gebhart/patrepeval huggingface dataset:
Assessment of<i>Chlamydia trachomatis</i>infection among Eastern European and West African women immigrants in South Italy (2011)

Chlamydia trachomatis infection is the most common sexually transmitted bacterial infection with an estimated incidence of 50 million cases in the world.1 The infection may remain asymptomatic or, if not treated, can lead to severe clinical manifestations including acute urethral syndrome, urethritis, bartholinitis, cervicitis, upper genital tract infections and perihepatitis.2 Despite the recognised need for early diagnosis and treatment of C trachomatis and other curable sexually transmitted infections, the strategies for detection of these infections are currently limited, …
Roots and Panicles of the C4 Model Grasses Setaria viridis (L). and S. pumila Host Distinct Bacterial Assemblages With Core Taxa Conserved Across Host Genotypes and Sampling Sites (2018)

Virtually all studied plant tissues are internally inhabited by endophytes. Due to their relevance for plant growth and health, bacterial microbiota of crop plants have been broadly studied. In plant microbiome research the root is the most frequently addressed environment, whereas the ecology of microbiota associated with reproductive organs still demands investigation. In this work, we chose the model grasses <i>Setaria viridis</i> and <i>Setaria pumila</i> to better understand the drivers shaping bacterial communities associated with panicles (representing a reproductive organ) as compared to those associated with roots. We collected wild individuals of both grass species from 20 different locations across Austria and investigated the bacterial assemblages within roots and ripe grain-harboring panicles by 16S rRNA gene-based Illumina sequencing. Furthermore, plant samples were subjected to genotyping by genetic diversity-focused Genotyping by Sequencing. Overall, roots hosted more diverse microbiota than panicles. Both the plant organ and sampling site significantly shaped the root and panicle-associated microbiota, whereas the host genotype only affected root communities. In terms of community structure, root-specific assemblages were highly diverse and consisted of conserved bacterial taxa. In contrast, panicle-specific communities were governed by <i>Gammaproteobacteria</i>, were less diverse and highly origin-dependent. Among OTUs found in both plant tissues, relative abundances of <i>Gammaproteobacteria</i> were higher in panicles, whereas <i>Rhizobiales</i> dominated root communities. We further identified core and non-core taxa within samples of both <i>Setaria</i> species. Non-core taxa included members of the <i>Saccharibacteria</i> and <i>Legionelalles</i>, while core communities encompassed eleven OTUs of seven bacterial orders, together with a set of ten panicle-enriched OTUs. These communities were widespread across root and panicle samples from all locations, hinting toward an evolved form of mutualism through potential vertical transmission of these taxa within <i>Setaria</i> species.
Fault or Frac? Source Mechanism and B-value Detection of Fault Fracturing - A Barnett Case Study (2011)

Microseismic monitoring is necessary to optimize hydraulic stimulation in unconventional reservoirs. Recognizing the difference between reactivating pre-existing joints and tectonic faults allows engineers to improve efficiency by avoiding stimulation of faults that may intersect aquifers and do not contribute to hydrocarbon production. Gutenberg and Richter (1954) proposed a relationship of size of events and number of events for a given area to be log N = A -bMs, where the slope b≈1 for tectonic fault earthquakes. Maxwell et al. (2009) and Downie et al. (2010) observed a slope of b≈2 for hydraulically stimulated fracture events. We show that source mechanism inversion of wide azimuth microseismic data acquired with buried array technology can provide this information in real time for each event. We do this on the basis that observed fracture and fault events exhibit unique source mechanisms, allowing us to calculate b values for thousands of events grouped by their source mechanism. The calculated slopes are consistent with previously published works regarding differentiation of fracture and fault activity. This knowledge will allow engineers to make more informed decisions to reduce the volume of fluids and proppants lost to reactivated faults.
Effect of Extraction Methodology on the Phytochemical Composition for Camelia sinensis “Powdered Tea Extracts” from Different Provenances (2022)

