gebhart/patrepeval huggingface dataset:
Infection of primary human hepatocytes with recombinant hepatitis C virus (2008)

Attachment of the virus to the cell surface followed by viral entry is the first step in a cascade of events required for initiation of infection. Results obtained with surrogate model systems for HCV infection using human hepatoma cell lines suggest that HCV entry is most likely a multi-step process which requires a set of initial binding molecules such as glycosaminoglycans, as well as (co)-receptors for viral entry such as CD81, SR-BI and claudin–1. However, it still remains elusive which host cell factors are required for HCV entry into its natural target cell, the human hepatocyte. In this study, we used the recently established HCV-JFH–1 based-infectious tissue culture model system to generate high titer virion preparations (HCVcc) for infection of primary human hepatocytes (PHH). Cells were incubated with cell culture adapted JFH–1 with proven in vivo viability in the presence or absence of an NS3 protease inhibitor. Infection was assessed by measuring HCV RNA by quantitative RT-PCR at different time-points post infection. PHH could be reproducibly infected with HCVcc as shown by a time-dependent increase of HCV RNA in infected hepatocytes which was not observed when cells were treated with the NS3 protease inhibitor. Studies to assess the impact of CD81, SR-BI and claudin–1 as host entry factor for HCV infection of primary human hepatocytes are ongoing. In conclusion, our results suggest that PHH can be infected with cell culture grown HCV. This model system will allow further dissecting molecular mechanisms of HCV infection of its natural target cell – the human hepatocyte.
Regeneration of Zinc Titanate H<sub>2</sub>S Sorbents (1998)

Zinc titanate is one of the leading regenerable sorbent candidates for high-temperature hydrogen sulfide (H2S) removal from coal gasifier gas. Temperatures in excess of 625 °C are required for regeneration of sulfided zinc titanate using air. However, hot-gas desulfurization processes require initiation of regeneration at temperatures below 550 °C. Modified zinc titanate sorbents were prepared by coprecipitation with Cu, Ni, Co, Fe, and Mo at levels up to 10 wt % to reduce the regeneration temperature. The maximum reduction in regeneration temperature was achieved for a zinc titanate sorbent with 5 wt % Co and 5 wt % Ni, which could be regenerated at temperatures as low as 475 °C.
Aflibercept Traps Galectin-1, an Angiogenic Factor Associated with Diabetic Retinopathy (2015)

Vascular endothelial growth factor (VEGF)-A-driven angiogenesis contributes to various disorders including cancer and proliferative diabetic retinopathy (PDR). Among several VEGF-A blockers clinically used is aflibercept, a chimeric VEGFR1/VEGFR2-based decoy receptor fused to the Fc fragment of IgG1 (i.e., VEGFR1/VEGFR2-Fc). Here, we revealed a novel anti-angiogenic function for aflibercept beyond its antagonism against VEGF family members. Immunoprecipitation and mass spectrometry analyses identified galectin-1 as an aflibercept-interacting protein. Biolayer interferometry revealed aflibercept binding to galectin-1 with higher affinity than VEGFR1-Fc and VEGFR2-Fc, which was abolished by deglycosylation of aflibercept with peptide:N-glycosidase F. Retinal LGALS1/Galectin-1 mRNA expression was enhanced in vitro by hypoxic stimulation and in vivo by induction of diseases including diabetes. Galectin-1 immunoreactivity co-localized with VEGFR2 in neovascular tissues surgically excised from human eyes with PDR. Compared with non-diabetic controls, intravitreal galectin-1 protein levels were elevated in PDR eyes, showing no correlation with increased VEGF-A levels. Preoperative injection of bevacizumab, a monoclonal antibody to VEGF-A, reduced the VEGF-A, but not galectin-1, levels. Galectin-1 application to human retinal microvascular endothelial cells up-regulated VEGFR2 phosphorylation, which was eliminated by aflibercept. Our present findings demonstrated the neutralizing efficacy of aflibercept against galectin-1, an angiogenic factor associated with PDR independently of VEGF-A.
Status of the transcription factors database (TFD) (1993)

