gebhart/patrepeval huggingface dataset:
NMR observation of HIV‐1 gp120 conformational flexibility resulting from V3 truncation (2014)

The envelope spike of HIV-1, which consists of three external gp120 and three transmembrane gp41 glycoproteins, recognizes its target cells by successively binding to its primary CD4 receptor and a coreceptor molecule. Until recently, atomic-resolution structures were available primarily for monomeric HIV-1 gp120, in which the V1, V2 and V3 variable loops were omitted (gp120core ), in complex with soluble CD4 (sCD4). Differences between the structure of HIV gp120core in complex with sCD4 and the structure of unliganded simian immunodeficiency virus gp120core led to the hypothesis that gp120 undergoes a major conformational change upon sCD4 binding. To investigate the conformational flexibility of gp120, we generated two forms of mutated gp120 amenable for NMR studies: one with V1, V2 and V3 omitted ((mut) gp120core ) and the other containing the V3 region [(mut) gp120core (+V3)]. The TROSY-(1)H-(15)N-HSQC spectra of [(2)H, (13)C, (15)N]Arg-labeled and [(2)H, (13)C, (15)N]Ile-labeled unliganded (mut) gp120core showed many fewer crosspeaks than the expected number, and also many fewer crosspeaks in comparison with the labeled (mut) gp120core bound to the CD4-mimic peptide, CD4M33. This finding suggests that in the unliganded form, (mut) gp120core shows considerable flexibility and motions on the millisecond time scale. In contrast, most of the expected crosspeaks were observed for the unliganded (mut) gp120core (+V3), and only a few changes in chemical shift were observed upon CD4M33 binding. These results indicate that (mut) gp120core (+V3) does not show any significant conformational flexibility in its unliganded form and does not undergo any significant conformational change upon CD4M33 binding, underlining the importance of V3 in stabilizing the gp120core conformation.
Tips on speaker recognition by autoregressive parameters and connectionist methods (2003)

This study reveals more interesting aspects on speaker and speech recognition as: 1. different importance of certain spectral frequency bands on the process of speaker and speech recognition; 2. signal phase has a significant importance; and 3. vowel recognition is preponderant in the decision weighting. To resolve the paradox described in A.J. Grichnik (2000), autoregressive (AR) coefficients were used to compute feature vectors in order to teach neural networks (NN). Tests made by using a two layer perceptron (MLP) were compared to a radial basis function (RBF) network in order to obtain the best recognition results.
Modifying Calf Lung Surfactant by Hexadecanol (2005)

Monolayer properties such as phase behavior, collapse pressure, and surface viscosity are determined by monolayer composition. Learning how to control these properties through simple additives is important to understanding lung surfactant monolayers and to designing optimal replacement surfactants for treatment of disease. The properties of Infasurf, a replacement lung surfactant derived from calf lung lavage organic extract, can be modified in a controlled fashion by adding hexadecanol (HD). Grazing incidence X-ray diffraction shows that the HD preferentially interacts with dipalmitoylphosphatidylcholine (DPPC), the main phospholipid component of Infasurf, in the same way as in binary mixtures of DPPC and HD. HD intercalates between the DPPC chains, which leads to a tighter packing of the two-dimensional lattice and greater stability of the solid phase. This molecular reorganization triggers changes at the macroscopic scale, leading to a greatly increased solid-phase fraction at a given surface pressure and order of magnitude increases in the surface shear viscosity. However, the collapse pressure decreases, and, hence, the minimum surface tension of the film increases.
A Study of the Opening Displacement of Transverse Cracks in Cross-Ply Laminates (1993)

Transverse cracks in cross-ply laminates are investigated experimentally to reveal the essential characteristics of their opening displacement under tensile loads. The average crack opening displacement is studied as a function of the longitudinal overall strain and the effects of matrix toughness and transverse ply thickness on this parameter are examined. The interactive effects between closely spaced transverse cracks are also ex amined and found to be significant. Implications of the experimentally observed features on the micromechanics and continuum damage type models are discussed.
Comparison of CpG s-ODNs, chromatin immune complexes, and dsDNA fragment immune complexes in the TLR9-dependent activation of rheumatoid factor B cells (2004)

