gebhart/patrepeval huggingface dataset:
A comparative radiation hybrid map of sheep chromosome 10 (2008)

Comparative radiation hybrid (RH) maps of individual ovine chromosomes are essential to identify genes governing traits of economic importance in sheep, a livestock species for which whole genome sequence data are not yet available. The USUoRH5000 radiation hybrid panel was used to generate a RH map of sheep chromosome 10 (OAR10) with 59 markers that span 1,422 cR over an estimated 92 Mb of the chromosome, thus providing markers every 2 Mb (equivalent to every 24 cR). The markers were derived from 46 BAC end sequences (BESs), a single EST, and 12 microsatellites. Comparative analysis showed that OAR10 shares remarkable conservation of gene order along the entire length of cattle chromosome 12 and that OAR10 contains four major homologous synteny blocks, each related to segments of the homologous human chromosome 13. Extending the comparison to the horse, dog, mouse, and chicken genome showed that these blocks share conserved synteny across species.
Research in Numerical Linear Algebra and Numerical Methods for Large-Scale Least Squares and Other Problems. (1983)

Abstract : The research problems studied for the U. S. Army Research Office over the six year period of these grants are each in the research area of Numerical Linear Algebra and Applications. The objectives of the research were to develop new techniques for handling large-scale problems which involve interative or direct methods for solving large sparse systems of linear equations or least squares problems. The topics to be studied included: (1) the convergence of iterative methods for solving systems of linear equations, (2) hyperbolic systems of partial differential equations, (3) large-scale least squares computations, (4) M-matrices and related topics on nonegativity, (5) the computation of stationary distributions for Markov chains and (6) sparse matrix computations in structural optimization. Research on these topics was to be coordinated with associated scientists and engineers from some of the application areas such as queueing network analysis, compartmental analysis of biological systems, geodetic adjustment methods and structural analysis. Some theoretical research was to be done and certain algorithms and software were to be developed and tested on real problems from these areas.
Constant-Tissue Model for Comparison of Supine and Prone Breast Coil SNR (2023)

Recent work has developed supine breast imaging for improved correlation with surgery and comfort but will likely require breast-specific coils to maximize the SNR. Comparing prone and supine SNR can be difficult due to substantial deformation between the positions and heterogeneity of the patient population. We measured SNR in a constant-tissue model to reduce dependence on tissue heterogeneity and provide an overall SNR across the volume of interest. We compared SNR of a novel 60-channel supine coil and a standard prone coil. In the cosntant-tissue images, the supine 60-channel coil increased SNR by 33%, 78% and 80% across 3 volunteers.
A randomized pilot study of Repetitive Transcranial Magnetic Stimulation for Adolescents with Major Depressive Disorder. (2022)

Objectives: Up to 40% of adolescents with Major Depressive Disorder (MDD) do not respond to treatment. Repetitive Transcranial Magnetic Stimulation (rTMS) is an effective treatment in adults for MDD which shows promising efficacy in adolescents, however additional controlled investigations are needed. This pilot study compared rTMS applied to the left-side of the head and right-side in a randomized controlled trial. We hypothesized rTMS treatment would lead to an improvement in Children’s Depression Rating Scale Revised (CDRS-R) depression scores of adolescents with MDD at 1-month follow-up compared to baseline. No difference in response between left- and right-sided rTMS was expected.Methods: Fourteen adolescents who had been previously treated for MDD but had continued to suffer with MDD for an average of 2 years were randomly allocated to right (low frequency) or left (high frequency) rTMS. rTMS was applied to the scalp over the dorsolateral prefrontal cortex over 20 treatments given over four weeks. The primary outcome measure was the CDRS-R. Outcome assessments occurred at 10 sessions and 20 sessions, with follow-up at one month and six months.Results: CDRS-R scores improved significantly across the 20 rTMS treatments, with peak response at 1-month follow-up. Two (14%) adolescents had ≥ 50% score improvement and a further four (29%) demonstrated partial response (between 25 and 50% reduction) by 1-month follow-up. Treatment gains were sustained at 6-month follow-up. There was no significant difference in efficacy between left- and right-sided treatment.Conclusion: This small study found preliminary evidence that adolescents with MDD benefited from rTMS.
Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics (2016)

