gebhart/patrepeval huggingface dataset:
Bactericidal Mechanism of Ag/Al<sub>2</sub>O<sub>3</sub> against <i>Escherichia coli</i> (2007)

The bactericidal process of Ag/Al2O3 to Escherichia coli has been investigated to clarify the bactericidal mechanism. In SEM images, the configuration of E. coli cells contacting with the catalyst surface was quite different from that contacting with AgNO3 solution, which indicated that the Ag+ eluted from the catalyst did not play an important role in the bactericidal process. The bactericidal experiments strongly confirmed the contribution of multiform reactive oxygen species (ROS) (super oxide dismutase (SOD) and catalase as the scavengers for O2*- and H2O2, respectively) to bactericidal effect on the catalyst surface. Furthermore, the surface modification of Ag/Al2O3 by ultraviolet and formaldehyde influenced the bactericidal effect obviously, which not only confirmed the bactericidal mechanism of catalytic oxidation but also provided evidence for the synergistic effect between Ag and Al2O3 on the catalyst surface.
Yield-centric layout optimization with precise quantification of lithographic yield loss (2008)

Continuous shrinkage of the design rule in LSI devices brings about greater difficulty in the manufacturing process. Since not only process engineers' efforts but also yield-centric layout optimization is becoming increasingly important, such optimization has recently become a focus of interest. One of the approached is lithographic hotspot modification in design data. Using lithography compliance check and a hotspot fixing system in the early stage of design, design with wider process margin can be obtained. In order to achieve higher process yield after hotspot fixing, layout should be carefully optimized to decrease pattern-dependent yield loss. Since yield value for the design will fluctuate sensitively as designed pattern are modified, pattern should be optimized based on a comprehensive consideration of yield loss covering parametric, systematic and random effects. In this work, using lithography simulation, a lithographic yield loss model is defined and applied for precise quantification of process yield loss in 45 nm logic design. Yield loss values of each cell for lithographic, parametric and random effects are estimated, and then layouts through multiple layers are optimized to decrease total yield loss. As a result, litho-yield loss is greatly improved without deteriorating total yield value. Thus, layout is obtained that reflects an awareness of overall process yield.
Cascaded systems analysis of the 3D noise transfer characteristics of flat‐panel cone‐beam CT (2008)

The physical factors that govern 2D and 3D imaging performance may be understood from quantitative analysis of the spatial-frequency-dependent signal and noise transfer characteristics [e.g., modulation transfer function (MTF), noise-power spectrum (NPS), detective quantum efficiency (DQE), and noise-equivalent quanta (NEQ)] along with a task-based assessment of performance (e.g., detectability index). This paper advances a theoretical framework based on cascaded systems analysis for calculation of such metrics in cone-beam CT (CBCT). The model considers the 2D projection NPS propagated through a series of reconstruction stages to yield the 3D NPS and allows quantitative investigation of tradeoffs in image quality associated with acquisition and reconstruction techniques. While the mathematical process of 3D image reconstruction is deterministic, it is shown that the process is irreversible, the associated reconstruction parameters significantly affect the 3D DQE and NEQ, and system optimization should consider the full 3D imaging chain. Factors considered in the cascade include: system geometry; number of projection views; logarithmic scaling; ramp, apodization, and interpolation filters; 3D back-projection; and 3D sampling (noise aliasing). The model is validated in comparison to experiment across a broad range of dose, reconstruction filters, and voxel sizes, and the effects of 3D noise correlation on detectability are explored. The work presents a model for the 3D NPS, DQE, and NEQ of CBCT that reduces to conventional descriptions of axial CT as a special case and provides a fairly general framework that can be applied to the design and optimization of CBCT systems for various applications.
Photochemistry of the Nonspecific Hydroxyl Radical Generator,<i>N</i>-Hydroxypyridine-2(1<i>H</i>)-thione (1996)

