gebhart/patrepeval huggingface dataset:
Accurate identification of centromere locations in yeast genomes using Hi-C (2015)

Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation capture assay, Hi-C, has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromeres' tendency to cluster in three-dimensional space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use Centurion to infer centromere locations in 14 yeast species. Across all microbes that we consider, Centurion predicts 89% of centromeres within 5 kb of their known locations. We also demonstrate the robustness of the approach in datasets with low sequencing depth. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results show that Centurion can be used for centromere identification for diverse species of yeast and possibly other microorganisms.
On Asymptotic Behaviors of Graph CNNs from Dynamical Systems Perspective (2019)

Graph Neural Networks (graph NNs) are a promising deep learning approach for analyzing graph-structured data. However, it is known that they do not improve (or sometimes worsen) their predictive performance as we pile up many layers and add non-lineality. To tackle this problem, we investigate the expressive power of graph NNs via their asymptotic behaviors as the layer size tends to infinity. Our strategy is to generalize the forward propagation of a Graph Convolutional Network (GCN), which is a popular graph NN variant, as a specific dynamical system. In the case of a GCN, we show that when its weights satisfy the conditions determined by the spectra of the (augmented) normalized Laplacian, its output exponentially approaches the set of signals that carry of the connected components and node degrees only for distinguishing nodes. Our theory enables us to relate the expressive power of GCNs with the topological of the underlying graphs inherent in the graph spectra. To demonstrate this, we characterize the asymptotic behavior of GCNs on the Erdős -- Renyi graph. We show that when the Erdős -- Renyi graph is sufficiently dense and large, a broad range of GCNs on it suffers from the information loss in the limit of infinite layers with high probability. Based on the theory, we provide a principled guideline for weight normalization of graph NNs. We experimentally confirm that the proposed weight scaling enhances the predictive performance of GCNs in real data. Code is available at this https URL.
Effect of Ternary Alloying Elements on Microstructure and Mechanical Property of Nb-Si Based Refractory Intermetallic Alloy (2005)

Microstructure and mechanical property at room temperature and at 1773 K of Nb-Si based refractory intermetallic alloys were investigated in terms of compression and fracture toughness test. Mo and V were chosen as ternary alloying elements because of their high melting points, atomic sizes smaller than Nb. Both ternary alloying elements were found to have a significant role in modifying the microstructure from dispersed structure to eutectic-like structure in Nb solid solution/Nb5Si3 intermetallic composites. The 0.2% offset yield strength at room temperature increased with increasing content of ternary elements in Nb solid solution and volume fraction of Nb5Si3. At 1773 K, Mo addition has a positive role in increasing the yield strength. On the other hand, V addition has a role in decreasing the yield strength. The fracture toughness of ternary alloys was superior to binary alloys. Details will be discussed in correlation with ternary alloying, volume fraction of constituent phase, and the microstructure.
Bioinspired polyimide film with fire retardant and gas barrier properties by gravity-induced deposition of montmorillonite (2023)

Flame retardants play a crucial role in improving the flame retardant properties of polymer materials. In recent years, environmental problems caused by flame retardants have attracted widespread attention. It is urgent to use green and effective methods to prepare flame retardant polymers. Bioinspired nanocomposites with layered structures seem to provide an effective idea, but in general, the hydrophilic properties of their raw materials limit their applications in certain fields. Here, we prepared biomimetic composites with a layered “brick-and-mortar” structure by gravity-induced deposition using polyimide as the polymer matrix and montmorillonite (MMT) as the filler. The well-arranged structures of the composite material could isolate oxygen and prevent combustible gases from escaping. The gas barrier performance has been greatly improved, in which the water vapor transmission rate (WVTR) and the oxygen transmission rate (OTR) decreased by 99.18% and three orders of magnitude, respectively. The flame retardant performance has also been improved, and its limiting oxygen index can reach 67.9%. More importantly, the polyimide matrix can be converted to water-insoluble by thermal imidization of water-soluble poly (amic acid) salt precursors, which endows the composites with low hygroscopicity. Such coating containing MMT can protect against polyurethane (PU) foam from fire. During the conical calorimetric test, the coated sample self-extinguished, and the peak heat release rate, total heat release, total smoke production is significantly decreased by 53.39%, 40.69%, and 53.03%, respectively. Taking advantage of these properties, this work utilizes a facile method to prepare biomimetic composites with low moisture absorption, excellent gas barrier properties, and flame retardancy, which have great application potential.
Visualizing Collagen Network within Human and Rhesus Monkey Vocal Folds Using Polarized Light Microscopy (2013)

The differences between the collagen networks in human and rhesus monkey vocal folds provide a morphological basis for differences in viscoelastic properties between species.
ChemInform Abstract: Novel Rearrangements of Enynes Catalyzed by PtCl<sub>2</sub>. (2000)

