gebhart/patrepeval huggingface dataset:
Rift valley fever virus L segment: correction of the sequence and possible functional role of newly identified regions conserved in RNA-dependent polymerases (1994)

The sequence of Rift Valley fever virus L segment that we published in a previous paper was erroneous in the 3'-terminal region of the antigenomic RNA molecule. Here, we have shown that the L segment is in fact 6404 nucleotides long and encodes a polypeptide of 237.7K in the viral complementary sense. Sequence comparisons performed between the RNA-dependent RNA polymerases of 22 negative-stranded RNA viruses revealed the existence of two novel regions located at the amino termini of the proteins and conserved only in the polymerases of bunya- and arenaviruses. In the region conserved in all RNA-dependent polymerases, corresponding to the so-called 'polymerase module', we identified a new motif, designated premotif A, common to all RNA-dependent polymerases, as well as amino acids located in the region between motifs preA and A which are strictly conserved for segmented negative-stranded RNA viruses. Using the recently released coordinates of human immunodeficiency virus reverse transcriptase and the alignment between all RNA-dependent polymerases in the 'polymerase module', we have determined the position of the conserved residues in these polymerases and discuss their possible functions in light of the available structural information.
Electronic Structure, Oxidation State of Sn, and Chemical Stability of Photovoltaic Perovskite Variant Cs2SnI6 (2015)

This paper has been published in Bulletin of the Chemical Society of Japan, which can be viewed at the following URL: this http URL Cs2SnI6, a variant of perovskite CsSnI3, is expected for a photovoltaic material. Based on a simple ionic model, it is expected that Cs2SnI6 is composed of Cs+, I-, and Sn4+ ions and that the band gap is primarily made of occupied I- 5p6 valence band maximum (VBM) and unoccupied Sn4+ 5s conduction band minimum (CBM) similar to SnO2. In this work, we performed density functional theory (DFT) calculations and revealed that the real oxidation state of the Sn ion in Cs2SnI6 is +2 similar to CsSnI3. The +2 oxidation state of Sn originates from 2 ligand holes in the [SnI6]2- octahedron unit, where the ligand [I6] cluster has the apparent [I66-L+2]4- oxidation state, because the band gap is formed mainly by occupied I 5p VBM and unoccupied I 5p CBM. The +2 oxidation state of Sn and the band gap are originated from the intracluster hybridization and stabilized by the strong covalent interaction between Sn and I.
An Environmental Shiga Toxin-Producing Escherichia coli O145 Clonal Population Exhibits High-Level Phenotypic Variation That Includes Virulence Traits (2015)

Shiga toxin-producing Escherichia coli (STEC) serotype O145 is one of the major non-O157 serotypes associated with severe human disease. Here we examined the genetic diversity, population structure, virulence potential, and antimicrobial resistance profiles of environmental O145 strains recovered from a major produce production region in California. Multilocus sequence typing analyses revealed that sequence type 78 (ST-78), a common ST in clinical strains, was the predominant genotype among the environmental strains. Similarly, all California environmental strains belonged to H28, a common H serotype in clinical strains. Although most environmental strains carried an intact fliC gene, only one strain retained swimming motility. Diverse stx subtypes were identified, including stx1a, stx2a, stx2c, and stx2e. Although no correlation was detected between the stx genotype and Stx1 production, high Stx2 production was detected mainly in strains carrying stx2a only and was correlated positively with the cytotoxicity of Shiga toxin. All environmental strains were capable of producing enterohemolysin, whereas only 10 strains were positive for anaerobic hemolytic activity. Multidrug resistance appeared to be common, as nearly half of the tested O145 strains displayed resistance to at least two different classes of antibiotics. The core virulence determinants of enterohemorrhagic E. coli were conserved in the environmental STEC O145 strains; however, there was large variation in the expression of virulence traits among the strains that were highly related genotypically, implying a trend of clonal divergence. Several cattle isolates exhibited key virulence traits comparable to those of the STEC O145 outbreak strains, emphasizing the emergence of hypervirulent strains in agricultural environments.
Ab initio IGLO study of the syn/anti dependence of the 13C NMR chemical shifts in simple amides (1993)