The photochemistry of N-hydroxypyridine-2(1H)-thione (N-HPT) has been investigated in aqueous and organic solvents using laser flash photolysis (λexc = 308 or 355 nm). Independent of the environment, UV excitation of N-HPT causes homolytic N−O bond cleavage, which leads to formation of the 2-pyridylthiyl (PyS•) and hydroxyl (•OH) radicals. In aqueous media, this process occurs efficiently from both the anionic and neutral forms (ΦN-O ≈ 0.20−0.30). In addition to N−O bond scission, N-HPT undergoes other primary photoprocesses which are pH-dependent. At pH = 7, photoionization (Φe− = 0.09 (λexc = 308 nm) and 0.05 (λexc = 355 nm)) of the anionic form generates the hydrated electron as well as the semioxidized radical of N-HPT. Fast rearrangement of the latter species produces the N-oxy-2-pyridylthiyl radical. At pH = 2, where the uncharged structure predominates, formation of an excited triplet state (ET ≥ 59.5 kcal mol-1) is observed (ΦT ≥ 0.05 using λexc = 355 nm) but photoionization does not take place. The neutral form of N-HPT displays similar photochemical behavior in organic solvents, generating •OH, PyS•, and the triplet state (ΦN-O = 0.30−0.45 and ΦT = 0.03−0.05 using λexc = 355 nm). In nonpolar, aprotic media, the subsequent reaction of PyS• with the thiol tautomer of N-HPT leads to the formation of an unsymmetric disulfide radical. Reactivities of the different transient species toward potential scavengers have also been investigated. The results obtained show that the simultaneous generation of several highly reactive intermediates is a major drawback in the use of N-HPT as a clean and simple photolytic source of •OH.
Three-Dimensional Imaging of Hepatic Sinusoids in Mice Using Synchrotron Radiation Micro-Computed Tomography (2013)

Hepatic sinusoid, the smallest vessel in the liver, plays important roles in hepatic microcirculation. Although the structure of the hepatic sinusoids affects diverse functions of the liver, little is known about morphological alterations in the sinusoids under pathological conditions. In this study, we show that the structure of hepatic sinusoids can be identified three-dimensionally in normal and carbon tetrachloride-injured mouse liver, using the absorption mode of synchrotron radiation micro-computed tomography. We observed that the hepatic sinusoidal structure on tomographic slice images was similar to that on histological images of normal and acutely injured mice. Moreover, centrilobular necrosis and structural alterations of the sinusoids in the necrotic region were detectable on tomographic slice and volume-rendered images of the acutely injured mice. Furthermore, quantitative analyses on 3D volume-rendered images of the injured sinusoid revealed decrease in the volume of the sinusoid and connectivity of the sinusoidal network. Our results suggest that the use of synchrotron radiation micro-computed tomography may improve our understanding of the pathogenesis of hepatic diseases by detecting the hepatic sinusoids and their alterations in three-dimensional structures of the damaged liver.
Abstract 815: CBL0137 demonstrates significant antitumor activity against hepatocellular carcinoma alone and in combination with sorafenib (2014)

Abstract Primary hepatocellular carcinoma (HCC) is the 6th most common malignancy diagnosed worldwide with an incidence that continues to rise. Even with the use of the current standard of care drug sorafenib, survival of patients remains at ∼10-11 months and sorafenib toxicity results in dose interruptions and delays. Therefore, tolerable, effective therapies against HCC are greatly needed. CBL0137 represents a novel class of small molecules that simultaneously activate p53 and inhibit cancer-associated stress response pathways, such as NF-κB and HSF-1, and has demonstrated broad range antitumor activity against pre-clinical tumor models. The effects of CBL0137 are mediated by the inhibition of the chromatin remodelling factor FACT (FAcilitates Chromatin Transcription) comprised of SSRP1 and SPT16 subunits. FACT is expressed in undifferentiated progenitors and stem cells of adult tissues, but is almost undetectable in differentiated cells. It is expressed in many tumor types, including HCC, and is correlated with high grade and worse overall survival. Thus, FACT represents a potentially important target for cancer therapy. We investigated the effect of CBL0137 on HCC using HepG2 and Hep3B xenograft models. Treatment of tumor bearing mice intravenously with 60-70 mg/kg CBL0137 every 4th day resulted in ∼88-94% tumor growth inhibition in both models, including tumor regression in 60-80% of tumors during the course of treatment. Furthermore, combination of suboptimal doses of CBL0137 with sorafenib had greater efficacy compared to either drug alone (tumor growth inhibition: HepG2- 87.9% combination vs 73.6% CBL0137 only (P=0.0014), 75.7% sorafenib only (P=0.0006); Hep3B- 79.6% combination vs 38.2% CBL0137 only (P=0.003), 51.4% sorafenib only (P=0.032)). Although the mechanism resulting in the combination effect is unknown, in vitro analysis of markers of CBL0137 and sorafenib activity revealed that both drugs caused a marked decrease in the basal and induced expression of NF-κB target genes (IL-8 and TNF). Furthermore, the combination of CBL0137 and sorafenib almost completely abolished the expression of these genes in both HCC cell lines, suggesting that the combination effect may be in part mediated through inhibition of the NF-κB pathway. Together, these data indicate that CBL0137 may provide a clinical benefit for the treatment of HCC both alone and in combination with sorafenib. Citation Format: Catherine Burkhart, Rachael Kohrn, Brittany Walker, Katerina Gurova, Andrei Purmal, Andrei Gudkov. CBL0137 demonstrates significant antitumor activity against hepatocellular carcinoma alone and in combination with sorafenib. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 815. doi:10.1158/1538-7445.AM2014-815
Coupled drift-diffusion/quantum transmitting boundary method simulations of thin oxide devices with specific application to a silicon based tunnel switch diode (2000)