The Transcription Factors Database is a specialized database focusing on transcription factors and their properties. This report describes the present status of this database and developments during the past year. Within this time, the size of this database has increased by a 2799 total records, and has become accessible through a number of new mechanisms.
Über Peptidsynthesen, XXII. Synthese von Eledoisin und Glu‐Eledoisin (1964)

Abstract Es wird über die Darstellung von Eledoisin und Glu 5 ‐Eledoisin berichtet. Die biologische Aktivität beider Verbindungen wird verglichen.
Mammary Cancer Promotion and MAPK Activation Associated With Consumption of a Corn Oil-Based High-Fat Diet (1999)

Our earlier work has shown a selective promotional effect on the genesis of mammary carcinomas bearing a wild-type, but not mutant, Ha-ras codon 12 in a 1-methyl-1-nitrosourea (MNU)-induced carcinogenesis model by high-fat diets (Nutr Cancer 23, 283-290, 1995). To test the hypothesis that activation of the mitogen-activated protein kinase (MAPK) pathway is associated with this promotional effect, we compared the in vivo MAPK phosphorylation state of carcinomas from rats consuming a low-fat (5% corn oil, modified AIN-93G) with that from rats consuming a high-fat (25% corn oil) diet. Specifically, 21-day-old female Sprague-Dawley rats were given an intraperitoneal injection of MNU and one week later were randomized to the two diets for six weeks. The number of mammary carcinomas per rat was 68% greater in the high-fat group, and Ha-ras mutation was rare in this short-term model. The levels of the phosphorylated MAPK2 (active) and of proliferating cell nuclear antigen (PCNA) were significantly higher in carcinomas from the high-fat group, and the two parameters were substantially correlated (r2 = 0.43, p < 0.01). The expression level of c-Raf was fourfold higher in the high-fat group but was only modestly associated with MAPK activation (r2 = 0.35, p < 0.05). The levels of the total MAPK1 and MAPK2, guanosine triphosphatase-activating protein, Ha-Ras, and MAPK kinase did not change. These results suggest that an upregulation of c-Raf expression by high fat may in part account for the in vivo MAPK activation, which in turn may enhance cell proliferation and mammary carcinogenesis.
Vibrational Modes of Nano-Template Viruses (2005)

Viruses have recently attracted attention as biological templates for assembly of nanostructures and nanoelectronic circuits. They can be coated with metals, silica or semiconductor materials and form end-to-end nanorod assemblies. Such viruses as tobacco mosaic virus (TMV) and M13 bac-teriophage have appropriate cylindrical shape and particularly suitable dimensions: M13 is 860 nm long and 6.5 nm in diameter, while TMV is 300 nm long, 18 nm in diameter and with a 4 nm in diameter axial channel. The knowledge of vibrational, i.e. quasi-acoustic phonon, modes of these viruses is important for material and structural characterization of the virus-based nano-templates and for in-situ control of the nanostructure self-assembly. In this paper we report on calculation of the dispersion relations for the lowest vibrational frequencies of TMV and M13 bacteriophage immersed in air and water. We analyze the damping of vibrations in water and discuss application of micro-Raman spectroscopy for control of the virus-based self-assembly processes.
IT Project Evaluation: Is More Formal Evaluation Necessarily Better? (2007)

This paper explores effective IT project evaluation practices in Australia among 36 companies operating in three industry sectors: Finance and Insurance; Mining; and Electricity, Gas and Water Supply. Qualitative analysis of 78 interviews was used to determine characteristics of effective evaluation practices. The study suggests that more formal and sophisticated evaluation methods do not necessarily result in more effective evaluation or better IT project outcomes. Rather, effective IT project evaluation outcomes are more closely related to the drivers of behaviour in organisations such as accountability for results, top-leadership commitment, a strong IT-Business relationship, alignment to strategy, an effective measurement regime, and a willingness to take action. Simplicity and flexibility were also key characteristics underlying effective practices. These conclusions provide both theoretical and practical insights into the evaluation of IT projects in complex environments.
Hydroplane polishing of semiconductor crystals (1981)

