gebhart/patrepeval huggingface dataset:
Apoptosis Genes in Human Alveolar Macrophages Infected with Virulent or Attenuated Mycobacterium tuberculosis (2003)

Tumor necrosis factor (TNF)-alpha-dependent apoptosis of alveolar macrophages (AM) after infection with avirulent Mycobacterium tuberculosis (Mtb) results in bacillary death and the destruction of a growth niche for the pathogen. This response is minimized after infection with virulent strains of Mtb. To study the genetic control of Mtb-induced apoptosis, we used microarrays to interrogate the expression profile of infected human AM. Although we found variation in gene expression between different donors of AM, a set of genes were constant for each condition. A group of proapoptotic genes were downregulated after infection by virulent Mtb strain H37Rv, whereas infection with avirulent Mtb H37Ra led to a gene expression profile that would favor macrophage apoptosis. Neutralizing TNF in macrophage cultures infected with H37Ra changed the gene expression profile to one that resembled the profile of macrophages infected with H37Rv. These data reveal that apoptosis-related genes are regulated differently by virulent or attenuated Mtb strains, and are consistent with the hypothesis that virulent Mtb interfere with TNF death signaling. Given the importance of TNF in host defense against tuberculosis, the ability to repress the expression of genes activated by TNF may constitute a bacillary virulence mechanism.
The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections (2022)

We developed high-accuracy multi-parametric machine learning classifiers to differentiate bacterial from viral infections in LRTI patients of various ages. We demonstrated the predictive value of four easy-to-collect clinical variables which facilitate personalized and accurate clinical decision-making. We observed that nasal cavity microbiota correlate with the clinical variables and thus may not add significant value to diagnostic algorithms that aim to differentiate bacterial from viral infections.
Eliminating dielectric degradation of low-k organosilicate glass by trimethylchlorosilane treatment (2002)

The interaction between low-k organosilicate glass (OSG) and photoresist removal is investigated. O2 plasma ashing and chemical wet stripper are commonly performed to remove photoresist (PR) in integrated circuit fabrication. However, O2 plasma or wet stripper will attack function groups and cause Si–OH group formation in OSG film during PR removal processing. The Si–OH groups often lead to moisture uptake and consequently dielectric degradation will occur in OSG film. Trimethylchlorosilane (TMCS) treatment can negate the damage in the OSG film after the PR removal process. In addition, chemical TMCS can react with Si–OH groups and reduces moisture uptake so that the dielectric characteristic of OSG can be maintained. Hence, TMCS treatment is a promising method for photoresist removal.
Imprint of gravitational waves on the cosmic microwave background (1993)

Long-wavelength gravitational waves can induce significant temperature anisotropy in the cosmic microwave background. Distinguishing this from anisotropy induced by energy density fluctuations is critical for testing inflationary cosmology and theories of large-scale structure formation. We describe full radiative transport calculations of the two contributions and show that they differ dramatically at angular scales below a few degrees. We show how anisotropy experiments probing large- and small-angular scales can combine to distinguish the imprint due to gravitational waves.
Prevention of postischemic tissue injury by controlled reperfusion: A preliminary study (2004)

Restoration of arterial blood flow to severely and acutely ischemic extremities results in tissue necrosis and systemic-metabolic complications associated with multiorgan failure and death. Surgical revascularization alone (SRA) was compared with revascularization and controlled reperfusion using standard cardiopulmonary bypass (R-CPB) in 41 patients with acute lower limb ischemia and ischemia-induced neurological dysfunction. The mean ischemia time was 17 ± 10 hours. Eighteen patients (44%) had unilateral femoral artery occlusion, 23 (56%) had distal aortic occlusion. Eleven patients (27%) presented ischemia-induced paraplegia. SRA was performed in 23 patients (56%), and R-CPB in 18 (44%). End-points were hospital mortality, lower limb amputation, the number of surgical fasciotomies, and the incidence of permanent neurological morbidity. Hospital mortality was 19.5%; it was 33% after SRA, and 5.5% with R-CPB (p = 0.007). R-CBP was superior to SRA in terms of amputation rate (0% vs. 21.7%, p = 0.056), number of fasciotomies performed (7% vs. 64%, p = 0.002), and neurological recovery (86% vs. 19%, p = 0.000). After acute lower limb ischemia controlled reperfusion using standard cardiopulmonary bypass techniques preserves skeletal muscle and nerve function and prevents local as well as systemic complications of postischemic restoration of bloodflow.
Fluidic Oscillators for Bluff Body Drag Reduction in Water (2016)

