gebhart/patrepeval huggingface dataset:
Glycosylation of the Hemagglutinin Protein of H5N1 Influenza Virus Increases Its Virulence in Mice by Exacerbating the Host Immune Response (2017)

The highly pathogenic avian influenza (HPAI) H5N1 viruses continue to circulate in nature and threaten public health. Although several viral determinants and host factors that influence the virulence of HPAI H5N1 viruses in mammals have been identified, the detailed molecular mechanism remains poorly defined and requires further clarification. In our previous studies, we characterized two naturally isolated HPAI H5N1 viruses that had similar viral genomes but differed substantially in their lethality in mice. In this study, we explored the molecular determinants and potential mechanism for this difference in virulence. By using reverse genetics, we found that a single amino acid at position 158 of the hemagglutinin (HA) protein substantially affected the systemic replication and pathogenicity of these H5N1 influenza viruses in mice. We further found that the G158N mutation introduced an N-linked glycosylation at positions 158 to 160 of the HA protein and that this N-linked glycosylation enhanced viral productivity in infected mammalian cells and induced stronger host immune and inflammatory responses to viral infection. These findings further our understanding of the determinants of pathogenicity of H5N1 viruses in mammals.<b>IMPORTANCE</b> Highly pathogenic avian influenza (HPAI) H5N1 viruses continue to evolve in nature and threaten human health. Key mutations in the virus hemagglutinin (HA) protein or reassortment with other pandemic viruses endow HPAI H5N1 viruses with the potential for aerosol transmissibility in mammals. A thorough understanding of the pathogenic mechanisms of these viruses will help us to develop more effective control strategies; however, such mechanisms and virulent determinants for H5N1 influenza viruses have not been fully elucidated. In this study, we identified glycosylation at positions 158 to 160 of the HA protein of two naturally occurring H5N1 viruses as an important virulence determinant. This glycosylation event enhanced viral productivity, exacerbated the host response, and thereby contributed to the high pathogenicity of H5N1 virus in mice.
PicASHOW (2001)

Article Share on PicASHOW: pictorial authority search by hyperlinks on the Web Authors: Ronny Lempel Department of Computer Science, The Technion, Haifa 32000, Israel Department of Computer Science, The Technion, Haifa 32000, IsraelView Profile , Aya Soffer IBM Research Lab in Haifa, Matam, Haifa 31905, Israel IBM Research Lab in Haifa, Matam, Haifa 31905, IsraelView Profile Authors Info & Claims WWW '01: Proceedings of the 10th international conference on World Wide WebMay 2001 Pages 438–448https://doi.org/10.1145/371920.372098Online:01 April 2001Publication History 37citation449DownloadsMetricsTotal Citations37Total Downloads449Last 12 Months15Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Hypoxia drives glucose transporter 3 expression through hypoxia-inducible transcription factor (HIF)–mediated induction of the long noncoding RNA NICI (2019)

Hypoxia-inducible transcription factors (HIFs) directly dictate the expression of multiple RNA species including novel and as yet uncharacterized long noncoding transcripts with unknown function. We used pan-genomic HIF-binding and transcriptomic data to identify a novel long noncoding RNA <u>N</u>oncoding <u>I</u>ntergenic <u>C</u>o-<u>I</u>nduced transcript (NICI) on chromosome 12p13.31 which is regulated by hypoxia via HIF-1 promoter-binding in multiple cell types. CRISPR/Cas9-mediated deletion of the hypoxia-response element revealed co-regulation of NICI and the neighboring protein-coding gene, solute carrier family 2 member 3 (<i>SLC2A3</i>) which encodes the high-affinity glucose transporter 3 (GLUT3). Knockdown or knockout of NICI attenuated hypoxic induction of SLC2A3, indicating a direct regulatory role of NICI in SLC2A3 expression, which was further evidenced by CRISPR/Cas9-VPR-mediated activation of NICI expression. We also demonstrate that regulation of <i>SLC2A3</i> is mediated through transcriptional activation rather than posttranscriptional mechanisms because knockout of NICI leads to reduced recruitment of RNA polymerase 2 to the <i>SLC2A3</i> promoter. Consistent with this we observe NICI-dependent regulation of glucose consumption and cell proliferation. Furthermore, NICI expression is regulated by the von Hippel-Lindau (VHL) tumor suppressor and is highly expressed in clear cell renal cell carcinoma (ccRCC), where SLC2A3 expression is associated with patient prognosis, implying an important role for the HIF/NICI/SLC2A3 axis in this malignancy.
Low power wireless readout of autonomous sensor wafer using MEMS grating light modulator (2002)

