gebhart/patrepeval huggingface dataset:
Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance (2023)

Protein space is a rich analogy for genotype-phenotype maps, where amino acid sequence is organized into a high-dimensional space that highlights the connectivity between protein variants. It is a useful abstraction for understanding the process of evolution, and for efforts to engineer proteins towards desirable phenotypes. Few framings of protein space consider how higher-level protein phenotypes can be described in terms of their biophysical dimensions, nor do they rigorously interrogate how forces like epistasis-describing the nonlinear interaction between mutations and their phenotypic consequences-manifest across these dimensions. In this study, we deconstruct a low-dimensional protein space of a bacterial enzyme (dihydrofolate reductase; DHFR) into "subspaces" corresponding to a set of kinetic and thermodynamic traits [(<i>k</i><sub><i>cat</i></sub>, <i>K</i><sub><i>M</i></sub>, <i>K</i><sub><i>i</i></sub>, and <i>T</i><sub><i>m</i></sub> (melting temperature)]. We then examine how three mutations (eight alleles in total) display pleiotropy in their interactions across these subspaces. We extend this approach to examine protein spaces across three orthologous DHFR enzymes (<i>Escherichia coli, Listeria grayi,</i> and <i>Chlamydia muridarum</i>), adding a genotypic context dimension through which epistasis occurs across subspaces. In doing so, we reveal that protein space is a deceptively complex notion, and that the process of protein evolution and engineering should consider how interactions between amino acid substitutions manifest across different phenotypic subspaces.
Adherence to postresection colorectal cancer surveillance at National Cancer Institute‐designated Comprehensive Cancer Centers (2018)

Guidelines recommend surveillance after resection of colorectal cancer (CRC), but rates of adherence to surveillance are variable and have not been studied at National Cancer Institute (NCI)-designated Comprehensive Cancer Centers. The aim of this study was to determine rates of adherence to standard postresection CRC surveillance recommendations including physician visits, carcinoembryonic antigen (CEA), computed tomography (CT), and colonoscopy after CRC resection at three NCI-designated centers. Data on patients with resected CRC from 2010 to 2017 were reviewed. Adherence to physician visits was defined as having at least two visits within 14 months after surgical resection. CEA adherence was defined as having at least four CEA levels drawn within 14 months. CT and colonoscopy adherence were defined as completing each between 10 and 14 months from surgical resection. Chi-square test and logistic regression analyses were performed for overall adherence and adherence to individual components. A total of 241 CRC patients were included. Overall adherence was 23%. While adherence to physician visits was over 98%, adherence to CEA levels, CT, and colonoscopy were each less than 50%. Center was an independent predictor of adherence to CEA, CT, and/or colonoscopy. Stage III disease predicted CT adherence, while distance traveled of 40 miles or less predicted colonoscopy adherence. Overall adherence to postresection CRC guideline-recommended care is low at NCI-designated centers. Adherence rates to surveillance vary by center, stage, and distance traveled for care. Understanding factors associated with adherence is critical to ensure CRC patients benefit from postresection surveillance.
Natural Convective Heat Transfer in an Inclined Rectangular Cavity (1984)

Experiments of the convective heat transfer in an inclined air filled rectangular cavity were carried out under the conditions of angle of inclination from 0° to 180° and a wide range of aspect-ratios (H/W = 5 ∼ 83). Depending on the angle of inclination, three flow pattern modes of a three-dimensional Benard cellular flow, a screw type flow with the axis parallel to the direction of inclination and a two-dimensional boundary layer flow were identified by visual observations of two directions. In addition, useful correlations of non-dimensional heat transfer coefficients were derived in the relations between Nusselt number NuW and modified Rayleigh number RaW cosθ or NuW and RaW sineθ.
Stability of the Cyclotron Resonance Scattering Feature in Hercules X‐1 withRXTE (2001)