The presented work examines the application of fluidic oscillators for active flow control in water. The oscillators are installed into a bluff body to reduce the pressure induced drag force. Experiments in water are accompanied by challenges such as cavitation and scaling effects. However, the properties of the investigated oscillator design agree with other publications with air as working fluid. Therefore, the transferability between different working fluids can be used for parametrization and scaling. Cavitation is detected at the external nozzle by means of hydrophone measurements. No significant influence on the natural oscillation of the fluidic oscillators and on the efficacy of the actuation is detected. The measured momentum agrees well with theoretical values. Based on these bench tests, the feasibility of the actuation is proven by towing tank measurements. The net drag of the bluff body is considerably reduced by the actuation. The drag improvements agree well with previous wind tunnel experiments on the same model.
Production of a Micro-Scale Linear Density Wedge (1978)

In the evaluation of conventional photographic imaging systems the non-linearity of the macroscopic curve can easily be dealt with by examining the "effective exposure" rather than expressing the density or transmittance. Dealing with the nonlinearities on a microscopic level, however, is very difficult since they result from development adjacency effects. A tool was made using a "V-shaped" groove design by G.W. Schumann which consists of a series of microscopic linear density wedges. The density wedges were made by filling V-cut grooves in a high quality acrylic plastic with a carbon-epoxy dispersion. The density wedges have been produced at the frequencies of 0.98. cy/mm and 0.57 cy/mm. These wedges have effective diffuse density ranges between 0.21 and 1.18. Their density gradient has been varied from .28 to 2.58 density units per mm. The wedges were then tested for their practicality for use in image evaluation. It was found that the characteristic curve for a small image area with a low surrounding density is higher in contrast and shifted to a higher speed when compared to a conventionally produced curve. When the micro scale density wedges were imaged with a high surrounding density, the results were not significantly different from those obtained with the conventional step wedge. There are several drawbacks attributed to the V-groove design that are discussed. The results from the practical application tests, however, suggest that there is significant merit for the micro scale wedges for use in the study of chemical adjacency effects. The micro-scale continuous density wedges are found to present a new concept to sensitometry where the characteristic curve can be related to some of the adjacency effects encountered in specific applications.
Workflow agents (1998)

Software agents as user agents, resource agents, and brokers may be able to enhance usefulness of workflow applications. Workflow technology is important to network computing because workflows exist naturally wherever distributed resources are interrelated. The problem with current workflow technology is that it is often too rigid. The lack of freedom accorded to human participants causes workflow management systems to appear unfriendly. As a result, they are often ignored or circumvented. This rigidity also causes productivity losses by making it harder to accommodate the flexible, ad hoc reasoning of human intelligence. Another challenge is that system requirements are rarely static. Software agents promise to address these challenges. The roles of greatest interest to a workflow setting are user agents, resource agents, and brokers. When a workflow is constituted in terms of distinct roles that agents can instantiate, the agents can be set up to respect the constraints of their users and resources. User agents negotiate with one another and with resource agents to ensure that global constraints are not violated and that global efficiencies can be achieved. Agents can include functionality to identify different kinds of exception conditions and react appropriately, possibly by negotiating a special sequence of actions. More importantly, agents can learn from repeated instances of the same kinds of exceptions. With this learning ability, agents can process the updated set of constraints when system requirements change.
Using security metrics coupled with predictive modeling and simulation to assess security processes (2009)

It is hard for security practitioners and decision-makers to know what level of protection they are getting from their investments in security, especially when they have invested in a number of technologies and processes which interact and combine together. It is even harder to estimate how well these investments can be expected to protect their organizations in the future as security policies, regulations and the threat environment are constantly changing. In this paper we propose that for measuring the effectiveness of security processes in large organizations, a greater emphasis needs to be put on process-based metrics, in contrast to the more commonly used symptomatic lagging indicators. We show, by means of two case studies, how these process-based metrics can be combined with executable, predictive models, based on a sound mathematical foundation, to both assess organizations' security processes under current conditions and predict how well they are likely to perform in potential future scenarios, which may include changes in working practices, policies or threat levels, or new investments in security. We present two case studies, in the areas of vulnerability threat management, and identity and access management, as significant examples to illustrate how this modeling and simulation-based approach can be used to provide a rich picture of how well existing security processes are protecting the organization and to answer "what-if" questions, such as exploring the effects of a change in security policy or an investment in new security technology. Our approach enables the organization to apply the metrics that are most relevant to its business, and provide a comprehensive view that shows the benefits and losses to the different stakeholders.
Tri-Band Mm-wave Directional Channel Measurements in Indoor Environment (2018)

