gebhart/patrepeval huggingface dataset:
Online autoadmin (2007)

Existing solutions for the automated physical design problem require explicit invocations of tuning tools and critically depend on DBAs gathering representative workloads manually. In this demonstration, we show an alternative approach to the physical design problem. Specifically, we demonstrate a novel monitoring/tuning DBMS component that we prototyped in Microsoft SQL Server 2005 as a server-side extension. This component is always-on and continuously modifies the current physical design reacting to varying workload or data characteristics. Our solution imposes low overhead and takes into account storage constraints, update statements, and the cost to create physical structures.
Conversion of Guaiacol on Noble Metal Catalysts: Reaction Performance and Deactivation Studies (2014)

Guaiacol, a phenol derived compound produced by the thermal degradation of lignin, was selected as a model compound to study the catalytic hydrodeoxygenation (HDO) process for upgrading pyrolysis bio-oils. Guaiacol is among the major components of bio-oils; however, it is thermally unstable which leads to catalyst deactivation. In the present study, four noble metal catalysts (Pt, Pd, Rh, and Ru) supported on activated carbon were tested in a fixed-bed reactor at atmospheric pressure and their performance for the guaiacol HDO process was measured. Our results showed that, among the tested catalysts, Pt has higher deoxygenation activity and shows little deactivation for 5 h. Additionally, the operating temperature for the Pt catalyst was optimized and found to be 300 °C. Finally, results from catalyst characterization demonstrated that polyaromatic deposits, especially the condensed ring compounds, are the most likely cause for catalyst deactivation.
Isolation and Characterization of Clostridium difficile Toxin-Specific Single-Domain Antibodies (2012)

Camelidae single-domain antibodies (VHHs) are a unique class of small binding proteins that are promising inhibitors of targets relevant to infection and immunity. With VHH selection from hyperimmunized phage display libraries now routine and the fact that VHHs possess long, extended complementarity-determining region (CDR3) loop structures that can access traditionally immunosilent epitopes, VHH-based inhibition of targets such as bacterial toxins are being explored. Toxin A and toxin B are high molecular weight exotoxins (308 kDa and 269 kDa, respectively) secreted by Clostridium difficile that are the causative agents of C. difficile-associated diseases in humans and in animals. Here, we provide protocols for the rapid generation of C. difficile toxin A- and toxin B-specific VHHs by llama immunization and recombinant antibody/phage display technology approaches and for further characterization of the VHHs with respect to toxin-binding affinity and specificity and the conformational nature of their epitopes.
Growth-induced anisotropy in bismuth: Rare-earth iron garnets (1986)

The bismuth-doped rare-earth iron garnets, (R3−x−yBixPby)Fe5O12 (Bi:RIG, R=Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, and Y), were prepared under constant growth conditions to investigate the influence of ionic species on the bismuth-based growth-induced uniaxial anisotropy Kgu. The effect of ionic species on growth-induced anisotropy in Bi:RIG was not consistent with the ionic size model of site ordering. In particular, Bi:SmIG, Bi:EuIG, and Bi:TbIG displayed high growth-induced anisotropies, up to 331 000 erg/cm3 at room temperature for x≊0.5. The temperature dependence of these Kgu’s was somewhat higher than that of the well studied Bi:YIG. The site ordering of Bi can be modeled by assuming that small, low-oxygen-coordination BiO+3−2ww melt complexes have a strong site selectivity for small, high-oxygen coordination sites at the growth interface.
High Power Explosive with Good Sensitivity: A 2:1 Cocrystal of CL-20:HMX (2012)

