gebhart/patrepeval huggingface dataset:
Structural Biology of Glycoproteins (2012)

In recent years, the field of structural biology has seen many advances in technology for the production of recombinant proteins, mainly led by the high-throughput techniques of the structural genomics community. These technologies have largely focussed on expression using Escherichia coli with around 88 % of the protein chains in the Protein Data Bank (PDB) in 2010 being produced using this bacterium [1]. However, many proteins require posttranslational modification for correct folding and/or activity. By far the most common modification is glycosylation and it has been estimated that over half of all human proteins including many membrane proteins are glycosylated [2-3]. Therefore, the production of correctly glycosylated proteins for functional and structural studies requires the use of eukaryotic systems [4].
Control of Downy Brome (Bromus tectorum) in Conservation Fallow Systems (1991)

Field studies were conducted to determine the most effective rate of several herbicides applied at various growth stages to control downy brome in conservation fallow programs. Downy brome growth stage affected the efficacy of all herbicides. All herbicides were less effective when application was delayed until the boot stage of downy brome. Fluazifop-P and sethoxydim must be applied prior to tillering to effectively control downy brome. Glyphosate, the commercial mixture of glyphosate plus 2,4-D, paraquat, and HOE-39866 consistently controlled downy brome up to the 3- to 5-tiller stage. Glyphosate at 180 to 200 g ha -1 , paraquat at 250 to 300 g ha -1 , and the commercial mixture of glyphosate plus 2,4-D at 600 to 660 g ha -1 controlled downy brome 80 to 90%. The effective rates were lower than rates currently registered for downy brome control in western Canada, and thus there is potential for making conservation fallow programs more economical when downy brome is the predominant weed.
Flow of Hydrates Dispersed in Production Lines (2003)

Abstract This paper presents some results obtained in a Research project managed by IFP (Institut Français du Pétrole) and IFE (Institute for Energy Technology), where the objective is to study the transport of hydrates in production lines. A number of research projects are devoted to the study of thermodynamic equilibrium in the presence of hydrates, and the kinetics of hydrate formation, in order to develop prevention tools like hydrates inhibitors, insulation.... But with the development of deep water and ultra deep water production schemes where these technologies become expensive and some times limited, a fair prediction of hydrate formation and transport conditions becomes necessary for anticipating the design of the production facilities and could help the production engineers to make the appropriate decisions. In the literature, however little efforts have been directed towards the hydrodynamic modeling of hydrate transport. This project aims at the study of hydrate slurries in flowing conditions and particularly in multiphase flow lines. Experimental data in flow loop are presented. Comparisons have been made with flow models. In presence of hydrate crystals, the production fluid resembles a slurry with effective transport properties. This study indicates that the presence of particles in the flow tends to increase the wall drag and, consequently, influences the production capacity of the line. Moreover the settling trends of these solid particles can complicate the problem. Discussions about these issues have been done.
The EST Model for Predicting Progressive Damage and Failure of Open Hole Bending Specimens (2016)

Progressive damage and failure in open hole composite laminate coupons subjected to flexural loading is modeled using Enhanced Schapery Theory (EST). Previous studies have demonstrated that EST can accurately predict the strength of open hole coupons under remote tensile and compressive loading states. This homogenized modeling approach uses single composite shell elements to represent the entire laminate in the thickness direction and significantly reduces computational cost. Therefore, when delaminations are not of concern or are active in the post-peak regime, the version of EST presented here is a good engineering tool for predicting deformation response. Standard coupon level tests provides all the input data needed for the model and they are interpreted in conjunction with finite element (FE) based simulations. Open hole bending test results of three different IM7/8552 carbon fiber composite layups agree well with EST predictions. The model is able to accurately capture the curvature change and deformation localization in the specimen at and during the post catastrophic load drop event.
Elongated VCE blast waves and structural response (2017)

