gebhart/patrepeval huggingface dataset:
Inhibition of passive cutaneous anaphylaxis by synthetic human immunoglobulin E peptide fragments (1992)

In an attempt to determine the regions responsible for type I immediate hypersensitivity, a total of 42 peptide fragments, which cover the CH3-CH4 domains in human immunoglobulin E (IgE), were chemically synthesized. Several peptide fragments located in the amino acid sequences Ala329-Thr357 and Arg419-Ala463, inhibited passive cutaneous anaphylaxis (PCA) in vivo. In order to pinpoint the sites responsible for the inhibition of the PCA reaction, various fragment peptides in these two regions were synthesized. As a result, residues Pro343-Leu348, Pro426-Thr433, and Ser456-Thr461 were suggested to be involved in type I immediate hypersensitivity.
Nanogaps for Sensing (2009)

Modern resistive chemical sensors include discontinuous nano/mesostructures. Sensing performances are then governed by the chemical nature of the nanostructure gap as well as by the sensor design at the nanogap scale. Various top-down, bottom-up and hybrid fabrication routes of discontinuous/nanogaped metal nano and mesostructures have been developed. These structures are assembled/organized on insulating surfaces for integration of resistor based devices for the specific sensing of chemicals in gaseous as well as in liquid media. Hydrogen sensing based on discontinuous/gaped palladium nano/mesostructures is a chosen case-study for the evaluation of various nano/mesogap fabrication methods.
Enhancing Local Linear Models Using Functional Connectivity for Brain State Decoding (2013)

The authors propose a statistical learning model for classifying cognitive processes based on distributed patterns of neural activation in the brain, acquired via functional magnetic resonance imaging (fMRI). In the proposed learning machine, local meshes are formed around each voxel. The distance between voxels in the mesh is determined by using functional neighborhood concept. In order to define functional neighborhood, the similarities between the time series recorded for voxels are measured and functional connectivity matrices are constructed. Then, the local mesh for each voxel is formed by including the functionally closest neighboring voxels in the mesh. The relationship between the voxels within a mesh is estimated by using a linear regression model. These relationship vectors, called Functional Connectivity aware Mesh Arc Descriptors (FC-MAD) are then used to train a statistical learning machine. The proposed method was tested on a recognition memory experiment, including data pertaining to encoding and retrieval of words belonging to ten different semantic categories. Two popular classifiers, namely k-Nearest Neighbor and Support Vector Machine, are trained in order to predict the semantic category of the item being retrieved, based on activation patterns during encoding. The classification performance of the Functional Mesh Learning model, which range in 62-68% is superior to the classical multi-voxel pattern analysis (MVPA) methods, which range in 40-48%, for ten semantic categories.
ChemInform Abstract: AUTOCATALYTIC DEPOSITION OF GOLD‐COPPER ALLOYS (1983)

Abstract Während es unmöglich ist, reines Au stromlos aus einer KAu(CN)2‐Lösung mit Formaldehyd abzuscheiden, können Au‐Cu‐Legierungen nach Zusatz von Cu‐Salzen und EDTA als Komplexbildungsreagenz auf Glassubstrate aufgebracht werden.
tBID Homooligomerizes in the Mitochondrial Membrane to Induce Apoptosis (2002)

Activation of the tumor necrosis factor R1/Fas receptor results in the cleavage of cytosolic BID to truncated tBID. tBID translocates to the mitochondria to induce the oligomerization of BAX or BAK, resulting in the release of cytochrome c (Cyt c). Here we demonstrate that in tumor necrosis factor alpha-activated FL5.12 cells, tBID becomes part of a 45-kDa cross-linkable mitochondrial complex that does not include BAX or BAK. Using fluorescence resonance energy transfer analysis and co-immunoprecipitation, we demonstrate that tBID-tBID interactions occur in the mitochondria of living cells. Cross-linking experiments using a tBID-GST chimera indicated that tBID forms homotrimers in the mitochondrial membrane. To test the functional consequence of tBID oligomerization, we expressed a chimeric FKBP-tBID molecule. Enforced dimerization of FKBP-tBID by the bivalent ligand FK1012 resulted in Cyt c release, caspase activation, and apoptosis. Surprisingly, enforced dimerization of tBID did not result in the dimerization of either BAX or BAK. Moreover, a tBID BH3 mutant (G94E), which does not interact with or induce the dimerization of either BAX or BAK, formed the 45-kDa complex and induced both Cyt c release and apoptosis. Thus, tBID oligomerization may represent an alternative mechanism for inducing mitochondrial dysfunction and apoptosis.
Fabrication of Ni Sulfides by Thermal Sulfidation (2006)

