gebhart/patrepeval huggingface dataset:
Characterization of AlGaN layer with high Al content grown by mixed‐source HVPE (2005)

Abstract Using mixed‐source hydride vapor‐phase epitaxy (HVPE), an AlGaN layer with high Al content on GaN/Al 2 O 3 substrate is obtained. The AlGaN layer grown by mixed‐source HVPE is characterized by X‐ray diffraction (XRD) measurements and cathodoluminescence (CL) spectra. In the mixed‐source HVPE technique, the AlGaN material is compounded from the chemical reaction between NH 3 and an aluminum–gallium chloride formed using HCl that is flowed over metallic Ga mixed with Al. The XRD measurements indicate that single‐crystal hexagonal AlGaN with high Al content had been grown. The CL spectra at 4 K show that the distribution of the Al on the AlGaN surface for very high Al content ( x = 0.8 in Al x Ga 1– x N) is not uniform. (© 2005 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Second‐Generation Inhibitors of the Mitochondrial Permeability Transition Pore with Improved Plasma Stability (2019)

Excessive mitochondrial matrix Ca<sup>2+</sup> and oxidative stress leads to the opening of a high-conductance channel of the inner mitochondrial membrane referred to as the mitochondrial permeability transition pore (mtPTP). Because mtPTP opening can lead to cell death under diverse pathophysiological conditions, inhibitors of mtPTP are potential therapeutics for various human diseases. High throughput screening efforts led to the identification of a 3-carboxamide-5-phenol-isoxazole compounds as mtPTP inhibitors. While they showed nanomolar potency against mtPTP, they exhibited poor plasma stability, precluding their use in in vivo studies. Herein, we describe a series of structurally related analogues in which the core isoxazole was replaced with a triazole, which resulted in an improvement in plasma stability. These analogues were readily generated using the copper-catalyzed "click chemistry". One analogue, N-(5-chloro-2-methylphenyl)-1-(4-fluoro-3-hydroxyphenyl)-1H-1,2,3-triazole-4-carboxamide (TR001), was efficacious in a zebrafish model of muscular dystrophy that results from mtPTP dysfunction whereas the isoxazole isostere had minimal effect.
Intra-host evolution during SARS-CoV-2 prolonged infection (2021)

Long-term infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents a challenge to virus dispersion and the control of coronavirus disease 2019 (COVID-19) pandemic. The reason why some people have prolonged infection and how the virus persists for so long are still not fully understood. Recent studies suggested that the accumulation of intra-host single nucleotide variants (iSNVs) over the course of the infection might play an important role in persistence as well as emergence of mutations of concern. For this reason, we aimed to investigate the intra-host evolution of SARS-CoV-2 during prolonged infection. Thirty-three patients who remained reverse transcription polymerase chain reaction (RT-PCR) positive in the nasopharynx for on average 18 days from the symptoms onset were included in this study. Whole-genome sequences were obtained for each patient at two different time points. Phylogenetic, populational, and computational analyses of viral sequences were consistent with prolonged infection without evidence of coinfection in our cohort. We observed an elevated within-host genomic diversity at the second time point samples positively correlated with cycle threshold (Ct) values (lower viral load). Direct transmission was also confirmed in a small cluster of healthcare professionals that shared the same workplace by the presence of common iSNVs. A differential accumulation of missense variants between the time points was detected targeting crucial structural and non-structural proteins such as Spike and helicase. Interestingly, longitudinal acquisition of iSNVs in Spike protein coincided in many cases with SARS-CoV-2 reactive and predicted T cell epitopes. We observed a distinguishing pattern of mutations over the course of the infection mainly driven by increasing A→U and decreasing G→A signatures. G→A mutations may be associated with RNA-editing enzyme activities; therefore, the mutational profiles observed in our analysis were suggestive of innate immune mechanisms of the host cell defense. Therefore, we unveiled a dynamic and complex landscape of host and pathogen interaction during prolonged infection of SARS-CoV-2, suggesting that the host's innate immunity shapes the increase of intra-host diversity. Our findings may also shed light on possible mechanisms underlying the emergence and spread of new variants resistant to the host immune response as recently observed in COVID-19 pandemic.
Visual hierarchical dimension reduction for exploration of high dimensional datasets (2003)