Elongated congested volumes are common at chemical processing and petroleum refining facilities due to the arrangement of processing units, but there have been relatively few evaluations reported for the blast loads produced by elongated vapor cloud explosions (VCEs). The accidental VCE that occurred at the Buncefield, UK facility in 2005 involved an elongated congested volume formed by the trees and undergrowth along a portion of the site boundary. Some of near‐field damage indicators present at the Buncefield site could not be reasonably explained using existing standard VCE blast load prediction techniques that are based on an assumption that the congested volume filled with flammable gas cloud is hemispherical and located at grade level. This paper summarizes recent work to define the characteristics associated with elongated congested volume VCEs and identify differences relative to standard VCEs involving compact congested volume geometries. The main conclusions from this work with regard to the blast wave shape for an elongated congested volume deflagration are: (1) the blast wave behaves as an acoustic wave along the long axis, (2) the blast wave has a very quick transition from the positive phase peak pressure to the negative phase peak pressure (i.e., quick relative to the positive phase duration), and (3) the magnitude of the pressure drop between the peak positive and negative pressures diminishes quickly with distance outside the congested volume. These observations are not consistent with the behavior of a compact congested volume geometry VCE blast wave. Deflagration and deflagration‐to‐detonation transition (DDT) regimes were also identified for unconfined elongated congested volume VCEs as a function of the normalized flame travel distance and flame speed. These regimes were verified with existing test data, including data from the on‐going RPSEA test program. These observations and the DDT regime identification provide a frame of reference to develop a better understanding of elongated congested volume VCEs. Generic structures, with properties typical of conventional construction, were analyzed to illustrate the effect of the elongated congested volume VCE blast loads on structural response. The results show that, for an elongated congested volume VCE, a high flame speed deflagration may result in more severe structural response in the near‐field than for a detonation (i.e., due to a DDT). These results provide an alternative near‐field damage indicator analysis approach for the investigation of elongated congested volume VCE incidents. © 2017 American Institute of Chemical Engineers Process Saf Prog 37: 283–293, 2018
DAMGO-induced expression of chemokines and chemokine receptors: the role of TGF-β1 (2008)

Studies from a number of laboratories suggest that modulation of cytokine expression plays an integral role in the immunomodulatory activity of opioids. Previously, our laboratory reported that activation of the mu-opioid receptor induced the expression of CCL2, CCL5, and CXCL10, as well as CCR5 and CXCR4. Previous work has also suggested the possibility that TGF-beta may participate in the opioid-induced regulation of immune competence, and in the present study, we set out to determine the role of this cytokine in the control of chemokine and chemokine receptor expression. We found that D-ala(2),N-Me-Phe(4)-Gly-ol(5)enkephalin (DAMGO), a highly selective mu-opioid agonist, induced the expression of TGF-beta1 expression at the protein and mRNA levels. In turn, the addition of TGF-beta1 was found to induce CCL5 and CXCR4 expression but not CCL2, CXCL10, or CCR5. Further analysis showed that pretreatment with neutralizing anti-TGF-beta1 blocked the ability of DAMGO to induce CCL5 or CXCR4. Similarly, pretreatment with cycloheximide prevented CCL5 or CXCR4 mRNA expression, consistent with the observation that DAMGO induction of chemokine and chemokine receptor expression requires newly synthesized TGF-beta1 protein. These results describe a common molecular basis for the activation of chemokine and chemokine receptor expression and may permit the development of strategies to inhibit certain undesirable immunological properties of micro-opioid agonists such as morphine and heroin.
High-performance GaAs/AlGaAs graded refractive index separate confinement heterostructure lasers grown by molecular-beam epitaxy on Si3N4 masked substrates (1989)

High-performance single quantum well graded refractive index separate confinement heterostructure lasers have been grown by molecular-beam epitaxy on Si3 N4 masked substrates. Lateral optical, carrier, and current confinement is supplied by the faceting which occurs during growth. Stripe lasers fabricated on 10-μm-wide openings in the [011̄] direction have threshold currents as low as 15 mA and internal quantum efficiency of 81% for a 500-μm-long cavity.
Comparative study of fusion algorithms and implementation of new efficient solution (2014)

