gebhart/patrepeval huggingface dataset:
Abstract 27: Label-free, real-time analysis of endothelial cell morphogenesis using iPSC-derived endothelial cells (2014)

Abstract Endothelial cell (EC) morphogenesis during the early stages of angiogenesis is a highly dynamic process tightly regulated by growth factor activity in the extracellular milieu. Other in vitro models for the analysis of EC morphogenesis have previously been developed to understand the cellular processes and the impact of soluble cues and pharmacological inhibitors. However, these assays typically utilize end-point analysis of primary endothelial cells (eg. HUVEC), which are a physiologically relevant vascular cell type but do exhibit variability from the diversity of donors. Additionally, current methods for measuring morphogenesis (eg. proliferation and migration) only capture a snapshot of cell function owing to potentially destructive labeling of the cells and do not capture the complexity of cellular processes involved in EC morphogenesis Here, we describe use of a real-time system for monitoring of cellular processes using electronic cell sensor array technology. The cellular model tested on this impedance-based platform was a well-defined human induced pluripotent stem cell (iPSC)-derived endothelial cells. Following assay optimization and workflow improvement, we assessed the impact of serum, growth factors (e.g. VEGF, EGF, FGF-2), and small-molecule angiogenesis inhibitors (e.g. Sunitinib, SU1498) on the proliferation, migration, and invasion of iPSC-derived ECs compared to primary cells. We observed that real-time monitoring of such cellular processes offers distinct and important advantages over traditional end-point assays - specifically, the ability to measure receptor activation and quantify morphologic and adhesive remodeling of EC upon growth factor activation or signaling inhibition. By better understanding cellular morphogenesis in vitro, we can generate a picture of what soluble cues regulate the process and how pharmacological agents can modulate the different cell fates underlying morphogenesis. The use of iPSC-derived endothelial cells provides a robust and reproducible source of cells that perform equivalently to the standard that is HUVEC. The combination of iPSC-derived EC together with a real time monitoring system provides a biologically relevant human model system. Citation Format: David Mann, David Belair, Coby Carlson, Arne Thompson, Yama Abassi, Jeff Irelan. Label-free, real-time analysis of endothelial cell morphogenesis using iPSC-derived endothelial cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 27. doi:10.1158/1538-7445.AM2014-27
A new test facility for efficient evaluation of MEMS contact materials (2007)

A novel test facility for the efficient evaluation of microelectromechanical system (MEMS) switches and the development of alternative contact materials is described. The facility utilizes the upper cantilever from commercial MEMS contact switches, and tests these against alternative bottom contact materials within a modified atomic force microscope (AFM). The test closely approximates the real switch, but can accommodate a wider range of test conditions and contact materials. The facility allows alternative contact materials to be easily and quickly incorporated, and therefore evaluated by measuring the number of cycles to failure. The evolution of the wear surfaces of the switch contact materials under test can also be easily examined. In order to demonstrate the facility, the evolution of the contact resistance and wear of a commercial RF MEMS cantilever with Au contacts was monitored under accelerated test conditions, comparing the behavior of Au bottom contacts to an alternative Au–Ni alloy contact material. The Au–Ni (20 at.%) alloy displayed reduced wear rates and improved switch cycle lifetimes compared to pure Au, while retaining acceptable values of contact resistance.
Disintermediated Active Communication (2006)

Disintermediated active communication (DAC) is a new paradigm of communication in which a sending thread actively engages a receiving thread when sending it a message via shared memory. DAC is different than existing approaches that use passive communication through shared-memory - based on intermittently checking for messages - or that use preemptive communication but must rely on intermediaries such as the operating system or dedicated interrupt channels. An implementation of DAC builds on existing cache coherency support and exploits light-weight user-level interrupts. Inter-thread communication occurs via monitored memory locations where the receiver thread responds to invalidations of monitored addresses with a light-weight user-level software-defined handler. Address monitoring is supported by cache line user-bits, or CLUbits. CLUbits reside in the cache next to the coherence state, are private per thread, and maintain user-defined per-cache-line state. A light weight software library can demultiplex asynchronous notifications and handle exceptional cases. In DAC-based programs threads coordinate with one another by explicit signaling and implicit resource monitoring. With the simple and direct communication primitives of DAC, multi-threaded workloads synchronize at a finer granularity and more efficiently utilize the hardware of upcoming multi-core designs. This paper introduces DAC, presents several signaling models for DAC-based programs, and describes a simple memory-based framework that supports DAC by leveraging existing cache-coherency models. Our framework is general enough to support uses beyond DAC
Lipooligosaccharide is required for the generation of infectious elementary bodies in Chlamydia trachomatis (2011)

