gebhart/patrepeval huggingface dataset:
Identification of the Receptor-Binding Protein in Lytic Leuconostoc pseudomesenteroides Bacteriophages (2013)

Two phages, P793 and ΦLN04, sharing 80.1% nucleotide sequence identity but having different strains of Leuconostoc pseudomesenteroides as hosts, were selected for identification of the host determinant gene. Construction of chimeric phages leading to the expected switch in host range identified the host determinant genes as ORF21P793/ORF23ΦLN04. The genes are located in the tail structural module and have low sequence similarity at the distal end.
Graphical Models for Inference with Missing Data (2013)

We address inference problems associated with missing data using causal Bayesian networks to model the data generation process. We show that procedures based on graphical models can overcome limitations of conventional missing data methods and provide meaningful performance guarantees even when data are Missing Not At Random (MNAR). In particular, we identify conditions that guarantee consistent estimation of parameters of interest in broad categories of missing data problems, and derive procedures for implementing this estimation. We derive testable implications for missing data problems in both MAR (Missing At Random) and MNAR categories. Finally, we apply these techniques to develop a suite of algorithms for closed form estimation of Bayesian network parameters.
(.+-.)-Carbocyclic 5'-nor-2'-deoxyguanosine and related purine derivatives: synthesis and antiviral properties (1992)

Beginning with 3-cyclopenten-1-ylamine hydrochloride, the 5'-nor derivatives of carbocyclic 2'-deoxyguanosine (2), 2'-deoxyadenosine (3), and 2,6-diaminopurine 2'-deoxyribofuranoside (4) have been prepared. These compounds were evaluated for antiviral potential versus herpes simplex virus, varicella-zoster virus, cytomegalovirus, vaccinia virus, vesicular stomatitis virus, and human immunodeficiency virus and found to lack activity. Also, compounds 2-4 were virtually nontoxic toward the host (human diploid fibroblast ESM and HEL) cells. These biological properties may be due to the inability of 2-4 to be phosphorylated to the requisite nucleotide level that is likely to be necessary for biological activity by correlation to carbocyclic 2'-deoxyguanosine (1), which possesses significant antiviral properties as a result of conversion to its 5'-triphosphate derivative.
The role of tissue ischemia in the pathogenesis of anastomotic stricture. (1988)

In a chronic dog model, colocolostomies with intact blood supplies were constructed with the circular stapler. By means of "tight" stapling, an ischemic suture line was induced (suture line blood flow reduced to less than 10% of baseline mucosal blood flow). Under these conditions, only one of 20 anastomoses resulted in stenosis at 1 month. Correctly stapled colocolostomies were then performed in bowels rendered ischemic by removal of all mesenteric arcades for 4 to 6 cm. Mucosal blood flow in such ischemic bowels was reduced to 30% and 16% of control, respectively, and suture line blood flow was as low as that of the tightly stapled anastomoses. Significant stenosis (more than 68% reduction of the lumen) was observed in the group with 6 cm of mesenteric clearance. In no dogs did peritonitis or colonic gangrene develop. Gross and histologic revascularization was evident when dogs were killed at 6 weeks. These findings suggest that it is ischemia of the bowel, rather than ischemia at the suture line itself, that leads to anastomotic stricture. In view of the known susceptibility of the human intestine to ischemia, the model may have overstated the degree of ischemia necessary to produce strictures in clinical practice. Since the induced acute ischemia did not persist in the chronic state, we conclude that it is the adequacy of collateral development that determines the outcome in this model.
Introduction to Programmable Logic Controllers (1998)

From the Publisher:
This book offers an introduction to programmable logic controllers. It is a comprehensive source where the beginner can learn what a programmable logic controller is, how it works, programming, editing, PLC interface, I/O module selection and PLC hardware configuration. The extensive review questions at the end of each chapter and over 40 hands-on lab manual exercises give users the tools to learn the topic at hand.
Features: 
-state-of-the-art information on PLC's 
-thorough coverage of Allen-Bradley SLC 500 series controllers 
-extensive review questions insures the reader has a solid grasp of materials presented in each chapter 
-hands-on exercises allow the reader to learn by doing 
-current product photos and illustrations aid the visual learner 
ALSO AVAILABLE 
Lab Manual,ISBN: 0-8273-7867-X 
INSTRUCTOR SUPPLEMENTS 
Instructor's Manual, ISBN: 0-8273-7868-8
Absence of Natural Killer Cells during Murine Pregnancy is Associated with Reproductive Compromise in TgE26 Mice1 (1997)

