gebhart/patrepeval huggingface dataset:
Data System and Data Management in a Federation of HPC/Cloud Centers (2022)

This chapter describes the federation of high-performance computing/data centers by a highly reliable distributed data infrastructure (DDI) as part of the LEXIS project (Large-Scale EXecution for Industry and Society, H2020 GA 825532). LEXIS offers user-friendly, cross-site orchestration for simulation and big data workflows, as well as data management, currently implemented at the IT4Innovations National Supercomputing Center (IT4I, CZ) and the Leibniz Supercomputing Centre (LRZ, DE). The chapter outlines requirements and implementation for such an infrastructure in the European context, considering the FAIR principles of modern research data management. Our high-reliability setup of iRODS (Integrated Rule-Oriented Data System) as data middleware is described, as well as the hardware behind the DDI, including burst buffers. A unified user access is ensured using the LEXIS authentication and authorization infrastructure. The LEXIS DDI has been integrated successfully into the LEXIS platform via REST APIs, and into the European data management landscape via EUDAT interfaces and tools.
Situational language training for hotel receptionists (2005)

This paper presents the lessons learned in experimenting with Thetis, an EC project focusing on the creation and localization of enhanced on-line pedagogical content for language learning in tourism industry. It is based on a general innovative approach to language learning that allows employees to acquire practical oral and written skills while navigating a relevant professional scenario. The approach is enabled by an underlying platform (EXILLS) that integrates virtual reality with a set of linguistic, technologies to create a new form of dynamic, extensible, goal-directed e-content.
The optical and detector properties of the PbS-Si heterojunction (1980)

Related optical and detector properties of the PbS-Si heterojunction (HJ) are presented and discussed. A direct optical bandgap at 300 K of 0.44 eV has been measured for PbS-Si versus 0.42 eV for PbS-sapphire. The HJ photocurrent frequency response has been determined to consist of two waveform components: Type A, a "spike" present only during the turn-on and turn-off stages of a radiation pulse, is bias independent; Type B, a continuous response, which increases with reverse bias. The temperature characteristic of the photocurrent has been observed to be strongly dependent on which waveform type dominates. The HJ noise current is Johnson noise limited at zero bias and 1/ <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</tex> noise limited under reverse bias. The HJ dark current is postulated to have four main generation mechanisms depending on temperature: Si-generated current, diffusion current from the PbS, PbS depletion or surface-generation current, and surface leakage. The PbS-Si HJ spectral response combines the effect of intrinsic absorption in Si and PbS and transitions between the Si and PbS valence bands. A detectivity of 1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sup> cm . Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sup> /W has been obtained at 3 µm.
Family History and Cardiovascular Risk in Familial Hypercholesterolemia (2003)

In FH families, LDL-C levels allow accurate diagnosis of FH in childhood. Moreover, increased LDL-C and lipoprotein(a) and decreased HDL-C levels in children identify FH kindreds with the highest CVD risk.
Anion recognition by a bidentate chalcogen bond donor (2016)

Perfluoroaryl-substituted tellurophenes act as anion receptors through noncovalent chalcogen bonding interactions. Linking two tellurophenes through an ethynylene group results in a significant level of chelate cooperativity, thus demonstrating that chalcogen bonding can be used to achieve multidentate anion recognition.
Rate-Equilibrium Relationships in Hydride Transfer Reactions:  The Role of Intrinsic Barriers (2002)

A literature survey on the kinetics of hydride abstractions from CH-groups by carbocations reveals a general phenomenon: Variation of the hydride acceptor affects the rates of hydride transfer to a considerably greater extent than an equal change of the thermodynamic driving force caused by variation of the hydride donor. The origin of this relationship was investigated by quantum chemical calculations on various levels of ab initio and DFT theory for the transfer of an allylic hydrogen from 1-mono- and 1,1-disubstituted propenes (XYC=CH-CH(3)) to the 3-position of 1-mono- and 1,1-disubstituted allyl cations (XYC=CH-CH(2)(+)). The discussion is based on the results of the MP2/6-31+G(d,p)//RHF/6-31+G(d,p) calculations. Electron-releasing substituents X and Y in the hydride donors increase the exothermicity of the reaction, while electron-releasing substituents in the hydride acceptors decrease exothermicity. In line with Hammond's postulate, increasing exothermicity shifts the transition states on the reaction coordinate toward reactants, as revealed by the geometry parameters and the charge distribution in the activated complexes. Independent of the location of the transition state on the reaction coordinate, a value of 0.72 is found for Hammond-Leffler's alpha = deltaDeltaG/deltaDelta(r)G degrees when the hydride acceptor is varied, while alpha = 0.28 when the hydride donor is varied. The value of alpha thus cannot be related with the position of the transition state. Investigation of the degenerate reactions XYC=CH-CH(3) + XYC=CH-CH(2)(+) indicates that the migrating hydrogen carries a partial positive charge in the transition state and that the intrinsic barriers increase with increasing electron-releasing abilities of X and Y. Substituent variation in the donor thus influences reaction enthalpy and intrinsic barriers in the opposite sense, while substituent variation in the acceptor affects both terms in the same sense, in accord with the experimental findings. Marcus theory is employed to treat these effects quantitatively.
Magneto-Mechanical Model of an Enzyme (2002)

