gebhart/patrepeval huggingface dataset:
Global Proteomics: Pharmacodynamic Decision Making via Geometric Interpretations of Proteomic Analyses (2008)

Disease and drugs can modulate the concentrations of hundreds of proteins in the blood which can be accurately measured using contemporary proteomic methods. Nevertheless, it is common practice to reduce the plurality of disease and drug effects by a few proteins for the pragmatic purposes of immunoassay development. The vast majority of putative biomarkers discovered by this reductionist approach never reach the clinic for two reasons: the prohibitive time and cost of assay development and the acute risk of a reduced protein panel failing when validated on a broader cross-section of the population. Global Proteomics is an alternate methodology where all blood proteins modulated by disease or drug are used to r esolve pharmacodynamic questions without the time, cost, and risk of developing an immunoassay . The Global Proteomic approach was applied to an Alzheimer study where it was demonstrated that a large panel of plasma proteins is pr edictive of disease severity (as measured by the Mini Mental State Examination). Furthermore, a subset of this panel was shown to be modulated by disease treatment (donepezil), thereby providing a means to quantify response to tr eatment. Finally, to establish that the Global Proteomics methodology has broad utility, it was also applied to a Hypertension study, illustrating that a panel of plasma proteins can also be derived that are corr elated with disease severity (as measured by blood pressure). In par ticular, the Global Proteomics methodology can readily distinguish patients responsive and non-responsive to hypertension therapies. The Global Proteomics approach is based upon a bioinformatics analysis approach which clusters samples by proteomic similarity and then uses a geometric representation of sample similarity to answer common pharmacodynamic questions.
Monitoring the regional spread of the invasive leafminer Cameraria ohridella Deschka and Dimic (Lepidoptera: Gracillariidae) by damage assessment and pheromone trapping (2004)

The leafminer Cameraria ohridella Deschka &amp; Dimic is an invasive pest of horse chestnut, Aesculus hippocastanum L., trees that has spread rapidly across Europe over the past 19 yr. It was recently reported in the United Kingdom, Denmark, and the Ukraine, and this spread is expected to continue through the Scandinavian countries until the northern limit of the host tree distribution is reached. The presence of the species is generally reported first in the cities, either as consequence of human-related transportation or because of the higher number of host trees in these areas. As a consequence, detailed studies of the spread of this pest through rural areas have not yet been carried out. We have monitored the spread of the moth at the fringe of its known distribution in eastern France during the period 2001-2003. The population was estimated by observing the damage caused by the pest and by establishing a network of pheromone traps. Pheromone traps were set up to measure two generations in 2001 and 2002, whereas the spatial pattern of the spread of the species measured by damage assessment was followed for each generation between 2001 and 2003 (nine generations). Spatial and temporal patterns in the population estimates made using these two methods were compared. We found that estimates made from damage assessment correlated with log-transformed estimates from pheromone trap catches, suggesting that both techniques can be used to monitor the spread of this pest. Over the period 2001-2003, the spread rate ranged from 17.0 to 37.9 km/yr, depending on the population threshold and method used.
Data from CXCR4 Is a Novel Target of Cancer Chemopreventative Isothiocyanates in Prostate Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Isothiocyanates (ITCs) derived from cruciferous vegetables, including phenethyl isothiocyanate (PEITC) and sulforaphane (SFN), exhibit &lt;i&gt;in vivo&lt;/i&gt; activity against prostate cancer in a xenograft and transgenic mouse model, and thus are appealing for chemoprevention of this disease. Watercress constituent PEITC and SFN-rich broccoli sprout extract are under clinical investigations but the molecular mechanisms underlying their cancer chemopreventive effects are not fully understood. The present study demonstrates that chemokine receptor CXCR4 is a novel target of ITCs in prostate cancer cells. Exposure of prostate cancer cells (LNCaP, 22Rv1, C4-2, and PC-3) to pharmacologically applicable concentrations of PEITC, benzyl isothiocyanate (BITC), and SFN (2.5 and 5 μmol/L) resulted in downregulation of CXCR4 expression. None of the ITCs affected secretion of CXCR4 ligand (stromal-derived factor-1). &lt;i&gt;In vivo&lt;/i&gt; inhibition of PC-3 xenograft growth upon PEITC treatment was associated with a significant decrease in CXCR4 protein level. A similar trend was discernible in the tumors from SFN-treated TRAMP mice compared with those of control mice, but the difference was not significant. Stable overexpression of CXCR4 in PC-3 cells conferred significant protection against wound healing, cell migration, and cell viability inhibition by ITCs. Inhibition of cell migration resulting from PEITC and BITC exposure was significantly augmented by RNAi of CXCR4. This study demonstrates, for the first time, that cancer chemopreventive ITCs suppress CXCR4 expression in prostate cancer cells &lt;i&gt;in vitro&lt;/i&gt; as well as &lt;i&gt;in vivo&lt;/i&gt;. These results suggest that CXCR4 downregulation may be an important pharmacodynamic biomarker of cancer chemopreventative ITCs in prostate adenocarcinoma. &lt;i&gt;Cancer Prev Res; 8(5); 365–74. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Sense and Shoot: Simultaneous Detection and Degradation of Low-Level Contaminants Using Graphene-Based Smart Material Assembly (2014)

