gebhart/patrepeval huggingface dataset:
A new architecture for supporting group work in the field of health care (2002)

The term of Groupware concerns software supporting cooperative group work. In contrast, CSCW (Computer-Supported Cooperative Work) is the scientific field that motivates and validates groupware design. The goal of our research is to study the software architectures providing coordination between task and managing conflicts within a distributed environment. We intend, in our project, to propose the computer solution that could answer the user requirements and avoid breakdowns in Critical Care Units (CCUs). This paper describes the Workflow management approach for supporting group work in the medical field. The emphasis will be put especially on asynchronous cooperation. To this aim, we propose a cooperative architecture which is based on the Blackboard model and uses the Object-Oriented approach (shared and active objects).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Microlith Based Sorber for Removal of Environmental Contaminants (2004)

<div class="htmlview paragraph">The development of energy efficient, lightweight sorption systems for removal of environmental contaminants in space flight applications is an area of continuing interest to NASA. The current CO<sub>2</sub> removal system on the International Space Station employs two pellet bed canisters of 5A molecular sieve that alternate between regeneration and sorption. A separate disposable charcoal bed removes trace contaminants.</div> <div class="htmlview paragraph">An alternative technology has been demonstrated using a sorption bed consisting of metal meshes coated with a sorbent, trademarked and patented [<span class="xref">1</span>] as Microlith<sup>®</sup> by Precision Combustion, Inc. (PCI); these meshes have the potential for direct electrical heating for this application. This allows the bed to be regenerable via resistive heating and offers the potential for shorter regeneration times, reduced power requirement, and net energy savings vs. conventional systems. The capability of removing both CO<sub>2</sub> and trace contaminants within the same bed has also been demonstrated. Thus, the need for a separate trace contaminant unit is eliminated resulting in an opportunity for significant weight savings. Unlike the charcoal bed, zeolites for trace contaminant removal are amenable to periodic regeneration. This paper describes the design and performance of a prototype sorber device for simultaneous CO<sub>2</sub> and trace contaminant removal and its attendant weight and energy savings.</div>
Novel aqueous nano-scaled formulations of oleic acid stabilized hydrophobic superparamagnetic iron oxide nanocrystals (2012)

This study revealed that mixed lipid-based amphiphiles allow stable aqueous formulations of the normally challenging hydrophobic magnetite nanocrystals with potential in vivo MRI contrast applications.
Towards Keratan Sulfate – Chemoenzymatic Cascade Synthesis of Sulfated <i>N</i>‐Acetyllactosamine (LacNAc) Glycan Oligomers (2016)

Abstract We report on a novel chemoenzymatic cascade for the synthesis of sulfated N ‐acetyllactosamine [(3Galβ1,4GlcNAcβ1,) n , LacNAc] oligomer structures. Starting from a linker modified GlcNAc substrate di‐ and trisaccharides were first synthesized by sequential use of human β4‐galactosyltransferase‐1 (β4GalT‐1) and β3‐ N ‐acetylglucosaminyltransferase from Helicobacter pylori (β3GlcNAcT). Subsequent regioselective chemical sulfation rendered the C‐6 mono‐, di‐, and tri‐ O ‐sulfated products in good yields. Further enzymatic elongation by β4GalT‐1 and β3GlcNAcT in a sequential mode yielded 6‐ O ‐sulfated LacNAc oligomers up to hexasaccharide length with variable degrees of sulfation. These carbohydrate structures mimic the sulfation pattern found in keratan sulfate and are potential ligands for different classes of glycan binding proteins. magnified image
Research Progress in Tobacco Fermentation (2018)

Flue-cured tobacco fermentation is one of the important processes in cigarette manufacturing production. In this thesis, the author interviewed the flue-cured tobacco fermentation mechanism, quality changes of fermentation process, environmental influences on fermentation quality, and fermentation method. By aiming at shortcomings of the current study, the author proposed the near-infrared means to judge the best period of fermentation and provided reference for cigarette enterprises.
Effect of Honey on Streptococcus mutans Growth and Biofilm Formation (2011)