The microstructure of Ni sulfides prepared by thermal sulfidation of pure Ni and their dependence of fabrication parameters were investigated by means of scanning electron microscopy and X-ray diffractions. Sulfidation was made by isothermally annealing Ni with the sulfur in vacuum sealed glass ampoules at 673 K for 120 – 600s under the sulfur pressure of 100 and 220 kPa. The sulfide layers formed in the early stage were found to consist of spherical particles smaller than 0.5um, which were grown and agglomerated with increasing annealing temperature. Thickness of sulfides developed on Ni substrate was found to increase with increasing annealing time and sulfur pressure. It was also found that compositions of dominant Ni sulfides changed with varying annealing time. At the initial stage, only Ni3S2 sulfide was formed on pure Ni, which was tightly bonded to Ni substrate. On increasing annealing time, NiS sulfide was formed. On further increasing annealing time, NiS1.97 sulfide was formed, which always coexisted with NiS sulfide. A mechanism for sulfidation of Ni is proposed as follows: 3Ni + 2S Ni3S2, Ni3S2 +S NiS, NiS + S NiS1.97
Suggested Procedures for the Reproducible Synthesis of Poly(d,l-lactideco-glycolide) Nanoparticles Using the Emulsification Solvent Diffusion Platform (2018)

Emulsification-diffusion with ethyl acetate is, therefore, a more reliable alternative to sev-eral existing procedures for the reproducible and refined synthesis of PLGA nanoparticles.
Structural Analysis and Physiological Properties of Exopolysaccharides Secreted by a Newly Isolated Pseudomonas stutzeri Bl58 under Alkaline Conditions (2016)

We have identified an ethanol-assimilating bacterial strain of Pseudomonas stutzeri that produces copious amounts of an exopolysaccharide when cultured in 5% ethanol under the alkaline condition of pH 10. The objective of this study was to evaluate the potential industrial applications of this exopolysaccharide designated BL58 by characterization of its chemical, rheological and physiological properties. The polymer was purified from the 72 h culture broth with periodic feeding of ethanol and the chemical structure of the polymer was determined by NMR spectroscopy, GC-mass spectrometry and alditol-acetate analysis of methylated hydrolyzates. The analytical data showed the presence of glucose, mannose and 3-O-carboxyethyl rhamnose and suggested that the main chain consists primarily of 1,4-linked glucose and mannose units with unique branching of 3-O-[(R)carboxyethyl] rhamnose at the 3 position of the glucose unit, a structure not previously reported. The polysaccharide has an average molecular weight of 1,800 kDa and the rheological behavior of the aqueous solution from high viscosity sol to viscoelastic gel depended on temperature and pH. Although no overt cytotoxicity was observed, the polymer displayed anti-proliferative activity when tested with leukemia, liver carcinoma and normal pulmonary cells, indicating potential pharmaceutical applications.
In-Vivo Charakterisierung der Herzfunktion der Desmin Knock-out Maus an einem klinischen 3T MR-Tomographen – Kardiale Kleintierbildgebung an einem klinischen 3T MRT (2010)

Ziel: Die MRT wird zunehmend für die Kleintierbildgebung in der kardiovaskulären Forschung eingesetzt. Ziel dieser Studie war erstens, die Etablierung eines Untersuchungsprotokolls für die funktionelle Herzbildgebung von Mäusen an einem klinischen 3T MRT und zweitens die Anwendung bei einem bisher nicht in-vivo untersuchten Desmin-/- Maus-Modell.
A Hybrid Heuristic in GPU-CPU Based on Scatter Search for the Generalized Assignment Problem (2017)

