gebhart/patrepeval huggingface dataset:
Adenovirus-mediated gene transfer of the tumor suppressor, p53, induces apoptosis in postmitotic neurons. (1996)

Programmed cell death is an ongoing process in both the developing and the mature nervous system. The tumor suppressor gene, p53, can induce apoptosis in a number of different cell types. Recently, the enhanced expression of p53 has been observed during acute neurological disease. To determine whether p53 overexpression could influence neuronal survival, we used a recombinant adenovirus vector carrying wild type p53 to transduce postmitotic neurons. A control consisting of the same adenovirus vector background but carrying the lacZ reporter expression cassette was used to establish working parameters for the effective genetic manipulation of sympathetic neurons. We have found that recombinant adenovirus can be used at titers sufficiently high (10 to 50 multiplicity of infection) to transduce the majority of the neuronal population without perturbing survival, electrophysiological function, or cytoarchitecture. Moreover, we demonstrate that overexpression of wild type p53 is sufficient to induce programmed cell death in neurons. The observation that p53 is capable of inducing apoptosis in postmitotic neurons has major implications for the mechanisms of cell death in the traumatized mature nervous system.
Incidence and diagnosis of anosognosia for hemiparesis revisited (2005)

Patients who do not mention their paresis spontaneously but do so when questioned about it directly should not be diagnosed having "anosognosia." If this more conservative cut off criterion is applied to the data of the present as well as previous studies, a frequency of between 10% and 18% for anosognosia for hemiparesis is obtained in unselected samples of acute hemiparetic stroke patients. The incidence thus seems smaller than previously assumed.
Xenobiotic CAR Activators Induce Dlk1-Dio3 Locus Noncoding RNA Expression in Mouse Liver (2017)

Derisking xenobiotic-induced nongenotoxic carcinogenesis (NGC) represents a significant challenge during the safety assessment of chemicals and therapeutic drugs. The identification of robust mechanism-based NGC biomarkers has the potential to enhance cancer hazard identification. We previously demonstrated Constitutive Androstane Receptor (CAR) and WNT signaling-dependent up-regulation of the pluripotency associated Dlk1-Dio3 imprinted gene cluster noncoding RNAs (ncRNAs) in the liver of mice treated with tumor-promoting doses of phenobarbital (PB). Here, we have compared phenotypic, transcriptional ,and proteomic data from wild-type, CAR/PXR double knock-out and CAR/PXR double humanized mice treated with either PB or chlordane, and show that hepatic Dlk1-Dio3 locus long ncRNAs are upregulated in a CAR/PXR-dependent manner by two structurally distinct CAR activators. We further explored the specificity of Dlk1-Dio3 locus ncRNAs as hepatic NGC biomarkers in mice treated with additional compounds working through distinct NGC modes of action. We propose that up-regulation of Dlk1-Dio3 cluster ncRNAs can serve as an early biomarker for CAR activator-induced nongenotoxic hepatocarcinogenesis and thus may contribute to mechanism-based assessments of carcinogenicity risk for chemicals and novel therapeutics.
17β-Estradiol Improves Survival in Male Mice with Cardiomyopathy Induced by Cardiac-Specific Tumor Necrosis Factor-α Overexpression (2005)

A transgenic mouse model of congestive heart failure (CHF) consequent to cardiac-specific overexpression of tumor necrosis factor-alpha (TNF-alpha) (TNF1.6) displays marked sex-related phenotypic differences. To clarify the potential contributions of estrogen to these sex-specific differences, male TNF1.6 mice were treated with 17beta- estradiol (E2). E2 treatment started at 25 +/- 1 days old (group A), but not at 36 +/- 2 days old (group B), significantly improved survival rate (p < 0.05). Furthermore, ventricular weight/body weight ratio was significantly decreased by E2 treatment in group A (p < 0.05). Echocardiography revealed that E2-treated hearts in group A exhibited less left ventricular dilatation (p < 0.05) relative to untreated male TNF1.6 mice (control). Moreover, in group A, E2 treatment partially reversed basal and isoproterenol-stimulated fractional shortening in TNF1.6 mice (p < 0.05). The cardiac content of TNF-alpha and interleukin-1beta (IL-1beta) was not changed by E2 treatment regardless of the timing of treatment. Thus, E2 exposure prior to puberty can limit the severity of cardiomyopathy in male TNF1.6 mice.
Multicomponent domino reactions for the synthesis of biologically active natural products and drugs (2000)

