gebhart/patrepeval huggingface dataset:
Size and morphology of toxic oligomers of amyloidogenic proteins: a case study of human stefin B (2008)

Amyloid-induced toxicity is a well-known phenomenon but the molecular background remains unclear. One hypothesis relates toxicity to amyloid-membrane interactions, predicting that amyloid oligomers make pores into membranes. Therefore, the toxicity and membrane interaction of prefibrillar aggregates and individual oligomers of a non-pathological yet highly amyloidogenic protein human stefin B (cystatin B) was examined. By monitoring caspase-3 activity and by testing cell viability, we showed that the lag phase aggregates obtained at pH 5 and 3 were toxic to neuroblastoma cells. Of equal toxicity were the higher-order oligomers prepared at pH 7 by freeze-thaw cycles. The higher-order oligomers eluted on size-exclusion chromatography (SEC) as a broad peak comprising hexamers, octamers, 12- and 16-mers, well separated from monomers, dimers and tetramers. Only oligomers higher than the tetramers (Rh >3.5 nm) proved toxic, in contrast to dimers and tetramers. In accordance with data from SEC, dynamic light scattering and atomic force microscopy data indicate that the toxic oligomers have diameters larger than 4 nm. Critical pressure measurements showed that the toxic higher-order oligomers inserted more effectively into model lipid monolayers than dimers and tetramers. They also bound, similarly to prefibrillar aggregates, to the plasma membrane and became internalized. Taken together, our results confirm the importance of membrane interaction and perforation in the phenomenon of cytotoxicity.
Synthesis and biological properties of vasopressin analogues containing 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (1990)

Solid phase synthesis methodology on a benzhydrylamine resin was used for the synthesis of three analogues of vasopressin with the non-coded amino acid, 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic), in the position 2 ([Tic 2 , Lys 8 ]VP ( I )) and in the position 3 ([Tic 3 , Lys 8 ]VP ( II )). The analogue containing only one Tic in place of both aromatic residues was also isolated (des-Tyr 2 -[Tic 3 , Lys 8 ]VP ( III )). The biological activities of all analogues were negligible.
STT MRAM patterning challenges (2013)

In this paper we report on the patterning challenges for the integration of Spin-Transfer Torque Magneto-Resistive- Random-Access Memory (STT MRAM). An overview of the different patterning approaches that have been evaluated in the past decade is presented. Plasma based etching, wet echting, but also none subtractive pattering approaches are covered. The paper also reports on the patterning strategies, currently under investigation at imec.
Real time spectroscopic ellipsometry of CuInSe2: Growth dynamics, dielectric function, and its dependence on temperature (2011)

Abstract This Letter reports real time spectroscopic ellipsometry studies of copper indium diselenide (CuInSe 2 ; CIS). A Volmer‐Weber nucleation process was identified from the measured thickness dynamics, and accurate dielectric functions were obtained in‐situ , avoiding oxidation while correcting for surface roughness. The energy and broadening parameters of the critical points in the dielectric functions obtained versus measurement temperature (including three previously unreported ones) yield a database that is valuable for on‐line materials analysis. (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Assistive technology for cognitive rehabilitation: State of the art (2004)

(2004). Assistive technology for cognitive rehabilitation: State of the art. Neuropsychological Rehabilitation: Vol. 14, Technology in Cognitive Rehabilation, pp. 5-39.
Immunological Effects of Hemoglobin, Encapsulated Hemoglobin, Polyhemoglobin and Conjugated Hemoglobin Using Different Immunization Schedules (1992)

Repeated subcutaneous immunizing injections into rats of Freund's adjuvant containing rat hemoglobin or o-raffinose rat polyhemoglobin did not result in increase in IgG antibody titers. However, heterologous hemoglobin injected as above is antigenic (49.50 + 6.70 % CPM). Crosslinking heterologous hemoglobin into o-raffinose polyhemoglobin further increased its antigenicity (75.60 + 4.08). Thus, unlike homologous hemoglobin, cross-linking of heterologous hemoglobin increased its antigenicity. Liposome encapsulated homologous hemoglobin injected subcutaneously with or without Freund's adjuvant did not show antigenicity. Encapsulated heterologous hemoglobin resulted in a minimal increase in antibody titers (10.73 + 4.64) only with Freund's adjuvant, but no increase when injected without Freund's adjuvant. Conjugated heterologous hemoglobin (PEG-Hb) injected intravenously by itself at weekly intervals did not result in significant increase in antibody titers on the 5th week.
STATISTICAL OPTIMIZATION OF FIXED DOSE COMBINATION OF GLIMEPIRIDE AND ATORVASTATIN CALCIUM IN IMMEDIATE RELEASE TABLET FORMULATION (2010)

