gebhart/patrepeval huggingface dataset:
Genetic engineering and stem cells: combinatorial approaches for cardiac cell therapy [Cellular/Tissue Engineering] (2008)

The use of genetic engineering to induce or alter specific protein expression in stem cells has already facilitated research in this field and may, additionally, offer a potential route for designing more efficient cell sources for cardiac repair. As the feasibility of stem cell genetic manipulation has already been proved and as genetic techniques continue to advance, the combinatorial approach for cardiac cell therapy is promising. This review will thus describe the applications of genetic engineering to improve the isolation, selection, and differentiation of stem cells prior to implantation as well as strategies to promote the retention, mobilization, survival, integration, and tracking of stem cells after implantation.
Picosecond Coherent and Incoherent Dynamics in Proteins (2006)

Abstract : There are two critical questions in the quantum protein dynamics: (1) the time scale of decoherence of coherent vibrational excitations of proteins, and (2) the rate of transport of quantum vibrations along the amide I polymer chain. We have carried out a series of experiments at FELIX, a free-electron laser (FEL) in the Netherlands which attacked these critical questions. We found that there does not exist a highly narrow and long-lived coherent state in the amide I band, in spite of Austin's initial excitement that he had stumbled upon this effect. It remains a mystery why this large and narrow scattering signal appears exactly where one would NOT expect to see a temperature grating signal, namely at the temperature isosbestic point.
Updating the IANA MPLS LSP Ping Parameters (2020)

This document updates RFC 8029 and RFC 8611 that define IANA
registries for MPLS LSP Ping. The updates are mostly for clarification
and to align this registry with recent developments..
Tpl-2 kinase downregulates the activity of p53 and enhances signaling pathways leading to activation of activator protein 1 induced by EGF (2009)

Tumor progression locus-2 (Tpl-2) kinase is a member of the mitogen-activated protein kinase kinase kinase family that has been implicated in cellular transformation. The enhanced expression of this protein has been shown to activate both the mitogen-activated protein kinase and c-Jun N-terminal kinase pathways. However, the molecular mechanisms responsible for the oncogenic potential of Tpl-2 are still largely unknown. Here, we showed that Tpl-2 interacted with p53 both in vitro and ex vivo. The overexpression of Tpl-2 inhibited the epidermal growth factor (EGF)-induced p53 phosphorylation (Ser15) through upregulating the activity of protein phosphatase 2A, which interacted with p53 stimulated by EGF. Also, the EGF-induced p53 activity was suppressed in the Tpl-2 wild-type (WT)-transfected HEK 293 cells, but had no effect in the Tpl-2-mutant (S413A)-transfected cells. Furthermore, introduction of small interfering RNA-Tpl-2 into HEK 293 cells resulted in decreased cell viability compared with only adenovirus-p53-infected cells. In addition, the Tpl-2 WT, but not Tpl-2 mutant (S413A), showed increased EGF-induced c-fos promoter activity, followed by activator protein 1 (AP-1) transactivation activity, which was associated with the cell transformation prompted by the H-Ras-Tpl-2-AP-1 signaling axis. These results indicated that the Ser413 of Tpl-2 plays an important role in EGF-induced carcinogenesis as well as inactivation of the p53.
Wideband Characterization of Backscatter Channels (2011)

The wireless channel of backscatter radio systems is a two-way pinhole channel, created by the concatenation of two standard wireless channels. Pinhole channels cause higher attenuation and deeper fades than common wireless channels. Passive ultra-high frequency radio-frequency identification (UHF RFID) is such a backscatter radio system, with the backscattering tag acting as pinhole. While the effects of this type of channel are well-known in terms of fading statistics, the impact of the pinhole channel on wideband parameters is unknown. We present a method to calculate wideband backscatter channel parameters from the parameters of the constituent channels to and from the pinhole, with a focus on characteristics that are vital for narrowband and wideband ranging. The approximations are verified by simulations and by measurements in a UHF RFID warehouse portal.
Synthesis and Solution Conformation of Cyclo[RGDRGD]:  A Cyclic Peptide with Selectivity for the αVβ3 Receptor (1996)