Lipopolysaccharides (LPS) and lipooligosaccharides (LOS) are the main lipid components of bacterial outer membranes and are essential for cell viability in most Gram-negative bacteria. Here we show that small molecule inhibitors of LpxC [UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase], the enzyme that catalyzes the first committed step in the biosynthesis of lipid A, block the synthesis of LOS in the obligate intracellular bacterial pathogen Chlamydia trachomatis. In the absence of LOS, Chlamydia remains viable and establishes a pathogenic vacuole ("inclusion") that supports robust bacterial replication. However, bacteria grown under these conditions were no longer infectious. In the presence of LpxC inhibitors, replicative reticulate bodies accumulated in enlarged inclusions but failed to express selected late-stage proteins and transition to elementary bodies, a Chlamydia developmental form that is required for invasion of mammalian cells. These findings suggest the presence of an outer membrane quality control system that regulates Chlamydia developmental transition to infectious elementary bodies and highlights the potential application of LpxC inhibitors as unique class of antichlamydial agents.
Effect of conagenin on thrombocytopenia induced by antitumor agents in mice. (1994)

The effect of conagenin (CNG) on myelosuppression induced by antitumor agents was investigated. The daily administration of CNG prevented reduction in the number of platelets (PLT) observed in peripheral blood of mice given mitomycin C (10 mg/kg) but did not prevent reduction in the number of leukocytes (WBC). The effect on PLT was also confirmed in mice given cyclophosphamide (100 mg/kg). In mice given repeated doses of 5-fluorouracil (10 mg/kg), CNG prevented the reduction of PLT as well as WBC and maintained them at normal levels. CNG prevented reduction of the production of interleukin-2, 3 and 6 in cultured supernatants of spleen cells taken from mice given 5-fluorouracil. These results suggest that CNG modulates production of lymphokines which are responsible for thrombopoiesis.
RNA structure and scalar coupling constants (2018)

Signs and magnitudes of scalar coupling constants-spin-spin splittings-comprise a very large amount of data that can be used to establish the conformations of RNA molecules. Proton-proton and proton-phosphorus splittings have been used the most, but the availability of {sup 13}C-and {sup 15}N-labeled molecules allow many more coupling constants to be used for determining conformation. We will systematically consider the torsion angles that characterize a nucleotide unit and the coupling constants that depend on the values of these torsion angles. Karplus-type equations have been established relating many three-bond coupling constants to torsion angles. However, one- and two-bond coupling constants can also depend on conformation. Serianni and coworkers measured carbon-proton coupling constants in ribonucleosides and have calculated their values as a function of conformation. The signs of two-bond coupling can be very useful because it is easier to measure a sign than an accurate magnitude.
New record of Dendronephthya hemprichi (Family: Nephtheidae) from Mediterranean, Israel- an evidence for tropicalization? (2023)

Abstract Bioinvasions have the potential to provoke cascade effects that can disrupt natural ecosystems, and cause ecological regime shifts. The Mediterranean Sea is particularly prone to bioinvasions as the changing water conditions, evoked by climate change, are creating advantageous conditions for Lessepsian migrants from the Red Sea. Recently, in May 2023, a new alien species was documented in the Mediterranean Sea - a soft coral of the genus Dendronephthya . This discovery was made by divers conducting ‘Long Term Ecological Research’ surveys, along the coast of Israel, at a depth of 42 m. Genetic and morphological testing were utilized to confirm the species identity as Dendronepthya hemprichi , an Indo-Pacific coral, common in the Red Sea. According to life history traits of this species such as accelerated attachment to available surfaces and fast growth, we expect it to rapidly expand its distribution and abundance across the Mediterranean. Highlights Potential ‘Tropicalization’ of the Mediterranean Sea Increasing water temperatures are an important vector for marine bioinvasion A second soft coral species, associated with Lessepsian migration, was identified in the Mediterranean The importance of a long-term ecological monitoring program for identifying ecosystem changes
Data from Bacterial-Driven Inflammation and Mutant <i>BRAF</i> Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy (2023)