A main issue in modern synthetic organic chemistry, which deals with the preparation of natural products, pharmaceuticals, diagnostics, agrochemicals, and other important materials, is the improvement of efficiency, the avoidance of toxic reagents, the reduction of waste, and the responsible treatment of our resources. One of the ways to fulfill these goals is the development and use of domino processes, which consist of several bond-forming reactions and which allow the highly efficient synthesis of complex molecules starting from simple substrates. Herein, the combination of several catalytic bond-forming transformations is clearly most appropriate. The synthesis of the enantiopure alkaloid (-)-hirsutine 22, which has a strong inhibitorial effect on influenza A viruses, was accomplished using a biomimetic domino Knoevenagel-hetero-Diels Alder-solvolysis-hydrogenation process. In a similar way the alkaloids (+)-dihydrocorynantheine 23 and (-)-dihydroantirhine 24 as well as heterosteroids 62, D-homosteroids 65 and 68, and azasteroids 25 are prepared. In addition, novel steroid alkaloids 26 are accessible by a combination of the formation of an iminium salt, a hydride shift, and an alkylation. The anti-leukemic pentacyclic (-)-cephalotaxine 27 is obtained by a combination of two Pd-catalyzed reactions.
LIDAR and vision‐based pedestrian detection system (2009)

Abstract A perception system for pedestrian detection in urban scenarios using information from a LIDAR and a single camera is presented. Two sensor fusion architectures are described, a centralized and a decentralized one. In the former, the fusion process occurs at the feature level, i.e., features from LIDAR and vision spaces are combined in a single vector for posterior classification using a single classifier. In the latter, two classifiers are employed, one per sensor‐feature space, which were offline selected based on information theory and fused by a trainable fusion method applied over the likelihoods provided by the component classifiers. The proposed schemes for sensor combination, and more specifically the trainable fusion method, lead to enhanced detection performance and, in addition, maintenance of false‐alarms under tolerable values in comparison with single‐based classifiers. Experimental results highlight the performance and effectiveness of the proposed pedestrian detection system and the related sensor data combination strategies. © 2009 Wiley Periodicals, Inc.
Supporting the clinical use of the ICF in Japan – Development of the Japanese version of the simple, intuitive descriptions for the ICF Generic-30 Set, its operationalization through a rating reference guide, and interrater reliability study (2019)

Abstract Background: The World Health Organization developed the International Classification of Functioning, Disability, and Health (ICF) in 2001 and has been in the process of implementing it in clinics since then. Current international efforts to implement ICF in rehabilitation clinics include the implementation of ICF Core Sets and the development of simple, intuitive descriptions for the ICF Generic-30 Set (also called Rehabilitation Set). The present study was designed to operationalize these ICF tools for clinical practice in Japan. This work included 1) the development of the Japanese version of the simple, intuitive descriptions for the ICF Generic-30 Set, 2) the development of a rating reference guide for Activity and Participation categories, and 3) the examination of the interrater reliability of rating Activity and Participation categories. Methods: The Japanese version of the simple, intuitive descriptions for the ICF Generic-30 Set was developed following the process employed to develop the Chinese and Italian versions. For further operationalization of this ICF Set in practice, a rating reference guide was developed. The development of the rating reference guide involved the following steps: 1) a trial of rating patients by several raters, 2) cognitive interviewing of the raters to analyze the thinking process involved in rating, 3) drafting of the rating reference guide, and 4) review by ICF specialists to confirm consistency with the original ICF concepts. After the rating reference guide was developed, interrater reliability of the rating with the reference guide was determined. Interrater reliability was examined using weighted kappa statistics with linear weight. Results: Through the pre-defined process, the Japanese version of the simple, intuitive descriptions for 30 categories of the ICF Generic-30 Set and the rating reference guides for 21 Activity and Participation categories were successfully developed. The weighted kappa statistics ranged from 0.61 to 0.85, showing substantial to excellent agreement of the ratings between raters. Conclusions: The present study demonstrates that ICF categories can be translated into clinical practice. Collaboration between clinicians and researchers would further enhance the implementation of the ICF in Japan. Trial registration: not applicable
High-power piezoelectric behavior of acceptor-doped 〈001〉 and 〈111〉 textured piezoelectric ceramics (2022)