Three peptides, cyclo[RGDRGD], cyclo[RGDRGd] (d = D-Asp), and the linear sequence RGDRGD, were prepared via solid phase syntheses. These were tested in binding assays based upon the alpha IIb/beta 3-fibrinogen and the alpha V beta 3-vitronectin interactions and found to be selective for the alpha V beta 3 integrin. The alpha V beta 3-vitronectin is important in bone regeneration, hence the compounds were also tested in an osteoclast regeneration assay; all three compounds, cyclo-[RGDRGD], cyclo[RGDRGd], and RGDRGD, showed modest activities. Molecular modeling, NMR, and CD studies were undertaken to elucidate the conformational preferences of cyclo-[RGDRGD], in aqueous solutions. Results from these studies strongly suggest that the molecule tends to adopt a type I beta-turn conformation with a relatively short distance between the Asp and Arg side chains. These observations are in harmony with the first correlations made between alpha V beta 3 selectivity and solution conformation for a peptide ligand (Pfaff, M.; et al. J. Biol. Chem. 1994, 269, 20233).
Unveiling the Merger Dynamics of the Most Massive MaDCoWS Cluster at z = 1.2 from a Multiwavelength Mapping of Its Intracluster Medium Properties (2020)

Abstract The characterization of the Intracluster Medium (ICM) properties of high-redshift galaxy clusters is fundamental to our understanding of large-scale structure formation processes. We present the results of a multiwavelength analysis of the very massive cluster MOO J1142+1527 at a redshift z = 1.2 discovered as part of the Massive and Distant Clusters of WISE Survey. This analysis is based on high angular resolution Chandra X-ray and NIKA2 Sunyaev–Zel’dovich (SZ) data. The cluster thermodynamic radial profiles have been obtained with unprecedented precision at this redshift and up to 0.7 R 500 , thanks to the combination of high-resolution X-ray and SZ data. The comparison between the galaxy distribution mapped in infrared by Spitzer and the morphological properties of the ICM derived from the combined analysis of the Chandra and NIKA2 data leads us to the conclusion that the cluster is an ongoing merger. We have estimated a systematic uncertainty on the cluster total mass that characterizes both the impact of the observed deviations from spherical symmetry and of the core dynamics on the mass profile. We further combine the X-ray and SZ data at the pixel level to obtain maps of the temperature and entropy distributions. We find a relatively low-entropy core at the position of the X-ray peak and high-temperature regions located on its south and west sides. This work demonstrates that the addition of spatially resolved SZ observations to low signal-to-noise X-ray data brings a high information gain on the characterization of the evolution of ICM thermodynamic properties at z &gt; 1.
Nitrogen fertilization of intercropped cereal-legume: A potassium, sulfur, magnesium and calcium plant acquisition dataset (2022)

Cereal-legume mixture is a well-known successful intercrop model for an efficient use of soil nutrients [1,2]. Effects of mineral N gradient on the acquisition of major nutrients: potassium (K), calcium (Ca), magnesium (Mg) and sulfur (S) is presented. A greenhouse pot experiment was conducted with wheat (Triticum aestivum L. cv. Lennox) and white lupin (Lupinus albus L. cv. Feodora) grown as sole crops and intercropped along a soil mineral N gradient obtained by <sup>15</sup>N addition. Plants were harvested at flowering stage and dry weights of shoots and roots were measured. Potassium, calcium, magnesium and sulfur concentrations in shoots and roots were determined by Inductively Coupled Plasma Mass Spectrometry (ICP-MS).
Pitchfork Bifurcation and Zharov Splitting in Nonlinear Mid-infrared Photothermal Spectroscopy in a liquid crystal using a Quantum Cascade Laser (2013)

