gebhart/patrepeval huggingface dataset:
IN-SITU SYNTHESIZED AND PATTERNED NANOWIRE ARRAYS IN MICROFLUIDIC CHANNEL FOR PARTICLE TRAPPING AND CELL LYSIS APPLICATIONS (2011)

Cell trapping and preparation (ex. lysis, separation, filtering etc.) becomes important tasks for bioassays as the needs of single cell study are increased. We introduce a novel and simple nanowire-integrated microfluidic device that can be applied to the biological cell assay. Nanowires were grown in the microchannel by in-situ nanowire synthesis method or conventional hydrothermal method on microscale post arrays. We demonstrated preliminary results of particle trapping and cell lysis with nanowireintegrated microfluidic devices. Nanowire bundle-based particle trapping shows good trapping performance. Also, cell lysis by using nanowire-integrated microfluidics shows good mechanical lysis performance.
A Public Dataset for YouTube's Mobile Streaming Client (2018)

Datasets are a valuable resource to analyze, model and optimize network traffic. This paper describes a new public dataset for YouTube's popular video streaming client on mobile devices. At the moment, we are providing 374 hours of time-synchronous measurements at the network, transport and application layer from two controlled environments in Europe. After describing our experimental design in detail, we discuss how to use our dataset for the analysis and optimization of HTTP Adaptive Streaming (HAS) traffic and point to specific use cases. To assure reproducibility and for community benefit, we publish the dataset at [1].
Differential Contributions of<i>Caenorhabditis elegans</i>Histone Deacetylases to Huntingtin Polyglutamine Toxicity (2006)

Expansion of a polyglutamine tract in the huntingtin protein causes neuronal degeneration and death in Huntington's disease patients, but the molecular mechanisms underlying polyglutamine-mediated cell death remain unclear. Previous studies suggest that expanded polyglutamine tracts alter transcription by sequestering glutamine rich transcriptional regulatory proteins, thereby perturbing their function. We tested this hypothesis in Caenorhabditis elegans neurons expressing a human huntingtin fragment with an expanded polyglutamine tract (Htn-Q150). Loss of function alleles and RNA interference (RNAi) were used to examine contributions of C. elegans cAMP response element-binding protein (CREB), CREB binding protein (CBP), and histone deacetylases (HDACs) to polyglutamine-induced neurodegeneration. Deletion of CREB (crh-1) or loss of one copy of CBP (cbp-1) enhanced polyglutamine toxicity in C. elegans neurons. Loss of function alleles and RNAi were then used to systematically reduce function of each C. elegans HDAC. Generally, knockdown of individual C. elegans HDACs enhanced Htn-Q150 toxicity, but knockdown of C. elegans hda-3 suppressed toxicity. Neuronal expression of hda-3 restored Htn-Q150 toxicity and suggested that C. elegans HDAC3 (HDA-3) acts within neurons to promote degeneration in response to Htn-Q150. Genetic epistasis experiments suggested that HDA-3 and CRH-1 (C. elegans CREB homolog) directly oppose each other in regulating transcription of genes involved in polyglutamine toxicity. hda-3 loss of function failed to suppress increased neurodegeneration in hda-1/+;Htn-Q150 animals, indicating that HDA-1 and HDA-3 have different targets with opposing effects on polyglutamine toxicity. Our results suggest that polyglutamine expansions perturb transcription of CREB/CBP targets and that specific targeting of HDACs will be useful in reducing associated neurodegeneration.
An Enantioselective Synthesis of (<i>S</i>)-(+)-3-Aminomethyl-5-methylhexanoic Acid via Asymmetric Hydrogenation (2003)

A concise enantioselective synthesis of (S)-(+)-3-aminomethyl-5-methylhexanoic acid (1, Pregabalin) has been developed. The key step is the asymmetric hydrogenation of a 3-cyano-5-methylhex-3-enoic acid salt 2 with a rhodium Me-DuPHOS catalyst, providing the desired (S)-3-cyano-5-methylhexanoate 3 in very high ee. Subsequent hydrogenation of the nitrile 3 with a heterogeneous nickel catalyst provides Pregabalin 1 in excellent overall yield and purity.
Textual analysis for code smell detection (2015)