Five observations of the hard X-ray spectrum of Her X-1 from \xte show that the $\sim 41$ keV energy of the cyclotron scattering line is constant within statistics of a few percent per observtion. Comparison with other observations over many years indicates strongly that the centroid energy of this absorption line has increased some time between 1991 and 1993 by 23%, from 34 keV to 41 keV. Moreover, the cutoff energy of the spectral continuum increased at the same time from 16 keV to 20 keV, which is, within the statistical error of 5%, in direct proportion to the centroid. This may be a sign thatboth these characteristics of the spectrum are controlled in the same way by the magnetic field strength in the region of scattering.
PARTIAL COHERENCE MATCHING OF SYNTHETIC SEISMOGRAMS WITH SEISMIC TRACES* (1980)

A bstract A crucial step in the use of synthetic seismograms is the estimation of the filtering needed to convert the synthetic reflection spike sequence into a clearly recognizable approximation of a given seismic trace. In the past the filtering has been effected by a single wavelet, usually found by trial and error, and evaluated by eye. Matching can be made more precise than this by using spectral estimation procedures to determine the contribution of primaries and other reflection components to the seismic trace. The wavelet or wavelets that give the least squares best fit to the trace can be found, the errors of fit estimated, and statistics developed for testing whether a valid match can be made. If the composition of the seismogram is assumed to be known (e.g. that it consists solely of primaries and internal multiples) the frequency response of the best fit wavelet is simply the ratio of the cross spectrum between the synthetic spike sequence and the seismic trace to the power spectrum of the synthetic spike sequence, and the statistics of the match are related to the ordinary coherence function. Usually the composition cannot be assumed to be known (e.g. multiples of unknown relative amplitude may be present), and the synthetic sequence has to be split into components that contribute in different ways to the seismic trace. The matching problem is then to determine what filters should be applied to these components, regarded as inputs to a multichannel filter, in order to best fit the seismic trace, regarded as a noisy output. Partial coherence analysis is intended for just this problem. It provides fundamental statistics for the match, and it cannot be properly applied without interpreting these statistics. A useful and concise statistic is the ratio of the power in the total filtered synthetic trace to the power in the errors of fit. This measures the overall goodness‐of‐fit of the least squares match. It corresponds to a coherent (signal) to incoherent (noise) power ratio. Two limits can be set on it: an upper one equal to the signal‐to‐noise ratio estimated from the seismic data themselves, and a lower one defined from the distribution of the goodness‐of‐fit ratios yielded by matching with random noise of the same bandwidth and duration as the seismic trace segment. A match can be considered completely successful if its goodness‐of‐fit reaches the upper limit; it is rejected if the goodness‐of‐fit falls below the lower one.
An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme (2018)

Cyanuric acid is a metabolic intermediate of <i>s</i>-triazines, such as atrazine (a common herbicide) and melamine (used in resins and plastics). Cyanuric acid is mineralized to ammonia and carbon dioxide by the soil bacterium <i>Pseudomonas</i> sp. strain ADP via three hydrolytic enzymes (AtzD, AtzE, and AtzF). Here, we report the purification and biochemical and structural characterization of AtzE. Contrary to previous reports, we found that AtzE is not a biuret amidohydrolase, but instead it catalyzes the hydrolytic deamination of 1-carboxybiuret. X-ray crystal structures of apo AtzE and AtzE bound with the suicide inhibitor phenyl phosphorodiamidate revealed that the AtzE enzyme complex consists of two independent molecules in the asymmetric unit. We also show that AtzE forms an α2β2 heterotetramer with a previously unidentified 68-amino acid-long protein (AtzG) encoded in the cyanuric acid mineralization operon from <i>Pseudomonas</i> sp. strain ADP. Moreover, we observed that AtzG is essential for the production of soluble, active AtzE and that this obligate interaction is a vestige of their shared evolutionary origin. We propose that AtzEG was likely recruited into the cyanuric acid-mineralizing pathway from an ancestral glutamine transamidosome that required protein-protein interactions to enforce the exclusion of solvent from the transamidation reaction.
Gastrointestinale Onkologie – Therapieupdate 2008 / 2009 (2009)