A measurement campaign has been carried out in a reference indoor environment - a medium-size meeting room - using an ultra-wideband channel sounder operating at 3 different frequency bands: 10 GHz, 60 GHz and 300 GHz. Automatic rotational units are used at Tx and Rx side to perform a full horizontal scanning with directional antennas, in order to achieve a double-directional channel characterization. Preliminary results show that multipath is mainly affected by few single or double-bounce components, and significant contributions may come from objects other than the walls, e.g. TV monitor and entrance door. Most of the contributions are clearly identifiable at all the considered frequencies, although they appear to be stronger at 60 GHz compared to 10 GHz. The radio channel's multipath richness appears to be frequency dependent, and in particular it decreases when comparing 60 GHz to 300 GHz.
A novel class of allosteric ligands modulating TRPA1: discovery of a switch in agonist‐antagonist function (1061.7) (2014)

TRPA1 functions as a ligand‐gated cation channel in sensory neurons and is an important drug discovery target for identification of novel analgesics. We report identification of a novel structural class of ligands reversibly modulating TRPA1 channel function. Using intracellular calcium measurement and whole cell patch clamp recording of HEK293 cells expressing human TRPA1, we characterized the structure‐activity relationships among a group of amino‐triarylmethane analogs. A minimal structural change switched a full agonist to antagonist and small changes in side chain substituents in the same ring greatly altered affinity among antagonists. The agonists, ALGX‐2014 and ALGX‐2015, only elicited TRPA1 currents when applied extracellularly. Their stimulatory effect was blocked by TRPA1 antagonists and unaffected by substituting the three cysteine residues of TRPA1 critical for covalent stimulation by electrophilic agonists, such as AITC and PGJ2, with alanines, suggesting channel activation occurs in a noncovalent manner. This novel class of allosteric agonists and antagonist ligands also interact with other well‐defined TRPA1 ligands and results suggest a highly conserved binding site among TRPA1 and other members of the thermo‐TRP family which may reside in the channel domain. Grant Funding Source : Supported by NIDA grant (DA031516) to JMH and NIDDK grant (DK081654) to MXZ
Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, Beta, Delta, and Omicron variants (2022)

This research was funded by the Canadian Institutes of Health Research (CIHR). VIDO receives operational funding from the Government of Saskatchewan through Innovation Saskatchewan and the Ministry of Agriculture and from the Canada Foundation for Innovation through the Major Science Initiatives for its CL3 facility.
Data from Predictive Signatures Inform the Effective Repurposing of Decitabine to Treat KRAS–Dependent Pancreatic Ductal Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Mutated KRAS protein is a pivotal tumor driver in pancreatic cancer. However, despite comprehensive efforts, effective therapeutics that can target oncogenic KRAS are still under investigation or awaiting clinical approval. Using a specific KRAS–dependent gene signature, we implemented a computer-assisted inspection of a drug–gene network to &lt;i&gt;in silico&lt;/i&gt; repurpose drugs that work like inhibitors of oncogenic KRAS. We identified and validated decitabine, an FDA-approved drug, as a potent inhibitor of growth in pancreatic cancer cells and patient-derived xenograft models that showed KRAS dependency. Mechanistically, decitabine efficacy was linked to KRAS–driven dependency on nucleotide metabolism and its ability to specifically impair pyrimidine biosynthesis in KRAS–dependent tumors cells. These findings also showed that gene signatures related to KRAS dependency might be prospectively used to inform on decitabine sensitivity in a selected subset of patients with KRAS–mutated pancreatic cancer. Overall, the repurposing of decitabine emerged as an intriguing option for treating pancreatic tumors that are addicted to mutant KRAS, thus offering opportunities for improving the arsenal of therapeutics for this extremely deadly disease.&lt;/p&gt;Significance:&lt;p&gt;Decitabine is a promising drug for cancer cells dependent on RAS signaling.&lt;/p&gt;&lt;/div&gt;
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection (2020)

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.
Influence of interfacial copper on the room temperature oxidation of silicon (1996)

Thick (∼1.3 μm) oxide films were grown by room-temperature oxidation of silicon after low-energy copper-ion implantation. The structural properties of the silicon dioxide layer and the implanted silicon were characterized by Rutherford backscattering spectrometry and transmission-electron microscopy. During the room temperature oxidation a portion of the implanted copper resided on the surface and a portion moved with the advancing Si/SiO2 interface. This study revealed that the oxide growth rate was dependent on the amount of Cu present at the moving interface. The surface copper is essential for the dissociation of oxygen at the surface, and it is this oxygen that participates in the oxidation process. The resulting oxide formed was approximately stoichiometric silicon dioxide.
Composites with extremal thermal expansion coefficients (1996)

We design three-phase composites having maximum thermal expansion, zero thermal expansion, or negative thermal expansion using a numerical topology optimization method. It is shown that composites with effective negative thermal expansion can be obtained by mixing two phases of positive thermal expansions with a void phase. We also show that there is no mechanistic relationship between negative thermal expansion and negative Poisson’s ratio.
Engineering Gender-Inclusivity into Software: Tales from the Trenches (2019)