Smart material nanoassemblies that can simultaneously sense and shoot low-level contaminants from air and water are important for overcoming the threat of hazardous chemicals. Graphene oxide (GO) sheets deposited on mesoscopic TiO2 films that underpin the deposition of Ag nanoparticles with UV irradiation provide the foundation for the design of a smart material. The Ag particle size is readily controlled through precursor concentration and UV irradiation time. These semiconductor–graphene oxide–metal (SGM) films are SERS-active and hence capable of sensing aromatic contaminants such as 4-nitrobenzenethiol (4-NBT) in nanomolar range. Increased local concentration of organic molecules achieved through interaction with 2-D carbon support (GO) facilitates low-level detection of contaminants. Upon UV irradiation of 4-NBT-loaded SGM film, one can induce photocatalytic transformations. Thus, each component of the SGM film plays a pivotal role in aiding the detection and degradation of a contaminant dispersed in aqueous solutions. The advantage of using SGM films as multipurpose “detect and destroy” systems for nitroaromatic molecules is discussed.
Yet Faster Ray-Triangle Intersection (Using SSE4) (2009)

Ray-triangle intersection is an important algorithm, not only in the field of realistic rendering (based on ray tracing) but also in physics simulation, collision detection, modeling, etc. Obviously, the speed of this well-defined algorithm's implementations is important because calls to such a routine are numerous in rendering and simulation applications. Contemporary fast intersection algorithms, which use SIMD instructions, focus on the intersection of ray packets against triangles. For intersection between single rays and triangles, operations such as horizontal addition or dot product are required. The SSE4 instruction set adds the dot product instruction which can be used for this purpose. This paper presents a new modification of the fast ray-triangle intersection algorithms commonly used, which-when implemented on SSE4-outperforms the current state-of-the-art algorithms. It also allows both a single ray and ray packet intersection calculation with the same precomputed data. The speed gain measurements are described and discussed in the paper.
Xenotransplantation and Xenogeneic Infections (1995)

The ongoing shortage of human organs and tissues for transplantation, coupled with scientific and biotechnological advances, has catalyzed new attempts to use animal tissues in humans — a field known as xenotransplantation. Pigs and nonhuman primates have been used as sources of organs, with limited success.1,2 Recently, the transplantation of baboon bone marrow to attempt to reconstitute the immune system in patients with AIDS was proposed,3 and fetal-pig mesencephalon cells are being studied for the treatment of patients with refractory parkinsonism.The use of xenogeneic tissues in transplantation has raised concern about potential infection with both recognized zoonotic pathogens . . .
ChemInform Abstract: Stereoselective Synthesis of Side Chain‐Functionalized Tetrahydropyrans from 5‐Hexenols. (2014)

