gebhart/patrepeval huggingface dataset:
Supplementary Figure 1 from Cotargeting Stress-Activated Hsp27 and Autophagy as a Combinatorial Strategy to Amplify Endoplasmic Reticular Stress in Prostate Cancer (2023)

&lt;p&gt;PDF file - 58K, PC-3 cells stably overexpressing Hsp27 show similar cell growth and apoptotic rates compared to parental or empty vector under basal, unstressed conditions&lt;/p&gt;
Self‐Condensation of N‐tert‐Butanesulfinyl Aldimines: Application to the Rapid Asymmetric Synthesis of Biologically Important Amine‐Containing Compounds. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
High-Efficiency Stacked Shorted Annular Patch Antenna Feed for Ku-Band Satellite Communications (2016)

Reflector-based satellite communication (SatCom) terminals require high sensitivity to minimize overall antenna size, and in view of their simplicity and high radiation efficiency, horn antennas are used almost exclusively as reflector feeds. As these terminals become more complex, smaller and more compact feeds that can be directly integrated with microstrip circuits are desirable. Standard microstrip antennas (MSAs) have unacceptably low radiation efficiency for use as reflector feeds. We show that the stacked shorted annular patch (SSAP) can be used as a replacement for horn feeds and achieves higher radiation and spillover efficiencies than conventional patch antennas due to the absence of distribution networks and dielectric substrates. Using a half-wavelength stacked patch as a director realizes a pattern that achieves high illumination efficiency with standard parabolic reflector geometries. Simulation and measurements show that the compact SSAP may be the first reported nonwaveguide feed antenna to achieve sensitivity comparable to that of a conventional horn feed.
Compact lens with circular spot profile for square die LEDs in multi-LED projectors (2011)

In the stage illumination industry, LED technology is promising both in terms of energy use and novel features, but it also has inherent issues. This paper presents a solution to the poor color homogeneity arising when multiple rectangular images formed from LED dies are combined into a circular spot profile. Using ray tracing, a nonrotationally symmetric collimating lens was optimized to round off such die images. The result is a high-output lens with an almost perfectly circular spot. In a simulated red green blue color mixing projector with seven LEDs, the lens reduced measurable color inhomogeneity by ≈24.1%, with a 5.3% luminous gain, compared to the best rotationally symmetric benchmark lens.
An Obligatory Role of Mind Bomb-1 in Notch Signaling of Mammalian Development (2007)

Our data provide the first evidence that Mib1 is essential for Jagged as well as Deltalike ligand-mediated Notch signaling in mammalian development, while Neur1, Neur2, and Mib2 are dispensable.
Integrated Dynamic Thermo-Mechanical Modeling of High Speed Spindles, Part 1: Model Development (2004)

This paper presents a comprehensive integrated thermo-dynamic model for various high speed spindles. The entire model consists of fully coupled three sub-models: bearing, spindle dynamic and thermal models. Using a finite element approach, a new thermal model has been generated, which can describe complex structures of high-speed motorized spindles, and can predict more accurate temperature distributions. The spindle dynamic model is constructed using finite elements based on Timoshenko beam theory and has been improved by considering shear deformation, material and bearing damping, and the spindle/tool-holder interface. Using the new thermo-dynamic model, more general and detailed bearing configurations can be modeled through a systematic coupling procedure. The thermal expansions of the shaft, housing and bearings are calculated based on predicted temperature distributions and are used to update the bearing preloads depending on the operating conditions, which are again used to update the thermal model. Therefore, the model is fully integrated and can provide solutions in terms of all the design parameters and operating conditions.
Mechanism of Action of and Mechanism of Reduced Susceptibility to the Novel Anti-Clostridium difficile Compound LFF571 (2012)

LFF571 is a novel semisynthetic thiopeptide and potent inhibitor of Gram-positive bacteria. We report that the antibacterial activity of LFF571 against Clostridium difficile is due to inhibition of translation. Single-step mutants of C. difficile with reduced susceptibility to LFF571 were selected at frequencies of <4.5 × 10(-11) to 1.2 × 10(-9). Sequencing revealed a G260E substitution in the thiopeptide-binding pocket of elongation factor Tu. Importantly, this mutation did not confer cross-resistance to clinically used antimicrobials. These results support the development of LFF571 as a treatment for C. difficile infection.
What patient and surgical factors contribute to implant wear and osteolysis in total joint arthroplasty? (2008)