The high-power piezoelectric properties of MnO 2 -doped 〈001〉 and 〈111〉 textured 0.24PIN–0.42PMN–0.34PT ceramics are compared to understand the orientation dependence.
Hemodynamic Characterization of Patients with Severe Emphysema (2002)

In 120 patients with severe emphysema evaluated for participation in the National Emphysema Treatment Trial, pulmonary hemodynamics and ventricular function were assessed. Pulmonary function tests were (%predicted): FEV(1) = 27%; residual volume = 224.6%; diffusion capacity = 26.7%. In 90.8% of patients, end-expiratory pulmonary artery mean pressure was > 20 mm Hg; in 61.4%, end-expiratory wedge pressure was > 12 mm Hg. Cardiac index was normal. Mean pulmonary artery pressure correlated inversely with arterial PO(2), and severity of emphysema, and directly with wedge pressure. Multiple stepwise regression revealed that arterial PO(2) was not an independent predictor of mean pulmonary artery pressure. No correlation was found between indices of emphysema severity and PA pressures. Diastolic ventricular pressures were increased without evidence of systolic dysfunction. We conclude that (1) elevations of pulmonary vascular pressures are common, (2) pulmonary hypertension may be related to factors other than hypoxia, (3) pulmonary hypertension does not impair resting systemic O(2) delivery, and (4) elevated cardiac diastolic pressures do not represent systolic dysfunction.
Quantitative Genetics and Heterosis Discussion Session (1999)

This chapter talks about a question-and-answer session with K. R. Lamkey, J. F. Crow, C. J. Goodnight, J. B. Miranda Filho, and M. Cooper on quantitative genetics and heterosis. Lamkey comments on heterosis for species that do not show inbreeding depression, the term functional heterosis and the quantitative genetics of heterosis in the graph of inbreds versus hybrids. The absence of inbreeding depression means there is no baseline level of heterosis in the species, unless there is something going on during the inbreeding process that we do not understand. The only way to have heterosis without having inbreeding depression is with additive × additive epistasis. Goodnight shares his knowledge on how much importance one gives to epistasis for the expression of heterosis in comparison to dominance and overdominance and how much importance can one gives to epistasis in the expression of panmictic heterosis compared with dominance and overdominance.
Supplementary Figures S1-7 from Trifluridine Induces p53-Dependent Sustained G<sub>2</sub> Phase Arrest with Its Massive Misincorporation into DNA and Few DNA Strand Breaks (2023)

&lt;p&gt;Supplementary Figures S1-7. Supplementary Figure S1. The cellular response of RKO cells to IC50 concentration of FdUrd or FTD. Supplementary Figure S2. The cellular responses of A549 cells to IC50 concentration of FdUrd or FTD. Supplementary Figure S3. A549 cells either treated with siGL2 or siTP53 were cultured in the presence of IC50 concentration of FdUrd or FTD. Supplementary Figure S4. RKO (A) or A549 (B) cells were cultured in the presence of IC50 concentration of FdUrd or FTD. Supplementary Figure S5. Immunoflurorescent images of Cyclin B1 in exponentially growing (A) or FTD-treated (B,C) HCT-116 cells. Supplementary Figure S6. Immunoflurorescent images of Cyclin B1 in FTD-treated HCT-116 cells with or without MG132. Supplementary Figure S7. Representative images of alkaline or neutral comet assay in camptothecin-treated HCT-116 cells.&lt;/p&gt;
“Plug and Play”-expression systems for high-quality production of recombinant proteins for structural analysis (2002)

Determining the structures of proteins of entire proteomes is a formidable endeavour. High throughput structural genomics correspondingly requires the development of highly efficient methods to streamline every step in progressing from the individual gene expression to refined three-dimensional protein structure. A major bottleneck in structural biology is the production of sufficient amounts of correctly folded and functional protein. Here, we present a simple “Plug and Play”-expression system that allows for parallel gene expression in E. coli, yeast and insect cells to rapidly select the best strategy for the production of high-quality protein.
Changes in the Prevalence of Weed Species in the Major Agronomic Crops of the Southern United States: 1994/1995 to 2008/2009 (2012)