Malaria parasite infection is initiated by the mosquito-transmitted sporozoite stage, a highly motile invasive cell that targets hepatocytes in the liver for infection. A promising approach to developing a malaria vaccine is the use of proteins located on the sporozoite surface as antigens to elicit humoral immune responses that prevent the establishment of infection. Very little of the P. falciparum genome has been considered as potential vaccine targets, and candidate vaccines have been almost exclusively based on single antigens, generating the need for novel target identification. The most advanced malaria vaccine to date, RTS,S, a subunit vaccine consisting of a portion of the major surface protein circumsporozoite protein (CSP), conferred limited protection in Phase III trials, falling short of community-established vaccine efficacy goals. In striking contrast to the limited protection seen in current vaccine trials, sterilizing immunity can be achieved by immunization with radiation-attenuated sporozoites, suggesting that more potent protection may be achievable with a multivalent protein vaccine. Here, we provide the most comprehensive analysis to date of proteins located on the surface of or secreted by Plasmodium falciparum salivary gland sporozoites. We used chemical labeling to isolate surface-exposed proteins on sporozoites and identified these proteins by mass spectrometry. We validated several of these targets and also provide evidence that components of the inner membrane complex are in fact surface-exposed and accessible to antibodies in live sporozoites. Finally, our mass spectrometry data provide the first direct evidence that the Plasmodium surface proteins CSP and TRAP are glycosylated in sporozoites, a finding that could impact the selection of vaccine antigens.
A transformation method from UML statechartto Petri nets (2012)

Petri nets can be used to build an executable model of software system, to support the simulation of model, to ensure the accuracy and reliability of software system. This paper brings forward the transformation rules from Unified Modeling Language (UML) statechart to colored Petri nets, presents mapping of the statechart and colored Petri nets according to transformation rules, builds an automatic transform platform, implements the automatic conversion from statechart to colored Petri nets and uses Point to Point Protocol (PPP) to verify the feasibility of the transformation method.
Dark current analysis of Quantum Cascade Detectors by Magneto-Resistance measurements (2008)

International audience
Methods for Reducing Hydrogen Outgassing (2003)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Changkun Dong, Parixit Mehrotra, Ganapati Rao Myneni; Methods for Reducing Hydrogen Outgassing. AIP Conf. Proc. 11 July 2003; 671 (1): 307–312. https://doi.org/10.1063/1.1597378 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Self-Assembly of Monolayer-Coated Silver Nanoparticles on Gold Electrodes. An Electrochemical Investigation (2003)

Redox behaviour of an array of dodecanethiol-coated silver nanoparticles, self-assembled on the gold electrode surface by dithiol linkers, is dominated in aqueous electrolytes by a reversible faradaic process that has been attributed to the anodic oxidation of silver nanoparticles. The nanoparticle array may be switched between the oxidised and reduced states repeatedly without any significant loss of electroactive material, thus showing a remarkable stability under electrochemical conditions. The mainly capacitive high-frequency electrical response of the nanoparticle array/electrolyte interface is characterised by a low value of capacitance, typical of a self assembled monolayer (SAM) of long-chain alkanethiols on gold; it has been associated with the compact organic layer interposed between the nanoparticles and the gold substrate. At lower frequencies, the interface displays a poorer electrical behaviour with both capacitive and resistive elements, which was associated with the more disordered organic layer located on the outer side of the film.
Aminal linked inorganic–organic hybrid nanoporous materials (HNMs) for CO2 capture and H2 storage applications (2016)

Cyclophosphazene based nitrogen-rich aminal-linked inorganic–organic hybrid nanoporous materials were synthesized by a Schiff-base condensation reaction, which captures 18.9 wt% of CO<sub>2</sub>.
Ex-Vivo and In-Vitro Evidence that Low Molecular Weight Heparins Exhibit Less Binding to Plasma Proteins than Unfractionated Heparin (1994)