Strategies of cell depletion were pursued to extend understanding of the functions of natural killer (NK) cell-like large granulated lymphocytes found in the rodent uterus during pregnancy. Repeated infusions of antibody to Ly-49G2, a surface marker thought to be expressed by the progenitor forms of these cells, removed Ly-49G2+ cells from the virgin but not the pregnant uterus. Large granulated uterine lymphocytes also differentiated during pregnancy in transgenic mice that carried a deletion in the IL-2 gene. This cell population was absent in two strains of mice, p56lck-/lck-.IL-2Rbeta-/IL-2Rbeta- and TgE26. Implantation sites in both of these strains had histopathological anomalies in the zone of decidualization. In TgE26 mice, a sudden onset of fetal loss began at Day 10 of gestation. Fetal death was associated with progressive changes in the maternal uterine arterioles, suggestive of localized arteriosclerosis associated with hypertension. TgE26 females carried immune-competent fetuses to term, apparently through preventive or compensatory mechanisms that may modify the uterine vasculature after the onset of vascular pathology. These studies are the first to suggest a vital role for large granulated lymphocytes in the promotion of fetal survival and pregnancy success.
Template-based, format-extensible authoring for BS digital data broadcast service (2002)

This paper describes the outline of a template-based authoring system for BS digital data broadcast service starting from December 2000 in Japan. The system is designed to compose multimedia documents in BML (Broadcast Markup Language) format. BML is an XML based data specification language adopted as Japanese standard for the service. The authoring system provides template functions to combine XML data sources with BML style templates. Also it provides data-binding rules with the templates to generate BML instances automatically. The templates and the rules are extensible so that they can generate multi-format contents written in BML and HTML for cross-media services.
Feature-based human motion parameter estimation with radar (2008)

Radar can be an extremely useful sensing technique to observe persons. It perceives persons behind walls or at great distances and in situations where persons have no or poor visibility. Human motion modulates the radar signal which can be observed in the spectrogram of the received signal. Extraction of these movements enables the animation of a person in virtual reality. The authors focus on a fast feature-based approach to estimate human motion features for real-time applications. The human walking model of Boulic is used, which describe the human motion with three parameters. Personification information is obtained by estimating the individual leg and torso parameters. These motion parameters can be estimated from the temporal maximum, minimum and centre velocity of the human motion distribution. Three methods are presented to extract these velocities. Additionally, we extract an independent human motion repetition frequency estimate based on velocity slices in the spectrogram. Kalman filters smooth the parameters and estimate the global Boulic parameters. These estimated parameters are input to the human model of Boulic which forms the basis for animation. The methods are applied to real radar measurements. The animated person generated with the extracted parameters provides a realistic look-alike of the real motion of the person.
Career racing performance in Thoroughbreds treated with prosthetic laryngoplasty for laryngeal neuropathy: 52 cases (1981–1989) (2000)

In addition to warning clients of the complications associated with prosthetic laryngoplasty, it may be prudent to provide a guarded prognosis for full restoration of racing performance in older horses, unless they are especially talented and are free of other racing-related problems.
Of inflammasomes and pathogens – sensing of microbes by the inflammasome (2013)

Inflammasomes are signalling platforms that sense a diverse range of microbial products and also a number of stress and damage associated endogenous signals. Inflammasome complexes can be formed by members of the Nod-like receptor family or the PYHIN family member AIM2. Upon formation, inflammasomes trigger proteolysis of caspase-1, which subsequently leads to a potent inflammatory response through the maturation and secretion of IL-1 family cytokines, which can be accompanied by an inflammatory cell death termed pyroptosis. Here, we review the sensing mechanisms of the currently characterized inflammasome complexes and discuss how they are involved in the innate immune response against microbial pathogens. We especially highlight recent advances in the molecular understanding of how microbial patterns are detected and discriminated from endogenous compounds by inflammasome sensors. Further, we review how inflammasomes contribute to the anti microbial host defense by cytokine-dependent and cell autonomous mechanisms.
Quartz-crystal microbalance study for characterizing atomic oxygen in plasma ash tools (2001)