In the Generalized Assignment Problem (GAP), tasks must be allocated to machines with limited resources, in order to minimize processing costs. This problem has several industrial applications and often appears as a substructure in other combinatorial optimization problems. We propose a hybrid method inspired by Scatter Search metaheuristic, that efficiently generates a pool of solutions using a Tabu list criteria and an Ejection Chain mechanism. Common characteristics are extracted from the pool and solutions are combined by exploring a restricted search space, as a Binary Programming (BP) model. This method was implemented as a parallel approach to run in a Graphics Processing Unit (GPU). Experimental results show that the proposed method is very competitive to the algorithms found in the literature. On average, a gap of 0.09% is obtained over a set of 45 instances, when compared to lower bounds. Due to the integration of the method with an exact BP solver, it was capable of proving the optimality of small size instances, also finding new best known solutions for 21 instances. In terms of computational times, the proposed method performs on average 8 times faster than literature, also indicating that the proposed approach is scalable and robust for practical applications.
Identification of 7B04 aluminum alloy anisotropy yield criteria with conventional test and Pottier test at elevated temperature (2019)

7B04 aluminum alloy is widely used for strength critical aerospace structural applications. In this paper, the plastic anisotropy of this alloy at 200 °C was investigated based on Hill’48 and Yld2000-2D yield criteria. Thermal tensile test at setting temperature was carried out by a designed electrical heating system and the strain field was measured by the digital image correlation system simultaneously. Parameters of Hill’48 yield criterion with Voce hardening were determined directly based on the thermal tensile test. The parameters of Yld2000-2D criterion were obtained by the inverse identification method with Pottier test at elevated temperature which can generate heterogeneous strain fields. Deep drawing test was carried out at 200 °C and the earing heights were measured. The accuracy of the determined yield criteria parameters was validated by numerical and experimental deep drawing test results.
A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus (2023)

Cytomegalovirus (CMV) is a leading cause of infant hearing loss and neurodevelopmental delay, but there are no clinically licensed vaccines to prevent infection, in part due to challenges eliciting neutralizing antibodies. One of the most well-studied targets for CMV vaccines is the viral fusogen glycoprotein B (gB), which is required for viral entry into host cells. Within gB, antigenic domain 2 site 1 (AD-2S1) is a target of potently neutralizing antibodies, but gB-based candidate vaccines have yet to elicit robust responses against this region. We mapped the genealogy of B cells encoding potently neutralizing anti-gB AD-2S1 antibodies from their inferred unmutated common ancestor (UCA) and characterized the binding and function of early lineage ancestors. Surprisingly, we found that a single amino acid heavy chain mutation A33N, which was an improbable mutation rarely generated by somatic hypermutation machinery, conferred broad CMV neutralization to the non-neutralizing UCA antibody. Structural studies revealed that this mutation mediated key contacts with the gB AD-2S1 epitope. Collectively, these results provide insight into potently neutralizing gB-directed antibody evolution in a single donor and lay a foundation for using this B cell-lineage directed approach for the design of next-generation CMV vaccines.
Low- and Zero-Cobalt Layered Oxide Cathodes for Lithium-Ion Batteries (2021)

Lithium-ion batteries have become an integral part of our daily life, powering portable electronic devices. They are in the process of transforming the transportation sector through electrification. They are also being intensively pursued for grid storage of electricity produced from renewable sources. Cost, sustainability, and supply-chain issues are major considerations in employing lithium-ion batteries for electric vehicle (EV) and grid storage applications. In the case of EVs, energy density or driving distance between charges is a critical parameter as well. These considerations have created immense interest to reduce cobalt content or eliminate cobalt altogether in layered oxide cathodes. With this perspective, the research and development trend has been to increase the nickel content and lower the cobalt content in LiNi 1-y-x Mn y -Co z O 2 (NMC) cathodes. For instance, the industry has been gradually moving from LiCoO 2 with 100% Co to NMC-111 with 33% Ni and 33% Co to NMC-622 with 60% Ni and 20% Co to NMC-811 with 80% Ni and 10% Co. While the increase in Ni content offers both an increase in capacity and a reduction in cost, it is also met with serious technical challenges. As the Ni content increases beyond 60%, the cathodes suffer from poor cycle, thermal, and air stabilities. The problems become exponentially challenging as the Ni content increases. This presentation will focus on improving the cycle, thermal, and air stabilities through compositional and controlled synthesis approaches, while reducing the Co content significantly as well as eliminating it altogether to give low- and zero-cobalt layered oxide cathodes with high capacities. The low- and zero-cobalt layered oxide cathodes are synthesized by a coprecipitation of the hydroxide precursors with appropriate doping, employing a tank reactor, followed by calcining with lithium hydroxide at optimal temperatures under a flowing oxygen atmosphere. As the Ni content increases, the calcining temperature and conditions need to be sensitively controlled to obtain high-quality samples. The presentation will particularly focus on the performance evaluation and a fundamental understanding of the degradation mechanisms with cathodes containing &gt; 90% nickel, including LiNiO 2 . The electrochemical performances are evaluated with full pouch cells by pairing the cathodes with graphite anode. The bulk and surface instabilities are assessed by employing a suite of advanced analytical methodologies, including X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), time-of-flight – secondary ion mass spectrometry (TOF-SIMS), high-resolution transmission electron microscopy (HR-TEM), etc. before and after extended cycling of full pouch cells. The presentation will also focus on assessing and improving the air stability as well as thermal stability of various compositions. Approaches to realize capacity values as high as 220 mAh/g will be presented.
Biomechanical implications of unilateral facetectomy, unilateral facetectomy plus partial contralateral facetectomy, and complete bilateral facetectomy in minimally invasive transforaminal interbody fusion (2019)

