gebhart/patrepeval huggingface dataset:
Biochemical Characterization and Substrate Specificity of Autophagin-2 from the Parasite Trypanosoma cruzi (2015)

The genome of the parasite Trypanosoma cruzi encodes two copies of autophagy-related cysteine proteases, Atg4.1 and Atg4.2. T. cruzi autophagin-2 (TcAtg4.2) carries the majority of proteolytic activity and is responsible for processing Atg8 proteins near the carboxyl terminus, exposing a conserved glycine. This enables progression of autophagy and differentiation of the parasite, which is required for successful colonization of humans. The mechanism of substrate hydrolysis by Atg4 was found to be highly conserved among the species as critical mutations in the TcAtg4.2, including mutation of the conserved Gly-244 residue in the hinge region enabling flexibility of the regulatory loop, and deletion of the regulatory loop, completely abolished processing capacity of the mutants. Using the positional scanning-substrate combinatorial library (PS-SCL) we determined that TcAtg4.2 tolerates a broad spectrum of amino acids in the P4 and P3 positions, similar to the human orthologue autophagin-1 (HsAtg4B). In contrast, both human and trypanosome Atg4 orthologues exhibited exclusive preference for aromatic amino acid residues in the P2 position, and for Gly in the P1 position, which is absolutely conserved in the natural Atg8 substrates. Using an extended P2 substrate library, which also included the unnatural amino acid cyclohexylalanine (Cha) derivative of Phe, we generated highly selective tetrapeptide substrates acetyl-Lys-Lys-Cha-Gly-AFC (Ac-KKChaG-AFC) and acetyl-Lys-Thr-Cha-Gly-AFC (Ac-KTChaG-AFC). Althoughthese substrates were cleaved by cathepsins, making them unsuitable for analysis of complex cellular systems, they were recognized exclusively by TcAtg4.2, but not by HsAtg4B nor by the structurally related human proteases SENP1, SENP2, and UCH-L3.
Regulation of Cerebral Microcirculation. Update. (2000)

The present symposium during Brain 99 was convened to explore the current aspects of the neural (extrinsic and intrinsic) and chemical control of the microvasculature in the brain with specific relevance to stimuli and rapid flow responses. N. Suzuki demonstrated the presence of neurokinin-1 receptors along the axons of vasoactive intestinal polypeptide-containing cerebrovascular parasympathetic nerves. Since the receptors were activated by substance P, calcitonin gene-related peptide and neurokinin released from coexisting sensory nerve fibers, the parasympathetic (vasodilating) fibers could effect rapid local flow increases. N. Suzuki, however, considered this as part of an elaborate defensive network protecting the brain from invasions by noxious substances. E. Hamel discussed the responses of the microvessels to neurotransmitters and suggested that nitric oxide (NO) released from intrinsic neurons may serve as a relay in the flow activation responses by intracerebral cholinergic fibers originating in the basal forebrain nuclei. D. Busija summarized a vasodilating system of activated N-methyl-D-asparate receptors located on neurons involving Ca influx-NO production, and activated ATP-sensitive potassium channels located in the vascular system. According to Busija, such interactions were disrupted during hypoxia and ischemia due to cyclooxygenase-derived superoxide anion. M. Lauritzen observed a 10 times larger increase in blood flow on stimulation of the climbing nerve as compared with that following the parallel nerve stimulation. The former transmitters are considered by him to be NO and K, and the latter NO and adenosine. Each speaker singled out NO as a common mediator for the microvasculature in the rapid local flow increases.
Classification of Breast Tumors by Grade and Steroid Receptor Status Using Pattern Recognition Analysis of Infrared Spectra (1999)

Infrared (IR) spectroscopy applied to tissue sections yields complex spectra that provide a molecular fingerprint of the tissue. We have studied a cohort of 77 breast tumors by IR spectroscopy to develop an objective method for the assignment of grade of breast tumors. Although the major variations between spectra from different tumors were in absorptions arising from triglycerides (adipose tissue) and collagen, subtle changes in spectra could be detected that were independent of cellularity and tissue composition. Using a specific multivariate pattern recognition strategy to associate these changes in spectra with different tumor grades, we then were able to accurately reclassify tumors by grade (87% accuracy; kappa = 0.835). A similar approach allowed classification of steroid receptor status (93% accuracy; kappa = 0.852). We conclude that IR spectroscopy may have clinical utility in the objective assignment of breast tumor grade.
Clonal Evolution in Ph-Negative, bcr-Positive Chronic Myeloid Leukaemia before and after Bone Marrow Transplantation (1989)

