gebhart/patrepeval huggingface dataset:
The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives (2020)

African swine fever virus (ASFV) is a highly contagious nucleocytoplasmic large DNA virus (NCLDV) that causes nearly 100% mortality in swine. The development of effective vaccines and drugs against this virus is urgently needed. pA104R, an ASFV-derived histone-like protein, shares sequence and functional similarity with bacterial HU/IHF family members and is essential for viral replication. Herein, we solved the crystal structures of pA104R in its apo state as well as in complex with DNA. Apo-pA104R forms a homodimer and folds into an architecture conserved in bacterial heat-unstable nucleoid proteins/integration host factors (HUs/IHFs). The pA104R-DNA complex structure, however, uncovers that pA104R has a DNA binding pattern distinct from its bacterial homologs, that is, the β-ribbon arms of pA104R stabilize DNA binding by contacting the major groove instead of the minor groove. Mutations of the basic residues at the base region of the β-strand DNA binding region (BDR), rather than those in the β-ribbon arms, completely abolished DNA binding, highlighting the major role of the BDR base in DNA binding. An overall DNA bending angle of 93.8° is observed in crystal packing of the pA104R-DNA complex structure, which is close to the DNA bending angle in the HU-DNA complex. Stilbene derivatives SD1 and SD4 were shown to disrupt the binding between pA104R and DNA and inhibit the replication of ASFV in primary porcine alveolar macrophages. Collectively, these results reveal the structural basis of pA104R binding to DNA highlighting the importance of the pA104R-DNA interaction in the ASFV replication cycle and provide inhibitor leads for ASFV chemotherapy.
Controllable fabrication of bent near-field optical fiber probes by electric arc heating (1998)

We describe the construction of a high voltage electric arc puller for controllable fabrication of bent near-field optical fiber probes. Various probes with bent angles ranging from 30° to 75° and bent lengths between 600 and 900 μm were successfully produced. The tip diameters achieved are between 100 and 200 nm. These bent type probes can be made into cantilevered probes that can be used for any dynamic mode atomic force microscope, and make the construction of a scanning near-field optical microscope easily attainable.
Molecular imaging: a FLIM-based FRET assay to identify novel protein-protein interactions between Cx43 and Cdo during myoblast differentiation (2010)

Previous studies of our group have shown that connexin43 (Cx43), besides forming gap junction channels, serves as a signaling center by binding to proteins of the actin cytoskeleton during skeletal myoblast differentiation. There is also evidence that Cdo (CAM-related/down regulated by oncogenes), a member of the Ig/FNIII family of cell surface receptors, exerts its promyogenic effects acting as a component of multiprotein complexes containing cytoskeletal components. Within these signaling platform, the interaction of Cdo and the cell-cell adhesion molecule N-cadherin is essential for the activation p38MAPK and the induction of myogenesis. Of interest, cadherins are also closely associated with Cx43 at sites of cell-to-cell contacts to ensure gap junction intercellular trafficking and functional integration. On these bases, in the present study we searched for a possible interaction of Cx43 and Cdo in differentiating C2C12 cells, using either optical methods such as confocal microscopy, fluorescence spectral analysis, FLIM-FRET (Fluorescence Lifetime Imaging -Fluorescence Resonance Energy Transfer) techniques and co-immunoprecipitation experiments. It was found that Cx43 and Cdo expression significantly correlated with each other during myoblast differentiation; both molecules reached the highest expression levels at 24 h and gradually disappeared with the ongoing of differentiation. Interestingly, stimulation with S1P, a bioactive lipid and a potent stimulator of myogenesis greatly potentiated the expression of Cx43 and Cdo in differentiating C2C12 cells. Moreover, Cx43 and Cdo co-localized at the plasma membrane and generated, especially in the cells stimulated with S1P, a strong FRET signal, as judged by either spectral and FLIM analyses, consistent with a physical interaction between the two proteins. These results matched the immunoprecipitation data. In conclusion, these results provide the first evidence for a direct interaction between Cx43 and Cdo in differentiating myoblasts and raise the intriguing hypothesis that this interaction may be a key step in the gap junction independent Cx43-mediated signaling.
Neurovascular injury associated non-apoptotic endothelial caspase-9 and astroglial caspase-9 mediate inflammation and contrast sensitivity decline (2022)