&lt;div&gt;Abstract&lt;p&gt;Colorectal cancer is multifaceted, with subtypes defined by genetic, histologic, and immunologic features that are potentially influenced by inflammation, mutagens, and/or microbiota. Colorectal cancers with activating mutations in &lt;i&gt;BRAF&lt;/i&gt; are associated with distinct clinical characteristics, although the pathogenesis is not well understood. The Wnt-driven multiple intestinal neoplasia (Min&lt;sup&gt;ApcΔ716/+&lt;/sup&gt;) enterotoxigenic &lt;i&gt;Bacteroides fragilis&lt;/i&gt; (ETBF) murine model is characterized by IL17-dependent, distal colon adenomas. Herein, we report that the addition of the &lt;i&gt;BRAF&lt;/i&gt;&lt;sup&gt;V600E&lt;/sup&gt; mutation to this model results in the emergence of a distinct locus of midcolon tumors. In ETBF-colonized &lt;i&gt;BRAF&lt;/i&gt;&lt;sup&gt;V600E&lt;/sup&gt;&lt;i&gt;Lgr5&lt;/i&gt;&lt;sup&gt;Cre&lt;/sup&gt;Min (BLM) mice, tumors have similarities to human &lt;i&gt;BRAF&lt;/i&gt;&lt;sup&gt;V600E&lt;/sup&gt; tumors, including histology, CpG island DNA hypermethylation, and immune signatures. In comparison to Min ETBF tumors, BLM ETBF tumors are infiltrated by CD8&lt;sup&gt;+&lt;/sup&gt; T cells, express IFNγ signatures, and are sensitive to anti–PD-L1 treatment. These results provide direct evidence for critical roles of host genetic and microbiota interactions in colorectal cancer pathogenesis and sensitivity to immunotherapy.&lt;/p&gt;Significance:&lt;p&gt;Colorectal cancers with &lt;i&gt;BRAF&lt;/i&gt; mutations have distinct characteristics. We present evidence of specific colorectal cancer gene–microbial interactions in which colonization with toxigenic bacteria drives tumorigenesis in &lt;i&gt;BRAF&lt;/i&gt;&lt;sup&gt;V600E&lt;/sup&gt;&lt;i&gt;Lgr5&lt;/i&gt;&lt;sup&gt;Cre&lt;/sup&gt;Min mice, wherein tumors phenocopy aspects of human &lt;i&gt;BRAF&lt;/i&gt;-mutated tumors and have a distinct IFNγ-dominant immune microenvironment uniquely responsive to immune checkpoint blockade.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 1601&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Error Suppression of Last-Programmed Word-Line for Real Usage of 3D-NAND Flash Memory (2021)

Blocks of 3D-NAND flash memory are programmed in order of WL. In real usage of 3D-NAND flash memory, a block contains both programmed WLs and not programmed WLs because the programmed data do not always fill the block. In the block, the last data are programmed at 'last-programmed WL' where the upper WL is not programmed. The last programmed data are supposed to have high reliability owing to shorter data-retention time. However, when upper WL is not programmed, BER of last-programmed WL largely increases because upper WL has less electrons and causes lateral charge migration. To suppress the errors at last-programmed word-line, this paper proposes Last-programmed Word-line Protection (LWLP). Proposed LWLP suppresses BER by 37% at last-programmed WL and extends data-retention time by more than 4 times.
Thermoplastic Elastomers (2004)