Abstract The syn / anti dependences of the alkyl 13 C chemical shifts provide a useful probe of stereochemistry around the amide bonds in peptides and proteins. To investigate these dependences the ab initio IGLO method was used to obtain the 13 C chemical shielding for the following series of amide molecules as models for the peptide bond: syn ‐ and anti ‐ N ‐methylformamide (NMF), cis ‐ and trans ‐ N ‐methylacetamide (NMA), N , N ‐dimethylformamide (DMF) and N , N ‐dimethylacetamide (DMA). Molecular geometries for shielding calculations are optimized ones at the HF/6–31G* level. Good correlations were observed between the calculated 13 C chemical shift results and the experimental data. The syn / anti dependence of 13 C chemical shifts around amide bonds is perdicted either with double‐ζ or triple‐ζ quality basis sets. Based on an analysis of the paramagnetic bond contributions (PBC) to the chemical shieldings, it is concluded that the syn / anti dependence of the 13 C chemical shifts in amides arises almost entirely from the PBC of the syn and anti NC bonds, and is completely analogous to the electronic origin for the cis / trans γ‐effect in hydrocarbons.
Oxygen-Transport and Solution Properties of Polylipid/HB Vesicles (ARC) (1992)

Polymerized phospholipid vesicle encapsulating Hb (polylipid/Hb vesicle) was prepared from a mixture of unsaturated phospholipid, cholesterol and unsaturated fatty acid and polymerization by gamma-ray irradiation. The average radius of resulting vesicles was 203 +/- 39 nm and concentrated Hb (30 wt%) was efficiently encapsulated. gamma-Ray polymerization proceeds theoretically at low temperature (4 degrees C). P50 and oxygen transporting efficiency were adjusted to 40 mmHg and 40%, respectively. Oncotic pressure and solution viscosity can be controlled to the same values as blood.
Electroacupuncture for Acute Ischemic Stroke: A Meta-Analysis of Randomized Controlled Trials (2015)

Electroacupuncture (EA) is an extension technique of acupuncture based on traditional acupuncture combined with modern electrotherapy. Here, we conducted a systematic review specifically to assess the effectiveness and safety of EA for acute ischemic stroke. Eight databases were searched for randomized-controlled clinical trials (RCTs) of EA for acute ischemic stroke published from inception to June 2013. Ultimately, 67 studies claimed to be RCTs. Eighteen studies with 1411 individuals were selected for the analyses, which got ≥ 4 "yes" in the domains of Cochrane risk of bias tool. The meta-analysis showed a significant effect of EA for improving Barthel Index (p < 0.00001), Fugl-Meyer Assessment (p < 0.00001), National Institutes of Health Stroke Scale (p < 0.00001), and Revised Scandinavian Stroke Scale (p < 0.00001) compared with western conventional treatments (WCTs). In an analysis of the total clinical efficacy rate, there was a significant difference between EA and WCTs (p=0.0002). Adverse effects were monitored in 6 studies, and were well tolerated in all stroke patients. According to the GRADE approach, the quality of evidence was mostly high or moderate. In conclusion, this systematic review revealed the evidence in support of the use of EA for acute ischemic stroke, although further larger sample-size and rigorously designed RCTs are required.
Adult Stem Cells (2007)

This chapter contains sections titled: Adult Stem Cells The Niche Hematopoietic Stem Cells Neural Stem Cells Epithelial Stem Cells Intestinal Stem Cells Cancer Stem Cells Summary References
<title>Polymer dynamics and fluid flow in microfabricated devices</title> (1998)

We will discuss two recent directions of our work: (1) The influence of submicron length scales on polymer dynamics, (2) Ultra-rapid mixing via sub-micron hydrodynamic focusing. (1) Polymer dynamics at sub-micron length scales. We have explored the changes in the dynamics of long polymers as the thickness of the quasi-2 dimensional space is varied from 0.09 microns to 10 microns. We will show how the thickness of this space, scaled with the persistence length of the polymer, changes the dynamics of the polymer. The consequences of this qualitative change in polymer dynamics is quite important, since it controls the elongation of the polymer at a given force field and hence the ability of he array to fractionate the polymer. (2) Mixing at the sub- micron length scale cannot be tubulent but only diffusive in nature. We will show how it is possible using hydrodynamics to produce liquid jets of width under 20 nanometers which can mix fluids in under 1 microsecond times.
Intramolecular Hydrogen Bonding Restricts Gd–Aqua‐Ligand Dynamics (2017)

