gebhart/patrepeval huggingface dataset:
Basic fibroblast growth factor inhibits osteoclast-like cell formation (1996)

Basic fibroblast growth factor (bFGF) inhibited osteoclast-like cell formation in co-cultures of mouse bone marrow cells either with the mouse stromal cell line, ST2, or with primary osteoblastic cells. Basic FGF significantly inhibited the osteoclast-like cell formation, induced by 1 alpha,25-dihydroxyvitamin D3[1 alpha, 25(OH)2D3] when the cytokine was added to the culture, at an intermediate stage, suggesting that bFGF inhibits the differentiation of the osteoclast progenitors. With regard to target cells, bFGF directly affected ST2; it increased [3H] thymidine uptake and decreased the number of alkaline phosphatase-positive cells. In contrast, bFGF had no inhibitory effect on the colony formation of bone marrow cells induced by macrophage colony stimulating factor in methylcellulose culture. In addition, ST2 cells treated with bFGF produced similar amounts of colony forming activity to those without the cytokine. These findings indicated that the bFGF is not involved in the proliferation of progenitor cells even in the presence of ST2 cells. Furthermore, bFGF inhibited osteoclast-like cell formation induced not only by 1 alpha,25(OH)2D3, but also by prostaglandin E2 and by interleukin-11. These results suggest that bFGF inhibits the common site of osteoclast-like cell formation, as induced by different mechanisms. Our data also indicated that the target cells for bFGF in inhibiting osteoclast formation are not osteoclast progenitors but stromal cells such as ST2 and osteoblastic cells, which support osteoclast development.
Hydrophobic analogues of rhodamine B and rhodamine 101: potent fluorescent probes of mitochondria in living C. elegans (2012)

Mitochondria undergo dynamic fusion and fission events that affect the structure and function of these critical energy-producing cellular organelles. Defects in these dynamic processes have been implicated in a wide range of human diseases including ischemia, neurodegeneration, metabolic disease, and cancer. To provide new tools for imaging of mitochondria in vivo, we synthesized novel hydrophobic analogues of the red fluorescent dyes rhodamine B and rhodamine 101 that replace the carboxylate with a methyl group. Compared to the parent compounds, methyl analogues termed HRB and HR101 exhibit slightly red-shifted absorbance and emission spectra (5-9 nm), modest reductions in molar extinction coefficent and quantum yield, and enhanced partitioning into octanol compared with aqueous buffer of 10-fold or more. Comparison of living C. elegans (nematode roundworm) animals treated with the classic fluorescent mitochondrial stains rhodamine 123, rhodamine 6G, and rhodamine B, as well as the structurally related fluorophores rhodamine 101, and basic violet 11, revealed that HRB and HR101 are the most potent mitochondrial probes, enabling imaging of mitochondrial motility, fusion, and fission in the germline and other tissues by confocal laser scanning microscopy after treatment for 2 h at concentrations as low as 100 picomolar. Because transgenes are poorly expressed in the germline of these animals, these small molecules represent superior tools for labeling dynamic mitochondria in this tissue compared with the expression of mitochondria-targeted fluorescent proteins. The high bioavailabilty of these novel fluorescent probes may facilitate the identification of agents and factors that affect diverse aspects of mitochondrial biology in vivo.
The collision of cotranscribing E. coli RNA polymerases studied in vitro. (1993)

The collision of cotranscribing E. coli ternary complexes was brought about in vitro by forcing the first "leading" complex to stall before first template C, due to the absence of CTP, and then permitting initiation of a second "following" complex. Following collision, the transcript of the leading complex was increased in length by as much as 7 nt., despite the absence of CTP, but did not dissociate. Upon addition of CTP, the leading complex aborted at exactly the positions requiring incorporation of the next Cs', the following complex continued transcription. The observations point to the importance of linking appropriate promoter efficiency with transcriptional pausing times, and the role of transcriptional collisions in termination events.
Genotyping of Acantamoeba spp. from rhisophere in Hungary (2019)