Retinal neurovascular injuries are a leading cause of vision loss in young adults presenting unmet therapeutic needs. Neurovascular injuries damage homeostatic communication between endothelial, pericyte, glial, and neuronal cells through signaling pathways that remain to be established. To understand the mechanisms that contribute to neuronal death, we use a mouse model of retinal vein occlusion (RVO). Using this model, we previously discovered that after vascular damage, there was non-apoptotic activation of endothelial caspase-9 (EC Casp9); knock-out of EC Casp9 led to a decrease in retinal edema, capillary ischemia, and neuronal death. In this study, we aimed to explore the role of EC Casp9 in vision loss and inflammation. We found that EC Casp9 is implicated in contrast sensitivity decline, induction of inflammatory cytokines, and glial reactivity. One of the noted glial changes was increased levels of astroglial cl-caspase-6, which we found to be activated cell intrinsically by astroglial caspase-9 (Astro Casp9). Lastly, we discovered that Astro Casp9 contributes to capillary ischemia and contrast sensitivity decline after RVO (P-RVO). These findings reveal specific endothelial and astroglial non-apoptotic caspase-9 roles in inflammation and neurovascular injury respectively; and concomitant relevancy to contrast sensitivity decline.
Machine learning approach for skill evaluation in robotic-assisted surgery (2016)

Evaluating surgeon skill has predominantly been a subjective task. Development of objective methods for surgical skill assessment are of increased interest. Recently, with technological advances such as robotic-assisted minimally invasive surgery (RMIS), new opportunities for objective and automated assessment frameworks have arisen. In this paper, we applied machine learning methods to automatically evaluate performance of the surgeon in RMIS. Six important movement features were used in the evaluation including completion time, path length, depth perception, speed, smoothness and curvature. Different classification methods applied to discriminate expert and novice surgeons. We test our method on real surgical data for suturing task and compare the classification result with the ground truth data (obtained by manual labeling). The experimental results show that the proposed framework can classify surgical skill level with relatively high accuracy of 85.7%. This study demonstrates the ability of machine learning methods to automatically classify expert and novice surgeons using movement features for different RMIS tasks. Due to the simplicity and generalizability of the introduced classification method, it is easy to implement in existing trainers.
Pharmacological and molecular activity of methanolic extract of Cichorium intybus Linn seeds (2015)

The oxidative damage of cellular tissue by reacting active species causes various human diseases like cardiovascular disease, cancer, aging and nephropathy. The antioxidant supplements obtained from plants are useful to cure the oxidative damage in cells. Recently, attention has focused on phytochemicals as new sources of natural antioxidant agent. The plant Cichorium intybus L., commonly denoted as chicory which belongs to family Asterac eae and geographically found in Asia and Europe. Chicory have medicinally active constituent like flavonoids, saponins tannins, alkaloids, inulin, sesquiterpene lactones, coumarins, vitamins, chlorophyll pigments and unsaturated sterols. Hence, in the present study methanolic extract of Cichorium intybus Linn seeds was evaluated for antioxidant invitro method and molecular activity using RAPD electrophoresis methods
Long-range Ordering in Water–Halide Ion Interactions: A Database Study (2004)

Abstract A detailed analysis of water–halide ion interactions using the Cambridge Structural Database reveals predominant cyclic hydrogen-bonded (H2O·X−)2 clusters and isostructural tapes of 4,5,6-membered rings leading to channel hydrates.
SHAARP: An Open-Source Package for Analytical and Numerical Modeling of Optical Second Harmonic Generation in Anisotropic Crystals (2022)

