gebhart/patrepeval huggingface dataset:
Colletotrichum graminicola as a system for studying the molecular genetics of conidial development in phytopathogenic fungi (1989)

Like many fungal pathogens of plants, Colletotrichum graminicola is dispersed and infects through asexually derived spores called conidia. The objectives of my thesis research were to: (1) characterize conidial development in C. graminicola; (2) develop techniques for studying the molecular genetics of conidial development; and (3) use these techniques to study genes that may be involved in conidiation. My results demonstrate the C. graminicola produces two different types of conidia. The two types have distinct ontogenies and are induced by different environmental cues. Techniques were developed for recovery of nonconidiating cultures, cultures producing exclusively one or the other type of conidium, or cultures producing both types of conidia. The cultures were suitable for the isolation of state-specific RNA. To manipulate the fungus genetically, I developed a DNA-demiated transformation system. A $\beta$-tubulin gene cloned from a benomyl-resistant mutant of the fungus conferred benomyl resistance in wild-type strains. Integration of circular plasmids carrying this gene was random. However, linearized and circular plasmids carrying other C. graminicola sequences were targeted to their respective homologous regions. During the cloning of the $\beta$-tubulin gene, and studies on its integration, it became apparent that C. graminicola contains a second $\beta$-tubulin gene. Because of the role of different $\beta$-tubulin isotypes in conidial development in other fungi, I studied the two C. graminicola $\beta$-tubulin genes. I cloned and sequenced both genes (TUB1 and TUB2). The deduced amino acid sequence of TUB2 is very similar to those of other fungal $\beta$-tubulins; the TUB1 sequence is much less conserved. Hybridization of TUB1 and TUB2 to poly (A) $\sp+$RNA indicated that TUB2 mRNA was more abundant than TUB1 mRNA in conidiating and nonconidiating cultures. There appeared to be a two- to three-fold increase in the level of TUB2 transcript relative to that of TUB1 in cultures producing one type of conidium. Disruption of TUB2 by site-specific integration did not result in any obvious changes in the fungus, including the development and germination of conidia. The data suggest that the divergent TUB1 product can function in place of the conserved TUB2 product.
Transformation by Cloned Harvey Murine Sarcoma Virus DNA: Efficiency Increased by Long Terminal Repeat DNA (1980)

The coding sequences for the transforming (src) protein (p21) of Harvey murine sarcoma virus have been localized to a 1.3 kilobase pair segment near the 5' end of the viral genome. Ligation of the viral terminal repeat DNA to the left end of the src region DNA markedly enhanced the low transforming efficiency of the src region DNA.
Use of epitaxial ZnSe films, grown from organoelemental compounds, in electron-beam-pumped lasers (1982)

An analysis is made of the feasibility of using epitaxial ZnSe films grown from organoelemental compounds in semiconductor lasers excited by electron beams. The first report is given of lasing as a result of longitudinal electron-beam excitation of such target films.
Chapter 9: Analyses Using Disease Ontologies (2012)

Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of "significant genes." One way to gain insight into the significance of altered expression levels is to determine whether Gene Ontology (GO) terms associated with a particular biological process, molecular function, or cellular component are over- or under-represented in the set of genes deemed significant. This process, referred to as enrichment analysis, profiles a gene-set, and is widely used to makes sense of the results of high-throughput experiments. The canonical example of enrichment analysis is when the output dataset is a list of genes differentially expressed in some condition. To determine the biological relevance of a lengthy gene list, the usual solution is to perform enrichment analysis with the GO. We can aggregate the annotating GO concepts for each gene in this list, and arrive at a profile of the biological processes or mechanisms affected by the condition under study. While GO has been the principal target for enrichment analysis, the methods of enrichment analysis are generalizable. We can conduct the same sort of profiling along other ontologies of interest. Just as scientists can ask "Which biological process is over-represented in my set of interesting genes or proteins?" we can also ask "Which disease (or class of diseases) is over-represented in my set of interesting genes or proteins?". For example, by annotating known protein mutations with disease terms from the ontologies in BioPortal, Mort et al. recently identified a class of diseases--blood coagulation disorders--that were associated with a 14-fold depletion in substitutions at O-linked glycosylation sites. With the availability of tools for automatic annotation of datasets with terms from disease ontologies, there is no reason to restrict enrichment analyses to the GO. In this chapter, we will discuss methods to perform enrichment analysis using any ontology available in the biomedical domain. We will review the general methodology of enrichment analysis, the associated challenges, and discuss the novel translational analyses enabled by the existence of public, national computational infrastructure and by the use of disease ontologies in such analyses.
Coadministration of Endothelial and Smooth Muscle Progenitor Cells Enhances the Efficiency of Proangiogenic Cell-Based Therapy (2008)

