gebhart/patrepeval huggingface dataset:
High-level synthesis of digital circuits using genetic algorithms (2002)

Describes a high-level synthesis system that uses genetic algorithms (GAs). The use of GAs allows for a synthesis method that is more flexible and more adaptable to new constraints than the traditional heuristic and integer linear programming approaches. The proposed GA tool is suitable for large, realistic problems. It performs simultaneous scheduling, allocation and binding of functional and storage units minimizing multiple related performance constraints such as latency, area throughput and power. The synthesis tool is capable of performing with control/data flow graphs.
Noninvasive Follow-Up of Simian Immunodeficiency Virus Infection in Wild-Living Nonhabituated Western Lowland Gorillas in Cameroon (2012)

Simian immunodeficiency viruses infecting western lowland gorillas (SIVgor) are closely related to HIV-1 and are most likely the ancestors of HIV-1 groups O and P. At present, limited data are available on genetic diversity, transmission, viral evolution, and pathogenicity of SIVgor in its natural host. Between 2004 and 2011, 961 putative gorilla fecal samples were collected at the Campo Ma'an National Park, Cameroon. Among them, 16% cross-reacted with HIV-1 antibodies, corresponding to at least 34 infected gorillas. Combining host genotyping and field data, we identified four social groups composed of 7 to 15 individuals each, with SIV rates ranging from 13% to 29%. Eleven SIVgor-infected gorillas were sampled multiple times; two most likely seroconverted during the study period, showing that SIVgor continues to spread. Phylogenetic analysis of partial env and pol sequences revealed cocirculation of closely related and divergent strains among gorillas from the same social group, indicating SIVgor transmissions within and between groups. Parental links could be inferred for some gorillas infected with closely related strains, suggesting vertical transmission, but horizontal transmission by sexual or aggressive behavior was also suspected. Intrahost molecular evolution in one gorilla over a 5-year period showed viral adaptations characteristic of escape mutants, i.e., V1V2 loop elongation and an increased number of glycosylation sites. Here we show for the first time the feasibility of noninvasive monitoring of nonhabituated gorillas to study SIVgor infection over time at both the individual and population levels. This approach can also be applied more generally to study other pathogens in wildlife.
Red-light emission induced by Mn-doped magnesium fluorogermanate (2015)

As a potential red-light source in the white light emitting diodes (LEDs), Mn-doped magnesium fluorogermanate (Mg28Ge7.5O38F10) are investigated by the first principles calculation with the Heyd-Scuseria-Ernzerhof (HSE) functional. The results demonstrate that the neutral Mn substitutions at the Mg (Mn), octahedral Ge (Mn) and tetrahedral Ge (Mn) sites are all energetically favorable. However, only Mn could create proper transition levels leading to the experimentally observed red-light emission under near ultra-violet (UV) excitation. Our results provide fundamental understanding of the Mn defects behavior and the corresponding red-light emission in Mn-doped magnesium fluorogermanate.
Migration ofAntigen-Specific T Cells Away from CXCR4-Binding Human ImmunodeficiencyVirus Type 1gp120 (2004)

Cell-mediated immunity depends in part on appropriate migration and localization of cytotoxic T lymphocytes (CTL), a process regulated by chemokines and adhesion molecules. Many viruses, including human immunodeficiency virus type 1 (HIV-1), encode chemotactically active proteins, suggesting that dysregulation of immune cell trafficking may be a strategy for immune evasion. HIV-1 gp120, a retroviral envelope protein, has been shown to act as a T-cell chemoattractant via binding to the chemokine receptor and HIV-1 coreceptor CXCR4. We have previously shown that T cells move away from the chemokine stromal cell-derived factor 1 (SDF-1) in a concentration-dependent and CXCR4 receptor-mediated manner. Here, we demonstrate that CXCR4-binding HIV-1 X4 gp120 causes the movement of T cells, including HIV-specific CTL, away from high concentrations of the viral protein. This migratory response is CD4 independent and inhibited by anti-CXCR4 antibodies and pertussis toxin. Additionally, the expression of X4 gp120 by target cells reduces CTL efficacy in an in vitro system designed to account for the effect of cell migration on the ability of CTL to kill their target cells. Recombinant X4 gp120 also significantly reduced antigen-specific T-cell infiltration at a site of antigen challenge in vivo. The repellant activity of HIV-1 gp120 on immune cells in vitro and in vivo was shown to be dependent on the V2 and V3 loops of HIV-1 gp120. These data suggest that the active movement of T cells away from CXCR4-binding HIV-1 gp120, which we previously termed fugetaxis, may provide a novel mechanism by which HIV-1 evades challenge by immune effector cells in vivo.
Impact of diagnostic misclassification on estimation of genetic correlations using genome-wide genotypes (2012)