High Dynamic Range (HDR) imaging has been the subject of significant researches over the past years, the goal of acquiring the best cinema-quality HDR images of fast-moving scenes using an efficient merging algorithm has not yet been achieved. In fact, through the years, many efficient algorithms have been implemented and developed. However, they are not yet efficient since they don't treat all the situations and they have not enough speed to ensure fast HDR image reconstitution. In this paper, we will present a full comparative analyze and study of the available fusion algorithms. Also, we will implement our personal algorithm which can be more optimized and faster than the existed ones. We will also present our investigated algorithm that has the advantage to be more optimized than the existing ones. This merging algorithm is related to our hardware solution allowing us to obtain four pictures with different exposures.
Structure-Activity Analysis of Microcin J25: Distinct Parts of the Threaded Lasso Molecule Are Responsible for Interaction with Bacterial RNA Polymerase (2005)

Peptide microcin J25 (MccJ25) inhibits bacterial RNA polymerase. We show that thermolysin-cleaved MccJ25 and MccJ25 lacking amino acids 13 to 17 also inhibit transcription. Our data and structural analysis of intact and thermolysin-digested MccJ25 suggest that distinct regions of MccJ25 are involved in transcription inhibition and cell entry.
Efficient 1.3 μm-band amplification in a Nd 3+ -doped single-mode fluoride fibre (1990)

A maximum gain of 5.5 dB was observed in a Nd3+-doped fluoride fibre around the 1.3 μm wavelength for a practical signal input level of −10 dBm. The pump power used was only 50 mW in a 820 nm wavelength, and a pumping efficiency of 0.13 dB/mW was attained.
The Diagnostic Utility of RAS Q61R Mutation-specific Immunohistochemistry in Epithelial-Myoepithelial Carcinoma (2021)

Epithelial-myoepithelial carcinoma (EMC) is a rare salivary gland cancer characterized by biphasic tubular structures composed of inner ductal and outer clear myoepithelial cells. Because of its histologic variety and overlap of histologic features with other salivary gland tumors, there are broad differential diagnoses. The HRAS Q61R mutation has been reported to be frequent in and specific to EMC. We evaluated the usefulness of RAS Q61R mutant-specific immunohistochemical (IHC) staining for detecting this genetic alteration in EMC. We investigated 83 EMC cases and 66 cases of salivary gland tumors with an EMC-like component, including pleomorphic adenoma, adenoid cystic carcinoma, basal cell adenoma/adenocarcinoma, and myoepithelial carcinoma. Sanger sequencing was performed for HRAS, KRAS, and NRAS. The diffuse and membranous/cytoplasmic RAS Q61R IHC expression was observed in 65% of EMC cases, in which all cases harbored the HRAS Q61R mutation. IHC-positive cases were present only in de novo EMCs (54/76 cases, 71%) but not in EMCs ex pleomorphic adenoma. The immunoreactivity was almost always restricted to the myoepithelial cells. Conversely, all EMC cases lacking the HRAS Q61R mutation were negative on IHC. In addition, only 3% of EMC-like tumors showed the abovementioned immunopositivity. None of the cases examined carried KRAS or NRAS mutations. IHC for RAS Q61R is highly sensitive and specific for detecting the HRAS Q61R mutation in EMC. Since significant immunopositivity was almost exclusively identified in nearly two thirds of EMCs but seldom in the histologic mimics, the IHC of RAS Q61R is a useful tool for diagnosing EMC in general pathology laboratories.
How to use information technology in the clinic to improve patient experience: Table 1 (2016)

The electronic patient record (EPR) software used by sexual and reproductive health (SRH) services has functionality that varies significantly and many are unable to meet all the patient and staff requirements; consequently, there is a real need to complement the EPR systems with additional information technology (IT) solutions. A successful IT solution needs to start with a pressing problem that can be clearly defined. Table 1 shows nine different problems that have been addressed in the last 5 years using a …
Prognostic G leason grade grouping: data based on the modified G leason scoring system (2013)