Although UF/PF and CBF may require slightly more time and effort and incur more risk than UF, the potential improvement in sagittal balance may be worthwhile for select patients.
A genome-wide SNP panel for mapping and association studies in the rat (2008)

We provide a fast and cost-effective platform for genome-wide SNP typing, which can be used for first-pass genetic mapping and association studies in a wide variety of rat strains.
Cooperativity in Solid-State Squaramides (2011)

Using a dipyridyl squaramide derivative as a model, we have shown that cooperativity in hydrogen-bonded catemers plays a crucial role in defining the solid-state synthon of disecondary squaramides, overriding the preferred association mode in solution.
JSNP: a database of common gene variations in the Japanese population (2002)

JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence the coding sequence of the genes. The project has been carried out by a collaboration between the Human Genome Center (HGC) in the Institute of Medical Science (IMS) at the University of Tokyo and the Japan Science and Technology Corporation (JST). JSNP serves as both a storage site for the Japanese SNPs obtained from the ongoing project and as a facility for public dissemination to allow researchers access to high quality SNP data. A primary motivation of the project is the construction of a basic data set to identify relationships between polymorphisms and common diseases or the reaction to drugs. As such, emphasis has been placed on the identification of SNPs that lie in candidate regions which may affect phenotype but which would not necessarily directly cause disease. Unrestricted access to JSNP and any associated files is available at http://snp.ims.u-tokyo.ac.jp/.
Beneficial Effects of Immunoisolated Fetal and Neonatal Pig Liver Fragments on Acute Liver Failure in a Large Animal (1999)

Xenogeneic cell (fragment) transplantation may be used as an interim therapy until the organ allotransplanation. Immunologic rejection, however, constitutes the major hurdle. To overcome this problem, "xeno" fetal and neonatal liver fragments (FLF, NLF) were encapsulated into separate micropore devices that protect them from immunological attack by the recipient. The FLF or NLF were then transplanted into beagles with hepatic failure to observe their biological effects. In Experiment 1 (n = 5) beagles were injected IV with D-galactosamine (D-gal, 1.0 g/kg) on day 0 and then received FLF grafts (0, 0.3, 0.8, 1.0, 2.0 g/kg). In Experiment 2 (n = 6) beagles received NLF grafts (1.8 g/kg) and on the following day were injected with D-gal (1.0 g/kg). In Experiment 1 only the high dose of xeno-FLF (2.0 g/kg) decreased the elevated ALT (GPT) and T. Bil. levels. Histologic examination showed that some of the hepatocytes of the host liver survived only in the high-dose graft. In Experiment 2, at 36 and 48 h after D-gal injection, the transplanted group had a significantly lower AST (GOT) level than the control. The grafted NLF survived for 14 days, according to histologic examinations. Thus, encapsulated FLF and NLF xenotransplantation can prevent liver dysfunction in a large animal hepatic failure model.
A GC-FID Validated Method for the Quality Control of Eucalyptus globulus Raw Material and its Pharmaceutical Products, and GC-MS Fingerprinting of 12 Eucalyptus Species (2014)