Changes in the weed flora of cropping systems reflect the impacts of factors that create safe sites for weed establishment and facilitate the influx and losses to and from the soil seedbank. This analysis of the annual surveys of the Southern Weed Science Society documents changes in the weed flora of the 14 contiguous southern states since the advent of transgenic, herbicide-resistant crops. In 1994 and 2009, the top five weeds in corn were morningglories, Texas millet, broadleaf signalgrass, johnsongrass, and sicklepod; in this same period Palmer amaranth, smartweeds, and goosegrass had the greatest increases in importance in corn. In cotton, morningglories and nutsedges were among the top five most troublesome weeds in 1995 and 2009. Palmer amaranth, pigweeds, and Florida pusley were also among the five most troublesome species in 2009; the weeds with the largest increases in importance in cotton were common ragweed and two species with tolerance to glyphosate, Benghal dayflower and Florida pusley. In soybean, morningglories, nutsedges, and sicklepod were among the top five weed species in 1995 and 2009. Two species with glyphosate resistance, Palmer amaranth and horseweed, were the second and fourth most troublesome weeds of soybean in 2009. In wheat, the top four weeds in 2008 were the same as those in 1994 and included Italian ryegrass, wild garlic, wild radish, and henbit. Crop production in the southern region is a mosaic of various crop rotations, soil types, and types of tillage. During the interval between the surveys, the predominant change in weed management practices in the region and the nation was the onset and rapid dominance of the use of glyphosate in herbicide-resistant cultivars of corn, cotton, and soybean. Because of the correspondence between the effects of glyphosate on the respective weed species and the observed changes in the weed flora of the crops, it is likely the very broad use of glyphosate was a key component shaping the changes in weed flora. Only eight of the top 15 most troublesome weeds of cotton and soybean, the crops with the greatest use of glyphosate, were the same in 1995 and 2009. In contrast, in corn and wheat where adoption of glyphosate-resistant cultivars lags or is absent, 12 of the 15 most troublesome weeds were the same in 1994 and 2008. These findings show on a regional scale that weeds adapt to recurrent selection from herbicides, currently the predominant weed management tool. Future research should seek methods to hinder the rapid spread of herbicide-tolerant and evolution of herbicide-resistant weed species. As new tools are developed, research should focus on ways to preserve the efficacy of those tools through improved stewardship.
Selected cholesterol biosynthesis inhibitors produce accumulation of the intermediate FF-MAS that targets nucleus and activates LXRα in HepG2 cells Molecular and cell biology of lipids (2017)

Sterol intermediates of the cholesterol biosynthetic pathway have drawn attention for novel biological activities. Follicular fluid meiosis activating sterol (FF-MAS) is a LXRα ligand and a potential modulator of physiologic processes regulated by nuclear receptors, such as lipid homeostasis and cell proliferation. In this work, we established a model to selectively accumulate FF-MAS in HepG2 cells, by using a combination of the inhibitors AY9944 and 17-hydroxyprogesterone to block C14-sterol reductases and the downstream C4-demethylase complex. We investigated the effects produced by altered levels of cholesterol biosynthesis intermediates, in order to dissect their influence on LXRα signaling. In particular, endogenously accumulated FF-MAS was able to modulate the expression of key genes in cholesterol metabolism, to activate LXRα nuclear signaling resulting in increased lipogenesis, and to inhibit HepG2 cells proliferation. Moreover, a fluorescent ester derivative of FF-MAS localized in nuclear lipid droplets, suggesting a role for these organelles in the storage of signaling lipids interacting with nuclear partners.
Color Textured Image Retrieval By Combining Texture And Color Features (2012)

Publication in the conference proceedings of EUSIPCO, Bucharest, Romania, 2012
Correction to: Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin (2021)

An amendment to this paper has been published and can be accessed via the original article.
A field study of modellers at work (2015)