Aqua ligands can undergo rapid internal rotation about the M-O bond. For magnetic resonance contrast agents, this rotation results in diminished relaxivity. Herein, we show that an intramolecular hydrogen bond to the aqua ligand can reduce this internal rotation and increase relaxivity. Molecular modeling was used to design a series of four Gd complexes capable of forming an intramolecular H-bond to the coordinated water ligand, and these complexes had anomalously high relaxivities compared to similar complexes lacking a H-bond acceptor. Molecular dynamics simulations supported the formation of a stable intramolecular H-bond, while alternative hypotheses that could explain the higher relaxivity were systematically ruled out. Intramolecular H-bonding represents a useful strategy to limit internal water rotational motion and increase relaxivity of Gd complexes.
Breaking the Silence (1995)

Public hearings are an effective way of forcing society to confront the problems facing large numbers of women. Linda Neuman reports on one such hearing designed to increase the awareness of violence against Asian women
High SNR CMOS S/H IC for multi-carrier direct RF under sampling receiver (2016)

Direct RF under sampling reception has been developed to reduce the size and the power consumption of the terrestrial wireless terminals. The system is suitable for multi-carrier operation. Some sample and hold (S/H) IC was reported to operate in high frequency or wideband operation. However the signal-noise ratio (SNR) has limitation caused by output buffer. We proposed high SNR S/H circuit with small gain ripple at the MHz to GHz frequency band for multi-carrier reception. The proposed S/H IC is designed and fabricated in 90 nm CMOS process. The fabricated IC performs improving of the output power and SNR about 23Bm and 10dB, respectively. Moreover, the maximum frequency with |S11| of less than −10dB is 11.5GHz.
Efficient Antibody Selection and Quantitation Using Microcapillary Cytometry (B209) (2007)

Abstract Optimal selection of antibodies for therapy or research utilizes information from relative affinity measurements, specificity, functional studies and antibody isotype. All of the above are further dependant on accurate quantitative levels of antibodies utilized in the experiments so that a proper comparison of clones may be performed. Guava® RapidQuant™ IgG assays are novel bead-based assays that use microcapillary cytometry to provide quantitation of mouse or human IgG. In this study, mice were immunized with human CD80 and supernatant from each resulting hybridoma was subjected to multiple analyses on the Guava EasyCyte™ platform. The antigen specificity was obtained using a cell-based Guava Express™ assay and quantitative levels of IgG in supernatant were determined using the Guava RapidQuant Mouse IgG Assay. Antibody isotype and relative affinity were also ascertained. From these analyses, top ranking clones from 455 tested were identified based on specificity and productivity data. This study demonstrates the utility of microcapillary cytometry in combination with bead-based and cell-based assays to obtain multiple layers of information in the ranking and selection of the best clones.
ChemInform Abstract: PRACTICAL ENZYMIC SYNTHESES OF RIBULOSE 1,5 BISPHOSPHATE AND RIBOSE 5‐PHOSPHATE (1981)

Abstract Die Gewinnung des für biochemische Untersuchungen wichtigen (teuren) Ribulose‐1,5‐bis‐phosphats (IV) auf 2 enzymatischen Synthesewegen sowie die Darstellung von Ribose‐S‐phosphat (VI) werden beschrieben: Das Oxidationsprodukt (II) des Glucosephosphats (I) bzw. das Ribosephosphat (VI) ‐ erhältlich aus AMP (V) oder enzymatisch aus (II) ‐ werden unter den angegebenen Bedingungen jeweils zu (IV) umgesetzt.
Computed Tomography Honeycombing Identifies a Progressive Fibrotic Phenotype with Increased Mortality across Diverse Interstitial Lung Diseases (2019)

