gebhart/patrepeval huggingface dataset:
Evidence for grading at polished surfaces from grazing-incidence X-ray scattering (1996)

Grazing-incidence specular and diffuse X-ray scattering has been performed on polished surfaces of the glass ceramic Zerodur (registered trademark of Schott Glaswerke, Mainz). Analysis using a distorted-wave Born approximation showed that satisfactory fits to the data could be obtained only if grading was included at the surface. A new formulation of the scattering model has been derived, incorporating such grading. When this was applied, excellent agreement between experiment and theory was obtained with one set of model parameters fitting at all scattering vectors.
Comparative Genomics of the Sigatoka Disease Complex on Banana Suggests a Link between Parallel Evolutionary Changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and Increased Virulence on the Banana Host (2016)

The Sigatoka disease complex, caused by the closely-related Dothideomycete fungi Pseudocercospora musae (yellow sigatoka), Pseudocercospora eumusae (eumusae leaf spot), and Pseudocercospora fijiensis (black sigatoka), is currently the most devastating disease on banana worldwide. The three species emerged on bananas from a recent common ancestor and show clear differences in virulence, with P. eumusae and P. fijiensis considered the most aggressive. In order to understand the genomic modifications associated with shifts in the species virulence spectra after speciation, and to identify their pathogenic core that can be exploited in disease management programs, we have sequenced and analyzed the genomes of P. eumusae and P. musae and compared them with the available genome sequence of P. fijiensis. Comparative analysis of genome architectures revealed significant differences in genome size, mainly due to different rates of LTR retrotransposon proliferation. Still, gene counts remained relatively equal and in the range of other Dothideomycetes. Phylogenetic reconstruction based on a set of 46 conserved single-copy genes strongly supported an earlier evolutionary radiation of P. fijiensis from P. musae and P. eumusae. However, pairwise analyses of gene content indicated that the more virulent P. eumusae and P. fijiensis share complementary patterns of expansions and contractions in core gene families related to metabolism and enzymatic degradation of plant cell walls, suggesting that the evolution of virulence in these two pathogens has, to some extent, been facilitated by convergent changes in metabolic pathways associated with nutrient acquisition and assimilation. In spite of their common ancestry and shared host-specificity, the three species retain fairly dissimilar repertoires of effector proteins, suggesting that they likely evolved different strategies for manipulating the host immune system. Finally, 234 gene families, including seven putative effectors, were exclusively present in the three Sigatoka species, and could thus be related to adaptation to the banana host.
Three-electrode-per-pel AC plasma display panel (1986)

A new ac plasma display technique is described in which the alternating sustain function is achieved on the back or substrate glass surface and the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x-y</tex> selected write-addressing uses a transparent front cover electrode and a substrate electrode. The three-electrode-per-pel structure achieves high overall emission efficiency as a result of nonshielded sustain discharges and low electrode capacitances.
Controllable fabrication of fiber nano-tips by dynamic chemical etching based on siphon principle (2004)

A dynamic chemical etching method based on siphon principle has been developed for controllable fabrication of fiber nano-tips, which could be used in near-field optical microscope and optical nanosensors. Compared with traditional static chemical etching, this method has advantages such as reproducibility, controllability, convenience, less cost, and making tip surface smooth. The overall shape and the tape angle of the tip can be effectively controlled through the speed and direction of water flux. Tips with taper angles from 20° to 55°, and tips with double tapers have been achieved by this method.
The orthotopic xenotransplant of human glioblastoma successfully recapitulates glioblastoma-microenvironment interactions in a non-immunosuppressed mouse model (2014)

This study demonstrated that the xenografted tumor in mouse brain parenchyma develops in a very similar manner to those found in patients affected by GBM and can be used to better understand the biology of GBM as well as testing potential therapies.
Touch screens now offer compelling uses (1991)

Research on improving the user interfaces of touch screen applications is described. The advantages of touch screens are discusses, their current capabilities are examined, and possible future developments are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Use of the EVTA process in the evaluation of human/system interaction and performance (1989)

The EVTA process generates a task-descriptive data base (Dury et al., 1987, page 375) from a detailed analysis of operator's observable activities and communications. The essential features of the EVTA process are the use of video/audio equipment to gather permanent records of operator activities from operational environments, and the generation of an empirical record of activity times through a software package which builds, manages and analyzes the resulting data base.
Factors that influence the intention to use mobile phone caller tunes for patient reporting of adverse drug reactions: a qualitative study (2019)

