gebhart/patrepeval huggingface dataset:
Generalized Time-Dependent Model of Radiation-Induced Chromosomal Aberrations in Normal and Repair-Deficient Human Cells (2014)

We have developed a model that can simulate the yield of radiation-induced chromosomal aberrations (CAs) and unrejoined chromosome breaks in normal and repair-deficient cells. The model predicts the kinetics of chromosomal aberration formation after exposure in the G0/G1 phase of the cell cycle to either low- or high-LET radiation. A previously formulated model based on a stochastic Monte Carlo approach was updated to consider the time dependence of DNA double-strand break (DSB) repair (proper or improper), and different cell types were assigned different kinetics of DSB repair. The distribution of the DSB free ends was derived from a mechanistic model that takes into account the structure of chromatin and DSB clustering from high-LET radiation. The kinetics of chromosomal aberration formation were derived from experimental data on DSB repair kinetics in normal and repair-deficient cell lines. We assessed different types of chromosomal aberrations with the focus on simple and complex exchanges, and predicted the DSB rejoining kinetics and misrepair probabilities for different cell types. The results identify major cell-dependent factors, such as a greater yield of chromosome misrepair in ataxia telangiectasia (AT) cells and slower rejoining in Nijmegen (NBS) cells relative to the wild-type. The model's predictions suggest that two mechanisms could exist for the inefficiency of DSB repair in AT and NBS cells, one that depends on the overall speed of joining (either proper or improper) of DNA broken ends, and another that depends on geometric factors, such as the Euclidian distance between DNA broken ends, which influences the relative frequency of misrepair.
Natural enemies of natural enemies: the potential top‐down impact of predators on entomopathogenic nematode populations (2014)

Top‐down population regulation can influence the success of biological control agents when they are released into the field. Entomopathogenic nematodes ( EPN s) are used commonly in biological control programmes, but their efficacy suffers from poor persistence. Although abiotic soil conditions have been shown to reduce EPN persistence, consumption of infected insects by scavengers and of infective juvenile ( IJ ) nematodes by predators may also regulate these populations. In the present study, the effects of different soil arthropods on EPN s in laboratory conditions were measured. It was hypothesised that arthropods commonly found in soil communities where EPN s are applied would consume cadavers of insects parasitised by the nematodes and the IJ s themselves. Some species of scavengers consume EPN ‐infected insects. Crickets ( Gryllus bimaculatus De Geer), A merican cockroaches [ Periplaneta Americana (Linnaeus)], ants [ Tetramorium chefketi Forel and Pheidole pallidula (Nylander)], earwigs ( Labidura riparia Pallas), mites ( Sancassania polyphyllae Zachvatkin), and springtails ( Sinella curviseta Brook and Folsomia candida Willem) have different responses to nematode‐killed insects. Results suggested that ants ( T. chefketi ), cockroaches, mites, and earwigs fed on Steinernema ‐killed insects whereas neither crickets nor springtails consumed them. In the second part of the study, experiments were conducted to determine whether mites and springtails consumed IJ EPN s. Results showed that S. polyphyllae mites do not consume infective juveniles in soil, whereas both springtail species consumed significant numbers of the IJ s. Top‐down regulatory processes can be a limiting factor for EPN populations under laboratory conditions. Both host cadavers and IJ s are consumed (albeit by different arthropods), so these results may help explain the difficulties associated with the persistence of EPN application to soil.
Aerococcus vaginalis sp. nov., isolated from the vaginal mucosa of a beef cow, and emended descriptions of Aerococcus suis, Aerococcus viridans, Aerococcus urinaeequi, Aerococcus urinaehominis, Aerococcus urinae, Aerococcus christensenii and Aerococcus sanguinicola (2014)

