gebhart/patrepeval huggingface dataset:
Identification of <i>Erwinia amylovora</i> Genes Induced during Infection of Immature Pear Tissue (2005)

The enterobacterium Erwinia amylovora is a devastating plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. In this study, we used a modified in vivo expression technology system to identify E. amylovora genes that are activated during infection of immature pear tissue, a process that requires the major pathogenicity factors of this organism. We identified 394 unique pear fruit-induced (pfi) genes on the basis of sequence similarity to known genes and separated them into nine putative function groups including host-microbe interactions (3.8%), stress response (5.3%), regulation (11.9%), cell surface (8.9%), transport (13.5%), mobile elements (1.0%), metabolism (20.3%), nutrient acquisition and synthesis (15.5%), and unknown or hypothetical proteins (19.8%). Known virulence genes, including hrp/hrc components of the type III secretion system, the major effector gene dspE, type II secretion, levansucrase (lsc), and regulators of levansucrase and amylovoran biosynthesis, were upregulated during pear tissue infection. Known virulence factors previously identified in E. (Pectobacterium) carotovora and Pseudomonas syringae were identified for the first time in E. amylovora and included HecA hemagglutinin family adhesion, Peh polygalacturonase, new effector HopPtoC(EA), and membrane-bound lytic murein transglycosylase MltE(EA). An insertional mutation within hopPtoC(EA) did not result in reduced virulence; however, an mltE(EA) knockout mutant was reduced in virulence and growth in immature pears. This study suggests that E. amylovora utilizes a variety of strategies during plant infection and to overcome the stressful and poor nutritional environment of its plant hosts.
Effects of pulsed ultrasound and temperature on the development of rat embryos in culture (1990)

Rat embryos in culture were exposed to pulsed ultrasound at SPTA intensity of 1.2 W/cm2 for 5, 15, and 30 min on day 9.5 of development. The whole embryo culture system allowed precise temperature control for directly examining the effects of ultrasound on the developing neural plate. After exposure, embryos were maintained in culture for a further 48 hr. No major morphological abnormalities were observed but a reduction in somite number occurred in the group insonated for 30 min, which was equivalent to a 2 hr delay in embryonic development. Similar delay in growth and "blistering" in the prosencephalon region of some embryos were observed after insonation for 15 min at 40.0 degrees C, an elevation of 1.5 degrees C over the temperature used for controls. Exposure to ultrasound for 15 min at 40 degrees C caused significant reduction in the growth of the head compared with that of control embryos. Heat shock genes for hsps 71/73 and 88 kD were induced after insonation for 30 min at 38.5 degrees C. Insonation did not cause any temperature changes in the culture medium. However, when the temperature of the culture medium was increased during insonation, defective development occurred. The results of these in vitro experiments suggest that ultrasound if resulting in significant hyperthermia could affect the development during early organogenesis of the neural plate and in particular they suggest that the embryo is at greater risk of damage during hyperthermic conditions. These results should provoke discussion of the concept that ultrasound in the febrile patient may present an increased embryonic risk which should be considered when deliberating on the use of diagnostic ultrasound procedures in the pregnant patient.
Rev. Griffith Hughes (1918)

Journal Article Rev. Griffith Hughes Get access Aneurin Williams Aneurin Williams 1Menai View, North Road, Carnarvon Search for other works by this author on: Oxford Academic Google Scholar Notes and Queries, Volume s12-IV, Issue 79, April 1918, Page 105, https://doi.org/10.1093/nq/s12-IV.79.105a Published: 01 April 1918
Computer assisted tracing of text evolution (1971)

Many situations exist in which convenient access to the detailed evolutionary information associated with a text's development is desirable:
A physical map of the genome of Mycoplasma mycoides subspecies mycoides Y with some functional loci (1988)

A physical map is presented for the 1200 kb genome of Mycoplasma mycoides subsp. mycoides Y, locating 32 cleavage sites for 8 restriction endonucleases. The large restriction fragments involved were separated and sized by pulsed-field agarose gel electrophoresis. Their locations on the map were determined by probing Southern blots of digests with individual fragments isolated from other digests and by correlating the products of double and triple digestions. Loci for 2 ribosomal RNA operons and 2 tRNA operons have been determined by probing with cloned genes and the broad regions of the replication origin and terminus have also been outlined by in vivo labelling studies.
Black garlic: A critical review of its production, bioactivity, and application (2016)