Total joint arthroplasty has been a successful operation for decades. Our current patients are younger and more active than those in the past. They place higher demands on themselves and have expectations commensurate with their lifestyles. Time-limited longevity with the large number of anticipated total joint replacement procedures and their potential burden to health care is a growing concern. In the past two decades, implant wear and osteolysis have been identified as major causes for the failure of otherwise well-functioning implants. Osteolysis can be divided into several categories: patient-specific, implant-specific, and the result of surgical factors. Although these categories are interrelated and not mutually exclusive, they enable us to build a framework in which to further advance our understanding of osteolysis and apply this information in a clinically relevant manner.
Digital microfluidic hydrogel microreactors for proteomics (2012)

Proteolytic digestion is an essential step in proteomic sample processing. While this step has traditionally been implemented in homogeneous (solution) format, there is a growing trend to use heterogeneous systems in which the enzyme is immobilized on hydrogels or other solid supports. Here, we introduce the use of immobilized enzymes in hydrogels for proteomic sample processing in digital microfluidic (DMF) systems. In this technique, preformed cylindrical agarose discs bearing immobilized trypsin or pepsin were integrated into DMF devices. A fluorogenic assay was used to optimize the covalent modification procedure for enzymatic digestion efficiency, with maximum efficiency observed at 31 μg trypsin in 2-mm diameter agarose gel discs. Gel discs prepared in this manner were used in an integrated method in which proteomic samples were sequentially reduced, alkylated, and digested, with all sample and reagent handling controlled by DMF droplet operation. Mass spectrometry analysis of the products revealed that digestion using the trypsin gel discs resulted in higher sequence coverage in model analytes relative to conventional homogenous processing. Proof-of-principle was demonstrated for a parallel digestion system in which a single sample was simultaneously digested on multiple gel discs bearing different enzymes. We propose that these methods represent a useful new tool for the growing trend toward miniaturization and automation in proteomic sample processing.
Hepatic Steatosis Alleviated in Diabetic Mice upon Dietary Exposure to Fibroin via Transgenic Rice: Potential STAMP2 Involvement in Hepatocytes (2020)

Many benefits of silk protein fibroin (SPF) have been suggested in biomedical applications; and notably, significant SPF effects have been observed for metabolic syndromes that are directly linked to insulin resistance, such as type 2 diabetes mellitus (T2DM). Based on our previous findings, we believe that SPF from spiders exhibits outstanding glucose-lowering effects in diabetic BKS.Cg-m+/+Lepr<sup>db</sup> mice. In order to evaluate the dietary effects of SPF in diabetic animals, we generated several lines of transgenic rice (TR) that expresses SPF, and the feeding of TR-SPF to diabetic animals decreased blood glucose levels, but did not change insulin levels. Western blot analyses of hepatic proteins showed that AMP-activated protein kinase (AMPK) expression and phosphorylation both decreased in TR-SPF-fed groups, compared with controls. This finding suggests that the glucose-lowering effects in this diabetic animal model might be AMPK-independent. In contrast, six-transmembrane protein of prostate 2 (STAMP2) was upregulated after TR-SPF exposure. Together with STAMP2, the Akt protein phosphorylation increased after TR-SPF exposure, which indicates that STAMP2 leads to Akt phosphorylation and thus increases insulin sensitivity in hepatocytes. Importantly, the hepatic steatosis that was seen in the liver of diabetic mice was remarkably alleviated in TR-SPF-fed mice. Hepatocytes that were immunopositive for STAMP2 were overwhelmingly observed in hepatic tissues from TR-SPF-fed mice compared to the control. Taken together, these results suggest that feeding diabetic mice with TR-SPF upregulates STAMP2 expression and increases Akt phosphorylation in hepatic tissues and thus potentially alleviates insulin resistance and hepatic steatosis.
Biomedical Applications: Engineering of Mature Human Induced Pluripotent Stem Cell‐Derived Cardiomyocytes Using Substrates with Multiscale Topography (Adv. Funct. Mater. 19/2018) (2018)