Traditional visualization techniques for multidimensional data sets, such as parallel coordinates, glyphs, and scatterplot matrices, do not scale well to high numbers of dimensions. A common approach to solving this problem is dimensionality reduction. Existing dimensionality reduction techniques usually generate lower dimensional spaces that have little intuitive meaning to users and allow little user interaction. In this paper we propose a new approach to handling high dimensional data, named Visual Hierarchical Dimension Reduction (VHDR), that addresses these drawbacks. VHDR not only generates lower dimensional spaces that are meaningful to users, but also allows user interactions in most steps of the process. In VHDR, dimensions are grouped into a hierarchy, and lower dimensional spaces are constructed using clusters of the hierarchy. We have implemented the VHDR approach into XmdvTool, and extended several traditional multidimensional visualization methods to convey dimension cluster characteristics when visualizing the data set in lower dimensional spaces. Our case study of applying VHDR to a real data set supports our belief that this approach is effective in supporting the exploration of high dimensional data sets.
Innovation in drug development: applying human factors to understand asthmatic patients’ needs. (2022)

<b>Aim:</b> Pharmacological therapy is crucial in the management of asthma, however understanding patient journey and exploring their perceptions is key to improve drug development. The objective of this human factors research was to identify the unmet needs of patients’ with asthma. <b>Methods:</b> Interviews were conducted in the United Kingdom, Italy and Germany with mild (N=20) and severe (N=28) asthma patients. <b>Results:</b> The study gathered patient perspective on the diagnosis process, symptoms, treatments, disease management and challenges with leaving with the disease. Participants mentioned that the diagnosis process could be improved by providing more information on asthma (33%), about the different available treatments (33%) and by receiving a faster diagnosis (17%). The most reported symptoms were difficulty breathing (more than 85% of participants mentioned it), coughing (&gt; 40%) and heavy feeling in the chest (&gt; 32%). The most common causes for triggering symptoms were related to allergies (34% of responses), the weather (26%) and&nbsp;physical exertion (15%).&nbsp;Several participants suggested to improve the medication focusing on dose frequency and effectiveness of the drug while some participants struggled with having numerous inhalers/treatments to manage, as well as the poor aesthetic of the inhaler and the non-discreetness. Overall challenges were associated to physical limitation (36%), social limitations (24%) and management of persistent symptoms (16%). <b>Conclusions:</b> Findings from this study could help pharmaceutical industries to improve the development of their products and generate new innovative solutions and concepts to enhance the patients’ quality of life.
A RANDOMIZED DOUBLE‐BLIND TRIAL OF TWO LOW DOSE COMBINED ORAL CONTRACEPTIVES (1979)

Fifty-five women using Loestrin-20 (20 microgram ethinyl oestradiol and 1 mg norethisterone acetate) as an oral contraceptive have been compared with a like number using Microgynon-30 (30 microgram ethinyl oestradiol and 150 microgram levonorgestrel) in a randomized, double-blind trial. Despite the small sample size, the main finding in the trial is clear-cut; Loestrin-20 provides poor cycle control and is thus less acceptable as an oral contraceptive than Microgynon-30. Although there is also a suggestion that Loestrin-20 may be less effective than Microgynon-30, the difference in the accidental pregnancy rates is not statistically significant.
Isolation and characterization of an abundant and novel 22-kDa protein (SM22) from chicken gizzard smooth muscle. (1987)

