gebhart/patrepeval huggingface dataset:
Piezotronic Effect in Solution-Grown p-Type ZnO Nanowires and Films (2013)

Investigating the piezotronic effect in p-type piezoelectric semiconductor is critical for developing a complete piezotronic theory and designing/fabricating novel piezotronic applications with more complex functionality. Using a low temperature solution method, we were able to produce ultralong (up to 60 μm in length) Sb doped p-type ZnO nanowires on both rigid and flexible substrates. For the p-type nanowire field effect transistor, the on/off ratio, threshold voltage, mobility, and carrier concentration of 0.2% Sb-doped sample are found to be 10(5), 2.1 V, 0.82 cm(2)·V(-1)·s(-1), and 2.6 × 10(17) cm(-3), respectively, and the corresponding values for 1% Sb doped samples are 10(4), 2.0 V, 1.24 cm(2)·V(-1)·s(-1), and 3.8 × 10(17) cm(-3). We further investigated the universality of piezotronic effect in the as-synthesized Sb-doped p-type ZnO NWs and reported for the first time strain-gated piezotronic transistors as well as piezopotential-driven mechanical energy harvesting based on solution-grown p-type ZnO NWs. The results presented here broaden the scope of piezotronics and extend the framework for its potential applications in electronics, optoelectronics, smart MEMS/NEMS, and human-machine interfacing.
Transcription Profiling of Signal Transduction-Related Genes in Sugarcane Tissues (2005)

A collection of 237,954 sugarcane ESTs was examined in search of signal transduction genes. Over 3500 components involved in several aspects of signal transduction, transcription, development, cell cycle, stress responses and pathogen interaction were compiled into the Sugarcane Signal Transduction (SUCAST) Catalogue. Sequence comparisons and protein domain analysis revealed 477 receptors, 510 protein kinases, 107 protein phosphatases, 75 small GTPases, 17 G-proteins, 114 calcium and inositol metabolism proteins, and over 600 transcription factors. The elements were distributed into 29 main categories subdivided into 409 sub-categories. Genes with no matches in the public databases and of unknown function were also catalogued. A cDNA microarray was constructed to profile individual variation of plants cultivated in the field and transcript abundance in six plant organs (flowers, roots, leaves, lateral buds, and 1st and 4th internodes). From 1280 distinct elements analyzed, 217 (17%) presented differential expression in two biological samples of at least one of the tissues tested. A total of 153 genes (12%) presented highly similar expression levels in all tissues. A virtual profile matrix was constructed and the expression profiles were validated by real-time PCR. The expression data presented can aid in assigning function for the sugarcane genes and be useful for promoter characterization of this and other economically important grasses.
Proteomic Analysis of Fractionated Toxoplasma Oocysts Reveals Clues to Their Environmental Resistance (2012)

Toxoplasma gondii is an obligate intracellular parasite that is unique in its ability to infect a broad range of birds and mammals, including humans, leading to an extremely high worldwide prevalence and distribution. This work focuses on the environmentally resistant oocyst, which is the product of sexual replication in felids and an important source of human infection. Due to the difficulty in producing and working with oocysts, relatively little is known about how this stage is able to resist extreme environmental stresses and how they initiate a new infection, once ingested. To fill this gap, the proteome of the wall and sporocyst/sporozoite fractions of mature, sporulated oocysts were characterized using one-dimensional gel electrophoresis followed by LC-MS/MS on trypsin-digested peptides. A combined total of 1021 non-redundant T. gondii proteins were identified in the sporocyst/sporozoite fraction and 226 were identified in the oocyst wall fraction. Significantly, 172 of the identified proteins have not previously been identified in Toxoplasma proteomic studies. Among these are several of interest for their likely role in conferring environmental resistance including a family of small, tyrosine-rich proteins present in the oocyst wall fractions and late embryogenesis abundant domain-containing (LEA) proteins in the cytosolic fractions. The latter are known from other systems to be key to enabling survival against desiccation.
Factor XIIIa formation promoted by complexing of alpha-thrombin, fibrin, and plasma factor XIII. (1987)

