gebhart/patrepeval huggingface dataset:
Reply (2013)

Dear Sir,We appreciate the comments and suggestions offered by Dr. Askoy and colleagues in their letter entitled ‘Corrected VEGF levels based on platelet count should be calculated'. There is support in the literature for correcting serum VEGF for platelet count, but not for correcting urine VEGF. VEGF is stored in the α-granules of platelets, and VEGF is released by degranulation when platelets are activated. Blood samples are allowed to clot when forming serum and this activates the platelets and causes release of platelet VEGF into the sample; serum VEGF therefore reflects the sum of plasma and platelet VEGF. Platelet VEGF is not released when blood samples are correctly processed for plasma with platelet-stabilizing anticoagulants (specifically, citrate-theophylline-adenosine-dipyridamole, CTAD) [1], but CTAD is not always used. As some studies report serum VEGF and some report plasma VEGF (using various techniques), there is currently substantial variability in the published literature. Correcting serum VEGF for platelet count has been proposed as a means to improve the consistency of serum VEGF measurements [2]. In our study, we measured urine VEGF, not serum VEGF. Urine VEGF is thought to reflect free circulating VEGF, not VEGF stored in platelets. Since platelet activation does not occur during the collection or processing of urine samples, we believe we have avoided this potentially confounding variable. While platelets are important reservoirs and scavengers of circulating VEGF, and thrombocytopenia has been suggested as a risk factor for ROP [3,4,5], there is currently no data in the literature to support correcting urine VEGF measurements for platelet count. Regardless, platelet counts were not simultaneously obtained along with urine samples, so we are not able to test this hypothesis using our current data.
Figures S2-S3-S4 from Silencing the Snail-Dependent RNA Splice Regulator ESRP1 Drives Malignant Transformation of Human Pulmonary Epithelial Cells (2023)

&lt;p&gt;Figures S2-S3-S4 provide additional evidence that Snail is a potent driver of EMT, carcinogenic signaling programs, and stem cell expansion in vitro.&lt;/p&gt;
Supplementary Figure 3 from Adoptive Cell Therapy for Lymphoma with CD4 T Cells Depleted of CD137-Expressing Regulatory T Cells (2023)

&lt;p&gt;PDF file - 352K, Memory markers do not identify distinct subsets of T cells in vaccinated vs. unvaccinated donors.&lt;/p&gt;
Optimizing Scalable Video Compression for Efficient Implementation on a VLIW Media Processor (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> State-of-the-art digital multimedia platforms contain a powerful Very-Long Instruction Word (VLIW) processing core. To obtain optimum performance on such a platform, a media-processing algorithm should exploit all the advantages provided by the VLIW processor's architecture. This paper focuses on a method for adapting a video compression algorithm for implementation on a VLIW processor using algorithm-architecture co-design. We demonstrate the importance of our adaptation approach and show the improved efficiency of the algorithm implementation. </para>
Diastolic Ventricular Interaction (1997)

Diastolic ventricular interaction in patients with chronic heart failure is associated with attenuated forearm vasoconstriction or paradoxical vasodilation during LBNP. This may explain the apparent derangement in baroreflex control of sympathetic outflow during acute volume unloading in heart failure.
Congener Response Reduces Risks from Bottom-Up and Top-Down Forces: Behavioral Parsimony by a Xylophage (2012)