A novel energetic cocrystal predicted to exhibit greater power and similar sensitivity to that of the current military standard explosive 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX) is presented. The cocrystal consists of a 2:1 molar ratio of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20), a powerful explosive too sensitive for military use, and HMX. A predicted detonation velocity 100 m/s higher than that of β-HMX, the most powerful pure form of HMX, was calculated for the cocrystal using Cheetah 6.0. In small-scale impact drop tests the cocrystal exhibits sensitivity indistinguishable from that of β-HMX. This surprisingly low sensitivity is hypothesized to be due to an increased degree of hydrogen bonding observed in the cocrystal structure relative to the crystals of pure HMX and CL-20. Such bonding is prevalent in this and other energetic cocrystals and may be an important consideration in the design of future materials. By being more powerful and safe to handle, the cocrystal presented is an attractive candidate to supplant the current military state-of-the-art explosive, HMX.
HBV 2021: New therapeutic strategies against an old foe (2021)

Hepatitis B virus (HBV) affects more than 250 million people worldwide, and is one of the major aetiologies for the development of cirrhosis and hepatocellular carcinoma (HCC). In spite of universal vaccination programs, HBV infection is still a public health problem, and the limited number of available therapeutic approaches complicates the clinical management of these patients. Thus, HBV infection remains an unmet medical need that requires a continuous effort to develop new individual molecules, treatment combinations and even completely novel therapeutic strategies to achieve the goal of HBV elimination. The following review provides an overview of the current situation in chronic HBV infection, with an analysis of the scientific rationale of certain clinical interventions and, more importantly, explores the most recent developments in the field of HBV drug discovery.
Inhibition of acute leukemia with attenuated Salmonella typhimurium strain VNP20009 (2020)

Acute leukemia is a common hematological malignancy. Despite recent promising progress, the prognosis of acute leukemia patients remains to be improved. New therapies are therefore still needed. Salmonella typhimurium has been shown to be highly effective as an anti-tumor agent in many solid cancer models, but it has not been applied in acute leukemia. Here, we report an attenuated Salmonella typhimurium strain, VNP20009, can induce apoptosis in multiple types of leukemia cells both in vivo and in vitro. Furthermore, VNP20009 significantly inhibited the proliferation of MLL-AF9-induced acute myeloid leukemia cells and prolonged the survival of the AML-carrying mice. VNP20009 restored the counts of white blood cell (WBC) and its five subsets in peripheral blood (PB) to near-physiological values, and elevated the levels of certain cytokines, such as tumor necrosis factor-α (TNF-α), leukemia inhibitory factor (LIF), interferon-γ (IFN-γ), chemokine C-X-C motif ligand-10 (CXCL-10) and C-C motif ligand-2 (CCL-2). Moreover, the ratio of immune cells, including natural killer cells (NKs), CD4<sup>+</sup> Th1-type cells and CD8<sup>+</sup> IFN-γ-producing effector T cells were highly upregulated in the AML mice treated with VNP20009. The results of the present study potentially provide an alternative therapeutic strategy for hematologic malignancies through boosting the innate and adaptive anti-tumor immunity.
Effect of tissue mechanical properties on cuff-based blood pressure measurements (2011)

This paper presents a 3D finite element upper arm model, validated by experiments as well as clinical data, used to study the error introduced in blood pressure measurements due to variability of arm tissue mechanical properties. The model consists of three separate cylindrical parts: soft tissue, bone and brachial artery. The artery volume changes under the cuff are used to represent the cuff pressure oscillations for analyzing blood pressure measurements. These oscillation trends are identical to observed clinical data. Also an upper arm simulator is designed and built for model validation. The model shows that the variation of soft tissue compressibility introduces an error up to 5% in blood pressure measurements. It is also revealed that the variation of the brachial artery and arm tissue stiffness has an insignificant effect on oscillometric blood pressure measurement method.
SaferCity: A System for Detecting and Analyzing Incidents from Social Media (2013)

This paper presents a system to identify and characterise public safety related incidents from social media, and enrich the situational awareness that law enforcement entities have on potentially-unreported activities happening in a city. The system is based on a new spatio-temporal clustering algorithm that is able to identify and characterize relevant incidents given even a small number of social media reports. We present a web-based application exposing the features of the system, and demonstrate its usefulness in detecting, from Twitter, public safety related incidents occurred in New York City during the Occupy Wall Street protests.
Face detection in the near-IR spectrum (2003)