This article discusses the measurement of atomic oxygen (AO) concentrations in an oxygen discharge using a quartz-crystal microbalance (QCM). This is a device that has been previously used for monitoring thin-film deposition, among several other applications. The sensor consists of a silver-coated quartz crystal that oscillates at its specific resonant frequency (typically, at about 6 MHz), which is dependent on the mass of the crystal. When exposed to AO, the silver oxidizes rapidly, resulting in a change in its mass, and a consequent change in this frequency. The frequency change is measured with a counter, and when plotted versus time, it may be fit to a standard diffusion-limited oxide-growth model. This model is then used to determine the specific AO flux to the crystal, and by inference, to the wafer. Initial results of QCM measurements in the FusionGemini Plasma Asher (GPL™-standard downstream microwave asher) and FusionGemini Enhanced Strip (GES™-fluorine compatible enhanced strip asher) are presented in this article. The results indicate AO densities of the order of 1012 cm−3 on the wafer. There is a marked increase in AO concentration with addition of nitrogen into the plasma, and a decrease in AO concentration with increasing pressure at constant flow. Effects of increasing the total plasma volume in the enhanced strip tool on AO production are discussed.
MicroRNAs are significantly influenced by p53 and radiation in HCT116 human colon carcinoma cells (2009)

Ionizing radiation is genotoxic to the cell, and p53 is commonly considered to be a key regulator that controls gene expression responding to the genotoxity of radiation. The expression profiles of microRNAs (miRNAs), which are small non-coding RNAs regulating the translation of target mRNAs, were analyzed to determine whether any correlation exists between miRNA expression, radiation response, and/or p53. The miRNA profiles were analyzed by microarray containing 470 human miRNA probes in HCT116 human colon carcinoma cells and their p53-null derivative. Thirty-eight miRNAs among the 138 flagged human miRNAs were selected by fold-change analysis. The expression levels of these 38 miRNAs were changed more than two-fold, and a total of 12 miRNAs were significantly affected by p53, radiation, and the combination of both. All 12 miRNAs had expression patterns correlated to p53, while two miRNAs were affected by radiation or the combined action of radiation and p53. In bioinformatics studies, these miRNAs had p53-binding sites with scores higher than 85% in their upstream regions, and some of their target genes were found to be involved in genotoxic responses. In conclusion, we have identified miRNAs influenced significantly by p53 and/or radiation in the HCT116 human colon carcinoma cell line model, and these miRNAs may have important roles in the regulation of genes involved the cellular responses to radiation.
Functional domain structure of calcineurin A: mapping by limited proteolysis (1989)

Limited proteolysis of calcineurin, the Ca2+/calmodulin-stimulated protein phosphatase, with clostripain is sequential and defines four functional domains in calcineurin A (61 kDa). In the presence of calmodulin, an inhibitory domain located at the carboxyl terminus is rapidly degraded, yielding an Mr 57,000 fragment which retains the ability to bind calmodulin but whose p-nitrophenylphosphatase is fully active in the absence of Ca2+ and no longer stimulated by calmodulin. Subsequent cleavage(s), near the amino terminus, yield(s) an Mr 55,000 fragment which has lost more than 80% of the enzymatic activity. A third, slower, proteolytic cleavage in the carboxyl-terminal half of the protein converts the Mr 55,000 fragment to an Mr 42,000 polypeptide which contains the calcineurin B binding domain and an Mr 14,000 fragment which binds calmodulin in a Ca2+-dependent manner with high affinity. In the absence of calmodulin, clostripain rapidly severs both the calmodulin-binding and the inhibitory domains. The catalytic domain is preserved, and the activity of the proteolyzed 43-kDa enzyme is increased 10-fold in the absence of Ca2+ and 40-fold in its presence. The calcineurin B binding domain and calcineurin B appear unaffected by proteolysis both in the presence and in the absence of calmodulin. Thus, calcineurin A is organized into functionally distinct domains connected by proteolytically sensitive hinge regions. The catalytic, inhibitory, and calmodulin-binding domains are readily removed from the protease-resistant core, which contains the calcineurin B binding domain. Calmodulin stimulation of calcineurin is dependent on intact inhibitory and calmodulin-binding domains, but the degraded enzyme lacking these domains is still regulated by Ca2+.
Advanced Functional Fibrous Materials for Enhanced Thermoregulating Performance (2019)

