gebhart/patrepeval huggingface dataset:
The metabolic regulator CodY links L isteria monocytogenes metabolism to virulence by directly activating the virulence regulatory gene prfA (2014)

Metabolic adaptations are critical to the ability of bacterial pathogens to grow within host cells and are normally preceded by sensing of host-specific metabolic signals, which in turn can influence the pathogen's virulence state. Previously, we reported that the intracellular bacterial pathogen Listeria monocytogenes responds to low availability of branched-chain amino acids (BCAAs) within mammalian cells by up-regulating both BCAA biosynthesis and virulence genes. The induction of virulence genes required the BCAA-responsive transcription regulator, CodY, but the molecular mechanism governing this mode of regulation was unclear. In this report, we demonstrate that CodY directly binds the coding sequence of the L. monocytogenes master virulence activator gene, prfA, 15 nt downstream of its start codon, and that this binding results in up-regulation of prfA transcription specifically under low concentrations of BCAA. Mutating this site abolished CodY binding and reduced prfA transcription in macrophages, and attenuated bacterial virulence in mice. Notably, the mutated binding site did not alter prfA transcription or PrfA activity under other conditions that are known to activate PrfA, such as during growth in the presence of glucose-1-phosphate. This study highlights the tight crosstalk between L. monocytogenes metabolism and virulence, while revealing novel features of CodY-mediated regulation.
Ultrasound‐assisted Extraction of Gymnemic Acids from Gymnema sylvestre Leaves and its Effect on Insulin‐producing RINm‐5 F β Cell Lines (2014)

Response surface methodology was successfully used to improve the extraction of gymnemic acids from G. sylvestre leaves. The ultrasound-assisted extraction process may be a better alternative to prepare such herbal extracts because it saves time and may prevent excess degradation of the target analytes.
<title>Confocal imaging through scattering media with a volume holographic filter</title> (2000)

The use of a volume holographic filter as collector element in a confocal system imaging through scattering (turbid) material is described. We show that the penetration depth of the volume holographic system is de-coupled from the scatter noise discrimination properties, and is potentially more advantageous than the traditional confocal microscope. Since the volume-holographic filter is a matched-filter, the penetration depth is dependent on the mismatch of the refractive index of the sample being imaged relative to the recording conditions. We present a method to overcome this limitation based on using a pre-compensating index matching film during the recording of the volume hologram. An improvement of the penetration depth is shown experimentally.
Minimizing Carbon Footprint by Smart Sustainable Reservoir Management (2021)

Abstract Sustainability and reducing carbon footprint has attracted attention in the oil and gas industry to optimize recovery and increase efficiency. The 4th Industrial Revolution has made an enormous impact in the oil and gas industry and on analyzing carbon footprint reduction opportunities. This allows classification of various reservoir operations, installation of permanent sensors and robots on the field, and reduction of overall power consumption. We present an overview of new AI approaches for optimizing reservoir performance while reducing their carbon footprint. We will outline the significant carbon emissions contributors for field operations and how their impact will change throughout the production's lifecycle from a reservoir. Based on this analysis, we will outline via an AI-driven optimization framework areas of improvement to reduce the carbon footprint considering the uncertainty. We analyzed the framework's performance on a synthetic reservoir model with several producing wells, water, and CO2 injecting wells. Beneficial in reducing carbon emissions from the field is the reuse and injection of CO2 for enhancing hydrocarbon production from the reservoir. One hundred different scenarios were then investigated utilizing an innovative autoregressive network model to determine the impact of these components on the overall carbon emission of the field and determine its uncertainty. The conclusions from the analysis were then incorporated into a data-driven optimization routine to minimize carbon footprint while maximizing reservoir performance. The final optimization results of the showcase outlined the ability to reduce the carbon footprint significantly.
The Second Synthetic Microstructures in Biological Research Conference. (1988)

Not available.
Antibacterial Activity of Polymer Coated Cerium Oxide Nanoparticles (2012)

Cerium oxide nanoparticles have found numerous applications in the biomedical industry due to their strong antioxidant properties. In the current study, we report the influence of nine different physical and chemical parameters: pH, aeration and, concentrations of MgSO(4), CaCl(2), KCl, natural organic matter, fructose, nanoparticles and Escherichia coli, on the antibacterial activity of dextran coated cerium oxide nanoparticles. A least-squares quadratic regression model was developed to understand the collective influence of the tested parameters on the anti-bacterial activity and subsequently a computer-based, interactive visualization tool was developed. The visualization allows us to elucidate the effect of each of the parameters in combination with other parameters, on the antibacterial activity of nanoparticles. The results indicate that the toxicity of CeO(2) NPs depend on the physical and chemical environment; and in a majority of the possible combinations of the nine parameters, non-lethal to the bacteria. In fact, the cerium oxide nanoparticles can decrease the anti-bacterial activity exerted by magnesium and potassium salts.
SpecHammer: Combining Spectre and Rowhammer for New Speculative Attacks (2022)