We have compared the non-specific binding of unfractionated heparin (UFH) with that of low molecular weight heparin (LMWH) to plasma proteins both ex-vivo and in-vitro. Non-specific binding to plasma proteins was assessed by comparing the heparin levels measured as anti-factor Xa activity before and after the addition of low affinity heparin, which is essentially devoid of anti-factor Xa activity, in order to displace heparin bound to plasma proteins. For the ex-vivo studies, we compared the recovery of UFH and a LMWH (ardeparin) from the plasma of patients participating in a randomized trial of post-operative venous thrombosis prophylaxis. For the in-vitro studies, we compared the recovery of UFH and 4 different LMWHs when added to the plasma from healthy volunteers and from patients with suspected venous thromboembolic disease. The results indicate that the recovery of LMWH is much less affected by nonspecific binding to plasma proteins both ex-vivo and in-vitro. In addition, there are differences between the LMWHs with respect to their plasma protein-binding.
Increased Leptin Expression in Common Carp ( Cyprinus carpio ) after Food Intake But Not after Fasting or Feeding to Satiation (2006)

Leptin is a key factor in the regulation of food intake and is an important factor in the pathophysiology of obesity. However, more than a decade after the discovery of leptin in mouse, information regarding leptin in any nonmammalian species is still scant. We report the identification of duplicate leptin genes in common carp (Cyprinus carpio). The unique gene structure, the conservation of both cysteines that form leptin's single disulfide bridge, and stable clustering in phylogenetic analyses substantiate the unambiguous orthology of mammalian and carp leptins, despite low amino acid identity. The liver is a major yet not the only site of leptin expression. However, neither 6 d nor 6 wk of fasting nor subsequent refeeding affected hepatic leptin expression, although the carp predictably shifted from carbohydrate to lipid metabolism. Animals that were fed to satiation grew twice as fast as controls; however, they did not show increased leptin expression at the termination of the study. Hepatic leptin expression did, however, display an acute and transient postprandial increase that follows the postprandial plasma glucose peak. In summary, leptin mRNA expression in carp changes acutely after food intake, but involvement of leptin in the long-term regulation of food intake and energy metabolism was not evident from fasting for days or weeks or long-term feeding to satiation. These are the first data on the regulation of leptin expression in any nonmammalian species.
Strain Identification of Newcastle Disease Virus in Tissue Culture (1970)

A procedure was developed that enabled the investigator to isolate and to identify virus and virus type in one cultural step. The development and morphology of each virus was studied on monolayers of chicken embryo fibroblasts. The response of individual plaques were compared in several tests. Samples from seven of ten serials of vaccines contaminated with Newcastle disease virus (NDV) were found to contain a lentogenic strain of NDV. Six tissue-culture procedures were used. Six isolates were typed as NDV-LaSota-like, and one was typed as NDV-BI-like.
A predictive blind equalizer based in Godard's criterion for 256-QAM digital radio systems (2002)

This paper develops the theory of complex finite-length linear equalization based in predictive filter structures and Godard's (1980) criterion. The complex equalizer is composed by a cascade of a forward and backward prediction-error filters plus a complex gain responsible for both power and carrier phase recovery. It can be updated adaptively at the same low computational cost as any other classical blind technique. Simulation results for digital radio links show that this technique performs very well with severe channel fadings in high-order QAM systems. In this case, some classical blind equalizers do not perform as well.
Operative Therapie des Ovarialkarzinoms (2016)