The negative impact of smells on the quality of a software systems has been empirical investigated in several studies. This has recalled the need to have approaches for the identification and the removal of smells. While approaches to remove smells have investigated the use of both structural and conceptual information extracted from source code, approaches to identify smells are based on structural information only. In this paper, we bridge the gap analyzing to what extent conceptual information, extracted using textual analysis techniques, can be used to identify smells in source code. The proposed textual-based approach for detecting smells in source code, coined as TACO (Textual Analysis for Code smell detectiOn), has been instantiated for detecting the Long Method smell and has been evaluated on three Java open source projects. The results indicate that TACO is able to detect between 50% and 77% of the smell instances with a precision ranging between 63% and 67%. In addition, the results show that TACO identifies smells that are not identified by approaches based on solely structural information.
Synthesis of Single-Crystal Gold Nanosheets of Large Size in Ionic Liquids (2005)

Large-size single-crystal gold nanosheets have been successfully prepared by microwave heating of HAuCl(4) in ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate, without any additional template agent. Transmission electron microscopy (TEM), electron diffraction (ED), scanning electron microscopy (SEM), and X-ray powder diffraction (XRD) were used to characterize the resultant gold nanosheets. It was demonstrated that the ionic liquid could act as template agent for the formation of gold nanosheets. The present synthesis route is very simple and fast. It can be expected that the method can be extended to the fabrication of other metal nanosheets in ionic liquids.
Redox‐ and pH‐Controlled Mechanized Nanoparticles (2009)

Abstract A new class of mechanized silica nanoparticles, which exploits the stability of the inclusion complexes formed between ferrocenedicarboxylic acid and both cucurbit[7]uril (CB7) and β‐cyclodextrin (β‐CD), are described. Mesoporous silica nanoparticles, capable of storing a payload of small molecules and releasing it following particular activation processes, have been designed and decorated with ferrocenecarboxylic acid stalks. The storage and release of the payload is controlled by the host–guest interaction between the ferrocene moiety (guest) and the ring moiety (CB7 or β‐CD). Ferrocene‐based Mechanized NanoParticles (FMNPs) were efficiently prepared, loaded with Rhodamine dye, and then tested under different activation procedures. The systems operated successfully under redox control (oxidation of ferrocenedicarboxylic acid) in the presence of β‐CD and under pH control (deprotonation of ferrocenedicarboxylic acid pH > 4) in the presence of CB7.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
The endotoxin of Helicobacter pylori is a modulator of host-dependent gastritis (1997)

Atrophic gastritis caused by Helicobacter pylori is the precursor lesion in the development of intestinal-type gastric adenocarcinoma. In animal models, atrophic gastritis induced by Helicobacter felis has been shown to be host dependent, developing in some mouse strains and not in others. The lipopolysaccharide (LPS) of H. pylori has been suggested to play a role in the induction of gastritis. The goal of this study was to compare the inflammation induced by long-term infection of the C3H/He and the C3H/HeJ strains of mice with H. felis. C3H/HeJ mice are unresponsive to LPS. Six months after infection, severe atrophic gastritis had developed in the body mucosae of all infected C3H/He mice, with replacement of parietal and chief cells. Atrophy was associated with a loss of the H. felis from the antral mucosa. In contrast, no atrophy was seen in the infected C3H/HeJ non-LPS responder animals, and heavy colonization of the antrum remained. There were no significant differences between both the quantitative and qualitative serum immunoglobulin G (IgG) and salivary IgA levels in both strains of mice. The main difference between the two strains of long-term-infected mice was a lack of macrophage infiltration in the lamina propria. Immunization induced good protective immunity to challenge with viable H. felis. Helicobacter-induced, host-dependent gastritis is likely to be cell mediated. The C3H/He and C3H/HeJ mouse model provides an excellent opportunity to investigate the cellular basis of atrophic gastritis.
A crucial role of caspase-3 in osteogenic differentiation of bone marrow stromal stem cells (2004)