Organisms must find food and avoid enemies. Homalodisca vitripennis (Germar) is a primary vector of Xylella fastidiosa , the causal agent of Pierce's disease, a deadly disease of grapevines and other plants. H. vitripennis feeds on xylem tissue depauperate in nutrients and has evolved many specialized physiological and behavioral adaptations. Bottom-up mortality risks to H. vitripennis include starvation and reduced fecundity through loss of quality hosts. Top-down risks include predation, egg parasitism by Hymenoptera, and fungal pathogens. Visual behavior of H. vitripennis in response to congeners, common heterospecifics, and artificial models of conspecifics was investigated. Behaviors and the physical properties of the visual cues involved were characterized. H. vitripennis adults exhibited highly significant, positive responses to conspecifics, a heterospecific species, Oncometopia nigricans , and artificial models the size of adult leafhoppers. Significant response was not observed to a congeneric, Homalodisca insolita , with a smaller body size, or to models of sizes, shapes, and colors other than black and red. Cadavers of leafhoppers placed on a novel and nutritionally poor host plant stimulated H. vitripennis adults to land on branches containing the cadavers. H. vitripennis also landed preferentially on branches containing conspecific cadavers despite the presence of a cadaver of a major predator, Anolis carolinensis lizards, or artificial lures resembling spiders. This consistent visual response was independent of variable bottom-up (host quality) and top-down (predator presence) risks, and it suggests for the first time such parsimonious behavior in insects, i.e., sole use of a live visual cue as a means to reduce mortality risks from bottom-up and top-down forces.
<title>Propagation analysis of the truncated second-order moment</title> (1996)

We discuss the use of the truncated second-order moment as an appropriate way of getting rid of the troublesome divergence problem caused by hard-edge diffraction. This approach preserves the simplicity of the propagation law of the beam size and makes the beam-propagation factor nearly invariant when propagation in ABCD systems is considered.
Front Cover: Isoliquiritigenin Attenuates Adipose Tissue Inflammation and Metabolic Syndrome by Modifying Gut Bacteria Composition in Mice (2022)

Mol. Nutr. Food Res. 2022, 66, 202101119 DOI: 10.1002/mnfr.202101119 Isoliquiritigenin (ILG), a flavonoid with a chalcone structure derived from Glycyrrhiza uralensis, beneficially modified gut microbiota by increasing the abundance of Akkermansia muciniphila and Parabacteroides goldsteinii. The altered composition of the gut bacteria by ILG restored impaired gut barrier function and prevented metabolic disorder in high fat diet-fed mice. This is reported by Riko Ishibashi and co-workers in article number 2101119.
High-Resolution Gamma-Ray Spectrometry of Pebble Bed Reactor Fuel Using Adaptive Digital Pulse Processing (2023)

In this work, an investigation was performed to assess the feasibility of passive gamma-ray spectrometry using adaptive digital pulse processing for online interrogation of pebble bed reactor (PBR) fuel. This work incorporates the physics of the radiation emission phenomenon with advanced pulse processing techniques to develop a high-resolution gamma-spectrometry system capable of handling ultrahigh count rates in various applications of nuclear science and technology. Computational modeling was used to simulate the irradiation of PBR fuel and to design the adaptive digital pulse processing–based gamma-ray spectrometry system. Monte Carlo simulations were performed to study the gamma-ray spectra of the PBR fuel and to perform coupled photon-electron transport analysis to calculate the pulse-height spectrum of PBR fuel. A Monte Carlo computer routine was used to predict the effect of pulse pileup at high-count-rate conditions. This code utilizes the random interval distribution function based on Poisson statistics to simulate the pileup behavior. Combined with pileup logic, a recursive trapezoid filter with adaptive shaping parameters was implemented to simulate the pileup behavior of a digital gamma-ray spectrometry system. The adaptive shaping algorithm selects the rise time of the trapezoid shaping filter based on the separation between the input pulses for each incoming signal. The simulation results using the proposed adaptive digital pulse processing demonstrated that with the improved energy resolution, the burnup information can be more accurately determined on a pebble-by-pebble basis as compared to fixed shaping, and tasks related to in-core fuel management, safeguards, and waste management become feasible to perform efficiently and accurately.
Supplementary Tables S1 and S2 from Inhibition of Melanoma Growth by Small Molecules That Promote the Mitochondrial Localization of ATF2 (2023)

&lt;p&gt;Supplementary Tables S1 and S2 - PDF file 100K, Supplementary Table S1. The top 20 upregulated genes in WM793 cells treated for 24 h with SBI-087702 as compared to DMSO-treated cells; Supplementary Table S2. The top 20 downregulated genes in WM793 cells treated for 24 h with SBI-0087702 as compared to DMSO-treated cells&lt;/p&gt;
Optoelectronic Properties of Mixed Iodide–Bromide Perovskites from First-Principles Computational Modeling and Experiment (2022)