Abstract Aerial oxygen stereoselectively converts 5‐hexenols into 2‐methyltetrahydropyrans via oxidative cyclization/radical functionalization cascades, when activated by a fluoro‐substituted cobalt(II) bis‐(β‐diketonate) complex in solutions of cyclohexa‐1,4‐diene (CHD).
Facile synthesis of comb, star, and graft polymers via reversible addition–fragmentation chain transfer (RAFT) polymerization (2002)

Abstract Reversible addition–fragmentation chain transfer (RAFT) polymerization has been shown to be a facile means of synthesizing comb, star, and graft polymers of styrene. The precursors required for these reactions were synthesized readily from RAFT‐prepared poly(vinylbenzyl chloride) and poly(styrene‐ co ‐vinylbenzyl chloride), which gave intrinsically well‐defined star and comb precursors. Substitution of the chlorine atom in the vinylbenzyl chloride moiety with a dithiobenzoate group proceeded readily, with a minor detriment to the molecular weight distribution. The kinetics of the reaction were consistent with a living polymerization mechanism, except that for highly crowded systems, there were deviations from linearity early in the reaction due to steric hindrance and late in the reaction due to chain entanglement and autoacceleration. A crosslinked polymer‐supported RAFT agent was also prepared, and this was used in the preparation of graft polymers with pendant polystyrene chains. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2956–2966, 2002
A Comparison of Acquired Port-wine Stain with Congenital Port-wine Stain Using an Image Analyzer (2008)

The mean vessel area in APWS was 1014.7 ± 782.5µm(2) and that of CPWS was 1341.5 ± 689.9µm(2). The mean percentage of vascular area in APWS was 2.02 ± 1.38% and that of CPWS was 2.65 ± 1.56%. The mean vessel depth in APWS was 327.5 ± 120.7µm and 321.7 ± 93.1µm in CPWS. No histopathologic variable was statistically significant using the Mann-Whitney test (p>0.05).
Analysis of loss to prevent oscillations in the slow wave cyclotron amplifier (1982)

Abstract An analysis of loss applied to the dielectric loaded waveguide slow wave cyclotron amplifier for the purpose of suppressing oscillations due to reflections from input/output couplers is presented. Both graphite type and ferrite type losses are considered. The appropritate waveguide dispersion relation is derived in the absence of an electron beam for each case and solved for the TEol and TE02, modes. An example attenuator design is also given.
Excellent uniformity and reproducible resistance switching characteristics of doped binary metal oxides for non-volatile resistance memory applications (2006)

We have investigated various doped metal oxides such as copper doped molybdenum oxide, copper doped Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , copper doped ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , aluminium doped ZnO, and Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> O for novel resistance memory applications. Compared with non-stoichiometric oxides (Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5-x</sub> , ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> , SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> ), doped metal oxides show higher device yield. Moreover, Cu:MoO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> have demonstrated excellent memory characteristics such as reliability under programming cycles, potential multi-bit operation, good data retention, highly scalable property, and fast switching speed. The switching mechanism of the copper doped molybdenum oxide can be explained by the generation and rupture of multi-filaments under the electrical stress
Impact of permethrin‐impregnated mosquito nets compared with DDT house‐spraying against malaria transmission by Anopheles farauti and An.punctulatus in the Solomon Islands (1993)

In villages of northern Guadalcanal in the Solomon Islands, where the predominant malaria vector is An.farauti No. 1 and An.puctulatus is also involved, malaria transmission rates were compared for three zones: (1) non-intervention: 438 people in seventeen villages; (2) residual DDT house-spraying two cycles per year: 644 people in thirty villages; (3) bednets impregnated with permethrin 0.5 g/m2 twice per year, used by 580 people in sixteen villages. Regular DDT spraying in zones 1 and 3 had been withdrawn 18 months previously. Malariological blood smear surveys of children aged 1-9 years in August 1986 to January 1987 showed a mean baseline malaria parasite rate of 38% (32/84). By February 1988, 18 months after introduction of impregnated bednets, the Plasmodium falciparum infection rate in children was lowest in the zone using impregnated bednets (21% of 29), intermediate in the untreated zone (29% of 34) and highest in the DDT zone (46% of 53), but these differences were not statistically significant. P. vivax infection rates were 9-14%. Using ELISA tests for malaria circumsporozoite antigen in the vectors, overall positivity rates were 0.7% of 49,902 An.farauti and 2.54% of 118 An.punctulatus, comprising 228 P.falciparum and 124 P.vivax infections. In the study zones, vector positivity rates were 0.93% of 31,615 An.farauti in the untreated zone; 0.32% of 16,883 An.farauti in the DDT zone; 0.07% of 1404 An.farauti and 2.54% of 118 An.puctulatus in the impregnated bednet zone. here was no significant correlation between malaria parasite rates in the vectors and the children.(ABSTRACT TRUNCATED AT 250 WORDS)
Inactivation of p21Sensitizes Cells to Apoptosis via an Increase of Both p14ARF and p53 Levels and an Alteration of the Bax/Bcl-2 Ratio (2002)