Caspase-3 is a critical enzyme for apoptosis and cell survival. Here we report delayed ossification and decreased bone mineral density in caspase-3-deficient (Casp3 -/-and Casp3 +/-) mice due to an attenuated osteogenic differentiation of bone marrow stromal stem cells (BMSSCs). The mechanism involved in the impaired differentiation of BMSSCs is due, at least partially, to the overactivated TGF-/Smad2 signaling pathway and the upregulated expressions of p53 and p21 along with the downregulated expressions of Cdk2 and Cdc2, and ultimately increased replicative senescence. In addition, the overactivated TGF-/Smad2 signaling may result in the compromised Runx2/Cbfa1 expression in preosteoblasts. Furthermore, we demonstrate that caspase-3 inhibitor, a potential agent for clinical treatment of human diseases, caused accelerated bone loss in ovariectomized mice, which is also associated with the overactivated TGF-/Smad2 signaling in BMSSCs. This study demonstrates that caspase-3 is crucial for the differentiation of BMSSCs by influencing TGF-/Smad2 pathway and cell cycle progression.
A Novel Biochemical Route for Fuels and Chemicals Production from Cellulosic Biomass (2012)

The conventional biochemical platform featuring enzymatic hydrolysis involves five key steps: pretreatment, cellulase production, enzymatic hydrolysis, fermentation, and product recovery. Sugars are produced as reactive intermediates for subsequent fermentation to fuels and chemicals. Herein, an alternative biochemical route is proposed. Pretreatment, enzymatic hydrolysis and cellulase production is consolidated into one single step, referred to as consolidated aerobic processing, and sugar aldonates are produced as the reactive intermediates for biofuels production by fermentation. In this study, we demonstrate the viability of consolidation of the enzymatic hydrolysis and cellulase production steps in the new route using Neurospora crassa as the model microorganism and the conversion of cellulose to ethanol as the model system. We intended to prove the two hypotheses: 1) cellulose can be directed to produce cellobionate by reducing β-glucosidase production and by enhancing cellobiose dehydrogenase production; and 2) both of the two hydrolysis products of cellobionate--glucose and gluconate--can be used as carbon sources for ethanol and other chemical production. Our results showed that knocking out multiple copies of β-glucosidase genes led to cellobionate production from cellulose, without jeopardizing the cellulose hydrolysis rate. Simulating cellobiose dehydrogenase over-expression by addition of exogenous cellobiose dehydrogenase led to more cellobionate production. Both of the two hydrolysis products of cellobionate: glucose and gluconate can be used by Escherichia coli KO 11 for efficient ethanol production. They were utilized simultaneously in glucose and gluconate co-fermentation. Gluconate was used even faster than glucose. The results support the viability of the two hypotheses that lay the foundation for the proposed new route.
The design for a high-T<sub>c</sub>superconducting magnetic separator (1992)

A number of options for the design of a superconducting high-Tc magnetic separator have been considered and it is suggested that, when material properties have improved sufficiently, a separator based on a flux tube with a flux pump will offer significant advantages. Another design for a more detailed evaluation was chosen based on an iron magnetic circuit in which amper-turns were supplied by a superconducting BSCCO-Ag tape wound coil operating at 77 K. Two configurations for the separator were considered, a ball matrix separator and a wire matrix high-gradient separator. Practical separations will be possible with such a system.
Indexing of multidimensional discrete data spaces and hybrid extensions (2009)

In this thesis various indexing techniques are developed and evaluated to support efficient queries in different vector data spaces. Various indexing techniques have been introduced for the (ordered) Continuous Data Space (CDS) and the Non-ordered Discrete Data Space (NDDS). All these techniques rely on special properties of the CDS or the NDDS to optimize data accesses and storage in their corresponding structures. Besides conventional exact match queries, the similarity queries and the box queries are two types of fundamental operations widely supported by modern indexing techniques. A box query is different from a similarity query in that the box query in multidimensional spaces tries to look up indexed data which meet query conditions on each and every dimension. The difference between similarity queries and box queriessuggests that indexing techniques which work well for similarity queries may not necessarily support efficient box queries. In this thesis, we propose the BoND-tree, a new indexing technique designed for supporting box queries in an NDDS. Both our theoretical analysis and experimental results demonstrate that the new heuristics proposed for the BoND-tree improve the performance of box queries in an NDDS significantly. The Hybrid
Probabilistic region-based localization for wireless networks (2007)