The recent Spectre attacks have revealed how the performance gains from branch prediction come at the cost of weakened security. Spectre Variant 1 (v1) shows how an attacker-controlled variable passed to speculatively executed lines of code can leak secret information to an attacker. Numerous defenses have since been proposed to prevent Spectre attacks, each attempting to block all or some of the Spectre variants. In particular, defenses using taint-tracking are claimed to be the only way to protect against all forms of Spectre v1. However, we show that the defenses proposed thus far can be bypassed by combining Spectre with the well-known Rowhammer vulnerability. By using Rowhammer to modify victim values, we relax the requirement that the attacker needs to share a variable with the victim. Thus, defenses that rely on this requirement, such as taint-tracking, are no longer effective. Furthermore, without this crucial requirement, the number of gadgets that can potentially be used to launch a Spectre attack increases dramatically; those present in Linux kernel version 5.6 increases from about 100 to about 20,000 via Rowhammer bit-flips. Attackers can use these gadgets to steal sensitive information such as stack cookies or canaries, or use new triple gadgets to read any address in memory. We demonstrate two versions of the combined attack on example victims in both user and kernel spaces, showing the attack’s ability to leak sensitive data.
Colonic Endometriosis Mimicking Colon Cancer on a Virtual Colonoscopy Study: A Potential Pitfall in Diagnosis (2009)

Colonic endometriosis has been reported in the literature to mimic colon cancer. Patients can present with symptoms almost identical to colon cancer. We present an exemplary case of a woman who was found to have a mass on conventional colonoscopy. Virtual colonoscopy was instrumental in characterizing the obstructive sigmoid mass. A biopsy of the mass revealed sigmoid endometriosis.
Workload-driven floorplanning for MIPS optimization (2003)

An approach to early floorplanning in which optimization of a CPU chip floorplan is done in the context of a program benchmark (workload) is presented. The methodology integrates workload-driven cycles-per-instruction estimation into the traditional cycle-time evaluation process implied by an (early) floorplanning tool. This effectively adds an extra dimension to the floorplanning optimization cost function and search space, allowing superior MIPS-tuning of the VLSI chip.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficient techniques for comprehensive protection from memory error exploits (2005)

Despite the wide publicity received by buffer overflow attacks, the vast majority of today&amp;apos;s security vulnerabilities continue to be caused by memory errors, with a significant shift away from stacks-mashing exploits to newer attacks such as heap overflows, integer overflows, and format-string attacks. While comprehensive solutions have been developed to handle memory errors, these solutions suffer from one or more of the following problems: high overheads (often exceeding 100%), incompatibility with legacy C code, and changes to the memory model to use garbage collection. Address space randomization (ASR) is a technique that avoids these drawbacks, but existing techniques for ASR do not offer a level of protection comparable to the above techniques. In particular, attacks that exploit relative distances between memory objects aren&amp;apos;t tackled by existing techniques. Moreover, these techniques are susceptible to information leakage and brute-force attacks. To overcome these limitations, we develop a new approach in this paper that supports comprehensive randomization, whereby the absolute locations of all (code and data) objects, as well as their relative distances are randomized. We argue that this approach provides probabilistic protection against all memory error exploits, whether they be known or novel. Our approach is implemented as a fully automatic source-to-source transformation which is compatible with legacy C code. The address-space randomizations take place at load-time or runtime, so the same copy of the binaries can be distributed to everyone -- this ensures compatibility with today&amp;apos;s software distribution model. Experimental results demonstrate an average runtime overhead of about 11%.
Multimodal Nonlinear Optical Imaging for Sensitive Detection of Multiple Pharmaceutical Solid-State Forms and Surface Transformations (2017)

Two nonlinear imaging modalities, coherent anti-Stokes Raman scattering (CARS) and sum-frequency generation (SFG), were successfully combined for sensitive multimodal imaging of multiple solid-state forms and their changes on drug tablet surfaces. Two imaging approaches were used and compared: (i) hyperspectral CARS combined with principal component analysis (PCA) and SFG imaging and (ii) simultaneous narrowband CARS and SFG imaging. Three different solid-state forms of indomethacin-the crystalline gamma and alpha forms, as well as the amorphous form-were clearly distinguished using both approaches. Simultaneous narrowband CARS and SFG imaging was faster, but hyperspectral CARS and SFG imaging has the potential to be applied to a wider variety of more complex samples. These methodologies were further used to follow crystallization of indomethacin on tablet surfaces under two storage conditions: 30 °C/23% RH and 30 °C/75% RH. Imaging with (sub)micron resolution showed that the approach allowed detection of very early stage surface crystallization. The surfaces progressively crystallized to predominantly (but not exclusively) the gamma form at lower humidity and the alpha form at higher humidity. Overall, this study suggests that multimodal nonlinear imaging is a highly sensitive, solid-state (and chemically) specific, rapid, and versatile imaging technique for understanding and hence controlling (surface) solid-state forms and their complex changes in pharmaceuticals.
Characterization of the Asian Citrus Psyllid (2013)