As a consequence of recent studies the treatment of gastrointestinal cancers has become challenging and is undergoing constant changes on the basis of the results of new trials. The steering committee of the working group on gastrointestinal cancers of the Deutsche Gesellschaft für Verdauungs- und Stoffwechselkrankheiten has decided to summarise and present recent updates of the current treatment guidelines and recommendations for the most relevant gastrointestinal malignancies. In this review we have included recent findings from large trials on esophageal, gastric, pancreatic, cholangiocellular and liver cancers, as well as colorectal cancers, neuroendocrine tumours and lymphomas. This includes an update on the combination with novel targeted agents and the introduction of potential predictive biomarkers in the selection of the appropriate treatment strategy.
Poly(2,5-benzimidazole)-Grafted Graphene Oxide as an Effective Proton Conductor for Construction of Nanocomposite Proton Exchange Membrane (2017)

To improve proton conduction properties of conventional sulfonated poly(ether ether ketone) (SPEEK), poly(2,5-benzimidazole)-grafted graphene oxide (ABPBI-GO) was prepared to fabricate nanocomposite membranes, which then were further doped with phosphoric acid (PA). The ABPBI-GO was synthesized through the reaction of 3,4-diaminobenzoic acid with the carboxyl acid groups present on the GO surface. The simultaneous incorporation of ABPBI-GO and PA into SPEEK did not only improve the physicochemical performance of the membranes in terms of thermal stability, water uptake, dimensional stability, proton conductivity, and methanol permeation resistance but also relieve PA leaching from the membranes though acid-base interactions. The resulting composite membranes exhibited enhanced proton conductivities in extended humidity ranges thanks to the hygroscopic character of PA and the increased water uptake. Moreover, the unique self-ionization, self-dehydration, and nonvolatile properties of PA improved the high-temperature proton conductivities (σ) of PA-doped membranes. The PA-doped SPEEK/ABPBI-GO-3.0 delivered a σ of 7.5 mS cm<sup>-1</sup> at 140 °C/0% RH. This value was fourfold higher than that of pristine SPEEK membranes. The PA-doped SPEEK/ABPBI-GO-3.0 based fuel cell membranes delivered power densities of 831.06 and 72.25 mW cm<sup>-2</sup> at 80 °C/95% RH and 120 °C/0% RH, respectively. By contrast, the PA-doped SPEEK membrane generated only 655.63 and 44.58 mW cm<sup>-2</sup> under the same testing conditions.
Incrimination of Phlebotomus kandelakii and Phlebotomus balcanicus as Vectors of Leishmania infantum in Tbilisi, Georgia (2012)

A survey of potential vector sand flies was conducted in the neighboring suburban communities of Vake and Mtatsminda districts in an active focus of visceral Leishmaniasis (VL) in Tbilisi, Georgia. Using light and sticky-paper traps, 1,266 male and 1,179 female sand flies were collected during 2006-2008. Five Phlebotomus species of three subgenera were collected: Phlebotomus balcanicus Theodor and Phlebotomus halepensis Theodor of the subgenus Adlerius; Phlebotomus kandelakii Shchurenkova and Phlebotomus wenyoni Adler and Theodor of the subgenus Larroussius; Phlebotomus sergenti Perfil'ev of the subgenus Paraphlebotomus. Phlebotomus sergenti (35.1%) predominated in Vake, followed by P. kandelakii (33.5%), P. balcanicus (18.9%), P. halepensis (12.2%), and P. wenyoni (0.3%). In Mtatsminda, P. kandelakii (76.8%) comprised over three fourths of collected sand flies, followed by P. sergenti (12.6%), P. balcanicus (5.8%), P. halepensis (3.7%), and P. wenyoni (1.1%). The sand fly season in Georgia is exceptionally short beginning in early June, peaking in July and August, then declining to zero in early September. Of 659 female sand flies examined for Leishmania, 12 (1.8%) specimens without traces of blood were infected including 10 of 535 P. kandelakii (1.9%) and two of 40 P. balcanicus (5.0%). Six isolates were successfully cultured and characterized as Leishmania by PCR. Three isolates from P. kandelakii (2) and P. balcanicus (1) were further identified as L. infantum using sequence alignment of the 70 kDa heat-shock protein gene. Importantly, the sand fly isolates showed a high percent identity (99.8%-99.9%) to human and dog isolates from the same focus, incriminating the two sand fly species as vectors. Blood meal analysis showed that P. kandelakii preferentially feeds on dogs (76%) but also feeds on humans. The abundance, infection rate and feeding behavior of P. kandelakii and the infection rate in P. balcanicus establish these species as vectors in the Tbilisi VL focus.
Multiple-Phase-Shift Control for a Dual Active Bridge to Secure Zero-Voltage Switching and Enhance Light-Load Performance (2017)