Immaturity of cardiomyocytes derived from induced pluripotent stem cells is an important issue in the field of cell therapeutics. In article number 1707378, Morteza Mahmoudi and co-workers develop substrates with multi-scale topography resembling the three-dimensional features of the native heart environment to address the issue of immaturity of cardiomyocytes. The results show faster differentiation, enhanced maturity, and improved beating.
RTM noise attenuation and image enhancement using time-shift gathers (2014)

PreviousNext No AccessBeijing 2014 International Geophysical Conference & Exposition, Beijing, China, 21-24 April 2014RTM noise attenuation and image enhancement using time-shift gathersAuthors: Adel KhalilJames Sun*Yu ZhangGordon PooleAdel KhalilCGG, James Sun*CGG, Yu ZhangCGG, and Gordon PooleCGGhttps://doi.org/10.1190/IGCBeijing2014-127 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InReddit Abstract Reverse time migration (RTM) has become a central tool in seismic imaging, especially in complex geologies where other migration methods fail. However, the way RTM is generally formulated introduces various types of artifacts, these include low-frequency noise in high velocity-contrast areas and shear-wave-like noise when anisotropy is included in the formulation. Using time-shift gathers from the extended imaging condition, we develop a method to effectively attenuate these artifacts and further enhance the final image by refocusing the migrated energy. We demonstrate the results of our method on both real and synthetic data sets. Keywords: time migration, attenuation, imagingPermalink: https://doi.org/10.1190/IGCBeijing2014-127FiguresReferencesRelatedDetails Beijing 2014 International Geophysical Conference & Exposition, Beijing, China, 21-24 April 2014 ISSN (online):2159-6832 Copyright: 2014 Pages: 1360 publication data© 2014 Published in electronic format with permission by the Society of Exploration Geophysicists and Chinese Petroleum SocietyPublisher:Society of Exploration Geophysicists HistoryPublished Online: 24 Apr 2014 CITATION INFORMATION Adel Khalil, James Sun*, Yu Zhang, and Gordon Poole, (2014), "RTM noise attenuation and image enhancement using time-shift gathers," SEG Global Meeting Abstracts : 494-498. https://doi.org/10.1190/IGCBeijing2014-127 Plain-Language Summary Keywordstime migrationattenuationimagingPDF DownloadLoading ...
Pre-mRNA splicing by complementation with purified human UI, U2, U4/U6 and U5 snRNPs (1988)

The four major nucleoplasmic small nuclear ribonucleoprotein particles U1, U2, U4/U6 and U5 can be extensively purified from HeLa cells by immunoaffinity chromatography using a monoclonal anti-trimethylguanosine antibody. The snRNP particles in active splicing extracts are selectively bound to the immunoaffinity matrix, and are then gently eluted by competition with an excess of free nucleoside. Biochemical complementation studies show that the purified snRNPs are active in pre-mRNA splicing, but only in the presence of additional non-snRNP protein factors. All the RNPs that are necessary for splicing can be purified in this manner. The active snRNPs are characterized with respect to their polypeptide composition, and shown to be distinct from several other activities implicated in splicing.
Development Control Thermoelectric Technique Using Customized Proportional Controller and Disturbance Observer (2011)

This paper proposes a development method to control thermoelectric by using customization proportional controller. Moreover, the system applied heat disturbance observer to estimation value heat disturbance outside object into the system. In the equipment part, Peltier device is selected to be the thermoelectric module device. This device is a type suitable for analysis thermal system, because the device has a fast respond and good stability, it is comparison with the device in this group. Also this proposal used high speed controller (FPGA) for the programming to control system. Moreover, about the circuit driver current and sensor temperature used digital system. It protected noise working well and easy to program with FPGA. The result of this research can be guideline for analysis to control thermal systems or to control temperature for various applications.
Metal Ion Dependence of Oligosaccharyl Transferase: Implications for Catalysis (1995)