Optical second harmonic generation is a second-order nonlinear process that combines two photons of a given frequency into a third photon at twice the frequency. Due to the symmetry constraints, it is widely used as a sensitive probe to detect broken inversion symmetry and local polar order. Analytical modeling of the electric-dipole SHG response is essential to extract fundamental properties of materials from experiments. However, complexity builds up dramatically in the analytical model when the probed crystal is of a low bulk crystal symmetry, with a low-symmetry surface orientation, exhibits absorption and dispersion, and consists of multiple interfaces. As a result, there is a largely uneven landscape in the literature on the SHG modeling of new materials, involving numerous approximations and a wide range of (in)accuracies, leading to a rather scattered dataset of reported SHG nonlinear susceptibility. Towards streamlining the reliability and accuracy of this process, we have developed an open-source package called the Second Harmonic Analysis of Anisotropic Rotational Polarimetry (SHAARP) which derives analytical solutions and performs numerical simulations of reflection SHG from a single interface for homogeneous crystals. Five key generalizations in SHG modeling are implemented, including all crystal symmetries down to triclinic, any crystal orientation, complex dielectric tensor (refractive indices) with frequency dispersion, and general polarization states of the light. SHAARP enables accurate anisotropic modeling of SHG response for a broad range of materials systems. The method is extendible to multiple interfaces. The code is free to download from https://github.com/Rui-Zu/SHAARP
ANÁLISE DAS MANIFESTAÇÕES PATOLÓGICAS PRESENTES NA PONTE SITUADA SOBRE O RIO TOCANTINS EM PORTO NACIONAL-TO (2020)

cinco anos aps a sua inaugurao vem apresentando problemas, que foram agravados devido ausncia de manuteno, comprometendo a sua durabilidade e vida til,
The General Transfer Matrix for Networks with Open-Circuited or Short-Circuited Stubs (1969)

Analysis and synthesis of distributed transmission line networks with open or short circuited shunts or series stubs, describing composite transfer matrices
Identification of an RNA Hairpin in Poliovirus RNA That Serves as the Primary Template in the In Vitro Uridylylation of VPg (2000)

The first step in the replication of the plus-stranded poliovirus RNA is the synthesis of a complementary minus strand. This process is initiated by the covalent attachment of UMP to the terminal protein VPg, yielding VPgpU and VPgpUpU. We have previously shown that these products can be made in vitro in a reaction that requires only synthetic VPg, UTP, poly(A), purified poliovirus RNA polymerase 3D(pol), and Mg(2+) (A. V. Paul, J. H. van Boom, D. Filippov, and E. Wimmer, Nature 393:280-284, 1998). Since such a poly(A)-dependent process cannot confer sufficient specificity to poliovirus RNA replication, we have developed a new assay to search for a viral RNA template in conjunction with viral or cellular factors that could provide this function. We have now discovered a small RNA hairpin in the coding region of protein 2C as the site in PV1(M) RNA that is used as the primary template for the in vitro uridylylation of VPg. This hairpin has recently been described in poliovirus RNA as being an essential structure for the initiation of minus strand RNA synthesis (I. Goodfellow, Y. Chaudhry, A. Richardson, J. Meredith, J. W. Almond, W. Barclay, and D. J. Evans, J. Virol. 74:4590-4600, 2000). The uridylylation reaction either with transcripts of cre(2C) RNA or with full-length PV1(M) RNA as the template is strongly stimulated by the addition of purified viral protein 3CD(pro). Deletion of the cre(2C) RNA sequences from minigenomes eliminates their ability to serve as template in the reaction. A similar signal in the coding region of VP1 in HRV14 RNA (K. L. McKnight and S. M. Lemon, RNA 4:1569-1584, 1998) and the poliovirus cre(2C) can be functionally exchanged in the assay. The mechanism by which the VPgpUpU precursor, made specifically on the cre(2C) template, might be transferred to the site where it serves as primer for poliovirus RNA synthesis, remains to be determined.
Microstructural characterization of α-GaN films grown on sapphire by organometallic vapor phase epitaxy (1995)

Microstructure of α-GaN films grown by organometallic vapor phase epitaxy on sapphire substrates using low temperature AlN (or GaN) buffer layers has been studied by transmission electron microscopy. The defects which penetrate the GaN films are predominantly perfect edge dislocations with Burgers vectors of the 1/3〈112̄0〉 type, lying along the [0001] growth direction. The main sources of threading dislocations are the low angle grain boundaries, formed during coalescence of islands at the initial stages of GaN growth. The grain sizes range from 50 to 500 nm, with in-plane misorientations of less than 3°. The nature of these threading dislocations suggests that the defect density would not likely decrease appreciably at increasing film thickness, and the suppression of these dislocations could be more difficult.
Interference-constrained wireless coverage in a protocol model (2006)