We report on the mid-infrared nonlinear photothermal spectrum of the neat liquid crystal 4-Octyl-4'-Cyanobiphenyl (8CB) using a tunable Quantum Cascade Laser (QCL). The nonequilibrium steady state characterized by the nonlinear photothermal infrared response undergoes a supercritical pitchfork bifurcation. The bifurcation, observed in heterodyne two-color pump-probe detection, leads to ultrasharp nonlinear infrared spectra similar to those reported in the visible region. A systematic study of the peak splitting as function of absorbed infrared power shows the bifurcation has a critical exponent of 0.5. The surprising observation of an apparently universal critical exponent in a nonequilibrium state is explained using a simple model reminiscent of mean field theory. Apart from the intrinsic interest for nonequilibrium studies, nonlinear photothermal methods lead to a dramatic narrowing of spectral lines, giving rise to a potential new contrast mechanism for the rapidly emerging new field of mid-infrared microspectroscopy using QCLs.
Identification and Privacy: Zero-Knowledge is not Enough. (2008)

At first glance, privacy and zero-knowledgeness seem to be similar properties. A scheme is private when no information is revealed on the prover and in a zero-knowledge scheme, communications should not leak provers&amp;apos; secrets. Until recently, privacy threats were only partially formalized and some zero-knowledge (ZK) schemes have been proposed so far to ensure privacy. We here explain why the intended goal is not reached. Following the privacy model proposed by Vaudenay at Asiacrypt 2007, we then reconsider the analysis of these schemes and thereafter introduce a general framework to modify identification schemes leading to different levels of privacy. Our new protocols can be useful, for instance, for identity documents, where privacy is a great issue. Furthermore, we propose efficient implementations of zero-knowledge and private identification schemes based on modi cations of the GPS scheme. The security and the privacy are based on a new problem: the Short Exponent Strong Diffie-Hellman (SESDH) problem. The hardness of this problem is related to the hardness of the Strong Diffie-Hellman (SDH) problem and to the hardness of the Discrete Logarithm with Short Exponent (DLSE) problem. The security and privacy of these new schemes are proved in the random oracle paradigm.
Cellulose Nanofiber Orientation in Nanopaper and Nanocomposites by Cold Drawing (2012)

To exploit the mechanical potential of native cellulose fibrils, we report on the preparation of nanopaper with preferred orientation of nanofibrillated cellulose (TEMPO-NFC) by cold drawing. The preparation route is papermaking-like and includes vacuum filtering of a TEMPO-oxidated NFC water dispersion, drawing in wet state and drying. The orientation of the fibrils in the nanopaper was assessed by AFM and wide-angle X-ray diffraction analysis, and the effect on mechanical properties of the resulting nanopaper structure was investigated by tensile tests. At high draw ratio, the degree of orientation is as high as 82 and 89% in-the-plane and cross-sectional planes of the nanopaper, respectively, and the Young's modulus is 33 GPa. This is much higher than mechanical properties of isotropic nanopaper. The cold drawing method can be also applied to NFC nanocomposites as demonstrated by preparation of TEMPO-NFC/hydroxyethyl cellulose (HEC) nanocomposites. The introduction of the soft HEC matrix allows further tailoring of the mechanical properties.
An Agent-Based Simulation of SOA-Ready Devices (2008)

In the future Internet of Things, intelligent embedded devices are expected to not only offer their functionality as a web service, but also to be able to discover and cooperate with other devices and services in a peer-to-peer way. The new capabilities of the emerging infrastructure will have a significant impact on industrial applications, services and business practices. In this paper we explore the simulation of such an infrastructure composed of heterogeneous web-service enabled (SOA-ready) devices with the help of a multi-agent system.
Video-rate photoacoustic microscopy of micro-vasculatures (2013)

We report the development of photoacoustic microscopy capable of video-rate high-resolution <i>in-vivo</i> imaging in deep tissue. A lightweight photoacoustic probe is made of a single-element broadband ultrasound transducer, a compact photoacoustic beam combiner, and a bright-field light delivery system. Focused broadband ultrasound detection provides a 44-&mu;m lateral resolution and a 28-&mu;m axial resolution. A multimode optical fiber is used to deliver laser pulses. The bright-field light delivery system can effectively improve the illumination efficiency. The photoacoustic probe weighs less than 40 grams and is mounted on a voice-coil scanner to acquire 40 cross-sectional images per second over several-mm range. The fast speed can effectively improve imaging throughput, reduce motion artifacts, and enable the visualization of highly dynamic biomedical processes. High-resolution micro-vascular imaging is successfully demonstrated.
CD3 and CD2 Ligation Alters CD49d Epitope Expression (1995)

