gebhart/patrepeval huggingface dataset:
Insights On Mammalian Glycosylation Enzymes From High‐Throughput Expression Studies (2016)

Glycan structures on cell surface and secreted glycoproteins play critical roles in biological recognition and targeting events in animal systems. The enzymes that synthesize these structures reside in membranes of the secretory pathway and modify glycoproteins in transit to the cell surface. These enzymes are generally poorly understood largely because they are challenging targets for functional expression even in eukaryotic hosts. We have established library of expression constructs encoding all human glycosylation enzymes (target gene list of ~350 coding regions) as secreted catalytic domain fusion proteins for recombinant production in HEK293 cells and baculovirus‐infected insect cells. Comparison of expression levels in each host system indicates similar trends where most proteins are well‐expressed, but only a subset are efficiently secreted. This presentation will summarize our strategies for expression and downstream workflows for biochemical and structural studies. Discussion of resulting structures and insights into catalytic mechanisms and substrate recognition will focus on recently determined structures of sialyltransferases and fucosyltransferases coming from the mammalian expression platform. Support or Funding Information (supported by NIH grants P41GM103390 and P01GM107012).
Inhibition of RNA synthesis in vitro by 9-aminoacridine carboxamide antitumor agents. Effects on overall RNA synthesis and synthesis of the initiating dinucleotide. (1990)

A series of 9-aminoacridine carboxamide derivatives of systematically varied structure was assayed in an RNA synthesis in vitro system. Escherichia coli DNA-dependent RNA polymerase and DNA derived from phage T7 or calf thymus were used to measure the effect of the drugs on overall RNA and the initiating dinucleotide (pppApU) syntheses. By means of multiple linear regression analysis it was shown that the inhibition of these reactions depends both on the drug equilibrium binding constant and kinetic parameters of dissociation of drug-DNA complexes.
A modified colorectal screening score for prediction of advanced neoplasia: A prospective study of 5744 subjects (2017)

Abstract Background and Aim We validated a modified risk algorithm based on the Asia‐Pacific Colorectal Screening (APCS) score that included body mass index (BMI) for prediction of advanced neoplasia. Methods Among 5744 Chinese asymptomatic screening participants undergoing a colonoscopy in Hong Kong from 2008 to 2012, a random sample of 3829 participants acted as the derivation cohort. The odds ratios for significant risk factors identified by binary logistic regression analysis were used to build a scoring system ranging from 0 to 6, divided into “average risk” (AR): 0; “moderate risk” (MR): 1–2; and “high risk” (HR): 3–6. The other 1915 subjects formed a validation cohort, and the performance of the score was assessed. Results The prevalence of advanced neoplasia in the derivation and validation cohorts was 5.4% and 6.0%, respectively ( P = 0.395). Old age, male gender, family history of colorectal cancer, smoking, and BMI were significant predictors in multivariate regression analysis. A BMI cut‐off at &gt; 23 kg/m 2 had better predictive capability and lower number needed to screen than that of &gt; 25 kg/m 2 . Utilizing the score developed, 8.4%, 57.4%, and 34.2% in the validation cohort were categorized as AR, MR, and HR, respectively. The corresponding prevalence of advanced neoplasia was 3.8%, 4.3%, and 9.3%. Subjects in the HR group had 2.48‐fold increased prevalence of advanced neoplasia than the AR group. The c‐statistics of the modified score had better discriminatory capability than that using predictors of APCS alone (c‐statistics = 0.65 vs 0.60). Conclusions Incorporating BMI into the predictors of APCS score was found to improve risk prediction of advanced neoplasia and reduce colonoscopy resources.
Physical impairment aware planning of next generation WDM backbone networks (2012)

We discuss and illustrate the evolution of the "Quality of Transmission" estimators suitable for optimized planning of next generation WDM networks featuring coherent detection, elastic spectral efficiency, and flexible optical network nodes.
Síntesis de un silicoaluminotitanato isomorfo a la zeolita Beta, activo para la oxidación selectiva de compuestos orgánicos (1994)

Referencia OEPM: P9101798.-- Fecha de solicitud: 31/07/1991.-- Titular: Universidad Politécnica de Valencia (UPV).
Interactive Digital Receiver Simulator (IDRS) System User's Manual and Software Documentation, (1978)