The protista Acanthamoeba is a free-living amoeba existing in various environments. A number of species among protista are recognized as human pathogens, potentially causing Acanthamoeba keratitis (AK), granulomatous amoebic encephalitis (GAE), and chronic granulomatous lesions. In this study, 10 rhizosphere samples were collected from maize and alfalfa plants in experimental station at Institute of Genetics, Microbiology and Biotechnology, Szent István University. We detected Acanthamoeba based on the quantitative real-time PCR assay and sequence analysis of the 18S rRNA gene. All studied molecular biological methods are suitable for the detection of Acanthamoeba infection in humans. The quantitative real-time PCR-based methods are more sensitive, simple, and easy to perform; moreover, these are opening avenue to detect the effect of number of parasites on human disease. Acanthamoeba species were detected in five (5/10; 50%) samples. All Acanthamoeba strains belonged to T4 genotype, the main AK-related genotype worldwide. Our result confirmed Acanthamoeba strains in rhizosphere that should be considered as a potential health risk associated with human activities in the environment.
STEM-01. TARGETING BRAIN METASTASIS-INITIATING CELLS: A PREVENTATIVE APPROACH (2020)

Abstract BACKGROUND The incidence of brain metastases (BM) is tenfold higher than primary brain tumors. BM commonly originate from primary lung, breast, and melanoma tumors with a 90% mortality rate within one year of diagnosis. Current standard of care for BM includes surgical resection with concurrent chemoradiation, but does not extend median survival past 16 months, posing a large unmet need to identify novel therapies against BM. METHODS From a large in-house biobank of patient-derived BM cell lines, the Singh Lab has generated murine orthotopic patient-derived xenograft (PDX) models of lung, breast, and melanoma BM that recapitulate the stages of BM progression as seen in humans. Using these three PDX models, we identified a population of “pre-metastatic” brain metastasis-initiating cells (BMICs) that are newly arrived in the brain but have yet to form detectable tumors. Pre-metastatic BMICs are not detectable in human patients but are important therapeutic targets with the potential to prevent BM in at-risk patients. RESULTS RNA sequencing of pre-metastatic BMICs from all three PDX primary tumor models with subsequent Connectivity Map analysis identified novel compounds that have the potential of killing all three types of BMICs. In particular, we identified two compounds that have selective killing of BMICs in vitro from all three primary tumor cohorts while sparing non-cancerous cells. We further characterized their ability to inhibit the self-renewal and proliferative properties of BMICs. Ongoing in vivo work will investigate the compounds’ preclinical utilities in preventing BM. CONCLUSION Identification of novel small molecules that target BMICs could prevent the formation of BM completely and dramatically improve the prognosis of at-risk cancer patients.
In Vivo Suppression of Hormone-Refractory Prostate Cancer Growth by Inositol Hexaphosphate (2004)

IP6 suppresses hormone-refractory PCA growth accompanied by inhibition of tumor cell proliferation and angiogenesis and increased apoptosis. IP6-caused increase in IGFBP-3 and decrease in VEGF might have a role in PCA growth control.
Dual analysis for recommending developers to resolve bugs (2015)

Abstract Bug resolution refers to the activity that developers perform to diagnose, fix, test, and document bugs during software development and maintenance. Given a bug report, we would like to recommend the set of bug resolvers that could potentially contribute their knowledge to fix it. We refer to this problem as developer recommendation for bug resolution . In this paper, we propose a new and accurate method named DevRec for the developer recommendation problem. DevRec is a composite method that performs two kinds of analysis: bug reports based analysis (BR‐Based analysis) and developer based analysis (D‐Based analysis). We evaluate our solution on five large bug report datasets including GNU Compiler Collection, OpenOffice, Mozilla, Netbeans, and Eclipse containing a total of 107,875 bug reports. We show that DevRec could achieve recall@5 and recall@10 scores of 0.4826–0.7989, and 0.6063–0.8924, respectively. The results show that DevRec on average improves recall@5 and recall@10 scores of Bugzie by 57.55% and 39.39%, outperforms DREX by 165.38% and 89.36%, and outperforms NonTraining by 212.39% and 168.01%, respectively. Moreover, we evaluate the stableness of DevRec with different parameters, and the results show that the performance of DevRec is stable for a wide range of parameters. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Successful Microbubble Sonothrombolysis Without Tissue-Type Plasminogen Activator in a Rabbit Model of Acute Ischemic Stroke (2011)