Halogen mixing in lead-halide perovskites is an effective route for tuning the band gap in light emission and multijunction solar cell applications. Here we report the effect of halogen mixing on the optoelectronic properties of lead-halide perovskites from theory and experiment. We applied the virtual crystal approximation within density functional theory, the <i>GW</i> approximation, and the Bethe-Salpeter equation to calculate structural, vibrational, and optoelectronic properties for a series of mixed halide perovskites. We separately perform spectroscopic measurements of these properties and analyze the impact of halogen mixing on quasiparticle band gaps, effective masses, absorption coefficients, charge-carrier mobilities, and exciton binding energies. Our joint theoretical-experimental study demonstrates that iodide-bromide mixed-halide perovskites can be modeled as homovalent alloys, and local structural distortions do not play a significant role for the properties of these mixed species. Our study outlines a general theoretical-experimental framework for future investigations of novel chemically mixed systems.
A synthetic peptide containing a predominant protein kinase C site within p47phox inhibits the NADPH oxidase in intact neutrophils (1996)

In vivo loading of a synthetic peptide (peptide 4) corresponding to residues 314-331 (RSRKRLSQDAYRRNSVRF) consistently diminished the oxidative burst in response to either phorbol 12-myristate 13-acetate (PMA) or formylmethionyl-leucyl-phenylalanine and cytochalasin B (fMLP/CB) compared to other synthetic peptides derived from the p47phox sequence. The effects of peptide 4 were concentration dependent with respect to both PMA and fMLP/CB. In contrast, peptide 4 enhanced the oxidative burst in response to fMLP alone. Peptide 4 inhibited the PMA and fMLP-mediated phosphorylation of endogenous neutrophil cytosolic proteins including p47phox. The PMA-induced translocation of p47phox to the plasma membrane was diminished in neutrophils loaded with peptide 4. These data represent the first report of a synthetic peptide derived from p47phox that inhibits the NADPH oxidase in intact neutrophils and inhibits the protein kinase C-mediated phosphorylation of endogenous p47phox.
The Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface is Altered by Hydrolyzed Glycosidic Bonds (2009)

A multiscale simulation model is used to construct potential and free energy surfaces for the carbohydrate-binding module [CBM] from an industrially important cellulase, Trichoderma reesei cellobiohydrolase I, on the hydrophobic face of a coarse-grained cellulose Ibeta polymorph. We predict from computation that the CBM alone exhibits regions of stability on the hydrophobic face of cellulose every 5 and 10 A, corresponding to a glucose unit and a cellobiose unit, respectively. In addition, we predict a new role for the CBM: specifically, that in the presence of hydrolyzed cellulose chain ends, the CBM exerts a thermodynamic driving force to translate away from the free cellulose chain ends. This suggests that the CBM is not only required for binding to cellulose, as has been known for two decades, but also that it has evolved to both assist the enzyme in recognizing a cellulose chain end and exert a driving force on the enzyme during processive hydrolysis of cellulose.
Quantum signal processing (2002)

In this article we present a signal processing framework that we refer to as quantum signal processing (QSP) (Eldar 2001) that is aimed at developing new or modifying existing signal processing algorithms by borrowing from the principles of quantum mechanics and some of its interesting axioms and constraints. However, in contrast to such fields as quantum computing and quantum information theory, it does not inherently depend on the physics associated with quantum mechanics. Consequently, in developing the QSP framework we are free to impose quantum mechanical constraints that we find useful and to avoid those that are not. This framework provides a unifying conceptual structure for a variety of traditional processing techniques and a precise mathematical setting for developing generalizations and extensions of algorithms, leading to a potentially useful paradigm for signal processing with applications in areas including frame theory, quantization and sampling methods, detection, parameter estimation, covariance shaping, and multiuser wireless communication systems. We present a general overview of the key elements in quantum physics that provide the basis for the QSP framework and an indication of the key results that have so far been developed within this framework. In the remainder of the article, we elaborate on the various elements in this figure.
Optical Interconnects for Future Advanced Antenna Systems: Architectures, Requirements and Technologies (2021)