The concept of thermoregulating textiles capable of providing personal thermal management property (PTM) has attracted significant attention in recent years. It is considered as an emerging approach to promote the comfort and general well-being of wearers and also to mitigate the energy consumption load for indoor living space conditioning. Regulating the heat exchange between human body and environment has been the core subject of many studies on introducing the PTM functionality to textiles. This work provides an overview of the latest literature, summarizing the recent innovations and state-of-the-art approaches of controlling the heat gain and loss of textiles. To this end, methods to control the fundamental aspects of heat gain and loss of fabrics such as using near-infrared reflective materials and conductive nanomaterials, designing photonic structures of fabrics, and engineering nanoporous structures for passive cooling and heating effects will be discussed. Moreover, specific attention is given to the application of phase change materials in textiles, their integration methods, and the associated mechanisms. Several commercial methods such as adapting the innovative designs, introducing moisture management capability, and using air/liquid thermoregulating systems will also be discussed. This review article provides a clear picture of the concept of thermoregulating textiles and recommends some future research trajectories for this emerging field.
Credit card fraud detection with a neural-network (1994)

Using data from a credit card issuer, a neural network based fraud detection system was trained on a large sample of labelled credit card account transactions and tested on a holdout data set that consisted of all account activity over a subsequent two-month period of time. The neural network was trained on examples of fraud due to lost cards, stolen cards, application fraud, counterfeit fraud, mail-order fraud and NRI (non-received issue) fraud. The network detected significantly more fraud accounts (an order of magnitude more) with significantly fewer false positives (reduced by a factor of 20) over rule-based fraud detection procedures. We discuss the performance of the network on this data set in terms of detection accuracy and earliness of fraud detection. The system has been installed on an IBM 3090 at Mellon Bank and is currently in use for fraud detection on that bank's credit card portfolio.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthesis of Human Immunodeficiency Virus DNA In a Cell-to-Cell Transmission Model (1992)

Cell-to-cell transmission of human immunodeficiency virus type 1 (HIV-1) was modelled by coculturing virus-infected cells with uninfected target cells at a ratio of 1:4. While H9 cells persistently infected with HTLV-IIIB did not contain unintegrated viral DNA detectable by Southern blotting, when cocultured with uninfected HUT-78 cells the mixed culture effectively underwent a new round one-step virus replication which began de novo synthesis of free viral DNA within 4 hours. Linear DNA was synthesized before the accumulation of circular DNA, and two seemingly distinct phases of viral DNA synthesis were involved. When both virus donor cells and recipient cells were arrested in the G0/G1 phase of the cell cycle, accumulation of circular viral DNA was inhibited. In contrast to cell-free virus infection of resting human peripheral blood mononuclear cells (PBMC), where no free viral DNA of discrete sizes could be detected by Southern blot, cell-to-cell transmission infection of resting PBMC resulted in the synthesis of full-length linear as well as circular viral DNA. The efficiency with which cell-to-cell transmission of HIV initiates virus replication underlines the importance of this mode of transmission in virus dissemination in vivo.
Effect of nitrogen‐mediated changes in alkalinity on pH control and CO<sub>2</sub> supply in intensive microalgal cultures (1982)

