gebhart/patrepeval huggingface dataset:
Comparison of sporulation and germination conditions for <i>Clostridium perfringens</i> strains (2023)

Abstract Clostridium perfringens is a spore forming, obligate anaerobe, Gram-positive bacterium that causes a range of diseases in humans and animals. The infectious form of C. perfringens is the spore, a structure that is derived from the vegetative cell under conditions of nutrient deprivation. The first step in C. perfringens pathogenesis is the differentiation of spores into replicating bacteria. Previous work in analyzing C. perfringens spore germination has produced contradictory, strain-specific results. Hence, we analyzed the requirements for spore formation and germination in seven different C. perfringens strains. Our data showed that C. perfringens sporulation conditions are strain specific, but germination responses are homogenous. C. perfringens spores can germinate using two distinct pathways. The first germination pathway (the amino acid-only pathway or AA) requires L-alanine, L-phenylalanine, and sodium ions (Na + ) as co-germinants. L-arginine is not a required germinant but potentiates germination. The AA pathway is inhibited by aromatic amino acids and potassium ions (K + ). Bicarbonate (HCO3-), on the other hand, bypasses potassium-mediated inhibition of C. perfringens spore germination through the AA pathway. The second germination pathway (the bile salt and amino acid pathway or BA) is more promiscuous and is activated by several bile salts and amino acids. In contrast to the AA pathway, the BA pathway is insensitive to Na + , but can be activated by either K + or HCO3-. We hypothesize that C. perfringens may have evolved these two distinct germination pathways to ensure spore response to different host environments. Manuscript contribution to the field Clostridium perfringens is a ubiquitous bacterium that can infect a wide variety of animal hosts, including humans. C. perfringens counts with a veritable arsenal of toxins that are differentially expressed depending on the host infected. Besides toxin production, C. perfringens can also form dormant and resistant spores that serve as infective vehicles. C. perfringens spores need to germinate back into vegetative cells to cause disease. Befitting to its wide host range, C. perfringens spore germination seems to use strain specific. In this study, we tested the ability of seven C. perfringens strains to produce spores under different conditions. We also tested the requirements for spore germination. We found that while C. perfringens sporulation was highly varied, the germination response for all strains could be divided into two distinct pathways. Since C. perfringens spores need to germinate to cause infection, understanding the germination behavior could lead to approaches for the prevention of diseases in humans and veterinary animals.
Secure Blue: an architecture for a scalable, reliable high volume SSL Internet server (2005)

Although there exist accelerator products to increase throughput of encrypted transactions produced by an Internet HTTP server there are no current architectures that provide a truly coordinated and scalable solution for Secure Socket Layer (SSL) encrypted communications. This paper presents an architecture that facilitates high volume SSL Internet serving, scaling from thousands to millions of independently active SSL sessions. Reliability, availability, serviceability, and on-line error recovery requirements for such an application are also addressed. Our approach is to offload SSL set-up protocol activity that was traditionally executed by transaction engines (and dedicated co-processors), to a scalable array of SSL handshake protocol-specific servers. This significantly reduces utilization on the transaction engines since SSL session set-up is a CPU intensive operation. Additionally, the actual encryption/decryption processing is offloaded as well, to a dedicated and scalable array of in-line encryption engine(s). The in-line encryption engine is architected such that requests and responses flowing to and from the transaction servers are in clear text. A benefit of this arrangement is that transaction engines (as well as Web accelerator proxies) will retain the ability to cache Web objects, while firewalls will retain the ability to perform packet level inspection of all traffic directed to the transaction engines. Such features have been sacrificed in prior SSL implementations.
Thermoelectric properties of Zn-doped Ca_5In_2Sb_6 (2013)