Cell-based therapy is a promising approach designed to enhance neovascularization and function of ischemic tissues. Interaction between endothelial and smooth muscle cells regulates vessels development and remodeling and is required for the formation of a mature and functional vascular network. Therefore, we assessed whether coadministration of endothelial progenitor cells (EPCs) and smooth muscle progenitor cells (SMPCs) can increase the efficiency of cell therapy. Unilateral hindlimb ischemia was surgically induced in athymic nude mice treated with or without intravenous injection of EPCs (0.5 x 10(6)), SMPCs (0.5 x 10(6)) and EPCs+SMPCs (0.25 x 10(6)+0.25 x 10(6)). Vessel density and foot perfusion were increased in mice treated with EPCs+SMPCs compared to animals receiving EPCs alone or SMPCs alone (P<0.001). In addition, capillary and arteriolar densities were enhanced in EPC+SMPC-treated mice compared to SMPC and EPC groups (P<0.01). We next examined the role of Ang-1/Tie2 signaling in the beneficial effect of EPC and SMPC coadministration. Small interfering RNA directed against Ang-1-producing SMPCs or Tie2-expressing EPCs blocked vascular network formation in Matrigel coculture assays, reduced the rate of incorporated EPCs within vascular structure, and abrogated the efficiency of cell therapy. Production of Ang-1 by SMPCs activates Tie2-expressing EPCs, resulting in increase of EPC survival and formation of a stable vascular network. Subsequently, the efficiency of EPC- and SMPC-based cotherapy is markedly increased. Therefore, coadministration of different types of vascular progenitor cells may constitute a novel therapeutic strategy for improving the treatment of ischemic diseases.
Differential Expression and Pharmacology of Native P2X Receptors in Rat and Primate Sensory Neurons (2012)

Evidence suggesting the involvement of P2X2 and P2X3 in chronic pain has been obtained mostly from rodent models. Here we show that rodents may be poor predictors of P2X3 pharmacology in human. We demonstrate that monkey and human dorsal root ganglion (DRG) neurons do not express appreciable levels of P2X2 subunit, contrary to rat sensory neurons. Additionally, we report functional P2X3 activity in monkey DRG neurons and confirm the absence of functional P2X2/3 receptors. Interestingly, native P2X3 receptors in rat and monkey DRGs show similar agonist potency, but different antagonist potencies for TNP-ATP [2-O-(2,4,6-trinitrophenyl)-ATP] and RO51. This unexpected difference in antagonist potency was confirmed by comparing rat and human P2X3 receptors in HEK293 cells. Mutagenesis studies reveal that two extracellular residues, A197 and T202, are synergistically responsible for the potency drop in primate P2X3 receptors. These results uncover species-specific P2X3 pharmacology and identify key mechanisms impacting the translatability of potential analgesics targeting P2X3 receptors.
Nanoscale Raman Characterization of a 2D Semiconductor Lateral Heterostructure Interface (2021)