Synthetic single-stranded oligodeoxynucleotides (15-30 bp) containing CpG motifs and phosphorothioate backbones (CpG s-ODN), immune complexes consisting of anti-nucleosome mAbs and mammalian chromatin (chromatin IC), and immune complexes consisting of anti-hapten mAbs and haptenated-double stranded DNA fragments ( approximately 600 bp) can all effectively stimulate transgenic B cells expressing a rheumatoid factor receptor by a TLR9-dependent process. However, differential sensitivity to both s-ODN and small molecule inhibitors suggests that stimulatory CpG sODN and chromatin IC may either access TLR9 via different routes or depend on discrete activation parameters. These data have important implications regarding the therapeutic application of TLR9 inhibitors to the treatment of systemic autoimmune diseases.
Determining the mechanism of intracellular pathogenesis in Yersinia enterocoli-ca. (2019)

Abstract not provided.
Enhanced FcγRIII/CD16 activation by discrete ligands as independent correlates of disease severity in COVID-19 patients (2021)

Abstract A dysregulated immune response with high levels of SARS-CoV-2 specific IgG antibodies is a common and distinctive feature of severe or critical COVID-19. Although a robust IgG response is typically considered to be beneficial, an overshooting activation mediated by immune receptors recognizing the Fc part of IgG (FcγRs) is thought to be detrimental and associated with immunopathology. However, direct evidence of FcγR driven immunopathology in COVID-19 is still sparse. Here, we used a cell-based FcγR activation reporter system to systematically analyze SARS-CoV-2 specific IgG responses and IgG-mediated FcγRIII (CD16) activation profiles in COVID-19 patient cohorts categorized by severity of disease. We found that increased CD16 activation by SARS-CoV-2 specific IgG is associated with a known pro-inflammatory IgG modification, namely afucosylation. Further, we identified CD16-reactive soluble IgG immune complexes (sICs) to be present in the serum of COVID-19 patients and show that the resulting CD16 activation by sICs is strongly related to disease severity. Our results provide evidence that CD16 activation by pro-inflammatory SARS-CoV-2 specific IgG together with circulating sICs is a major contributor to COVID-19 immunopathology. These findings highlight the importance of FcγR driven immunopathology in COVID-19. Further, our data highly warrant the development of targeted intervention strategies against IgG driven immunopathology following SARS-CoV-2 infection. One sentence summary Severity of disease in COVID-19 patients is associated with enhanced CD16 activation by afucosylated S-specific IgG and CD16-reactive circulating IgG-complexes.
Hydrogen Bond Directed Nitrile Oxide Cycloaddition Reactions of Allylic 2°-Amides (1993)

The ability of allylic and homoallylic 2°-amides to direct nitrile oxide cycloaddition reactions has been studied. For N-cyclopentenyl amides, good regio- and stereochemical control are observed and mechanistic studies suggest that hydrogen bonding in the transition state selectively accelerates formation of one isomer. Acyclic allylic and homoallylic 2°-amides do not exhibit high regio- or stereoselectivity
Direct Observation of the Formation Pathway of [Mo132] Keplerates (2016)

The formation pathway of a closed spherical cluster [Mo132], starting from a library of building blocks of molybdate anions, has been reported. Electrospray ionization mass spectrometry, Raman spectroscopy, and theoretical studies describe the formation of such a complex cluster from a reduced and acidified aqueous solution of molybdate. Understanding the emergence of such an enormous spherical model cluster may lead to the design of new clusters in the future. Formation of such a highly symmetric cluster is principally controlled by charge balance and the emergence of more symmetric structures at the expense of less symmetric ones.
A chunk-based caching algorithm for streaming video (2010)

Session 05 : Streaming applications
Cyclic Adenosine 5′-Diphosphate Ribose Analogs without a “Southern” Ribose Inhibit ADP-ribosyl Cyclase–Hydrolase CD38 (2014)