The Zintl compound Ca_5Al_2Sb_6 is a promising thermoelectric material with exceptionally low lattice thermal conductivity resulting from its complex crystal structure. In common with the Al analogue, Ca_5In_2Sb_6 is naturally an intrinsic semiconductor with a low p-type carrier concentration. Here, we improve the thermoelectric properties of Ca_5In_2Sb_6 by substituting Zn^(2+) on the In^(3+) site. With increasing Zn substitution, the Ca_5In_(2−x)Zn_xSb_6 system exhibits increased p-type carrier concentration and a resulting transition from non-degenerate to degenerate semiconducting behavior. A single parabolic band model was used to estimate an effective mass in Ca_5In_2Sb_6 of m^* = 2m_e, which is comparable to the Al analogue, in good agreement with density functional calculations. Doping with Zn enables rational optimization of the electronic transport properties and increased zT in accordance with a single parabolic band model. The maximum figure of merit obtained in optimally Zn-doped Ca_5In_2Sb_6 is 0.7 at 1000 K. While undoped Ca_5In_2Sb_6 has both improved electronic mobility and reduced lattice thermal conductivity relative to Ca_5Al_2Sb_6, these benefits did not dramatically improve the Zn-doped samples, leading to only a modest increase in zT relative to optimally doped Ca_5Al_2Sb_6.
Active Learning for Skewed Data Sets (2020)

Consider a sequential active learning problem where, at each round, an agent selects a batch of unlabeled data points, queries their labels and updates a binary classifier. While there exists a rich body of work on active learning in this general form, in this paper, we focus on problems with two distinguishing characteristics: severe class imbalance (skew) and small amounts of initial training data. Both of these problems occur with surprising frequency in many web applications. For instance, detecting offensive or sensitive content in online communities (pornography, violence, and hate-speech) is receiving enormous attention from industry as well as research communities. Such problems have both the characteristics we describe -- a vast majority of content is not offensive, so the number of positive examples for such content is orders of magnitude smaller than the negative examples. Furthermore, there is usually only a small amount of initial training data available when building machine-learned models to solve such problems. To address both these issues, we propose a hybrid active learning algorithm (HAL) that balances exploiting the knowledge available through the currently labeled training examples with exploring the large amount of unlabeled data available. Through simulation results, we show that HAL makes significantly better choices for what points to label when compared to strong baselines like margin-sampling. Classifiers trained on the examples selected for labeling by HAL easily out-perform the baselines on target metrics (like area under the precision-recall curve) given the same budget for labeling examples. We believe HAL offers a simple, intuitive, and computationally tractable way to structure active learning for a wide range of machine learning applications.
“Snap-n-Eat” (2015)

We present snap-n-eat, a mobile food recognition system. The system can recognize food and estimate the calorific and nutrition content of foods automatically without any user intervention. To identify food items, the user simply snaps a photo of the food plate. The system detects the salient region, crops its image, and subtracts the background accordingly. Hierarchical segmentation is performed to segment the image into regions. We then extract features at different locations and scales and classify these regions into different kinds of foods using a linear support vector machine classifier. In addition, the system determines the portion size which is then used to estimate the calorific and nutrition content of the food present on the plate. Previous approaches have mostly worked with either images captured in a lab setting, or they require additional user input (eg, user crop bounding boxes). Our system achieves automatic food detection and recognition in real-life settings containing cluttered backgrounds. When multiple food items appear in an image, our system can identify them and estimate their portion size simultaneously. We implemented this system as both an Android smartphone application and as a web service. In our experiments, we have achieved above 85% accuracy when detecting 15 different kinds of foods.
Multi-layer multi-instance kernel for video concept detection (2007)