This paper aims to give an outlook of future advanced antenna systems for 5G and 6G wireless networks. The trend to increase the peak data rate and to reduce latency and power consumption will continue in the future. This will be made possible by the exploitation of millimeter wave frequency bands and by the introduction of massive multiple-input multiple-output antenna technology which requires a transformation of the antenna hardware architectures and technologies. Advanced antenna systems based on arrays of several hundreds of antenna elements are under development and to keep the fronthaul throughput manageable, some digital signal processing functions have been moved inside the antenna, creating the need to distribute very big volumes of data at high bit rate across the antenna. The characteristics and hardware architecture of future advanced antenna systems are discussed and the relevant interconnect requirements are presented. A new type of monolithically integrated optical transceiver is presented, integrating electronic and photonic circuits on the same chip with high bandwidth density, high energy efficiency and low latency. The transceiver technology is discussed and results of experimental demonstrations are given.
Analysis of Al2O3 Atomic Layer Deposition on ZrO2 Nanoparticles in a Rotary Reactor (2007)

Abstract Al 2 O 3 atomic layer deposition (ALD) is analyzed on ZrO 2 nanoparticles in a rotary reactor. This rotary reactor allows for static exposures and efficiently utilizes the reactants for ALD on high surface area nanoparticles. The Al 2 O 3 ALD is performed using exposures to Al(CH 3 ) 3 and H 2 O reactants. The pressure transients during these exposures are examined using a sequence of reactant micropulses. These micropulses are less than the required exposures for the ALD surface chemistry to reach completion. The pressure transients during identical sequential Al(CH 3 ) 3 and H 2 O micropulses change as the surface chemistry progresses to completion. These pressure transients allow the required saturation reactant exposure to be determined to maximize reactant usage. The ZrO 2 nanoparticles are coated using various numbers of Al(CH 3 ) 3 and H 2 O reactant exposures. The Al 2 O 3 ALD‐coated ZrO 2 nanoparticles are subsequently analyzed using a number of techniques including scanning electron microscopy (SEM), transmission electron microscopy (TEM), Auger electron spectroscopy (AES), scanning AES (SAES), and X‐ray photoelectron spectroscopy (XPS). The TEM images reveal very conformal Al 2 O 3 ALD on the ZrO 2 nanoparticles. The Al 2 O 3 ALD thicknesses versus number of Al(CH 3 ) 3 and H 2 O reactant exposures yielded an Al 2 O 3 ALD growth rate of 2.0 Å per reactant cycle. The AES and XPS results are consistent with an Al 2 O 3 ALD film that completely and conformally covered the underlying ZrO 2 nanoparticle. The SAES measurements show that the Al 2 O 3 ALD films are continuous and homogeneous on the ZrO 2 nanoparticles. These results demonstrate that a rotary reactor can successfully perform ALD with high reactant efficiency on high surface area nanoparticles.
Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism (2020)

The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN) of the influenza RNA dependent RNA polymerase, and we report here complexes of PAN with RNA and DNA oligonucleotides to understand its specificity and the structural basis of baloxavir resistance mutations. The RNA and DNA oligonucleotides bind within the substrate binding groove of PAN in a similar fashion, explaining the ability of the enzyme to cleave both substrates. The individual nucleotides occupy adjacent conserved pockets that flank the two-metal active site. However, the 2' OH of the RNA ribose moieties engage in additional interactions that appear to optimize the binding and cleavage efficiency for the natural substrate. The major baloxavir resistance mutation at position 38 is at the core of the substrate binding site, but structural studies and modeling suggest that it maintains the necessary virus fitness via compensating interactions with RNA. These studies will facilitate the development of new influenza therapeutics that spatially match the substrate and are less likely to elicit resistance mutations.
Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling (2021)