Chicken gizzard smooth muscle contains a highly abundant protein (SM22) with an apparent Mr on sodium dodecyl sulfate-polyacrylamide electrophoretic gels of 23,000. The ratio of actin:SM22:tropomyosin in this tissue is estimated to be 6.5(+/- 0.8):2.0(+/- 0.2):1.0. At least three isoelectric isoforms are present in ratios of alpha:beta:gamma of 14:5:1 with alpha the most basic and gamma the most acidic. A method for the purification of SM22 and partial separation of its isoforms is described. Amino acid analyses of purified alpha and beta demonstrate the presence of 1 and 2 half-cystines, respectively, and a lower content of basic amino acids in beta. A value of 22,000 for the Mr of alpha estimated by sedimentation equilibrium indicated its presence as a monomer at physiological ionic strengths. Estimates of the translational frictional coefficient (f/fmin) of alpha calculated from its Stokes radius (25.5 A) and Mr were consistent with its existence as a moderately asymmetric globular protein. Calculations based on its far-ultraviolet CD spectrum provided values of 37% alpha-helix, 31% beta-sheet, 5% beta-turn, and 27% random coil. SM22 was shown not to share functional properties with several proteins of similar Mr and isoelectric point such as myokinase, brain 23-kDa protein, and troponin I. We conclude that it is a novel protein not previously isolated or characterized from any tissue.
A new simulation method for nonlinear characteristics of SAW devices (2013)

In recent years, the linearity performance of the RF front end part of mobile phone handsets is a one of very hot topics. In such a situation, the requirement of high linearity to SAW duplexers has become strong. In this paper, a novel simulation method for nonlinear signals has been proposed. The nonlinear stress and current are represented by introducing nonlinear terms into the piezoelectric fundamental equations. They are connected as voltage and current sources in the electrical equivalent circuit of a SAW device, and the nonlinear signals observed at arbitrary external terminals are estimated. Very good agreement between the simulation and the measured values has been obtained for the third-order harmonic and IMD of SAW resonators.
An Antibody that Reconstitutes the “Base-On” Form of B12 Coenzymes (2002)

A monoclonal antibody, raised against coenzyme B12, binds natural “base-off” analogues 1 of coenzyme B12 and restructures them into the “base-on” form 2.
Designing of the Urban Public Bus Operation Dispatch System (2012)

The urban public bus operation dispatch system is one of the most important systems in ITS (Intelligent Transportation System). This paper describes the system in detail, including the system’s architecture, the bus onboard equipment and the system’s software part etc. Through integrating the single chip module, GPRS module, GPS module and other modules, the bus onboard equipment is designed. According to the object-oriented software engineering ideas and using UML (Unified Model language), the software system is designed. Finally, the bus onboard equipment and the system software part can send information each other using GPRS technology. The system has been implemented using Visual Studio 2005 C# language and tested in laboratory.
An area minimizer for floorplans with L-shaped regions (2003)

Given a floorplan with L-shaped regions, the problem considered is to choose an implementation from a set of possible implementations for each module such that the resultant floorplan will have minimum area, subject to the constraint that the dual polar graphs of the floorplan must be preserved. The concept of a cut line is extended, and eight types of cut lines that are used to decompose floorplans with L-shaped regions are defined. An O(n/sup 3/) time algorithm for deciding whether a given floorplan is decomposable is presented. A heuristic algorithm, which uses the cut tree obtained by the decomposition algorithm to solve the area minimization problem, is proposed. For floorplans that can not be decomposed by the decomposition algorithm, a branch-and-bound algorithm can be incorporated into the algorithm to solve the area minimization problem. The results obtained are superior to those obtained by running an existing mathematical programming package for at least 1 h, and the execution time is less than 3 min for the most complex test problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Penalized Preimage Learning in Kernel Principal Component Analysis (2010)