p21(WAF1) appears to be a major determinant of the cell fate in response to anticancer therapy. It was shown previously that HCT116 human colon cancer cells growing in vitro enter a stable arrest upon DNA damage, whereas cells with a defective p21(WAF1) response undergo apoptosis. Here we report that the enhanced sensitivity of HCT116/p21(-/-) cells to chemotherapeutic drug-induced apoptosis correlates with an increased expression of p53 and a modification of their Bax/Bcl-2 ratio in favor of the pro-apoptotic protein Bax. Treatment of HCT116/p21(-/-) cells with daunomycin resulted in a reduction of the mitochondrial membrane potential and in activation of caspase-9, whereas no such changes were observed in HCT116/p21(+/+) cells, providing evidence that p21(WAF1) exerts an antagonistic effect on the mitochondrial pathway of apoptosis. Moreover, the role of p53 in activation of this pathway was demonstrated by the fact that inhibition of p53 activity by pifithrin-alpha reduced the sensitivity of HCT116/p21(-/-) cells to daunomycin-induced apoptosis and restored a Bax/Bcl-2 ratio similar to that observed in HCT116p21(+/+) cells. Enhancement of p53 expression after disruption of p21(WAF1) resulted from a stabilization of p53, which correlated with an increased expression of the tumor suppressor p14(ARF), an inhibitor of the ubiquitin ligase activity of Mdm2. In accordance with the role of p14(ARF) in p53 stabilization, overexpression of p14(ARF) in HCT116/p21(+/+) cells resulted in a strong increase in p53 activity. Our results identify a novel mechanism for the anti-apoptotic effect of p21(WAF1) consisting in maintenance of mitochondrial homeostasis that occurs in consequence of a negative control of p14(ARF) expression.
Dynamics of laser-induced cavitation bubbles at a solid–liquid interface in high viscosity and high capillary number regimes (2020)

No unified model is available yet to explain the dynamics of laser-induced cavitation bubbles during laser ablation of solid targets in liquids, when an extremely high capillary number is achieved (&amp;gt;100), i.e., when the viscous forces strongly contribute to the friction. By investigating laser-induced bubbles on gold and yttrium-iron-garnet targets as a function of the liquid viscosity, using a nanosecond laser and an ultrafast shadowgraph imaging setup, we give a deeper insight into what determines the bubble dynamics. We find that the competition between the viscous forces and the surface tension (capillary number Ca), on the one hand, and the competition between the viscous forces and inertia (Reynolds number Re), on the other hand, are both key factors. Increasing the viscous forces, and hereby Ca up to 100 has an impact on the bubble shape and results in a very pronounced rim, which separates the bubble in a spherical cap driven by inertia and an interlayer. The temporal evolution of the footprint radius of the interlayer can be addressed in the framework of the inertiocapillary regime. For an intermediate viscosity, the thickness of the interlayer is consistent with a boundary layer equation. Interestingly, our data cannot be interpreted with simplified hydrodynamic (Cox–Voinov) or molecular-kinetic theory models, highlighting the originality of the dynamics reported when extremely high capillary numbers are achieved. Upon bubble collapse, spherical persistent microbubbles are created and partly dispersed in water, whereas the high-viscous polyalphaolefines lead to long-standing oblate persistent bubbles sticking to the target’s surface, independent of the ablated target. Overall, liquid’s viscosity determines laser ablation-induced cavitation.
Anytime coding for distributed computation (2016)

