gebhart/patrepeval huggingface dataset:
The serine-rich cytoplasmic domain of the interleukin-2 receptor beta chain is essential for interleukin-2-dependent tyrosine protein kinase and phosphatidylinositol-3-kinase activation. (1993)

The biological activity of interleukin-2 receptors (IL-2R) is dependent on the functional coupling of IL-2R beta molecules to intracellular enzymes such as protein tyrosine kinase. The serine-rich, S-domain within the cytosolic portion of IL-2R beta plays an essential role in transduction of the IL-2 proliferative signal. Cells bearing either wild type IL-2R beta (Baf alpha/beta) or deletions within the S-domain (Baf alpha/beta SD1) were used to evaluate the importance of the S-domain in linking ligand binding to protein tyrosine kinase induction. Multiparameter, side by side comparisons showed that only those cells that expressed wild type IL-2R beta responded to IL-2 by increased cellular proliferation, accumulation of the c-myc proto-oncogene, and activation of protein tyrosine kinase. Activation of protein tyrosine kinase was, in turn, linked to increased tyrosine phosphorylation and activation of phosphatidylinositol-3-kinase. These findings indicate that the S-domain of the IL-2R beta chain is an essential component in the signal transduction cascade that links IL-2 binding to tyrosine kinase and phosphatidylinositol-3-kinase activation.
A Second Look at Neutron Resonance Transmission Analysis as a Spent Fuel NDA Technique (2011)

Many different nondestructive analysis techniques are currently being investigated as a part of the United States Department of Energy's Next Generation Safeguards Initiative (NGSI) seeking methods to quantify plutonium in spent fuel. Neutron Resonance Transmission Analysis (NRTA) is one of these techniques. Having first been explored in the mid-1970s for the analysis of individual spent-fuel pins a second look, using advanced simulation and modeling methods, is now underway to investigate the suitability of the NRTA technique for assaying complete spent nuclear fuel assemblies. The technique is similar to neutron time-of-flight methods used for cross-section determinations but operates over only the narrow 0.1-20 eV range where strong, distinguishable resonances exist for both the plutonium (239, 240, 241,242Pu) and uranium (235,236,238U) isotopes of interest in spent fuel. Additionally, in this energy range resonances exists for six important fission products (99Tc, 103Rh, 131Xe, 133Cs, 145Nd, and 152Sm) which provide additional information to support spent fuel plutonium assay determinations. Initial modeling shows excellent agreement with previously published experimental data for measurements of individual spent-fuel pins where plutonium assays were demonstrated to have a precision of 2-4%. Within the simulation and modeling analyses of this project scoping studies have explored fourteen different aspects of the technique including the neutron source, drift tube configurations, and gross neutron transmission as well as the impacts of fuel burn up, cooling time, and fission-product interferences. These results show that NRTA may be a very capable experimental technique for spent-fuel assay measurements. The results suggest sufficient transmission strength and signal differentiability is possible for assays through up to 8 pins. For an 8-pin assay (looking at an assembly diagonally), 64% of the pins in a typical 17 ? 17 array of a pressurized water reactor fuel assembly can be part of a complete transmission assay measurement with high precision. Analysis of rows with up to 12 pins may also be feasible but with diminished precision. Preliminary data analysis of an NRTA simulation has demonstrated the simplicity of the technique.
LightSNiP assay is a good strategy for pharmacogenetics test (2015)

OPINION article Front. Pharmacol., 02 June 2015Sec. Pharmacogenetics and Pharmacogenomics https://doi.org/10.3389/fphar.2015.00114
Impact of Transceiver Power Consumption on the Energy Efficiency of Zero-Forcing Detector in Massive MIMO Systems (2014)

We consider the impact of transceiver power consumption on the energy efficiency (EE) of the zero-forcing (ZF) detector in the uplink of massive MIMO systems, where a base station (BS) with M antennas communicates coherently with K single antenna user terminals (UTs). We consider the problem of maximizing the EE with respect to (M, K) for a fixed sum spectral efficiency. Through analysis, we study the impact of system parameters on the optimal EE. System parameters consists of the average channel gain to the users and the power consumption parameters (PCPs) (e.g., power consumed by each RF antenna/ receiver at BS). When the average user channel gain is high or else the BS/UT design is power inefficient, our analysis reveals that it is optimal to have a few BS antennas and a single user, i.e., nonmassive MIMO regime. Similarly, when the channel gain is small or else the BS/UT design is power efficient, it is optimal to have a larger (M, K), i.e., massive MIMO regime. Tight analytical bounds on the optimal EE are proposed for both these regimes. The impact of the system parameters on the optimal EE is studied, and several interesting insights are drawn.
Chemical reactivity between sol‐gel deposited Pb(Zr, Ti)O3 layers and their GaAs substrates (2016)