Cyclic adenosine 5'-diphosphate ribose (cADPR) analogs based on the cyclic inosine 5'-diphosphate ribose (cIDPR) template were synthesized by recently developed stereo- and regioselective N1-ribosylation. Replacing the base N9-ribose with a butyl chain generates inhibitors of cADPR hydrolysis by the human ADP-ribosyl cyclase CD38 catalytic domain (shCD38), illustrating the nonessential nature of the "southern" ribose for binding. Butyl substitution generally improves potency relative to the parent cIDPRs, and 8-amino-N9-butyl-cIDPR is comparable to the best noncovalent CD38 inhibitors to date (IC50 = 3.3 μM). Crystallographic analysis of the shCD38:8-amino-N9-butyl-cIDPR complex to a 2.05 Å resolution unexpectedly reveals an N1-hydrolyzed ligand in the active site, suggesting that it is the N6-imino form of cADPR that is hydrolyzed by CD38. While HPLC studies confirm ligand cleavage at very high protein concentrations, they indicate that hydrolysis does not occur under physiological concentrations. Taken together, these analogs confirm that the "northern" ribose is critical for CD38 activity and inhibition, provide new insight into the mechanism of cADPR hydrolysis by CD38, and may aid future inhibitor design.
Shorter Hospital Stays and Lower Costs for Rivaroxaban Compared With Warfarin for Venous Thrombosis Admissions (2016)

Rivaroxaban was associated with significantly shorter hospital LOS and lower hospitalization costs compared with warfarin.
Performance of frequency offset estimation in the presence of IQ imbalance for OFDM direct conversion receivers (2009)

In WLAN receivers, a direct conversion architecture has been implemented in recent years. Though this architecture reduces cost and power consumption, it may suffer from direct current (DC) offset and frequency offset. To reduce the effect of DC offset, a frequency offset estimation scheme with a differential filter for orthogonal frequency division multiplexing (OFDM) direct conversion receivers has been proposed. However, the receiver may also suffer from IQ imbalance, which deteriorates the performance of frequency offset estimation. In this paper, the performance analysis of the frequency offset estimation scheme with the differential filter in the presence of IQ imbalance is derived. The numerical results obtained through computer simulations show that the derived analysis provides close approximation to the performance of the frequency offset estimation scheme. It also clarifies the dependency of the mean square error on the waveform of the preamble symbols, which is caused by IQ imbalance.
Size-Dependent Chemical Reactivity of Silicon Nanocrystals with Water and Oxygen (2014)

A detailed investigation examines how the size of allylbenzene-capped silicon nanocrystals (ncSi:AB) affects their chemical reactivity with gaseous O2, H2O, and O2/H2O as probed by in situ luminescence spectroscopy. Specifically, changes in the photoluminescence (PL) of size-separated ncSi:AB are monitored through alterations of their PL absolute quantum yield (AQY) as well as the wavelength and intensity of their PL spectra over time. These experiments, conducted under both continuous and intermittent illumination, help elucidate the roles of O2, H2O, and mixtures of O2/H2O, with respect to oxidation of ncSi:AB as a function of their size, providing vital information for any perceived application in advanced materials and biomedical devices.
An integrated 2.5 GHz ΣΔ frequency synthesizer with 5 μs settling and 2 Mb/s closed loop modulation (2002)

Three radio communication standards that share common performance requirements are gaining momentum. The 802.11 wireless LAN standard, the Bluetooth radio connectivity protocol, and the HomeRF SWAP home networking protocol all specify frequency hopping radios in the 2.4 GHz band using FSK modulation in a 1 MHz bandwidth. These standards require modest radio performance (compared to cellular systems), but demand small size and low cost. This paper describes a CMOS /spl Sigma//spl Delta/ fractional-N (/spl Sigma//spl Delta/FN) frequency synthesizer. In contrast to prior art, its 700 kHz bandwidth type-1 phase-locked loop (PLL) enables sub-5 /spl mu/s frequency hops plus 2- and 4-level digital Gaussian frequency shift keying (GFSK) modulation at 1 or 2 Mb/s.
Poloidal variations in toroidal fusion reactor wall power loadings (1985)

A geometric formulation is developed by the authors for determining poloidal variations in bremmstrahlung, cyclotron radiation, and neutron wall power loadings in toroidal fusion devices. Assuming toroidal symmetry and utilizing a numerical model which partitions the plasma into small cells, it was generally found that power loadings are highest on the outer surface of the torus, although variations are not as large as some have predicted. Results are presented for various plasma power generation configurations, plasma volume fractions, and toroidal aspect ratios, and include plasma and wall blockage effects.
ACI-35 elicits robust and specific antisera against Tau in wild-type and Tau.P301L mice. (2015)