(1) Background: beverages based on extracts from Camellia sinensis are popular worldwide. Due to an increasing number of processed teas on the market, there is a need to develop unified classification standards based on chemical analysis. Meanwhile, phytochemical characterizations are mainly performed on tea samples from China (~80%). Hence, data on teas of other provenances is recommended. (2) Methods: in the present investigation, we characterized lyophilised extracts obtained by infusion, maceration and methanolic extraction derived from tea samples from China, Japan, Sri Lanka and Portugal by phytochemistry (catechins, oxyaromatic acids, flavonols, alkaloids and theanine). The real benefits of drinking the tea were analysed based on the bioavailability of the determined phytochemicals. (3) Results: the infusions revealed the highest total phenolic contents (TPC) amounts, while methanolic extracts yielded the lowest. The correlation matrix indicated that the levels of phenolic compounds were similar in the infusions and methanolic samples, while extractions made by maceration were significantly different. The differences could be partially explained by the different amounts of (-)-epigallocatechin gallate (EGCG), (-)-epicatechin gallate (ECG) and gallic acids (GA). The catechin percentages were significantly lower in the macerations, especially the quantity of EGCG decreases by 4- to 5-fold after this process. (4) Conclusions: the results highlight the importance of the processing methodology to obtain “instant tea”; the composition of the extracts obtained with the same methodology is not significantly affected by the provenance of the tea. However, attention should be drawn to the specificities of the Japanese samples (the tea analysed in the present work was of Sencha quality). In contrast, the extraction methodology significantly affects the phytochemical composition, especially concerning the content of polyphenols. As such, our results indicate that instant tea classification based on chemical composition is sensible, but there is a need for a standard extraction methodology, namely concerning the temperature and time of contact of the tea leaves with the extraction solvent.
On the surprising difficulty of simple things (2015)

Partitioning a dataset into ranges is a task that is common in various applications such as sorting [1,6,7,8,9] and hashing [3] which are in turn building blocks for almost any type of query processing. Especially radix-based partitioning is very popular due to its simplicity and high performance over comparison-based versions [6].
UV Spectrophotometers as Detectors for Size Exclusion Chromatography of Styrene—Acrylonitrile (SAN) Copolymers (1982)

The application of UV spectrophotometers to the analysis of styrene containing copolymers has been extensively reported in the literature. However, hypochromic effects and band shifts which result in deviations from Beer's Law have limited the use of UV detectors as mass or composition detectors in size exclusion chromatography applications. Deviations from Beer's Law for low conversion styrene-acrylonitrile copolymers in tetrahydrofuran have been experimentally investigated and compared with results previously reported in the literature. The behaviour of the extinction coefficient as a function of the copolymer composition is discussed in view of the information obtained from infrared and nuclear magnetic resonance measurements on the same polymers. As a result of this investigation, a quantitative correlation of the extinction coefficients of styrene-acrylonitrile copolymers with the length of the styrene sequences has been obtained which, in turn, allows for the use of UV spectrophotometers as sequence length detectors.
Utilisation des zéolithes comme filtre catalytique des polluants organiques persistants (2009)

This study deals with the catalytic oxidation of 1-methylnaphtalene (1. MN) a modele molecule of polycyclics aromatics hydrocarbons (PAHs) over USHY faujasite zeolite doped or not with platinium. The aim of this study was the use of the USHY zeolite as catalytic filter for the destruction of persistant organic pollutants (POPs) fromm incineration processes. In a first time we evaluated the potential of the USHY zeolite for the destruction of 1-MN alone into carbon dioxide and water, then in the presence of 1. 2-dichlorobenzene, a precursor of dioxin and finally in the presence of a complex mixture of HCI, NO, SO2 and NH3
Mercury in UK imported fish and shellfish and UK-farmed fish and their products (2003)