We present an O(nlogn) algorithm to compute the coverage map of a given set of transmitters under interference constraints. That is, we compute the set of points that lie within the transmission range of one transmitter and lie outside the interference range of every other transmitter. To our knowledge, there is no existing satisfactory algorithm for this purpose. We assume that the transmission and interference ranges of each transmitter are circular disks.We show that for an appropriate choice of 'distance measure', coverage at each point can be computed by considering only certain 'proximate' transmitters. Hence, we partition the plane into proximity regions and the coverage in these proximity regions is computed considering only proximate transmitters. We use an extension of Voronoi diagrams, called 'Power' diagrams, to represent the proximity regions.
Findings, Gaps, and Future Direction for Research in Nonpharmaceutical Interventions for Pandemic Influenza (2010)

Charles J. Vukotich, Jr., Rebecca M. Coulborn, Tomas J. Aragon, Michael G. Baker, Barri B. Burrus, Allison E. Aiello, Benjamin J. Cowling, Alasdair Duncan, Wayne Enanoria, M. Patricia Fabian, Yu-hui Ferng, Elaine L. Larson, Gabriel M. Leung, Howard Markel, Donald K. Milton, Arnold S. Monto, Stephen S. Morse, J. Alexander Navarro, Sarah Y. Park, Patricia Priest, Samuel Stebbins, Alexandra M. Stern, Monica Uddin, and Scott F. Wetterhall Author affiliations: University of Pittsburgh, Pennsylvania, USA (C.J. Vukotich, S. Stebbins); University of Michigan, Ann Arbor, Michigan, USA (R.M. Coulborn, A.E. Aiello, H. Markel, A.S. Monto, J.A. Navarro, A.M. Stern, M. Uddin); University of California, Berkeley, California, USA (T.J. Aragon, W. Enanoria); University of Otago, Dunedin, New Zealand (M.G. Baker, A. Duncan, P. Priest); RTI International, Research Triangle Park, North Carolina, USA (B.B. Burrus, S.F. Wetterhall); University of Hong Kong, Hong Kong, People's Republic of China (B.J. Cowling, G. M. Leung); University of Massachusetts, Lowell, Massachusetts, USA (M.P. Fabian); Columbia University, New York, New York, USA (Y. Ferng, E.L. Larson, S.S. Morse); University of Maryland, College Park, Maryland, USA (D.K. Milton); and Hawaii Department of Health, Honolulu, Hawaii (S.Y. Park)
The radial distribution of magnetic helicity in the solar convective zone: observations and dynamo theory (2005)

We continue our attempt to connect observational data on current helicity in solar active regions with solar dynamo models. In addition to our previous results about temporal and latitudinal distributions of current helicity, we argue that some information concerning the radial profile of the current helicity averaged over time, and latitude can be extracted from the available observations. The main feature of this distribution can be presented as follows. Both shallow and deep active regions demonstrate a clear dominance of one sign of current helicity in a given hemisphere during the whole cycle. Broadly speaking, current helicity has opposite polarities in the Northern and Southern hemispheres, although there are some active regions that violate this polarity rule. The relative number of active regions violating the polarity rule is significantly higher for deeper active regions. A separation of active regions into ‘shallow’, ‘middle’ and ‘deep’ is made by comparing their rotation rate and the helioseismic rotation law. We use a version of Parker's dynamo model in two spatial dimensions, which employs a non-linearity based on magnetic helicity conservation arguments. The predictions of this model about the radial distribution of solar current helicity appear to be in remarkable agreement with the available observational data; in particular the relative volume occupied by the current helicity of ‘wrong’ sign grows significantly with the depth.
Thermodynamic aspects of the vitrification of toluene, and xylene isomers, and the fragility of liquid hydrocarbons (1990)