In video concept detection, most existing methods have not well studied the intrinsic hierarchical structure of video content. However, unlike flat attribute-value data used in many existing methods, video is essentially a structured media with multi-layer representation. For example, a video can be represented by a hierarchical structure including, from large to small, shot, key-frame, and region. Moreover, it fits the typical Multi-Instance (MI) setting in which the "bag-instance" correspondence is embedded among contiguous layers. We call such multi-layer structure and the "bag-instance" relation embedded in the structure as Multi-Layer Multi-Instance (MLMI) setting in this paper. We formulate video concept detection as an MLMI learning problem in which a rooted tree with MLMI nature embedded is devised to represent a video segment. Furthermore, by fusing the information from different layers, we construct a novel MLMI kernel to measure the similarities between the instances in the same and different layers. In contrast to traditional MI learning, both the Multi-Layer structure and Multi-Instance relations are leveraged simultaneously in the proposed kernel. We applied MLMI kernel to concept detection task on TRECVID 2005 corpus and reported superior performance (+25% in Mean Average Precision) to standard Support Vector Machine based approaches.
A Wireless Magnetic Resonance Device for Optogenetic Applications in an Animal Model (2020)

The currents of optical stimulation devices with tethered or untethered systems have various disadvantages, including optical fiber breakage, disrupted animal movements, heavy batteries carried on heads, and high-frequency electromagnetic impacts. Our novel wireless remote control was developed to address these issues. The novel wireless device uses a magnetic resonance technique to modify the deficits of the conventional magnetic induction or radio-frequency power sources. The present device emits a strong and steady electromagnetic power. It is cheaper than previous versions, and the receiver coil on its head is very light (≦ 1 g). For the present wireless remote-controlled device, the electromagnetic field's range (i.e., +5 cm and -5 cm of the outside coil) is larger than the range for the magnetic induction and radio-frequency power sources. The present device controls animals' behavior by the electromagnetic field's effective range via photostimulation. The novel wireless remote-controlled device with a magnetic resonance technique can be applied in many behavioral tasks in mice and rats. To avoid the adverse effects of high radio frequency and to extend the electromagnetic field's range, this novel technique serves as a helpful tool to modulate the neuronal activity of target neurons in specific brain areas for optogenetic experiments.
Use of feed enzymes in feedlot finishing diets (1999)

An enzyme mixture with predominantly xylanase and cellulase activities was added to a high concentrate diet (92.2%, dry matter basis) and fed to growing heifers (370 kg) reared in a commercial feedlot. Enzyme supplementation had no effect on dry matter intake but increased (P < 0.01) average daily gain by 9% (1.40 to 1.53 kg d −1 ) and numerically improved feed-to-gain ratio by 10% (7.72 to 6.95 kg dry matter kg −1 gain). Feed enzyme technology can improve efficiency of commercial feedlot cattle production. Key words: Beef cattle, feedlot cattle, enzymes, barley
Thermostable Flap Endonuclease from the Archaeon,Pyrococcus horikoshii, Cleaves the Replication Fork-like Structure Endo/Exonucleolytically (1999)

The flap endonuclease gene homologue from the hyperthermophilic archaeon, Pyrococcus horikoshii, was overexpressed in Escherichia coli and purified. The results of gel filtration indicated that this protein was a 41-kDa monomer. P. horikoshii flap endonuclease (phFEN) cleaves replication fork-like substrates (RF) and 5' double-strand flap structures (DF) using both flap endonuclease and 5'-3'-exonuclease activities. The mammalian flap endonuclease (mFEN) is a single-strand flap-specific endonuclease (Harrington, J. J., and Lieber, M. R. (1994) EMBO J. 13, 1235-1246), but the action patterns of phFEN appear to be quite different from those of mFEN at this point. The DF-specific flap endonuclease and 5'-exonuclease activities have not yet been reported. Therefore, this is the first report of the specific endo/exonuclease activities of phFEN. The DF-specific 5'-exonuclease activity degraded the downstream primer of 3' single-flap structure and was 15 times higher than the activities against nicked substrates without 3' flap strand. DF-specific flap endonuclease cleaved the 5' double-flap strand in DF and the lagging strand in RF at the junction portion. Because the RF appears to be the intermediate structure, due to the arrest of the replication fork, the double strand breaks after the arrests of the replication forks are probably caused by phFEN.
Controlled biosynthesis of neoviridogriseins, new homologues of viridogrisein. I. Taxonomy and fermentation. (1979)