The combination of anti-CD2 plus anti-CD3 monoclonal antibodies (mAbs) synergistically prolongs allograft survival and induces antigen-specific tolerance. Since altered expression of cell surface molecules might be important for tolerance induction, the effect of anti-CD2 and anti-CD3 mAbs on the expression of adhesion molecules was analyzed on splenic T cells with an in vitro model. The anti-CD2 mAb, 12-15, alone had no effect on the expression of integrin alpha 4-chain epitopes recognized by two anti-CD49d (VLA-4 alpha) mAbs, R1-2 and PS/2. The anti-CD3 mAb, 2C11, caused R1-2 epitope expression to decrease, while PS/2 epitope expression remained unchanged. The combination of anti-CD2 and anti-CD3 mAbs further decreased R1-2 epitope expression while preserving PS/2 epitope expression. The expression of integrin beta 1 and beta 7 chains, each of which form heterodimers with alpha 4 chains, also remained unchanged. Expression of other integrin, selectin, or immunoglobulin superfamily molecules (CD11a, CD18, CD44, CD45, CD48, CD54 and CD62L) were all significantly increased by anti-CD2 or anti-CD3 mAbs. Decreased R1-2 epitope expression was anti-CD3 dependent and specifically augmented by anti-CD2 mAb. CD2-regulated decreases in R1-2 epitope expression correlated with increased cAMP and could be prevented by addition of high doses of IL-2 but was not affected by the addition of other cytokines. R1-2 alpha 4 epitope expression could be specifically restored by the divalent cation Mn2+, which also increased functional binding to the VCAM-1 ligand. Significantly, the R1-2 but not the PS/2 mAb prolonged graft survival in a cardiac allograft model. These results show that anti-CD2 and anti-CD3 mAbs selectively decrease integrin alpha 4 chain epitope expression on T cells through conformational regulation. Decreased expression of a CD49d epitope is unique in comparison to the up-modulation of other T-cell adhesion receptors. These changes correlate with functional effects and provide an additional mechanistic explanation for the synergistic effect of anti-CD2 plus anti-CD3 in producing tolerance.
Geographic Variation and Bias in the Polygenic Scores of Complex Diseases and Traits in Finland (2019)

Polygenic scores (PSs) are becoming a useful tool to identify individuals with high genetic risk for complex diseases, and several projects are currently testing their utility for translational applications. It is also tempting to use PSs to assess whether genetic variation can explain a part of the geographic distribution of a phenotype. However, it is not well known how the population genetic properties of the training and target samples affect the geographic distribution of PSs. Here, we evaluate geographic differences, and related biases, of PSs in Finland in a geographically well-defined sample of 2,376 individuals from the National FINRISK study. First, we detect geographic differences in PSs for coronary artery disease (CAD), rheumatoid arthritis, schizophrenia, waist-hip ratio (WHR), body-mass index (BMI), and height, but not for Crohn disease or ulcerative colitis. Second, we use height as a model trait to thoroughly assess the possible population genetic biases in PSs and apply similar approaches to the other phenotypes. Most importantly, we detect suspiciously large accumulations of geographic differences for CAD, WHR, BMI, and height, suggesting bias arising from the population's genetic structure rather than from a direct genotype-phenotype association. This work demonstrates how sensitive the geographic patterns of current PSs are for small biases even within relatively homogeneous populations and provides simple tools to identify such biases. A thorough understanding of the effects of population genetic structure on PSs is essential for translational applications of PSs.
Stress-induced activation of sympathetic nervous system is attenuated by the delta-opioid receptor agonist deltorphin in healthy man. (1993)

To examine the role of delta-opioid receptors in the regulation of the sympathoadrenomedullary system, the effects of the highly selective delta-opioid receptor agonist deltorphin (DT) on plasma catecholamine responses to insulin-induced hypoglycemia (IIH) and cold pressor test (CPT) have been investigated in normal subjects in two separate studies. DT failed to modify basal plasma levels of both norepinephrine (NE) and epinephrine (E). DT completely suppressed the IIH-evoked elevation of NE, whereas it attenuated the E response by 20%, with the DT-induced decrease in E release failing to achieve statistical significance. DT completely blocked the release of both NE and E elicited by CPT. We conclude that specific delta-opioid receptor stimulation exerts an inhibitory effect on NE release induced by both IIH and CPT. These findings provide evidence that delta-opioid receptors may influence the autonomic sympathetic reactivity.
Automated Decision-based Adversarial Attacks (2021)