We demonstrate remote data acquisition from an autonomous sensor module over a low power wireless optical link. The communication link is based on a grating light modulator. The high data rate, low power consumption, compactness and ease of fabrication make this wireless optical link a promising candidate for a wide range of remote-sensing and sensor-network applications.
Approach to the patient after relapse of hairy cell leukemia (2009)

The current hairy cell leukemia (HCL) treatment is excellent, but evidence of cure with purine analogs cladribine and pentostatin, is lacking. Significant long-term immune suppression, particularly to CD4+ T-cells, and declining complete remission rates with each course, make the identification of new therapies an important goal. The anti-CD20 monoclonal antibody (Mab) rituximab displays significant activity, and, while causing prolonged normal B-cell depletion, spares T-cells. Recombinant immunotoxins, containing an Fv fragment of a Mab fused to truncated Pseudomonas exotoxin, have shown efficacy in HCL resistant to both purine analogs and rituximab. LMB-2 targets CD25 and can induce remission providing the HCL cells are CD25+. All HCL cells display CD22. Recombinant anti-CD22 immunotoxin BL22, targeting CD22, has shown significant efficacy in phase I and II testing, and avoids prolonged suppression of both normal B- and T-cells. An improved high-affinity version of BL22, termed HA22, is currently undergoing phase I testing.
Association Between Earlier Introduction of Peanut and Prevalence of Peanut Allergy in Infants in Australia (2022)

In cross-sectional analyses, introduction of a guideline recommending early peanut introduction in Australia was not associated with a statistically significant lower or higher prevalence of peanut allergy across the population.
Transposition of vertical recti for residual tropias. (1976)

Transposition of vertical muscles for residual tropia was performed: nasal displacement for exotropia and temporal displacement for esotropia. Five millimeter equal displacement of superior and inferior recti corrected 10 to 14 prism diopter while equal displacement of 7 to 8 mm resulted in correction of 25 prism diopter. Special indications of this procedure may be: (1) residual tropia in cases with severe intractable ambylopia or pathology in one eye where patient and surgeon may be reluctant to operate on the sound eye, or (2) residual tropias of the alternating type in patients who underwent operations in all horizontal muscles of both eyes.
Static Route Optimization For Waste Collection In Mecca City (2020)

Waste collection is a key component of the municipal service to the community within the urban set-up. It is a visible service that requires surmountable expenditures while ensuring that clients are satisfied with the service. As outlined in the paper, static route optimization is implemented by adopting the traveling salesman problem to enhance the development of a cost-effective route. The study takes a case of the Al Awali district, Mecca City and attempts to establish the best outlay of the waste collection vehicle movement to optimize their operational route besides ensuring that customers are assured the quality of service. The study focused on utilizing the static route optimization with the traveling salesman problem, which was solved through the incorporation of the Hamiltonian path and the Nearest Neighbor algorithm. Finally, it became clear that an optimized route is achievable with a concerted approach to an examination of various routes by performing several trials to trace out a cost-effective route that serves all clients efficiently.
Characterization of the Prion Protein Binding Properties of Antisense Oligonucleotides (2019)