The combination on the same wafer of materials having different physical properties is a key challenge. In particular, functional oxides of the perovskite family are very attractive for applications in the micro‐optoelectronic field since they present a variety of physical properties (ferroelectricity, ferromagnetism, superconductivity, high Pockels coefficients, …). They are classically grown on SrTiO 3 (STO) substrates, but molecular beam epitaxy (MBE) allows their epitaxy on Si and GaAs platforms, providing that specific interface engineering strategies are used. However, even in this case, chemical reactions between the growing oxide and the substrate strongly impact the epitaxy process and impose using specific growth procedures that are detrimental to the oxide crystal quality. Amongst the oxides that can be integrated on STO templates, Pb(Zr,Ti)O 3 (PZT) is of particular interest because of its high remanent polarization (P r ), its low coercive field (E c ) and its outstanding piezoelectric properties In this contribution, we report the study of sol‐gel prepared PZT thin films on STO/GaAs templates grown by molecular beam epitaxy (MBE). The spin‐coated layers were calcined at 350°C under air for 5 minutes to dty the sol film. The crystallization of the PZT have been studied in function of post‐annealings at three different temperatures ranging (405°C, 420°C and 510 °C). High angle annular dark field scanning transmission electron microscopy (HAADF‐STEM) and energy dispersive X‐ray spectroscopy (EDXS) have been used to study the structure and the chemical composition of the layers. High resolution HAADF images coupling to geometrical phase analysis (GPA) show that PZT is locally strained on the STO/GaAs during the first steps of crystallization. Complete crystallization of the PZT laeyrs cannot be achieved due to a significant oxidation of the GaAs substrate which enhances As diffusion through the structure and further formation of parasitic PbAs and SrAs compounds.
Core-binding factor leukemia hijacks the T-cell–prone PU.1 antisense promoter (2021)

The blood system serves as a key model for cell differentiation and cancer. It is orchestrated by precise spatiotemporal expression of crucial transcription factors. One of the key master regulators in the hematopoietic systems is PU.1. Reduced levels of PU.1 are characteristic for human acute myeloid leukemia (AML) and are known to induce AML in mouse models. Here, we show that transcriptional downregulation of PU.1 is an active process involving an alternative promoter in intron 3 that is induced by RUNX transcription factors driving noncoding antisense transcription. Core-binding factor (CBF) fusions RUNX1-ETO and CBFβ-MYH11 in t(8;21) and inv(16) AML, respectively, activate the PU.1 antisense promoter that results in a shift from sense toward antisense transcription and myeloid differentiation blockade. In patients with CBF-AML, we found that an elevated antisense/sense transcript and promoter accessibility ratio represents a hallmark compared with normal karyotype AML or healthy CD34+ cells. Competitive interaction of an enhancer with the proximal or the antisense promoter forms a binary on/off switch for either myeloid or T-cell development. Leukemic CBF fusions thus use a physiological mechanism used by T cells to decrease sense transcription. Our study is the first example of a sense/antisense promoter competition as a crucial functional switch for gene expression perturbation by oncogenes. Hence, this disease mechanism reveals a previously unknown Achilles heel for future precise therapeutic targeting of oncogene-induced chromatin remodeling.
Paxillin controls endothelial cell migration and tumor angiogenesis by altering neuropilin 2 expression (2014)

Although a number of growth factors and receptors are known to control tumor angiogenesis, relatively little is known about the mechanism by which these factors influence the directional endothelial cell migration required for cancer microvessel formation. Recently, it has been shown that the focal adhesion protein paxillin is required for directional migration of fibroblasts in vitro. Here, we show that paxillin knockdown enhances endothelial cell migration in vitro and stimulates angiogenesis during normal development and in response to tumor angiogenic factors in vivo. Paxillin produces these effects by decreasing expression of neuropilin 2 (NRP2). Moreover, soluble factors secreted by tumors that stimulate vascular ingrowth, including vascular endothelial growth factor (VEGF), also decrease endothelial cell expression of paxillin and NRP2, and overexpression of NRP2 reverses these effects. These results suggest that the VEGF-paxillin-NRP2 pathway could represent a new therapeutic target for cancer and other angiogenesis-related diseases.
Normalized Diastolic Properties After Left Ventricular Assist Result From Reverse Remodeling of Chamber Geometry (2001)

These findings are all consistent with the hypothesis that early normalization of diastolic properties after LV assist device support results from remodeling of chamber geometry, not from changes in tissue stiffness. These data emphasize the importance of geometry to ventricular mechanics and demonstrate that reduction of heart size does not necessarily produce a reduction in wall stress.
Search for a heavy Higgs boson decaying into a Z boson and another heavy Higgs boson in the $$\ell \ell bb$$ and $$\ell \ell WW$$ final states in pp collisions at $$\sqrt{s}=13$$ $$\text {TeV}$$ with the ATLAS detector (2021)

