gebhart/patrepeval huggingface dataset:
Genetic Process Engineering (2004)

In this chapter we present an engineering discipline to obtain complex, predictable, and reliable cell behaviors by embedding biochemical logic circuits and programmed intercellular communications into cells. To accomplish this goal, we provide a well-characterized component library, a biocircuit design methodology, and software design tools. Using the cellular gates,we introduce genetic process engineering, a methodology for modifying the DNA encoding of existing genetic elements to achieve the desired input/output behavior for constructing reliable circuits of significant complexity.We also describe BioSpice, a prototype software tool for biocircuit design that supports both static and dynamic simulations and analysis of singlecell environments and small cell aggregates. The goal of our research is to lay the foundations of an engineering discipline for building novel living systems with well-defined purposes and behaviors using standardized, well-characterized components. Cells are miniature, energy efficient, self-reproduce, and can manufacture biochemical products. These unique characteristics make cells attractive for many novel applications that require precise programmed control over the behavior of the cells. The applications include nanoscale fabrication, embedded intelligence in materials, sensor/effector arrays, patterned biomaterial manufacturing, improved pharmaceutical synthesis, programmed therapeutics, and as a sophisticated tool for in vivo studies of genetic regulatory networks. These applications require synthesis of sophisticated and reliable cell behaviors that instruct cells to make logic decisions based on factors such as existing environmental conditions and current cell state. For example, a cell may be programmed to secrete particular timed sequences of biochemicals depending on the type of messages sent by its neighbors. The approach proposed here for engineering the requisite precision control is to embed internal computation and programmed intercellular communications into the cells. The challenge is to provide robust computation and communications using a substrate where reliability and reproducible results are difficult to achieve. Biological organisms as an engineering substrate are currently difficult to modify and control because of the poor understanding of their complexity. Genetic modifications to cells often result in unpredictable and unreliable behavior. A single Escherichia coli bacterial cell contains approximately 1010 active molecules, about 107 of which are protein molecules.
Integrated number portability protocols for wire and wireless network (2002)

Naturally, wireless network is similar to wire network in the point of supporting number portability. Thus, in this paper, we proposed the integrated number portability protocols for wire and wireless network using the intelligent network. For this, we integrated the LNP DB of wire network and home location register/visited location register (HLR/VLR) of a wireless network. We proposed the methods for the wireless call setup protocol to use the IN service. Through this research, we examine the support of more efficient number portability services for wire and wireless telephone subscribers.
Multi-sensor Integrated System for Reverse Engineering (2013)

Application of multiple sensors in Reverse Engineering (RE) has been effective approach to meet increasing demands of both complexity and accuracy. However, methodology to plan RE steps using systems combining different sensors has been a serious challenge. This paper presents hybrid system that integrates laser line scanning probe and touch trigger probe of coordinate measuring machine for RE of complex part. As a result of integration, this system utilizes strength of one system to overcome limitation of other. In this paper, RE methodology using hybrid system has been described through a part case study. The primary objective of this paper is to retrieve lost 2D drawings as well as damaged portion of mechanical part efficiently and accurately using hybrid system.
MWD determination of ultra high MFR polypropylene by melt rheology (1994)

Abstract A rheological technique of determining molecular weight distribution (MWD) of ultra high MFR polypropylene (PP) is presented. The development of this new technique was needed for two reasons. First, the advent of high activity catalyst made possible the direct polymerization and thus the commercialization of very high MFR PP. Secondly, the polydispersity index (PI) measurement based on crossover modulus from G′ and G″ curves, which was developed by Zeichner and Patel in 1981, was proven to be inapplicable to resins with MFR higher than about 40, due to instrument limitations. This new technique utilizes G′ and G″ data at low frequencies which are obtained from a dynamic frequency sweep test at 200°C. PI values, a measure of MWD, determined by this method are proven to have an excellent correlation with those obtained by gel permeation chromatography (GPC). This method has been very useful in determining MWD of melt brown fiber resins whose MFR is normally between 30 and 1000. It has also been used as a quality control tool during the resin production in a commercial plant. © 1994 John Wiley & Sons, Inc.
Quinolone‐Resistant<i>Salmonella typhi</i>in Viet Nam: Molecular Basis of Resistance and Clinical Response to Treatment (1997)