Fibrin polymers (des A,B fibrinogen) reduced the concentration of alpha-thrombin required for 50% activation of plasma factor XIII (a2b2 tetramer) by approximately 100-fold. In the presence of fibrin, the amount of gamma-thrombin required for activation was not affected. Catalytically inactive i-Pr2P- and D-Phe-Pro-Arg-CH2-alpha-thrombin were found to inhibit over 95% of the activation by alpha-thrombin in the presence of fibrin. Unlike plasma factor XIII, the concentration of alpha-thrombin required for 50% activation of platelet factor XIII (a2 dimer) was lower, and the activation was not enhanced by fibrin. However, when the a2 platelet factor XIII was incubated with purified b-chains, the alpha- and gamma-thrombin concentrations required for activation increased tenfold and reached levels similar to those required for activation of the plasma factor XIII. When fibrin was present, the alpha-thrombin concentrations needed for activation of the a2b2 complexes were reduced, and the presence of fibrin had no effect on gamma-thrombin cleavage of the a2b2 complexes. Therefore, the b-chains must inhibit a-chain cleavage by alpha-thrombin in the absence of fibrin. These results imply that the formation of a cocomplex involving alpha-thrombin, fibrin, and plasma factor XIII causes some conformational change in plasma factor XIII such that the b-chains no longer inhibit cleavage of the a-chains.
Highly Conducting Water-Soluble Polythiophene Derivatives (1997)

Water-soluble sodium poly(2-(3-thienyloxy)ethanesulfonate) and sodium poly(2-(4-methyl-3-thienyloxy)ethanesulfonate) have been synthesized. The sulfonic acid form of these new polymers has revealed a self-acid-doping reaction that leads to stable, highly conducting (0.5−5 S/cm) materials together with low absorption in the visible range. This process is reversible, and upon deprotonation, the insulating and dark polymers are recovered. The high doping and conductivity levels seem to be related to the relatively low oxidation potentials (0.44−0.50 V vs Ag/AgCl) of these polymers, which allows an almost complete (reversible) oxidation reaction in air (oxygen), catalyzed by the presence of the sulfonic acid moiety.
Sensitivity Enhancement of Photothermoelectric Terahertz Detectors with Series Combination between Carbon Nanotubes and Metals (2018)

This paper presents highly flexible terahertz (THz) detectors based on single-walled carbon nanotube (SWNT) films. Based on detection mechanism of the photothermoelectric effect, the effective Seebeck coefficient between the SWNT film and the electrode metal is a key parameter for sensitive THz detection. We proposed and demonstrated that the effective Seebeck coefficient was increased by employing the combination with the electrode in series, and achieved raising the sensitivity of THz detection. Particularly utilizing metals (nickel, bismuth) with negative Seebeck coefficient for the series electrode led to the sensitivity enhancement by a factor of 17 times compared to conventional parallel combination.
Mechanism-Based Covalent Neuraminidase Inhibitors with Broad-Spectrum Influenza Antiviral Activity (2013)

Influenza antiviral agents play important roles in modulating disease severity and in controlling pandemics while vaccines are prepared, but the development of resistance to agents like the commonly used neuraminidase inhibitor oseltamivir may limit their future utility. We report here on a new class of specific, mechanism-based anti-influenza drugs that function through the formation of a stabilized covalent intermediate in the influenza neuraminidase enzyme, and we confirm this mode of action with structural and mechanistic studies. These compounds function in cell-based assays and in animal models, with efficacies comparable to that of the neuraminidase inhibitor zanamivir and with broad-spectrum activity against drug-resistant strains in vitro. The similarity of their structure to that of the natural substrate and their mechanism-based design make these attractive antiviral candidates.
Paramagnetic metalloporphyrins as potential contrast agents in NMR imaging (1984)

Several water-soluble paramagnetic metalloporphyrins were found to increase significantly the relaxation rate (1/T1) of water. Such compounds are known to be selectively retained by tumors in animals, and consequently we identify them as potential contrast agents for tumors in NMR imaging.
Fast 3D-Vision System to Classify Metallic Coins by their Embossed Topography (2006)