Kernaussagen Der postoperative Tumorrest stellt in der Behandlung des Ovarialkarzinoms den wichtigsten Prognosefaktor dar. Das Ziel einer jeden zytoreduktiven Operation sollte daher das Erreichen einer makroskopischen Tumorfreiheit sein („R0-Resektion“). Eine „R1-Resektion“ (postoperativ makroskopisch sichtbarer Tumor vorhanden) kann nicht durch eine nachfolgende adjuvante Chemotherapie ausgeglichen werden. Bei Patientinnen mit Ovarialkarzinom kommt es nach laparoskopischen Eingriffen in vielen Fällen innerhalb kürzester Zeit zur Ausbildung von Bauchdeckenmetastasen im Bereich der Trokareinstichstelle. Bei hochgradigem Verdacht auf ein Ovarialkarzinom sollte deshalb auf die Durchführung einer diagnostischen Laparoskopie nach Möglichkeit verzichtet werden. Die operative Versorgung des Ovarialkarzinoms sollte in einem Zentrum für gynäkologische Onkologie erfolgen. Mit der jungen Patientin kann unter der Voraussetzung eines adäquaten chirurgischen Stagings und hierbei gesichertem Stadium FIGO IA, G1 eine fertilitätserhaltende Operation besprochen werden. Aufgrund erhöhter Rezidivraten ist nach abgeschlossener Familienplanung die Durchführung einer Komplettierungsoperation dringend anzuraten. Eine Kombination aus Allgemein- und Epiduralanästhesie verbessert die postoperative Schmerztherapie und verringert Komplikationen wie Pneumonien, postoperative Übelkeit/Erbrechen und Motilitätsstörungen des Darmes.
Low secondary electron yield carbon coatings for electron cloud mitigation in modern particle accelerators (2011)

In order to upgrade the Large Hadron Collider (LHC) performance to be oriented towards higher energies and higher intensities in the future, a series of improvements
of the existing LHC injectors is planned to take place over the next few years. Electron cloud effects are expected to be enhanced and play a central role in limiting the
performance of the machines of the CERN complex.

Electron cloud phenomena in beam pipes are based on electron multiplication and can be sufficiently suppressed if the Secondary Electron Yield (SEY) of the surface of the beam pipes is lower than unity. The goal of this work is to find and study a thin film coating with reliably low initial SEY, which does not require bake-out or conditioning in situ with photons, is robust against air exposure and can easily be applied in the beam pipes of accelerators. In this work, amorphous carbon (a-C) thin films have been prepared by DC magnetron sputtering for electron cloud mitigation and antimultipactor applications.

In the first part of this thesis, the experimental set-ups for the a-C thin film coatings used in this work are described. In the second part, a summary of all the key
experimental findings obtained on the a-C thin films in the laboratory, as well as the results of the measurements carried out with LHC type beams in the Super Proton
Synchrotron (SPS), i.e. the last injector before the LHC are shown. The influence of different coating parameters, such as power, discharge gas pressure and substrate
temperature on SEY has been investigated. The a-C thin films have been characterized by SEY measurements, Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Nuclear Reaction Analysis (NRA), X-ray Photoelectron Spectroscopy (XPS) and Raman Spectroscopy. The SEY of the a-C samples after long termexposure to various atmospheres has been studied. Different surface treatments,
such as conditioning by electron beam, annealing under vacuum and ion bombardment, on the sample surfaces have been investigated. Apart from the characterizations
in laboratory, a-C thin films have also been applied to the liners in the electron cloud monitors and to vacuum chambers of three dipole magnets in the SPS. The
electron cloud effect has been studied in the SPS with LHC type beams.

In the third and final part, several other coating techniques as well as materials have been investigated for low SEY applications are presented. To gain a deep
understanding of the properties of our amorphous carbon coating, the amorphous carbon thin film has been compared with other pure graphite samples.

In conclusion, the present study has largely improved the knowledge of the electron cloud understanding with LHC type beams in the SPS. Amorphous carbon coatings are believed to be a potential solution for the electron cloud in the high-energy particle accelerators.
E-101 Preventative HIV Vaccine Progress (2014)

Effective vaccines often generate protective antibody responses that are similar to those produced during natural infection. For HIV-1, the isolation of broadly reactive neutralizing monoclonal antibodies (bNAbs) has provided a template for the kind of immune response we aim to elicit via immunization. The analysis of bNAb structural mode of recognition and genetic pathways of antigen recognition and affinity maturation can impact HIV vaccine design and prevention efforts in several ways, including (1) structure-based vaccine design, (2) understanding antibody evolution to optimize immunization strategies, and (3) direct immunoprophylaxis by passive antibody or gene-based vectors. Highlights from each of these areas will be reviewed, including recent advances in immunogen design, antibody optimization, non-human primate immunogenicity and passive protection data.
Diaminomaleonitrile-based Schiff bases: aggregation-enhanced emission, red fluorescence, mechanochromism and bioimaging applications (2016)