Long term administration of oral hypoglycemic drugs has been reported to be associated with increased cardiovascular mortality as compared to treatment with diet alone or diet with insulin. For this complication atorvastatin calcium can be used to reduce the cardiovascular mortility. The objective of the present study was to evaluate the effects of two factors (amount of carboxymethylcellulose sodium and sodium starch glycolate) on drug release of atorvastatin calcium and glimepiride from the tablet in order to optimize the formulation by 2 factor 3 level factorial design. Two independent variables taken were carboxymethylcellulose sodium (10mg, 12.5mg and 15 mg) and sodium starch glycolate (2.5 mg, 5mg and 7.5mg). The evaluated response were percentage release of atorvastatin ca in 60 min (Y1) and percentage release of glimepiride in 60 min (Y2) was taken as the response variables. Drug release was measured in USP 2 (paddle type) apparatus using 900 ml 0.05 M phosphate buffer (pH 6.8) solution at a rotation speed 75 rpm. The dissolution data revealed that amount of carboxymethylcellulose sodium and sodium starch glycolate are very important to achieve optimum formulation. Using responses and resulted statistical equations, optimum formulation was predicted. It shows that sodium starch glycolate has more effect than carboxymethylcellulose sodium on the tablet formulation and formulation with 14.78 mg of carboxymethylcellulose sodium and 7.5 mg of sodium starch glycolate is the optimized formulation. The optimized formulation produced dissolution profiles that were closed to predicted values.
Large image reconstruction using small holograms (1989)

Large image reconstruction using a factor of 5 smaller hologram is realized with an optical system which consists of two Fresnel lenses and one common lens. The secondary Fresnel lens also serves as a projection screen. Furthermore, using the same optical system, a true color hologram is achieved by using three primary color lasers. Reconstruction is by the same lasers or white light. The stringent requirement for the optics is discussed.
Enhanced Susceptibility to Superantigen‐Associated Streptococcal Sepsis in Human Leukocyte Antigen–DQ Transgenic Mice (2001)

Bacterial superantigens are believed to cause septic shock, although, because of the lack of superantigen-sensitive infection models, proof that superantigenicity underlies shock pathogenesis is lacking. This work demonstrates a clear superantigen effect in septic shock resulting from bacterial infection. Transgenic expression of human leukocyte antigen (HLA)-DQ, but not HLA-DR, specifically augments lymphocyte responses to streptococcal pyrogenic exotoxin A (SPEA). HLA-DQ transgenic mice had increased mortality after administration of SPEA or infection with Streptococcus pyogenes. Immune activation during infection was HLA-DQ transgene-dependent and was manifested by Vbeta-specific T cell repertoire changes and widespread lymphoblastic tissue infiltration. Unlike earlier models, which used toxin-induced shock, these T cell superantigen responses and lymphoblastoid changes were observed during invasive streptococcal sepsis. Lymphoid activation was undetectable in HLA-DQ mice infected with an isogenic SPEA(-) strain, which proves that a single superantigen can play a role in sepsis pathogenesis.
CuInSe2 quantum dots grown by molecular beam epitaxy on amorphous SiO2 surfaces (2019)