Sonothrombolysis without tPA using these MB is effective in decreasing infarct volumes. Study of human application and further MB technique development are justified.
Association of posterior p-values of S.A.G.E. SIBPAL proportion-IBD and Haseman-Elston statistics for ACTHR112 (1997)

A common practice among researchers performing linkage studies is the use of equal allele frequencies as input when reporting p-values from computer linkage programs such as S.A.G.E. SIBPAL. Our results, using 5,000 sets from a uniform-prior distribution of allele frequencies, showed that such input may be problematic. Further, we found that the S.A.G.E. SIBPAL test for proportion of alleles shared identical by descent among concordantly affected sib pairs showed a greater percentage of significant p-values with decreasing parental genotype information (Table III), while the S.A.G.E. SIBPAL Haseman-Elston test produced significant p-values comparatively less frequently (Table IV).
A cross section of alpha -particle-induced soft-error phenomena in VLSIs (1989)

The alpha -particle-induced soft-error phenomena for VLSIs are investigated using a three-dimensional device simulator and a new experimental method. The scope of the present work includes a description of: the scalability of the funneling length (size effects and proximity effects), the effects of reduced supply voltages, the potential barrier effect of an n/sup +/-p/sup +/-p (substrate) structure, compulsory exposure experiments, and a new effect that causes the soft error ( alpha -particle source-drain penetration effect, or ALPEN). A new funneling length behavior that cannot be explained by Hu's model (1982) is discussed. According to this behavior, it was found that a critical charge for a given soft-error rate, which determines the limitation of planar and trench memory cells, can be scaled down. Furthermore, it is shown that the ALPEN effect, which occurs when an effective channel length of a MOSFET is comparable to the effective funneling length, puts a new constraint on deep submicrometer VLSI design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enhanced recovery of unconventional gas. The methodology--Volume III (of 3 volumes) (1979)

The methodology is described in chapters on the analytic approach, estimated natural gas production, recovery from tight gas sands, recovery from Devonian shales, recovery from coal seams, and recovery from geopressured aquifers. (JRD)
Deriving prognostic continuous time Bayesian networks from D-matrices (2015)

Probabilistic graphical models are widely used in the context of fault diagnostics and prognostics, providing a framework to model the relationships between faults and tests in complex systems. Bayesian networks have sufficient representational power as a model for system-level diagnosis but are inadequate for domains involving prognosis. In order to perform fault prognostics, a model must have the capability to perform probabilistic reasoning over time. One model well suited to this problem is the continuous time Bayesian network (CTBN). In this paper, we propose a method of constructing a continuous time Bayesian network from a D-matrix, a common matrix representation of a diagnostic model. Additionally, we provide procedures for parameterizing the CTBN using reliability information such as the mean time between failures, as well as the false alarm and non-detect probabilities. Through experiments on two different datasets, we demonstrate the correctness of our parameterization process. We also explore the ways in which applying evidence impacts the query results over the network. Finally, we demonstrate the real-world applicability of this approach by performing incremental tests for the purpose of diagnosing and prognosing a fault in the system.
N1-Substituted Quinoxaline-2,3-diones as Kainate Receptor Antagonists: X-ray Crystallography, Structure–Affinity Relationships, and in Vitro Pharmacology (2019)