Nalidixic acid-resistant Salmonella typhi (NARST) was first isolated in Viet Nam in 1993. Analysis of the quinolone resistance-determining region of gyrA in 20 NARST isolates by polymerase chain reaction and single-stranded conformational polymorphism yielded two novel patterns: pattern II corresponding to a point mutation at nucleotide 87 Asp-->Gly (n = 17), and pattern III corresponding to a point mutation at nucleotide 83 Ser-->Phe (n = 3). In trials of short-course ofloxacin therapy for uncomplicated typhoid, 117 (78%) of 150 patients were infected with multidrug-resistant S. typhi, 18 (15%) of which were NARST. The median time to fever clearance was 156 hours (range, 30-366 hours) for patients infected with NARST and 84 hours (range, 12-378 hours) for those infected with nalidixic acid-susceptible strains (P < .001). Six (33.3%) of 18 NARST infections required retreatment, whereas 1 (0.8%) of 132 infections due to susceptible strains required retreatment (relative risk = 44; 95% confidence interval = 5.6-345; P < .0001). We recommend that short courses of quinolones not be used in patients infected with NARST.
Systems Biology Approaches Reveal a Specific Interferon-Inducible Signature in HTLV-1 Associated Myelopathy (2012)

Human T-lymphotropic virus type 1 (HTLV-1) is a retrovirus that persists lifelong in the host. In ∼4% of infected people, HTLV-1 causes a chronic disabling neuroinflammatory disease known as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The pathogenesis of HAM/TSP is unknown and treatment remains ineffective. We used gene expression microarrays followed by flow cytometric and functional assays to investigate global changes in blood transcriptional profiles of HTLV-1-infected and seronegative individuals. We found that perturbations of the p53 signaling pathway were a hallmark of HTLV-1 infection. In contrast, a subset of interferon (IFN)-stimulated genes was over-expressed in patients with HAM/TSP but not in asymptomatic HTLV-1 carriers or patients with the clinically similar disease multiple sclerosis. The IFN-inducible signature was present in all circulating leukocytes and its intensity correlated with the clinical severity of HAM/TSP. Leukocytes from patients with HAM/TSP were primed to respond strongly to stimulation with exogenous IFN. However, while type I IFN suppressed expression of the HTLV-1 structural protein Gag it failed to suppress the highly immunogenic viral transcriptional transactivator Tax. We conclude that over-expression of a subset of IFN-stimulated genes in chronic HTLV-1 infection does not constitute an efficient host response but instead contributes to the development of HAM/TSP.
Structural Requirements for the Cooling Activity of Cyclic α-Keto Enamines (2003)

3-Methyl- and 5-methyl-2-(l-pyrrolidinyl)-2-cyclopenten-1-one were recently identified as cooling compounds formed by Maillard reaction in heated glucose/L-proline mixtures, as well as in roasted malt. To gain more insights into the molecular requirements of this cooling effect, a range of cyclic keto enamine derivatives were synthesized, and their physiological cooling activities were evaluated. Any modification of the amino moiety, the carbocyclic ring size, or the alkyl substitution led to an increase of the cooling threshold. Insertion of an oxygen atom into the carbocycle, however, increased the cooling activity, e.g. the threshold of the corresponding3(2H)-furanone was 16-fold below the threshold concentration found for the 2-cyclopenten-1-one. Incorporation of an oxygen into the 5-position of the cyclopentenone resulted in a even more drastic effect, e.g. the 2(5H)-furanone exhibited the strongest cooling effect at the low threshold of 0.02-0.06 mmol/L. In contrast to the minty smelling (—)-menthol, these keto enamines are odorless, but impart a cooling sensation to the oral cavity and to the skin.
Rapid Prototyping of Augmented Reality & Virtual Reality Interfaces (2019)