Abstract : This report describes the design and implementation of the Interactive Digital Receiver Simulator (IDRS). The IDRS is a computer program that is capable of processing predetected signals that have been converted to digital format and recorded. It allows a user to computer interactively produce (1) desired hardcopy patterns of signals for a detailed analysis of modulation characteristics and (2) processed signal segments for processing by pattern analysis/recognition programs for feature extraction. In essence, the IDRS program provides the user with the capability of interactively creating a digital receiver to his specifications. (Author)
19-Tungstodiarsenate(III) Functionalized by Organoantimony(III) Groups: Tuning the Structure–Bioactivity Relationship (2015)

A family of three discrete organoantimony(III)-functionalized heteropolyanions-[Na{2-(Me2HN(+)CH2)C6H4Sb(III)}As(III)2W19O67(H2O)](10-) (1), [{2-(Me2HN(+)CH2)C6H4Sb(III)}2As(III)2W19O67(H2O)](8-) (2), and [{2-(Me2HN(+)CH2)C6H4Sb(III)}{WO2(H2O)}{WO(H2O)}2(B-β-As(III)W8O30)(B-α-As(III)W9O33)2](14-) (3)-have been prepared by one-pot reactions of the 19-tungstodiarsenate(III) precursor [As(III)2W19O67(H2O)](14-) with 2-(Me2NCH2)C6H4SbCl2. The three novel polyanions crystallized as the hydrated mixed-alkali salts Cs3KNa6[Na{2-(Me2HN(+)CH2)C6H4Sb(III)}As(III)2W19O67(H2O)]·43H2O (CsKNa-1), Rb2.5K5.5[{2-(Me2HN(+)CH2)C6H4Sb(III)}2As(III)2W19O67(H2O)]·18H2O·Me2NCH2C6H5 (RbK-2), and Rb2.5K11.5[{2-(Me2HN(+)CH2)C6H4Sb(III)}{WO2(H2O)}{WO(H2O)}2(B-β-As(III)W8O30)(B-α-As(III)W9O33)2]·52H2O (RbK-3), respectively. The number of incorporated {2-(Me2HN(+)CH2)C6H4Sb(III)} units could be tuned by careful control of the experimental parameters. Polyanions 1 and 2 possess a dimeric sandwich-type topology, whereas 3 features a trimeric, wheel-shaped structure, representing the largest organoantimony-containing polyanion. All three compounds were fully characterized in the solid state via single-crystal X-ray diffraction (XRD), infrared (IR) spectroscopy, and thermogravimetric analysis, and their aqueous solution stability was validated by ultraviolet-visible light (UV-vis) and multinuclear ((1)H, (13)C, and (183)W) nuclear magnetic resonance (NMR) spectroscopy. Effective inhibition against six different types of bacteria was observed for 1 and 2, and we could extract a structure-bioactivity relationship for these polyanions.
Microstructural and micromagnetic characterization of thin film magnetic tunnel junctions (1999)

High-resolution electron microscopy, Lorentz microscopy, and off-axis electron holography have been used to characterize magnetic tunnel junctions. Observations in cross section show that the tunnel barriers are slightly narrower and smoother after annealing at temperatures up to 350 °C. The demagnetization of a magnetically hard CoPtCr reference layer through repeated magnetization reversal of a soft layer of either Co or Ni40Fe60 is likely to originate from magnetic fringing fields at Néel walls, which form in the soft layers close to the coercive field.
Frequency-domain periodic active noise control and equalization (1997)

This paper analyzes a frequency-domain periodic active noise control (ANC) system. The adaptive filter employs the frequency domain complex least mean square (LMS) algorithm driven by a unit value at each frequency bin. The synchronously sampled frequency-domain adaptive structure acts as a comb filter to cancel narrowband noises with harmonically related frequencies. A frequency-domain periodic active noise equalization (ANE) system, which reshapes the residual noise by controlling the output of the adaptive comb filter at each frequency bin, is also developed and analyzed in this paper. Computer simulations and real-time experiments conducted attest to the practical usefulness of the proposed ANC and ANE systems.
Security Information Architecture for Automation and Control Networks (2008)

