gebhart/patrepeval huggingface dataset:
Supplementary Table and Figures from Changes in the Glycosylation of Kininogen and the Development of a Kininogen-Based Algorithm for the Early Detection of HCC (2023)

&lt;p&gt;Supplementary Table S1. Patient Characteristics for patients from the University of California at San Diego; Supplementary Table S2. Fitness of algorithms; Supplementary Table S3. Cross validations of potential models; Supplementary Table S4. Statistical inference of comparing models; Supplementary Figure S1. Scheme of study design;Supplementary Figure S2. Scatter plot; Supplementary Figure S3. AUROC for the individual components analyzed; Supplementary Figure S4. MALDI-TOF analysis of low molecular weight kininogen; Supplementary Figure S5. Glycopeptide analysis of tryptic glycopeptide 44-58; Supplementary Figure S6. Glycopeptide analysis of tryptic glycopeptide 197-208 showing identification of fucosylated glycopeptides; Supplementary Figure S7. Glycopeptide analysis of tryptic glycopeptide 289-300;&lt;/p&gt;
Proposal for Neutron Scattering Systems for Calibration of Dark Matter Search and Low-Energy Neutrino Detectors (2013)

The proposal of two neutron scattering systems for calibration of two-phase cryogenic avalanche detectors with high sensitivity being developed at Budker INP is presented. This kind of detectors is designed for the search of dark matter and low energy neutrino detection, in particular, coherent neutrino scattering on nuclei. Detector calibration is made with a measurement of ionization yield and scintillation quenching factor for low energy recoiling nuclei (in 0.5 to 100 keV range) originating from elastic scattering of neutrons. To provide wide range of recoiling nuclei energies two systems of neutron scattering are proposed. The first one is based on small-sized DD generator of fast (2.45 MeV) monoenergetic neutrons operating on sealed neutron tube. The second one is based on tandem proton accelerator and lithium target and capable of generation of monoenergetic epithermal neutrons with energy up to 100 keV
High fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo (2020)

Abstract The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved high signal to noise ratio in vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise that present analysis challenges, namely light scattering, out-of-focus sources, motion, and blood flow. We present a novel signal extraction methodology, Spike-Guided Penalized Matrix Decomposition-Nonnegative Matrix Factorization (SGPMD-NMF), which resolves supra- and sub-threshold voltages with high fidelity, even in the presence of correlated noise. The method incorporates biophysical constraints (shared soma profiles for spiking and subthreshold dynamics) and optical constraints (smoother spatial profiles from defocused vs. in-focus sources) to cleave signal from background. We validated the pipeline using simulated and composite datasets with realistic noise properties. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon, mouse cortex expressing SomArchon or Voltron, and zebrafish spine expressing zArchon1.
Microsoft Indoor Localization Competition (2015)

column Share on Microsoft Indoor Localization Competition: Experiences and Lessons Learned Authors: Dimitrios Lymberopoulos Microsoft Research Microsoft ResearchView Profile , Jie Liu Microsoft Research Microsoft ResearchView Profile , Xue Yang Intel Labs Intel LabsView Profile , Romit Roy Choudhury UIUC, Urbana-Champaign UIUC, Urbana-ChampaignView Profile , Souvik Sen HP Labs HP LabsView Profile , Vlado Handziski Technical University of Berlin Technical University of BerlinView Profile Authors Info & Claims GetMobile: Mobile Computing and CommunicationsVolume 18Issue 4October 2014 pp 24–31https://doi.org/10.1145/2721914.2721923Published:13 January 2015Publication History 40citation706DownloadsMetricsTotal Citations40Total Downloads706Last 12 Months31Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Results of the Latarjet procedure for recurrent anterior dislocation of the shoulder in patients with epilepsy (2012)