An ac/dc + dual active bridge (DAB) circuit was found as one solution for the high-efficiency and high-power-density electric vehicle charger. One control option is to let the ac/dc part only convert the grid voltage to a double-line-frequency folded sine wave and let the DAB stage handle both the power factor (PF) and power delivery. While conventional single-phase-shift tends to lose zero-voltage switching (ZVS) at light load and the variable-switching-frequency dual-phase-shift (DPS) sacrifices the light-load performance, this letter proposes a multiple-phase-shift control, which allows for a fixed-switching-frequency triple-phase-shift (TPS) control at the light load to enhance the grid power quality. At medium- and heavy-load conditions, a phase-shift jump from TPS to DPS is performed to reduce the circulating current and improve efficiency. The proposed control strategy secures ZVS, realizes unity PF accurately and minimizes the control complexity. Experimental results on a SiC-based 7.2-kW charger validated its effectiveness and the smooth transition between the heavy load and light load.
A Portable Needle-free Jet Injector Based on a Custom High Power-density Voice-coil Actuator (2006)

We have constructed a portable needle-free drug injection (NFI) device based upon a custom voice-coil linear actuator. Our actuator is optimized to provide high instantaneous force (>200 N) and power (4 kW) while still allowing a total stroke of 25 mm. The actuator is relatively inexpensive, compact, and lightweight, allowing it to serve as the force generator in a portable, reusable, handheld NFI system. The actuator is capable of accelerating liquid drug in quantities of up to 250 microL to a speed of more than 200 ms(-1). The repeatability of a 50 microL volume ejection is better than +/-1 microL.
Electrospinning of palladium/silica nanofibers for catalyst applications (2015)

A new inorganic supported catalyst of silica (SiO<sub>2</sub>)-supported palladium (Pd) nanofibers was successfully fabricated by the electrospinning followed by the calcination at high temperature and the reduction in H<sub>2</sub> atmosphere.
<title>High-frame-rate low-latency hardware-in-the-loop image generation: an illustration of the particle method and DIME</title> (2000)

New computing architectures based on the DIME standard have been previously introduced which allow for processing of high frame rate imaging systems which may also need low latency capability, a common requirement for HWIL systems. This paper is presented in two sections: To achieve future realism in image generation systems for hardware-in-the-loop (HWIL) testing a significant increase in processing power is required, but additionally a suitable architecture is essential to provide low latency response on the data flow. Nallatech previously introduced DIME as a novel platform for HWIL systems which is capable of handling sub-frame latencies and greater than 100 Hz frame rates. We will demonstrate the system operating on traditional complex imaging problems, such as large convolution masks of 13 X 13 and also on new image generation techniques such as the particle method which is being developed by Matra British Aerospace Dynamics UK (MBDUK). MBDUK are proceeding on upgrading existing HWIL image generation systems for real-time particle models, to higher frame rates and increased complexity. Using Nallatech's latest DIME based architectures, models containing thousands of individual particles can be created at frame rates over 100 Hz and a resolution of 1024 X 1024 oversampled 4 times. This is possible because particle models exhibit high levels of parallelism ideal for exploiting the architecture of an FPGA. This paper will demonstrate the versatility of these particle models to create highly realistic signatures in terms of spatial dynamics and IR signature. Particle models are ideal for simulating dynamic objects such as flares, exhaust plumes, fires and explosions.
Reflectance (2016)