A 26-year-old man, who presented with bilateral fundal haemorrhages, was found to have chronic myeloid leukaemia (CML). The Ph chromosome was not present but a clone with t(1;9) (p32;q34) was detected. On referral for bone marrow transplant (BMT) he was found to be in accelerated phase with clonal evolution in three cell lines inv(3)(q21q26); inv(3)(q),i(17q); inv(3q)+8. Molecular investigation revealed a breakpoint on chromosome 22 within the breakpoint cluster region (bcr) similar to that found in Ph+ cases. After BMT, from an HLA-identical sister, successful engraftment (46,XX) was accompanied by evidence of a residual host cell population with further evolution (del(7)(q22)) and persistence of the bcr+ clone. Acute myeloid leukaemia, detected 5 months later, was associated with predominance of the clone 46XY,t(1;9),inv(3q),del(7)(q22) which failed to respond to treatment and the patient died 6.5 months after BMT. This case indicates that BMT, after the acquisition of additional chromosomal change in accelerated phase, may fail owing to persistence of the leukaemic clone. In addition the BMT conditioning regimen may produce further abnormalities which confer drug resistance on the persisting clone, which can emerge as an intractable myeloid blast crisis.
Migration velocity analysis in factorized VTI media (2004)

Abstract One of the main challenges in anisotropic velocity analysis and imaging is simultaneous estimation of velocity gradients and anisotropic parameters from reflection data. Approximating the subsurface by a factorized VTI (transversely isotropic with a vertical symmetry axis) medium provides a convenient way of building vertically and laterally heterogeneous anisotropic models for prestack depth migration. The algorithm for P-wave migration velocity analysis (MVA) introduced here is designed for models composed of factorized VTI layers or blocks with constant vertical and lateral gradients in the vertical velocity VP0. The anisotropic MVA method is implemented as an iterative two-step procedure that includes prestack depth migration (imaging step) followed by an update of the medium parameters (velocity-analysis step). The residual moveout of the migrated events, which is minimized during the parameter updates, is described by a nonhyperbolic equation whose coefficients are determined by 2D semblance scanning. For piecewise-factorized VTI media without significant dips in the overburden, the residual moveout of P-wave events in image gathers is governed by four effective quantities in each block: (1) the normal-moveout velocity Vnmo at a certain point within the block, (2) the vertical velocity gradient kz, (3) the combination k^x = kx1 + 2δ of the lateral velocity gradient kx and the anisotropic parameter δ, and (4) the anellipticity parameter η. We show that all four parameters can be estimated from the residual moveout for at least two reflectors within a block sufficiently separated in depth. Inversion for the parameter η also requires using either long-spread data (with the maximum offset-to-depth ratio no less than two) from horizontal interfaces or reflections from dipping interfaces. To find the depth scale of the section and build a model for prestack depth migration using the MVA results, the vertical velocity VP0 needs to be specified for at least a single point in each block. When no borehole information about VP0 is available, a well-focused image can often be obtained by assuming that the vertical-velocity field is continuous across layer boundaries. A synthetic test for a three-layer model with a syncline structure confirms the accuracy of our MVA algorithm in estimating the interval parameters Vnmo, kz, k^x, and η and illustrates the influence of errors in the vertical velocity on the image quality.
Advanced Optical Techniques for Sensing and Imaging in Harsh Environments (2019)

Advances in aircraft propulsion technologies require new techniques for performance evaluation of aircraft components and subsystems as well as reliable in-flight control and health management. Those components and subsystems operate in harsh environments and for a proper operation these environments should be constantly monitored to obtain the designed performance of the engine. Optical techniques due to their immunity to electromagnetic radiation, chemical stability, and other unique features pose to meet the ever increasing requirements of the industry.The presentation will address applications of advanced optical techniques for both for sensing and imaging. In the process we will address fiber optics Bragg temperature sensors that were developed at NASA Glenn Research Center and tested at NASA Armstrong Flight Research Center as well as other advanced techniques for sensing and imaging in harsh environments. The presentation will also include discussion on various applications of presented techniques and proposed directions for future development.
Signaling Components in Bacterial Locomotion and Sensory Reception (2000)