Black garlic is obtained from fresh garlic (Allium sativum L.) that has been fermented for a period of time at a controlled high temperature (60-90°C) under controlled high humidity (80-90%). When compared with fresh garlic, black garlic does not release a strong offensive flavor owing to the reduced content of allicin. Enhanced bioactivity of black garlic compared with that of fresh garlic is attributed to its changes in physicochemical properties. Studies concerning the fundamental findings of black garlic, such as its production, bioactivity, and applications, have thus been conducted. Several types of black garlic products are also available in the market with a fair selling volume. In this article, we summarize the current knowledge of changes in the components, bioactivity, production, and applications of black garlic, as well as the proposed future prospects on their possible applications as a functional food product.
The replicometer is broken: telomeres activate cellular senescence in response to genotoxic stresses (2014)

Telomeres, the ends of our linear chromosomes, can function as 'replicometers', capable of counting cell division cycles as they progressively erode with every round of DNA replication. Once they are critically short, telomeres become dysfunctional and consequently activate a proliferative arrest called replicative senescence. For many years, telomeres were thought to be autonomous structures, largely isolated from cell intrinsic and extrinsic signals, whose function is to prevent limitless cellular proliferation, a characteristic of most cancer cells. It is becoming increasingly evident, however, that telomeres not only count cell divisions, but also function as sensors of genotoxic stresses to stop cell cycle progression prematurely and long before cells would have entered replicative senescence. This stable growth arrest, triggered by dysfunctional telomeres that are not necessarily critically short, likely evolved as a tumor-suppressing mechanism as it prevents proliferation of cells that are at risk for acquiring potentially hazardous and transforming mutations both in vitro and in vivo. Here, we review studies supporting the concept that telomeres are important cellular structures whose function not only is to count cell divisions, but also to act as molecular switches that can rapidly stop cell cycle progression permanently in response to a variety of stresses, including oncogenic signals.
Applications of a theory of ferromagnetic hysteresis (1988)

The differential equation that underlies the theory of rate-independent hysteresis for isoperm ferromagnetic materials is modified and extended to rate-dependent nonisoperm materials. The theory and its extension exhibit all of the important features of ferromagnetic hysteresis, including the existence and stability of minor loops. Both are well suited for use in numerical field-solving codes. Examples in which the material functions are simple combinations of analytic functions are presented for MnZn ferrite, NiZn ferrite, NiFe tape, and CoCr thin film. Also presented is a procedure for constructing a two-dimensional vector model that yields bell-shaped and M-shaped curves for graphs of the angular variation of the coercive field.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
HIV Treatment and Associated Mitochondrial Pathology (2013)

Antiretroviral therapy has dramatically reduced mortality in human immunodeficiency virus (HIV) infection. In 1988, the suggestion that the first antiretroviral drug, zidovudine, was the potential cause of muscle pathology in HIV-infected persons resulted in structural and biochemical patient studies demonstrating acquired mitochondrial dysfunction. Assessment of subsequent nucleoside analog reverse transcriptase inhibitor (NRTI) antiretroviral drugs has indicated that mitochondria are a common target of NRTI toxicity in multiple tissues, leading to a wide variety of pathology ranging from lipodystrophy to neuropathy. Overwhelmingly, these complications have emerged during post-licensing human studies. Subsequent animal and in vitro studies have then elucidated the potential pathological mechanisms, suggesting that NRTI-associated mitochondrial toxicity arises principally from inhibition of the sole mitochondrial DNA (mtDNA) polymerase gamma, leading to a reduction in mtDNA content (depletion). Millions of patients have been treated with mitochondrially toxic NRTIs and these drugs remain the backbone of antiretroviral rollout in much of sub-Saharan Africa. Here we describe the 25-year history of antiretroviral associated mitochondrial pathology and critically review the strength of evidence linking clinical, histopathological, and molecular data. We discuss recently described novel mechanisms of NRTI-associated mitochondrial damage and whether or not recently licensed NRTIs may be considered free from mitochondrial toxicity.
Raptor: integrating checkpoints and thread migration for cluster management (2004)