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.
Broadband omnidirectional antireflection coatings optimized by genetic algorithm (2009)

An optimized graded-refractive-index (GRIN) antireflection (AR) coating with broadband and omnidirectional characteristics--as desired for solar cell applications--designed by a genetic algorithm is presented. The optimized three-layer GRIN AR coating consists of a dense TiO2 and two nanoporous SiO2 layers fabricated using oblique-angle deposition. The normal incidence reflectance of the three-layer GRIN AR coating averaged between 400 and 700 nm is 3.9%, which is 37% lower than that of a conventional single-layer Si3N4 coating. Furthermore, measured reflection over the 410-740 nm range and wide incident angles 40 degrees -80 degrees is reduced by 73% in comparison with the single-layer Si3N4 coating, clearly showing enhanced omnidirectionality and broadband characteristics of the optimized three-layer GRIN AR coating.
Smart Three Axis Compliant (STAC) Interconnect: An Ultra-High Density MEMS Based Interconnect for Wafer-Level Ultra-Thin Die (2005)

This paper described a novel smart three axis compliant (STAC) interconnect targeted to revolutionize chip-to-chip and chip-to-board high-density 3D integration for ultra-thin Si dies (les75mum) at the wafer level. The STAC interconnect is a three dimensionally compliant interconnect which allows stacked ultra-thin chips to move or flex freely during operation with negligible stress imposed on the die. The paper showed that these interconnects could accommodate mismatches of board or package coefficient of thermal expansion (CTE) from chip CTE. STAC interconnects were fabricated using MEMS technologies to support super-fine-pitch (ap20mum pitch) interconnection. These interconnects are batch processed and die containing them can be stacked either at the wafer-level or at the die-level
O-glycans direct selectin ligands to lipid rafts on leukocytes (2015)

Palmitoylated cysteines typically target transmembrane proteins to domains enriched in cholesterol and sphingolipids (lipid rafts). P-selectin glycoprotein ligand-1 (PSGL-1), CD43, and CD44 are O-glycosylated proteins on leukocytes that associate with lipid rafts. During inflammation, they transduce signals by engaging selectins as leukocytes roll in venules, and they move to the raft-enriched uropods of polarized cells upon chemokine stimulation. It is not known how these glycoproteins associate with lipid rafts or whether this association is required for signaling or for translocation to uropods. Here, we found that loss of core 1-derived O-glycans in murine C1galt1(-/-) neutrophils blocked raft targeting of PSGL-1, CD43, and CD44, but not of other glycosylated proteins, as measured by resistance to solubilization in nonionic detergent and by copatching with a raft-resident sphingolipid on intact cells. Neuraminidase removal of sialic acids from wild-type neutrophils also blocked raft targeting. C1galt1(-/-) neutrophils or neuraminidase-treated neutrophils failed to activate tyrosine kinases when plated on immobilized anti-PSGL-1 or anti-CD44 F(ab')2. Furthermore, C1galt1(-/-) neutrophils incubated with anti-PSGL-1 F(ab')2 did not generate microparticles. In marked contrast, PSGL-1, CD43, and CD44 moved normally to the uropods of chemokine-stimulated C1galt1(-/-) neutrophils. These data define a role for core 1-derived O-glycans and terminal sialic acids in targeting glycoprotein ligands for selectins to lipid rafts of leukocytes. Preassociation of these glycoproteins with rafts is required for signaling but not for movement to uropods.
Holographic-Based mmW-Wideband Bidirectional Frequency Scanning Leaky Wave Antenna (2020)

Utilizing the holography theory, a bidirectional wideband leaky wave antenna in the millimetre wave (mmW) band is presented. The antenna includes a printed pattern of continuous metallic strips on an Alumina 99.5% sheet, and a surface wave launcher (SWL) to produce the initial reference waves on the substrate. To achieve a bidirectional radiation pattern, the fundamental TE mode is excited by applying a Vivaldi antenna (as the SWL). The proposed holographic-based leaky wave antenna (HLWA) is fabricated and tested and the measured results are aligned with the simulated ones. The antenna has 22.6% fractional bandwidth with respect to the central frequency of 30 GHz. The interference pattern is designed to generate a 15 deg backward tilted bidirectional radiation pattern with respect to the normal of the hologram sheet. The frequency scanning property of the designed HLWA is also investigated.
Proteomes of Residual Tumors in Curcumin-Treated Rats Reveal Changes in Microenvironment/Malignant Cell Crosstalk in a Highly Invasive Model of Mesothelioma (2022)