The Fifth Biennial Conference on Bacterial Locomotion and Signal Transduction was held on 16 to 21 January 1999 in Cuernavaca, Mexico. The meeting brought together 202 researchers in the fields of bacterial motility, transcription control by environmental signals, and bacterial behavior and
Horizontal and Vertical Scaling of Cloud Geometry Inferred from CloudSat Data (2018)

Abstract A method is described to characterize the scale dependence of cloud chord length using cloud-type classification reported with the 94-GHz CloudSat radar. The cloud length along the CloudSat track is quantified using horizontal and vertical structures of cloud classification separately for each cloud type and for all clouds independent of cloud type. While the individual cloud types do not follow a clear power-law behavior as a function of horizontal or vertical scale, a robust power-law scaling of cloud chord length is observed when cloud type is not considered. The exponent of horizontal length is approximated by β ≈ 1.66 ± 0.00 across two orders of magnitude (~10–1000 km). The exponent of vertical thickness is approximated by β ≈ 2.23 ± 0.03 in excess of one order of magnitude (~1–14 km). These exponents are in agreement with previous studies using numerical models, satellites, dropsondes, and in situ aircraft observations. These differences in horizontal and vertical cloud scaling are consistent with scaling of temperature and horizontal wind in the horizontal dimension and with scaling of buoyancy flux in the vertical dimension. The observed scale dependence should serve as a guide to test and evaluate scale-cognizant climate and weather numerical prediction models.
Amplification of stimulated soft x-ray emission in a confined plasma column (1985)

An enhancement of \ensuremath{\sim}100 of stimulated emission over spontaneous emission of the C vi 182-A\r{} line (one-pass gain \ensuremath{\sim}6.5) was measured in a recombining, magnetically confined plasma column by two independent techniques involving intensity calibrated extreme xuv monochromators. Additional confirmation that the enhancement was due to stimulated emission has been obtained with a soft x-ray mirror; with 12% measured effective reflectivity of the mirror, a 120% increase in intensity of the C vi 182-A\r{} line in the axial direction was observed.
Preconditioned Newton Methods for Fully Coupled Reservoir and Surface Facility Models (1998)

Abstract The fully implicit coupling of surface facilities with a reservoir model can lead to a significant increase in computing time. The focus of this paper is on the development of methods that can minimize the impact of the facility model on the global solution procedure. A local grid refinement preconditioner is developed to accelerate convergence of the full flow field implicit simulation. P. 181
Effect of Estriol on Bone Loss in Postmenopausal Japanese Women: A Multicenter Prospective Open Study (1996)

Estriol prevented postmenopausal bone loss and improved climacteric symptoms effectively with low incidence of genital bleeding.
Chelating‐agent suppression of cadmium‐induced hepatotoxicity (1987)

The administration of sodium N-methyl-N-dithiocarboxy-D-glucamine (NaG) at 500 mg/kg, i.p., or sodium calcium diethylenetriaminepentaacetic acid (DTPA) at 632.5 mg/kg, i.p., reduces the serum enzyme levels characteristic of hepatic damage following the intravenous administration of cadmium chloride (3.5 mg CdCl2.2.5H2O/kg). Some effect on serum enzyme levels was found even when the interval between administration of cadmium chloride and that of the antagonist was as great as 4 h. The enzymes examined included aspartate aminotransferase (AST), gamma-glutamyl transpeptidase (GGT), alanine aminotransferase (SGPT), and alkaline phosphatase (AP). A histopathological examination of the livers of such animals also reveals the presence of a significant protective action.
De-emulsifiers for water-in-crude oil-emulsions (1997)