A new technique for obtaining optically flat, damage-free surfaces on semiconductor crystals has been developed. The polishing is very fast, being capable of removing over 30 μm of materials per minute in the case of GaAs and InP. Initial results indicate that the technique can also be used in the polishing of HgCdTe.
Electrochemical Degradation of Acid Blue 41 on Ti/Sb-SnO<sub>2</sub> Anodes (2012)

The electrochemical degradation of the wastewater of acid blue 41 was studied with Ti/Sb-SnO 2 as an anode in which the Sb-SnO 2 coating was prepared with a polymeric precursor method. The conversion of acid blue 41 was carried out under galvanostatic control. The effects of current density, initial concentration of acid blue 41 and the concentration of supporting electrolyte on color removal, COD removal and instantaneous current efficiency (ICE) were investigated. The experimental results show that the color removal and COD removal enhance with increasing current density, but ICE decreases. Acid blue 41 can firstly be oxidized by the destroying the conjugated chromophore group and it is difficult that the intermediates produced during the degradation process of cid blue 41 is further degraded.
Sonar Grid Map Based Localization for Autonomous Mobile Robots (2008)

A mobile robot must be able to build a reliable map of surroundings and estimate its position. We have developed a technique for a grid-based localization of a mobile robot with ultrasonic sensors using extended Kalman filter (EKF). For this, we used grids themselves as landmarks of the environment. The grid-based localization can minimize the use of computer resources for localization because this approach does not rely on exact geometric representation of a landmark. Experiments were performed in a real environment to verify the methodology developed in this study, and the results indicate that the grid-based localization can be useful for a practical application.
Performability-based quality of service metrics for communication services (2002)

The paper defines new performability-based QOS (quality of service) metrics to characterize the quality of services offered over telecommunication and computer communication networks. Performability metrics used to characterize fault-tolerant computer systems are not directly applicable to services. This paper discusses the various challenges that arise in defining performability metrics for services. These metrics are defined both from a service provider perspective as well as a customer perspective. In order to model real-world service offerings, which often involve multiple vendor networks, we define service segment metrics from which overall service metrics can be obtained. Additionally, these service segment metrics can be used in negotiations between the different vendors participating in the joint service offering.
Formation of Porcine Hepatocyte Spheroids for use in a Bioartificial Liver (1995)

Xenogeneic hepatocytes have recently been used in a bioartificial liver device as a potential short-term extracorporeal support of acute liver failure. Scaling up the system requires large quantities of viable and highly active cells. Hepatocytes grown as spheroids manifest higher metabolic activities for longer time periods as compared to those in monolayer cultures. Use of hepatocyte spheroids for application in a bioartificial liver can possibly alleviate the need of scaling up. Porcine hepatocytes when cultured under stirred conditions, form multicellular spheroids in a defined culture medium. Spheroids were formed 24 h after cell inoculation with an efficiency of 80-90% and a mean diameter of about 135 μm. Scanning electron microscopy revealed numerous microvilli projecting from the entire surface of the spheroids. Transmission electron microscopy revealed differentiated hepatocytes which displayed well-developed cytoplasmic structures separated by bile canaliculus-like structures. The morphological studies show a resemblance between cells in the spheroids and in the liver in vivo. Ureagenesis by spheroids was twice as active and was sustained for a longer culture period than that by hepatocytes cultured as monolayers. Preparation of porcine hepatocyte spheroids in an agitated vessel is simple efficient and reproducible. It will allow for preparation of large quantities of spheroids to be employed in a bioartificial liver device as well as in liver metabolism studies.
Modification of the pulmonary renin–angiotensin system and lung structural remodelling in congestive heart failure (2006)