Disorders that share genetic risk factors often are placed in closely related diagnostic categories and treated similarly. Until recently, evidence for shared genetic etiology derived from classical research strategies--coaggregation in family and twin studies. Accumulating sufficient numbers of families was often problematic. However, in the era of genome-wide genotyping, we can now directly estimate the degree of sharing of genetic risk factors between disorders. This strategy is practical even for very rare disorders, where it is infeasible to ascertain informative families. Importantly, the estimates of genetic correlations from genome-wide genotypes are derived using such distant relatives that contamination by shared environmental factors seems unlikely. However, any method that seeks to quantify the shared etiology of disorders assumes they can be distinguished diagnostically from one another without error. Here we investigate the impact of misdiagnosis on estimates of genetic correlation both from traditional family data and from genome-wide genotypes of case-control samples from unrelated individuals. Our analyses show similar results for levels of misdiagnosis in both types of data. In both scenarios, genetic variances and heritabilities tend to be slightly underestimated but genetic correlations are overestimated, sometimes substantially so. For example, two genetically distinct but equally heritable disorders each with prevalence 1%, can generate false-positive estimates of genetic correlations of >0.2 in the presence of 10% reciprocal misdiagnosis. Strategies for minimizing the effects of misdiagnosis in cross-disorder genetic studies are discussed.
Role of<i>Bacillus anthraci</i>s Spore Structures in Macrophage Cytokine Responses (2007)

The innate immune response of macrophages (Mphi) to spores, the environmentally acquired form of Bacillus anthracis, is poorly characterized. We therefore examined the early Mphi cytokine response to B. anthracis spores, before germination. Mphi were exposed to bacilli and spores of Sterne strain 34F2 and its congenic nongerminating mutant (DeltagerH), and cytokine expression was measured by real-time PCR and an enzyme-linked immunosorbent assay. The exosporium spore layer was retained (exo+) or removed by sonication (exo-). Spores consistently induced a strong cytokine response, with the exo- spores eliciting a two- to threefold-higher response than exo+ spores. The threshold for interleukin-1beta (IL-1beta) production by wild-type Mphi was significantly lower than that required for tumor necrosis factor alpha expression. Cytokine production was largely dependent on MyD88, suggesting Toll-like receptor involvement; however, the expression of beta interferon in MyD88-/- Mphi suggests involvement of a MyD88-independent pathway. We conclude that (i) the B. anthracis spore is not immunologically inert, (ii) the exosporium masks epitopes recognized by the Mphi, (iii) the Mphi cytokine response to B. anthracis involves multiple pattern recognition receptors and signaling pathways, and (iv) compared to other cytokines, IL-1beta is expressed at a lower spore concentration.
Acute respiratory distress syndrome in acute pyelonephritis during pregnancy: ten-year review (2014)

Acute pyelonephritis (AP) is one of the most common medical complications of pregancy. About 20% of women with severe pyelonephritis during pregnancy develop complications that include anaemia, septic shock syndrome, acute respiratory distress syndrome (ARDS), preterm labour, intrauterine growth retardation... AP may result in significant maternal morbidity and fetal morbidity and mortality. An early diagnosis and treatment with parenteral antibiotics are essential to avoid complicated AP and obstetric complications.
Pd/P(<i>t</i>-Bu)<sub>3</sub>:  A Mild and General Catalyst for Stille Reactions of Aryl Chlorides and Aryl Bromides (2002)