It has always been difficult to clearly explain to biochemistry students how enzymes work. The idea of enzyme-substrate stereospecificity, active site, coupled reactions, inhibitor or activator effects, mono- and bisubstrate reactions or any other aspect related to the mechanism of action of enzymes are in general abstract and difficult concepts for students taking introductory courses in biochemistry. On the other hand, students are more familiar with mechanical or magnetic objects, and normally they have no problem understanding how they work. Accordingly, a magneto-mechanical model is proposed as a didactic resource to show in class how enzymes can catalyze biochemical reactions. This model is also helpful for introducing the concept of coupled reactions and many other structural and mechanistic aspects of enzyme reactions.
Large area molded silicon nitride micro mirrors (2003)

Large area molded torsional micromirrors have been fabricated from thin films of low-pressure chemical vapor deposition silicon nitride. Optical surfaces as large as 400 μm in diameter with surface deviations less than 0.33 μm have been fabricated from 1.5-μm-thick layers of silicon nitride. Surface flatness was achieved by molding latticed silicon nitride fins to the backside of the mirrors. Fins as deep as 28 μm were constructed by deep reactive ion etching bulk silicon to produce molds for the fins prior to silicon nitride deposition. Mirrors with fins were shown to be insensitive to temperature effects within the range of 50-120 /spl deg/C. An optical switch with insertion loss less than 2 dB was constructed with the mirrors, demonstrating their potential as switch elements in optical systems.
Potential Role of Abnormal Ion Transport in the Pathogenesis of Chronic Sinusitis (2006)

We established methods for well-differentiated sinus epithelial cultures. The cells exhibited Na(+) absorption and Cl(-) secretion, and elevated rates of ion transport may be pathophysiologically relevant in chronic sinusitis.
Metastatic Dedifferentiated Chordoma With Elevated β-hCG (2002)

Chordomas are relatively uncommon bone tumors, and fewer than 10% of cases are classified as dedifferentiated chordomas. These tumors tend to be more clinically aggressive than chordomas and have a higher incidence of early distant metastases. In this case report, we describe a 24-year-old man with dedifferentiated chordoma and multiple pulmonary metastases. Further laboratory analysis revealed an elevated serum beta-human chorionic gonadotropin level. Unfortunately, the patient's clinical condition deteriorated rapidly and he died before receiving any treatment for his cancer. However, chemotherapy may play a useful role in the management of systemic disease in patients with dedifferentiated chordoma.
Faculty Opinions recommendation of Distinct compartmentalization of the chemokines CXCL1 and CXCL2 and the atypical receptor ACKR1 determine discrete stages of neutrophil diapedesis. (2019)

Highlights d The CXCR2 ligands CXCL1 and CXCL2 play distinct roles in neutrophil diapedesis d Endothelial cell (EC)-and
Applying video annotation technology on web-based multimedia learning framework (2008)

With the Web and hypertext technology, we can obtain many kinds of information and data on Web. Moreover, streaming and compression technology enable us to access multimedia data through network more easily than before. Hypertext technology has been used in linking Web resources popularly. However, we usually only can follow the original sequence of a video to browse it. Our research extends Hypervideo concept and combines hypertext concept and video presentation to give a different presentation style. We constructed a framework for our Web-based Hypervideo system which is mainly used for instruction. The system offers an easy-to-use interface for teachers to annotate and add information on video. The player tool designed for students can re-present the provided annotations and information. A prototype system has been built for evaluating the proposed framework. According to the experiment result, the proposed framework is feasible for this kind of application. The prototype system also verifies that the user-interface and data model are designed in a good way.
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. (2017)

In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository.
Supplementary material from "Flagellar kinematics reveals the role of environment in shaping sperm motility" (2020)