This course introduces participants to rapid prototyping techniques for augmented reality and virtual reality interfaces. Participants will learn about both physical prototyping with paper and Play-Doh as well as digital prototyping via new visual authoring tools for AR/VR. The course is structured into four sessions. After an introduction to AR/VR prototyping principles and materials, the next two sessions are hands-on, allowing participants to practice new physical and digital prototyping techniques. These techniques use a combination of new paper-based AR/VR design templates and smartphone-based capture and replay tools, adapting Wizard of Oz for AR/VR design. The fourth and final session will allow participants to test and critique each other's prototypes while checking against emerging design principles and guidelines. The instructor has previously taught the techniques to broad student audiences with a wide variety of non-technical backgrounds, including design, architecture, business, medicine, education, and psychology, who shared a common interest in user experience and interaction design. The course is targeted at non-technical audiences including HCI practitioners, user experience researchers, and interaction design professionals and students. A useful byproduct of the course will be a small portfolio piece of a first AR/VR interface designed iteratively and collaboratively in teams.
Dietary fiber modulates intestinal proglucagon messenger ribonucleic acid and postprandial secretion of glucagon-like peptide-1 and insulin in rats. (1996)

Intestinal hormones stimulate more than 50% of the insulin response after oral glucose administration. Short chain fatty acids stimulate mucosal adaptation and may alter proglucagon messenger RNA and release of the insulin secretagogue, glucagon-like peptide-1 (GLP-1). Sprague-Dawley rats ingested a fiber-free elemetnal diet or an elemental diet supplemented with 30% fiber providing similar energy and nutrients for 14 days. The cecal and colonic short chain fatty acids contents were significantly higher in the 30% fiber group. Ileal proglucagon messenger RNA levels were significantly higher in the 30% group vs. the 0% group (11.47 +/- 0.87 vs. 6.52 +/- 0.87 densitometer units), respectively. Similar trends were seen in the colon (13.36 +/- 1.0 vs. 10.90 +/- 0.77 densitometer units; P = 0.07). Plasma GLP-1, insulin, and C peptide levels 30 min postoral glucose were significantly higher in the 30% fiber group vs. the 0% group (19.8 +/- 1.2 vs. 15.4 +/- 1.2 pg/ml, 2.67 +/- 0.4 vs. 1.29 +/- 0.5 ng/ml, and 964.4 +/- 94.4 vs. 530.2 +/- 120.4 pM, respectively). Plasma glucose and glucagon did not differ between groups. A diet supplemented with fiber is able to significantly alter proglucagon gene expression and modulate GLP-1 and insulin secretion. These novel findings deepen our understanding of the beneficial role of fiber in improving glucose homeostasis.
Technology of Wide-Bandgap Diode Structures for Highfrequency Operation (2006)

This paper reports on technology development aspects for GaN-based diodes in view of their application at high frequencies. The investigated devices include structures for transferred electron effects for operation at high electric-fields as well as heterostructure varactors (HBV) and Schottky diodes for frequency multiplication function. The impact of factors such as high threshold voltage for transferred electron effects, strong piezoelectric effects and Schottky barrier properties on device technologies and performances are addressed
Thinking Straight about Calcium (1993)

For the past 10 years, both scientists and the lay public have been subjected to a spate of claims and counterclaims about the value of ensuring an adequate intake of calcium throughout life. Although the role of calcium in the health of adult bone has been called controversial, it may be more accurate to say that it has been confusing. Is it possible to straighten out the apparent conflicts?A recent review identified 43 studies published since 1988 that related calcium intake to bone mass, bone loss, or bone fragility1. Twenty-six reported that calcium intake was associated in some . . .
Lack of Toll-like Receptor 4 and 2 Polymorphisms in Korean Patients with Bacteremia (2006)