Face detection is an important prerequisite step for successful face recognition. Face detection methods reported in the literature are far from perfect and deteriorate ungracefully where lighting conditions cannot be controlled. We propose a method that could potentially outperform state-of-the-art face detection methods in environments with dynamic lighting conditions. The approach capitalizes upon our near-IR skin and face detection methods reported elsewhere. It ascertains the existence of a face within a skin region by finding the eyes and eyebrows. The eye-eyebrow pairs are determined by extracting appropriate features from multiple near-IR bands. In this paper we introduce a novel feature extraction method we call <i>dynamic integral projection</i>. The method is relatively simple but highly effective because the processing is constrained within the skin region and aided by the near-IR phenomenology.
Free form V-groove reflector design with the SMS method (2009)

The Simultaneous Multiple Surface design method (SMS) is applied to the design of free-form V-groove reflectors. The general design problem is to achieve perfect coupling of two wavefronts after two reflections at the groove, no matter which side of the groove the rays hit first. All possible 2D designs are listed and used as a basis for the 3D free-form reflector analysis. The extension to the 3D case is given, and illustrative particular canonical examples are developed. Besides the theory and design work, first prototypes were produced of a mirrorless TIR device using V-grooves that emulates a parabolic reflector. The experimental measurements of the TIR reflector show reflectance up to 98%.
Efficient Magnetron With a Virtual Cathode (2016)

We use particle-in-cell (PIC) computer simulations to demonstrate high-efficiency operation of a magnetron with diffraction output (MDO) that uses a virtual cathode in the interaction space instead of a physical cathode. The cathode generating the electron beam is external to the MDO interaction space and, therefore, is immune from electron bombardment, pulse shortening, decreasing electron efficiency, and frequency shift attributed to expanding cathode plasma. Electronic efficiencies comparable to those achieved with the MDO with a transparent cathode have been achieved in the simulations.
In situ detection of individual mRNA molecules with single nucleotide resolution (2009)

The human body contains a variety of different cell types that share a common genome, but differ in how they use the information encoded therein. Variation in molecular content exists even at the level of individual cells, and to provide deeper insight into complex cellular processes methods that permit analysis of each cell on its own are needed. This thesis presents molecular methods for localized detection of individual nucleic acid molecules. The developed methods are based on padlock probes and target-primed rolling circle amplification. Single-molecule detection sensitivity in combination with single-nucleotide genotyping selectivity enables detection of allelic DNA variants and closely related target sequences directly in cells. Padlock probes further enable multiplex detection of targets, and in combination with image analysis quantitative molecular data for individual cells can be acquired for large cell populations at a resolution that no other in situ detection method can provide at present. In this thesis, the in situ target-primed rolling circle amplification technique was first used for genotyping of a point mutation in the mitochondrial genome with padlock probes. This displayed mitochondrial DNA heterogeneity in cell populations. Application of the method on comet assay preparations showed that mitochondrial genomes are lost from these samples prior to analysis. Nuclear DNA targets, however, can be efficiently detected in corresponding samples. Padlock probes and rolling circle amplification are thus an attractive alternative to FISH analysis for localized DNA detection in comet assay samples. A method was also developed for localized detection of individual mRNA molecules with padlock probes and rolling circle amplification. This method provides unique possibilities to genotype allelic variants of transcripts in situ. mRNA expression is associated with substantial cell-to-cell variation and our presented method permits simultaneous visualization of multiple transcripts directly in complex tissue samples. Application of the methods presented in this thesis will enable new types of studies of biological samples from both normal and disease states.
Phased Array System Design and Modeling (2007)

This paper describes a hardware architecture for a phase array system implemented at 2.425 GHz, discusses beam formation with mutual coupling effects, modulation formats, and provides a test bench for automated testing of the phase array system
Progression of Behavioral and CNS Deficits in a Viable Murine Model of Chronic Neuronopathic Gaucher Disease (2016)