The nature of the interface in lateral heterostructures of 2D monolayer semiconductors including its composition, size, and heterogeneity critically impacts the functionalities it engenders on the 2D system for next-generation optoelectronics. Here, we use tip-enhanced Raman scattering (TERS) to characterize the interface in a single-layer MoS2/WS2 lateral heterostructure with a spatial resolution of 50 nm. Resonant and non-resonant TERS spectroscopies reveal that the interface is alloyed with a size that varies over an order of magnitude-from 50-600 nm-within a single crystallite. Nanoscale imaging of the continuous interfacial evolution of the resonant and non-resonant Raman spectra enables the deconvolution of defect-activation, resonant enhancement, and material composition for several vibrational modes in single-layer MoS2, MoxW1-xS2, and WS2. The results demonstrate the capabilities of nanoscale TERS spectroscopy to elucidate macroscopic structure-property relationships in 2D materials and to characterize lateral interfaces of 2D systems on length scales that are imperative for devices.
ChemInform Abstract: Electrophilic Coordination Catalysis: A Summary of Previous Thought and a New Angle of Analysis (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Probing the functional role of phenylalanine-31 of Escherichia coli dihydrofolate reductase by site-directed mutagenesis (1987)

The role of Phe-31 of Escherichia coli dihydrofolate reductase in binding and catalysis was probed by amino acid substitution. Phe-31, a strictly conserved residue located in a hydrophobic pocket and interacting with the pteroyl moiety of dihydrofolate (H2F), was replaced by Tyr and Val. The kinetic behavior of the mutant enzymes in general is similar to that of the wild type. The rate-limiting step for both mutant enzymes is the release of tetrahydrofolate (H4F) from the E X NADPH X H4F ternary complex as determined for the wild type. The 2-fold increase in V for the two mutant enzymes arises from faster dissociation of H4F from the enzyme-product complex. The quantitative effect of these mutations is to decrease the rate of hydride transfer, although not to the extent that this step becomes partially rate limiting, but to accelerate the dissociation rates of tetrahydrofolate from product complexes so that the opposing effects are nearly compensating.
Removal of Shallow and Deep Scratches and Pits from Polished Copper Films (2003)

Chemical mechanical polishing of scratched and pitted copper films was performed with a chemical solution containing 3 wt % hydrogen peroxide 2 mM benzotriazole, and a complexing agent, at pH 4, in the presence and absence of 0.1 wt % of ∼10 to 20 nm colloidal silica particles. While the chemical solution alone was able to clear shallow scratches and pits, some as deep as 40 nm, the addition of 0.1 wt % of colloidal silica allowed the planarization of scratches as deep as ∼320 nm and pits as deep as 350 nm, all after a 60 s polish time. © 2003 The Electrochemical Society. All rights reserved.
CCTV and night-time observations (2004)

Is it ethical–and practical–to use closed-circuit television in place of traditional methods to observe psychiatric inpatients at night? Mathew Page and colleagues describe a research project, led by Bournemouth University, designed to seek answers
<title>Combined SPECT and x-ray CT medical imaging system</title> (1995)

We have designed and built a system for correlated x ray CT transmission and SPECT emission imaging with an array of photon counting detectors. The scanner operates in a third generation fan beam geometry by translating a 23 element high purity germanium detector across the fan to image phantoms and small animals. The x ray CT image is used to obtain an object specific, i.e., anatomically accurate, attenuation map for the reconstruction of the SPECT image. SPECT images are reconstructed with an MLEM code and the pixel values are scaled in physical units by determining a scaling factor from a uniform water phantom with homogeneous and known attenuation. Single myocardial slices of several pigs were imaged with a 99mTc sestamibi imaging agent which is taken up in proportion to regional myocardial blood flow. The results show that 99mTc uptake and regional myocardial blood flow, determined in vivo from reconstructed SPECT images, correlate with the measured in vitro data. Furthermore, the correlation is markedly improved by reconstructing the images with an object specific attenuation map obtained from the coregistered x ray CT image. We were also able to restore the 99mTc sestamibi uptake from the reconstructed images to an accuracy between 40% and 90% of the true in vitro value, depending on the selection of maximum or mean pixel values in the regions of interest.© (1995) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Design Space Exploration of 3D Network-on-Chip (2018)