We present a method of coupling drift-diffusion simulations with quantum transmitting boundary method (QTBM) tunnel current calculations. This allows self-consistent simulation of thin oxide devices in which large tunnel currents can flow. Simulated results are presented for a thin oxide Al/SiO/sub 2//Si structure and an Al/SiO/sub 2//n-Si/p-Si tunnel switching diode. We demonstrate the careful use of the recombination lifetime as an adjustable or relaxable parameter in order to obtain converging solutions.
Role of Cyclic AMP in Leukemias (2016)

In leukemias, cyclic adenosine monophosphate (cAMP) can play a role in cancer cell maturation and can be both pro- and antiapoptotic.
KHEDA (KAIRA) (2012)

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First-Principles Study of Iron Oxide Polytypes: Comparison of GGA+<i>U</i> and Hybrid Functional Method (2014)

Iron oxides are materials of wide interest that exhibit diverse electric, magnetic, optical, and catalytic properties; therefore, many studies to gain complete understanding of their polytypic phase boundary have been pursued. However, first-principles investigations of iron oxides using conventional density functional theory (DFT) calculations often yield a gross error due to the strong electron correlation that is poorly described within (semi) local approximations. This limitation often can be overcome using either the Hubbard correction (DFT+U) or a hybrid functional DFT method. Here, we investigate the diverse polytypic phases of iron monoxide (FeO) by comparing DFT+U and the hybrid-functional method (particularly B3PW91). We found that both methods show reasonable agreement in predicting the properties of the experimentally observed phases (B1, B8, iB8, and B2). However, the DFT+U method overestimates the equilibrium volume of B1 phase and predicts the experimentally undiscovered B4 phases to be nearly as stable as the naturally abundant B1 phase. In addition, B3PW91 predicts a local Jahn–Teller distortion pattern of the B1 phase that is more similar than that predicted by DFT+U to the result of a reported low-temperature neutron diffraction experiment. Using B3PW91, which is considered more convincing, we further discuss that there is no clear phase boundary between the monoclinic and rhombohedral B1 phases under compression but that the compression gradually reduces the local anisotropy to yield a rhombohedral-like phase, which agrees with previous experimental diffraction results. We expect that our comprehensive study demonstrates the virtue of using hybrid-functional DFT methods, particularly in exploring various known and unknown polytypic phases of transition-metal oxides.
Controlled phase separation in conjugated polymer blends induced by thermolithography (2008)

The big interest in conjugated polymers is due to their easy solution processability, which endows them with several prospects, from low-cost processing, to opportunity of creating materials with new properties by simple mixing solutions, so research has focused on to optimize the blends properties in order to enhance optoelectronic device performance. Possibility to rules a phase separation in conjugated polymer blends has wide range of applications in optoelectronics, because both charge transport and charge separation are influenced by presence of phase segregation. Here we present a new method of controlling phase segregation in conjugated polymer blends by using a scanning probe microscope.
An aromatic–antiaromatic switch in P-heteroles. A small change in delocalisation makes a big reactivity difference (2006)