Software distributed shared-memory (SDSM) provides the abstraction necessary to run shared-memory applications on cost-effective parallel platforms such as clusters of workstations. However, problems such as cluster component reliability and cluster management, which are not directly related to performance, need to be addressed before SDSM solutions can be widely adopted. This paper presents Raptor, an SDSM cluster management system based on checkpoint/recovery and thread migration. Raptor checkpoints decouple the runtime system and application data from application threads, allowing efficient load balancing, resource allocation, and rollback recovery. There are two important features of the system. First, it reduces checkpoint overhead by only saving application-specific data that cannot be recreated at recovery time. Second, by integrating thread migration capability both at running and recovery, it allows the addition or removal of computing resources from a running application, while adding little or no additional burden on the SDSM application programmer.
SyntaxSQLNet: Syntax Tree Networks for Complex and Cross-Domain Text-to-SQL Task (2018)

Most existing studies in text-to-SQL tasks do not require generating complex SQL queries with multiple clauses or sub-queries, and generalizing to new, unseen databases. In this paper we propose SyntaxSQLNet, a syntax tree network to address the complex and crossdomain text-to-SQL generation task. Syn-taxSQLNet employs a SQL specific syntax tree-based decoder with SQL generation path history and table-aware column attention encoders. We evaluate SyntaxSQLNet on a new large-scale text-to-SQL corpus containing databases with multiple tables and complex SQL queries containing multiple SQL clauses and nested queries. We use a database split setting where databases in the test set are unseen during training. Experimental results show that SyntaxSQLNet can handle a significantly greater number of complex SQL examples than prior work, outperforming the previous state-of-the-art model by 9.5% in exact matching accuracy. To our knowledge, we are the first to study this complex text-to-SQL task. Our task and models with the latest updates are available at https://yale-lily. github.io/seq2sql/spider.
A Signature Scheme Associated with Universal Re-signcryption (2009)

Today, with increasing deversity of network technologies, people have been likely to be interested in anonymity. The attacker might threaten anonymity of senders and receivers by confirming linkability between their sessions. Recently, Golle et al. proposed the re-encryption scheme applicable to Mix, called universal re-encryption. In this scheme, a ciphertext is supposed to be re-encrypted without public information corresponding to it. Moreover, only a subject that re-enctypts a ciphertext can know the correspondence of original ciphertext and it, and the computational complexity to break the unlinkability property is equal to the semantic secrecy. In this paper, we consider and improve the universal re-encryption scheme, and propose a scheme that can verify who transmit the message by adding the property of signature.
Detection of multivessel coronary artery disease by early exercise testing after first myocardial infarction. (1989)

The ability of a symptom limited treadmill exercise test (TMT) to predict the presence of multivessel coronary artery disease (MVD) three weeks after a first myocardial infarction was assessed in 76 male patients aged 25-65 (mean 40.9 +/- 10.1) years. There were 6 patients with normal coronaries, 36 with single vessel disease (SVD), 20 with double vessel disease (DVD), and 14 with three vessel disease (TVD). TMT was positive in 20/34 (58.8%) patients with MVD, and 4/42 (9%) patients with SVD or normal coronaries. The predictive accuracy of a positive TMT in detecting MVD was 83.3%, and the predictive accuracy of a negative TMT in excluding MVD was 73.1%. It is concluded that TMT is useful test for predicting the presence or absence of MVD in survivors of a first transmural myocardial infarction.
Clustering and the design of preference-assessment surveys in healthcare. (1999)

Employing a clustering algorithm to analyze health status survey data enables researchers to gain a data-driven, concise summary of the experiences of patients.
HcBench: Methodology, development, and characterization of a customer usage representative big data/Hadoop benchmark (2013)