Because of the tradition of using honey as an antimicrobial medicament, we investigated the effect of natural honey (NH) on Streptococcus mutans growth, viability, and biofilm formation compared to that of an artificial honey (AH). AH contained the sugars at the concentrations reported for NH. NH and AH concentrations were obtained by serial dilution with tryptic soy broth (TSB). Several concentrations of NH and AH were tested for inhibition of bacterial growth, viability, and biofilm formation after inoculation with S. mutans UA159 in 96-well microtiter plates to obtain absorbance and CFU values. Overall, NH supported significantly less (P < 0.05) bacterial growth than AH at 25 and 12.5% concentrations. At 50 and 25% concentrations, both honey groups provided significantly less bacterial growth and biofilm formation than the TSB control. For bacterial viability, the results for all honey concentrations except 50% NH were not significantly different from those for the TSB control. NH was able to decrease the maximum velocity of S. mutans growth compared to AH. In summary, NH demonstrated more inhibition of bacterial growth, viability, and biofilm formation than AH. This study highlights the potential antibacterial properties of NH and could suggest that the antimicrobial mechanism of NH is not solely due to its high sugar content.
Elastic moduli of the superhard cubic<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">BC</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mi mathvariant="normal">N</mml:mi></mml:math>phase by Brillouin scattering (2003)

Brillouin scattering measurements on the nanocrystalline cubic phase of ${\mathrm{BC}}_{2}\mathrm{N},$ the hardest known solid after diamond, have been successfully performed using the ``emulated'' platelet scattering geometry. We were able to measure both longitudinal ${(V}_{p})$ and shear ${(V}_{s})$ velocities independent of refractive index, and thus obtained values of $13.09\ifmmode\pm\else\textpm\fi{}0.22$ and $8.41\ifmmode\pm\else\textpm\fi{}0.14\mathrm{k}\mathrm{m}/\mathrm{s},$ respectively. Using these values, we calculated the bulk and the shear moduli as $259\ifmmode\pm\else\textpm\fi{}22$ and $238\ifmmode\pm\else\textpm\fi{}8\mathrm{GPa},$ respectively.
Prevention of sudden cardiac death by n‐3 polyunsaturated fatty acids (2006)

There were already several epidemiologic studies that showed eating fish frequently seemed to reduce deaths from coronary heart disease. There were also observational and clinical trials, which more specifically showed that the reduction in cardiovascular deaths from eating fish were largely the result of n-3 polyunsaturated fatty acids in fish oil for the prevention of sudden cardiac death (SCD). This led me to perform a clinical trial in which all subjects had an implanted cardioverter-defibrillator and were at very high risk of SCD. The results of this study and the mechanisms by which the n-3 fish oil fatty acids prevent fatal cardiac arrhythmias will be the subject of this review.
What's basic about basic emotions? (1990)

A widespread assumption in theories of emotion is that there exists a small set of basic emotions. From a biological perspective, this idea is manifested in the belief that there might be neurophysiological and anatomical substrates corresponding to the basic emotions. From a psychological perspective, basic emotions are often held to be the primitive building blocks of other, nonbasic emotions. The content of such claims is examined, and the results suggest that there is no coherent nontrivial notion of basic emotions as the elementary psychological primitives in terms of which other emotions can be explained. Thus, the view that there exist basic emotions out of which all other emotions are built, and in terms of which they can be explained, is questioned, raising the possibility that this position is an article of faith rather than an empirically or theoretically defensible basis for the conduct of emotion research. This suggests that perhaps the notion of basic emotions will not lead to significant progress in the field. An alternative approach to explaining the phenomena that appear to motivate the postulation of basic emotions is presented.
Internalization routes of cell‐penetrating melanoma antigen peptides into human dendritic cells (2013)