Lung structural remodelling, characterized by myofibroblast proliferation and collagen deposition, contributes to impaired functional capacity in CHF (congestive heart failure). As the lung is the primary site for the formation of Ang II (angiotensin II), local modifications of this system could contribute to lung remodelling. Rats with CHF, induced following myocardial infarction (MI) via coronary artery ligation, were compared with sham-operated controls. The MI group developed lung remodelling as confirmed by morphometric measurements and immunohistochemistry. Pulmonary Ang II concentrations increased more than 6-fold (P<0.01), and AT1 (Ang II type 1) receptor expression was elevated by 3-fold (P<0.01) with evidence of distribution in myofibroblasts. AT2 (Ang II type 2) receptor expression was unchanged. In isolated lung myofibroblasts, AT1 and AT2 receptors were expressed, and Ang II stimulated proliferation as measured by [3H]thymidine incorporation. In normal rats, chronic intravenous infusion of Ang II (0.5 mg.kg(-1) of body weight.day(-1)) for 28 days significantly increased mean arterial pressure (P<0.05), without pulmonary hypertension, lung remodelling or a change in AT1 receptor expression. We conclude that there is a modification of the pulmonary renin-angiotensin system in CHF, with increased Ang II levels and AT1 receptor expression on myofibroblasts. Although this may contribute to lung remodelling, the lack of effect of increased plasma Ang II levels alone suggests the importance of local pulmonary Ang II levels combined with the effect of other factors activated in CHF.
Multi-granularity sampling for simulating concurrent heterogeneous applications (2008)

Detailed or cycle-accurate/bit-accurate (CABA) simulation is a critical phase in the design flow of embedded systems. However, with increasing system complexity, full detailed simulation is prohibitively slower than the hardware being simulated. In this paper, we present an approach that uses the sampling technique to speed up the design flow of Multiprocessor System-on-Chip (MPSoC) systems. Based on the dynamic behavior of the applications running concurrently, our method dynamically chooses between multiple granularities of the sampling phase. The similarities of the execution phases for all possible granularities are first analyzed, then transitions between phase overlaps are discretized. To facilitate the detection of repetitions, one phase, with an appropriate granularity, is chosen per process. Unlike most other proposals, the associated performance is usually accurate enough not to need repeated resampling. The use of checkpointing in conjunction with our approach is simplified because the amount of the needed disk space is significantly reduced. Experimental results show that the simulation of concurrent heterogeneous applications can be accelerated by a factor of up to 60x, while maintaining an average performance estimation error lower than 5%.
Condensed-Phase and Oxidation Reaction Behavior of Ti/2B Foils in Varied Gaseous Environments (2012)

The effect of gaseous environment on self-propagating reactions in Ti/2B multilayer foils was studied. Multilayers with reactant layer periodicities from 50 to 3000 nm and a nominal stoichiometry of 1:2 Ti:B were grown using magnetron sputtering. Analysis through scanning transmission electron microscopy, differential scanning calorimetry, and X-ray diffraction revealed the as-deposited multilayers consisted of well-ordered layers of crystalline Ti and amorphous B with the amount of intermixed material negligibly affecting the exothermicity. Propagation rate testing was performed at varied vacuum pressures and studied by high-speed imaging. Propagation rates for foils with bilayer thicknesses 666 nm or thinner did not exhibit a pressure dependency, while foils with bilayer thicknesses 857 nm and larger did. The latter, thick-bilayer foils would not propagate below a characteristic pressure. After reaction, Auger electron spectroscopy revealed O penetration in the thicker bilayer designs and incomplete mixing of Ti and B, while the thinner bilayer foils were uniformly converted to single-phase, hexagonal TiB2. Increased air pressure was found to promote the propagating reaction of the thicker bilayer designs, likely due to increased heat release from oxidation that promotes intermixing and reaction between Ti and B.
Epidemiologic Features of Four Successive Annual Outbreaks of Bubonic Plague in Mahajanga, Madagascar (2002)

From 1995 to 1998, outbreaks of bubonic plague occurred annually in the coastal city of Mahajanga, Madagascar. A total of 1,702 clinically suspected cases of bubonic plague were reported, including 515 laboratory confirmed by Yersinia pestis isolation (297), enzyme-linked immunosorbent assay, or both. Incidence was higher in males and young persons. Most buboes were inguinal, but children had a higher frequency of cervical or axillary buboes. Among laboratory-confirmed hospitalized patients, the case-fatality rate was 7.9%, although all Y. pestis isolates were sensitive to streptomycin, the recommended antibiotic. In this tropical city, plague outbreaks occur during the dry and cool season. Most cases are concentrated in the same crowded and unsanitary districts, a result of close contact among humans, rats, and shrews. Plague remains an important public health problem in Madagascar, and the potential is substantial for spread to other coastal cities and abroad.
Single-pass GPU solid voxelization for real-time applications (2008)