This paper presents a security-related machine-vision solution for real-time classification of moving objects with highly reflective metallic surfaces and complex 3D-structures. As an application example of our so called Three-Color Selective Stereo Gradient Method (Three-Color SSGM) a classification system for three main coin denominations of Euro coins is presented. Such coins are quickly moving in a coin validation system. The objective is to decide only from comparison of specially measured and processed 3D-surface information with characteristic topographical data stored in a database whether a coin belongs to one of the reference classes or has to be rejected as a foreign or counterfeit coin. Under illumination from a three-color light emitting diode equipped ring a single image of the moving coin is captured by a digital color camera. Exploiting the spectral properties of the illumination sources, which correspond to the special spectral characteristics of the camera, three independent subimages can be extracted. Comparison between these subimages leads to a discrimination between a coin with real 3D-surface and a counterfeit coin based on a photographic image of a coin of the same type. After the coin has been located and segmented, grey value based rotation and translation invariant features are extracted froma normalized image. In combination with template matching methods, a coin can be classified. Classification results will be reported for the three main coin denominations of Euro coins.
Dynamic Record Blocking: Efficient Linking of Massive Databases in MapReduce (2012)

Record Linkage is the task of identifying which records in a database refer to the same entity. A standard machine learn-ing approach to this problem is to train a model that assigns scores to pairs of records where pairs scoring above a thresh-old are said to represent the same entity. However, it is too expensive to make pairwise comparisons among all records in large databases. \\Blocking &quot; is the process of grouping similar-seeming records into blocks that a machine learning component then explores exhaustively. In many blocking ap-proaches, records are grouped together into blocks by shared properties that are indicators of duplication. However, when dealing with very large data sources, it is nearly impossible to determine any xed set of properties at training time that will be optimal for the Zipan distribution of values for these properties that we will encounter at run time. In this paper, we propose a novel Dynamic Blocking algorithm which au-tomatically chooses the blocking properties in a data-driven way at execution time to eciently determine which pairs of records in a data set should be examined as potential du-plicates without creating the same pair across blocks. We demonstrate the viability of this algorithm for large data sets. We have scaled this system up to work on billions of records on an 80-node Hadoop cluster. 1.
Photospread (2008)

PhotoSpread is a spreadsheet system for organizing and analyzing photo collections. It extends the current spreadsheet paradigm in two ways: (a) PhotoSpread accommodates sets of objects (e.g., photos) annotated with tags (attribute-value pairs). Formulas can manipulate object sets and refer to tags. (b) Photos can be reorganized (tags and location changed) by drag-and-drop operations on the spreadsheet. The PhotoSpread design was driven by the needs of field biologists who have large collections of annotated photos. The paper describes the PhotoSpread functionality and the design choices made.
Newly Synthesized 3-Indolyl Furanoid Inhibits Matrix Metalloproteinase-9 Activity and Prevents Nonsteroidal Anti-inflammatory Drug-Induced Gastric Ulceration (2023)

Indomethacin, a known nonsteroidal anti-inflammatory drug (NSAID) induces gastric inflammation, causing degradation of the extracellular matrix by specific matrix metalloproteinases (MMPs). We investigated the antiulcer efficacy of 3-indolyl furanoids (<b>3g</b> and <b>3c</b>, i.e., methoxy substitution at 4- and 5-positions of the indole ring, respectively), derived from indomethacin. Interestingly, <b>3g</b> protected against indomethacin-induced gastropathy in vivo by inhibiting MMP-9. Our work established a chemical modification strategy for the development of safer NSAIDs. Moreover, in vitro and in silico studies confirmed that <b>3g</b> inhibited MMP-9 activity with an IC<sub>50</sub> value of 50 μM by binding to the catalytic cleft of MMP-9, leading to ulcer prevention. Pharmacokinetics was presented as the mean concentration-time profile in the rat plasma, and the extraction efficiency was greater than 70%, showing a <i>C</i><sub>max</sub> of 104.48 μg/mL after 6.0 h (<i>t</i><sub>max</sub>) treatment with half-life and area under the curve being 7.0 h and 1273.8 h μg/mL, respectively, indicating the higher antiulcer potency of <b>3g</b>.
Early non-invasive diagnosis of cervical cancer: Beyond Pap smears and human papilloma virus (HPV) testing (2005)