Background: Patient reporting of adverse drug reactions (ADRs) is low in low- and middle-income countries, in part because of poor awareness to report. With the increase in mobile subscription, mobile phones can be used as a platform to disseminate information on ADRs. The aim of this study was to qualitatively assess the potential of using mobile phone caller tunes (the message or sound the caller hears before the receiver answers the call) to encourage patient reporting of ADRs. Methods: A total of 38 key informant interviews and 12 focus group discussions (57 participants in groups of 4–5) were conducted in Accra, Ghana. The transcripts were analysed using key constructs of the Technology Acceptance Model (TAM) including perceived usefulness, perceived ease of use, and behavioural intention to use caller tunes for patient reporting of ADRs. Results: Respondents mentioned lack of knowledge on reporting ADRs, and their willingness to use mobile phone caller tunes to promote patient reporting of ADRs. Many respondents pointed out how ADRs usually led to discontinuity in medication use, usually without consultation with health professionals. Caller tunes were regarded an innovative, accessible and convenient platform to disseminate information on ADRs. Most respondents intended to use caller tunes with drug safety information to promote ADR reporting, particularly to help their friends and family members. Simplicity of the message, use of songs or messages in local languages and price of downloading the caller tunes were important considerations. Conclusion: There is a need for the creation and testing of caller tunes on ADRs in Ghana to promote patient or consumer reporting of ADRs. Further studies are needed to assess factors that could influence the creation and use of caller tunes to disseminate information on drug safety.
Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection (2010)

It is well known that light-sheet illumination can enable optically sectioned wide-field imaging of macroscopic samples. However, the optical sectioning capacity of a light-sheet macroscope is undermined by sample-induced scattering or aberrations that broaden the thickness of the sheet illumination. We present a technique to enhance the optical sectioning capacity of a scanning light-sheet microscope by out-of-focus background rejection. The technique, called HiLo microscopy, makes use of two images sequentially acquired with uniform and structured sheet illumination. An optically sectioned image is then synthesized by fusing high and low spatial frequency information from both images. The benefits of combining light-sheet macroscopy and HiLo background rejection are demonstrated in optically cleared whole mouse brain samples, using both green fluorescent protein (GFP)-fluorescence and dark-field scattered light contrast.
The farnesoid X receptor: a novel drug target? (2004)

Bile acids are end products of cholesterol metabolism. They are exclusively synthesised by the liver and subsequently secreted via the bile duct into the intestine to facilitate the absorption of dietary fat and fat-soluble vitamins. Nuclear receptors are ligand-activated transcription factors. The farnesoid X receptor (FXR) has recently been identified as a bile acid-activated nuclear receptor. FXR controls bile-acid synthesis, conjugation and transport, as well as lipid metabolism. Recent advances in FXR biology demonstrate that FXR may represent a valuable target for the identification of novel drugs to treat dyslipidaemia and cholestasis. However, for therapeutic purposes the development of selective FXR modulators, which only activate or inhibit specific FXR target genes and as such induce specific responses, will be required.
Design of Transformation-Processed $\hbox{Nb}_{3} \hbox{Al}$ Conductors to Balance Drawability and Inter-Filament Decoupling (2013)

Transformation-processed Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Al superconductors should be used in conjunction with a high-melting-point matrix material such as Nb. However, Nb is superconductive below 9 K, which causes low-field instability due to magnetic interfilament coupling at liquid He temperature. One alternative matrix material is Ta. However, the use of Ta sacrifices the drawability of the precursor wires, increasing the risk of wire breakage during drawing. In this work, a new layout intended to balance drawability and interfilament decoupling is proposed. In this new layout, Nb barrier filaments are concentrated around the central dummy core, and Ta barrier filaments are located so as to magnetically decouple the Nb barrier filaments in the outer filamentary region. The drawability and magnetization behavior of the newly designed Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Al wires are compared with those of conventional wires.
The versatility of the αβ T‐cell antigen receptor (2013)

The T-cell antigen receptor is a heterodimeric αβ protein (TCR) expressed on the surface of T-lymphocytes, with each chain of the TCR comprising three complementarity-determining regions (CDRs) that collectively form the antigen-binding site. Unlike antibodies, which are closely related proteins that recognize intact protein antigens, TCRs classically bind, via their CDR loops, to peptides (p) that are presented by molecules of the major histocompatibility complex (MHC). This TCR-pMHC interaction is crucially important in cell-mediated immunity, with the specificity in the cellular immune response being attributable to MHC polymorphism, an extensive TCR repertoire and a variable peptide cargo. The ensuing structural and biophysical studies within the TCR-pMHC axis have been highly informative in understanding the fundamental events that underpin protective immunity and dysfunctional T-cell responses that occur during autoimmunity. In addition, TCRs can recognize the CD1 family, a family of MHC-related molecules that instead of presenting peptides are ideally suited to bind lipid-based antigens. Structural studies within the CD1-lipid antigen system are beginning to inform us how lipid antigens are specifically presented by CD1, and how such CD1-lipid antigen complexes are recognized by the TCR. Moreover, it has recently been shown that certain TCRs can bind to vitamin B based metabolites that are bound to an MHC-like molecule termed MR1. Thus, TCRs can recognize peptides, lipids, and small molecule metabolites, and here we review the basic principles underpinning this versatile and fascinating receptor recognition system that is vital to a host's survival.
Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins (2013)