A gram-stain-positive, facultatively anaerobic, non-spore-forming, catalase-negative, coccoid-shaped bacterial strain, designated BV2(T), was isolated from the vaginal mucosa of a beef cow in Japan. Phylogenetic analysis showed that the isolate shared high 16S rRNA gene sequence similarity (92.9 %) with Aerococcus suis 1821/02(T) and low similarity (<92.7 %) with any other recognized species of the genus Aerococcus. The DNA G+C content was 44.7 mol%, which is within the range observed among species of the genus Aerococcus (37.5-48.4 mol%). The major cellular fatty acid was C18 : 1ω9c, similar to other type strains of species of the genus Aerococcus. The results of genotypic, phenotypic and chemotaxonomic analyses as well as the low degree of DNA-DNA relatedness with all recognized members of the genus Aerococcus indicate that strain BV2(T) represents a novel species of the genus Aerococcus, for which the name Aerococcus vaginalis sp. nov. is proposed. The type strain is BV2(T) ( = JCM 19163(T) = DSM 27293(T)). Emended descriptions of Aerococcus suis, Aerococcus viridans, Aerococcus urinaeequi, Aerococcus urinaehominis, Aerococcus urinae, Aerococcus christensenii and Aerococcus sanguinicola are also presented.
Anti‐cooperativity and cooperativity in hydrophobic interactions: Three‐body free energy landscapes and comparison with implicit‐solvent potential functions for proteins (2002)

Potentials of mean force (PMFs) of three-body hydrophobic association are investigated to gain insight into similar processes in protein folding. Free energy landscapes obtained from explicit simulations of three methanes in water are compared with that predicted by popular implicit-solvent effective potentials for the study of proteins. Explicit-water simulations show that for an extended range of three-methane configurations, hydrophobic association at 25 degrees C under atmospheric pressure is mostly anti-cooperative, that is, less favorable than if the interaction free energies were pairwise additive. Effects of free energy nonadditivity on the kinetic path of association and the temperature dependence of additivity are explored by using a three-methane system and simplified chain models. The prevalence of anti-cooperativity under ambient conditions suggests that driving forces other than hydrophobicity also play critical roles in protein thermodynamic cooperativity. We evaluate the effectiveness of several implicit-solvent potentials in mimicking explicit water simulated three-body PMFs. The favorability of the contact free energy minimum is found to be drastically overestimated by solvent accessible surface area (SASA). Both the SASA and a volume-based Gaussian solvent exclusion model fail to predict the desolvation barrier. However, this barrier is qualitatively captured by the molecular surface area model and a recent "hydrophobic force field." None of the implicit-solvent models tested are accurate for the entire range of three-methane configurations and several other thermodynamic signatures considered.
Pathomechanics of the pivot shift maneuver (1981)

This paper analyzes changes in instant centers of motion and joint surface velocity vectors in knees demonstrating a positive pivot shift test. Eight patients were studied on the basis of a sus pected tear of the anterior cruciate ligament. Clinical evaluation consisted of a history and examination with special attention to the anterior drawer test, Lach mann's test, and the pivot shift test. Control knees chosen had a negative history of injury and a normal examination. Serial roentgenograms were obtained on all knees through a range of motion from 0 to 90° of flexion, at increments of 7 to 10°. Internal rotation and valgus stress were applied to duplicate the pivot shift maneu ver during the filming. These serial studies were used to determine instant centers of motion, modifying the method of Rouleaux. Arthrography and arthoscopy were performed to document the pathologic anatomy. Alterations in instant center progression were noted in all patients with a clinically positive pivot shift as compared with the control group and a general pattern of progression was observed. From 0 to 20° of flexion the instant centers were located too near the joint line and displaced anteriorly. During the shift phase (from 20 to 45°) the instant centers were located posteriorly and proximally on the femur. These findings indicate that from 0 to 20° rolling predominated followed by a sudden change to gliding as the shift occurred. In a few cases the initial instant centers were actually located below the joint line, indicating a backwards glide phenomenon. From 50 to 90° the instant center progression was near normal. Surface velocity vectors were likewise abnormal in patients with pivot shift. During the initial phase of flexion the velocity vector was not tangential to the joint surface, indicating excessive friction and com pressive forces were present during knee motion. These findings demonstrate a possible mechanism for the development of posttraumatic arthritis of the tibial- femoral joint in patients with a positive pivot shift test. A quantitative analysis.of the pivot shift maneuver is shown which aids in understanding the pathomechan ics of the pivot shift maneuver. The method is also suggested for long-term evalu ation of anterior cruciate reconstructive procedures.
The self-programming thermostat (2009)