The 2005 ISUP modifications to the Gleason grading system for prostate carcinoma accurately categorize patients by pathological findings and short-term biochemical outcomes but, while retaining the essence of the Gleason system, there is a need for a change in its reporting to more closely reflect tumour behaviour. We propose reporting Gleason grades, including prognostic grade groups which accurately reflect prognosis as follows: Gleason score ≤ 6 (prognostic grade group I); Gleason score 3+4=7 (prognostic grade group II); Gleason score 4+3=7 (prognostic grade group III); Gleason score 4+4=8 (prognostic grade group (IV); and Gleason score 9-10 (prognostic grade group (V).
Interacción vía-estructura en puentes ferroviarios: algoritmos de cálculo paso a paso (2009)

espanolEl articulo describe un metodo de calculo basado en modelos numericos para el analisis del fenomeno de interaccion longitudinal via-estructura en puentes ferroviarios. Se analizan las acciones a considerar en el calculo y los metodos de combinacion. En este sentido los autores presentan un nuevo metodo de analisis completo de todas las acciones, que simula el paso del tren a lo largo del viaducto, mediante un algoritmo paso a paso. Se presentan ejemplos de aplicacion del nuevo metodo de calculo al diseno de viaductos y su comparacion con los resultados obtenidos mediante metodos de combinacion simplificados. EnglishThe article describes a calculation method based on numerical models for the analysis of longitudinal track-structure interaction in railway bridges. An analysis is made of the stresses to be considered in the calculation and the combination methods. The authors present a new method of complete analysis of all the stresses, simulating the passage of a train throughout a bridge, and employing a step-by-step algorithm. The paper present examples of the application of the new calculation method to the design of bridges and compares these with the results obtained from simplified combination models.
Functional activity of enucleated human polymorphonuclear leukocytes. (1983)

Enucleated human polymorphonuclear leukocytes (PMN) were prepared by centrifuging isolated, intact PMN over a discontinuous Ficoll gradient that contained 20 microM cytochalasin B. The enucleated cells (PMN cytoplasts) contained about one-third of the plasma membrane and about one-half of the cytoplasm present in intact PMN. The PMN cytoplasts contained no nucleus and hardly any granules. The volume of the PMN cytoplasts was about one-fourth of that of the original PMN. Greater than 90% of the PMN cytoplasts had an "outside-out" topography of the plasma membrane. Cytoplasts prepared from resting PMN did not generate superoxide radicals (O2-) or hydrogen peroxide. PMN cytoplasts incubated with opsonized zymosan particles or phorbol-myristate acetate induced a respiratory burst that was qualitatively (O2 consumption, O2- and H2O2 generation) and quantitatively (per unit area of plasma membrane) comparable with that of intact, stimulated PMN. Moreover, at low ratios of bacteria/cells, PMN cytoplasts ingested opsonized Staphylococcus aureus bacteria as well as did intact PMN. At higher ratios, the cytoplasts phagocytosed less well. The killing of these bacteria by PMN cytoplasts was slower than by intact cells. The chemotactic activity of PMN cytoplasts was very low. These results indicate that the PMN apparatus for phagocytosis, generation of bactericidal oxygen compounds, and killing of bacteria, as well as the mechanism for recognizing opsonins and activating PMN functions, are present in the plasma membrane and cytosol of these cells.
Porcine Circovirus Induces B Lymphocyte Depletion in Pigs with Wasting Disease Syndrome. (2000)

To disclose the mechanism of cellular injury following porcine circovirus(PCV)infection, 12 pigs were examined by the terminal deoxynucleotidyl transferase−mediated dUTP−nick end labeling(TUNEL)method and immunohistochemistry.Histologically, the lymphoid tissues were characterized by marked apoptosis of lymphocytes, lymphocyte depletion, and macrophages and giant cells containing numerous inclusion bodies with or without apoptotic bodies.Immunohistochemically, there were many lysozyme−positive macrophages in the lymphoid follicles, while the number of CD79a−positive B lymphocytes was scanty.Apoptotic cells, which were proved to be TUNEL positive, revealed CD79a positivity.Although detectable mainly in the cytoplasm of macrophages, PCV antigens were found also in the nuclei of macrophages and apoptotic lymphocytes.Ultrastructurally, the presence of PCV virions was confirmed in apoptotic bodies phagocytosed by macrophages.These findings suggested that lymphocyte depletion with apoptotic death of B lymphocytes was caused by PCV, and that some of the inclusion bodies were phagolysosomes derived from the apoptosis.Thus, PCV may trigger the development of wasting disease syndrome by producing an immunocompromised state in pigs.
Optical design study for the 1-5 μm spectral band (2009)