Pd/P(t-Bu)(3) serves as an unusually reactive catalyst for Stille reactions of aryl chlorides and bromides, providing solutions to a number of long-standing challenges. An unprecedented array of aryl chlorides can be cross-coupled with a range of organotin reagents, including SnBu(4). Very hindered biaryls (e.g., tetra-ortho-substituted) can be synthesized, and aryl chlorides can be coupled in the presence of aryl triflates. The method is user-friendly, since a commercially available complex, Pd(P(t-Bu)(3))(2), is effective. Pd/P(t-Bu)(3) also functions as an active catalyst for Stille reactions of aryl bromides, furnishing the first general method for room-temperature cross-couplings.
Tolerant parsing with a special kind of «Any» symbol: the algorithm and practical application (2018)

Tolerant parsing is a form of syntax analysis aimed at capturing the structure of certain points of interest presented in a source code. While these points should be welldescribed in the corresponding language grammar, other parts of the program are allowed to be not presented in the grammar or to be described coarse-grained, thereby parser remains tolerant to the possible inconsistencies in the irrelevant area. Island grammars are one of the basic tolerant parsing techniques. "Island" is used as the relevant code alias, while the irrelevant code is called "water". In the paper, a modified LL(1) parsing algorithm with built-in "Any" symbol processing is described. The "Any" symbol matches implicitly defined token sequences. The use of the algorithm for island grammars allows one to reduce irrelevant code description as well as to simplify patterns for relevant code matching. Our "Any" implementation is more accurate and less restrictive in comparison with the closest analogues implemented in Coco/R and LightParse parser generators. It also has potentially lower overhead than the "bounded seas" concept implemented in PetitParser. As shown in the experimental section, the tolerant parser generated by the C# island grammar is proven to be applicable for large-scale software projects analysis.
Applications of virtual reality for pain management in burn-injured patients (2008)

The pain associated with burn injuries is intense, unremitting and often exacerbated by anxiety, depression and other complicating patient factors. On top of this, modern burn care involves the repetitive performance - often on a daily basis for weeks to months - of painful and anxiety-provoking procedures that create additional treatment-related pain, such as wound care, dressing changes and rehabilitation activities. Pain management in burn patients is primarily achieved by potent pharmacologic analgesics (e.g., opioids), but is necessarily complemented by nonpharmacologic techniques, including distraction or hypnosis. Immersive virtual reality provides a particularly intense form of cognitive distraction during such brief, painful procedures, and has undergone preliminary study by several research groups treating burn patients over the past decade. Initial reports from these groups are consistent in suggesting that immersive virtual reality is logistically feasible, safe and effective in ameliorating the pain and anxiety experienced in various settings of post-burn pain. Furthermore, the technique appears applicable to a wide age range of patients and may be particularly well-adapted for use in children, one of the most challenging populations of burn victims to treat. However, confirmation and extension of these results in larger numbers of patients in various types of burn-related pain is necessary to more clearly define the specific benefits and limitations of virtual reality analgesia in the burn care setting.
Editorial-Analytical Chemistry in the Undergraduate Curriculum (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEditorial-Analytical Chemistry in the Undergraduate CurriculumHerbert A. LaitinenCite this: Anal. Chem. 1979, 51, 1, 1Publication Date (Print):January 1, 1979Publication History Published online12 July 2002Published inissue 1 January 1979https://pubs.acs.org/doi/10.1021/ac50037a601https://doi.org/10.1021/ac50037a601research-articleACS PublicationsRequest reuse permissionsArticle Views52Altmetric-Citations-LEARN 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-Alertsclose Get e-Alerts
Extensible circuit-QED architecture via amplitude- and frequency-variable microwaves (2022)