Abstract A search for a heavy neutral Higgs boson, A , decaying into a Z boson and another heavy Higgs boson, H , is performed using a data sample corresponding to an integrated luminosity of 139 fb $$^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:math> from proton–proton collisions at $$\sqrt{s} = 13$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>13</mml:mn></mml:mrow></mml:math> $$\text {TeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mtext>TeV</mml:mtext></mml:math> recorded by the ATLAS detector at the LHC. The search considers the Z boson decaying into electrons or muons and the H boson into a pair of b -quarks or W bosons. The mass range considered is 230–800 $$\text {GeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mtext>GeV</mml:mtext></mml:math> for the A boson and 130–700 $$\text {GeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mtext>GeV</mml:mtext></mml:math> for the H boson. The data are in good agreement with the background predicted by the Standard Model, and therefore 95% confidence-level upper limits for $$\sigma \times B(A\rightarrow ZH)\times B(H\rightarrow bb \; \text {or} \; H \rightarrow WW)$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>σ</mml:mi><mml:mo>×</mml:mo><mml:mi>B</mml:mi><mml:mo>(</mml:mo><mml:mi>A</mml:mi><mml:mo>→</mml:mo><mml:mi>Z</mml:mi><mml:mi>H</mml:mi><mml:mo>)</mml:mo><mml:mo>×</mml:mo><mml:mi>B</mml:mi><mml:mo>(</mml:mo><mml:mi>H</mml:mi><mml:mo>→</mml:mo><mml:mi>b</mml:mi><mml:mi>b</mml:mi><mml:mspace/><mml:mtext>or</mml:mtext><mml:mspace/><mml:mi>H</mml:mi><mml:mo>→</mml:mo><mml:mi>W</mml:mi><mml:mi>W</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math> are set. The upper limits are in the range 0.0062–0.380 pb for the $$H\rightarrow bb$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>H</mml:mi><mml:mo>→</mml:mo><mml:mi>b</mml:mi><mml:mi>b</mml:mi></mml:mrow></mml:math> channel and in the range 0.023–8.9 pb for the $$H\rightarrow WW$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>H</mml:mi><mml:mo>→</mml:mo><mml:mi>W</mml:mi><mml:mi>W</mml:mi></mml:mrow></mml:math> channel. An interpretation of the results in the context of two-Higgs-doublet models is also given.
Supplementary Figure Legends from FcRL5 as a Target of Antibody–Drug Conjugates for the Treatment of Multiple Myeloma (2023)

&lt;p&gt;PDF file - 25KB&lt;/p&gt;
Efficient fiber-coupled detection for multiphoton microscopy: characterization and comparison with air-coupled detection (2004)

The femtoliter excitation volume of multiphoton microscopy renders all emitted photons useful in detecting fluorescence signals. We have previously demonstrated the viability of transmitting the emitted fluorescence via multimode optical fibers onto a photomultiplier tube (PMT) in a full-field arrangement. A custom MPLSM, based on a commercially available confocal microscope was developed to readily switch between the regular descanned path for confocal microscopy and our non-descanned pathways (direct detection) supporting fiber-coupled detection. We now wish to demonstrate the efficacy of fiber-based detection using a side-by-side comparison of our fiber-coupled paradigm to the traditional method of directly focusing the fluorescence, through air, onto a PMT. To effectively compare the two methods, we have incorporated a second direct detection epi-fluorescence pathway for air-coupling onto a PMT that does not affect the performance of the fiber-based MPLSM. We found that fiber-based detection compares favorably against traditional direct detection. We demonstrate the viability of fiber-based detection for high-resolution neuronal brain slice imaging.
Benchmarking Super-Resolution Algorithms on Real Data (2017)

Over the past decades, various super-resolution (SR) techniques have been developed to enhance the spatial resolution of digital images. Despite the great number of methodical contributions, there is still a lack of comparative validations of SR under practical conditions, as capturing real ground truth data is a challenging task. Therefore, current studies are either evaluated 1) on simulated data or 2) on real data without a pixel-wise ground truth. To facilitate comprehensive studies, this paper introduces the publicly available Super-Resolution Erlangen (SupER) database that includes real low-resolution images along with high-resolution ground truth data. Our database comprises image sequences with more than 20k images captured from 14 scenes under various types of motions and photometric conditions. The datasets cover four spatial resolution levels using camera hardware binning. With this database, we benchmark 15 single-image and multi-frame SR algorithms. Our experiments quantitatively analyze SR accuracy and robustness under realistic conditions including independent object and camera motion or photometric variations.
X‐Ray Microanalysis of the Fingernails in Term and Preterm Infants (1988)