Swimming spermatozoa from diverse organisms often have very similar morphologies, yet different motilities as a result of differences in the flagellar waveforms used for propulsion. The origin of these differences has remained largely unknown. Using high-speed video microscopy and mathematical analysis of flagellar shape dynamics, we quantitatively compare sperm flagellar waveforms from marine invertebrates to humans by means of a novel phylokinematic tree. This new approach revealed that genetically dissimilar sperm can exhibit strikingly similar flagellar waveforms and identifies two dominant flagellar waveforms among the deuterostomes studied here, corresponding to internal and external fertilizers. The phylokinematic tree shows marked discordance from the phylogenetic tree, indicating that physical properties of the fluid environment, more than genetic relatedness, act as an important selective pressure in shaping the evolution of sperm motility. More broadly, this work provides a physical axis to complement morphological and genetic studies to understand evolutionary relationships.
Towards clean and atomically flat ZnO (000&1macr;) surfaces (2006)

Abstract We established a cleaning procedure to obtain atomically flat $000 \bar {1}$ surfaces from pressurized melt grown ZnO using ex‐situ and in‐situ processing. The ex‐situ chemical cleaning consisted in removing the surface fluid layer and contaminants from the surface. The physical in‐situ procedure used sputtering‐annealing cycles to clean and reconstruct the surface. 3 key parameters were in‐situ investigated: the annealing time, the annealing temperature and the sputtering energy. Investigations were carried out by means of Low Energy Electron Diffraction (LEED), Auger Electron Spectroscopy (AES), X‐ray Photoemission Spectroscopy (XPS), Time of Flight of Secondary Ion Mass Spectrometry (ToF‐SIMS), Atomic Force Microscopy and Spectroscopy (AFM and AFS) and Scanning Tunnelling Microscopy (STM). (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Corticopontine projection in the rat: The distribution of labelled cortical cells after large injections of horseradish peroxidase in the pontine nuclei (1989)

The distribution of cortical cells projecting to the pontine nuclei in rats was studied by making large injections of horseradish peroxidase that filled the basilar pons and measuring the density of labelled cells in each cortical area. All retrogradely labelled cells were layer V pyramidal cells. The highest densities of labelled cells were observed in the motor areas. The lowest densities were in temporal association cortex and perirhinal cortex. Visual cortical areas, including the primary visual cortex, provided a major source of pontine projections. The distribution of corticopontine cells within the primary visual cortex was studied in more detail. In all cases the highest density of labelled cells was observed in the region of cortex that represents the nasal visual field. Control injections into brainstem regions adjacent to the pontine nuclei produced a much lower absolute density of retrogradely labelled cortical cells and the distribution of those cells was different from that observed following pontine injections. We conclude that every area of the rat's cerebral cortex projects to the pontine nuclei and that there are consistent variations in the density of the projections both between and within areas.
A robust automated markerless registration framework for neurosurgery navigation (2014)

Our system can quickly reconstruct the intra-operative face, and then efficiently and accurately align it to the pre-operative image, meeting the registration requirements in neurosurgery navigation. It avoids a tedious set-up process for surgeons.
A multi-pronged investigation of option generation using depression, PET and modafinil (2021)

Option generation is a critical process in decision making, but previous studies have largely focused on choices between options given by a researcher. Consequently, how we self-generate options for behaviour remain poorly understood. Here, we investigated option generation in major depressive disorder and how dopamine might modulate this process, as well as the effects of modafinil (a putative cognitive enhancer) on option generation in healthy individuals. We first compared differences in self-generated options between healthy non-depressed adults [n = 44, age = 26.3 years (SD 5.9)] and patients with major depressive disorder [n = 54, age = 24.8 years (SD 7.4)]. In the second study, a subset of depressed individuals [n = 22, age = 25.6 years (SD 7.8)] underwent PET scans with 11C-raclopride to examine the relationships between dopamine D2/D3 receptor availability and individual differences in option generation. Finally, a randomized, double-blind, placebo-controlled, three-way crossover study of modafinil (100 mg and 200 mg), was conducted in an independent sample of healthy people [n = 19, age = 23.2 years (SD 4.8)] to compare option generation under different doses of this drug. The first study revealed that patients with major depressive disorder produced significantly fewer options [t(96) = 2.68, P = 0.009, Cohen's d = 0.54], albeit with greater uniqueness [t(96) = -2.54, P = 0.01, Cohen's d = 0.52], on the option generation task compared to healthy controls. In the second study, we found that 11C-raclopride binding potential in the putamen was negatively correlated with fluency (r = -0.69, P = 0.001) but positively associated with uniqueness (r = 0.59, P = 0.007). Hence, depressed individuals with higher densities of unoccupied putamen D2/D3 receptors in the putamen generated fewer but more unique options, whereas patients with lower D2/D3 receptor availability were likely to produce a larger number of similar options. Finally, healthy participants were less unique [F(2,36) = 3.32, P = 0.048, partial η2 = 0.16] and diverse [F(2,36) = 4.31, P = 0.021, partial η2 = 0.19] after taking 200 mg versus 100 mg and 0 mg of modafinil, while fluency increased linearly with dosage at a trend level [F(1,18) = 4.11, P = 0.058, partial η2 = 0.19]. Our results show, for the first time, that option generation is affected in clinical depression and that dopaminergic activity in the putamen of patients with major depressive disorder may play a key role in the self-generation of options. Modafinil was also found to influence option generation in healthy people by reducing the creativity of options produced.
Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2 (2020)