Antisense oligonucleotides (ASOs) designed to lower prion protein (PrP) expression in the brain through RNase H1-mediated degradation of PrP RNA are in development as prion disease therapeutics. ASOs were previously reported to sequence-independently interact with PrP and inhibit prion accumulation in cell culture, yet <i>in vivo</i> studies using a new generation of ASOs found that only PrP-lowering sequences were effective at extending survival. Cerebrospinal fluid (CSF) PrP has been proposed as a pharmacodynamic biomarker for trials of such ASOs, but is only interpretable if PrP lowering is indeed the relevant mechanism of action in vivo and if measurement of PrP is unconfounded by any PrP-ASO interaction. Here, we examine the PrP-binding and antiprion properties of ASOs in vitro and in cell culture. Binding parameters determined by isothermal titration calorimetry were similar across all ASOs tested, indicating that ASOs of various chemistries bind full-length recombinant PrP with low- to mid-nanomolar affinity in a sequence-independent manner. Nuclear magnetic resonance, dynamic light scattering, and visual inspection of ASO-PrP mixtures suggested, however, that this interaction is characterized by the formation of large aggregates, a conclusion further supported by the salt dependence of the affinity measured by isothermal titration calorimetry. Sequence-independent inhibition of prion accumulation in cell culture was observed. The inefficacy of non-PrP-lowering ASOs against prion disease in vivo may be because their apparent activity in vitro is an artifact of aggregation, or because the concentration of ASOs in relevant compartments within the central nervous system (CNS) quickly drops below the effective concentration for sequence-independent antiprion activity after bolus dosing into CSF. Measurements of PrP concentration in human CSF were not impacted by the addition of ASO. These findings support the further development of PrP-lowering ASOs and of CSF PrP as a pharmacodynamic biomarker.
Non-equilibrium trajectory dynamics and the kinematics of gliding in a flying snake (2011)

The supplementary data for the original article should have contained an additional movie. This can be found online at stacks.iop.org/BB/6/019501/mmedia.
Correlating Nanorod Structure with Experimentally Measured and Theoretically Predicted Surface Plasmon Resonance (2010)

The extinction spectra of Au nanorods electrochemically synthesized using anodic aluminum oxide templates are reported. Homogeneous suspensions of nanorods with average diameters of 35, 55, 80, and 100 nm and varying lengths were synthesized, and their resultant surface plasmon resonances were probed by experimental and theoretical methods. Experimental extinction spectra of the nanoparticles exhibit good overall agreement with those calculated using the discrete dipole approximation. We determine the dependence of the dipole plasmon wavelength on both rod length and diameter, and we then utilize these results to derive an equation for predicting longitudinal dipole resonance wavelength for nanorod dimensions beyond the quasistatic limit. On average, the equation allows one to predict plasmon resonance maxima within 25 nm of the experimentally measured values. An analysis of factors that are important in determining the plasmon width is also provided. For long rods, the width decreases with increasing length in spite of increased radiative damping due to increased frequency dispersion in the real part of the metal dielectric function.
Tratamiento de úlceras vasculares crónicas con equivalentes cutáneos obtenidos mediante ingeniería tisular (2003)

Split hand/split foot (SHSF; also known as ectrodactyly) is a human developmental disorder characterized by missing central digits and other distal limb malformations. An association between SHSF and cytogenetically visible rearrangements of chromosome 7 at bands q21-q22 provides compelling evidence for the location of a causative gene at this location, and the locus has been designated SHFD1. In the present study, marker loci were localized to the SHFD1 critical region through the analysis of somatic cell hybrids derived from individuals with SHSF and cytogenetic abnormalities involving the 7q21-q22 region. Combined genetic and physical data suggest that the order of markers in the SHFD1 critical region is cen-D7S492-D7S527-(D7S479-D7S491)-SHFD1-++ +D7S554-D7S518-qter. Dinucleotide repeat polymorphisms at three of these loci were used to test for linkage of SHSF to this region in a large pedigree that demonstrates autosomal dominant SHSF. Evidence against linkage of the SHSF gene to 7q21-q22 was obtained in this pedigree. Therefore, combined molecular and genetic data provide evidence for locus heterogeneity in autosomal dominant SHSF. We propose the name SHSF2 for this second locus.
Self-alignment of silicon chips on wafers: A capillary approach (2010)