A total of 12 epileptic patients (14 shoulders) with recurrent seizures and anterior dislocations of the shoulder underwent a Latarjet procedure and were reviewed at a mean of 8.3 years (1 to 20) post-operatively. Mean forward flexion decreased from 165° (100° to 180°) to 160° (90° to 180°) (p = 0.5) and mean external rotation from 54° (10° to 90°) to 43° (5° to 75°) (p = 0.058). The mean Rowe score was 76 (35 to 100) at the final follow-up. Radiologically, all shoulders showed a glenoid-rim defect and Hill-Sachs lesions pre-operatively. Osteo-arthritic changes of the glenohumeral joint were observed in five shoulders (36%) pre-operatively and in eight shoulders (57%) post-operatively. Re-dislocation during a seizure occurred in six shoulders (43%). Five of these patients underwent revision surgery using a bone buttress from the iliac crest and two of these patients re-dislocated due to a new seizure. Due to the unacceptably high rate of re-dislocation after surgery in these patients, the most important means of reducing the incidence of further dislocation is the medical management of the seizures. The Latarjet procedure should be reserved for the well-controlled patient with epilepsy who has recurrent anterior dislocation of the shoulder during activities of daily living.
Chain-Walking Polymerization of α-Olefins by α-Diimine Ni(II) Complexes: Effect of Reducing the Steric Hindrance of Ortho- and Para-Aryl Substituents on the Catalytic Behavior, Monomer Enchainment, and Polymer Properties (2018)

With Brookhart type α-diimine Ni(II) based catalysts, it is highly challenging to tune polymers branching level and branch-type distribution, which in turn strongly affects thermal and mechanical properties, through the aryl ortho-positions modification, while maintaining high turnover frequencies (TOFs). Herein, we are interested in performing a systematic investigation on the polymerization of 1-octene, 1-decene, and 1-octadecene catalyzed by a series of α-diimine nickel(II) complexes with methyl ligand backbone and different substituents in aryl positions (Ni1-Ni6). In addition to bulky isopropyl and tert-butyl substituents described in the original Brookhart's work, complexes with different aryl ortho- and para-substituted α-diimine ligands, including the less sterically demanding methyl and ethyl substituents, are investigated. The 13C NMR spectra of the polymers have been assigned in detail, and some unique features have been identified and related to the chain-walking coordination/insertion mechanism. Changes in the ligand structure and monomer size have important effects on the numerous combinations of insertion and chain-walking paths from which different branches are installed. We have also carried out a comprehensive investigation of the mechanical behavior of the polymers by means of uniaxial stretching until failure, step-cycle, and creep tensile tests. Overall, the resulting polymers exhibited a broad spectrum of tensile properties, depending on their microstructure and crystallinity which in turn are strongly affected by monomer length and type of α-diimine ligand. 1-Octene and 1-decene polymers behave as elastomers with excellent mechanical properties, i.e., high elongation at break (up to 2000%) and good strain recovery, while 1-octadecene polymers behave as plastomers.
Surface recombination velocity and bulk lifetime in GaAs and InP (1986)

An analytical expression is derived which allows the bulk minority carrier recombination lifetime tau and the surface recombination velocity S to be extracted from a single non-contact photoconductivity decay (PCD) measurement. This analytical expression is rather complex, but can be reduced to a first-order approximation. A comparison of the computer simulation of the more complex expression and the first-order approximation reveals that the first-order expression and the first-order approximation reveals that the first-order approximation model is accurate and is equally valid for both n-type and p-type materials.
Temperature‐dependences of cationic mobility and carrier generation in solid polyether media (1992)

Abstract The temperature‐dependences of cationic conductivity and mobility in a macromolecular lithium salt/copolyether blend were investigated by means of complex impedance analysis and a time‐of‐flight technique, respectively. The transient ionic current after reversing the d.c. bias polarity exhibits two peaks, corresponding to cationic and anionic movement respectively, and verifying a cationic transfer number of 0.99 at 50°C. The comparison between conductivity and mobility makes it possible to reveal the temperature‐dependence of the cation carrier number. As a result, the population of free ions was found to decrease exponentially with increasing temperature. However, this “anomalous” behavior of salt dissociation has little effect on the temperature‐dependence of conductivity, since it is cation carrier mobility rather than its number which is the main factor influencing the ion transport process.
Identification of Soat1 as a Quantitative Trait Locus Gene on Mouse Chromosome 1 Contributing to Hyperlipidemia (2011)