<b>Rationale:</b> Honeycombing on chest computed tomography (CT) has been described in diverse forms of interstitial lung disease (ILD); however, its prevalence and association with mortality across the spectrum of ILD remains unclear. <b>Objective:</b> To determine the prevalence and prognostic value of CT honeycombing and characterize associated mortality patterns across diverse ILD subtypes in a multicenter cohort. <b>Methods:</b> This was an observational cohort study of adult participants with multidisciplinary or adjudicated ILD diagnosis and documentation of chest CT imaging at index diagnosis across five U.S. hospitals (one tertiary and four nontertiary medical centers). Participants were stratified based on presence or absence of CT honeycombing. Vital status was determined from review of medical records and social security death index. Transplant-free survival was analyzed using univariate and multivariable Cox regression. <b>Results:</b> The sample comprised 1,330 participants (mean age, 66.8 yr; 50% men) with 4,831 person-years of follow-up. The prevalences of CT honeycombing were 42.0%, 41.9%, 37.6%, and 28.6% in chronic hypersensitivity pneumonitis, connective tissue disease-related ILD (CTD-ILD), idiopathic pulmonary fibrosis (IPF), and unclassifiable/other ILDs, respectively. Among those with CT honeycombing, cumulative mortality hazards were similar across ILD subtypes, except for CTD-ILD, which had a lower mortality hazard. Overall, the mean survival time was shorter among those with CT honeycombing (107 mo; 95% confidence interval [CI], 92-122 mo) than those without CT honeycombing (161 mo; 95% CI, 147-174 mo). CT honeycombing was associated with an increased mortality rate (hazard ratio, 1.72; 95% CI, 1.38-2.14) even after adjustment for center, sex, age, forced vital capacity, diffusing capacity, ILD subtype, and use of immunosuppressive therapy (hazard ratio, 1.62; 95% CI, 1.29-2.02). CT honeycombing was associated with an increased mortality rate within non-IPF ILD subgroups (chronic hypersensitivity pneumonitis, CTD-ILD, and unclassifiable/other ILD). In IPF, however, mortality rates were similar between those with and without CT honeycombing. <b>Conclusions:</b> CT honeycombing is prevalent in diverse forms of ILD and uniquely identifies a progressive fibrotic ILD phenotype with a high mortality rate similar to IPF. CT honeycombing did not confer additional risk in IPF, which is already known to be a progressive fibrotic ILD phenotype regardless of the presence of CT honeycombing.
Hepatic thrombopoietin gene silencing reduces platelet count and breast cancer progression in transgenic MMTV-PyMT mice (2019)

In humans, platelet count within the normal range is required for physiological hemostasis, but, adversely, platelets also support pathological thrombosis. Moreover, by releasing growth factors, they may enhance neoplastic proliferation. We hypothesize that platelet count correlates with platelet-dependent pathologies, even within the range of hemostatic competence. Because platelet production is promoted by thrombopoietin signaling through the myeloproliferative leukemia virus oncogene (cMPL), a receptor expressed on megakaryocytes, we evaluated the feasibility of selective targeting of hepatic thrombopoietin production to test this hypothesis. We synthesized murine- and primate-specific antisense oligonucleotides (THPO-ASO) that silence hepatic thrombopoietin gene (THPO) expression without blocking extrahepatic THPO. Repeated doses of THPO-ASO were administered to mice and a baboon, causing a sustained 50% decline in plasma thrombopoietin levels and platelet count within 4 weeks in both species. To investigate whether reducing platelet count within the translationally relevant hemostatic range could alter a neoplastic process, we administered THPO-ASO to 6-week-old transgenic MMTV-PyMT mice that develop early ductal atypia that progresses into cMPL-negative fatal metastatic breast cancer within 2 to 3 months. THPO-ASO treatment increased the average time to euthanasia (primary humane endpoint) at 2 cm3 combined palpable tumor volume. Our results show that THPO-ASO reduced blood platelet count, plasma platelet factor 4, vascular endothelial growth factor, thrombopoietin levels, bone marrow megakaryocyte density, tumor growth rate, proliferation index, vascularization, platelet and macrophage content, and pulmonary metastases vs untreated controls. These findings confirm that sustained and moderate pharmacological platelet count reduction is feasible with THPO-ASO administration and can delay progression of certain platelet-dependent pathological processes within a safe hemostatic platelet count range.
A novel additive manufacturing compression overmolding process for hybrid metal polymer composite structures (2023)