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et a ̀ la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
S6K Directly Phosphorylates IRS-1 on Ser-270 to Promote Insulin Resistance in Response to TNF-α Signaling through IKK2 (2008)

S6K1 (p70S6K) is a serine kinase downstream from Akt in the insulin signaling pathway that is involved in negative feedback regulation of insulin action. S6K1 is also activated by TNF-alpha, a pro-inflammatory cytokine. However, its role remains to be characterized. In the current study, we elucidated a mechanism for S6K1 to mediate TNF-alpha-induced insulin resistance in adipocytes and hepatocytes. S6K1 was phosphorylated at Thr-389 in response to TNF-alpha. This led to phosphorylation of IRS-1 by S6K1 at multiple serine residues including Ser-270, Ser-307, Ser-636, and Ser-1101 in human IRS-1 (Ser-265, Ser-302, Ser-632, and Ser-1097, in rodent IRS-1). Direct phosphorylation of these sites by S6K1 was observed in an in vitro kinase assay using purified IRS-1 and S6K1. Phosphorylation of all these serines was increased in the adipose tissue of obese mice. RNAi knockdown demonstrated an important role for S6K1 in mediating TNF-alpha-induced IRS-1 inhibition that led to impaired insulin-stimulated glucose uptake in adipocytes. A point mutant of IRS-1 (S270A) impaired association of IRS-1 with S6K1 resulting in diminished phosphorylation of IRS-1 at three other S6K1 phosphorylation sites (Ser-307, Ser-636, and Ser-1101). Expression of a dominant negative S6K1 mutant prevented TNF-induced Ser-270 phosphorylation and IRS-1 protein degradation. Moreover, in IKK2 (but not IKK1)-null cells, TNF-alpha treatment did not result in Thr-389 phosphorylation of S6K1. We present a new mechanism for TNF-alpha to induce insulin resistance that involves activation of S6K by an IKK2-dependent pathway. S6K directly phosphorylates IRS-1 on multiple serine residues to inhibit insulin signaling.
A Current View of the Mammalian Aquaglyceroporins (2007)

The discovery of aquaporin water channels by Agre and coworkers answered a long-standing biophysical question of how the majority of water crosses biological membranes. The identification and study of aquaporins have provided insight, at the molecular level, into the fundamental physiology of water balance regulation and the pathophysiology of water balance disorders. In addition to the originally identified classical aquaporins, a second class of aquaporins has been identified. Aquaporins in this latter class, the so-called aquaglyceroporins, transport small uncharged molecules such as glycerol and urea as well as water. Aquaglyceroporins have a wide tissue distribution, and emerging data suggest that several of them may play previously unappreciated physiological or pathophysiological roles. Analyses of transgenic mice have revealed potential roles of aquaglyceroporins in skin elasticity, gastrointestinal function and metabolism, and metabolic diseases such as diabetes mellitus. This review comprehensively discusses the recent discoveries in the field of aquaglyceroporins, alongside a brief overview of the so-called unorthodox aquaporins.
Field studies of color perception in the natural environment (2002)

The Clean Air Act protects visibility in national parks and wilderness areas. Effective strategies to protect and improve visibility depend on accurate models of the effect of sources of air pollution on haze and the perception of scenic vistas seen through the haze. Development of reliable models depends on the available observational data. Unfortunately, the psychophysics of color perception through atmospheric haze has been little studied in the natural environment. Over the years, three field studies of the relationship between atmospheric haze and perception of color have been carried out at the Grand Canyon National Park, the Great Smokey Mountains National Park, and in southern California (just this summer). Some of the problems of doing a visibility field study are described. Qualitatively, these studies show that the hue of a target seen through haze is constant as the haze increases even though the light coming from the target becomes blue due to the effect of light scattered by the haze. The colorfulness decreases exponentially as the optical depth of the haze increases. These results are discussed quantitatively in terms of the classical Metelli color scission formulation of transparency modified for atmospheric visibility and also in terms of recent laboratory work that relates transparency perception and Michelson contrast and convergence in a color space