Red-emissive diaminomaleonitrile-based Schiff bases with aggregation-enhanced emission, mechanochromism, and application in bioimaging were designed and readily synthesized.
Depletion of cardiolipin induces major changes in energy metabolism in Trypanosoma brucei bloodstream forms (2020)

The mitochondrial inner membrane glycerophospholipid cardiolipin (CL) associates with mitochondrial proteins to regulate their activities and facilitate protein complex and supercomplex formation. Loss of CL leads to destabilized respiratory complexes and mitochondrial dysfunction. The role of CL in an organism lacking a conventional electron transport chain (ETC) has not been elucidated. Trypanosoma brucei bloodstream forms use an unconventional ETC composed of glycerol-3-phosphate dehydrogenase and alternative oxidase (AOX), while the mitochondrial membrane potential (ΔΨm) is generated by the hydrolytic action of the F<sub>o</sub> F<sub>1</sub> -ATP synthase (aka F<sub>o</sub> F<sub>1</sub> -ATPase). We now report that the inducible depletion of cardiolipin synthase (TbCls) is essential for survival of T brucei bloodstream forms. Loss of CL caused a rapid drop in ATP levels and a decline in the ΔΨm. Unbiased proteomic analyses revealed a reduction in the levels of many mitochondrial proteins, most notably of F<sub>o</sub> F<sub>1</sub> -ATPase subunits and AOX, resulting in a strong decline of glycerol-3-phosphate-stimulated oxygen consumption. The changes in cellular respiration preceded the observed decrease in F<sub>o</sub> F<sub>1</sub> -ATPase stability, suggesting that the AOX-mediated ETC is the first pathway responding to the decline in CL. Select proteins and pathways involved in glucose and amino acid metabolism were upregulated to counteract the CL depletion-induced drop in cellular ATP.
Single-Stage Series-Connected Isolated Converters for MVAC to DC Applications (2022)

This paper presents an novel fast electric vehicle (EV) charger configuration suitable for direct medium voltage (MV) connection. The idea is based on the multi-cell boost (MCB) structure and shares its advantages in terms of modularity, low line inductor requirements, high-frequency isolation and good semiconductor utilization. However, instead of using a two-stage conversion approach, where each cell includes power factor correction (PFC) rectifier that is followed by isolated dc-dc converters, a single-sage approach is implemented. In this case both PFC and isolation functions are realized with a single cell based on isolated current source converters (CSCs). The topology structure and its possible configurations are presented, followed by some design considerations. Next, some of the possible CSC topologies suitable for the proposed single-stage MCB cell are described, followed by simulation and benchmarking of selected topologies.
Combined siRNA and Small-Molecule Phenotypic Screening Identifies Targets Regulating Rhinovirus Replication in Primary Human Bronchial Epithelial Cells (2020)

Human rhinovirus (RV) is the most common cause of acute upper respiratory tract infections and has recently been shown to play a significant role in exacerbations of asthma and chronic obstructive pulmonary disease (COPD). There is a significant unmet medical need for agents for the prevention and/or treatment of exacerbations triggered by human RV infection. Phenotypic drug discovery programs using different perturbation modalities, for example, siRNA, small-molecule compounds, and CRISPR, hold significant value for identifying novel drug targets. We have previously reported the identification of lanosterol synthase as a novel regulator of RV2 replication through a phenotypic screen of a library of siRNAs against druggable genes in normal human bronchial epithelial (NHBE) cells. Here, we describe a follow-up phenotypic screen of small-molecule compounds that are annotated to be pharmacological regulators of target genes that were identified to significantly affect RV2 replication in the siRNA primary screen of 10,500 druggable genes. Two hundred seventy small-molecule compounds selected for interacting with 122 target gene hits were screened in the primary RV2 assay in NHBE cells by quantifying viral replication via in situ hybridization followed by secondary quantitative PCR-based assays for RV2, RV14, and RV16. The described follow-up phenotypic screening allowed us to identify Fms-related tyrosine kinase 4 (FLT4) as a novel target regulating RV replication. We demonstrate that a combination of siRNA and small-molecule compound screening models is a useful phenotypic drug discovery approach for the identification of novel drug targets.