Ongoing automation and the open access implementation of critical systems are increasing security vulnerability in automation and control networks employed in the electric power sector. This work is of the view that the integration between policy-based management and access control mechanisms is necessary to take us closer to a more effective solution for the combat against security threats. This paper introduces a modular architecture based on the XACML framework and applies this to automation and control networks used in the electric power industry. This security architecture is described and its components are individually analyzed and tested in a real power production environment. This paper also describes relevant encountered difficulties, provides results and new insights into access control when applied to industrial critical network infrastructures.
Potential of memory steel reinforcement for shear strengthening of concrete bridge girders with I-sections (2022)

&lt;p&gt;This study was carried out to access the performance of near surface mounted (NSM) memory steel reinforcement for shear strengthening of concrete girders with I-sections. Specially designed/strengthened concrete I-sections were tested in tension and the bond behaviour of memory steel was observed and reported as failure mode, load displacement and strain variation. It has been demonstrated that the memory steel reinforcement has a great potential for active shear strengthening of concrete girders with I-section. The activation of memory steel apply prestress on the I-section that delays the cracking and increases the ultimate failure load. The delayed shear cracking will consequently retain the aggregate interlock mechanism that is the main component of shear strength. Besides the additional strength of the external reinforcement, the yielding of internal stirrups is also delayed that further retains the intrinsic shear strength.&lt;/p&gt;&lt;p&gt;The results reported in this paper are part of a wider study to investigate various shear strengthening configurations for precast prestressed I-girders using memory steel reinforcement and fibre reinforced polymers (FRPs).&lt;/p&gt;
Ni and Co Segregations on Selective Surface Facets and Rational Design of Layered Lithium Transition‐Metal Oxide Cathodes (2016)

The chemical processes occurring on the surface of cathode materials during battery cycling play a crucial role in determining battery's performance. However, the understanding of such surface chemistry is far from clear due to the complexity of redox chemistry during battery charge/discharge. Through intensive aberration corrected STEM investigation on ten layered oxide cathode materials, two important findings on the pristine oxides are reported. First, Ni and Co show strong plane selectivity when building up their respective surface segregation layers (SSLs). Specifically, Ni‐SSL is exclusively developed on (200) m facet in Li–Mn‐rich oxides (monoclinic C2/m symmetry) and on (012) h facet in Mn–Ni equally rich oxides (hexagonal R‐3m symmetry), while Co‐SSL has a strong preference to (20−2) m plane with minimal Co‐SSL also developed on some other planes in Li–Mn‐rich cathodes. Structurally, Ni‐SSLs tend to form spinel‐like lattice while Co‐SSLs are in a rock‐salt‐like structure. Second, by increasing Ni concentration in these layered oxides, Ni and Co SSLs can be suppressed and even eliminated. The findings indicate that Ni and Co SSLs are tunable through controlling particle morphology and oxide composition, which opens up a new way for future rational design and synthesis of cathode materials.
Healing of DSP Circuits Under Power Bound Using Post-Silicon Operand Bitwidth Truncation (2012)

Increasing device parameter variations in nanometer CMOS technologies cause large spread in circuit parameters such as delay and power, leading to parametric yield loss. For digital signal processing (DSP) hardware, variations in circuit parameters can significantly affect the quality of service (QoS). Existing post-silicon calibration and repair approaches rely on adaptation of circuit operating parameters such as voltage, frequency, or body bias and typically incur large delay or power overhead. This paper presents a novel low-overhead approach of healing DSP chips by commensurately truncating the operand width based on their process shifts. The proposed approach exploits the fact that critical timing paths in typical DSP datapaths originate from the least significant bits. Hence, truncation of these bits, by setting them at constant values, can effectively reduce the delay of a unit, thereby avoiding delay failures. The proposed technique is applied to two common DSP blocks, namely discrete cosine transform (DCT) and finite impulse response (FIR) filter. Simulation results show significant reduction in critical path delay along with a graceful degradation in the QoS. They also show large improvement in manufacturing yield (41.6%) with up to 5X savings in power compared to existing approaches such as voltage scaling and body biasing.
Two-dimensional dopant Profiling on Operating MOSFET by Scanning Capacitance Microscopy (2007)