Deep learning models are vulnerable to adversarial examples, which can fool a target classifier by imposing imperceptible perturbations onto natural examples. In this work, we consider the practical and challenging decision-based black-box adversarial setting, where the attacker can only acquire the final classification labels by querying the target model without access to the model's details. Under this setting, existing works often rely on heuristics and exhibit unsatisfactory performance. To better understand the rationality of these heuristics and the limitations of existing methods, we propose to automatically discover decision-based adversarial attack algorithms. In our approach, we construct a search space using basic mathematical operations as building blocks and develop a random search algorithm to efficiently explore this space by incorporating several pruning techniques and intuitive priors inspired by program synthesis works. Although we use a small and fast model to efficiently evaluate attack algorithms during the search, extensive experiments demonstrate that the discovered algorithms are simple yet query-efficient when transferred to larger normal and defensive models on the CIFAR-10 and ImageNet datasets. They achieve comparable or better performance than the state-of-the-art decision-based attack methods consistently.
Electroformed Multilayer Orifice Plate for Improved Fuel Injection Characteristics (1997)

&lt;div class="htmlview paragraph"&gt;A new orifice plate (OP) for advanced fuel injection characteristics is presented. The OP is designed to optimize the air-fuel mixture generation and transportation within individually shaped manifold geometries of spark-ignition engines. To generate the suitable spray characteristics, the basic OP design and its flow characteristics have some features originating from the well known turbulence nozzle principle:&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Turbulence generating flow deflections within the OP are achieved by superimposing layers containing flow cavities, which are displaced from one another. The flow deflections effect atomization and define the spatial spray beam orientation.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A great variety and a high volume of precisely structured, low cost OPs can be produced daily by micromachining the layers in electroformed nickel. The flow cavities and outer dimensions of each layer are shaped by photo-resist structures.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper describes the new OP's design development achieved through engine tests, flow simulations and experimental spray tests. A suitable OP manufacturing method is illustrated. For a wide range of flow rates, the new OP produces multiform spray shapes containing finely atomized, homogeneously distributed droplets. These characteristics are suitable for improving spray propagation and air-fuel mixture preparation.&lt;/div&gt;
Resolution and characterisation of multiple isoforms of bovine κ‐casein by 2‐DE following a reversible cysteine‐tagging enrichment strategy (2006)

Visualisation of multiple isoforms of kappa-casein on 2-D gels is restricted by the abundant alpha- and beta-caseins that not only limit gel loading but also migrate to similar regions as the more acidic kappa-casein isoforms. To overcome this problem, we took advantage of the absence of cysteine residues in alpha(S1)- and beta-casein by devising an affinity enrichment procedure based on reversible biotinylation of cysteine residues. Affinity capture of cysteine-containing proteins on avidin allowed the removal of the vast majority of alpha(S1)- and beta-casein, and on subsequent 2-D gel analysis 16 gel spots were identified as kappa-casein by PMF. Further analysis of the C-terminal tryptic peptide along with structural predictions based on mobility on the 2-D gel allowed us to assign identities to each spot in terms of genetic variant (A or B), phosphorylation status (1, 2 or 3) and glycosylation status (from 0 to 6). Eight isoforms of the A and B variants with the same PTMs were observed. When the casein fraction of milk from a single cow, homozygous for the B variant of kappa-casein, was used as the starting material, 17 isoforms from 13 gel spots were characterised. Analysis of isoforms of low abundance proved challenging due to the low amount of material that could be extracted from the gels as well as the lability of the PTMs during MS analysis. However, we were able to identify a previously unrecognised site, T(166), that could be phosphorylated or glycosylated. Despite many decades of analysis of milk proteins, the reasons for this high level of heterogeneity are still not clear.