To study the neuronal deficits in neuronopathic Gaucher Disease (nGD), the chronological behavioral profiles and the age of onset of brain abnormalities were characterized in a chronic nGD mouse model (9V/null). Progressive accumulation of glucosylceramide (GC) and glucosylsphingosine (GS) in the brain of 9V/null mice were observed at as early as 6 and 3 months of age for GC and GS, respectively. Abnormal accumulation of α-synuclein was present in the 9V/null brain as detected by immunofluorescence and Western blot analysis. In a repeated open-field test, the 9V/null mice (9 months and older) displayed significantly less environmental habituation and spent more time exploring the open-field than age-matched WT group, indicating the onset of short-term spatial memory deficits. In the marble burying test, the 9V/null group had a shorter latency to initiate burying activity at 3 months of age, whereas the latency increased significantly at ≥12 months of age; 9V/null females buried significantly more marbles to completion than the WT group, suggesting an abnormal response to the instinctive behavior and an abnormal activity in non-associative anxiety-like behavior. In the conditional fear test, only the 9V/null males exhibited a significant decrease in response to contextual fear, but both genders showed less response to auditory-cued fear compared to age- and gender-matched WT at 12 months of age. These results indicate hippocampus-related emotional memory defects. Abnormal gait emerged in 9V/null mice with wider front-paw and hind-paw widths, as well as longer stride in a gender-dependent manner with different ages of onset. Significantly higher liver- and spleen-to-body weight ratios were detected in 9V/null mice with different ages of onsets. These data provide temporal evaluation of neurobehavioral dysfunctions and brain pathology in 9V/null mice that can be used for experimental designs to evaluate novel therapies for nGD.
Thed Optimum Optical Geometry for Recording a Full Color Transmission type Holographic Screen of Larged Size (2000)

The main problem of image projection on a transmission type holographic screen is color sepa-ration. And it can be overcome by using a long narrow slit type diffuser as a source of the object beam when we record the screen. But that screen is not optimized and so needs changing several conditions. To set up the system many complicate things should be taken into accounted so it is very important to analyze the basic structure by simple concepts and calculations. We designed the system so that recording and projection axis coincide in one line and showed that the analysis of the system is very simple. We did it by a 1st order paraxial approximation calculation and it was good enough to describe the system. The photo-emulsion layer shrinks after processing of the hologram. It induced unsatisfactory color matching at the viewing zone. To overcome this effect, we pre-checked the shrinkage rate of an emulsion layer by experiments and modified the recording set up to compensate for the amount of shrinkage.
Separation of Genomic DNA from Plasmid DNA by Selective Renaturation with Immobilized Metal Affinity Capture (2005)

In contrast to proteins, many nucleic acids can undergo reversible modification of their conformations, and this flexibility can be used to facilitate purification. Selective renaturation with capture is a novel method of removing contaminating genomic DNA from plasmid samples. Plasmid DNA quickly renatures after thermal denaturation and cooling (or alkaline denaturation followed by neutralization), whereas genomic DNA remains locally denatured after rapid cooling in mismatch-stabilizing high ionic strength buffer. Partially denatured genomic DNA can be selectively bound to a metal chelate affinity adsorbent through exposed purine bases, while double-stranded renatured plasmid DNA is not bound. Using this method we have readily achieved 1,000,000-fold clearance of 71 wt % contaminating E. coli genomic DNA from plasmid samples.
Urine Proteomics Biomarkers in Renal Transplantation: An Overview (2009)

A major goal of clinical proteomics was to identify biomarkers that can aid in the diagnosis and prognosis of different conditions. These biomarkers will not only assist the clinician in the diagnosis of a disease but they will also give directions as to which therapy may be more appropriate for each patient, thus contributing to the development of personalized medicine. This review discusses the current concepts in urine proteomics aimed at identifying predictive biomarkers that could detect the presence of acute rejection or chronic allograft dysfunction early on and for instance be used to personalize immunosuppressive therapies for kidney transplant patients.
Engineering a Glucosamine-6-phosphate Responsive <i>glmS</i> Ribozyme Switch Enables Dynamic Control of Metabolic Flux in <i>Bacillus subtilis</i> for Overproduction of <i>N</i>-Acetylglucosamine (2018)