The low aromaticity of phosphole can be switched to low antiaromaticity by oxidizing the phosphorus atom. This subtle change in the mode of delocalisation alters substantially the chemical behaviour of these heteroles.
<i>Plasmodium</i>   <i>berghei</i> Infection in Mice Induces Liver Injury by an IL-12- and Toll-Like Receptor/Myeloid Differentiation Factor 88-Dependent Mechanism (2001)

Malaria, caused by infection with Plasmodium spp., is a life cycle-specific disease that includes liver injury at the erythrocyte stage of the parasite. In this study, we have investigated the mechanisms underlying Plasmodium berghei-induced liver injury, which is characterized by the presence of apoptotic and necrotic hepatocytes and dense infiltration of lymphocytes. Although both IL-12 and IL-18 serum levels were elevated after infection, IL-12-deficient, but not IL-18-deficient, mice were resistant to liver injury induced by P. berghei. Neither elevation of serum IL-12 levels nor liver injury was observed in mice deficient in myeloid differentiation factor 88 (MyD88), an adaptor molecule shared by Toll-like receptors (TLRs). These results demonstrated a requirement of the TLR-MyD88 pathway for induction of IL-12 production during P. berghei infection. Hepatic lymphocytes from P. berghei-infected wild-type mice lysed hepatocytes from both uninfected and infected mice. The hepatocytotoxic action of these cells was blocked by a perforin inhibitor but not by a neutralizing anti-Fas ligand Ab and was up-regulated by IL-12. Surprisingly, these cells killed hepatocytes in an MHC-unrestricted manner. However, CD1d-deficient mice that lack CD1d-restricted NK T cells, were susceptible to liver injury induced by P. berghei. Collectively, our results indicate that the liver injury induced by P. berghei infection of mice induces activation of the TLR-MyD88 signaling pathway which results in IL-12 production and activation of the perforin-dependent cytotoxic activities of MHC-unrestricted hepatic lymphocytes.
Augmenting SAT Solvers for Network Configuration/Planning (2006)

Abstract : This project explored the possibility of alternate encodings of the planning problem and extensions to satisfiability (SAT) solvers that can better capture the constraints and objectives for network configurations. For example, the ability to directly deal with arithmetic constraints dealing with configuration cost, or probabilistic failure modes may lead to more compact encodings that are then dealt with more sophisticated decision procedures. The end goal is to capture the constraints and objectives of network planning in a decision problem and then solve these using efficient decision procedures in a scalable way.
Update on vascular catheter infections (2004)

Purpose of review Extensive reviews of our current understanding of vascular catheter infections have recently been published. This update highlights 22 primary research articles selected from 415 randomized clinical trials and over 2500 other articles on vascular catheter infections published between January 2002 and March 2004. Recent findings Full sterile barriers are not necessary for the insertion of arterial catheters. Subcutaneous tunnels may decrease the risk of femoral catheter infection. The minocycline-rifampin catheter coating still appears to be the most efficacious. Further studies demonstrating that education of MD/RN personnel reduces the risk of catheter infection now exist. A number of studies show that the method of attaching IV tubing to catheters and certain catheter flush solutions can reduce the risk of infection. Differential time to positivity looks increasingly promising as a practical method for diagnosing catheter infection. All catheters suspected of infection do not need to be removed. The management of vascular catheter infections can be improved by a simple e-mail mechanism. Summary Abundant evidence now exists that there are many interventions that can reduce the risk of vascular catheter infections. The next phase of our understanding should include determining how many of these many interventions are necessary and under what circumstances.
Relative adipose tissue failure in Alström syndrome drives obesity-induced insulin resistance (2020)