Optimized delivery of antigens combined with sustainable maturation of dendritic cells (DCs) is crucial for generation of effective antitumoral immune responses. Multiple approaches for ex vivo antigen loading and improvement in immunogenicity have been described. We have recently established a single-step protocol consisting of a fusion peptide (a sequence of the melanoma antigen Melan-A and a cationic cell-penetrating HIV TAT domain) bound in complexes with a toll-like receptor agonist. As the exact cellular uptake mechanisms of TAT-coupled antigens have been a matter of considerable debate and significantly depend on cell type, cargo and concentrations, we evaluated internalization routes into human immature DCs in comparison with non-phagocytic cell lines. We found that Melan-A-TAT fusion peptide uptake by DCs is mainly energy dependent, superior compared with polylysine-coupled Melan-A and significantly higher in DCs as compared with Jurkat cells or HUVECs. Furthermore, we could track the uptake of the fusion peptide exclusively through early endosomes to lysosome compartments after 90 min by fluorescence microscopy and immunoelectron microscopy. Specific endocytosis inhibitors revealed major internalization of the fusion peptide by DCs via clathrin-mediated endocytosis, whereas uptake by non-phagocytic HUVECs differed significantly, involving macropinocytosis as well as clathrin-mediated endocytosis. As our understanding of the processes involved in internalization of TAT-coupled cargos by human DCs broadens, and DC activation becomes available by single-step procedures as described, further development of simultaneous DC maturation and intra-cellular peptide targeting is warranted.
Evacuation guidance support using cooperative agent-based IoT devices (2017)

It is an important task to prepare for unprecedented natural disasters. When natural disasters occur, indoor and outdoor situations greatly change. Therefore, it is difficult to provide evacuation guidance during sudden and unpredictable disasters. We propose an agent-based evacuation guidance support system, which autonomously determines the evacuation guidance plan based on the situation assessed by cooperating IoT devices, in order to support quick evacuation guidance. We describe an evacuation guidance support system based on agent-based IoT (AIoT), which consists of situation recognition and evacuation route planning. We performed some experiments to confirm the effectiveness of our proposal.
Active Oxygen in Plant Pathogenesis (1995)

Plant cells produce active oxygen during interactions with potential patho­ gens. Active oxygen species, including superoxide, hydrogen peroxide, and the hydroxyl radical, could potentially affect many cellular processes in­ volved in plant/pathogen interactions. Active oxygen can be difficult to monitor in plant cells because many of the species are short-lived and are subject to cellular antioxidant mechanisms such as superoxide dismutases, peroxidases, the ascorbate/glutathione cycle, and catalase. Modifications of the luminol-dependent chemiluminescence assay have facilitated studies on both the production and scavenging of active oxygen that occurs during incompatible plantlbacteria interactions. Many potential sources for active oxygen production have been identified such as NADPH oxidases and per­ oxidases, but it is still unclear which mechanisms predominate during plant! pathogen interactions. The active oxygen produced in response to pathogens and elicitors has been hypothesized to have direct antimicrobial effects and to play a role in other defense mechanisms including lignin production, lipid peroxidation, phytoalexin production, and the hypersensitive response. tThe US Govenunent has the right to retain a nonexclusive, royalty-free license in and to any copyright covering this paper.
On the Radio Resource Allocation in Enhanced Uplink UTRA-FDD with Fixed Relay Stations (2006)

In this paper, an integrated radio resource allocation (IRRA) algorithm is proposed for enhanced uplink UTRA-FDD with fixed relay stations (RSs). It comprises three entities: load based route manager (LBRM), base station resource scheduler (BSRS), and relay station load balancer (RSLB). LBRM is responsible for the selection of user transmission routes, BSRS is for the scheduling of user transmission time and rates based on the available base station (BS) capacity, and RSLB is for the fine-tuning of user resource assignments (e.g. assigned rates) so as to prevent the overloading of RSs. The three entities operate periodically, synchronously, and with coordinated interactions. By system level simulations, the proposed algorithm is evaluated and compared with two other cases: 1) non-relaying, 2) relaying with a benchmark approach. The results show that IRRA can ensure significant gains in terms of cell throughput.
Analysis of Apoptosis and Necroptosis by Fluorescence-Activated Cell Sorting (2016)