Neoviridogriseins, new homologues of viridogrisein, were produced with viridogrisein and griseoviridin by Streptomyces sp. P8648 which was identified as a strain of Streptomyces griseoviridus.
Mapping a Gene Defect in Absorptive Hypercalciuria to Chromosome 1q23.3-q24<sup>1</sup> (1999)

Absorptive hypercalciuria (AH), a common cause of kidney stones, is due to intestinal hyperabsorption of calcium. The presence of a family history of nephrolithiasis, in about half of the affected individuals studied indicates that an inherited genetic defect is one likely cause of AH. Although it is known that intestinal calcium absorption is regulated by a number of factors, the molecular biological basis for the increased calcium absorption in AH is unknown. This study was designed to determine the chromosomal locus of the gene defect linked to the AH phenotype in three families with a severe form of AH. Three kindreds were evaluated in a systematic autosomal genome-wide linkage analysis study. The AH phenotype, characterized by hyperabsorption of calcium and hypercalciuria, was linked to only one chromosomal locus, 1q23.3-q24. A 2-point logarithm of odds score of 3.3 was obtained with markers D1S318 and D1S196 at a recombination frequency of theta = 0. Nonparametric multipoint linkage analysis yielded a peak nonparametric linkage Z(all)-score of 12.7, P = 6 x 10(-6) Analysis of key recombinants within the families studied localized the gene to a 4.3-megabase region between markers D1S2681 (centromere) and D1S2815. A trait associated with intestinal hyperabsorption of calcium in a severe form of absorptive hypercalciuria has been mapped to chromosome 1q23.3-q24.
Cover Picture: Enantioselective Kita Oxidative Spirolactonization Catalyzed by In Situ Generated Chiral Hypervalent Iodine(III) Species (Angew. Chem. Int. Ed. 12/2010) (2010)

Conformationally flexible C2-symmetric chiral iodosylarene, which has been rationally designed based on secondary n–σ* or hydrogen-bonding interactions, is a highly effective catalyst for the Kita oxidative spirolactonization. As described by K. Ishihara and co-workers in their Communication on page 2175 ff., this catalysis provides the highest enantioselectivity (up to 92 % ee) among previous chiral hypervalent iodine-catalyzed reactions.
Distributed LC resonant clock tree synthesis (2011)

Clock networks in high-performance designs are extremely power hungry. One potential method for reducing the power consumption is to use distributed LC tanks in which energy is conserved by shifting it between electrical and magnetic forms at the resonant frequency. However, no physical algorithms to physically synthesize resonant trees have been proposed. In order to utilize such techniques in ASICs, this work presents the first algorithm to synthesize resonant regional clock trees. Our results suggest that, on average, we can reduce clock power consumption by 41.7% at 2Ghz with no degredation to skew compared to a minimum buffer insertion algorithm.
Linear Friction Stir Welding of Medium Carbon Steel at Low Temperature (2019)

Linear Friction Welding (LFW) is a solid-state joining process in which a joint is obtained through the relative motion of two components under a high contact load. The most important factor of this conventional method is to obtain a fresh surface at the interface by expelling the weld interface as flash. In this study, medium carbon steel was welded by LFW at a low frequency, low amplitude and high applied pressure. As a result of the temperature measurements and microstructure observations, the maximum temperature of the weld plane was confirmed to be below the A1 transformation temperature, and martensitic transformation was suppressed at the weld interface. The key concept of this method is applying a large strain deformation to the interfaces to recrystallize at a lower temperature which is different from the conventional LFW.
Densification, strengthening and toughening in hafnium carbide with the addition of silicon carbonitride (2019)