&lt;p&gt;(A) Vaccination schedule with ACI-35 in wild-type mice is shown schematically with s.c. injections represented by the syringes and the bleedings by the letter B with a number. Antisera titers were measured by ELISA on the phosphorylated antigenic sequence incorporated in the vaccine (pTau peptide), and on the non-phosphorylated peptide of the same primary amino acid sequence (Tau peptide) (see text for details). Data are presented as mean± SD. Statistical analysis: one-way ANOVA followed by Bonferroni multiple comparison test (**p&lt;0.01, **** p&lt;0.0001) and by unpaired student's t-test (**** p&lt;0.0001). (B) Similar vaccination with ACI-35 of Tau.P301L mice and analysis by ELISA. Data are presented as mean± SD. Statistical analysis by unpaired student's t-test (** p&lt;0.01; **** p&lt;0.0001) (C) TAUPIR with antisera from ACI-35 vaccinated wild-type mice and Tau.P301L mice demonstrated a specific reaction with neurofibrillary tangles and neuropil threads in forebrain of biGT mice. IHC with Mab AT100 is included for comparison. IHC with sera from Tau.P301L mice injected with PBS or from Tau.P301L mice that were not vaccinated, were devoid of specific antibodies and auto-antibodies against human protein Tau. Scale bars: 50 µm.&lt;/p&gt;
Particle size dependence of the dynamic photophysical properties of NaYF_4:Yb, Er nanocrystals (2010)

The effects of the nanocrystal size on the emission spectra and decay rates of upconverting hexagonal NaYF(4):Yb,Er nanocrystals are investigated. The influence of nanocrystal size is represented in terms of the surface area/volume ratio (SA/Vol). Our results show that a small nanocrystal size, or large SA/Vol ratio increases the decay rate, in particular, the green luminescence decay rate varies linearly with the SA/Vol ratio.
Heat Degradation of PVC Stabilized by Treatment with Alkylaluminum Compounds (1978)

Abstract Thermal degradation of PVC treated with alkylaluminum compounds has been studied. Four PVC samples of different molecular weights have been treated with Me3Al, and Et3A1, and the dehydrochlorination rates of the polymers were determined at 190 and 220°C under a nitrogen atmosphere. The alkylaluminum-treated low molecular weight samples show marked increase in thermal stability, i. e., slower rate of dehydrochlorination right from the beginning of degradation, whereas with the higher molecular weight samples stabilization becomes pronounced only after a few percent of dehydrochlorination. The color of R3Al-treated samples was much lighter (yellowish) than those of controls (dark brown) at 1% HCl loss. The average polyene sequence lengths formed during the early stages of dehydrochlorination are found to be much shorter with RsAl-treated PVC than with virgin samples. It appears as though polyene sequences which arose by zipping- initiation from allylic and/or tertiary chlorine sites are longer than those which form by random initiation along the chain. The autocatalytic (i. e., HC1-catalyzed) dehydrochlorination observed with virgin PVC disappears after treatment with R3A1. The HCl-catalyzed dehydrochlorination is minimized when thin films are used instead of powdery samples, which may be due to higher rates of HC1 diffusion through thin films. Autocatalysis of dehydrochlorination is affected by the concentrations of double bonds and HCl and the length of polyene sequences. Interaction between polyenes and HC1 by hydrogen transfer may lead to the re-initiation of unzipping, thus lengthening the polyene sequences.
Phytoremediation of Organic Pollutants (2008)

Doty will present an overview of phytoremediation and organic (degradable) pollutants. She will discuss the problem of pollution and present traditional as well as alternative solutions. She will outline the advantages and disadvantages of using phytoremediation. She will explain genetic engineering, which can be used to enhance plants' natural abilities to phytoremediate. Finally, she will review recent studies in the field.
Kinetics of Coarsening and Precipitation of Dilute Polymer Solutions:  Fluorescence Study of PEO in Toluene (2002)