Finding the preimage of a feature vector in kernel principal component analysis (KPCA) is of crucial importance when KPCA is applied in some applications such as image preprocessing. Since the exact preimage of a feature vector in the kernel feature space, normally, does not exist in the input data space, an approximate preimage is learned and encouraging results have been reported in the last few years. However, it is still difficult to find a "good" estimation of preimage. As estimation of preimage in kernel methods is ill-posed, how to guide the preimage learning for a better estimation is important and still an open problem. To address this problem, a penalized strategy is developed in this paper, where some penalization terms are used to guide the preimage learning process. To develop an efficient penalized technique, we first propose a two-step general framework, in which a preimage is directly modeled by weighted combination of the observed samples and the weights are learned by some optimization function subject to certain constraints. Compared to existing techniques, this would also give advantages in directly turning preimage learning into the optimization of the combination weights. Under this framework, a penalized methodology is developed by integrating two types of penalizations. First, to ensure learning a well-defined preimage, of which each entry is not out of data range, convexity constraint is imposed for learning the combination weights. More insight effects of the convexity constraint are also explored. Second, a penalized function is integrated as part of the optimization function to guide the preimage learning process. Particularly, the weakly supervised penalty is proposed, discussed, and extensively evaluated along with Laplacian penalty and ridge penalty. It could be further interpreted that the learned preimage can preserve some kind of pointwise conditional mutual information. Finally, KPCA with preimage learning is applied on face image data sets in the aspects of facial expression normalization, face image denoising, recovery of missing parts from occlusion, and illumination normalization. Experimental results show that the proposed preimage learning algorithm obtains lower mean square error (MSE) and better visual quality of reconstructed images.
A Double Planetary Gear Train-CVT Transmission with Multiple Applications (1995)

&lt;div class="htmlview paragraph"&gt;A family of transmission systems based on a “Planetary Gear - CVT” mechanism is presented here. The systems considered consist of two compound planetary gear trains connected through a CVT pulley system to provide the power/torque split and recirculation function, without the use of additional clutches and/or chain drives. A two degree of freedom system results in which one of the degrees of freedom is directly related to the CVT ratio.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The mechanisms considered here combine the gear reduction function of compound planetary gear trains with the continuously variable trans-&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;used as a circulating power control unit.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The kinematics and dynamics of this family of systems is presented with emphasis on the belt forces, torques on the various shafts and the overall input/output velocity ratios through the CVT ratio span.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Then a parametric analysis is conducted to characterize the effect of the various functional ratios and parameters of the system in terms of the overall performance. Finally, various potential applications are discussed and the associated design configurations are presented.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Specifically, some applications related to automotive auxiliary equipment and industrial equipment transmissions are presented.&lt;/div&gt;
Stress Fractures and the Female Athlete (2000)

Stress injury to bone is the result of a temporary disturbance in the equilibrium between bone resorption and bone regeneration. Knowledge of the pathophysiology of bone in health and disease currently encompasses an interactive mode that includes biomechanical, hormonal, nutritional, and genetic factors. The current study will review possible etiologic theories for stress injuries to bone with a special emphasis on gender-related factors. Females may be more at risk for a stress injury to bone because of their unique hormonal environment, and other anatomic and gender factors.
Phosphorylation-Dependent Degradation of p300 by Doxorubicin-Activated p38 Mitogen-Activated Protein Kinase in Cardiac Cells (2005)

p300 and CBP are general transcriptional coactivators implicated in different cellular processes, including regulation of the cell cycle, differentiation, tumorigenesis, and apoptosis. Posttranslational modifications such as phosphorylation are predicted to select a specific function of p300/CBP in these processes; however, the identification of the kinases that regulate p300/CBP activity in response to individual stimuli and the physiological significance of p300 phosphorylation have not been elucidated. Here we demonstrate that the cardiotoxic anticancer agent doxorubicin (adriamycin) induces the phosphorylation of p300 in primary neonatal cardiomyocytes. Hyperphosphorylation precedes the degradation of p300 and parallels apoptosis in response to doxorubicin. Doxorubicin-activated p38 kinases alpha and beta associate with p300 and are implicated in the phosphorylation-mediated degradation of p300, as pharmacological blockade of p38 prevents p300 degradation. p38 phosphorylates p300 in vitro at both the N and C termini of the protein, and enforced activation of p38 by the constitutively active form of its upstream kinase (MKK6EE) triggers p300 degradation. These data support the conclusion that p38 mitogen-activated protein kinase regulates p300 protein stability and function in cardiomyocytes undergoing apoptosis in response to doxorubicin.
Introduction to this special section: Case studies: Conventionals (2019)