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].
A metabolomic endotype of bioenergetic dysfunction predicts mortality in critically ill patients with acute respiratory failure (2021)

Acute respiratory failure (ARF) requiring mechanical ventilation, a complicating factor in sepsis and other disorders, is associated with high morbidity and mortality. Despite its severity and prevalence, treatment options are limited. In light of accumulating evidence that mitochondrial abnormalities are common in ARF, here we applied broad spectrum quantitative and semiquantitative metabolomic analyses of serum from ARF patients to detect bioenergetic dysfunction and determine its association with survival. Plasma samples from surviving and non-surviving patients (N = 15/group) were taken at day 1 and day 3 after admission to the medical intensive care unit and, in survivors, at hospital discharge. Significant differences between survivors and non-survivors (ANOVA, 5% FDR) include bioenergetically relevant intermediates of redox cofactors nicotinamide adenine dinucleotide (NAD) and NAD phosphate (NADP), increased acyl-carnitines, bile acids, and decreased acyl-glycerophosphocholines. Many metabolites associated with poor outcomes are substrates of NAD(P)-dependent enzymatic processes, while alterations in NAD cofactors rely on bioavailability of dietary B-vitamins thiamine, riboflavin and pyridoxine. Changes in the efficiency of the nicotinamide-derived cofactors' biosynthetic pathways also associate with alterations in glutathione-dependent drug metabolism characterized by substantial differences observed in the acetaminophen metabolome. Based on these findings, a four-feature model developed with semi-quantitative and quantitative metabolomic results predicted patient outcomes with high accuracy (AUROC = 0.91). Collectively, this metabolomic endotype points to a close association between mitochondrial and bioenergetic dysfunction and mortality in human ARF, thus pointing to new pharmacologic targets to reduce mortality in this condition.
Comportamiento de microcosmos agrícolas de microorganismos manipulados genéticamente (1994)

La ingenieria genetica ofrece las herramientas necesarias para la manipulacion de genes y la transferencia del adn recombinante a otros organismos. En este trabajo de tesis doctoral se ha explotado el potencial biodegradativo de las bacterias del genero pseudomonas para construir bacterias recombinantes que mineralizan alquiltoluenos del tipo de los etiltoluenos y 2,4,6- trinitrotulueno hasta anhidrido carbonico y agua. Los microorganismos recombinantes funcionan conforme a su diseno en condiciones de laboratorio, lo cual se ha puesto de manifiesto utilizando sustratos marcados con 14c y recogiendo 14co2. El comportamiento de los microorganismos recombinantes y el de sus parentales se ha estudiado en microcosmos constituidos por suelos agricolas de la provincia de granada ricos y pobres en materia organica. En general, no se han observado diferencias significativas en la capacidad de establecimiento, multiplicacion, supervivencia y funcionamiento de los organismos recombinantes y sus parentales no manipulados geneticamente. En general, los microorganismos se establecen y multiplican en suelos ricos en materia organica. En ambos tipos de suelos se ha observado transferencia intraespecifica del plasmido tol, aunque ello solo ocurre en condiciones de alta densidad celular.
In Memory of Our Mentor (2021)

This paper commemorates the life and work of L.A. Aksent'ev (1932–2020), the late professor of Kazan University. He was a brilliant mathematician, lecturer, and educator. L.A. Aksent'ev initiated the establishment of the well-known Russian Mathematical School of Complex Analysis. Over the years of the School's existence, its representatives have defended 31 candidate and 8 doctoral dissertations. Our research pathways are also associated with the School's activity.
Long-Lived Charge-Separated State Produced by Photoinduced Electron Transfer in a Zinc Imidazoporphyrin-C60Dyad (2003)

[reaction: see text] Photoexcitation of a zinc imidazoporphyrin-fullerene dyad with a short linkage results in formation of the charge-separated state by photoinduced electron transfer. The charge-separated state has a lifetime of 310 micros in benzonitrile at 278 K, which is the longest lifetime in solution ever reported for electron donor-acceptor-linked dyads.
Acoustic Microcannons: Toward Advanced Microballistics (2015)