We previously identified two closely linked quantitative trait loci (QTL) on distal chromosome 1 contributing to major variations in plasma cholesterol and triglyceride levels in an intercross derived from C57BL/6 (B6) and C3H/HeJ (C3H) apolipoprotein E-deficient (apoE(-/-)) mice. Soat1, encoding sterol o-acyltransferase 1, is a functional candidate gene located underneath the proximal linkage peak. We sequenced the coding region of Soat1 and identified four single nucleotide polymorphisms (SNPs) between B6 and C3H mice. Two of the SNPs resulted in amino-acid substitutions (Ile147Val and His205Tyr). Functional assay revealed an increased enzyme activity of Soat1 in peritoneal macrophages of C3H mice relative to those of B6 mice despite comparable protein expression levels. Allelic variants of Soat1 were associated with variations in plasma cholesterol and triglyceride levels in an intercross between B6.apoE(-/-) and C3H.apoE(-/-) mice. Inheritance of the C3H allele resulted in significantly higher plasma lipid levels than inheritance of the B6 allele. Soat1 variants were also significantly linked to major variations in plasma esterified cholesterol levels but not with free cholesterol levels. Trangenic expression of C3H Soat1 in B6.apoE(-/-) mice resulted in elevations of plasma cholesterol and triglyceride levels. These results indicate that Soat1 is a QTL gene contributing to hyperlipidemia.
MERS-CoV 4b protein interferes with the NF-κB-dependent innate immune response during infection (2018)

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that emerged in 2012, causing severe pneumonia and acute respiratory distress syndrome (ARDS), with a case fatality rate of ~36%. When expressed in isolation, CoV accessory proteins have been shown to interfere with innate antiviral signaling pathways. However, there is limited information on the specific contribution of MERS-CoV accessory protein 4b to the repression of the innate antiviral response in the context of infection. We found that MERS-CoV 4b was required to prevent a robust NF-κB dependent response during infection. In wild-type virus infected cells, 4b localized to the nucleus, while NF-κB was retained in the cytoplasm. In contrast, in the absence of 4b or in the presence of cytoplasmic 4b mutants lacking a nuclear localization signal (NLS), NF-κB was translocated to the nucleus leading to the expression of pro-inflammatory cytokines. This indicates that NF-κB repression required the nuclear import of 4b mediated by a specific NLS. Interestingly, we also found that both in isolation and during infection, 4b interacted with α-karyopherin proteins in an NLS-dependent manner. In particular, 4b had a strong preference for binding karyopherin-α4 (KPNA4), which is known to translocate the NF-κB protein complex into the nucleus. Binding of 4b to KPNA4 during infection inhibited its interaction with NF-κB-p65 subunit. Thereby we propose a model where 4b outcompetes NF-κB for KPNA4 binding and translocation into the nucleus as a mechanism of interference with the NF-κB-mediated innate immune response.
Protection againstStaphylococcus aureusSepsis by Vaccination with Recombinant Staphylococcal Enterotoxin A Devoid of Superantigenicity (1999)

Staphylococcal exotoxins are virulence determinants in Staphylococcus aureus arthritis and septicemia. To assess the utility of enterotoxins as vaccine candidates for these diseases, a genetically modified staphylococcal enterotoxin A (SEA) that lacks superantigenic properties was used. Mice immunized with recombinant (r) SEA had significantly longer survival than control immunized mice and lost significantly less weight than the controls. Transfer of SEA-specific antibodies to naive mice resulted in good protection against death in staphylococcal sepsis. In vitro proliferative responses to SEA by naive lymphocytes were almost totally abolished on incubation with serum from rSEA but not with control antigen-immunized mice. These results suggest that immunization with rSEA devoid of superantigenic properties provides good protection against S. aureus sepsis. In addition, the data indicate that the protection is at least in part mediated by SEA neutralizing antibodies.
Culture of human fetal B-cell precursors on bone marrow stroma maintains highly proliferative CD20dim cells (1993)

Growth of human B-cell precursors (BCP) was achieved by plating fetal CD10+ surface-mu (s mu)- cells in liquid medium onto bone marrow-derived fibroblastic stromal cell layers deprived of hematopoietic cells. Proliferation of the fetal BCP was strongly potentiated by the addition of interleukin-7 (IL-7) to the cultures. Cultures included both a stroma-adherent and -nonadherent fraction of lymphoid cells, allowing us to expand the number of input BCP to 13-fold. In the presence of exogenous IL-7, proliferation was dose-dependent relative to the number of stromal cells, demonstrating that soluble IL-7 does not act alone to promote optimal growth. We further showed that the lymphoid cells recovered remain CD10+ sIg- BCP and that most cells expressed the maturation-associated CD20 antigen when IL-7 was added to the cultures. Whereas both freshly isolated CD20- and CD20bright BCP proliferated in the presence of stroma, we observed that high-proliferative capacity CD20dim cells were maintained in the cultures. Finally, CD20dim sorted cells were shown to subsequently acquire high levels of CD20 expression in culture, thus demonstrating a partial maturation sequence. The present culture system thus represents a useful model for studying the regulatory signals in early human B lymphopoiesis.
New Substituted Piperazines as Ligands for Melanocortin Receptors. Correlation to the X-ray Structure of “THIQ” (2004)