Bacillus subtilis is a typical industrial microorganism and is widely used in industrial biotechnology, particularly for nutraceutical production. There are many studies on the static metabolic engineering of B. subtilis, whereas there are few reports on dynamic metabolic engineering due to the lack of appropriate elements. Here, we established a dynamic reprogramming strategy for reconstructing metabolic networks in B. subtilis, using a typical nutraceutical, N-acetylglucosamine (GlcNAc), as a model product and the glmS (encoding glucosamine-6-phosphate synthase) ribozyme as an engineering element. First, a trp terminator was introduced to effectively release the glmS ribozyme feedback inhibition. Further, we engineered the native glucosamine-6-phosphate (GlcN6P) responsive glmS ribozyme switch to dynamically control the metabolic flux in B. subtilis for overproduction of GlcNAc. With GlcN6P as a ligand, the native sensor glmS ribozyme is integrated at the 5'- of phosphoglucosamine mutase and 6-phosphofructokinase genes to decrease the flux dynamically toward the peptidoglycan synthesis and glycolysis pathway, respectively. The glmS ribozyme mutant M5 ( glmS ribozyme cleavage site AG → GG) with decreased ribozyme activity is integrated at the 5'- of glucose-6-phosphate isomerase gene to increase the flux dynamically toward the GlcNAc synthesis pathway. This strategy increased the GlcNAc titer from 9.24 to 18.45 g/L, and the specific GlcNAc productivity from 0.53 to 1.21 g GlcNAc/g cell. Since GlcN6P is involved in the biosynthesis of various products, here the developed strategy for multiple target dynamic engineering of metabolic pathways can be generally used in B. subtilis and other industrial microbes for chemical production.
Opioid receptor delta as a global modulator of skin differentiation and barrier function repair (2015)

In this research, we have demonstrated in vitro (on inflamed reconstructed human epidermis, RHE) and in vivo (on human aged volunteers) that activation by natural agonist peptide of opioid receptor delta reduces the skin inflammation thus leading to improvement in epidermis differentiation and skin barrier properties.
Investigation of changes in thickness and reflectivity from layered retinal structures of healthy and diabetic eyes with optical coherence tomography (2011)

OCT is usually employed for the measurement of retinal thickness. However, coherent reflected light carries more information characterizing the optical properties of tissue. Therefore, optical property changes may provide further information regarding cellular layers and early damage in ocular diseases. We investigated the possibility of OCT in detecting changes in the optical backscattered signal from layered retinal structures. OCT images were obtained from diabetic patients without retinopathy (DM, n = 38 eyes) or mild diabetic retinopathy (MDR, n = 43 eyes) and normal healthy subjects (n = 74 eyes). The thickness and reflectivity of various layered structures were assessed using a custom-built algorithm. In addition, we evaluated the usefulness of quantifying the reflectivity of layered structures in the detection of retinal damage. Generalized estimating equations considering within-subject inter-eye relations were used to test for differences between the groups. A modified p value of <0.001 was considered statistically significant. Receiver operating characteristic (ROC) curves were constructed to describe the ability of each parameter to discriminate between the eyes of DM, MDR and healthy eyes. Thickness values of the GCL + IPL and OPL showed a significant decrease in the MDR eyes compared to controls. Significant decreases of total reflectance average values were observed in all layers in the MDR eyes compared with controls. The highest AUROC values estimated for the total reflectance were observed for the GCL+IPL, OPL and OS when comparing MDR eyes with controls. Total reflectance showed a better discriminating power between the MDR eyes and healthy eyes compared to thickness values. Our results suggest that the optical properties of the intraretinal layers may provide useful information to differentiate pathological from healthy eyes. Further research is warranted to determine how this approach may be used to improve diagnosis of early retinal neurodegeneration.