Programmable thermostats offer large potential energy savings without sacrificing comfort, but only if setback schedules are defined correctly. We present the concept of a self-programming thermostat that automatically creates an optimal setback schedule by sensing the occupancy statistics of a home. The system monitors occupancy using simple sensors in the home, similar to those already used in typical security systems, and the user defines the desired balance between energy and comfort using a single, intuitive knob. Our preliminary results show that this approach can reduce heating and cooling demand by up to 15% over the default setback schedule recommended by EnergyStar.
Vertical profiles of environmental parameters measured from physical, optical and imaging sensors during station TARA_067 of the Tara Oceans expedition 2009-2013 (2014)

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set includes properties of seawater, particulate matter and dissolved matter from physical, optical and imaging sensors mounted on a vertical sampling system (Rosette) used during the 2009-2013 tara Oceans Expedition. It comprised 2 pairs of conductivity and temperature sensors (SEABIRD components), and a complete set of WEtLabs optical sensors, including chrorophyll and CDOM fluorometers, a 25 cm transmissiometer, and a one-wavelength backscatter meter. In addition, a SATLANTIC ISUS nitrate sensor and a Hydroptic Underwater Vision Profiler (UVP) were mounted on the rosette. In the Arctic Ocean and Arctic Seas (2013), a second oxygen sensor (SBE43) and a four frequency Aquascat acoustic profiler were added. The system was powered on specific Li-Ion batteries and data were self-recorded at 24HZ. Sensors have all been factory calibrated before, during and after the four year program. Oxygen was validated using climatologies (WOA09). Nitrate and Fluorescence data were adjusted with discrete measurements from Niskin bottles mounted on the Rosette, and optical darks were performed monthly on board. A total of 839 quality checked vertical profiles were made during the tara Oceans expedition 2009-2013.
Tritium Transport from a Solid Radioactive Waste Burial Ground Whose Heterogeneous Conductivity Field is Based on Site Lithologic Data: ABSTRACT (1996)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Development of the Vaccine Analytic Unit's research agenda for investigating potential adverse events associated with anthrax vaccine adsorbed (2006)

The experience described, while specific for establishing the VAU's research agenda for the safety of the current anthrax vaccine, may be useful and adapted for research planning in other areas of public health research.
Peroxynitrite preferentially oxidizes the dithiol redox motifs of protein-disulfide isomerase (2017)

Protein-disulfide isomerase (PDI) is a ubiquitous dithiol-disulfide oxidoreductase that performs an array of cellular functions, such as cellular signaling and responses to cell-damaging events. PDI can become dysfunctional by post-translational modifications, including those promoted by biological oxidants, and its dysfunction has been associated with several diseases in which oxidative stress plays a role. Because the kinetics and products of the reaction of these oxidants with PDI remain incompletely characterized, we investigated the reaction of PDI with the biological oxidant peroxynitrite. First, by determining the rate constant of the oxidation of PDI's redox-active Cys residues (Cys<sup>53</sup> and Cys<sup>397</sup>) by hydrogen peroxide (<i>k</i> = 17.3 ± 1.3 m<sup>-1</sup> s<sup>-1</sup> at pH 7.4 and 25 °C), we established that the measured decay of the intrinsic PDI fluorescence is appropriate for kinetic studies. The reaction of these PDI residues with peroxynitrite was considerably faster (<i>k</i> = (6.9 ± 0.2) × 10<sup>4</sup> m<sup>-1</sup> s<sup>-1</sup>), and both Cys residues were kinetically indistinguishable. Limited proteolysis, kinetic simulations, and MS analyses confirmed that peroxynitrite preferentially oxidizes the redox-active Cys residues of PDI to the corresponding sulfenic acids, which reacted with the resolving thiols at the active sites to produce disulfides (<i>i.e.</i> Cys<sup>53</sup>-Cys<sup>56</sup> and Cys<sup>397</sup>-Cys<sup>400</sup>). A fraction of peroxynitrite, however, decayed to radicals that hydroxylated and nitrated other active-site residues (Trp<sup>52</sup>, Trp<sup>396</sup>, and Tyr<sup>393</sup>). Excess peroxynitrite promoted further PDI oxidation, nitration, inactivation, and covalent oligomerization. We conclude that these PDI modifications may contribute to the pathogenic mechanism of several diseases associated with dysfunctional PDI.
Magnetische Sensoren auf Basis des AMR-Effekts (Magnetic Sensors Based on the AMR-Effect) (2001)