SHP2 is a protein tyrosine phosphatase that normally potentiates intracellular signaling by growth factors, antigen receptors, and some cytokines, yet is frequently mutated in human cancer. Here, we examine the role of SHP2 in the responses of breast cancer cells to EGF by monitoring phosphoproteome dynamics when SHP2 is allosterically inhibited by SHP099. The dynamics of phosphotyrosine abundance at more than 400 tyrosine residues reveal six distinct response signatures following SHP099 treatment and washout. Remarkably, in addition to newly identified substrate sites on proteins such as occludin, ARHGAP35, and PLCγ2, another class of sites shows reduced phosphotyrosine abundance upon SHP2 inhibition. Sites of decreased phospho-abundance are enriched on proteins with two nearby phosphotyrosine residues, which can be directly protected from dephosphorylation by the paired SH2 domains of SHP2 itself. These findings highlight the distinct roles of the scaffolding and catalytic activities of SHP2 in effecting a transmembrane signaling response.
Comparison of breast carcinomas diagnosed in the 1980s with those diagnosed in the 1940s to 1960s. (1991)

Improved survival with breast cancer can at least partially be explained by detection of increased numbers of small carcinomas with favourable histological characteristics.
In vivo changes of hemopoietic progenitors and the expression of the interleukin 5 gene in eosinophilic mice infected with Toxocara canis. (1990)

It has been demonstrated that purified recombinant interleukin 5 (rIL-5) supports the terminal differentiation and proliferation of eosinophilic precursors in vitro and plays an important role in increasing the functional activities of eosinophils. In this study, we examined the hemopoietic changes and analyzed murine (m) IL-5 mRNA expression in eosinophilic mice infected with the helminth Toxocara canis. In eosinophilic mice, eosinophils increased in number in both bone marrow and spleen. However, the number of eosinophilic precursors increased markedly in spleen cells of eosinophilic mice but remained relatively constant in the bone marrow. In the presence of granulocyte colony-stimulating factor (G-CSF), the number of granulocytic precursors increased in the spleen cells of eosinophilic mice. From these findings, the condition of eosinophilopoiesis in eosinophilic mice is accompanied by an increase in granulocyte-macrophage progenitors as well as eosinophil progenitors. Using Northern blot analysis, a weak but definite band corresponding to mIL-5 mRNA was detected in spleen cells of mice 4 and 5 days after helminthic infection. In addition, these data were confirmed by in vitro polymerase chain reaction (PCR) amplification of mRNA obtained from these spleen cells. Finally, injections of a monoclonal antibody against mIL-5 completely suppressed the blood eosinophilia in mice infected with T. canis. In conclusion, IL-5 is suggested to play a major role in eosinophilopoiesis in vivo.
Thermodynamic study on the role of hydrogen during hydride vapor phase epitaxy of Alx Ga1–xN (2006)

Abstract Thermodynamic study for the hydride vapor phase epitaxy (HVPE) of Al x Ga 1– x N was performed to realize the thick, large size AlGaN wafers. It was found that the hydrogen (H 2 ) in the carrier gas affected the resulting solid composition of the alloy. The solid composition x in Al x Ga 1– x N can be controlled by changing the H 2 mole fraction in the carrier gas. These facts would be explained by difference in the growth reactions between AlN and GaN. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Postoperative radiotherapy in Dukes' B and C carcinoma of the rectum and rectosigmoid: A randomized multicenter study (1986)

Results obtained during the first 5 years of a randomized study of postoperative radiotherapy (50 Gy) are presented. Criteria for randomization were fulfilled in 494 of 861 patients with Dukes' B and C tumors, when the trial was closed. Severe complications from radiotherapy approximated 10%. Probability of survival without local failure within 24 months was significantly higher after radiotherapy in patients with Dukes' C tumors, and the time of local failure was delayed 1 year. Patients with Dukes' B tumors had no benefit from radiotherapy. Risks of distant metastases and death were not influenced by radiotherapy in the main groups. Plasma-CEA measurements were evaluated blindly, and radiotherapy changed the critical levels of CEA for detection of recurrent cancer. It was concluded that patients with Dukes' C tumors may benefit from radiotherapy and plasma-CEA levels are influenced by radiotherapy, which may be important, when these are used in screening for recurrent cancer.
Nuclear Factor (Erythroid-Derived 2)-Like 2 Regulates the Hepatoprotective Effects of Remote Ischemic Conditioning in Hemorrhagic Shock (2018)

Our studies demonstrate the critical role of Nrf2 in the ability of RIC to prevent organ injury after S/R.