Fluorescence-activated cell sorting (FACS) is a laser-based, biophysical technology that allows simultaneous multiparametric analysis. For the analysis of dying cells, fluorescently labeled Annexin V (Annexin V(FITC)) and propidium iodide (PI) are the most commonly used reagents. Instead of PI, 4',6-diamidino-2-phenylindole (DAPI) can also be used. DAPI is a fluorescent stain that binds strongly to A-T-rich regions in DNA. DAPI and PI only inefficiently pass through an intact cell membrane and, therefore, preferentially stain dead cells. DAPI can be combined with Annexin V(FITC)and the potentiometric fluorescent dye, tetramethylrhodamine methyl ester (TMRM), which measures mitochondrial permeability transition and mitochondrial membrane depolarization. TMRM is a cell-permeable fluorescent dye that is sequestered to active mitochondria, and hence labels live cells. On apoptosis or necroptosis the TMRM signal is lost. The advantage of using Annexin V(FITC)/DAPI/TMRM is that the entire cell population is labeled, and it is easy to distinguish living (TMRM + /Annexin V(FITC)-/DAPI-) from dying or dead cells (apoptosis: TMRM-/Annexin V(FITC)+ /DAPI-; necrosis: TMRM-/Annexin V(FITC)+ /DAPI+). This is important because cell debris (fluorescent negative particles) must be avoided to establish the correct parameters for the FACS analysis, otherwise incorrect statistical values will be obtained. To obtain information on the cell concentration or absolute cell counts in a sample, it is recommended to add an internal microsphere counting standard to the flow cytrometric sample. This protocol describes the FACS analysis of cell death in HT1080 and L929 cells, but it can be readily adapted to other cell types of interest.
Characteristics and design of a current sensor using multilayer Co/Ni structures (2002)

Recent studies show the possibility of using amorphous materials as current sensors. In this paper, the magnetoresistance effect existing in multilayer (Co/sub 50/Ni/sub 25/)/sub 10/ structures has been used to develop a current sensor susceptible to be fully integrated. Experimental results have been obtained to compare the properties of the anisotropic magnetoresistance effect (AMR) with commercial ones.
Blastocyst trophectoderm biopsy and preimplantation genetic diagnosis for familial monogenic disorders and chromosomal translocations (2008)

Abstract Objective Modern in vitro fertilization practices involve transfer of embryos as blastocysts, when anabolic metabolism is well established and pregnancy rates can be maintained while transferring embryos singly to avoid multiple pregnancies. Embryo biopsy for preimplantation genetic diagnosis (PGD), however, is generally performed on day 3, when the embryo comprises just 6 to 8 cells, one or two of which are removed for testing. Implantation rates and clinical pregnancy rates have remained relatively low and a harmful effect from losing one or more cells from such early embryos has not been excluded. Methods We performed a sequential study involving 399 egg retrievals and 1879 embryo biopsies for patients undergoing PGD to avoid a serious monogenic disease or an unbalanced chromosomal translocation. We compared implantation and viable pregnancy rates after biopsies taken on day 3 (cleavage‐stage biopsy) with biopsies delayed until day 5 or 6, when the embryo is a blastocyst and 5 or more cells can be sampled from the trophectoderm while the inner cell mass, from which the fetus develops, remains intact. All embryos were transferred as blastocysts. Results Despite fewer blastocysts than cleavage embryos biopsied and tested (3.6 compared to 6.6), implantation rates per embryo transferred were 43.4% if biopsied at the blastocyst stage and 25.6% if biopsied at the cleavage stage (P < 0.01), with ongoing or live‐birth pregnancy rates per egg retrieval of 34.2% (average transfer number 1.1) for blastocyst biopsies and 25.5% (transfer number 1.6) for cleavage stage biopsies (P < 0.05, 1‐tailed). The multiple pregnancy rate for monogenic disease exclusion fell from 16.7% to 2% (P = 0.04, 1‐tailed). Conclusions For exclusion of genetic disease, day 5‐6 blastocyst‐stage biopsies are more likely to be followed by implantation and singleton births than is the case after PGD performed on day 3. Copyright © 2008 John Wiley & Sons, Ltd.
Predicting Functional Regions on Objects (2013)

We revisit the notion of object affordances, an idea that speaks to an object's functional properties more than its class label. We study the problem of spatially localizing affordances in the form of 2D segmentation masks annotated with discrete affordance labels. For example, we use affordance masks to denote on what surfaces a person sits, grabs, and looks at when interacting with a variety of everyday objects (such as chairs, bikes, and TVs). We introduce such a functionally-annotated dataset derived from the PASCAL VOC benchmark and empirically evaluate several approaches for predicting such functionally-relevant object regions. We compare "blind" approaches that ignore image data, bottom-up approaches that reason about local surface layout, and top-down approaches that reason about structural constraints between surfaces/regions of objects. We show that the difficulty of functional region prediction varies considerably across objects, and that in general, top-down functional object models do well, though there is much room for improvement.
High Performance LOBPCG Method for Solving Multiple Eigenvalues of Hubbard Model: Efficiency of Communication Avoiding Neumann Expansion Preconditioner (2018)