The three xylenes, 1,2-, 1,3-, and 1,4-dimethyl benzene, provide a well-characterized family of isomeric molecules within which the melting points vary greatly while fluid-state properties such as boiling points and viscosities remain very similar. Because all pure isomers crystallize rapidly on cooling, their behavior at the low-temperature end of the liquid state, i.e., near the glass transition, has not been studied. We report here differential scanning calorimetry studies of phase relations for the three mixed isomer systems, and identify composition regions in which emulsified and also bulk mixtures can be vitrified at ordinary cooling rates. For one of the latter, 70% m-xylene+ 30% o-xylene by volume, we determine the change in heat capacity through the glass transition. On the assumption that this is the same for pure m-xylene, we assess the Kauzmann limit on liquid behavior, TK, for m-xylene to fall at 104.6 K, Tg/TK to be 1.20, and the excess entropy at Tg to be 15.6 J/mol K or 30.5% of the entropy of fusion. Equivalent data are obtained for the better-known glass former toluene, for which we find Tg/TK=1.16. Comparisons of these results are made with literature data for some saturated analogs. From these comparisons emerges the simple rule that the excess heat capacity of supercooled liquid over crystal can be described as a hyperbolic function of temperature, the one parameter of which varies linearly with the carbon number of the molecule. The plot passes through the origin, and has a greater slope for aromatic than for paraffinic molecules. This is correlated both with the greater ‘‘fragility’’ of the aromatic liquids assessed from viscosity-temperature relations normalized by the calorimetric Tg, and with a simple ‘‘liquid range’’ index Tb/Tg, where Tb is the boiling point.
Software defined coherent lidar (SD-Cl) architecture (2017)

In recent years, thanks to the innovation in optical and electro-optical components, space based light detection and ranging (Lidar) systems are having great success, as a considerable alternative to passive radiometers or microwave sensors [1]. One of the most important applications, for space based Lidars, is the measure of target's distance and its relative properties as e.g., topography, surface's roughness and reflectivity, gravity and mass, that provide useful information for surface mapping, as well as semi-autonomous landing functionalities on lowgravity bodies (moons and asteroids). These kind of systems are often called Lidar altimeters or laser rangefinders.
Extremely highly isospecific polymerization of olefins using solvay‐type TiCl<sub>3</sub> and Cp<sub>2</sub>TiMe<sub>2</sub> as catalyst (1988)

Abstract Polymerizations of various olefins (ethylene, propene, 1‐butene, 4‐methyl‐1‐pentene,1‐hexene, and 1‐octene) were carried out using the Solvay‐type TiCl 3 catalyst combined with Cp 2 TiMe 2 . The polymers produced were characterized by DSC, solvent fractionation, GPC, and 13 C NMR. It was found that the present catalyst gives linear polyethylene without ethyl branches and extremely highly isotactic poly(α‐olefins) containing very few steric defects. The catalyst seems to be most isospecific among the Ziegler‐Natta catalysts reported so far.
ChemInform Abstract: Preparation of Potassium Azidoaryltrifluoroborates and Their Cross‐Coupling with Aryl Halides. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
FDG-PET as a Potential Tool for Selecting Patients with Advanced Non–Small Cell Lung Cancer Who May Be Spared Maintenance Therapy after First-Line Chemotherapy (2011)

Fractional decrease in SUVmax of the main lesion after completion of 4 cycles of chemotherapy may discriminate patients with TTP ≥8 weeks and predict TTP and OS in patients with advanced NSCLC.
A FLUSH-MOUNT SENSOR PACKAGE FOR A MEMS PIEZOELECTRIC MICROPHONE WITH THROUGH-SILICON-VIAS FOR AIRCRAFT FUSELAGE ARRAYS (2016)

This paper presents the design, fabrication and preliminary testing of a flush-mount sensor die and associated package for an aluminum nitride (AlN) based piezoelectric MEMS microphone for aircraft fuselage arrays. The optimal microphone design is determined using composite plate theory in combination with lumped element modeling. Through-silicon-vias are incorporated into the fabrication of the sensor thus eliminating front-side wire bonds and enabling an overall flush surface for the packaged sensor that minimizes flow disturbance.
ChemInform Abstract: Electroless Etching of ZnSe in Aqueous Ferricyanide Solutions. An Electrochemical Study. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.