Among the ionotropic glutamate receptors, the physiological role of kainate receptors is less well understood. Although ligands with selectivity toward the kainate receptor subtype GluK1 are available, tool compounds with selectivity at the remaining kainate receptor subtypes are sparse. Here, we have synthesized a series of quinoxaline-2,3-diones with substitutions in the N1-, 6-, and 7-position to investigate the structure–activity relationship (SAR) at GluK1–3 and GluK5. Pharmacological characterization at native and recombinant kainate and AMPA receptors revealed that compound 37 had a GluK3-binding affinity (Ki) of 0.142 μM and 8-fold preference for GluK3 over GluK1. Despite lower binding affinity of 22 at GluK3 (Ki = 2.91 μM), its preference for GluK3 over GluK1 and GluK2 was >30-fold. Compound 37 was crystallized with the GluK1 ligand-binding domain to understand the SAR. The X-ray structure showed that 37 stabilized the protein in an open conformation, consistent with an antagonist binding mode.
401 Development of New ELID Grinding Technique for Desk-Top Grinding System (2006)

A demand for the mold of micro-lens is on the increase. As a system for the machining of micro-lens mold, a desk-top machine tool is being expected. But, when the grinding wheel with the small diameter is used, the ELID grinding method has a problem about the installation setting place of the negative electrode along the wheel. In this research, we developed a system to electrolyze the small type ELID grinding wheel. This system was realized ELID grinding processing without using the negative electrode along the wheel, for the purpose of machining of micro lens mold. That result succeeded in the development of the SLID grinding system which uses nozzle type electrodes (new electrode less ELID grinding method). Then, the processing using this system could get the mirror surface of Ra 12nm without electric discharge scar. There was a small abrasion of SLID grinding wheel and abundant volume of material removed.
A performance evaluation of lock-free synchronization protocols (1994)

In this paper, we investigate the practicat performance of lock-free techniques that provide synchronization on shared-memory multiprocessors. Our goal is to provide a technique to allow designers of new protocols to quickly determine an algorithm's performance characteristics. We develop a simple analytical performance model based on the architectural observations that memory accesses are expensive, synchronization instructions
Thermo-mechanical simulation of plastic deformation during temperature cycling of bond wires for power electronic modules (2014)

Modelling was undertaken to investigate the role of bond wire size on reliability in power electronic converters. Experiments have shown that thin 125 μm Al wires used in place of 375 μm Al wires alleviate bond wire lift-off and further outlast other sources of failure such as solder degradation in a power module. To investigate the role of bond-wire size on wire lift-off, the effective plastic strain was estimated through thermo-mechanical simulation. Three-dimensional models were constructed for the thin and thick bond wires, respectively. For the critical deformation of the aluminium bond wires during thermal cycling, a temperature-dependent bi-linear plasticity model was used. The effect of a difference in yield strength for the thin wires was also investigated. Maximum as well as volumetrically averaged values of the effective plastic strain showed significant differences between the thick and thin wires and wires with different yield strengths. The modelling results show higher effective plastic strain for the thick wires - supporting the experimental findings.
Video denoising using separable 4D nonlocal spatiotemporal transforms (2011)

We propose a powerful video denoising algorithm that exploits temporal and spatial redundancy characterizing natural video sequences. The algorithm implements the paradigm of nonlocal grouping and collaborative filtering, where a higher-dimensional transform-domain representation is leveraged to enforce sparsity and thus regularize the data. The proposed algorithm exploits the mutual similarity between 3-D spatiotemporal volumes constructed by tracking blocks along trajectories defined by the motion vectors. Mutually similar volumes are grouped together by stacking them along an additional fourth dimension, thus producing a 4-D structure, termed group, where different types of data correlation exist along the different dimensions: local correlation along the two dimensions of the blocks, temporal correlation along the motion trajectories, and nonlocal spatial correlation (i.e. self-similarity) along the fourth dimension. Collaborative filtering is realized by transforming each group through a decorrelating 4-D separable transform and then by shrinkage and inverse transformation. In this way, collaborative filtering provides estimates for each volume stacked in the group, which are then returned and adaptively aggregated to their original position in the video. Experimental results demonstrate the effectiveness of the proposed procedure which outperforms the state of the art.
Optical Fiber Current Sensors for Electric Power Facilities (2005)