Case studies, with a focus on conventional systems, provide insight of seismic and well data sets in terms of characterizing reservoirs with innovative techniques and approaches. This special section contains three such papers from three different regions: offshore Brazil, the North Sea, and the Middle East. Each contribution presents a different geologic problem ranging from siliciclastics to volcanics to carbonates. The challenges faced in each paper were tackled using innovative approaches to reservoir characterization in complex geologic regions.
Mechanical properties of the P-selectin/PSGL-1 interaction (2003)

Using an Atomic Force Microscope (AFM), the mechanical properties of the P-selectin/PSGL-1 complex were studied with two separate methods. Both methods yielded similar results. The molecular complex displayed a linear relationship between force and molecular extension. The dimeric bond of the wild type PSGL-1 interaction resulted in a spring constant roughly double that of a recombinant monomeric PSGL-1 interaction, suggesting that the two subunits of the dimeric interaction act as springs in parallel. The P-selectin portion of the complex was found to contribute the most to the mechanical compliance of the molecular complex.
Synthesis of the Thomsen-Friedenreich-antigen (TF-antigen) and binding of Galectin-3 to TF-antigen presenting neo-glycoproteins (2020)

The Thomsen-Friedenreich-antigen, Gal(β1-3)GalNAc(α1-O-Ser/Thr (TF-antigen), is presented on the surface of most human cancer cell types. Its interaction with galectin 1 and galectin 3 leads to tumor cell aggregation and promotes cancer metastasis and T-cell apoptosis in epithelial tissue. To further explore multivalent binding between the TF-antigen and galectin-3, the TF-antigen was enzymatically synthesized in high yields with GalNAc(α1-EG3-azide as the acceptor substrate by use of the glycosynthase BgaC/Glu233Gly. Subsequently, it was coupled to alkynyl-functionalized bovine serum albumin via a copper(I)-catalyzed alkyne-azide cycloaddition. This procedure yielded neo-glycoproteins with tunable glycan multivalency for binding studies. Glycan densities between 2 and 53 glycan residues per protein molecule were obtained by regulated alkynyl-modification of the lysine residues of BSA. The number of coupled glycans was quantified by sodium dodecyl sulfate polyacrylamide gel electrophoresis and a trinitrobenzene sulfonic acid assay. The binding efficiency of the neo-glycoproteins with human galectin-3 and the effect of multivalency was investigated and assessed using an enzyme-linked lectin assay. Immobilized neo-glycoproteins of all modification densities showed binding of Gal-3 with increasing glycan density. However, multivalent glycan presentation did not result in a higher binding affinity. In contrast, inhibition of Gal-3 binding to asialofetuin was effective. The relative inhibitory potency was increased by a factor of 142 for neo-glycoproteins displaying 10 glycans/protein in contrast to highly decorated inhibitors with only 2-fold increase. In summary, the functionality of BSA-based neo-glycoproteins presenting the TF-antigen as multivalent inhibitors for Gal-3 was demonstrated.
New directions in teaching the fundamentals of computer science — discrete structures and computational analysis (1973)

Since the publication of the Curriculum 68 report of the ACM Committee [CUR 68], undergraduate computer science programs have undergone substantial changes. Notably, many courses previously taught at the graduate level have shifted down to the undergraduate level; new areas have developed and consolidated but were not covered by the ACM report. These facts make it necessary to revise and update the Curriculum 68 report. An important factor which could help the revision is the actual experience gained through the development of many new undergraduate computer science programs since the publication of Curriculum 68 report five years ago. More specifically, most recommendations of the ACM report contain just the subject areas to be taught. The actual teaching experiences of these courses have formulated certain basic philosophies and formats of presentation. It is helpful, in our opinion, to compare the merits of these philosophies and formats of presentation. In this paper, we shall discuss the basic philosophies and formats of presentation of two undergraduate computer science courses—Introduction to Discrete Structures, and Computational Analysis. The former coincides with the B3 course of the Curriculum 68 report; the latter is a new course not covered by the ACM report.
[Anti-tumor effects of DDP-PLLA-CNTs on human cholangiocarcinoma cell line in vitro]. (2014)

DDP-PLLA-CNTs have drug sustained-release characteristics and can significantly inhibit the proliferation of QBC939 cell line.