The efficiency of 18 different polyalkylphenols-polyalkylene-polyamines-formaldehyde ethoxylates (PAPAFE) in the deemulsification of water-in-crude oil-emulsion were studied. In this respect, two naturally occurring Egyptian water-in-crude oil-emulsions were used to test the investigated de-emulsifiers. The effect of the variation in the molecular structure of the (PAPAFE) on their de-emulsification potency is investigated. The investigation reveals that de-emulsifiers containing nonyl phenol reduce crude oil-water interfacial tension (IFT) and are more efficient than those containing dodecyl phenol. PAPAFE containing more amino groups are found to have better emulsion breaking ability. This is attributed to their enhanced ability to solubilize asphaltenes, which are the prime motivators for crude oil-water emulsion stability. They drag asphaltenes crosslinked at the water-crude oil interface and consequently, resulting in a substantial decrease in emulsion stability. There exists an optimum hydrophilic-lipophilic balance (HLB) for the investigated PAPAFE, ranging from 12 to 13.5 at which their maximum de-emulsification ability is attained. All studied APAFE showed increased de-emulsification performance by increasing the temperature from 50 to 70°C. Increasing the temperature reduces the viscosity of the crude oil continuous phase and increases the rate of diffusion of both the surfactant molecules and the dispersed water droplets. This will cause an increase in the rate of coalescence of the water droplets.
Improving the sensitivity of the heat‐transfer method (HTM) for cancer cell detection with optimized sensor chips (2015)

In this article, we increased the sensitivity of the heat‐transfer method (HTM) for the detection of breast cancer cells (ZR‐75‐1 cells, see figure) in phosphate buffered saline (PBS). The effect of small technological changes on the limit of detection (LoD) of the methodology was examined. To this extent, polished aluminum substrates with a mirror finish were used, replacing the unpolished chips used in previous studies. These chips were coated with a polyurethane layer and imprinted for the target cell type, creating a so‐called surface imprinted‐polymer (SIP). Binding of target cells to the SIP resulted in an increase of the thermal resistance at the solid‐liquid interface under study. Background thermal resistance measurements were performed with polished and unpolished aluminum substrates. In addition, the effect of using silver paste as thermal coupling between the aluminum chip and the copper heat provider was analyzed. The results of these experiments reveal that optimal thermal contact is achieved when directly coupling the copper heat provider to the polished side of the aluminum substrate as evidenced by a decrease in the baseline thermal resistance. In addition, noise levels on the heat‐transfer resistance ( R th ) signal decreased by a factor in the optimal configuration. Dose‐response curves were obtained using the optimized methodology and were compared with results obtained with the original substrates. These quantitative experiments demonstrated an improvement of the LoD by approximately thirty percent. ZR‐75‐1 cells applied onto a home‐made rubber stamp.
A Study on Zero Sensitive Control System (2009)

Since system uncertainties are unavoidable in the modeling, control systems are generally required to be insensitive to these uncertainties. In this paper, the problem of control system design which is insensitive to these uncertainties is studied, and a structure of system uncertainties which do not affect the control performance is clarified.
Interaction of Vasopressin and Splenda on Glucose Metabolism and Long-term Preferences under<i>Ad-libitum</i>and Food-restricted Conditions (1999)

Previous research has demonstrated that vasopressin-containing rats are capable of adapting to the stress of food restriction; whereas, vasopressin-deficient rats cannot adapt to this stressor. In the present study, the value of using a low-calorie (Splenda) or no-calorie (Equal) artificial sweetener to reverse the deleterious effects of food restriction in vasopressin-deficient rats was examined. In association with this effect, the role of vasopressin in long-term preferences for the two artificial sweeteners was studied. Vasopressin-deficient, Brattleboro (DI) rats and vasopressin-containing, Long-Evans (LE) rats underwent an habituation phase during which they had ad-libitum access to food. This was followed by an experimental phase during which the rats were divided into four groups. (1) DI rats continued with ad-libitum feeding, (2) LE rats continued with ad-libitum feeding, (3) DI rats subjected to 23 h of food restriction, and (4) LE rats subjected to 23 h of food restriction. All rats had ad-libitum access to an 8% Splenda solution, a 1% Equal solution, and water throughout both phases of the experiment. The deleterious effects of food restriction were completely reversed in DI rats, including survival, no stomach pathology, and normal plasma levels of glucose and urea nitrogen.
Distinct Subcellular Localization of Transiently Expressed Types 1 and 2 Iodothyronine Deiodinases as Determined by Immunofluorescence Confocal Microscopy (2000)