Toll-like receptors (TLRs) are pattern-recognition receptors that are important in innate immune responses to bacterial infection. The purpose of this study is to describe the prevalence of TLRs genetic variations in the bacteremic patients in Korea. A total of 154 patients with bacteremia and 179 healthy volunteers were included. The Asp299Gly and Thr399Ile allele of the TLR4 gene and Arg753Gln and Arg677Trp allele of the TLR2 gene were tested by PCR-RFLP. The DNA sequences were determined to confirm the PCR-RFLP results. Contrary to the expectation, no genetic polymorphisms were detected in both groups of this study, suggesting that it is very rare in Korean.
A new family of frequency-hop codes (2000)

We give an algebraic construction for a new family of frequency-hop codes. The construction is based on properties of finite fields: it is shown that for each field GF(p/sup m/), there exists a large number of codes of length p/sup m/. The codes are also shown to possess the best possible simultaneous two-dimensional autocorrelation and cross-correlation properties. Moreover, they include a family of codes: with a code length of a power of 2, which are ideally suitable for applications in digital communication systems.
Real-time application of advanced three-dimensional graphic techniques for research aircraft simulation (1990)

Visual aids are valuable assets to engineers for design, demonstration, and evaluation. Discussed here are a variety of advanced three-dimensional graphic techniques used to enhance the displays of test aircraft dynamics. The new software's capabilities are examined and possible future uses are considered.
Photic Induction of <i>mPer1</i> and <i>mPer2</i> in <i>Cry</i> -Deficient Mice Lacking a Biological Clock (1999)

Mice lacking mCry1 and mCry2 are behaviorally arrhythmic. As shown here, cyclic expression of the clock genes mPer1 and mPer2 (mammalian Period genes 1 and 2) in the suprachiasmatic nucleus and peripheral tissues is abolished and mPer1 and mPer2 mRNA levels are constitutively high. These findings indicate that the biological clock is eliminated in the absence of both mCRY1 and mCRY2 (mammalian cryptochromes 1 and 2) and support the idea that mammalian CRY proteins act in the negative limb of the circadian feedback loop. The mCry double-mutant mice retain the ability to have mPer1 and mPer2 expression induced by a brief light stimulus known to phase-shift the biological clock in wild-type animals. Thus, mCRY1 and mCRY2 are dispensable for light-induced phase shifting of the biological clock.
Study on stability of B-vitamins in processing methods of ginseng (1982)

B-vitamin contents in ginsengs ranged from 55.9 to 65.5 r/g and from 13.2 to 14.5 r/g for niacin and niacin amide, from 4.9 to 5.4 mr/g for cobalamine, and from 3.9 to 8.2 r/g and from 6.9 to 8.2 r/g for riboflavin and thiamine regardless processing. Especially, cobalamine was detected in ginseng. It is found that the contents of B-vitamins somewhat decreased according to processing methods, washing-dried and steaming-dried of fresh ginseng. Niacin, niacin amide and cobalamine decreased by . Therefore, it is approved that B-vitamins were stable in processing methods.
Knowledge Representation of Requirements Documents Using Natural Language Processing (2018)

Complex systems such as automotive software systems are usually broken down into subsystems that are specified and developed in isolation and afterwards integrated to provide the functionality of the desired system. This results in a large number of requirements documents for each subsystem written by different people and in different departments. Requirements engineers are challenged by comprehending the concepts mentioned in a requirement because coherent information is spread over several requirements documents. In this paper, we describe a natural language processing pipeline that we developed to transform a set of heterogeneous natural language requirements into a knowledge representation graph. The graph provides an orthogonal view onto the concepts and relations written in the requirements. We provide a first validation of the approach by applying it to two requirements documents including more than 7,000 requirements from industrial systems. We conclude the paper by stating open challenges and potential application of the knowledge representation graph.
Microsatellite variation in Central Africa: An analysis of intrapopulational and interpopulational genetic diversity (2000)