Oligosaccharyl transferase activity exhibits an absolute requirement for certain divalent metal cations. Studies with reconstituted enzyme suggest a preference for metal ions that can adopt an octahedral coordination geometry. In order to gain insight into the specific role of the metal cation in catalysis, we have investigated the influence of the metal cofactor on catalytic turnover of the tripeptide substrate Bz-Asn-Leu-Thr-NHMe (1) and a closely related sulfur-containing analog, Bz-Asn(gamma S)-Leu-Thr-NHMe (2). The metal ion substitution studies reveal that 1 is effectively turned over in the presence of several metal ions (Mn2+, Fe2+, Mg2+, and Ca2+). In contrast, 2 is only glycosylated in the presence of the thiophilic metal cations manganese and iron. When the enzyme is reconstituted with the oxophilic cations magnesium and calcium, 2 shows minimal substrate behavior. With the amide substrate 1, the distinct preference for manganese over magnesium may argue against direct coordination of the metal to the lipid-linked substrate pyrophosphate moiety. This fact, together with the comparative studies with asparagine- and thioasparagine-containing tripeptides, implicates the metal cofactor in a role that places it proximal to the peptide binding site.
<title>Water quality monitoring using an automated portable fiber optic biosensor: RAPTOR</title> (2001)

The RAPTOR is a portable, automated biosensor capable of performing rapid, ten-minute assays on a sample for four target analytes simultaneously. Samples are analyzed using a fluorescent sandwich immunoassay on the surface of short polystyrene optical probes with capture antibody adsorbed to the probe surface. Target analytes bound to the fiber by capture antibodies are detected with fluorescently labeled tracer antibodies, which are held in a separate reservoir. Since target recognition is a two-step process, selectivity is enhanced, and the optical probes can be reused up to forty times, or until a positive result is obtained. This greatly reduces the logistical burden for field operations. Numerous assays for toxins, such as SEB and ricin, and bacteria, such as Bacillus anthracis and Francisella tularensis, have been developed for the RAPTOR. An assay of particular interest for water quality monitoring and the screening of fruits and vegetables is detection of Giardia cysts. Giardia lamblia is a parasitic protozoan common in the developing world that causes severe intestinal infections. Thus, a simple field assay for screening water supplies would be highly useful. Such an assay has been developed using the RAPTOR. The detection limit for Giardia cysts was 5x104/ml for a 10-minute assay.
Kinetic model of impurity poisoning during growth of calcite (2004)

The central role of the organic component in biologically controlled mineralization is widely recognized. These proteins are characterized by a high proportion of acidic amino acid residues, especially aspartate, Asp. At the same time, biomineralization takes place in the presence of a number of naturally-occurring, inorganic impurities, particularly Mg and Sr. In an attempt to decipher the controls on calcite growth imposed by both classes of modifiers, we have used in situ AFM to investigate the dependence of growth morphology and step kinetics on calcite in the presence of Sr{sup 2+}, as well as a wide suite of Aspartic acid-bearing polypeptides. In each case, we observe a distinct and step-specific modification. Most importantly, we find that the step speed exhibits a characteristic dependence on impurity concentration not predicted by existing crystal growth models. While all of the impurities clearly induce appearance of a 'dead zone,' neither the width of that dead zone nor the dependence of step speed on activity or impurity content can be explained by invoking the Gibbs-Thomson effect, which is the basis for the Cabrera-Vermilyea model of impurity poisoning. Common kink-blocking models also fail to explain the observed dependencies. Here we propose a kinetic model of inhibition based on a 'cooperative' effect of impurity adsorption at adjacent kink sites. The model is in qualitative agreement with the experimental results in that it predicts a non-linear dependence of dead zone width on impurity concentration, as well as a sharp drop in step speed above a certain impurity content. However, a detailed model of impurity adsorption kinetics that give quantitative agreement with the data has yet to be developed.
PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq (2019)

Toolsets available for in-depth analysis of scRNA-seq datasets by biologists with little informatics experience is limited. Here, we describe an informatics tool (PyMINEr) that fully automates cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks in silico. We applied PyMINEr to interrogate human pancreatic islet scRNA-seq datasets and discovered several features of co-expression graphs, including concordance of scRNA-seq-graph structure with both protein-protein interactions and 3D genomic architecture, association of high-connectivity and low-expression genes with cell type enrichment, and potential for the graph structure to clarify potential etiologies of enigmatic disease-associated variants. We further created a consensus co-expression network and autocrine-paracrine signaling networks within and across islet cell types from seven datasets. PyMINEr correctly identified changes in BMP-WNT signaling associated with cystic fibrosis pancreatic acinar cell loss. This proof-of-principle study demonstrates that the PyMINEr framework will be a valuable resource for scRNA-seq analyses.
EXERT: EXhaustive IntEgRiTy Analysis for Information Flow Security (2022)