The currently most efficient polycrystalline solar cells are based on the Cu(In,Ga)Se<sub>2</sub> compound as a light absorption layer. However, in view of new concepts of nanostructured solar cells, CuInSe<sub>2</sub> nanostructures are of high interest. In this work, we report CuInSe<sub>2</sub> nanodots grown through a vacuum-compatible co-evaporation growth process on an amorphous surface. The density, mean size, and peak optical emission energy of the nanodots can be controlled by changing the growth temperature. Scanning transmission electron microscopy measurements confirmed the crystallinity of the nanodots as well as chemical composition and structure compatible with tetragonal CuInSe<sub>2</sub>. Photoluminescence measurements of CdS-passivated nanodots showed that the nanodots are optoelectronically active with a broad emission extending to energies above the CuInSe<sub>2</sub> bulk bandgap and in agreement with the distribution of sizes. A blue-shift of the luminescence is observed as the average size of the nanodots gets smaller, evidencing quantum confinement in all samples. By using simple quantum confinement calculations, we correlate the photoluminescence peak emission energy with the average size of the nanodots.
Scaffolds Based on Biopolymeric Foams (2005)

Abstract A new approach for the preparation of hydrophilic and biocompatible porous scaffolds is described. The procedure involves the derivatization of a biopolymer by the introduction of vinylic moieties, formation of a high‐internal‐phase oil‐in‐water emulsion, and its subsequent polymerization. The ensuing materials are characterized by a highly porous morphology represented by pores completely interconnected by a plurality of holes. The hydrophilic and biocompatible nature of these materials make them good candidates for application as scaffolds for tissue engineering.
Predicting Viewer Perceived Emotions in Animated GIFs (2014)

Animated GIFs are everywhere on the Web. Our work focuses on the computational prediction of emotions perceived by viewers after they are shown animated GIF images. We evaluate our results on a dataset of over 3,800 animated GIFs gathered from MIT's GIFGIF platform, each with scores for 17 discrete emotions aggregated from over 2.5M user annotations - the first computational evaluation of its kind for content-based prediction on animated GIFs to our knowledge. In addition, we advocate a conceptual paradigm in emotion prediction that shows delineating distinct types of emotion is important and is useful to be concrete about the emotion target. One of our objectives is to systematically compare different types of content features for emotion prediction, including low-level, aesthetics, semantic and face features. We also formulate a multi-task regression problem to evaluate whether viewer perceived emotion prediction can benefit from jointly learning across emotion classes compared to disjoint, independent learning.
FlexiBO: Cost-Aware Multi-Objective Optimization of Deep Neural Networks. (2020)

One of the key challenges in designing machine learning systems is to determine the right balance amongst several objectives, which also oftentimes are incommensurable and conflicting. For example, when designing deep neural networks (DNNs), one often has to trade-off between multiple objectives, such as accuracy, energy consumption, and inference time. Typically, there is no single configuration that performs equally well for all objectives. Consequently, one is interested in identifying Pareto-optimal designs. Although different multi-objective optimization algorithms have been developed to identify Pareto-optimal configurations, state-of-the-art multi-objective optimization methods do not consider the different evaluation costs attending the objectives under consideration. This is particularly important for optimizing DNNs: the cost arising on account of assessing the accuracy of DNNs is orders of magnitude higher than that of measuring the energy consumption of pre-trained DNNs. We propose FlexiBO, a flexible Bayesian optimization method, to address this issue. We formulate a new acquisition function based on the improvement of the Pareto hyper-volume weighted by the measurement cost of each objective. Our acquisition function selects the next sample and objective that provides maximum information gain per unit of cost. We evaluated FlexiBO on 7 state-of-the-art DNNs for object detection, natural language processing, and speech recognition. Our results indicate that, when compared to other state-of-the-art methods across the 7 architectures we tested, the Pareto front obtained using FlexiBO has, on average, a 28.44% higher contribution to the true Pareto front and achieves 25.64% better diversity.
Analysis of the bright fireball over Kola Peninsula on April 19, 2014 followed by successful meteorite recovery campaign (2014)

Detail záznamu - Analysis of the bright fireball over Kola Peninsula on April 19, 2014 Followed by successful meteorite recovery campaign - Detailní zobrazení záznamu - Knihovna Akademie věd České republiky
CHANGES IN THE SERUM ALPHA GLYCOPROTEIN DISTRIBUTION IN TRAUMA PATIENTS (1975)