As a part of a research project on molecular variation in Central Africa, we have analyzed 10 microsatellites (CD4, CSFO, D3S1358, D18S51, D21S11, F13A1, FES, TH01, TPOX, and VWA) in the Bamileke and Ewondo from Cameroon and the Sanga and Mbenzele Pygmies from the Central African Republic (a total of 390 chromosomes). A statistically significant trend towards heterozygote deficiency was detected in the Mbenzele Pygmies. This was established through the use of powerful exact tests for the Hardy-Weinberg equilibrium. A certain degree of isolation and a small effective size may explain this finding. However, the lack of any substantial reduction in allelic diversity in the Mbenzele does not support the possibility that this group has a smaller effective size in evolutionary terms. A possible explanation based on ethnographic studies suggests that the gene flow from non-Pygmies to Pygmies could have been interrupted only in relatively recent times. The analysis of association between genotypes at pairs of independent loci indicates that the level of subheterogeneity is markedly lower in the Bamileke than in other sampled populations. This may be explained by the combined effect of larger population size, more rigid respect of clanic exogamy, and higher matrimonial mobility of the Bamileke. Finally, we have analyzed interpopulational relationships among our sampled populations and other Central African populations. The results are consistent with a previous study of protein loci (Spedini et al. 1999), which suggests the recent history of the Bamileke and Ewondo has led them to aquire a substantial genetic similarity. Furthermore, the Mbenzele Pygmies diverge from Biaka Pygmies, despite their common origin and geographical proximity. This is probably due to the differentiating effect of genetic drift, which is enhanced by the small effective size of Pygmy populations.
The pupillary light reflex distinguishes between circadian and non-circadian delayed sleep phase disorder (DSPD) phenotypes in young adults (2018)

This study investigated the utility of the pupillary light reflex as a method of differentiating DSPD patients with delayed melatonin timing relative to desired/required sleep time (circadian type) and those with non-delayed melatonin timing (non-circadian type). All participants were young adults, with a total of 14 circadian DSPD patients (M = 28.14, SD = 5.26), 12 non-circadian DSPD patients (M = 29.42, SD = 11.51) and 51 healthy controls (M = 21.47 SD = 3.16) completing the protocol. All participants were free of central nervous system acting medications and abstained from caffeine and alcohol on the day of the assessment. Two pupillary light reflex measurements were completed by each participant, one with a 1s dim (~10 lux) light exposure, and one with a 1s bright (~1500 lux) light exposure. Circadian DSPD patients showed a significantly faster pupillary light reflex than both non-circadian DSPD patients and healthy controls. Non-circadian patients and healthy controls did not differ significantly. Receiver operating characteristic curves were generated to determine the utility of mean and maximum constriction velocity in differentiating the two DSPD phenotypes, and these demonstrated high levels of sensitivity (69.23--100%) and specificity (66.67-91.67%) at their optimal cut offs. The strongest predictor of DSPD phenotype was the mean constriction velocity to bright light (AUC = 0.87). These results support the potential for the pupillary light reflex to clinically differentiate between DSPD patients with normal vs. delayed circadian timing relative to desired bedtime, without the need for costly and time-consuming circadian assessments.
The p38α/β MAPK functions as a molecular switch to activate the quiescent satellite cell (2005)

Somatic stem cells cycle slowly or remain quiescent until required for tissue repair and maintenance. Upon muscle injury, stem cells that lie between the muscle fiber and basal lamina (satellite cells) are activated, proliferate, and eventually differentiate to repair the damaged muscle. Satellite cells in healthy muscle are quiescent, do not express MyoD family transcription factors or cell cycle regulatory genes and are insulated from the surrounding environment. Here, we report that the p38alpha/beta family of mitogen-activated protein kinases (MAPKs) reversibly regulates the quiescent state of the skeletal muscle satellite cell. Inhibition of p38alpha/beta MAPKs (a) promotes exit from the cell cycle, (b) prevents differentiation, and (c) insulates the cell from most external stimuli allowing the satellite cell to maintain a quiescent state. Activation of satellite cells and p38alpha/beta MAPKs occurs concomitantly, providing further support that these MAPKs function as a molecular switch for satellite cell activation.