A series of piperazine analogues of the melanocortin 4 receptor (MC4R) specific small-molecule agonist "THIQ" was synthesized and characterized structurally and pharmacologically. First, several THIQ imitations lacking the triazole moiety were prepared. Syntheses included acylation of 4-phenylpiperazine or 4-cyclohexylpiperazine. In two cases the tertiary amine function was replaced by the corresponding N-oxide. To obtain more complex structures, a 4-substituted piperazine ring was formed by alkylation of the primary amino group of cyclohexane-derived amino alcohols with N,N-bis(2-chloroethyl)benzylamine. The hydroxylic group of the intermediate was first activated with methanesulfonyl chloride, and the sulfonic ester formed in situ was introduced into the reaction with the sodium salt of 1,2,4-triazole. In one case (i.e., preparation of 23c) introduction of the 1,2,4-triazole moiety was performed at a carbon of the cyclohexane ring. In addition, this intermediate contained a piperazine moiety connected via its nitrogen atom to a cyclohexane ring carbon neighboring the reaction center. As established in NMR and X-ray investigations herein, this substitution proceeded with retention of the initial trans configuration of 1,2-disubstituted cyclohexane. To obtain pure enantiomers of 23c, its precursor 21c was subjected to chiral chromatography on a Chirobiotic V column. The derivatives (R,R)-21cand (S,S)-21c obtained were introduced into further syntheses steps, giving (R,R)-23c and (S,S)-23c, respectively. Melanocortin MC(1,3-5) receptor binding studies showed that all tested piperazine derivatives were active. Several compounds showed clear selectivity for MC4R, with submicromolar affinities being obtained. Among them, one substance, (R,R)-23c, displayed a biphasic curve in displacement of [125I]NDP-MSH on MC4R [K(i)high = 1 nM and K(i)low = 260 nM]. This biphasic competition curve was similarly biphasic to the competition curve obtained herein using THIQ. An X-ray study performed on crystals of the THIQ sulfate salt revealed two closely related conformations, which resemble the shape of the letter "Y", where piperidine and 4-chlorophenyl groups are situated close to each other, but the 1,2,3,4-tetrahydroisoquinoline residue is remote, the triazole function being highly exposed to the environment. The crystals of the dinitrate salt of (R,R)-23c showed a different conformation, where parts of the molecule are spread out almost symmetrically around the central section. Molecular modeling, based on the THIQ crystal structure and the functional similarity of THIQ and (R,R)-23c, allowed us to suggest a possible "bioactive" conformation of (R,R)-23c that is similar to the crystal conformation of THIQ.
Inhibition of Both the Autocrine and the Paracrine Growth of Human Leukemia with a Fully Human Antibody Directed Against Vascular Endothelial Growth Factor Receptor 2 (2004)

Vascular endothelial growth factor (VEGF) and its receptors (VEGFR) have been implicated in promoting solid tumor growth and metastasis via stimulating tumor-associated angiogenesis. Here we show that certain "liquid" tumors such as acute myeloid leukemia not only produce VEGF but also express functional VEGFR, resulting in an autocrine loop for tumor growth and propagation. In addition, the leukemia-derived VEGF can also stimulate the production of growth factors, including interleukin 6 (IL6) and granulocyte-macrophage colony stimulating factor (GM-CSF), by human endothelial cells, which in turn further promotes the growth of leukemia cells (the paracrine loop). A fully human anti-VEGFR2 (or kinase insert domain-containing receptor, KDR) antibody, IMC-2C6, strongly blocks KDR/VEGF interaction and neutralizes VEGF-stimulated activation of KDR in endothelial cells. In a system where leukemia cells are co-cultured with endothelial cells, IMC-2C6 inhibits both the production of IL6 and GM-CSF by endothelial cells and the growth of leukemia cells. Finally, IMC-2C6 effectively blocks VEGF-induced migration of KDR+ human leukemia cells, and when administered in vivo, significantly prolonged survival of mice inoculated with KDR+ human leukemia cells. Taken together, our data suggest that anti-KDR antibodies may have broad applications in the treatment of both solid tumors and certain types of leukemia.
First-principles pseudopotential calculations for hydrogen in 4d transition metals. II. Vibrational states for interstitial hydrogen isotopes (1992)