Bacterial microcompartments (MCPs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. MCPs carrying out three different metabolic functions have been characterized in some detail, while gene expression and bioinformatics studies have implicated other types, including one believed to perform glycyl radical-based metabolism of 1,2-propanediol (Grp). Here we report the crystal structure of a protein (GrpN), which is presumed to be part of the shell of a Grp-type MCP in Rhodospirillum rubrum F11. GrpN is homologous to a family of proteins (EutN/PduN/CcmL/CsoS4) whose members have been implicated in forming the vertices of MCP shells. Consistent with that notion, the crystal structure of GrpN revealed a pentameric assembly. That observation revived an outstanding question about the oligomeric state of this protein family: pentameric forms (for CcmL and CsoS4A) and a hexameric form (for EutN) had both been observed in previous crystal structures. To clarify these confounding observations, we revisited the case of EutN. We developed a molecular biology-based method for accurately determining the number of subunits in homo-oligomeric proteins, and found unequivocally that EutN is a pentamer in solution. Based on these convergent findings, we propose the name bacterial microcompartment vertex for this special family of MCP shell proteins.
Bordetella pertussis Isolates from Argentinean Whooping Cough Patients Display Enhanced Biofilm Formation Capacity Compared to Tohama I Reference Strain (2015)

Pertussis is a highly contagious disease mainly caused by Bordetella pertussis. Despite the massive use of vaccines, since the 1950s the disease has become re-emergent in 2000 with a shift in incidence from infants to adolescents and adults. Clearly, the efficacy of current cellular or acellular vaccines, formulated from bacteria grown in stirred bioreactors is limited, presenting a challenge for future vaccine development. For gaining insights into the role of B. pertussis biofilm development for host colonization and persistence within the host, we examined the biofilm forming capacity of eight argentinean clinical isolates recovered from 2001 to 2007. All clinical isolates showed an enhanced potential for biofilm formation compared to the reference strain Tohama I. We further selected the clinical isolate B. pertussis 2723, exhibiting the highest biofilm biomass production, for quantitative proteomic profiling by means of two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with mass spectrometry, which was accompanied by targeted transcriptional analysis. Results revealed an elevated expression of several virulence factors, including adhesins involved in biofilm development. In addition, we observed a higher expression of energy metabolism enzymes in the clinical isolate compared to the Tohama I strain. Furthermore, all clinical isolates carried a polymorphism in the bvgS gene. This mutation was associated to an increased sensitivity to modulation and a faster rate of adhesion to abiotic surfaces. Thus, the phenotypic biofilm characteristics shown by the clinical isolates might represent an important, hitherto underestimated, adaptive strategy for host colonization and long time persistence within the host.
Ubiquitin-EP52 fusion protein homologs from<i>Trypanosoma brucei</i> (1990)

Journal Article Ubiquitin-EP52 fusion protein homologs from Trypanosoma brucei Get access S. Wong, S. Wong Department of Microbiology and Immunology, University of CaliforniaLos Angeles, CA 90024, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar T.H. Morales, T.H. Morales Department of Microbiology and Immunology, University of CaliforniaLos Angeles, CA 90024, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar D.A. Campbell D.A. Campbell * Department of Microbiology and Immunology, University of CaliforniaLos Angeles, CA 90024, USA * To whom correspondence should be addresse Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 23, 1 December 1990, Page 7181, https://doi.org/10.1093/nar/18.23.7181 Published: 01 January 1990 Article history Published: 01 January 1990 Received: 12 October 1990
Analysis of Sources of Variability in Runoff Plots Studies Using a Numerical Model: A Case Study From a 40 Fallow Plots Experiment (2013)

Runoff volumes from plots can be quite variable. These variations can be important for understanding the hydrologic system, and also to evaluating the effectiveness of infiltration and runoff prediction models. We investigated the sources of variability among 40 replications in a previously reported experiment on fallow plots. A numerical model was calibrated using data from the experiment and from other published data. Approximately 70% of the observed variation among the replicated plots could be explained by the spatial variabilities of hydraulic conductivity, surface storage, and the depth to claypan. Changes in the relative differences in runoff among plots may be explainable by the modification of the spatial distribution of hydraulic conductivity and surface storage during tillage. The introduction of these sources of variability in the model formulation produced a realistic description of the variance of the observed values of runoff, as well as a relatively clear delineation between the explained and unexplained variability. These results can serve as an index of model performance in predicting observed data.
The interaction between Myc and Miz1 is required to antagonize TGFβ-dependent autocrine signaling during lymphoma formation and maintenance (2010)