We introduce a circuit-QED architecture combining fixed-frequency qubits and microwave-driven couplers. In the appropriate frame, the drive parameters appear as tunable knobs enabling selective two-qubit coupling and coherent-error suppression. We moreover introduce a set of controlled-phase gates based on drive-amplitude and drive-frequency modulation. We develop a theoretical framework based on Floquet theory to model microwave-activated interactions with time-dependent drive parameters, which we also use for pulse shaping. We perform numerical simulations of the gate fidelity for realistic circuit parameters, and discuss the impact of drive-induced decoherence. We estimate average gate fidelities beyond $99.9\%$ for all-microwave controlled-phase operations with gate times in the range $50-120\,\mathrm{ns}$. These two-qubit gates can operate over a large drive-frequency bandwidth and in a broad range of circuit parameters, thereby improving extensibility. We address the frequency allocation problem for this architecture using perturbation theory, demonstrating that qubit, coupler and drive frequencies can be chosen such that undesired static and driven interactions remain bounded in a multi-qubit device. Our numerical methods are useful for describing the time-evolution of driven systems in the adiabatic limit, and are applicable to a wide variety of circuit-QED setups.
Circulating p53 antibodies as early markers of oral cancer: correlation with p53 alterations. (1998)

p53 aberrations are early events in the pathogenesis of betel- and tobacco-related oral malignancies. Accumulation of p53 protein in oral lesions may elicit a humoral immune response against p53 protein in these patients. p53 antibodies (Abs) were analyzed in 183 sera obtained from patients with premalignant or malignant oral lesions and normal individuals by enzyme-linked immunoassay using recombinant p53 protein as antigen. These results were correlated with accumulation of p53 protein in patients' matched oral tissue specimens. Circulating p53 Abs were observed in 24 of 70 (34%) cancer patients and 15 of 50 (30%) patients with premalignant oral lesions. p53 Abs showed a significant association with increase in tumor size and dedifferentiation of tumors, factors indicative of poor prognosis. Expression of p53 protein was analyzed in 43 matched oral lesions (18 premalignant and 25 malignant cases). All the p53-seropositive patients (7 leukoplakia and 11 squamous cell carcinoma) showed elevated levels of p53 protein in matched oral lesions. However, the total number of patients seropositive for p53 Abs was lesser than that of patients exhibiting p53 protein accumulation in oral lesions. Four of the 63 normal healthy individuals who were heavy consumers of tobacco (smoking/chewing) and betel were found to be positive for p53 Abs. Detection of circulating p53 Abs in patients with premalignant oral lesions suggests that humoral immune response against p53 protein is an early event in oral oncogenesis and may be a surrogate marker for both p53 alteration and preclinical cancer.
Speaking on the record (2005)

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2005.
Managing Transport Energy (2007)

How can we provide clean, safe, sustainable energy supplies for transport systems in Britain, Europe and the world as a whole during the twenty-first century, despite rising population levels, increasing affluence and growing mobility? Managing Transport Energy reviews the effects of transport by focussing on the key factors which offer ways of decoupling transport from intensive energy use and shows how it is possible to analyse and model various scenarios. The overall approach is interdisciplinary - covering all aspects of managing ground transport energy. Technology driven issues, such as vehicle power-trains, fuels, future fuels are explained using extensive diagrams. ‘Softer’ issues such as car sharing, travel plans and mobility management are given equal coverage. Readers of this text should be to improve their understanding of the complex issues at stake as well as some of the potential solutions to reducing energy dependence in this growing field.
Activation regions in a yeast transposon have homology to mating type control sequences and to mammalian enhancers. (1985)

The DNA sequence of the Ty1 activating region from the CYC7-H2 mutant of Saccharomyces cerevisiae is presented. Analysis of the data revealed the presence of four simian virus 40-type enhancer core sequences. Two of the Ty1 enhancer cores are contiguous with sequences also homologous to the diploid control site at MAT alpha. We postulate that these two Ty1 regions of approximately equal to 30 base pairs are regulatory blocks, and we have analyzed deletions to ascertain whether they are necessary for effects of Ty1 on adjacent gene expression. We found that activation is lost when a restriction fragment encompassing both postulated regulatory blocks is deleted. Deletion of restriction fragments that remove only one of the two regulatory blocks has little or no effect on Ty1 activating ability in haploid yeast cells or on repression of this function in diploid yeast cells. Because the most significant internal homologies in the restriction fragments analyzed are the putative regulatory blocks, these observations suggest that enhancer-like sequences are involved in cell-type control of Ty1 effects on gene expression.
Rasterized Bounding Volume Hierarchies (2012)