In this second part of our first-principles study of hydrogen in transition metals within the framework of the Born-Oppenheimer and the local density-functional approximations, the mixed-basis pseudopotential method, which was outlined in the first part, is applied to calculate total energies and internal forces in Pd(n)H supercells with n less-than-or-equal-to 32 and Nb(n)H supercells with n less-than-or-equal-to 4. Adiabatic potentials for H in PdH and NbH are determined and the influence of lattice relaxations is discussed. Analytic model potentials are fitted to the first-principles results, and the importance of anharmonicity for vibrational states of interstitial H isotopes is investigated. By comparing our calculated vibrational energies with results from neutron-scattering experiments, we find that for NbH the anharmonicity is weak and the results obtained in harmonic approximation or via perturbation theory are in good agreement with experiment. For PdH the harmonic approximation as well as the perturbation theory are insufficient. The anharmonicity and the periodicity of the adiabatic potential need to be represented carefully by a Fourier series. Then the agreement with experiment is found to be as good as for NbH and even allows us to propose a reinterpretation of the experimental data.
Computational Fluid Dynamic Analysis for the Assessment of Experimental Design Risks and Flow Sensitivities for a Three-Dimensional Bump Flow (2020)

This paper studies the use of computational fluid dynamics in the design of a three-dimensional bump flow experiment whose purpose is to provide a benchmark set of data for computational fluid dynamics validation. CFD solutions are used as a predictive tool to anticipate flow sensitivities and potential sources of experimental risks. Solutions sensitivities to turbulence models and flow solvers are assessed. Flow sensitivities to Reynolds number and incoming boundary layer quantities are studied and an emphasis is given to solution verification and numerical error estimation. Computational solutions are compared to experimental data at full-scale Reynolds numbers.
Supramolecular Organization of α,α‘-Disubstituted Sexithiophenes (2002)

The self-assembly of alpha,alpha'-linked sexithiophenes with chiral and achiral penta(ethylene glycol) chains attached at the alpha-positions of the terminal rings, that is, 2,2':5',2'':5'',2''':5''',2'''':5'''',2'''''-sexithiophene-5,5'''''-dicarboxylic acid-2S)-2-methyl-3,6,9,12,15-pentaoxahexadecyl ester (1) and 2,2':5',2'':5'',2''':5'''',2''''':5''''',2'''''-sexithiophene-5,5'''''-dicarboxylic acid-3,6,9,12,15-pentaoxahexadecyl ester (2), respectively is described. Analysis of the UV/vis, fluorescence, circular dichroism, and circular polarization of luminescence spectroscopic data shows that these compounds form chiral aggregates in polar solvents and in the solid state. In n-butanol aggregation occurs at temperatures below 30 degrees C, while above this threshold temperature the aggregates break up without an intermediate disordered state of aggregation, and the compounds are molecularly dissolved. The "melting temperature" of the aggregates depends on the concentration of sexithiophene, indicating that the optical changes observed are a result of intermolecular processes. Mass spectrometric measurements reveal that 1 and 2 can form mixed aggregates. Analysis of the optical spectra reveals that in these mixed aggregates, chiral 1 molecules act as "sergeants" to direct the packing of the "soldiers" 2, illustrating cooperativity within the columns. In water, the same type of chiral aggregates are formed as in n-butanol below 30 degrees C; however, these aggregates are still present, but the chirality is lost above 30 degrees C. In spin-coated films of 1 chiral aggregates are present. AFM studies show that 1 self-organizes into chiral fiberlike structures in the solid state. Furthermore both 1 and 2 display thermotropic liquid crystalline behavior between 180 and 200 degrees C.
Improved Cardiac Magnetic Resonance-Thermometry and dosimetry for monitoring lesion formation during catheter ablation (2016)

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