We present a combinatorial machine learning method to evaluate and optimize peptide vaccine formulations, and we find for SARS-CoV-2 that it provides superior predicted display of viral epitopes by MHC class I and MHC class II molecules over populations when compared to other candidate vaccines. Our method is robust to idiosyncratic errors in the prediction of MHC peptide display and considers target population HLA haplotype frequencies during optimization. To minimize clinical development time our methods validate vaccines with multiple peptide presentation algorithms to increase the probability that a vaccine will be effective. We optimize an objective function that is based on the presentation likelihood of a diverse set of vaccine peptides conditioned on a target population HLA haplotype distribution and expected epitope drift. We produce separate peptide formulations for MHC class I loci (HLA-A, HLA-B, and HLA-C) and class II loci (HLA-DP, HLA-DQ, and HLA-DR) to permit signal sequence based cell compartment targeting using nucleic acid based vaccine platforms. Our SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA hits on average in an individual (≥ 1 peptide 99.91%) with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. Our MHC class II vaccine formulations provide 90.17% predicted coverage with at least five vaccine peptide-HLA hits on average in an individual with all peptides having observed mutation probability ≤ 0.001. We evaluate 29 previously published peptide vaccine designs with our evaluation tool with the requirement of having at least five vaccine peptide-HLA hits per individual, and they have a predicted maximum of 58.51% MHC class I coverage and 71.65% MHC class II coverage given haplotype based analysis. We provide an open source implementation of our design methods (OptiVax), vaccine evaluation tool (EvalVax), as well as the data used in our design efforts.
Experimental Quantification of Noise in Linear Ultrasonic Imaging (2018)

An efficient procedure for experimental-based quantification of statistical distributions of both the random and microstructural speckle noise within an ultrasonic image is presented. This is of particular interest in the multiview total focusing method, which enables many images (views) of the same region to be obtained by utilizing alternative ray paths and mode conversions. For example, in an immersion configuration, 21 separate views of the same region of a sample can be formed by exploiting direct and skip paths. These views can be combined through some form of data fusion algorithm to improve defect detection and characterization performance. However, the noise level is different in different views and this should be accounted for in any data fusion algorithm. It is shown that by using only one set of experimental data from a single measurement location, rather than numerous independent locations, it is possible to obtain accurate noise parameters at an imaging level. This is achieved by accounting for the spatial variation in the noise parameters within the image, due to beam spread, directivity, and attenuation with a simple empirical correction. An important feature of the process is the suppression of image artifacts caused by signal responses from other ray paths with the use of image masking. This masking process incorporates knowledge of the expected autocorrelation length (ACL) of image speckle noise and high-amplitude cluster suppression. The expected ACL is determined via a simple ray-based forward model of a single point scatterer. Compared to the estimates obtained using multiple independent locations, the speckle noise parameters estimated from a single measurement location were within 0.4 dB.
Manipulation of pyramidal cell firing in the hippocampus of freely behaving rats by local application of K+ via microdialysis (1996)

In this study, microdialysis was performed in the hippocampus of freely behaving rats, and the firing of pyramidal cells, including place cells, was recorded at the site of the microdialysis probe. For 10-min periods, the artificial cerebrospinal fluid (ACSF) in the microdialysis system was replaced with ACSF containing 50 mM K+(high K+ solution). Complementary in vitro tests determined that microdialysis with such high K+ solution produced an outflow of 5% of the perfused K+ from the microdialysis probe. Application of K+ with this method into the CA1 region significantly increased the firing of the local pyramidal cells, including place cells, during both movement and sleep. On average, K+ exposures increased the firing rate of the neurons to 306% and 448% of the control firing rate during movement and sleep, respectively. After the termination of the K+ outflow, the cells continued to discharge for 5–30 min with a significantly higher frequency than before the K+ challenge. This phenomenon also occurred in both behavioral states. During the period of enhanced firing, the out-of-field firing rate of the recorded place cells was dramatically increased. It was also found that during the K+ applications, otherwise silent pyramidal cells often became electrically active. The K+ -induced firing modifications were usually not accompanied by behavioral or EEG changes. The data raise the possibility that transient elevations in the extracellular K+ concentration contribute to the ionic/molecular processes which are responsible for plastic firing pattern modifications in hippocampus. Pharmacological manipulation of place cells with the described method offers a new strategy to understand the molecular bases of spatial memory. © 1996 Wiley-Liss, Inc.