Cervical cancer is a major gynecologic malignancy around the world. However, current diagnostic methods such as Pap smear and human papilloma virus (HPV) testing are insufficient for an early diagnosis of cervical cancer, follow-up on therapy efficacy or to identify the women who might progress to cervical cancer (only about 1-5% of the HPV-positive women will develop cervical cancer). Patients with atypical squamous cells of undetermined significance (ASC-US) clearly need a better screening test. Developing a non-invasive method for early diagnosis of cervical cancer is essential. Our in vitro and translational research data support the hypothesis that: 1. Squamous cell cervical cancer is related to specific upregulation of tissue and serum Insulin-like Growth Factor-II levels (IGF-II; 100% sensitivity and 100% specificity). Serum IGF-I, but not IGF-II levels are elevated in other gynecological, breast, lung and prostate cancers. Serum IGF-II test helps in diagnosing cervical cancer as early as ASC-US or cervical intraepithelial neoplasia (CIN)-I and in monitoring therapy efficacy (p < 0.001 by Student's 't' test and Chi-square analysis). 2. Concomittant to increased serum IGF-II levels, IGF-Binding Protein 3 (IGF-BP3) levels are significantly decreased in persistent CIN and cervical cancer (p < 0.0001). As IGF-BP3 modulates IGF-II biological activity, significantly decreased serum IGF-BP3 levels (levels normalize after therapy; p < 0.001) may indicate a poor prognosis. Similar to serum IGF-II, serum IGF-BP3 levels help monitoring therapy efficacy in cervical cancer and advanced CIN. Measurement of serum IGF-II levels will help in early diagnosis of cervical cancer and monitoring of therapy outcome. Serum IGF-BP3 in conjunction with IGF-II levels may help in predicting prognosis as well as monitoring therapy efficacy.
Image-based photo hulls (2003)

We present an efficient image-based rendering algorithm that computes photo hulls of a scene photographed from multiple viewpoints. Our algorithm, called image-based photo hulls (IBPH), like the image-based visual hulls (IBVH) algorithm from Matusik et. al. (2000) on which it is based, takes advantage of epipolar geometry to efficiently reconstruct the geometry and visibility of a scene. Our IBPH algorithm differs from IBVH in that it utilizes the color information of the images to identify the scene geometry. These additional color constraints often result in a more accurately reconstructed geometry, which projects to better synthesized virtual views of the scene. We demonstrate our algorithm running in a real-time 3D telepresence application using video data acquired from four viewpoints.
Robust and low-cost BIST architectures for sequential fault testing in datapath multipliers (2002)

The modified Booth array multiplier is the most ubiquitous multiplier architecture in the datapaths of either general purpose microprocessors or specialized Digital Signal Processors. Sequential fault testing for Booth array multipliers has never been proposed in the past. In this paper, we present two BIST architectures for modified Booth array multipliers with respect to the Realistic Sequential Cell Fault model (RS-CFM). The first BIST architecture aims to resolve the test invalidation problem to the largest possible extent, while the second one aims to test cost reduction. Both BIST architectures achieve very high sequential fault coverage and impose moderate hardware and delay overhead. Simplified variations of the two BIST architectures are also presented for the non-recoded signed array multipliers. Thus, the proposed BIST architectures offer a universal BIST solution that covers the totality of signed array multipliers: non-recoded and recoded.
Facilitating Remote Laboratory Deployments Using a Relay Gateway Server Architecture (2013)

Hands-on experiments prepare students to deal with real-world problems and help to efficiently digest theoretical concepts and relate those to practical tasks. However, shortage of equipment, high costs, and the lack of human resources for laboratory maintenance and assistance decrease the implementation capacity of the hands-on training laboratories. At the same time, the Internet has become a common networking medium and is increasingly used to enhance education and training. In addition, experimental equipment at many sites is typically underutilized. Thus, remote laboratories accessible through the Internet can resolve cost and access constraints as they can be used at flexible times and from various locations. While many solutions have been proposed so far, this paper addresses an important issue of facilitating remote lab deployments by providing remote connectivity services to lab providers using a Relay Gateway Server architecture. A proof-of-concept solution is described which also includes other previously reported useful features. The system has been tested in engineering labs and student assessment is provided.
<i>In vitro</i> anti-acne activity of phytoactives from the stem bark of <i>Artocarpus hirsutus</i> Lam<i>.</i> and characterisation of pyranocycloartobiloxanthone A as a mixture of two anomers (2017)