Abstract Hafnium carbide (HfC) possesses low toughness and damage tolerance, which limits its application as high‐temperature structural materials. Here we report a route to fabricate a dense HfC with high toughness by incorporating a two‐component SiCN (silicon carbonitride) sintering aid, which is composed of SiCN and turbostratic carbon in the spark plasma sintering. The addition of the SiCN not only enhances the density (up to ~97%) of the final product, but more importantly results in an increase in toughness from 4.3 to 8.5 MPa m 1/2 with only a 10% reduction in the flexural strength. The improvement has been attributed to the unique microstructure of the obtained samples, exhibiting several important characteristics: (a) homogeneously dispersed SiCN and C secondary phases in the HfC matrix to control grain size; (b) HfC grains contain different levels of Si, O, and N to form solid solution; (c) enrichment of free carbon at grain boundaries and triple junctions.
Terminal difluoro olefin analogs of squalene are time-dependent inhibitors of squalene epoxidase (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTerminal difluoro olefin analogs of squalene are time-dependent inhibitors of squalene epoxidaseWilliam R. Moore, Gerald L. Schatzman, Esa T. Jarvi, Raymond S. Gross, and James R. McCarthyCite this: J. Am. Chem. Soc. 1992, 114, 1, 360–361Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/ja00027a056https://doi.org/10.1021/ja00027a056research-articleACS PublicationsRequest reuse permissionsArticle Views584Altmetric-Citations116LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
High channel density optical interconnects using photonic crystal fibers (2006)

Demanding real-time data processing applications are driving the need for high-throughput programmable logic. Improvements to computing speed from reduction of processor feature sizes are predicted, but these are expected to be hampered within the next 2-5 years by the limitations of metallic interconnects between processors. Optical interconnect alternatives have been attempted, but independent optical channel densities are, at present, restricted by conventional fiber dimensions. In this paper a novel solution to this problem is presented employing a multi-core <i>microstructured</i> fiber. In this type of fiber, a <i>photonic crystal fiber</i> (PCF), the core is a solid silica region surrounded by air holes shot through the length of the fiber. This is created by stacking capillaries and solid canes of silica to create a preform, with the structure preserved after drawing down; a core may be created by replacing an air hole by a solid cane. The criteria for the fiber design are discussed: a bit error rate restriction leads to an upper limit for cross-coupling between cores and hence the distance (or number of air holes) between each channel. Modeling indicates a final fiber design containing 37 cores 31.25 microns apart, equivalent to a density of 1150 independent channels per millimeter squared. Details of an optical transmitting/receiving system utilizing four of the channels and arrays of VCSELs as transmitters and receivers are described. Future improvements to the system are discussed.
High-Performance Water-Based Mud Using Nanoparticles for Shale Reservoirs (2013)

Summary URTeC 1581549 Drilling through a shale formation can result in borehole instability problems, and this is known to add substantial costs to the operation. This is because conventional drilling fluids tend to interact with clay minerals in shales, and the mechanical properties of rock are changed by clay swelling. To avoid those problems, drilling fluid design is one of the most important factors that need to be considered. Oil-based muds (OBMs) are traditionally preferred due to their ability to minimize this interaction. However, OBMs are expensive and are subject to environmental constraints, so water-based muds (WBMs) are often preferred. To reduce the interaction between water-based muds and shales, we need to reduce water invasion into the shale. To reduce this invasion, internal or external filter cakes should be developed. Shale has extremely low permeability and a very small pore throat size, so normal mud cakes fail to stop or even reduce the fluid invasion. We have shown that the addition of nanoparticle additives to water-based drilling fluids can significantly reduce water invasion into shales. In this paper, we report results for shale permeability and pressure penetration though shales using different fluids: brine, base mud and nanoparticle based muds. To better define the effect of nanoparticles, we used different concentrations of nanoparticles in the mud. From the large reduction in permeability and the pressure response results, we clearly show that nanoparticles act as good shale inhibitors to ensure wellbore stability during drilling.