As the limits of Moore’s law are approached, three-dimensional integration appears as the key to advanced microelectronic systems. Die-to-wafer assembly appears to be an unavoidable step to reach full integration. While robotic methods experience difficulties to accommodate fabrication speed and alignment accuracy, self-assembly methods are promising due to their parallel aspect, which overcomes the main difficulties of current techniques. The aim of this work is the understanding of the mechanisms of self-alignment with an evaporating droplet technique. Stable and unstable modes are examined. Causes for misalignments of chips on wafers and their evolution are investigated with the help of the SURFACE EVOLVER numerical software. Precautions for suitable alignment are proposed.
Fast Three-Dimensional Position Detective Sensor with Disturbance Removal of Background Light (1990)

A new sensor for measuring the three-dimensional coordinates and the three-dimensional shape of an object was fabricated. A laser-spotlight was used as the light source. This laser-light is irradiated on a polygon mirror. As the mirror rotates, this light scans the object surface from the lower side to the upper side. The light reflected from the object scans the surface of the sensor developed in this study.On the sensor surface, 21times;21 phototransistor-elements are arranged two-dimensionally. Out of these phototransistor, only the elements receiving light operate and their output signals are sent to the digital parallel processing circuit.The role of this circuit is to detect the position (xs, ys) of the center element among the phototransistors, activated by the light reflected from the object. These detected values are then passed to a personal computer. By processing the values, xs and ys, with the computer program, the three-dimensional coordinates (X, Y, Z) of the center position of the laser-light spot on the object surface are calculated in a real-time fashion.The time required for the measurement of the (X, Y, Z) is as small as 3.3μs. In addition, even when the surface of the object is illuminated by the background light of the magnitude of 1, 000lx, there is no influence on the measured values (X, Y, Z).Furthermore, the data of many positions on the object surface are obtained and stored in the memory units of the computer by repeating the above-mentioned operations, the system can offer a display of the three-dimensional shape of the object on the CRT, but, the number of phototransistor elements are fow 21×21 elements. This causes that the maximum error ΔY (or ΔZ) in the measured value Y (or Z) becomes as large as 3.4mm for the distance of about 320mm between the object and the sensor.
Metabotyping of Biofluids Reveals Stress-Based Differences in Gut Permeability in Healthy Individuals (2009)

Life stress promotes gut dysfunction, but underlying biochemical events are not well-understood. In the present study, we describe the metabolic events associated with background stress and its potential influence on the response to novel incoming stress stimulus in healthy subjects. A 15 min cold pain test was carried out in healthy men and women stratified according to low (LS; n = 21) and moderate background stress (MS; n = 9) during jejunal segmental perfusion. Cold pain induced a stronger psychological response in MS compared to LS subjects, but similar increases in heart rate and blood pressure. Urine and plasma were analyzed using 1H NMR-based metabonomics. Basal stress levels were imprinted in the metabolic profiles indicating different energy and lipid homeostasis. Cold pain increased gut permeability, as determined by mannitol and xylose levels, the response being greater in LS subjects. Moreover, the rate of plasma clearance of mannitol and xylose was dependent on background stress level and gender. In addition, cold pain modulated the levels of circulating ketone bodies, Krebs's cycle intermediates, glucose, and the glucogenic alanine and lactate, which brings further evidence of an alteration of energy homeostasis. Therefore, unravelling life stress with metabonomics may provide a system biology basis for the clinical management and therapeutic surveillance of gut health and disorders.
Hypoxia activates the notch signaling pathway in cells of the intervertebral disc: Implications in degenerative disc disease (2011)

In intervertebral disc cells, hypoxia promotes expression of Notch signaling proteins. Notch signaling is an important process in the maintenance of disc cell proliferation, and thus offers a therapeutic target for the restoration of cell numbers during degenerative disc disease.
Differentiable Game Mechanics (2019)