Magnetoresistive Sensoren unter Nutzung des anisotropen magnetoresistiven Effekts (AMR-Effekts) finden sowohl im Automobil als auch im industriellen Bereich für vielfältige Messaufgaben Anwendung. Aufbauend auf den theoretischen Grundlagen des AMR-Effekts werden die unterschiedlichen Ausführungsformen und Messprinzipien von AMR-Sensoren dargestellt und diskutiert. Abschließend erfolgt die Vorstellung von AMR-Sensorsystemen zur berührungslosen Drehzahl- und Winkelmessung sowie zur Schwachfeldmessung für Kompassanwendungen.
Hybrid FE-WB methods for efficient vehicle interior cavity acoustic analysis (2010)

status: Published
Rare Earth Cobaltites as Oxygen Electrode Materials for Alkaline Solution (1977)

The perovskite‐type compounds (Ln = lanthanoid element, M = alkaline earth element, M' = transition metal element) are examined as oxygen electrode materials for an alkaline solution. A porous sintered electrode consisting of a compound like is satisfactory in both polarization characteristics and stability under working conditions. However, a polytetrafluoroethylene (PTFE) bonded type electrode barely functions as an oxygen electrode even at a current density as low as 10 mA/ cm2. The electrode oxide undergoes reduction instead of acting as a reduction catalyst for gaseous oxygen to hydroxy ions. From a practical point of view, the sinter‐type electrodes are promising as metal‐air secondary battery cathodes because they are stable to anodic oxidation during charge periods.
Counting 1D free electron laser growing modes in the presence of space charge (2012)

Knowing the number and structure of the free electron laser's (FEL) growing modes is of fundamental importance to its theoretical description and its applications. The one-dimensional FEL dispersion relation, including the space-charge effects, is well established in the FEL theory, but questions remain about the number of the growing solutions (modes). In this paper, we provide the definite answers to the latter question and identify the amplification bandwidth of these modes.
Open-Source JTAG Simulator Bundle for Labs (2012)

Abstract This paper presents a software/hardware bundle for studying, training and research related to IEEE 1149.1 Boundary Scan (BS) standard. The presented package includes a software environment Trainer 1149 that is capable to graphically visualize BS facilities and perform fine-grain simulation of BS test process. Trainer 1149 provides a cozy graphical design and simulation environment of BS-enabled chips and non-BS clusters. It provides the user with a full flexibility in working with any type of BS structures by supporting standard formats such as Boundary Scan Description Language and SVF (for defining test patterns). A special fault simulation mode allows injecting various types of interconnection faults to simulate their impact and inspect them using interactive tools. Trainer 1149 is the main component of a recent goJTAG initiative that aims at bringing JTAG tools closer to the user for both learning and experimental work purposes. The software part is implemented in multi-platform Java environment and distributed as an open-source freeware. Using a convenient low-cost USB-JTAG controller, one can also test real defects in real hardware. Such combination of features is unique for a public domain BS package.
Live-Load Response of a 65-Year-Old Pratt Truss Bridge (2014)