Total mercury concentrations were measured in fish and shellfish and their products imported into the UK and also in UK-produced farmed salmon and trout. Three hundred and thirty-six samples were collected using a two-stage sampling plan. The sample plan was weighted to reflect consumption, but with some bias towards fish that might accumulate higher levels of mercury, such as large predatory fish at the top of the food chain. The highest levels of total mercury were found in billfish (swordfish and marlin) and shark. Mercury concentrations in the five samples of fresh/frozen shark ranged from 1.006 to 2.200 mg kg(-1), all above the European Commission limit for the species, and concentrations in 20 samples of fresh/frozen billfish ranged from 0.153 to 2.706 mg kg(-1) with 13 samples above the 1.0 mg kg(-1) limit for the species. One sample of Antarctic ice fish was collected and had a mercury concentration of 0.664 mg kg(-1). The limit for this species was 0.5 mg kg(-1). One sample of fresh/frozen tuna out of the 20 collected had a mercury concentration above the limit of 1.0 mg kg(-1) (1.5 mg kg(-1)), but all other fresh tuna samples were well within the regulatory limit (average 0.4 mg kg(-1)). Mercury concentrations in canned tuna were lower with concentrations on average half that measured in fresh/frozen tuna. Mercury concentrations in UK-farmed salmon and trout were relatively low. The maximum concentration found in 46 samples of fresh/frozen or smoked trout and salmon was 0.103 mg kg(-1).
Detection and Quantitation of Genetically Modified Maize (Bt-176 Transgenic Maize) by Applying Ligation Detection Reaction and Universal Array Technology (2004)

We have applied the ligation detection reaction (LDR) combined with a universal array approach to the detection and quantitation of the polymerase chain reaction (PCR) amplified cry1A(b) gene from Bt-176 transgenic maize. We demonstrated excellent specificity and high sensitivity. Down to 0.5 fmol (nearly 60 pg) of PCR amplified transgenic material was unequivocally detected with excellent linearity within the 0.1-2.0% range with respect to wild-type maize. We suggest the feasibility of extending the LDR/universal array format to detect in parallel several transgenic sequences that are being developed for food applications.
Thermoelectric properties and electronic structure of the Zintl phase Sr<sub>5</sub>In<sub>2</sub>Sb<sub>6</sub>and the Ca<sub>5</sub>−<i>x</i>Sr<sub><i>x</i></sub>In<sub>2</sub>Sb<sub>6</sub>solid solution (2014)

The Zintl phase Sr5In2Sb6 is isostructural with Ca5In2Sb6-a promising thermoelectric material with a peak zT of 0.7 when the carrier concentration is optimized by doping. Density functional calculations for Sr5In2Sb6 reveal a decreased energy gap and decreased valence band effective mass relative to the Ca analog. Chemical bonding analysis using the electron localizability indicator was found to support the Zintl bonding scheme for this structure type. High temperature transport measurements of the complete Ca(5-x)Sr(x)In2Sb6 solid solution were used to investigate the influence of the cation site on the electronic and thermal properties of A5In2Sb6 compounds. Sr was shown to be fully miscible on the Ca site. The higher density of the Sr analog leads to a slight reduction in lattice thermal conductivity relative to Ca5In2Sb6, and, as expected, the solid solution samples have significantly reduced lattice thermal conductivities relative to the end member compounds.
Symbolic Arrays in Symbolic PathFinder (2017)

Symbolic Execution is a program analysis technique used to increase software reliability. Modern software often manipulate complex data structures, many of which being similar to arrays. We present a novel approach and implementation in Symbolic PathFinder for handling symbolic arrays in Java. It enables analyzing a broader class of programs that manipulates arrays. We also extend the Symbolic Pathfinder testcase generation to support numeric arrays.
Time to Onset of Sustained Postoperative Pain Relief (SuPPR) (2015)

*Department of Anesthesiology, Louisiana State University Health Science Center, New Orleans, LA †Pain Medicine Fellowship and Neuromodulation, Department of Anesthesiology, University of Michigan Health System, Back & Pain Center, Ann Arbor, MI The authors declare no conflict of interest.
Direct Organocatalytic Asymmetric α‐Hydroxymethylation of Ketones and Aldehydes. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Stereo optimal transport of the matching filter (2019)