Deep learning is built on the foundational guarantee that gradient descent on an objective function converges to local minima. Unfortunately, this guarantee fails in settings, such as generative adversarial nets, that exhibit multiple interacting losses. The behavior of gradient-based methods in games is not well understood -- and is becoming increasingly important as adversarial and multi-objective architectures proliferate. In this paper, we develop new tools to understand and control the dynamics in n-player differentiable games. The key result is to decompose the game Jacobian into two components. The first, symmetric component, is related to potential games, which reduce to gradient descent on an implicit function. The second, antisymmetric component, relates to Hamiltonian games, a new class of games that obey a conservation law akin to conservation laws in classical mechanical systems. The decomposition motivates Symplectic Gradient Adjustment (SGA), a new algorithm for finding stable fixed points in differentiable games. Basic experiments show SGA is competitive with recently proposed algorithms for finding stable fixed points in GANs -- while at the same time being applicable to, and having guarantees in, much more general cases.
Synthesis and Glycosidase Inhibition of the Enantiomer of (−)-Steviamine, the First Example of a New Class of Indolizidine Alkaloid (2010)

(+)-Steviamine, the enantiomer of the natural (-)-steviamine, and its corresponding C5 epimer have been synthesized from the D-ribose-derived cyclic nitrone. (-)-Steviamine was found to be the first naturally occurring iminosugar that causes any inhibition of alpha-galactosaminidases.
A Comparison of Continuous Wave Doppler Radar to Impedance Cardiography for Analysis of Mechanical Heart Activity (2005)

The paper compares the data obtained from a continuous wave Doppler radar sensor based on a commercially available microwave motion sensor KMY24 to an impedance cardiograph measured using a Cardiac Output Monitor (Medis Niccomo). Both sensors are used to analyze the mechanical activity of the heart. System parameters, signal content and robustness are discussed.
Residue analysis of thermally depolymerized phthalaldehyde‐based polymer thin films (2021)

Abstract In this study, thermolysis of poly(phthalaldehyde), pPHA, was investigated, and the nonvolatile residues produced were characterized by bulk and surface analyses to provide insight into its use as a resist material for thermal scanning probe lithography. A temperature of 300°C for a short time was required to remove nearly all of the residue produced from pPHA depolymerization. X‐ray photoelectron spectroscopy (XPS) was used to quantify the trace amount of hydrocarbon residue after thermolysis. Time‐of‐flight secondary ion mass spectrometry (SIMS) results show that the residue is largely PHA monomers and oligomers, but also include hydrocarbon char. Differences in molecular weight and composition of the residue as a function of copolymer composition were investigated to give insight into designing new thermal resist materials.
Integrated Interpretation for Pressure Transient Tests in Discretely Fractured Reservoirs (2012)

Abstract In this paper, we present the interpretation of pressure transient well test data from discretely fractured reservoirs, where the fractures provide conduits for fluid flow and displacement, but where the fracture network is poorly connected. For this reason, dual porosity models such as Warren and Root’s formulation are not usually applicable. We first outline the gaps in the existing pressure transient well test interpretation methodology for these reservoirs, then we introduce two new techniques developed to address these gaps: 1) a reservoir model-based inversion technique for the identification of spatial variation in reservoir parameters from pressure transient data, and 2) a boundary-element method for determining the pressure transient behavior of the reservoir with arbitrarily distributed finite and/or infinite conductivity vertical fractures. Using these two new techniques, we defined a new integrated interpretation methodology for reservoirs with discrete natural fractures and incorporating openhole log data, seismic, and the preliminary geological reservoir model. This is an important step in reconciling static and dynamic reservoir data to update the geological reservoir model with meaningful parameters. This methodology provides a direct means of calibrating the fracture model with the well test pressure and rate measurements- one of the few dynamic and deep-reading measurements for reservoir evaluation. Finally, we illustrated the use of the methodology, and demonstrated its robustness by using an example DST from a fractured carbonate reservoir in Campos Basin, Brazil. Results indicated the presence of discrete fractures close to and intersecting the well that do not form a connected fracture network.