Although the need for gender-inclusivity in software itself is gaining attention among both SE researchers and SE practitioners, and methods have been published to help, little has been reported on how to make such methods work in real-world settings. For example, how do busy software practitioners use such methods in low-cost ways? How do they endeavor to maximize benefits from using them? How do they avoid the controversies that can arise in talking about gender? To find out how teams were handling these and similar questions, we turned to 10 real-world software teams. We present these teams experiences "in the trenches," in the form of 12 practices and 3 potential pitfalls, so as to provide their insights to other real-world software teams trying to engineer gender-inclusivity into their software products.
A study of the alkaline proteases secreted by different Aspergillus species (1993)

Strains from several species of Aspergillus were grown in the presence of soluble collagen, and the major secreted proteins present in the culture fluid were examined for proteolytic activity. The possibility of relatedness among the alkaline proteases secreted by Aspergillus was studied by probing extracts from the various species with polyclonal antisera raised to the isolated alkaline proteases of A. fumigatus and A. oryzae. The pathogenic species A. flavus, A. terreus and A. nidulans hydrolyse collagen and were found to secrete an alkaline protease related to that of Aspergillus fumigatus. In contrast, A. niger and non-pathogenic species such A. glaucus, A. versicolor and A. clavatus were unable to degrade collagen in vitro. These findings suggest a possible pathogenic role for the secreted alkaline proteases of Aspergillus species.
A low-disturbance diagnostic function integrated in the PV arrays' MPPT algorithm (2011)

This paper focuses on the estimation of series resistance changes for flat silicone PV panels or arrays during operation, without moving the operating point far away from the Maximum Power Point <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> . The method is based on the measurement of the slope of the IV curve at a current level that differs from the short-circuit current with a fixed value, regardless of irradiance conditions. The method causes less power loss and power ripple due to measurements and it is easily integrated in a hill-climbing MPPT algorithm.
Electrical potential accelerates the E1P(Na)----E2P conformational transition of (Na,K)-ATPase in reconstituted vesicles. (1986)

We have used renal (Na,K)-ATPase, covalently labeled with fluorescein, and phospholipid vesicles reconstituted with labeled enzyme, to detect conformational transitions induced by acetyl phosphate in the presence of Mg2+ and Na+ ions. Equilibrium fluorescence measurements show quenching of the fluorescein fluorescence, which is thought to reflect conversion of the initial E1 form to the phosphorylated E2P form. These fluorescence changes occur on inside-out-oriented pumps. The rates of acetyl phosphate-induced fluorescence changes have been measured using a stopped-flow fluorimeter. The rate of fluorescence quenching (1.5-3 s-1) is a measure of the rate of the E1P(Na)----E2P transition. The quenching is preceded by a fast fluorescence increase (12.3 +/- 4 s-1) associated with phosphorylation of E1 to E1P(Na), shown clearly in experiments with enzyme treated with oligomycin. Oligomycin greatly reduces the rate of the fluorescence quenching (0.044 +/- 0.01 s-1). Using potassium-loaded vesicles treated with valinomycin or lithium-loaded vesicles treated with Li+ ionophore N,N'-diheptyl-N,N'-didiethyl ether, 5,5-dimethyl-3,7-dioxanonanediamide in order to induce electrical diffusion potentials, negative inside, the rates of the fluorescence quenching are accelerated by up to 4-fold. The experiments demonstrate that the conformational transition E1P(Na)----E2P, associated with transport of 3 Na+ ions, is a voltage-sensitive reaction, carrying a net positive charge. This confirms a prediction based on transport experiments. In experiments with fluorescein-labeled (Na,K)-ATPase, the use of acetyl phosphate rather than ATP, which does not bind, provides a valuable tool to detect fluorescence signals accompanying steps in the turnover cycle.
THICKNESS DEPENDENT PROPERTIES OF BARIUM STRONTIUM TITANATE THIN-FILM VARACTORS (2010)

Ba0.6Sr0.4TiO3 (BST) thin-films with large dielectric tunability as high as 5.8:1 were obtained using a large area pulsed laser deposition process, with low loss-tangents below 0.01 at zero-bias and 10 GHz. This paper summarizes experimental results obtained on large area processed BST thin film varactors. Varactors with 0.6 μm thick BST films exhibited large dielectric tunability, the relative dielectric permittivity at zero bias of 1280 tuned to 220 at 20 V, at an electric field of 333 kV/cm. The leakage current through the BST film was below 1 nA up to 10 V dc bias. The Quality factor (Q) exceeded 500 at relatively low 10 V dc bias for both 0.6 and 1 μm thick BST varactors.