A novel coding scheme is proposed to speed up distributed computation through a form of approximate computing. It is known that task replication can greatly mitigate the “straggler effect” in cloud computing, wherein an overall computation can be significantly delayed by slowed processing nodes (or “stragglers”). It has also been demonstrated that, in certain contexts, ideas of error-correction coding can more efficiently deal with stragglers than pure replication. The approach proposed herein builds on these earlier observations through an “anytime” approach to approximate computing. In this paradigm, over time one can produces approximate solutions of increasing accuracy. To accomplish this we first decompose a computational job in to tasks of various priorities. Next, we apply linear error correction coding to produce subtasks that are assigned to different processors. The decomposition used has a big effect on the type of anytime performance we attain. We study this scheme in a general framework in terms of the expected cost of the approximate solution. We further explore the approach in the context of vector-matrix multiplication. The proposed construction is numerically studied and, in comparison to previous work, demonstrates a significant improvement in the accuracy/latency trade-off.
Cooling Challenges in Military Helicopter Applications (2006)

Due to the unique operational environment, higher packaging density, and increasing power consumption, there is a growing cooling need for electronic equipment on board military helicopters. However, conduction remains to be the main cooling mechanism for electronic components in these applications. This paper attempts to address current thermal solutions and challenges along with system, mechanical, and reliability constraints. Future thermal management trends and needs are also discussed
Fingerprinting Codes Under the Weak Marking Assumption (2017)

Fingerprinting codes based on the marking assumption provide reliable security against collusion attacks, but lack resilience against channel errors such as symbol erasures or other forms of distortions introduced by transmission over noisy or insecure communication channels. This additional source of distortion errors can be addressed by relaxing the marking assumption. In this paper we examine the restrictions and limitations on the code construction in terms of accusation errors, alphabet size, and the distortion errors under this weaker form of the marking assumption as formulated by Guth and Pfitzmann, also deriving a theoretical minimum lower bound on the code length of q-ary fingerprinting codes. We provide the formulas for applying the already existing binary Tardos code with symmetric accusation function under the weaker form of the marking assumption along with numerical results proving the tightness of the derived bounds. We show that the code is still of asymptotically minimum code length under the relaxation of the marking assumption.
Down‐regulation of Glucan, Water‐Dikinase activity in wheat endosperm increases vegetative biomass and yield (2012)

A novel mechanism for increasing vegetative biomass and grain yield has been identified in wheat (Triticum aestivum). RNAi-mediated down-regulation of Glucan, Water-Dikinase (GWD), the primary enzyme required for starch phosphorylation, under the control of an endosperm-specific promoter, resulted in a decrease in starch phosphate content and an increase in grain size. Unexpectedly, consistent increases in vegetative biomass and grain yield were observed in subsequent generations. In lines where GWD expression was decreased, germination rate was slightly reduced. However, significant increases in vegetative growth from the two leaf stage were observed. In glasshouse pot trials, down-regulation of GWD led to a 29% increase in grain yield while in glasshouse tub trials simulating field row spacing and canopy development, GWD down-regulation resulted in a grain yield increase of 26%. The enhanced yield resulted from a combination of increases in seed weight, tiller number, spikelets per head and seed number per spike. In field trials, all vegetative phenotypes were reproduced with the exception of increased tiller number. The expression of the transgene and suppression of endogenous GWD RNA levels were demonstrated to be grain specific. In addition to the direct effects of GWD down-regulation, an increased level of α-amylase activity was present in the aleurone layer during grain maturation. These findings provide a potentially important novel mechanism to increase biomass and grain yield in crop improvement programmes.
Westinghouse Approach and Experience on Operating VVER (PWR)1000 I and C Modernization (2004)

The paper will describe the background, current implementation approach and experience on the largest ever modernization program on operating units VVER 1000 (PWR) at Kozloduy Nuclear Power Plant in Bulgaria. The Modernization Program itself includes more than 212 measures. Westinghouse is modernizing the major I and C Systems at VVER 1000. (authors)