The article contains sections titled: 1. Thermoplastic Polyolefin Elastomers 1.1. Introduction and Definition 1.2. Thermoplastic Polyolefin Blends 1.2.1. Morphology 1.2.2. Elastomer Component, Soft Domain 1.2.3. Plastic Component, Hard Domain 1.2.4. Compounds, Trade Names 1.2.5. Processing 1.3. Thermoplastic Vulcanizates 1.3.1. Dynamic Vulcanization 1.3.2. Production and Morphology 1.3.3. Types 1.3.4. Processing 1.3.5. Performance and Product Positioning 1.3.6. Uses 1.3.7. Commercial Products and Trade Names 2. Thermoplastic Polyurethane Elastomers 2.1. Introduction 2.2. Raw Materials 2.3. Production 2.4. Properties 2.5. Processing and Use 2.6. Economic Aspects 2.7. Toxicology and Occupational Health 3. Thermoplastic Copolyester Elastomers 3.1. Introduction 3.2. Raw Materials 3.3. Production 3.4. Microstructure and Composition of Segments 3.4.1. Short-Chain Ester Units (Hard Segments) 3.4.2. Long-Chain Polyether Soft Segments 3.4.3. Hydrocarbon Soft Segments 3.4.4. Polyester Soft Segments 3.5. Properties 3.6. Blends 3.7. Uses 3.8. Producers, Trade Names 4. Thermoplastic Polyamide Elastomers 4.1. Introduction 4.2. Raw Materials 4.3. Manufacture of Block Polyetheramides 4.3.1. Polyetheresteramides 4.3.2. Synthesis of Polyetheramides 4.4. Physical and Chemical Properties 4.4.1. Block Variations 4.4.2. Morphology 4.4.3. Outstanding Properties 4.4.4. Chemical Resistance 4.4.5. Processing 4.5. Uses 4.6. Trade Names 5. Styrenic Block Copolymers 5.1. Introduction 5.2. Synthesis 5.3. Properties 5.4. Uses 5.4.1. Adhesives, Sealants, and Coatings 5.4.2. Modification of Bitumen 5.4.3. Compounded Products 5.4.4. Modification of Plastics
Convenient Synthesis and Isolation of Conformationally Rigid Glutamic Acid Analogues (2004)

Abstract A convenient synthetic methodology for the synthesis of highly conformationally restricted tricyclic aminodicarboxylic acids bridged analogues of glutamic acid, is presented. The process can be used for preparation of the novel glutamate analogues.
Disrupted-in-schizophrenia 1 (DISC1) protein aggregates in cerebrospinal fluid are elevated in first-episode psychosis patients (2023)

Abstract The Disrupted-in-schizophrenia 1 (DISC1) protein is a key regulator at the intersection of signaling pathways relevant for adaptive behavior. It is prone to posttranslational changes such as misassembly and aggregation but the significance of such transformations for human mental illness has remained unclear. Here we demonstrate that DISC1 protein aggregates are increased in CSF samples of patients with first episode psychosis (n=50) compared to healthy controls (n=47), as measured by the highly sensitive surface-based fluorescence intensity distribution analysis technology that enables single aggregate detection. The concentration was in the low femtomolar range. No correlations were found to symptom levels, but the difference was particularly significant in the subset of patients receiving the diagnoses “schizophrenia, unspecified” (DSM IV 295.9) or schizoaffective disorder (DSM IV 295.70) at 18-month follow-up. The occurrence of protein aggregates in vivo in patients with psychotic disorders has not been previously reported. It underscores the significance of posttranslational modifications of proteins both as pathogenetic mechanisms and as potential diagnostic markers in these disorders.
Oncologists’ Use of Genomic Sequencing Data to Inform Clinical Management (2018)

Findings demonstrate that many oncologists view next-generation sequencing results to be potentially valuable in directing subsequent therapy for their patients; however, barriers in communicating results to patients and implementing them in clinical management remain.
The Effects of a 28-Hz Vibration on Arm Muscle Activity during Isometric Exercise (2009)

This study shows that V exercise at 28 Hz produces an increase of the activation and the coactivation of biceps and triceps. This exercise modality seems therefore suitable for various applications.
In vitro repair potential of articular cartilage: proteoglycan metabolism in the different areas of the femoral condyles in human cartilage explants. (1987)

We tested the hypothesis that metabolism of individual cartilage samples, such as those which might be taken at arthroscopy, could reflect the overall intrinsic reparative response of the cartilaginous tissue of that joint. Full thickness samples of articular cartilage, removed from the anteromedial, anterolateral and posterolateral areas of the femoral condyles of 2 normal knees, were placed in tissue culture separately. The incorporation of 14C-glucosamine into matrix molecules, especially proteoglycan, was measured. Three slices of each area were removed after one, 3 or 6 weeks of in vitro culture. The extracted matrix molecules and the media were analyzed and the relative amount of radioactive proteoglycan and proteoglycan aggregates, as well as the total amount of radiolabelled proteoglycan/mg dry weight, were calculated. A progressive increase in these variables during the culture period was demonstrated, suggesting an attempt at repair of the articular cartilage in this in vitro condition. No differences in the incorporation dynamics were found between the anteromedial, anterolateral and posterolateral areas of both subjects.
Dielectric ceramics based on the ZrO/sub 2/-SnO/sub 2/-TiO/sub 2/ ternary system for microwave and millimeter wave applications (2005)