Serum electropherograms of trauma patients, when stained for glycoproteins, show striking changes in the alpha glycoproteins of these patients which revert to normal if and when they recover. Thus monitoring of the glycoprotidograms of trauma patients (contrary to ordinary protidograms) is likely to afford important information on the course of these patients' recovery. Of two glycoproteins that have been more closely studied, one, alpha1A acid glycoprotein, is a phagocytosis inhibitor; it is increased in the sera of trauma patients. The other, alpha2HS glycoprotein, is a phagocytosis promotor (or opsonin); it is decreased in the sera of trauma patients. Both the increase of the first and the decrease of the second glycoprotein may thus contribute to the known increased proneness to bacterial infection among these patients.
Phase coexistence and properties of Pb(Zr/sub 1-x/Ti/sub x/)O/sub 3/-Sr(K/sub 0.25/Nb/sub 0.75/)O/sub 3/ (PZT-SKN) solid solutions (2000)

As known, coexistence of rhombohedral and tetragonal phases around morphotropic phase transition is the key in adjusting the set of material parameters to specific applications. In the present study, the correlation between the physical properties of 0.98Pb(Zr/sub 1-x/Ti/sub x/)O/sub 3/-0.02Sr(K/sub 0.25/Nb/sub 0.75/)O/sub 3/ (0.98PZT-0.02SKN) solid solution and Zr/Ti ratio around morphotropic phase transition has been studied in detail. Choosing the right stoichiometry the PZT-SKN system allows both excellent sensor as well as actuator materials.
Characterisation of sol–gel derived titanium oxopolymers: first evidence of Ti–OH groups through1H–17O CP NMR experiments (1998)

Titanium oxo based xerogels obtained through hydrolysis of titanium tetrabutoxide in acidic conditions have been characterised through FTIR,17O MAS and 1H–17O static CP NMR experiments. This latter technique allows the separation of the 17O NMR resonances corresponding to the protonated titanium oxo sites from those of the titanium oxo unprotonated sites, by varying the 1Hto 17O contact time in a cross-polarisation sequence. These experiments clearly evidence the presence of Ti–OH groups. Their characteristic 17O NMR resonance, in titanium based xerogels, is located at about 200 ppm.
Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system (1991)

Xylene monooxygenase, encoded by the TOL plasmid of Pseudomonas putida, catalyzes the oxidation of toluene and xylenes and consists of two different subunits encoded by xylA and xylM. In this study, the complete nucleotide sequences of these genes were determined and the amino acid sequences of the xylA and xylM products were deduced. The XylM sequence had a 25% homology with alkane hydroxylase, which catalyzes the omega-hydroxylation of fatty acids and the terminal hydroxylation of alkanes. The sequence of the first 90 amino acids of XylA exhibited a strong similarity to the sequence of chloroplast-type ferredoxins, whereas the rest of the XylA sequence resembled that of ferredoxin-NADP+ reductases. Based on this information, the structure and function of xylene monooxygenase were deduced. XylM may be a catalytic component for the hydroxylation of the carbon side chain of toluene and xylenes and, as is the alkane hydroxylase protein, may be a membrane-bound protein containing ferrous ion as a prosthetic group. XylA may have two domains consisting of an N-terminal region similar to chloroplast-type ferredoxins and a C-terminal region similar to ferredoxin-NADP+ reductases. The ferredoxin portion of XylA may contain a [2Fe-2S] cluster and reduce the oxidized form of the XylM hydroxylase. The activity determined by the C-terminal region of the XylA sequence may be the reduction of the oxidized form of ferredoxin by concomitant oxidation of NADH.
EVALUATION OF POST MORTEM SURVIVAL OF SKIN BY TISSUE CULTURE METHODS (1958)

KEPES, J. M.D.; GEORGIADE, N. M.D., A; EIRING, M. S. AND; PICKRELL, K. M.D. Author Information
Laboratory Evaluation of Thermophilic‐Anaerobic Digestion to Produce Class A Biosolids. 1. Stabilization Performance of a Continuous‐Flow Reactor at Low Residence Time (2005)