Big Data analytics using Map-Reduce over Hadoop has become a leading edge paradigm for distributed programming over large server clusters. The Hadoop platform is used extensively for interactive and batch analytics in ecommerce, telecom, media, retail, social networking, and being actively evaluated for use in other areas. However, to date no industry standard or customer representative benchmarks exist to measure and evaluate the true performance of a Hadoop cluster. Current Hadoop micro-benchmarks such as HiBench-2, GridMix-3, Terasort, etc. are narrow functional slices of applications that customers run to evaluate their Hadoop clusters. However, these benchmarks fail to capture the real usages and performance in a datacenter environment. Given that typical datacenter deployments of Hadoop process a wide variety of analytic interactive and query jobs in addition to batch transform jobs under strict Service Level Agreement (SLA) requirements, performance benchmarks used to evaluate clusters must capture the effects of concurrently running such diverse job types in production environments. In this paper, we present the methodology and the development of a customer datacenter usage representative Hadoop benchmark "HcBench" which includes a mix of large number of customer representative interactive, query, machine learning, and transform jobs, a variety of data sizes, and includes compute, storage 110, and network intensive jobs, with inter-job arrival times as in a typical datacenter environment. We present the details of this benchmark and discuss application level, server and cluster level performance characterization collected on an Intel Sandy Bridge Xeon Processor Hadoop cluster.
<title>Applications of x-ray and neutron capillary optics</title> (1993)

Discovery that wide energy and angular control of x ray and neutron trajectories can be achieved with high efficiency by the use of shaped arrays of hollow capillaries has made possible important new applications in science, medicine, and industry. These include medical diagnostic imaging, medical therapy, analysis of the composition and structure of materials, x-ray microscopy, x-ray astronomy, industrial process and fault analysis, and x-ray lithography. The status and prospects for this remarkable range of possibilities is summarized in this report.
Mesotrione Alone and in Mixtures with Glyphosate in Glyphosate-Resistant Corn (Zea mays)<sup>1</sup> (2003)

Field studies were conducted in 1999, 2000, and 2001 to investigate weed control and glyphosate-resistant corn tolerance to postemergence applications of mesotrione at 70, 105, and 140 g ai/ha applied with and without glyphosate at 560 g ai/ha. Mesotrione alone and mixed with glyphosate controlled smooth pigweed greater than 97% and common lambsquarters 93 to 99%. Control of common ragweed and morningglory species was variable. Common ragweed control was generally best when mesotrione was applied at 105 or 140 g/ha, and control increased only in 2000 with the addition of glyphosate. Giant foxtail control was below 25% with all rates of mesotrione, but mixtures of mesotrione plus glyphosate controlled giant foxtail 65 to 75%. Mesotrione injured glyphosate-resistant corn 4 to 24% when averaged over glyphosate rates, and injury was usually increased by higher mesotrione rates, with rainfall after herbicide applications, and in mixtures with glyphosate. Injury was transient and did not reduce corn yields. Mesotrione injury on glyphosate-resistant corn was confirmed in the greenhouse, where all mesotrione treatments reduced glyphosate-resistant corn biomass 9 to 23% compared with the nontreated check.Nomenclature: Glyphosate; mesotrione; common lambsquarters, Chenopodium album L. #3 CHEAL; common ragweed, Ambrosia artemisiifolia L. # AMBEL; giant foxtail, Setaria faberi Herrm. # SETFA; morningglory species, Ipomoea spp. # IPOSS; smooth pigweed, Amaranthus hybridus L. # AMACH; corn, Zea mays L. ‘Dekalb 626RR’, ‘Dekalb 5863RR’.Additional index words: IPOHE, IPOLA, Ipomoea hederacea (L.) Jacq., Ipomoea lacunosa L., Ipomoea purpurea L. Roth, IPOPU, total postemergence, transgenic crops, triketone herbicide.Abbreviations: DAT, days after treatment; POST, postemergence; WAT, weeks after treatment.
Lyme disease and relapsing fever<i>Borrelia</i>elongate through zones of peptidoglycan synthesis that mark division sites of daughter cells (2016)