Hardware information flow analysis detects security vulnerabilities resulting from microarchitectural design flaws, design-for-test/debug (DfT/D) backdoors, and hardware Trojans. Though information flow violations can be manifested through a multitude of possible ways, prior research has only focused on detecting the existence of such vulnerabilities and no approach has been proposed to exhaustively activate all vulnerable points and reduce false positives. In this paper, we propose EXERT, a novel analysis framework that combines ATPG, SAT, and FSM analysis to detect information flow violations and perform exhaustive analysis that reports the complete set of violating input patterns for vulnerable control points. The FSM analysis, in particular, can be performed offline and helps resolve scalability limitations in prior approaches while remaining exhaustive. As proof-of-concept, EXERT is evaluated on multiple Trojan benchmarks from Trust-Hub. It detects rare Trojan triggers (activation probability ≈ 1.4243e-70), generates all activation patterns within minutes, and shows a 15 x to 110 x faster run time compared with Cadence Jasper Security Path Verification (SPV). EXERT is also applied to a larger RISC-V benchmark to identify instruction sequences that result in privilege escalation.
Supplementary Information S1 from A Phase 1 First-in-Human Study of FS118, a Tetravalent Bispecific Antibody Targeting LAG-3 and PD-L1 in Patients with Advanced Cancer and PD-L1 Resistance (2023)

&lt;p&gt;Supplementary information&lt;/p&gt;
Neural network models for classifying immune cell subsets (2013)

The immune system is composed of heterogeneous cell populations and it includes several hundreds of distinct cells types such as neutrohils, eosinophils, basophils, macrophages, dendritic cells, CD4+ and CD8+ T cells, 7<5 T cells, mast cells, and B cells and each main cell type can be further differentiated into subsets with unique and overlapping functions. For example CD4+ T cells can be differentiated into T helper (Th)l, Th2, Thl7, and regulatory T cell (Treg) subsets. To study molecular mechanisms of cell differentiation, Systems Biology Markup Language (SBML) based Ordinary Differential Equation (ODE) models can be used for representing such processes. These intracellular signaling models often require many equations to accurately represent intracellular pathways and biochemical reactions. Another challenge in studying the immune system and immune responses is the need for integration of complex processes that occur at different time and space scales (i. e., populations, whole organism, tissue level, cellular and molecular) through multi-scale modeling. This study presents two novel neural network models for modeling CD4+ T cell differentiation and immune cell subset classification. The first model reduces the complex ODE intracellular model by focusing on the input and output cytokines and the second model establishes an automated subset classification based on molecular patterns expressed in immune cells. After training, the first model achieves small prediction errors of cytokine concentrations and the second model achieves 98% prediction rate for subset classification. Neural network algorithm and models have been widely used for many data mining tasks such as classification and pattern recognition. However, to the best of our knowledge this study is the first one applying the neural network algorithm for immune cell differentiation and subset classification. In addition, these novel neural network models can be computationally efficiently integrated into multi-scale models with limited computational costs.
Asymmetric Synthesis of (S)-3-Amino-4-methoxy-butan-1-ol by Way of Reductive Amination (2011)

A new synthesis of (S)-3-amino-4-methoxy-butan-1-ol is reported. The synthesis is based on the preparation of the primary, nonprotected enamine of the commercially available β-keto ester methyl 4-methoxy-3-oxo-butanoate and asymmetric catalytic enamine hydrogenation using a Ru-MeOBIPHEP catalyst. Alternatively, the process is performed by asymmetric catalytic reductive amination of the β-keto ester with ammonium acetate and hydrogen using a similar Ru catalyst. Both process versions provided initial ee values of 97−98% which were upgraded to ≥99% by product crystallization. Ester to alcohol conversion was best accomplished by LiBH4 reduction after transitory Boc protection of the amino group.