Curcumin exhibits both immunomodulatory properties and anticarcinogenic effects which have been investigated in different experimental tumor models and cancer types. Its interactions with multiple signaling pathways have been documented through proteomic studies on malignant cells in culture; however, in vivo approaches are scarce. In this study, we used a rat model of highly invasive peritoneal mesothelioma to analyze the residual tumor proteomes of curcumin-treated rats in comparison with untreated tumor-bearing rats (G1) and provide insights into the modifications in the tumor microenvironment/malignant cell crosstalk. The cross-comparing analyses of the histological sections of residual tumors from two groups of rats given curcumin twice on days 21 and 26 after the tumor challenge (G2) or four times on days 7, 9, 11 and 14 (G3), in comparison with G1, identified a common increase in caveolin-1 which linked with significant abundance changes affecting 115 other proteins. The comparison of G3 vs. G2 revealed additional features for 65 main proteins, including an increase in histidine-rich glycoprotein and highly significant abundance changes for 22 other proteins regulating the tumor microenvironment, linked with the presence of numerous activated T cells. These results highlight new features in the multiple actions of curcumin on tumor microenvironment components and cancer cell invasiveness.
Effect of die temperature on the flow of polymer melts. Part I: Flow inside the die (1987)

Abstract The effect of die wall temperature on the flow of polymer melts in circular capillary dies was studied. At constant flow rates, it was found that die wall temperature had a greater effect on the pressure drop than melt temperature. A capillary die with two circular channels with different diameters was designed to simulate the profile extrusion. Changes of wall temperature varied the flow rate ratio between the two channels. An implicit finite difference method was used to simulate the velocity and temperature profiles inside the die. Values predicted by this model matched well with experimental data for both dies.
Improving the performance of strained InGaAs/AlGaAs single quantum well lasers (1990)

By adjusting the carrier confining structure and the optical confining structure of strained InGaAs/AlGaAs single quantum well (QW) lasers, an improvement in performance has been obtained. First, the influence of optical confinement was examined by comparing two graded-index confining structures. For InxGa1−xAs QWs with either x=0.20 or x=0.25, lasers with greater optical confinement factor had improved performance, with both lower threshold (180 A/cm2 for x=0.20) and higher characteristic temperature (250 K for x=0.20), despite their reduced carrier confining potentials. Second, experiments on graded-composition quantum wells show that thin step-grading layers result in improved performance. In this structure, where the QW has x=0.35, and the step layers have x=0.15, the optimum step thickness is 30–40 Å. Thicker step layers appear to create too much strain, degrading the laser operation. These results indicate that step grading of strained QWs produces active region interfaces with lower defect density, and that step grading is especially useful in improving the performance of long-wavelength, highly strained InGaAs/AlGaAs QW lasers.
EFFECTS OF SILICA MODIFICATION ON THE STRUCTURE AND CRACKING PROPERTIES OF INDUSTRIAL ALUMINA MATERIALS (2010)

Three industrial alumina materials were modified by silica through hydrolysis of TEOS and activation of alumina under acid conditions.The structural properties of silica-modified alumina materials were characterized in detail by XRD,XRF,XPS,BET,FT-IR,NH3-TPD,and the catalytic cracking evaluations were proceeded on a microactivity reactor.The results revealed that the relative crystallinity of the alumina materials decreased after silica-modification,and Si—O—Al could be formed but the Si/Al molar ratio of the surface was higher than that of the body in the silica-modified alumina materials,which possessed both Lewis acid and Brnsted acid as well as high total acid content.The silica-modification improved the hydrothermal stabilities of alumina materials.The catalytic cracking activities of catalysts with the silica-modified alumina as the additive component,especially,for heavy oil conversion could be dramatically improved.
Grain Growth and Texture Evolution in Thin Films (1996)

Microstructural and texture evolution during grain growth in polycrystalline thin films was investigated. Grain growth in thin films is a coarsening process driven by the reduction of grain boundary energy, surface energies, and strain energy density. Because crystal properties can be anisotropic, grain growth in thin films is an orientation selective process. Surface and interfacial energy minimization or reduction favors the growth of grains with low combined surface and interfacial free energy. For the films and substrates investigated in this thesis, surface and interfacial energy promotes the growth of (111)-textured grains. Thin films on thick substrates are usually subjected to a non-zero state of strain, arising from differential thermal expansion between the film and the substrate, from densification and from intrinsic strains. For elastically deformed fcc metal films, strain energy density promotes the growth of (001)-textured grains. In plastically deformed films, strain energy density can favor the growth of (011)-textured grains; this results from the orientation dependence of the yield stress of grains in thin films. (111) grains are predicted to maximize the yield stress, and (011) grains are predicted to have low yield stress. An analytic model for texture evolution during grain growth in thin films can be developed by equating the magnitudes of the orientation-dependent driving forces, for pairs of orientations. The
Effects of multipath and base-station antenna arrays on uplink capacity of cellular CDMA (2002)