The element content of the fingernails of 10 term and 14 preterm infants, clipped for the first time after delivery, was determined by x-ray microanalysis. The results showed a decrease in sulfur and aluminum, and a higher chlorine content in term infants in comparison with preterm ones, the difference being statistically significant. Sodium, potassium, calcium, and zinc content did not differ in the two groups. Copper, iron, magnesium, aluminum, and phosphorus were detected in trace amounts only. Cobalt was not detected in the fingernails of newborns in either group. The elevated content of aluminum in the fingernails of preterm infants may be a clue to the osteopenia observed in these infants.
100 kW Coherently Combined Slab MOPAs (2009)

We are developing a 100-kW Nd:YAG cw solid-state laser system. Seven wavefront-corrected 15-kW MOPA (master oscillator power amplifier) laser chains are phase locked to achieve a single aperture output beam with good beam quality.
Mechanical Properties and Microstructure of Heat Treated and Quenched Ti-6Al-4V. (1977)

Contents: (a) The Fatigue Life of Ti-6Al-4V Tested at 260C in the Annealed and as Quenched Condition; (b) A Comparison of the Microstructure and Properties of Small Diameter Rod and Thick Plate; (c) Corrosion-Fatigue Properties of the Ti-6Al-4V Alloys; and (d) Microstructure and Properties of Ti-6Al-4V Heat Treated at 900C and 927C Followed by a Water Quench.
Structure and functional anatomy of the gas exchange apparatus of leafless orchids: evidence for a control mechanism? (2021)

Abstract It is assumed that special structures in aerial roots of leafless orchids, aeration units, are involved in gas exchange regulation. In this study, the structure of aeration units in three leafless taxa (Microcoelia exilis, M. aphylla, Dendrophylax funalis) and a leaf-bearing species (Campylocentrum micranthum) are investigated to obtain more evidence of a possible mechanism for gas exchange control in aerial orchid roots. Extensive analyses of the anatomy of the velamen radicum, exodermis and cortex were performed using light and electron microscopy and µCT. In all considered leafless taxa, the aeration unit consists of pneumathodes (non-wettable regions in the velamen radicum), an exodermal aeration cell (EAC) with a thin cell wall (often equipped with a special internal layer showing a fluffy structure) and specialized cortical cells (SCC). The SCC provide gaps for gas exchange, show differentially thickened cell walls and are arranged in a staggered manner. Based on the 3D structure of the aeration unit, we suggest the possibility of dehydration-triggered gap closure (driven by root shrinkage), in the process of which first the SCC are pushed against each other and second the EAC are squeezed shut by the exodermis.
Bosch's approach toward automated driving (2015)

Abstract Advanced driver assistance systems already help drivers reach their destinations safely and more comfortably. Future systems will evolve from driver assistance over highly automated vehicles to fully automated driving. With an increasing level of automation, automated functions will reduce the driver's burden more and more, thereby creating space for productivity, communication or entertainment while driving. In this article we outline our roadmap for future automated vehicles, assess the key challenges for introduction and give an overview of the major algorithmic components.
Evidence for a complex regulation of Pho4 action in S. cerevisiae (1998)

Transcriptional activation of the yeast PHO5 promoter upon phosphate starvation requires two transcriptional activators, the bHLH protein Pho4 and the homeodomain protein Pho2. The two proteins bind to the promoter in a cooperative manner. Cooperativity requires DNA binding of both proteins as well as specific Pho2-Pho4 interaction. The activity of Pho4 is regulated through phosphorylation by Pho80-Pho85, a cyclin-cdk complex. Under repressing conditions Pho4 is phosphorylated and located predominantly in the cytoplasm. However, although non-phosphorylatable Pho4 derivatives are constitutively localised in the nucleus, activity of PHO5 in a strain expressing such mutants still increases 4 times upon induction, showing that there is yet another mechanism regulating PHO5 expression which is independent of Pho80-Pho85. In addition to six Pho85 consensus target sites, Pho4 contains two putative PKA phosphorylation sites, one being located in the basic region (Ser 254), which is involved in interactions with Pho2. We have therefore examined the possible role of Ser254 phosphorylation in the regulation of Pho4-Pho2 interactions and consequently the ability of Pho4 to bind DNA and activate transcription. To this end, we introduced two mutations into Pho4 at this residue (S254A and S254D). Expression of PHO5 in a strain containing the Pho4 derivative (S254A) was 2-3 times higher at repressive conditions than with wt Pho4, but only slightly higher at induced conditions. On the other hand, the S254D mutation, which mimicks constitutively phosphorylated Ser254, was without a significant effect at repressive conditions, but results in more than 2-fold lower activation at induced conditions, indicating that phosphorylation of Ser254 is involved in the regulation of Pho4 activity. Experiments testing the ability of the mutant Pho4 proteins to interact with Pho2 and to bind DNA are in progress.
Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections (2021)

Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413–415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.