Determining the physical location of wireless nodes is important to a wide variety of applications. In this paper, we propose a series of probabilistic region-based localization algorithms, including using static grids, segments of grids, and dynamic meshes. These algorithms provide a wide range of trade-off between accuracy and cost, making them suitable for different types of networks, such as sensor networks and mesh networks. Furthermore, we propose several techniques to extract and leverage additional information on location constraints, which is shown to significantly improve the localization accuracy and can be applied to other localization schemes. Finally we develop techniques to enhance robustness of localization, and show that the enhanced scheme can achieve high accuracy even in the presence of significant measurement errors.
High performance solid polymer electrolyte with graphene oxide nanosheets (2014)

Two dimensional graphene oxide (GO) sheets with high surface area and excellent mechanical properties are introduced into a solid polyethylene oxide/lithium salt electrolyte.
Tribological Behaviors of Graphene and Graphene Oxide as Water-Based Lubricant Additives for Magnesium Alloy/Steel Contacts (2018)

The tribological behaviors of graphene and graphene oxide (GO) as water-based lubricant additives were evaluated by use of a reciprocating ball-on-plate tribometer for magnesium alloy-steel contacts. Three sets of test conditions were examined to investigate the effect of concentration, the capacity of carrying load and the endurance of the lubrication film, respectively. The results showed that the tribological behaviors of water can be improved by adding the appropriate graphene or GO. Compared with pure deionized water, 0.5 wt.% graphene nanofluids can offer reduction of friction coefficient by 21.9% and reduction of wear rate by 13.5%. Meanwhile, 0.5 wt.% GO nanofluids were found to reduce the friction coefficient and wear rate up to 77.5% and 90%, respectively. Besides this, the positive effect of the GO nanofluids was also more pronounced in terms of the load-carrying capacity and the lubrication film endurance. The wear mechanisms have been tentatively proposed according to the observation of the worn surfaces by field emission scanning electron microscope-energy dispersive spectrometer (FESEM-EDS) and Raman spectrum as well as the wettability of the nanofluids on the magnesium alloy surface by goniometer.
Single-pass online learning (2006)

To learn concepts over massive data streams, it is essential to design inference and learning methods that operate in real time with limited memory. Online learning methods such as perceptron or Winnow are naturally suited to stream processing; however, in practice multiple passes over the same training data are required to achieve accuracy comparable to state-of-the-art batch learners. In the current work we address the problem of training an on-line learner with a single passover the data. We evaluate several existing methods, and also propose a new modification of Margin Balanced Winnow, which has performance comparable to linear SVM. We also explore the effect of averaging, a.k.a. voting, on online learning. Finally, we describe how the new Modified Margin Balanced Winnow algorithm can be naturally adapted to perform feature selection. This scheme performs comparably to widely-used batch feature selection methods like information gain or Chi-square, with the advantage of being able to select features on-the-fly. Taken together, these techniques allow single-pass online learning to be competitive with batch techniques, and still maintain the advantages of on-line learning.
Cyclic GMP-specific, high affinity, noncatalytic binding sites on light-activated phosphodiesterase. (1980)

ROS, rod outer segment; cGMP, guanosine 3',5"monophosphoric acid; CAMP, adenosine 3',5'-monophosphoric acid; 8-N3-["P]cIMP, 8-a~ido-[~~P]inosine 3',5"monophosphoric acid EDTA, ethylenediaminetetraacetic acid; EGTA, eth-.ylene glycol bis(P
Stereo matching by compact windows via minimum ratio cycle (2002)

Window size and shape selection is a difficult problem in area based stereo. We propose an algorithm which chooses an appropriate window shape by optimizing over a large class of "compact" windows. We call them compact because their ratio of perimeter to area tends to be small. We believe that this is the first window matching algorithm which can explicitly construct non-rectangular windows. Efficient optimization over the compact window class is achieved via the minimum ratio cycle algorithm. In practice it takes time linear in the size of the largest window in our class. Still the straightforward approach to find the optimal window for each pixel-disparity pair is too slow. We develop pruning heuristics which gave practically the same results while reducing running time from minutes to seconds. Our experiments show that unlike fixed window algorithms, our method avoids blurring disparity boundaries as well as constructs large windows in low textured areas. The algorithm has few parameters which are easy to choose, and the same parameters work well for different image pairs.
Identification of Dermatophyte Species by 28S Ribosomal DNA Sequencing with a Commercial Kit (2003)