Acoustically triggered microcannons, capable of loading and firing nanobullets (Nbs), are presented as powerful microballistic tools. Hollow conically shaped microcannon structures have been synthesized electrochemically and fully loaded with nanobullets made of silica or fluorescent microspheres, and perfluorocarbon emulsions, embedded in a gel matrix stabilizer. Application of a focused ultrasound pulse leads to the spontaneous vaporization of the perfluorocarbon emulsions within the microcannon and results in the rapid ejection of the nanobullets. Such Nbs "firing" at remarkably high speeds (on the magnitude of meters per second) has been modeled theoretically and demonstrated experimentally. Arrays of microcannons anchored in a template membrane were used to demonstrate the efficient Nbs loading and the high penetration capabilities of the ejected Nbs in a tissue phantom gel. This acoustic-microcannon approach could be translated into advanced microscale ballistic tools, capable of efficient loading and firing of multiple cargoes, and offer improved accessibility to target locations and enhanced tissue penetration properties.
Ultrasonic Attenuation in n-Type Ge. III. Effects of Magnetic Field (1984)

The magnetic field dependence of ultrasonic attenuation α( B ) has been measured for Sb-doped Ge over the impurity concentration region 3.1 ×10 16 to 3.3 ×10 17 cm -3 . It is found that the results are sensitive to the impurity concentration ( N ), in particular the difference in the attenuation coefficient with and without magnetic field, Δ α( B )= α( B ) - α(0), has a peak around 1.5 ×10 17 cm -3 as a function of the concentration. It is pointed out that the attenuation coefficient per electron in the D - band should increase with the magnetic field. For N >2 ×10 17 cm -3 , Δ α( B ) exhibits the behavior expected from a simple free electron gas model.
Examples of Applying RWE Causal-Inference Roadmap to Clinical Studies (2023)

AbstractA Real-World Evidence (RWE) scientific working group of the American Statistical Association Biopharmaceutical Section endeavors to elevate statistical practices of generating real-world evidence to support regulatory decision making. Randomized clinical trials have been the gold standard for evaluating the safety and efficacy of medical products. However, in many cases, their costs, duration, limited generalizability, and ethical or technical infeasibility might have motivated some to consider alternatives, such as real-world studies. Yet, the studies conducted in a real-world setting may be susceptible to the lack of randomization and the presence of confounding bias. To generate robust real-world evidence (RWE) from analyzing real-world data (RWD), we have proposed an RWE Causal Inference Roadmap with targeted learning. Three key steps in the roadmap are (1) define a target estimand that aligns with the causal estimand of the study objective; (2) select an efficient estimator for estimating the target estimand and an estimator of its uncertainty; and (3) evaluate the robustness of conclusions to violations of untestable causal assumptions. In this article, we demonstrate how to apply the roadmap to generate RWE using synthetic data based on a real oncology trial.KEYWORDS: Causal inference roadmapClinical trialsEstimandReal-world evidenceTMLE Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Study of deep electronic states in CdTe solar cells through the detection and DLTS treatment of slow transients (2005)

We have designed and built a temperature controlled sample stage with automated data acquisition software to detect and study thin film solar cell deep electronic states (DES) with capacitance transients (CTr) that have characteristic times ranging from seconds to hours. Our studies on thin film CdTe solar cells regularly detect DES with concentrations exceeding the doping level and with characteristic times in the tens to hundreds of seconds at room temperature. An example is given of how this high concentration of DES with slow characteristic times can provide misleading C-V profile measurements. Also described are preliminary observations of Meyer-Neldel rule behavior and DLTS analysis of CdTe cells with and without copper and CdCl/sub 2/ treatment.
Do Gastroenterologists Adhere to Diagnostic and Treatment Guidelines for Celiac Disease? (2011)

There is significant disagreement between nonexperts and experts in diagnosis and management of CD. Promotion of existing guidelines and further research is advised.
Synthesis of Conformationally Restricted Dinucleotides by Ring-Closing Metathesis (2000)

[reaction:see text] The ring-closing metathesis reaction has been used in the synthesis of conformationally restricted dinucleotides as well as a 3'-nucleotide analogue. From bis-allylic nucleoside phosphates obtained from simple nucleoside precursors, the synthesis of unsaturated cyclophosphates has been accomplished using either Grubbs' catalyst or an improved analogue. Hereby, the conformational freedom of the nucleic acid phosphordiester linkage has been efficiently constrained.
Framework for Abstraction and Control of Traffic Engineered Networks (2016)

Traffic Engineered networks have a variety of mechanisms to facilitate
the separation of the data plane and control plane. They also have a
range of management and provisioning protocols to configure and
activate network resources. These mechanisms represent key
technologies for enabling flexible and dynamic networking. Abstraction
of network resources is a technique that can be applied