A recently introduced optimal transport of the matching filter (OTMF) provided us with a robust misfit function for reducing cycle skipping in Full-Waveform Inversion (FWI). Unlike the conventional L2-norm approach, OTMF computes a matching filter first by deconvolution of the predicted data with the measured ones and constructs the misfit function by measuring the Wasserstein distance W2 between the resulting preconditioned matching filter and the target, i.e., the Dirac delta function. Compared to the conventional application of the optimal transport (OT) misfit in the data domain directly, OTMF applies the OT to the resulting matching filter avoiding the modification of the amplitude or the phase of the original seismic data. Measuring the distance between the resulting matching filter and a Dirac delta function using Wasserstein metric W2 suggests a convex misfit function with respect to the time shifted signal. We propose a misfit function by stereo optimal transport of the matching filter (SOTMF), which takes the space coherency of the resulting matching filter into consideration. Compared to OTMF, SOTMF has an extra regularization term, which controls the variations of the resulting matching filter along the space (offset) axis, and the regularization term is formulated by Wasserstein distance between the matching filters of the nearby traces. Thus, in the framework of OT, SOTMF tries to focus the resulting matching filter to be a Dirac delta function in time and enhance its space coherency as well. We use the Marmousi example to show that SOTMF can reduce the cycleskipping, and at the same time its result shows less artifacts than OTMF. A result using an anisotropic version of SOTMF waveform inversion on a real dataset also demonstrates the good performance of the approach. Presentation Date: Tuesday, September 17, 2019 Session Start Time: 1:50 PM Presentation Time: 2:40 PM Location: 225B Presentation Type: Oral
Exploring polymorphism and solvate formation using high pressure (2007)

High-pressure X-ray single-crystal diffraction experiments on three different crystals of -K 4 Co(MoO 4 ) 3
Back Cover: Homotropic Allosterism: In-Depth Structural Analysis of the Gas-Phase Noncovalent Complexes Associating a Double-Cavity Cucurbit[<i>n</i>]uril-Type Host and Size-Selected Protonated Amino Compounds (ChemPlusChem 9/2013) (2013)

The back cover picture shows how a combination of experimental and theoretical tools proves attractive for the study of noncovalent interactions between a double-cavity cucurbit[n]uril-type receptor and size-selected guest molecules.In their Full Paper on page 959 ff., P. Gerbaux and co-workers describe that ternary complexes are smoothly transferred from aqueous solutions to the gas phase upon electrospray ionization.State-ofthe-art methods based on mass spectrometry associated with computational chemistry demonstrate the conservation of the condensed-phase structure during the transfer.
Atypical protein kinase C zeta as a target for chemosensitization of tumor cells. (2002)

Exposure of tumor cells to cytotoxic agents simultaneously activates a variety of intracellular signaling pathways. Some of these pathways involve enzymes from the protein kinase C (PKC) family of serine/threonine kinases. This family includes isoenzymes that negatively influence cell death, whereas other demonstrate an opposite effect. The present study analyzes the role of the zeta atypical PKC isoform in tumor cell response to cytotoxic agents. Using a histone H1 phosphorylation assay, we showed that both tumor necrosis factor alpha and etoposide activate PKCzeta in U937 human leukemic cells. Stable transfection of a kinase-dead, dominant-negative PKCzeta mutant in U937 cells decreases Bcl-2 expression while increasing the expression of Bax and several procaspases. This transfection also prevents etoposide-induced nuclear factor-kappaB nuclear translocation and accumulation of X-linked inhibitor of apoptosis protein. PKCzeta inhibition accelerates the occurrence of apoptosis in leukemic cells exposed to etoposide and tumor necrosis factor alpha. This sensitization was confirmed in vitro by use of a clonogenic assay. In addition, PKCzeta inhibition sensitized tumor cells grown in nude mice to etoposide. These results indicate that PKCzeta isoform is a protective signals that is activated in tumor cells exposed to a cytotoxic agent. This inducible resistance factor thus appears an attractive target for chemosensitization of tumor cells.
CAMK2G is identified as a novel therapeutic target for myelofibrosis (2021)