This work describes the investigations of (Zr/sub 0.8/Sn/sub 0.2/)TiO/sub 4/ compounds prepared by solid-state reaction techniques. The effect of La/sub 2/O/sub 3/, ZnO and NiO addition on microwave dielectric properties was investigated. The samples were sintered at temperatures T/sub s/=1280 -1400 /spl deg/C. The materials exhibit a dielectric constant /spl epsiv//sub r//spl sim/36 and high values of the Q/spl middot/f product from 30,000 to 55,000 at microwave frequencies. The measured temperature coefficient of the resonance frequency /spl tau//sub f/ takes values in the range (-2/spl divide/+4) ppm//spl deg/C.
DYNAMICAL FEATURES IN COARSENING SOAP FROTH: TOPOLOGICAL APPROACH (1996)

We summarize some recent developments in approximate descriptions of soap froth evolution in 2D. The questions addressed concern temporal correlations in the scaling state, characterization of transient behavior and evolution from very special initial states. We observed that for these delicate issues mean field theory fails; moreover, we found that widely accepted topological simulation methods also disagree significantly with experiments. We identified the source of these discrepancies in the manner the models select the topological rearrangement that follows a bubble’s disappearance. Properly modified topological simulations do yield agreement with experiments. Our analysis allows identification of the manner in which different aspects of the microscopic dynamics affect the long time behavior of the system.
A 3-D nanoribbon-like Pt-free oxygen reduction reaction electrocatalyst derived from waste leather for anion exchange membrane fuel cells and zinc-air batteries (2019)

Fe-Nx and Fe-S-based ORR electrocatalysts have emerged as rightful candidates to replace Pt in fuel cells to make the technology cheap and sustainable. Fe-N-C catalysts are generally prepared by the pyrolysis of conducting polymers, metal-organic frameworks, aerogels, etc., and the combination of multiple heteroatoms and metal precursors. These precursors are mostly expensive and their synthesis involves multiple steps. In this report, we have demonstrated the synthesis of a Fe-N-C catalyst from the waste leather obtained from the footwear and other leather-consuming industries. The pyrolysis of leather with FeCl3 (metal source) results in the formation of a highly thin and porous nano-ribbon like morphology. Waste leather acts as a cost-free single source of heteroatoms like N, S and carbon. The catalyst synthesized at a temperature of 900 °C shows an overpotential of 40 mV and better durability compared to the commercial Pt/C catalyst. The catalyst is demonstrated as the cathode for alkaline exchange membrane fuel cell (AEMFC) and zinc-air battery (ZAB) applications. In the AEMFC, a power density of 50 mW cm-2 and an OCV of 0.92 V are obtained whereas, in the ZAB, it exhibited a power density of 174 mW cm-2 compared to 160 mW cm-2 of the system based on the Pt/C catalyst.
Robust refraction statics solution and near-surface velocity model building using feedback from reflection data (2018)

An accurate near-surface velocity model is critical for weathering statics correction and initial model building for depth migration and full-waveform inversion. However, near-surface models from refraction inversion often suffer from errors in refraction data, insufficient sampling, and over-simplified assumptions used in refraction algorithms. Errors in refraction data can be caused by picking errors resulting from surface noise, attenuation, and dispersion of the first-arrival energy with offset. These errors are partially compensated later in the data flow by reflection residual statics. Therefore, surface-consistent residual statics contain information that can be used to improve the near-surface velocity model. We have developed a new dataflow to automatically include median and long-wavelength components of surface-consistent reflection residual statics. This technique can work with any model-based refraction solution, including grid-based tomography methods and layer-based methods. We modify the cost function of the refraction inversion by adding model and data weights computed from the smoothed surface-consistent residual statics. By using an iterative inversion, these weights allow us to update the near-surface velocity model and to reject first-arrival picks that do not fit the updated model. In this nonlinear optimization workflow, the refraction model is derived from maximizing the coherence of the reflection energy and minimizing the misfit between model arrival times and the recorded first-arrival times. This approach can alleviate inherent limitations in shallow refraction data by using coherent reflection data.