We evaluate the uplink capacity of a DS-CDMA cellular system using DPSK modulation with antenna array at base-station. A 2D-RAKE receiver structure with predetection equal gain combining is used for demodulation. We study both the outage and blocking probabilities of the system as a function of the cell loading and the number of array elements. Assuming perfect instantaneous power control and considering the effects of shadowing, multipath fading, path loss, and voice activity, we evaluate the system capacity in terms of the number of users per cell. Simulation results are also presented.
A Novel Approach for the Preparation of AgBr Nanoparticles from Their Bulk Solid Precursor Using CTAB Microemulsions (2006)

Microemulsions are suitable reaction media to prepare a wide variety of nanoparticles and provide control over their sizes. However, as typically used, microemulsions limit rates of rapid reactions and suffer from low reactant solubilization capacity. This work presents a new application of a novel approach aimed at minimizing these limitations. This approach, which was previously applied for AgCl nanoparticle preparation, involves solubilization of a bulk silver halide in the form of higher halides, by means of reaction with the surfactant counterion of a microemulsion, and the reprecipitation of silver halide nanoparticles in the water pools of individual reverse micelles. CTAB microemulsions were employed because they possess a reactive counterion and are known to have a high solubilization capacity for ionic reactants. Despite their high solubilization capacity, CTAB microemulsions achieved lower nanoparticles uptake (molar concentration of the colloidal nanoparticles) for the same surfactant concentration when compared to our previous study. The effect of the following variables on the nanoparticle uptake and the particle size was investigated: (1) operation variables, including rate of mixing and temperature; and (2) microemulsion variables, including CTAB and n-butanol concentrations, and water-to-surfactant mole ratio, R. These variables provide a comprehensive test to the proposed mechanism and expose the role of the surfactant layer rigidity. The nanoparticle uptake increased as the rate of mixing, temperature, and CTAB concentration increased, and decreased as n-butanol concentration and R increased. High n-butanol concentration and R values reduced the effective surfactant concentration and contributed to less surfactant layer rigidity and to particle aggregation.
Frequency of truly cryptic subtelomere abnormalities – a study of 534 patients and literature review (2005)

Frequency of truly cryptic subtelomere abnormalities - a study of 534 patients and literature review. Unbalanced subtelomere chromosome rearrangements are a significant cause of mental retardation with approximately 5% of over 3000 affected individuals tested worldwide having a chromosome rearrangement of this type. Many of these abnormalities are detectable using routine karyotyping at the 550 band level and therefore are not considered to be cryptic. The frequency of truly cryptic subtelomere abnormality should be less than 5% but has not been established. In this study, we defined 'cryptic abnormality' as one not detectable at the 550 band level on routine karyotyping. Using this as one of the selection criteria, we have studied 534 individuals with mental retardation/ developmental delay (MR/DD) and referred for subtelomere study by clinical geneticists. We have identified seven cases with cryptic subtelomere abnormalities. The clinical features of the seven abnormal cases are summarized. Literature review identified five publications on the identification of subtelomere abnormalities which used similar recruitment criteria: (a) normal karyotype at the 550 band level and (b) subjects were selected for subtelomere studies. Combining the data from these studies with those of the current study, 1154 patients were tested and 30 subtelomere abnormalities were identified. We estimate the frequency of truly cryptic subtelomere abnormality to be approximately 2.6% (30/1154) in children with MR/DD who are referred for subtelomere study.
Molecular evolution of enzymes involved in the arachidonic acid cascade (1992)

The metabolic pathway called the arachidonic acid cascade produces a wide range of eicosanoids, such as prostaglandins, thromboxanes and leukotrienes with potent biological activities. Recombinant DNA techniques have made it possible to determine the nucleotide sequences of cDNAs and/or genomic structures for the enzymes involved in the pathway. Sequence comparison analyses of the accumulated sequence data have brought great insights into the structure, function and molecular evolution of the enzymes. This paper reviews the sequence comparison analyses of the enzymes involved in the arachidonic acid cascade.
Excitons and the lifetime of organic semiconductor devices (2015)

While excitons are responsible for the many beneficial optical properties of organic semiconductors, their non-radiative recombination within the material can result in material degradation due to the dumping of energy onto localized molecular bonds. This presents a challenge in developing strategies to exploit the benefits of excitons without negatively impacting the device operational stability. Here, we will briefly review the fundamental mechanisms leading to excitonic energy-driven device ageing in two example devices: blue emitting electrophosphorescent organic light emitting devices (PHOLEDs) and organic photovoltaic (OPV) cells. We describe strategies used to minimize or even eliminate this fundamental device degradation pathway.