The freshwater alga Scenedesmus obliquus was grown in continuous culture at a fixed dilution rate of 0.5/day, but at varying pH in the range 4.17-10.67. The pH was regulated in the range 4.17-7.67 by continuously bubbling 1% CO(2)-enriched air into the cultures and by varying the source of nitrogen (NO(3) (-), NH(4) (+), or urea) in the growth medium, which, in turn, led to changes in culture alkalinity. Culture alkalinity and P(CO(2) ) were the sole determinants of pH. A pH-stat system, together with NO(3) (-) in the medium, was used to regulate the pH in the range 7.92-10.67. Maximum productivity, which occurred at pH 6.6, was dependent on N source only to the extent that culture alkalinity was a function of nitrogen uptake. The results demonstrate that the choice of N is a critical factor in controlling the pH of large-scale algal cultures. NH(4) (+) is a poor source of N because it leads to destruction of culture alkalinity and concomitant growth-inhibiting reductions in pH, whereas NO(3) (-) has an opposite effect, although pH is not so severely affected in this case. Urea is, by far, the most suitable N source for maximizing algal yield when it is supplied in combination with the proper amounts of HCO(3) (-) alkalinity in the growth medium and percent CO(2) in the bubbled gas that will lead to an equilibrium pH near the optimum pH.
Hardware-Assisted Dependable Systems (2017)

Unpredictable hardware faults and software bugs lead to application crashes, incorrect computations, unavailability of internet services, data losses, malfunctioning components, and consequently financial losses or even death of people. In particular, faults in microprocessors (CPUs) and memory corruption bugs are among the major unresolved issues of today. CPU faults may result in benign crashes and, more problematically, in silent data corruptions that can lead to catastrophic consequences, silently propagating from component to component and finally shutting down the whole system. Similarly, memory corruption bugs (memory-safety vulnerabilities) may result in a benign application crash but may also be exploited by a malicious hacker to gain control over the system or leak confidential data. Both these classes of errors are notoriously hard to detect and tolerate. Usual mitigation strategy is to apply ad-hoc local patches: checksums to protect specific computations against hardware faults and bug fixes to protect programs against known vulnerabilities. This strategy is unsatisfactory since it is prone to errors, requires significant manual effort, and protects only against anticipated faults. On the other extreme, Byzantine Fault Tolerance solutions defend against all kinds of hardware and software errors, but are inadequately expensive in terms of resources and performance overhead. In this thesis, we examine and propose five techniques to protect against hardware CPU faults and software memory-corruption bugs. All these techniques are hardware-assisted: they use recent advancements in CPU designs and modern CPU extensions. Three of these techniques target hardware CPU faults and rely on specific CPU features: ∆-encoding efficiently utilizes instruction-level parallelism of modern CPUs, Elzar re-purposes Intel AVX extensions, and HAFT builds on Intel TSX instructions. The rest two target software bugs: SGXBounds detects vulnerabilities inside Intel SGX enclaves, and “MPX Explained” analyzes the recent Intel MPX extension to protect against buffer overflow bugs. Our techniques achieve three goals: transparency, practicality, and efficiency. All our systems are implemented as compiler passes which transparently harden unmodified applications against hardware faults and software bugs. They are practical since they rely on commodity CPUs and require no specialized hardware or operating system support. Finally, they are efficient because they use hardware assistance in the form of CPU extensions to lower performance overhead.
Applying Morphology to English-Arabic Statistical Machine Translation (2011)

We introduce two approaches to augmenting English-Arabic statistical machine translation (SMT) with linguistic knowledge.The first approach improves SMT by adding linguistically motivated syntactic features to particular phrases.These added features are based on the English syntactic information, namely part-of-speech tags and dependency parse trees.We achieved improvements of 0.2 and 0.6 in BLEU score on two different data sets over the state-of-the-art SMT baseline system.The second approach improves morphological agreement in machine translation output through post-processing.Our method uses the projection of the English dependency parse tree onto the Arabic sentence in addition to the Arabic morphological analysis in order to extract the agreement relations between words in the Arabic sentence.Afterwards, classifiers for individual morphological features are trained using syntactic and morphological information from both the source and target languages.The predicted morphological features are then used to generate the correct surface forms.Our method achieves a statistically significant improvement over the baseline system according to human evaluation.i List of Tables5.1 Word classes for connectable phrases . . . . . . .