This study is aimed to isolate the phytoactives from the stem bark of Artocarpus hirsutus and evaluate their in vitro anti-acne activity. The ethanolic stem bark extract of A. hirsutus provided two major phytoactive constituents: (i) pyranocycloartobiloxanthone A, (1) and (ii) Artonine E, (2) whose structures were determined by NMR and MS spectroscopic analysis. The present study is the first to report compound 1 as a mixture of two anomers (α and β), approximately 70:30 ratio. Both compounds 1 and 2 were isolated for the first time from this plant. In vitro anti-acne activity of compounds 1 and 2 were evaluated by agar well diffusion method and the minimum inhibition was determined by broth micro dilution method. The result of anti-microbial activity (MIC = 2.0 μg/mL each) is comparable to antibiotic, Clindamycin (MIC = 0.03 μg/mL) and clearly demonstrate their potential as anti-acne agents.
P38α Regulates Expression of DUX4 in Facioscapulohumeral Muscular Dystrophy (2019)

ABSTRACT FSHD is caused by the loss of repression at the D4Z4 locus leading to DUX4 expression in skeletal muscle, activation of its early embryonic transcriptional program and muscle fiber death. While progress toward understanding the signals driving DUX4 expression has been made, the factors and pathways involved in the transcriptional activation of this gene remain largely unknown. Here, we describe the identification and characterization of p38α as a novel regulator of DUX4 expression in FSHD myotubes. By using multiple highly characterized, potent and specific inhibitors of p38α/β, we show a robust reduction of DUX4 expression, activity and cell death across FSHD1 and FSHD2 patient-derived lines. RNA-seq profiling reveals that a small number of genes are differentially expressed upon p38α/β inhibition, the vast majority of which are DUX4 target genes. Our results reveal a novel and apparently critical role for p38α in the aberrant activation of DUX4 in FSHD and support the potential of p38α/β inhibitors as effective therapeutics to treat FSHD at its root cause. VISUAL ABSTRACT
A synthetic, three-dimensional bone marrow hydrogel (2018)

Three-dimensional (3D) synthetic hydrogels have recently emerged as desirable in vitro cell culture platforms capable of representing the extracellular geometry, elasticity, and water content of tissue in a tunable fashion. However, they are critically limited in their biological functionality. Hydrogels are typically decorated with a scant 1-3 peptide moieties to direct cell behavior, which vastly underrepresents the proteins found in the extracellular matrix (ECM) of real tissues. Further, peptides chosen are ubiquitous in ECM, and are not derived from specific proteins. We developed an approach to incorporate the protein complexity of specific tissues into the design of biomaterials, and created a hydrogel with the elasticity of marrow, and 20 marrow-specific cell-instructive peptides. Compared to generic PEG hydrogels, our marrow-inspired hydrogel improves stem cell differentiation and proliferation. We propose this tissue-centric approach as the next generation of 3D hydrogel design for applications in tissue engineering.
Thoracic impedance measures tissue characteristics in the vicinity of the electrodes, not intervening lung water: implications for heart failure monitoring (2014)

The rationale for intrathoracic impedance (Z) detection of worsening heart failure (HF) presupposes that changes in Z reflect changes in pulmonary congestion, but is confounded by poor specificity in clinical trials. We therefore tested the hypothesis that Z is primarily affected by tissue/water content in proximity to electrodes rather than by lung water distribution between electrodes through the use of a new computational model for deriving the near-field impedance contributions from the various electrodes. Six sheep were implanted with a left atrial pressure (LAP) monitor and a cardiac resynchronization therapy device which measured Z from six vectors comprising of five electrodes. The vector-based Z was modelled as the summation of the near-field impedances of the two electrodes forming the vector. During volume expansion an acute increase in LAP resulted in simultaneous reductions in the near-field impedances of the intra-cardiac electrodes, while the subcutaneous electrode showed several hours of lag (all p<0.001). In contrast, during the simulated formation of device-pocket edema (induced by fluid injection) the near-field impedance of the subcutaneous electrode had an instantaneous response, while the intra-cardiac electrodes had a minimal inconsistent response. This study suggests that the primary contribution to the vector based Z is from the tissue/water in proximity to the individual electrodes. This novel finding may help explain the limited utility of Z for detecting worsening HF.