We compared the subcellular localization of FLAG-epitope tagged Types 1 and 2 deiodinases (D1 and D2) transiently expressed in human embryonic kidney (HEK-293) and mouse neuroblastoma (NB2A) cells. D2 is an integral membrane protein based on resistance to extraction at pH 11 with the NH2 terminus in the endoplasmic reticulum (ER). Immunofluorescence confocal microscopy using anti-FLAG and anti-GRP78/BiP antibodies showed the FLAG-D1 signal was found in the periphery of the cells and not co-localized with the ER specific marker GRP78/BiP. On the other hand, FLAG-D2 protein was found in the ER co-localized with the GRP78/BiP protein. These differential distribution patterns indicate subcellular sorting of D1 and D2 is determined by intrinsic protein sequence and can explain the ready access of D2-generated T3 to the nucleus.
Les chemins de fer du Mozambique (1930)

Célérier Jean. Les chemins de fer du Mozambique. In: Annales de Géographie, t. 39, n°222, 1930. pp. 665-666.
Critical Frequency of Photic Driving in the Diagnosis of Multiple Sclerosis (1986)

<h3>To the Editor.</h3> —Ramani et al<sup>1</sup>raised interesting questions in their article comparing critical frequency of photic driving (CFPD) with pattern visual evoked response (PVER) in the diagnosis of multiple sclerosis (MS). The authors reviewed the initial article by Celesia and Daly<sup>2</sup>and our initial study<sup>3</sup>and found "disagreement about the relative sensitivities" of PVER and CFPD testing. In reevaluating this technique, Ramani et al<sup>1</sup>reliably replicated our methods for testing CFPD, with only "minor differences." They state that their results and conclusions did not replicate those of our laboratory or those of Celesia and Daly.<sup>2</sup> There are several possible reasons for this that are not adequately discussed in their article. First, they report that we found CFPD to be "somewhat more sensitive than PVER." In fact, in our initial report on 27 patients, we found CFPD to be "slightly more sensitive" and we emphasized
HLA Reduces Killer Cell Ig-like Receptor Expression Level and Frequency in a Humanized Mouse Model (2013)

NK cells use NK cell receptors to be able to recognize and eliminate infected, transformed, and allogeneic cells. Human NK cells are prevented from killing autologous healthy cells by virtue of inhibitory NKRs, primarily killer cell Ig-like receptors (KIR) that bind "self" HLA class I molecules. Individual NK cells stably express a selected set of KIR, but it is currently disputed whether the fraction of NK cells expressing a particular inhibitory KIR is influenced by the presence of the corresponding HLA ligand. The extreme polymorphism of the KIR and HLA loci, with wide-ranging affinities for individual KIR and HLA allele combinations, has made this issue particularly hard to tackle. In this study, we used a transgenic mouse model to investigate the effect of HLA on KIR repertoire and function in the absence of genetic variation inside and outside the KIR locus. These H-2K(b-/-) and H-2D(b-/-) mice lacked ligands for inhibitory Ly49 receptors and were transgenic for HLA-Cw3 and a KIR B haplotype. In this reductionist system, the presence of HLA-Cw3 reduced the frequency of KIR2DL2(+) cells, as well as the surface expression levels of KIR2DL2. In addition, in the presence of HLA-Cw3, the frequency of NKG2A(+) cells and the surface expression levels of NKG2A were reduced. In line with these findings, both transgene-encoded KIR and endogenous NKG2A contributed to the rejection of cells lacking HLA-Cw3. These findings support the idea that HLA influences the human KIR repertoire.
Logical Path Delay Distribution And Transistor-Sizing (2005)

The merits of high performance design are high speed, low power consumption, and small silicon area. Area optimization could be achieved at different levels of the design abstraction. In this paper area-delay optimization technique that depends on library-free synthesis and transistor sizing is presented. This technique can be used to optimize the path delay or to minimize the path area for a specific given required time. It is generated depending on the CMOS inverter delay model, modified logical effort (MLE) model [A. Kabbani, D. Al-Khalili, and A. J. Al-Khalili (2004)] and the CMOS gate transition time model [A. Kabbani (2004)]. The proposed technique achieves better performance as compared to Synopsys's design compiler. For a given required time, the presented technique saves on area-delay product by about 50% on the average.