The increased desire for multispectral infrared optical systems in compact packages significantly complicates the optical design of such systems. Add in the fact that multiple spectral bands are now imaging on the same detector, and the optical designs become quite challenging. The availability of materials over the desired multiple spectral bands that transmit well with the desired dispersion properties further complicates the design. Designing optics for good performance in the SWIR (1.0 - 2.0&mu;m) and the MWIR (3.5 - 5.0&mu;m) bands is an example where this challenge can be significant. Many of the preferred optical materials in the MWIR start to cut off prior to reaching 1&mu;m, or have dispersions that are very difficult to control over this broad of a spectral band. Reflective designs are often limited because of packaging limitations. In this paper, multiple approaches are designed and examined to find the best balance between risk, performance, and size. The analyzed design studies include the use of traditional MWIR materials, harmonic diffractive lenses, and alternative materials that will require further development to be used in a tactical environment.
Improving temporal cognition by enhancing motivation. (2015)

Increasing motivation can positively impact cognitive performance. Here we employed a cognitive timing task that allows us to detect changes in cognitive performance that are not influenced by general activity or arousal factors such as the speed or persistence of responding. This approach allowed us to manipulate motivation using three different methods; molecular/genetic, behavioral and pharmacological. Increased striatal D2Rs resulted in deficits in temporal discrimination. Switching off the transgene improved motivation in earlier studies, and here partially rescued the temporal discrimination deficit. To manipulate motivation behaviorally, we altered reward magnitude and found that increasing reward magnitude improved timing in control mice and partially rescued timing in the transgenic mice. Lastly, we manipulated motivation pharmacologically using a functionally selective 5-HT2C receptor ligand, SB242084, which we previously found to increase incentive motivation. SB242084 improved temporal discrimination in both control and transgenic mice. Thus, while there is a general intuitive belief that motivation can affect cognition, we here provide a direct demonstration that enhancing motivation, in a variety of ways, can be an effective strategy for enhancing temporal cognition. Understanding the interaction of motivation and cognition is of clinical significance since many psychiatric disorders are characterized by deficits in both domains.
Significance of anterior Q waves in left anterior fascicular block—A clinical and noninvasive assessment (2002)

Patients with LAFB in the absence of MI may have Q waves in the V leads that are approximately 0.02 s in duration and restricted to one or two leads. This anomaly may represent a variation of conduction in the initial 0.02 s QRS vector due to LAFB.
Acid activation mechanism of the influenza A M2 proton channel (2016)

The homotetrameric influenza A M2 channel (AM2) is an acid-activated proton channel responsible for the acidification of the influenza virus interior, an important step in the viral lifecycle. Four histidine residues (His37) in the center of the channel act as a pH sensor and proton selectivity filter. Despite intense study, the pH-dependent activation mechanism of the AM2 channel has to date not been completely understood at a molecular level. Herein we have used multiscale computer simulations to characterize (with explicit proton transport free energy profiles and their associated calculated conductances) the activation mechanism of AM2. All proton transfer steps involved in proton diffusion through the channel, including the protonation/deprotonation of His37, are explicitly considered using classical, quantum, and reactive molecular dynamics methods. The asymmetry of the proton transport free energy profile under high-pH conditions qualitatively explains the rectification behavior of AM2 (i.e., why the inward proton flux is allowed when the pH is low in viral exterior and high in viral interior, but outward proton flux is prohibited when the pH gradient is reversed). Also, in agreement with electrophysiological results, our simulations indicate that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain; the four transmembrane helices flanking the channel lumen alone seem to determine the proton conduction mechanism.