Abstract We present the rasterized bounding volume hierarchy (RBVH), a compact data structure that accelerates approximate ray casting of complex meshes and provides adjustable level of detail. During construction, we identify subtrees of BVHs containing surfaces that can be represented by height fields. For these subtrees the conventional ray‐surface intersection, which possibly involves a large number of triangles, is replaced by a simple ray marching procedure to find the intersection with the surface. We describe GPU algorithms for construction, ray casting, and data querying of the RBVH that achieve comparable or higher performance than state of the art acceleration structures for triangle meshes. Moreover, RBVHs provide an inherent surface parameterization for storing data on the surfaces and natively handle triangle and point‐based surface representations. We also show that RBVHs support adaptive level‐of‐detail and can be combined with traditional BVHs to handle complex scenes.
Achieving Repeatability of Asynchronous Events in Wireless Sensor Networks with EnviroLog (2006)

Abstract : Sensing events from dynamic environments are normally asynchronous and non-repeatable. This lack of repeatability makes it particularly difficult to statistically evaluate the performance of sensor network applications. Hence, it is essential to have the capability to capture and replay sensing events, providing a basis not only for system evaluation, but also for realistic protocol comparison and parameter tuning. To achieve that, we design and implement EnviroLog, a distributed service that improves repeatability of experimental testing of sensor networks via asynchronous event recording and replay. To use EnviroLog, an application programmer needs only to specify two types of simple annotations to the source code. Automatically, the preprocessor embeds EnviroLog into any desired level of an event-driven architecture. It records all events generated by lower layers and can replay them later to upper layers on demand. We validate the accuracy and performance of recording and replay through a set of microbenchmarks, using the latest XSM platforms. We further demonstrate the strength of EnviroLog in system tuning and performance evaluation for sensor network applications in an outdoor environment with 37 XSMs.
Efecto del fotoperiodo en las truchas (Oncorhynchus mykiss) sobre la maduración gonadal para inducir al desove fuera de estación reproductiva (2023)

El objetivo de esta investigación fue evaluar el fotoperiodo con luz artificial en las truchas (Oncorhynchus mykiss) para la maduración sexual de las gónadas. Se trabajó con 240 reproductoras de 3 años, de segundo desove, que fueron sometidas al fotoperiodo con luz artificial. Los tratamientos fueron T0 con luz natural, T1 con 18HL:6H0 (fotoperiodo largo) y el T2 con 18HO:6HL (fotoperiodo corto), durante 6 meses. Se utilizó la energía fotovoltaica para cada cámara oscura, adaptada previamente. A los 3 meses, se realizó el cambio de fotoperiodo para el T1, fotoperiodo horas luz corto y T2 fotoperiodo de horas luz largo. La evaluación del desarrollo gonadal se realizó de manera manual mediante masajes ventrales en dirección opérculo-caudal. Cuando se obtuvieron las ovas maduras, se procedió a realizar el proceso de fertilización. Para ello, se utilizó semen de neomachos que fueron madurados con diferentes medios maduración, por 2 horas a 4 °C. Posteriormente, se realizó la fertilización a partir de ciertos parámetros. Los resultados no evidencian diferencias significativas (p<0.05) entre los tratamientos. Sin embargo, si la época de desove fue en diferentes meses para los tratamientos, para ambos tratamientos y en el testigo no se encontró óvulos maduros. Con respecto los siguientes parámetros número de ovas, volumen de ovas, total de ovas y el diámetro de ovas no fueron influenciados significativamente por los tratamientos (p-valor>0.05). Sin embargo, encontró una diferencia significativa que utilizaron diferentes medios maduración (p-valor<0.05).