Agents that cause Lyme disease, relapsing fever, leptospirosis, and syphilis belong to the phylum Spirochaetae-a unique lineage of bacteria most known for their long, spiral morphology. Despite the relevance to human health, little is known about the most fundamental aspects of spirochete growth. Here, using quantitative microscopy to track peptidoglycan cell-wall synthesis, we found that the Lyme disease spirochete Borrelia burgdorferi displays a complex pattern of growth. B. burgdorferi elongates from discrete zones that are both spatially and temporally regulated. In addition, some peptidoglycan incorporation occurs along the cell body, with the notable exception of a large region at the poles. Newborn cells inherit a highly active zone of peptidoglycan synthesis at midcell that contributes to elongation for most of the cell cycle. Concomitant with the initiation of nucleoid separation and cell constriction, second and third zones of elongation are established at the 1/4 and 3/4 cellular positions, marking future sites of division for the subsequent generation. Positioning of elongation zones along the cell is robust to cell length variations and is relatively precise over long distances (>30 µm), suggesting that cells ‟sense" relative, as opposed to absolute, cell length to establish zones of peptidoglycan synthesis. The transition from one to three zones of peptidoglycan growth during the cell cycle is also observed in relapsing fever Borrelia. However, this mode of growth does not extend to representative species from other spirochetal genera, suggesting that this distinctive growth mode represents an evolutionary divide in the spirochete phylum.
StretchEBand (2017)

The increased interest in interactive soft materials, such as smart clothing and responsive furniture, means that there is a need for flexible and deformable electronics. In this paper, we focus on stitch-based elastic sensors, which have the benefit of being manufacturable with textile craft tools that have been used in homes for centuries. We contribute to the understanding of stitch-based stretch sensors through four experiments and one user study that investigate conductive yarns from textile and technical perspectives, and analyze the impact of different stitch types and parameters. The insights informed our design of new stretch-based interaction techniques that emphasize eyes-free or causal interactions. We demonstrate with StretchEBand how soft, continuous sensors can be rapidly fabricated with different parameters and capabilities to support interaction with a wide range of performance requirements across wearables, mobile devices, clothing, furniture, and toys.
A generalized Markov Chain modeling approach for on board applications (2010)

This paper deals with a new class of Markov Chain type models that can be effectively used for real time modeling and on-line learning of nonlinear systems with uncertainties. We expand the concept of the generalized Markov Chain - a probabilistic model that synergistically combines the idea of transition probabilities with the information granulation paradigm. We consider generalized Markov chains based on two different types of information granules - intervals and fuzzy subsets - and the methods for their learning from data. We also analyze the relationship between the Markov chains and the fuzzy models and derive an alternative formulation of the Chapman-Kolmogorov equation that applies to stochastic models in fuzzy environment. As this approach is motivated by and intended for in-vehicle applications, results are illustrated on examples of granular models of vehicle speed and road grade.
Sustained inflammation after pericyte depletion induces irreversible blood-retina barrier breakdown (2017)

In the central nervous system, endothelial cells (ECs) and pericytes (PCs) of blood vessel walls cooperatively form a physical and chemical barrier to maintain neural homeostasis. However, in diabetic retinopathy (DR), the loss of PCs from vessel walls is assumed to cause breakdown of the blood-retina barrier (BRB) and subsequent vision-threatening vascular dysfunctions. Nonetheless, the lack of adequate DR animal models has precluded disease understanding and drug discovery. Here, by using an anti-PDGFRβ antibody, we show that transient inhibition of the PC recruitment to developing retinal vessels sustained EC-PC dissociations and BRB breakdown in adult mouse retinas, reproducing characteristic features of DR such as hyperpermeability, hypoperfusion, and neoangiogenesis. Notably, PC depletion directly induced inflammatory responses in ECs and perivascular infiltration of macrophages, whereby macrophage-derived VEGF and placental growth factor (PlGF) activated VEGFR1 in macrophages and VEGFR2 in ECs. Moreover, angiopoietin-2 (Angpt2) upregulation and Tie1 downregulation activated FOXO1 in PC-free ECs locally at the leaky aneurysms. This cycle of vessel damage was shut down by simultaneously blocking VEGF, PlGF, and Angpt2, thus restoring the BRB integrity. Together, our model provides new opportunities for identifying the sequential events triggered by PC deficiency, not only in DR, but also in various neurological disorders.