The Myc protein suppresses the transcription of several cyclin-dependent kinase inhibitors (CKIs) via binding to Miz1; whether this interaction is important for Myc's ability to induce or maintain tumorigenesis is not known. Here we show that the oncogenic potential of a point mutant of Myc (MycV394D) that is selectively deficient in binding to Miz1 is greatly attenuated. Binding of Myc to Miz1 is continuously required to repress CKI expression and inhibit accumulation of trimethylated histone H3 at Lys 9 (H3K9triMe), a hallmark of cellular senescence, in T-cell lymphomas. Lymphomas that arise express high amounts of transforming growth factor beta-2 (TGFbeta-2) and TGFbeta-3. Upon Myc suppression, TGFbeta signaling is required to induce CKI expression and cellular senescence and suppress tumor recurrence. Binding of Myc to Miz1 is required to antagonize growth suppression and induction of senescence by TGFbeta. We demonstrate that, since lymphomas express high levels of TGFbeta, they are poised to elicit an autocrine program of senescence upon Myc inactivation, demonstrating that TGFbeta is a key factor that establishes oncogene addiction of T-cell lymphomas.
Function of the Outer Membrane of <i>Escherichia coli</i> as a Permeability Barrier to Beta-Lactam Antibiotics (1977)

On the basis of a simple theoretical model, the ease of penetration of beta-lactam antibiotics through the outer membrane of Escherichia coli was measured. The cell envelope was found to act as a diffusion barrier to both penicillins and cephalosporins. The validity of the model and the cooperative action of cell-bound beta-lactamase and outer membrane were further verified by comparing calculated and experimentally determined velocities of beta-lactam hydrolysis by intact cells and sonically treated cell suspensions. The results showed good correspondence at five different antibiotic concentrations. Similar conclusions could be drawn from a comparison of beta-lactam concentrations on both sides of the outer membrane, calculated from enzyme kinetic measurements and minimal inhibitory concentrations for both a beta-lactamase-producing E. coli and its enzyme-negative variant. in the case of benzylpenicillin and cephalothin, however, no correspondence was found. The joint action of several parameters determining the efficacy of penicillins and cephalosporins against beta-lactamase-producing E. coli is discussed.
Progress towards reliable free-space optical networks (2011)

Free-space optical communications (FSOC) links provide an appealing and complementary enhancement to current radio frequency (RF) systems because of their inherent benefits of high-bandwidth and directional communication. Although FSOC systems can be inoperable through clouds or thick fog, employing them in a hybrid RF/optical link configuration can yield a system that can operate under most weather conditions and provide high-bandwidth, secure, jam-resistant communications under most conditions. Beyond attenuation effects and line-of-sight limitations, FSOC link performance is primarily driven by optical turbulence along the beam path, which leads to severe fluctuation of the communications channel and distortion of the signal wavefront. Many methods have been either modeled or field-tested to reduce this fading with varying degrees of success. The approach taken in the DARPA Free Space Optical Experimental Network Experiment (FOENEX) program is a continuance of systems development work funded and developed by DARPA, the Air Force Research Laboratory (AFRL), and the Naval Research Laboratories (NRL). The use of QoS-based link-level techniques was successfully demonstrated under the AFRL Iron T2 and DARPA ORCA programs. The FOENEX program extends these methods via technology developments at the physical layer as well as implementing the network methods to ensure end-to-end high bandwidth connectivity. This paper focuses on progress to date in networking technologies that will support free space optical networks (FSON) out to 200 km ranges even when individual links are disrupted up to 5% of the time.
Dramatic lithium chloride effect on the reaction stereocontrol in Zn-mediated asymmetric cinnamylation: highly practical synthesis of β-aryl homoallylic amines (2010)

An extremely mild and practical approach for the preparation of enantiomerically enriched β-aryl substituted homoallylic amines bearing two adjacent stereogenic centers was realized by room temperature zinc-mediated highly stereoselective cinnamylation of N-sulfinyl imines.
On exploiting declarative programming and parallel execution in computer based real-time systems (2002)

Presents experiences from modelling real-time applications in the declarative functional language H, developed hand-in-hand with a novel parallel graph reduction architecture called rp8601, both designed with the requirements of real-time embedded systems in mind. In rp8601, the analogue and digital interactions with the environment have been designed into the chips and into the language, and so have mechanisms to handle time constraints. Traditionally, declarative programming means that the programmer need not be aware of the processor operations. Instead, he can focus on the abstract relations between the input and output streams. The specific real-time requirements have normally not been taken into account in the declarative view. Our conclusion is that declarative functional programming is a viable technique for the development of complex software for embedded real-time systems. However, considerable efforts have to be spent on educating and training the application programmers in the new programming paradigm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>