The Kettle River Bridge is an arched, steel cantilevered deck, Pratt Truss bridge. To quantify the live-load performance of the bridge superstructure and provide a baseline for future comparisons, it was instrumented with 151 strain gauges on various beam, stringer, and truss members. In addition, 8 displacement gauges were attached along the truss. All gauges were simultaneously monitored while the bridge was subjected to a nondestructive, live-load test. The recorded bridge response was analyzed to quantify in situ behavior. The measured behavior was then used to validate a finite-element model using solid and frame elements, which was subsequently used to obtain an inventory- and operating-load rating of 2.03 and 2.64, respectively. Based on the results of the test, it was concluded that the large gusset plates added partial fixity to the truss members, as evident from the significant measured in-plane bending strains. However, the beam-and-stringer deck support system showed minimal rotational restraint between consecutive panels and behaved nearly simply supported. The validated finite-element model was used to determine distribution factors. The actual bridge distribution factors were found to be conservative in comparison to those calculated according the AASHTO LRFD specifications, by 17–44%.
Feminario Universidad Rural Paulo Freire, Serranía de Ronda: el reto imprescindible (2007)

Wild Cucumis species have been divided into Australian/Asian and African groups using morphological and phylogenetic characteristics, and new species have been described recently. No molecular cytogenetic information is available for most of these species. The crossability between 5 southern African Cucumis species (C. africanus, C. anguria, C. myriocarpus, C. zeyheri, and C. heptadactylus) has been reported; however, the evolutionary relationship among them is still unclear. Here, a molecular cytogenetic analysis using FISH with 5S and 45 S ribosomal DNA (rDNA) was used to investigate these Cucumis species based on sets of rDNA-bearing chromosomes (rch) types I, II and III. The molecular cytogenetic and phylogenetic results suggested that at least 2 steps of chromosomal rearrangements may have occurred during the evolution of tetraploid C. heptadactylus. In step 1, an additional 45 S rDNA site was observed in the chromosome (type III). In particular, C. myriocarpus had a variety of rch sets. Our results suggest that chromosomal rearrangements may have occurred in the 45 S rDNA sites. We propose that polyploid evolution occurred in step 2. This study provides insights into the chromosomal characteristics of African Cucumis species and contributes to the understanding of chromosomal evolution in this genus.
Peptide mimics for structural features in proteins (1993)

The crystal structure determination of three heptapeptides containing alpha-aminoisobutyryl (Aib) residues as a means of helix stabilization provides a high-resolution characterization of 6-->1 hydrogen-bonded conformations, reminiscent of helix-terminating structural features in proteins. The crystal parameters for the three peptides, Boc-Val-Aib-X-Aib-Ala-Aib-Y-OMe, where X and Y are Phe, Leu (I), Leu, Phe (II) and Leu, Leu (III) are: (I) space group P1, Z = 1, a = 9.903 A, b = 10.709 A, c = 11.969 A, alpha = 102.94 degrees, beta = 103.41 degrees, gamma = 92.72 degrees, R = 4.55%; (II) space group P21, Z = 2, a = 10.052 A, b = 17.653 A, c = 13.510 A, beta = 108.45 degrees, R = 4.49%; (III) space group P1, Z = 2 (two independent molecules IIIa and IIIb in the asymmetric unit), a = 10.833 A, b = 13.850 A, c = 16.928 A, alpha = 99.77 degrees, beta = 105.90 degrees, gamma = 90.64 degrees, R = 8.54%. In all cases the helices form 3(10)/alpha-helical (or 3(10)helical) structures, with helical columns formed by head-to-tail hydrogen bonding. The helices assemble in an all-parallel motif in crystals I and III and in an antiparallel motif in II. In the four crystallographically characterized molecules, I, II, IIIa and IIIb, Aib(6) adopts a left-handed helical (hL) conformation with positive phi, psi values, resulting in 6-->1 hydrogen-bond formation between Aib(2) CO and Leu(7)/Phe(7) NH groups. In addition a 4-->1 hydrogen bond is seen between Aib(3) CO and Aib(6) NH groups. This pattern of hydrogen bonding is often observed at the C-terminus of helices proteins, with the terminal pi-type turn being formed by four residues adopting the hRhRhRhL conformation.