Although JAK1/2 inhibition is effective in alleviating symptoms of myelofibrosis (MF), it does not result in the eradication of MF clones, which can lead to inhibitor-resistant clones emerging during the treatment. Here, we established induced pluripotent stem cells (iPSCs) derived from MF patient samples (MF-iPSCs) harboring JAK2 V617F, CALR type 1, or CALR type 2 mutations. We demonstrated that these cells faithfully recapitulate the drug sensitivity of the disease. These cells were used for chemical screening, and calcium/calmodulin-dependent protein kinase 2 (CAMK2) was identified as a promising therapeutic target. MF model cells and mice induced by MPL W515L, another type of mutation recurrently detected in MF patients, were used to elucidate the therapeutic potential of CAMK2 inhibition. CAMK2 inhibition was effective against JAK2 inhibitor-sensitive and JAK2 inhibitor-resistant cells. Further research revealed CAMK2 γ subtype was important in MF model cells induced by MPL W515L. We showed that CAMK2G hetero knockout in the primary bone marrow cells expressing MPL W515L decreased colony-forming capacity. CAMK2G inhibition with berbamine, a CAMK2G inhibitor, significantly prolonged survival and reduced disease phenotypes, such as splenomegaly and leukocytosis in a MF mouse model induced by MPL W515L. We investigated the molecular mechanisms underlying the therapeutic effect of CAMK2G inhibition and found that CAMK2G is activated by MPL signaling in MF model cells and is an effector in the MPL-JAK2 signaling pathway in these cells. These results indicate CAMK2G plays an important role in MF, and CAMK2G inhibition may be a novel therapeutic strategy that overcomes resistance to JAK1/2 inhibition.
A novel codesign approach based on distributed virtual machines (2002)

This paper describes a hardware/software codesign approach for the design of embedded systems based on digital signal processors and FPGAs. Our approach is based on distributed virtual machines for simulation and verification of the application on a Linux cluster and for running the application on different target architectures (DSPs, FPGAs) as well. The main focus is the description of the virtual machine, which was designed to make DSP applications portable across different platforms while maintaining optimal code.
Monolithic Perovskite Silicon Tandem Solar Cells with Advanced Optics (2016)

To realize high efficiency monolithic perovskite silicon tandem solar cells, we develop low-temperature processes for the perovskite top cell, rear-side light trapping, optimized perovskite growth, transparent contacts and recombination interconnection layers, and adapted characterization methods.
On Characterization of Vibration Measurement Using Microwave Doppler Radar (2018)

Doppler radar is a compact, microwave sensor for detecting vibration of the target object, from a distance. In this paper, Doppler only measurements are used to characterize the vibrational properties namely vibration amplitude and the frequency. The focus of the study is to understand the potential effect of the measurement environment on measurement quality. The investigations lead us to propose a system consisting of two single channel radars (in lieu of one quadrature radar), spatially separated both along range and azimuth directions. The proposed system introduces diversity, ensures robustness in detection while keeping the system design cost-effective in large scale deployments.
Abstract 1669: Identification of mutant KRas-Raf-1 binding disruptors (2018)

Abstract Mutant KRas is a major driver of human cancer, yet currently no clinically approved therapies that directly target mutant KRas are available. In order to identify novel drugs that bind either mutant KRas or its effector Raf-1, we used alpha-screen and GST-pull down assays to identify disruptors of KRas G12D binding to the Ras-binding domain of Raf-1. From a novel, natural product-inspired chemical library called Complexity To Diversity (CTD), we have identified a series of 5 hits that belong to a family of gibberellic acid-derived compounds and 2 hits from a family of pleuromutilin-derived compounds. At present we are using Differential Scanning Fluorimeter (DSF) and Isothermal calorimetry (ITC) assays to determine whether these hits bind to KRas G12D or Raf-1 RBD. These studies may lead to identifying chemical probes that can be developed to target mutant KRas-driven cancers. Citation Format: Rajanikanth Vangipurapu, Liwei Chen, Perry Kennedy, Karen C. Morrison, Paul J. Hergenrother, Said M. Sebti. Identification of mutant KRas-Raf-1 binding disruptors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1669.
Synthesis of Cyclic and Acyclic β-Amino Acids via Chelation-Controlled 1,3-Dipolar Cycloaddition (2003)

Isoxazolidines have been synthesized in diastereomeric excess up to 94% via a MgBr2-induced chelation-controlled 1,3-dipolar cycloaddition reaction with N-hydroxyphenylglycinol as a chiral auxiliary. The diastereomerically pure isoxazolidines were further transformed into cyclic and acyclic beta-amino acid derivatives.
HTS microwave cavity with temperature-independent frequencies (1995)

An HTS-walled and sapphire-loaded class of microwave cavities is described whose low TE modes show a frequency maximum at a controllable temperature. This makes the resonant frequencies of such passively compensated cavities independent or invariant of temperature at this point. Two different experimental realizations are presented. For a 7.8 GHz TE 011 mode, one cavity exhibited a frequency shift of less than 12 kHz over a 25 degree range, centered at 115 Kelvin.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>