Knowing the impact in real settings of a software development approach is beneficial to both the industry and the research community. In this paper, we report on a field study we conducted at General Motors with the intent of understanding whether the organization was achieving some of the intended benefits of introducing a model-driven approach to software engineering. This study involved both observations and interviews. We found that several factors are still limiting the productivity increase claimed by MDE.
Nano-Emulsions; Emulsification Using Low Energy Methods (2014)

Nano-emulsions are emulsions with droplet sizes from 20 nm up to 200-500 nm, thermodynamically unstable, and appear transparent or translucent to the naked eye. Nano-emulsions are very useful in many industries; such as food, pharmaceutical, cosmetic, and chemical. Forming nano-emulsions using a method that requires energy input from a mechanical device is known as a ‘high-energy method’, while a method using chemical energy stored in the components is referred to as a ‘low- energy method’. The low-energy method can be classified into three categories: the Phase Inversion Temperature method, Phase Inversion Composition method or Emulsion Inversion Point method and the Spontaneous Emulsification method. To study nano-emulsification using the low-energy methods, phase diagrams are used to determine the phase behavior of the components and specify the temperature and concentrations at which various structures exist at equilibrium with desired properties. Most research focuses on droplet size and polydispersibility of nano-emulsions, because these properties influence physicochemical properties, appearance and stability of nano-emulsions. There have been many studies on the effect of composition and the major determining factors in the emulsification process on droplet size and polydispersibility of nano-emulsions such as surfactant type, concentration, location, oil type, surfactant-to-oil ratio, salt, stirring speed, and temperature.
Antireflection coatings for submillimeter silicon lenses (2014)

Low-loss lenses are required for submillimeter astronomical applications, such as instrumentation for CCAT, a 25 m diameter telescope to be built at an elevation of 18,400 ft in Chile. Silicon is a leading candidate for dielectric lenses due to its low transmission loss and high index of refraction; however, the latter can lead to large reflection losses. Additionally, large diameter lenses (up to 40 cm), with substantial curvature present a challenge for fabrication of antireflection coatings. Three anti-reflection coatings are considered: a deposited dielectric coating of Parylene C, fine mesh structures cut with a dicing saw, and thin etched silicon layers (fabricated with deep reactive ion etching) for bonding to lenses. Modeling, laboratory measurements, and practicalities of fabrication for the three coatings are presented and compared. Measurements of the Parylene C anti-reflection coating were found to be consistent with previous studies and can be expected to result in a 6% transmission loss for each interface from 0.787 to 0.908 THz. The thin etched silicon layers and fine mesh structure anti-reflection coatings were designed and fabricated on test silicon wafers and found to have reflection losses less than 1% at each interface from 0.787 to 0.908 THz. The thin etched silicon layers are our preferred method because of high transmission efficiency while having an intrinsically faster fabrication time than fine structures cut with dicing saws, though much work remains to adapt the etched approach to curved surfaces and optics &lt; 4" in diameter unlike the diced coatings.
Effects of conventional and alternating cushion weight-shifting in persons with spinal cord injury (2014)

A repeated-measures study of 13 adult full-time wheelchair users with spinal cord injury (SCI) was carried out to determine whether alternating-pressure air cushion (APAC) use compared with independent pressure relief (IPR) provides reliable, effective pressure relief for individuals with SCI. Bilateral mean ischial interface pressure (IP), transcutaneous oxygen tension (TcPO2), and unilateral laser Doppler blood flow were evaluated. Blood flow component contributions were determined using short-time Fourier transform (STFT)-based spectral analysis. IPR assessment was carried out at recruitment. Study participants then used an APAC for 2 wk every 3 mo for 18 mo. IPR weight-shifting decreased mean ischial IP (p < 0.05) and increased mean TcPO2 (p < 0.05). All variables rapidly returned to preintervention levels following weight-shifting except for the cardiac component of blood flow. APAC-induced weight-shifting decreased mean ischial IP (p < 0.05). Mean TcPO2 increased and was higher than for IPR. STFT analysis indicated that quiet sitting following APAC-induced weight-shifting produced a higher neurogenic component of blood flow than following IPR (p = 0.02). Thus, IPR positively affects multiple aspects of tissue health but produces transient improvements and must be repeated regularly. APAC activation dynamically and continuously alters IP distribution with more sustained positive tissue health effects.