We introduce scanning capacitance force microscopy (SCFM), a newly developed dopant profiling method, and a 3-dimensional wiring procedure enabling evaluation of dopant profile under metal-oxide-semiconductor field-effect-transistor (MOSFET) operation. The principle of the SCFM is based on measurement of an electrostatic force (ESF) that is induced by bias voltage of angular frequency ω between a tip and a sample. The focused ion beam (FIB) technique was employed to evaluate dopant profile for the cross-section of MOSFET devices under the device operation. Local etching, deposition, and formation of small wiring for the specified MOSFET were successively carried out with the FIB, and the variation of dopant profiling was clearly shown with applying voltage to the MOSFET. These techniques are expected to be utilized for the failure analysis and the development of next-generation devices.
Sequence conservation at human and mouse orthologous common fragile regions, FRA3B / FHIT and Fra14A2 / Fhit (2001)

It has been suggested that delayed DNA replication underlies fragility at common human fragile sites, but specific sequences responsible for expression of these inducible fragile sites have not been identified. One approach to identify such cis-acting sequences within the large nonexonic regions of fragile sites would be to identify conserved functional elements within orthologous fragile sites by interspecies sequence comparison. This study describes a comparison of orthologous fragile regions, the human FRA3B/FHIT and the murine Fra14A2/Fhit locus. We sequenced over 600 kbp of the mouse Fra14A2, covering the region orthologous to the fragile epicenter of FRA3B, and determined the Fhit deletion break points in a mouse kidney cancer cell line (RENCA). The murine Fra14A2 locus, like the human FRA3B, was characterized by a high AT content. Alignment of the two sequences showed that this fragile region was stable in evolution despite its susceptibility to mitotic recombination on inhibition of DNA replication. There were also several unusual highly conserved regions (HCRs). The positions of predicted matrix attachment regions (MARs), possibly related to replication origins, were not conserved. Of known fragile region landmarks, five cancer cell break points, one viral integration site, and one aphidicolin break cluster were located within or near HCRs. Thus, comparison of orthologous fragile regions has identified highly conserved sequences with possible functional roles in maintenance of fragility.
Extracting the conduction band offset in strained FinFETs from subthreshold-current measurements (2011)

Subthreshold measurements can reveal key device parameters. We present a method to identify the region of the transfer characteristic where the drain current is affected by neither parasitic off-state leakage nor strong inversion current. Then we employ this method to obtain the conduction band edge shift for FinFETs with various fin widths using temperature dependent transfer characteristics. The results indicate lowering of the conduction band edge up to 40 meV, and hence threshold voltage, for fin widths down to 5 nm. This is explained by the combination of quantum confinement and strain effect on the band edges. We demonstrate a qualitative agreement between measurements, theory and simulation.
Improvement in UV Optical Properties of CsLiB6O10 by Reducing Water Molecules in the Crystal (2005)

We investigated the effects of water molecules in CsLiB 6 O 10 (CLBO) crystals on UV optical properties. Our results show that long-term heat treatment is necessary to adequately remove water molecules from inside the crystal. The reducing the number of water molecules contained in the crystal improves the transmittance at 266 nm. In addition, the long-term heat-treated crystal can generate three-times higher 266-nm output without bulk damage than a normal sample.
The expression of IL-1β, iNOS and COX-2 genes by human chondrocytes is differentially regulated by reactive oxygen species (2001)

peer reviewed
Types of Fluid Disorder in Children with Bacterial Meningitis (1991)

As part of a prospective study of children with bacterial meningitis we analyzed in 36 patients of our hospital the fluid balance on admission and during the first three days of treatment. On admission 10 of them (28%) had inappropriate antidiuretic hormone secretion SIADH, 10 (28%) hypo-osmolal and 10 (28%) iso-osmolal contraction. Six patients (17%) had no clear fluid disorder. The patients with SIADH had significantly lower mean serum NA+ (127 vs. 132 mEq/l, p less than 0.01) and higher mean urine Na+ (111 vs. 26 mEq/l, p less than 0.01) concentration as well as higher mean urinary Na+/K+ ratio (2.23 vs. 0.365, p less than 0.005) than the patients with hypo-osmolal contraction. They also tended to be younger and have a shorter history of fever. The patients with SIADH had a less strict fluid restriction than the patients with hypo-osmolal contraction, and their fluid balance normalized more slowly. Our findings support initial water restriction for all children with bacterial meningitis.
Quantifying distortions in two-photon remote focussing microscope images using a volumetric calibration specimen (2014)