We have shown that dermatophyte species can be easily identified on the basis of a DNA sequence encoding a part of the large-subunit (LSU) rRNA (28S rRNA) by using the MicroSeq D2 LSU rRNA Fungal Sequencing Kit. Two taxa causing distinct dermatophytoses were clearly distinguished among isolates of the Trichophyton mentagrophytes species complex.
Viral control of the SUMO pathway: Gam1, a model system (2007)

SUMO (small ubiquitin-related modifier) is a ubiquitin-like family member that is conjugated to its substrates through discrete enzymatic steps: activation, involving the E1 enzyme [SAE (SUMO-activating enzyme) 1-SAE2], conjugation, involving the E2 enzyme [Ubc9 (ubiquitin-conjugating enzyme 9)], and substrate modification, through the co-operation of Ubc9 and E3 protein ligases. Work from our laboratory has shown the first example of a viral protein, Gam1, that binds to the E1 heterodimer, inhibiting its function and causing a complete block of the SUMOylation pathway both in vivo and in vitro, followed by SAE1-SAE2 degradation. The mechanism by which a viral protein inactivates and subsequently degrades an essential cellular enzyme, arresting a key regulatory pathway, will be discussed. Although four distinct SUMO isoforms have been described, I will use SUMO to describe the entire system.
Liquid Imbibition in Ceramic-Coated Carbon Nanotube Films (2016)

Understanding of the liquid imbibition dynamics in nanoporous materials is important to advances in chemical separations, phase change heat transfer, electrochemical energy storage, and diagnostic assays. We study the liquid imbibition behavior in films of ceramic-coated vertically aligned carbon nanotubes (CNTs). The nanoscale porosity of the films is tuned by conformal ceramic coating via atomic layer deposition (ALD), enabling stable liquid imbibition and precise measurement of the imbibition dynamics without capillary densification of the CNTs. We show that the imbibition rate decreases as the ceramic coating thickness increases, which effectively changes the CNT-CNT spacing and therefore decreases the permeability. We derive a model, based on Darcy's law, that incorporates an expression for the permeability of nanoscale post arrays, and we show that the model fits the experimental results with high accuracy. The tailorable porosity, along with controllable surface wettability and mechanical stability of coated CNTs, suggest their suitability for application-guided engineering, and for further investigation of imbibition behavior at finer length scales.
The Soluble Guanylate Cyclase Stimulator Riociguat Ameliorates Pulmonary Hypertension Induced by Hypoxia and SU5416 in Rats (2012)

Riociguat and sildenafil significantly reduced RVSP and RVH, and improved RV function compared with vehicle. Riociguat had a greater effect on hemodynamics and RVH than sildenafil.
Analysing Survival Data From Clinical Trials and Observational Studies (1996)

"Analysing Survival Data From Clinical Trials and Observational Studies." Technometrics, 38(3), p. 299
Role of mTOR in the degradation of IRS‐1: Regulation of PP2A activity (2002)

We have investigated the role of PI 3-kinase and mTOR in the degradation of IRS-1 induced by insulin. Inhibition of mTOR with rapamycin resulted in approximately 50% inhibition of the insulin-induced degradation of IRS-1. In contrast, inhibition of PI-3 kinase, an upstream activator of mTOR, leads to a complete block of the insulin-induced degradation. Inhibition of either PI-3 kinase or mTOR prevented the mobility shift in IRS-1 in response to insulin, a shift that is caused by Ser/Thr phosphorylation. These results indicate that insulin stimulates PI 3-kinase-mediated degradation of IRS-1 via both mTOR-dependent and -independent pathways. Platelet-derived growth factor (PDGF) stimulation leads to a lower level of degradation, but significant phosphorylation of IRS-1. Both the degradation and phosphorylation of IRS-1 in response to PDGF are completely inhibited by rapamycin, suggesting that PDGF stimulates IRS-1 degradation principally via the mTOR-dependent pathway. Inhibition of the serine/threonine phosphatase PP2A with okadaic acid also induced the phosphorylation and degradation of IRS-1. IRS-1 phosphorylation and degradation in response to okadaic acid were not inhibited by rapamycin, suggesting that the action of mTOR in the degradation of IRS-1 results from inhibition of PP2A. Consistent with this, treatment of cells with rapamycin stimulated PP2A activity. While the role of mTOR in the phosphorylation of IRS-1 appears to proceed primarily through the regulation of PP2A, we also provide evidence that the regulation of p70S6 kinase phosphorylation requires the direct activity of mTOR.