In this work we have validated a method to standardize and control the quality of Eucalyptus globulus raw material and phytomedicines containing either the essential oil or the fluid extract of this plant in the final formulation. Internal standardization provided a simple, fast, and reproducible GC-FID analytical method that accurately quantified 1,8-cineol in different E. globulus sub-products, such as its essential oil, dried leaves, fluid extract, and syrup. In addition, GC-MS identification of the main compounds of E. globulus species afforded fingerprints for the qualitative analysis of different Eucalyptus species.
Fostamatinib, a Syk inhibitor prodrug for the treatment of inflammatory diseases. (2009)

Rigel Pharmaceuticals Inc is developing fostamatinib, a prodrug of the spleen tyrosine kinase (Syk) inhibitor R-406, for the potential treatment of autoimmune diseases such as rheumatoid arthritis (RA), idiopathic thrombocytopenic purpura (ITP) and B-cell lymphomas. Syk is a key mediator of Fc and B-cell receptor signaling in inflammatory cells, such as B-cells, mast cells, macrophages and neutrophils. Preclinical studies of R-406 or fostamatinib demonstrated a significant reduction in major inflammatory mediators such as TNFalpha, IL-1, IL-6 and IL-18, leading to reduced inflammation and bone degradation in models of RA. In a phase II clinical trial, fostamatinib treatment effectively improved American College of Rheumatology response rates in patients with RA. Preclinical studies and phase II trials also suggested the potential of using fostamatinib for the treatment of ITP and B-cell lymphomas, by increasing platelet counts and inducing response rates, respectively. Fostamatinib is orally bioavailable and was well tolerated in phase I and II trials, with the most common side effect being gastrointestinal symptoms. At the time of publication, phase II trials for fostamatinib were ongoing in patients with RA, ITP and B-cell lymphomas. The Syk inhibitor appears to be a promising therapeutic for immunological diseases, but further data are required to establish the efficacy and long-term safety of the drug in humans.
Lost in Transcription: p21 Repression, Mechanisms, and Consequences (2005)

The cyclin-dependent kinase inhibitor p21WAF1/CIP1 is a major player in cell cycle control and it is mainly regulated at the transcriptional level. Whereas induction of p21 predominantly leads to cell cycle arrest, repression of p21 may have a variety of outcomes depending on the context. In this review, we concentrate on transcriptional repression of p21 by cellular and viral factors, and delve in detail into its possible biological implications and its role in cancer. It seems that the major mode of p21 transcriptional repression by negative regulators is the interference with positive transcription factors without direct binding to the p21 promoter. Specifically, the negative factors may either inhibit binding of positive regulators to the promoter or hinder their transcriptional activity. The ability of p21 to inhibit proliferation may contribute to its tumor suppressor function. Because of this, it is not surprising that a number of oncogenes repress p21 to promote cell growth and tumorigenesis. However, p21 is also an inhibitor of apoptosis and p21 repression may also have an anticancer effect. For example, c-Myc and chemical p21 inhibitors, which repress p21, sensitize tumor cells to apoptosis by anticancer drugs. Further identification of factors that repress p21 is likely to contribute to the better understanding of its role in cancer.
Evaluation of a Vancomycin Chiral Stationary Phase in Capillary Electrochromatography Using Polar Organic and Reversed-Phase Modes (2000)

A vancomycin chiral stationary phase (CSP) was fully evaluated in capillary electrochromatography (CEC) in reversed-phase and polar organic modes for a number of racemic pharmaceutical compounds. High efficiency and resolution values were obtained for a number of compound classes including thalidomide in both the polar organic mode (190000 plates meter(-1) and Rs = 13.8) and reversed-phase mode (125000 plates meter(-1) and Rs = 13.0). Experimental parameters, including organic modifier, organic solvent ratio, ionic strength, pH, temperature, and voltage, were examined in both the aqueous and nonaqueous modes to deduce their effect on the resultant EOF, retention times, resolution, and efficiency of chiral separations. All results were consistent with and found to be a combination of what is known from existing literature on CEC theory and experience obtained with macrocyclic antibiotic CSPs in LC. Column stability was excellent, and each column packed was found to offer repeatable separations even when switching from the aqueous to the nonaqueous mode.