The exact diagonalization method is a high accuracy numerical approach for solving the Hubbard model of a system of electrons with strong correlation. The method solves for the eigenvalues and eigenvectors of the Hamiltonian matrix derived from the Hubbard model. Since the Hamiltonian is a huge sparse symmetric matrix, it was expected that the LOBPCG method with an appropriate preconditioner could be used to solve the problem in a short time. This turned out to be the case as the LOBPCG method with a suitable preconditioner succeeded in solving the ground state (the smallest eigenvalue and its corresponding eigenvector) of the Hamiltonian. In order to solve for multiple eigenvalues of the Hamiltonian in a short time, we use a preconditioner based on the Neumann expansion which uses approximate eigenvalues and eigenvectors given by LOBPCG iteration. We apply a communication avoiding strategy, which was developed considering the physical properties of the Hubbard model, to the preconditioner. Our numerical experiments on two parallel computers show that the LOBPCG method coupled with the Neumann preconditioner and the communication avoiding strategy improves convergence and achieves excellent scalability when solving for multiple eigenvalues.
Crystal structures of α‐dioxygenase from <i>Oryza sativa</i>: Insights into substrate binding and activation by hydrogen peroxide (2013)

α-Dioxygenases (α-DOX) are heme-containing enzymes found predominantly in plants and fungi, where they generate oxylipins in response to pathogen attack. α-DOX oxygenate a variety of 14-20 carbon fatty acids containing up to three unsaturated bonds through stereoselective removal of the pro-R hydrogen from the α-carbon by a tyrosyl radical generated via the oxidation of the heme moiety by hydrogen peroxide (H2 O2 ). We determined the X-ray crystal structures of wild type α-DOX from Oryza sativa, the wild type enzyme in complex with H2 O2 , and the catalytically inactive Y379F mutant in complex with the fatty acid palmitic acid (PA). PA binds within the active site cleft of α-DOX such that the carboxylate forms ionic interactions with His-311 and Arg-559. Thr-316 aids in the positioning of carbon-2 for hydrogen abstraction. Twenty-five of the twenty eight contacts made between PA and residues lining the active site occur within the carboxylate and first eight carbons, indicating that interactions within this region of the substrate are responsible for governing selectivity. Comparison of the wild type and H2 O2 structures provides insight into enzyme activation. The binding of H2 O2 at the distal face of the heme displaces residues His-157, Asp-158, and Trp-159 ≈ 2.5 Å from their positions in the wild type structure. As a result, the Oδ2 atom of Asp-158 interacts with the Ca atom in the calcium binding loop, the side chains of Trp-159 and Trp-213 reorient, and the guanidinium group of Arg-559 is repositioned near Tyr-379, poised to interact with the carboxylate group of the substrate.
Weighted Sampling for Combined Model Selection and Hyperparameter Tuning (2020)

The combined algorithm selection and hyperparameter tuning (CASH) problem is characterized by large hierarchical hyperparameter spaces. Model-free hyperparameter tuning methods can explore such large spaces efficiently since they are highly parallelizable across multiple machines. When no prior knowledge or meta-data exists to boost their performance, these methods commonly sample random configurations following a uniform distribution. In this work, we propose a novel sampling distribution as an alternative to uniform sampling and prove theoretically that it has a better chance of finding the best configuration in a worst-case setting. In order to compare competing methods rigorously in an experimental setting, one must perform statistical hypothesis testing. We show that there is little-to-no agreement in the automated machine learning literature regarding which methods should be used. We contrast this disparity with the methods recommended by the broader statistics literature, and identify a suitable approach. We then select three popular model-free solutions to CASH and evaluate their performance, with uniform sampling as well as the proposed sampling scheme, across 67 datasets from the OpenML platform. We investigate the trade-off between exploration and exploitation across the three algorithms, and verify empirically that the proposed sampling distribution improves performance in all cases.