Remote focussing microscopy allows sharp, in-focus images to be acquired at high speed from outside of the focal plane of an objective lens without any agitation of the specimen. However, without careful optical alignment, the advantages of remote focussing microscopy could be compromised by the introduction of depth-dependent scaling artifacts. To achieve an ideal alignment in a point-scanning remote focussing microscope, the lateral (XY) scan mirror pair must be imaged onto the back focal plane of both the reference and imaging objectives, in a telecentric arrangement. However, for many commercial objective lenses, it can be difficult to accurately locate the position of the back focal plane. This paper investigates the impact of this limitation on the fidelity of three-dimensional data sets of living cardiac tissue, specifically the introduction of distortions. These distortions limit the accuracy of sarcomere measurements taken directly from raw volumetric data. The origin of the distortion is first identified through simulation of a remote focussing microscope. Using a novel three-dimensional calibration specimen it was then possible to quantify experimentally the size of the distortion as a function of objective misalignment. Finally, by first approximating and then compensating the distortion in imaging data from whole heart rodent studies, the variance of sarcomere length (SL) measurements was reduced by almost 50%.
EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Labels (2015)

The genetic encoding of nitroxide amino acids in combination with electron paramagnetic resonance (EPR) distance measurements enables precise structural studies of native proteins, i.e. without the need for mutations to create unique reactive sites for chemical labeling and thus with minimal structural perturbation. We here report on in vitro DEER measurements in native E. coli thioredoxin (TRX) that establish the nitroxide amino acid SLK-1 as a spectroscopic probe that reports distances and conformational flexibilities in the enzyme with nonmutated catalytic centers that are not accessible by the use of the traditional methanethiosulfonate spin label (MTSSL). We generated a rotamer library for SLK-1 that in combination with molecular dynamics (MD) simulation enables predictions of distance distributions between two SLK-1 labels incorporated into a target protein. Toward a routine use of SLK-1 for EPR distance measurements in proteins and the advancement of the approach to intracellular environments, we study the stability of SLK-1 in E. coli cultures and lysates and establish guidelines for protein expression and purification that offer maximal nitroxide stability. These advancements and insights provide new perspectives for facile structural studies of native, endogenous proteins by EPR distance measurements.
Mechanisms of apoptosis in T cells from patients with renal cell carcinoma. (1999)

Tumors may escape immune recognition and destruction through the induction of apoptosis in activated T lymphocytes. Results from several laboratories suggest that FasL (L/CD95L) expression in tumors may be responsible for this process. In this study of patients with renal cell carcinoma (RCC), we provide evidence for two mechanisms of T-cell apoptosis. One mechanism involves the induction of apoptosis via FasL expression in tumor cells. This is supported by several observations, including the fact that tumor cells in situ as well as cultured cell lines expressed FasL mRNA and protein by a variety of techniques. The FasL in RCC is functional because in coculture experiments, FasL+ tumors induced apoptosis in Fas-sensitive Jurkat T cells and in activated peripheral blood T cells but not in resting peripheral blood T cells. Most importantly, antibody to FasL partially blocked apoptosis of the activated T cells. Moreover, Fas was expressed by T cells derived from the peripheral blood (53% median) and tumor (44.3% median) of RCC patients. Finally, in situ staining for DNA breaks demonstrated apoptosis in a subset of T cells infiltrating renal tumors. These studies also identified a second mechanism of apoptosis in RCC patient peripheral T cells. Whereas these cells did not display DNA breaks when freshly isolated or after culture for 24 h in medium, peripheral blood T cells from RCC patients underwent activation-induced cell death after stimulation with either phorbol 12-myristate 13-acetate/ionomycin or anti-CD3/CD28 antibodies. Apoptosis mediated by exposure to FasL in tumor cells or through T-cell activation may contribute to the failure of RCC patients to develop an effective T-cell-mediated antitumor response.