Fluorescence was used to follow the late stage phase demixing of a very dilute toluene solution of a poly(ethylene oxide) (PEO) chain labeled at one end with pyrene. The excimer to monomer fluorescence intensities ratio is proportional to the average volume of the aggregates. From the linear region of the fluorescence intensity ratio variation with time the apparent rate constants of coarsening were calculated. The apparent rates of coarsening increase with the temperature quench depth, owing to the decrease of the solvent quality to the polymer. At long times, large aggregates are formed and precipitate. From the variation of the light-scattering intensity the apparent rates of precipitation were calculated. A linear correlation was observed between the apparent rates of coarsening and precipitation.
Myocardial infarction induces structural and functional remodelling of the intrinsic cardiac nervous system (2015)

Autonomic dysregulation following myocardial infarction (MI) is an important pathogenic event. The intrinsic cardiac nervous system (ICNS) is a neural network located on the heart that is critically involved in autonomic regulation. The aims of this study were to characterize structural and functional remodelling of the ICNS post-MI in a porcine model (control (n = 16) vs. healed anteroapical MI (n = 16)). In vivo microelectrode recordings of basal activity, as well as responses to afferent and efferent stimuli, were recorded from intrinsic cardiac neurons. From control 118 neurons and from MI animals 102 neurons were functionally classified as afferent, efferent, or convergent (receiving both afferent and efferent inputs). In control and MI, convergent neurons represented the largest subpopulation (47% and 48%, respectively) and had enhanced transduction capacity following MI. Efferent inputs to neurons were maintained post-MI. Afferent inputs were attenuated from the infarcted region (19% in control vs. 7% in MI; P = 0.03), creating a 'neural sensory border zone', or heterogeneity in afferent information. MI reduced transduction of changes in preload (54% in control vs. 41% in MI; P = 0.05). The overall functional network connectivity, or the ability of neurons to respond to independent pairs of stimuli, within the ICNS was reduced following MI. The neuronal response was differentially decreased to ventricular vs. atrial pacing post-MI (63% in control vs. 44% in MI to ventricular pacing; P < 0.01). MI induced morphological and phenotypic changes within the ICNS. The alteration of afferent neural signals, and remodelling of convergent neurons, represents a 'neural signature' of ischaemic heart disease.
HPACK: Header Compression for HTTP/2 (2015)

This specification defines HPACK, a compression format for efficiently
representing HTTP header fields, to be used in HTTP/2.
Effects of Single vs. Multiple Sets of Weight Training: Impact of Volume, Intensity, and Variation (1997)

ABSTRACTThis study examined the effects of a single set of weight training exercise to failure and 2 multiple-set protocols (not to failure) on the 1-RM parallel squat. Forty-three men were randomly assigned to 1 of 3 weight training protocols emphasizing leg and hip strength: SS = single set to fai
Low-drive-voltage 40 Gb/s modulator on X-cut LiNbO/sub 3/ wafer (2002)

A 40 Gb/s X-cut LiNbO/sub 3/ modulator based on a two-step back-slot structure provides low drive voltage of 2.8 V. No DC drift phenomena are observed during more than 100 hours of operation at 100 degree C. These performances indicate high potential for 40 Gb/s transmission system application.
Supplementary Figure 2 from Stearoyl-CoA Desaturase 1 Is a Novel Molecular Therapeutic Target for Clear Cell Renal Cell Carcinoma (2023)

&lt;p&gt;Supplementary Figure 2: Inhibition of SCD1 induces ER stress - PDF file 1316K, Inhibition of SCD1 activity in ccRCC induces endoplasmic reticulum stress response in ccRCC&lt;/p&gt;
Rapid Circadian Entrainment in Models of Circadian Genes Regulation (2019)

The light-based minimum-time circadian entrainment problem for mammals, Neurospora, and Drosophila is studied based on the mathematical models of their circadian gene regulation. These models contain high order nonlinear differential equations. Two model simplification methods are applied to these high-order models: the phase response curves (PRC) and the Principal Orthogonal Decomposition (POD). The variational calculus and a gradient descent algorithm are applied for solving the optimal light input in the high-order models. As the results of the gradient descent algorithm rely heavily on the initial guesses, we use the optimal control of the PRC and the simplified model to initialize the gradient descent algorithm. In this paper, we present: (1) a general process for solving the minimum-time optimal control problem on highorder models; (2) the impacts of minimum-time optimal light on circadian gene transcription and protein synthesis.