This glossary of terms covers phenomena considered under the very wide terms photocatalysis and radiation catalysis. A clear distinction is made between phenomena related to either photochemistry and photocatalysis or radiation chemistry and radiation catalysis. The term “radiation” is used here as embracing electromagnetic radiation of all wavelengths, but in general excluding fast-moving particles. Consistent definitions are given of terms in the areas mentioned above, as well as definitions of the most important parameters used for the quantitative description of the phenomena. Terms related to the up-scaling of photocatalytic processes for industrial applications have been included. This Glossary should be used together with the Glossary of terms used in photochemistry, 3rd edition, IUPAC Recommendations 2006: (doi:10.1351/pac200779030293) as well as with the IUPAC Compendium of Chemical Terminology, 2nd ed. (the “Gold Book” 2006–; doi:10.1351/goldbook), because many terms used in photocatalysis are defined in these documents.
Le virome cutané de la poule analysé par séquençage à haut débit: des virus différents de la peau humaine (2015)

Epidémiologie/Virus et Environnement - Session I
Nieustalone przewodzenie ciepła ciał o dużej przewodności cieplnej w warunkach konwekcji swobodnej w powietrzu (1974)

The paper presents a solution of the problem of unsteady heat transfer in bodies of high thermal conducitivity; at the surface of the body the heat is exchanged under the conditions of free convection. Calculations are made in the case of air convection. The results obtained are compared with those evaluated under the assumption of a constant heat transfer coefficient.
Power Control and Maximum Flows of Wireless Lattice Networks (2007)

In this paper we investigate the power control problem associated with a special class of Wireless Mesh Networks, known as the Wireless Lattice Networks. These networks function mainly as backbone networks. A natural question for a network in such a class is to determine its maximum flow for a given an end-to-end traffic distribution. For a given set of self-interfering links, known as a web, the maximum flow is shown to be the solution of a nonlinear matrix equation. The maximum flow of the network can then be determined from the maximum flows of the webs it contains.
Oleanolic Acid Enhances Mesenchymal Stromal Cell Osteogenic Potential by Inhibition of Notch Signaling (2017)

Oleanolic acid (OA), a pentacyclic triterpenoid, has been shown to modulate multiple signaling pathways in a variety of cell linages. But the mechanisms underlying OA-mediated mesenchymal stromal cell (MSC) osteogenic differentiation are not known. In this study, we examined effects of OA on cell viability, osteogenic differentiation in MSCs, and the involvement of Notch and BMP signaling. OA induced bone marrow derived MSC differentiation towards osteoprogenitor cells and inhibited Notch signaling in a dose dependent manner. Constitutive activation of Notch signaling fully blocked OA induced MSC osteogenic differentiation. The expression level of early osteogenic marker genes, ALP, Runx2, and type I collagen, which play a critical role in MSC to osteoblast transition and servers as a downstream target of BMP signaling, was significantly induced by OA. Furthermore, BMP2 mediated MSC osteogenic differentiation was significantly enhance by OA treatment, indicating a synergistic effect between BMP2 and OA. Our results suggest that OA is a promising bioactive agent for bone tissue regeneration, and inhibition of Notch signaling is required for its osteogenic effects on MSCs.
Biology and control of burcucumber (2001)

Research was initiated to determine the periodicity of emergence, seasonal plant growth and reproductive potential, and response to selected preemergence (PRE) and postemergence (POST) herbicides for burcucumber. Under Indiana conditions, burcucumber germinated from late April to October and was stimulated by periodic rainfall. Relative growth rates of plants were greatest up to 10 wk after establishment and declined when flowering was initiated. Without competition, early spring (May)–established burcucumber plants attained a fresh weight of up to 86 kg and produced almost 80,000 seeds. With later establishment, less biomass and and a smaller number of seeds were produced. Seedlings emerging up to mid-August produced germinable seed prior to frost, thus indicating that season-long control strategies are needed to minimize reproduction. A PRE application of atrazine, metribuzin plus chlorimuron, or linuron plus chlorimuron provided greater than 90% visual control up to 8 wk after treatment (WAT). Greater than 80% visual control was obtained with POST applications of glyphosate or with combinations of glyphosate plus dicamba or glyphosate plus 2,4-D; chlorimuron, metribuzin plus chlorimuron; or paraquat. Both imazaquin and bentazon provided less than 70% control. Results indicate that burcucumber displays rapid development with periodic germination throughout the growing season and is capable of producing large amounts of plant biomass and seed.