There is increasing interest in the United States in producing biosolids from municipal wastewater treatment that meet the criteria for Class A designation established by the U.S. Environmental Protection Agency. Class A biosolids are intended to be free of pathogens and also must meet requirements for reduction of the vector-attraction potential associated with untreated sludge. High-temperature processes are considered to produce Class A biosolids if the combination of operating temperature and treatment time exceeds minimum criteria, but this option is not applicable to mixed, continuous-flow reactors. Such reactors, or any combination of reactors that does not meet the holding time requirement at a specific temperature, must be demonstrated to inactivate pathogens to levels consistent with the Class A criteria. This study was designed to evaluate pathogen inactivation by thermophilic anaerobic digestion in a mixed, continuous-flow reactor followed by batch or plug-flow treatment. In this first of a two-part series, we describe the performance of a continuous-flow laboratory reactor with respect to physical and chemical operating parameters; microbial inactivation in the combined continuous-flow and batch treatment system is described in the second part. Sludges from three different sources were treated at 53 degrees C, while sludge from one of the sources was also treated at 55 and 51 degrees C. Relatively short hydraulic retention times (four to six days) were used to represent a conservative operating condition with respect to pathogen inactivation. Treatment of a fermented primary sludge led to an average volatile-solids (VS) destruction efficiency of 45%, while VS destruction for the other two sources was near or below 38%, the Class A criterion for vector attraction reduction. Consistent with other studies on thermophilic anaerobic digestion of sludges at short residence times, effluent concentrations of volatile fatty acids (VFAs) were relatively high. Also consistent with other studies, the most abundant VFA in the effluent was propionate. Gas production ranged from 0.3 to 0.5 m3/kg VS fed and from 0.8 to 1.3 m3/kg VS destroyed.
Abstract P3-10-38: Histopathological Subclassification of Triple Negative Breast Carcinoma Using Prognostic Scoring System (2010)

Abstract Purpose: Triple negative breast carcinoma (TNBC) is currently being required to be classified pluralistically in order to provide the most appropriate therapy to the patients. We attempted to subclassify TNBC cases into subgroups based on clinical outcome or prognosis of the patients with TNBC using archival specimens. Materials and Methods: We analyzed 102 Japanese cases of invasive TNBC who underwent surgery between January 1998 and December 2007. The clinicopathological factors and clinical information of these patients were retrospectively retrieved from charts of the patients. Immunohistochemical staining was performed for estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), epidermal growth factor receptor 1 (EGFR1), CK5/6, Ki-67 and CD31 for microvessel density (MVD). Results: Median follow-up time of the patients was 68.5 months. Multivariable analysis demonstrated that the pathologic node status was the most significantly associated with relapse-free survival (RFS) and breast cancer-specific survival (BCSS) of the patients. Pathological tumor size, basal-like type, Ki-67 labeling index (LI) and MVD were also independently associated with RFS and BCSS. Based on these results, we devised the Risk Score system reflecting Hazard ratios (HRs) of these prognostic factors above. Multivariate analysis and the Risk Score for TNBC patients. With this system, TNBC patients in this study were classified into three subgroups; patients with score 0-3 are in low risk group, score 4-7 in intermediate risk group and score 8- in high risk group. These three groups had statistically significant differences for risk of relapse and breast cancer-specific death, respectively. Conclusions: We propose the Risk Score system, which incorporated pathologic nodal status, size of the primary tumor, the presence or absence of basal-like features, Ki67 LI and MVD of the patients in order to predict postoperative clinical course of the Japanese patients with TNBC. Such a classification which can be performed in diagnostic pathology laboratory can be useful as a decision-making tool for triple negative patients. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-10-38.
Donor transaminase and recipient hepatitis. Impact on blood transfusion services (1981)

To assess the relationship of donor alanine aminotransferase (ALT) level to recipient hepatitis, 283 transfused patients were prospectively followed up after open heart surgery; hepatitis developed in 12.7%, of which 97% was non-A, non-B. The ALT tests on 3,359 donors to these patients indicated that risk of hepatitis was significantly associated with the level of donor ALT; 29% of 52 patients receiving at least 1 unit of blood with an ALT level greater than 53 IU/L had hepatitis develop (20.7 cases per 1,000 units), compared with 9% of 231 recipients of only blood with an ALT level of 53 IU/L or less (7.8 cases per 1,000 units). Calculation of corrected efficacy predicts that, at an exclusion level equivalent to 2.25 SDs above the mean log for normal subjects, ALT testing of donors could prevent 29% of posttransfusion hepatitis at the loss of 1.6% of donor units. (<i>JAMA</i>1981;246:630-634)