High-performance and energy-efficient Network-on-Chip (NoC) architecture is one of the crucial components of the manycore processing platforms. A very promising NoC architecture recently proposed in the literature is the three-dimensional small-world NoC (3D SWNoC). Due to short vertical links in 3D integration and the robustness of small-world networks, the 3D SWNoC architecture outperforms its other 3D counterparts. However, the performance of 3D SWNoC is highly dependent on the placement of the links and associated routers. In this article, we propose a sensitivity-based link placement algorithm (SEN) to optimize the performance of 3D SWNoC. The sensitivity of a link in a NoC measures the importance of the link. The SEN algorithm optimizes the performance of 3D SWNoC by calculating the sensitivities of all the links in the NoC and removing the least important link repeatedly. We compare the performance of SEN algorithm with simulated annealing- (SA) and recently proposed machine-learning-based (ML) optimization algorithm. The optimized 3D SWNoC obtained by the proposed SEN algorithm achieves, on average, 11.5% and 13.6% lower latency and 18.4% and 21.7% lower energy-delay product than those optimized by the SA and ML algorithms respectively. In addition, the SEN algorithm is 26 to 33 times faster than the SA algorithm for the optimization of 64-, 128-, and 256-core 3D SWNoC designs. The performance gain provided by the SEN-, SA-, and ML-based methods also depend on the characteristics of the benchmarks under consideration. If the traffic pattern generated by a benchmark does not have enough variation, then the ML-based method does not have adequate opportunity to optimize the network. However, we find that ML-based methodology has faster convergence time than SEN and SA for bigger systems. The ML-based optimization algorithm is almost 4 and 97 times faster than the SEN- and SA-based algorithm for a system with 256 cores.
RFID based systematic livestock health management system (2014)

Nowadays many farmers have adopted various means in the context of good farming practices to ensure the health of their livestock in good condition and healthy. Failure to ensure the health of livestock would cause to the death of animals and lead to decreased in productivity. Conventional methods by incorporating livestock data information on paper is a huge waste of time and not safe, therefore not effective for a good farming practiced. Hence, the electronic-based livestock management systems are needed to help farmers and livestock veterinary to share information for the purpose of early prevention of dangerous diseases from infected their livestock. In this project, the extensively use of Radio Frequency Identification (RFID) technology for livestock health management in the preparation of animal profile has created a fast and efficient method, but several conditions have to be set such as the RFID frequency selection and numbers of livestock in the farms. In current practice, even though the RFID systems in animal rearing is not a new approach, but this project has successfully demonstrated the effectiveness of RFID technology comes to solve daily problems on farms. In developing this monitoring system, web-based application platform likes MySQL, Apache and JSP has been used in an integrated methods for reporting and recording of livestock health records. Furthermore, Java programming act as a script, MySQL as database and NetBeans IDE 7.2 is used for the development of the whole system. In order to ensure this system development costs can be reduced as much as possible, the RFID Based Livestock Health Management System was built using open source software. The use of laptops and portable RFID reader has made farmers easier to access their livestock health information in real time and then can be shared to the other interested parties.
Reciprocal signaling between translational control pathways and synaptic proteins in autism spectrum disorders (2014)

Autism spectrum disorder (ASD) is a heterogeneous group of heritable neurodevelopmental disorders. Symptoms of ASD, which include deficits in social interaction skills, impaired communication ability, and ritualistic-like repetitive behaviors, appear in early childhood and continue throughout life. Genetic studies have revealed at least two clusters of genes frequently associated with ASD and intellectual disability: those encoding proteins involved in translational control and those encoding proteins involved in synaptic function. We hypothesize that mutations occurring in these two clusters of genes interfere with interconnected downstream signaling pathways in neuronal cells to cause ASD symptomatology. In this review, we discuss the monogenic forms of ASD caused by mutations in genes encoding for proteins that regulate translation and synaptic function. Specifically, we describe the function of these proteins, the intracellular signaling pathways that they regulate, and the current mouse models used to characterize the synaptic and behavioral features associated with their mutation. Finally, we summarize recent studies that have established a connection between mRNA translation and synaptic function in models of ASD and propose that dysregulation of one has a detrimental impact on the other.
Caractérisation de l'auto-échauffement des TBHs SiGe:C par l'extraction de l'impédance thermique (2013)

