, where an expected vehicle state is augmented by its associated uncertainty. The so-called beliefs are obtained by propagating a Gaussian probability distribution along the nominal path of the steering function while taking into account the control and localization uncertainty. A novel concept for collision avoidance in Gaussian belief space is then introduced that considers the shape of the vehicle and the full information about the uncertainty of a state. Together with the sampling-based motion planner RRT*, the proposed realtime capable methodology reduces the collision probability by an order of magnitude in three challenging automated driving scenarios.
Identification of Bacillus Strains for Biological Control of Catfish Pathogens (2012)

Bacillus strains isolated from soil or channel catfish intestine were screened for their antagonism against Edwardsiella ictaluri and Aeromonas hydrophila, the causative agents of enteric septicemia of catfish (ESC) and motile aeromonad septicaemia (MAS), respectively. Twenty one strains were selected and their antagonistic activity against other aquatic pathogens was also tested. Each of the top 21 strains expressed antagonistic activity against multiple aquatic bacterial pathogens including Edwardsiella tarda, Streptococcus iniae, Yersinia ruckeri, Flavobacterium columnare, and/or the oomycete Saprolegnia ferax. Survival of the 21 Bacillus strains in the intestine of catfish was determined as Bacillus CFU/g of intestinal tissue of catfish after feeding Bacillus spore-supplemented feed for seven days followed by normal feed for three days. Five Bacillus strains that showed good antimicrobial activity and intestinal survival were incorporated into feed in spore form at a dose of 8×10(7) CFU/g and fed to channel catfish for 14 days before they were challenged by E. ictaluri in replicate. Two Bacillus subtilis strains conferred significant benefit in reducing catfish mortality (P<0.05). A similar challenge experiment conducted in Vietnam with four of the five Bacillus strains also showed protective effects against E. ictaluri in striped catfish. Safety of the four strains exhibiting the strongest biological control in vivo was also investigated in terms of whether the strains contain plasmids or express resistance to clinically important antibiotics. The Bacillus strains identified from this study have good potential to mediate disease control as probiotic feed additives for catfish aquaculture.
Clinical manifestations, risk factors, and maternal and perinatal outcomes of coronavirus disease 2019 in pregnancy: living systematic review and meta-analysis (2020)

This article is a living systematic review that will be updated to reflect emerging evidence. Updates may occur for up to two years from the date of original publication. This version is update 1 of the original article published on 1 September 2020 (BMJ 2020;370:m3320), and previous updates can be found as data supplements (https://www.bmj.com/content/370/bmj.m3320/related#datasupp). When citing this paper please consider adding the update number and date of access for clarity.
Coupling geomechanical modeling with seismic pressure prediction (2018)

We couple geomechanical modeling with seismic velocity to enhance the prediction of pressure and stresses in complex geologic settings. In these settings, pressure is controlled by mean and shear stresses rather than by only the vertical (overburden) stress. We estimate total mean and shear stresses from a geomechanical model. Effective mean and shear stresses are calculated from velocity using a relationship that we develop between velocity and these stresses. The pressure prediction process is iterated to attain convergence between the predicted pressure field and the one input in the geomechanical model. We also explicitly predict the full stress tensor. We apply our method along with the standard, vertical-effective-stress method to a salt basin beneath the Sigsbee Escarpment in the Mad Dog field, Gulf of Mexico. The methods are constrained to the same pressure data along a calibration well and are then used to predict pressure and stresses across the basin. We find that salt and basin bathymetry substantially perturb the stress field. The pressures predicted by the two methods differ the least at the calibration well and the most in areas where the total mean and shear stresses are the most different from those at the same burial depth at the calibration well. Our method is shown to predict pressures measured along a subsalt well better than the standard, vertical method. We calculate minimum stress and the drilling window along a vertical profile near salt and find that they significantly differ from the ones predicted by the standard, vertical method.