Metal polymer composites combining low density, high strength composites with highly ductile and tough metals have gained traction over the last few decades as lightweight and high-performance materials for industrial applications. However, the mechanical properties are limited by the interfacial bonding strength between metals and polymers achieved through adhesives, welding, and surface treatment processes. In this paper, a novel manufacturing process combining additive manufacturing and compression molding to obtain hybrid metal polymer composites with enhanced mechanical properties is presented. Additive manufacturing enabled deposition of polymeric material with fibers in a predetermined pattern to form tailored charge or preform for compression molding. A grade 300 maraging steel triangular lattice is first fabricated using AddUp FormUp350 laser powder bed system and compression overmolded with additively manufactured long carbon fiber-reinforced polyamide-6,6 (40% wt. CF/PA66) preform. The fabricated hybrid metal polymer composites showed high stiffness and tensile strength. The stiffness and failure characteristics determined from the uniaxial tensile tests were correlated to a finite element model within 20% deviation. Fractographic analyses was performed using microscopy to investigate failure mechanisms of the hybrid structures.
Numerical Simulations of the Flow Past Crescent Cylinders for Flow Metering Purposes (2018)

Abstract The present study is devoted to the flow peoperties of a vortex shedding system behind a bluff body that has a crescent cross-section, facing downstream of the flow. The investigation is conducted numerically using a lattice Boltzmann method. As a benchmark validation, the studied system was compared to the system of vortices formed behind the classical case of a circular cylinder for the same flow configuration and dynamic conditions, while varying the Reynolds number. The flow simulations have revealed that the crescent body affected substantially the shedding mechanism with remarkable differences when compared to the classical cylindrical case. There was a clear decrease in the shedding frequency with the crescent body that is beneficial when using this system as a metering tool.
Real-time in vivo Cherenkoscopy imaging during external beam radiation therapy (2013)

Cherenkov radiation is induced when charged particles travel through dielectric media (such as biological tissue) faster than the speed of light through that medium. Detection of this radiation or excited luminescence during megavoltage external beam radiotherapy (EBRT) can allow emergence of a new approach to superficial dose estimation, functional imaging, and quality assurance for radiation therapy dosimetry. In this letter, the first in vivo Cherenkov images of a real-time Cherenkoscopy during EBRT are presented. The imaging system consisted of a time-gated intensified charge coupled device (ICCD) coupled with a commercial lens. The ICCD was synchronized to the linear accelerator to detect Cherenkov photons only during the 3.25-μs radiation bursts. Images of a tissue phantom under irradiation show that the intensity of Cherenkov emission is directly proportional to radiation dose, and images can be acquired at 4.7 frames/s with SNR>30. Cherenkoscopy was obtained from the superficial regions of a canine oral tumor during planned, Institutional Animal Care and Use Committee approved, conventional (therapeutically appropriate) EBRT irradiation. Coregistration between photography and Cherenkoscopy validated that Cherenkov photons were detected from the planned treatment region. Real-time images correctly monitored the beam field changes corresponding to the planned dynamic wedge movement, with accurate extent of overall beam field, and expected cold and hot regions.
Yellow Light Negative-index Metamaterials (2009)

A well established silver based fishnet design was further miniaturized. By studying its transmittance, reflectance, and corresponding numerical simulations, we reported a negative refractive index of −0.25 at yellow light of 580 nm.
Trigger for the occurrence of grain coarsening phenomenon of BS304S31 austenite stainless steel under small plastic strain at high temperature (2003)

Observation by optical microscopy and EBSP have made it clear that the trigger for the grain coarsening phenomenon of austenite stainless steel BS304S31 may be the stacking faults concentrating selectively in a thin layer lying just beneath the grain boundary. When macroscopic plastic strain reached 6 percent, selective concentration of stacking faults was observed. When it reached 20 percent, the distribution of stacking faults became uniform in each grain. After these specimens were heated, concentration of stacking faults disappeared, and grain coarsening occurred at the point with 6 percent strain, but no grain coarsening occurred at the point with 20 percent strain. In order to investigate this concentration of stacking faults, an attempt was made to analyze the deformation in each crystal by using image‐based FEM. The result suggested that there is a possibility that plastic strain concentrates in the vicinity of the grain boundary when the macroscopic plastic strain is small.
Supplementary Figure Legend from Dual mTORC1/2 and HER2 Blockade Results in Antitumor Activity in Preclinical Models of Breast Cancer Resistant to Anti-HER2 Therapy (2023)

&lt;p&gt;PDF file, 85KB.&lt;/p&gt;