This paper describes development of optical fiber current sensors along with some of their applications. Optical fiber current sensors based on the Faraday effect have long been expected to replace conventional current transformers as compact and high performance current sensors. Yet because they require complex means for achieving stable characteristics, this type of sensor has never come into widespread practical use. To solve these problems we developed a special sensor fiber made from flint glass and created sensor systems whose sensing method ideally matches the characteristics of the fiber. These sensors we developed are immune to environmental effects such as vibration and temperature changes. They are also compact and flexible, and attach easily around conductors. This paper also introduces some typical applications of these sensors including cable current measurement using a portable type sensor, a fault section locating system for power transmission lines using these sensors, and sensor applications to protective relay systems as verified in field tests.
Efficient formation of pure helical beams from a Gaussian beam (2003)

Summary from only given. We verified our approach experimentally with spiral phase elements (SPEs) and a cw Nd-YAG laser. The experimental intensity distribution at the far field when passing the incident shifted-Gaussian beam through SPE was detected by a CCD camera.
Differential vasoconstrictor activity of human urotensin‐II in vascular tissue isolated from the rat, mouse, dog, pig, marmoset and cynomolgus monkey (2000)

1. Urotensin-II (U-II) and its G-protein-coupled receptor, GPR14, are expressed within mammalian cardiac and peripheral vascular tissue and, as such, may regulate mammalian cardiovascular function. The present study details the vasoconstrictor profile of this cyclic undecapeptide in different vascular tissues isolated from a diverse range of mammalian species (rats, mice, dogs, pigs, marmosets and cynomolgus monkeys). 2. The vasoconstrictor activity of human U-II was dependent upon the anatomical origin of the vessel studied and the species from which it was isolated. In the rat, constrictor responses were most pronounced in thoracic aortae and carotid arteries: -log[EC(50)]s 9.09+/-0.19 and 8.84+/-0.21, R(max)s 143+/-21 and 67+/-26% 60 mM KCl, respectively (compared, for example, to -log[EC(50)] 7.90+/-0.11 and R(max) 142+/-12% 60 mM KCl for endothelin-1 [ET-1] in thoracic aortae). Responses were, however, absent in mice aortae (-log[EC(50)] <6.50). These findings were further contrasted by the observation that U-II was a 'coronary-selective' spasmogen in the dog (-log[EC(50)] 9.46+/-0.11, R(max) 109+/-23% 60 mM KCl in LCX coronary artery), yet exhibited a broad spectrum of vasoconstrictor activity in arterial tissue from Old World monkeys (-log[EC(50)]s range from 8.96+/-0.15 to 9.92+/-0.13, R(max)s from 43+/-16 to 527+/-135% 60 mM KCl). Interestingly, significant differences in reproducibility and vasoconstrictor efficacy were seen in tissue from pigs and New World primates (vessels which responded to noradrenaline, phenylephrine, KCl or ET-1 consistently). 3. Thus, human U-II is a potent, efficacious vasoconstrictor of a variety of mammalian vascular tissues. Although significant species/anatomical variations exist, the data support the hypothesis that U-II influences the physiological regulation of mammalian cardiovascular function.
Tungsten Hexachloride-catalyzed Decomposition of Diazo Compounds. A Novel Oxazole Synthesis (1977)

Abstract Benzoylphenyldiazomethane and diazoacetophenone react with several nitriles in the presence of WCl6 catalyst to produce 2-substituted 4,5-diphenyloxazoles (1a–d) and 2-methyl-5-phenyloxazole (2) in good yields. The remarkable catalysis is ascribed to the good affinity of tungsten with carbenes. The catalytic decomposition of diphenyldiazomethane yields diphenylcarbenium ion, which is transformed into triarylmethanes in aromatic solvents.
Large‐Area Vapor‐Phase Growth and Characterization of MoS2 Atomic Layers on a SiO2 Substrate (2012)

Atomic-layered MoS(2) is synthesized directly on SiO(2) substrates by a scalable chemical vapor deposition method. The large-scale synthesis of an atomic-layered semiconductor directly on a dielectric layer paves the way for many facile device fabrication possibilities, expanding the important family of useful mono- or few-layer materials that possess exceptional properties, such as graphene and hexagonal boron nitride (h-BN).