National audience
A Novel Segment-Based Protection Algorithm for Multicast Sessions in Optical Networks with Mesh Topologies (2011)

This work examines protection of multicast sessions in optical networks utilizing a novel segment-based algorithm called Level Protection. Our proposed scheme exhibits improved performance compared to other segment-based multicast protection schemes.
Control configuration selection for integrating processes using graphs (2015)

Recently, methods for Control Configuration Selection (CCS) using weighted graphs have been introduced. These methods were integrated in a software tool which allows systematic CCS in industry processes by choosing a simplified model with a reduced structure on which control will be based. This paper addresses the extension of these graph-based methods to be applied to integrating systems, which often appear in industry processes, e.g. at storage vessels. The extension is based on restricting the analysis to a set of frequencies of interest which omits the infinite DC-gain. The results are validated and illustrated using a real-life case, namely the secondary heating system of a pulp & paper mill.
RADIOCHEMICAL SEPARATION OF Ag, Au, Cd, Co, Fe, In, AND Zn PRESENT AS TRACE IMPURITIES IN GALLIUM. (1966)

Cytomegalovirus (CMV) pneumonitis is one of the most severe manifestations of CMV disease among immunocompromised patients. The diagnosis of CMV pneumonitis traditionally has required the use of invasive procedures such as lung biopsy. In this retrospective study, we evaluated a centrifugation culture method in samples of bronchoalveolar fluid for the noninvasive diagnosis of CMV pneumonitis. During a 9-mo period, 75 bronchoalveolar lavage samples were collected from 58 patients with pneumonitis. We analyzed the data from 21 patients in whom lung tissue samples were obtained within 14 days of the bronchoalveolar lavage. Centrifugation cultures of bronchoalveolar fluid were positive for CMV in 12 cases. CMV pneumonitis was confirmed in samples of lung tissue from five (42%) of the 12 patients, whereas no evidence of CMV pneumonitis was found in the remaining seven (58%) cases. Of nine patients with negative centrifugation cultures, CMV pneumonitis was confirmed in two (22%). When compared with conventional cultures, we found bronchoalveolar lavage fluid centrifugation cultures to be highly sensitive (100%) and specific (92%) for the detection of CMV infection. However, detection of CMV by centrifugation culture proved to be only moderately sensitive (71%) and nonspecific (50%) for the diagnosis of CMV pneumonitis.
Quantitative Nanostructural and Single-Molecule Force Spectroscopy Biomolecular Analysis of Human-Saliva-Derived Exosomes (2011)

Exosomes are naturally occurring nanoparticles with unique structure, surface biochemistry, and mechanical characteristics. These distinct nanometer-sized bioparticles are secreted from the surfaces of oral epithelial cells into saliva and are of interest as oral-cancer biomarkers. We use high- resolution AFM to show single-vesicle quantitative differences between exosomes derived from normal and oral cancer patient's saliva. Compared to normal exosomes (circular, 67.4 ± 2.9 nm), our findings indicate that cancer exosome populations are significantly increased in saliva and display irregular morphologies, increased vesicle size (98.3 ± 4.6 nm), and higher intervesicular aggregation. At the single-vesicle level, cancer exosomes exhibit significantly (P < 0.05) increased CD63 surface densities. To our knowledge, it represents the first report detecting single-exosome surface protein variations. Additionally, high-resolution AFM imaging of cancer saliva samples revealed discrete multivesicular bodies with intraluminal exosomes enclosed. We discuss the use of quantitative, nanoscale ultrastructural and surface biomolecular analysis of saliva exosomes at single-vesicle- and single-protein-level sensitivities as a potentially new oral cancer diagnostic.