Obesity is a major risk factor for insulin resistance (IR) and its attendant complications. The pathogenic mechanisms linking them remain poorly understood, partly due to a lack of intermediary monogenic human phenotypes. Here, we report on a monogenic form of IR-prone obesity, Alström syndrome (ALMS). Twenty-three subjects with monogenic or polygenic obesity underwent hyperinsulinaemic-euglycemic clamping with concomitant adipose tissue (AT) microdialysis and an in-depth analysis of subcutaneous AT histology. We have shown a relative adipose tissue failure in monogenic obese cohort; a finding supported by observations in a novel conditional mouse model (&lt;i&gt;Alms&lt;sup&gt;flin/flin&lt;/sup&gt;&lt;/i&gt;) and ALMS1-silenced human primary adipocytes. Whereas, selective reactivation of ALMS1 gene in adipose tissue of an ALMS conditional knockdown mice model (&lt;i&gt;Alms&lt;sup&gt;flin/flin&lt;/sup&gt;;Adipo-Cre&lt;sup&gt;+/-&lt;/sup&gt;&lt;/i&gt;) restores systemic insulin sensitivity and glucose tolerance. Hence, we show for the first time the relative adipose tissue failure in human obese cohorts to be a major determinant of accelerated IR without evidence of lipodystrophy. These new insights into adipocyte driven insulin resistance may assist development of adipose tissue targeted therapeutic strategies for diabetes.
Using approximate models for engineering design (1998)

Engineers and designers use complicated computer simulations to model physical phenomenon. They evaluate many designs as they search for the design. Because the definition of best changes during the design process, they have to evaluate even more designs. This can be a very costly and time consuming task. Approximate models can help them get more information from the simulations and make better decisions. This can result in getting the same or better information in a shorter time. We have used approximate models with over twenty applications. This paper focuses on how we have used multi-objective optimization and approximate models with three applications. We show how these mathematical methods can be used to explore complex relationships.
L'instabilite Lombaire Intervertebrale Etude D'un Systeme Souple de Stabilisation Systeme de Graf® (1995)

"L'instabilite Lombaire Intervertebrale Etude D'un Systeme Souple de Stabilisation Systeme de Graf®." Archives of Physiology and Biochemistry, 103(3), p. C160
Influence of apolipoprotein E genotype on the transmission of Alzheimer disease in a community-based sample. (1996)

The epsilon 4 allele of the apolipoprotein E locus (APOE) has been found to be an important predictor of Alzheimer disease (AD). However, linkage analysis has not clarified the role of APOE in the transmission of AD. The results of the current study provide evidence that the pattern of transmission of memory disorders differs in nuclear families in which the AD-affected proband did carry an epsilon 4 allele versus those families in which the AD-affected proband did not carry an epsilon allele. Further, risk of AD due to APOE genotype in the probands is modified by family history of memory disorders, suggesting gene-by-gene interactions. Family history remained a significant predictor of AD for affected probands with some, but not all, APOE genotypes in a logistic regression analysis. Though nonadditive in the prediction of AD, APOE genotype and family history acted additively in the prediction of age at AD onset. The results of complex segregation analysis were inconsistent with Mendelian segregation of memory disorders both in families of affected probands who did or did not carry an epsilon 4 allele, yet these two groups had significantly different parameter estimates for their transmission models. These results are consistent with gene-by-gene interactions, but also could result from common elements in the familial environment.
Conformational effects on electrical and spectroscopic properties of 1,2‐di(2‐thienyl)ethylenes and corresponding poly[(2,2′‐dithienyl)‐5,5′‐diylvinylenes] (1996)

Abstract 1,2‐Dialkyl‐substituted 1,2‐di(2‐thienyl)ethylenes have been synthesized and investigated by cyclic voltammetry. The bulk of the alkyl substituents was modulated in order to progressively increase the torsional angle between the thiophene rings and the plane of the olefinic bond, from a fully planar structure to highly twisted systems. Distortion markedly affects the UV spectra and the oxidation peak potentials of the monomers. The electro‐chemical polymerization experiments gave the following results: (i) ( E )‐ and ( Z )‐dithienyl‐ethylene systems produced polymers with identical properties; (ii) progressive deviation from planarity increased the oxidation peak potential of the monomer, as far as the polymerization was inhibited; (iii) long and rigid monomeric units reduced chain flexibility, leading to materials with low conductivity and unsatisfactory mechanical properties.