gebhart/patrepeval huggingface dataset:
Nuclear orphan receptor TR3/Nur77 mediates melanoma cell apoptosis (2007)

TR3 was originally recognized for its role in the regulation of cell survival and differentiation, however, it was recently found to be a potent pro-apoptotic protein. In order to characterize the role of TR3 in melanoma cell apoptosis, we studied expression of TR3 in melanoma cell lines and tissues, its subcellular distribution and function during apoptosis using various expression and RNA interference vectors. We found that TR3 was constitutively expressed in both cultured melanoma cells and melanoma tissues. TR3 expression was significantly decreased in advanced melanomas comparing to benign nevi. Over-expression of wild type TR3 or mutant TR3 lacking the DNA binding domain resulted in massive apoptosis in melanoma cells, whereas stable knockdown of TR3 using RNA interference resulted in melanoma cell resistance to apoptosis induced by chemotherapeutic agents ATRA and cisplatin. We further demonstrated that apoptosis in melanoma cells was mediated, at least partially, through TR3 mitochondrial translocation but not alteration in TR3 expression levels. Our results suggest that TR3 is an important apoptosis inducing factor in melanoma cells. Decreased expression of TR3 in metastatic melanoma cells may contribute to their reduced apoptotic potential and increased resistance to chemotherapy.
A comprehensive review of endpoint detection in chemical mechanical planarisation for deep-submicron integrated circuits manufacturing (2003)

As the number of metal levels and the wafer size increase, the need for global planarity across the wafer becomes more crucial. Chemical mechanical planarisation (CMP) is considered the key technique to achieve this goal. Accurate in situ end point detection and monitoring method can reduce the product variance, improve the yield and throughput. During CMP process, the wafer is brought downward against the polishing pad completely. The monitoring of the wafer polishing in such a configuration becomes a difficult task. Many methods have been proposed in the past years, including the optical, electrical, acoustical/vibrational, thermal, frictional, chemical/electrochemical methods and others, which are critically reviewed in this study. The mainstream of the industrial application and the future trend are investigated.
An electro-conductive fluid as a responsive implant for the controlled stimuli-release of diclofenac sodium (2015)

The purpose of this study was to develop an electro-responsive co-polymeric (ERP) implantable gel from polyethylene glycol (PEG), sodium polystyrene sulphonate (NaPss), polyvinyl alcohol (PVA), and diethyl acetomidomalonate (DAA) for electro-liberation of the model drug diclofenac sodium. Various physicochemical and physicomechanical characterization tests were undertaken on the synthesized drug-free gel (ERP G1) and drug-loaded gel (ERP G2). The ability of the gel to release diclofenac sodium following electrical stimulation was evaluated using a galvanostat while Molecular Mechanics (MM) simulations were performed to elucidate the experimental mechanisms. A stable electro-active gel exhibiting superior cycling stability was produced with desirable rheological properties, rigidity (BHN = 35.4 N ± 0.33 N/mm<sup>2</sup>; resilience = 10.91 ± 0.11%), thermal properties (T<sub>g</sub> ≈ 70 °C; T<sub>c</sub> ≈ 200 °C) and homogeneous morphology. "ON-OFF" pursatile gradual drug release (37-94% from t<sub>30 min</sub>-t<sub>180</sub> <sub>min</sub>) kinetics was observed upon applying electric stimulation intermittently, indicating that drug release from the gel was electrically controlled. Overall, the galvanometric and MM evaluation ascertained the suitability of the PEG/NaPss/PVA ERP-Gel for application as a subcutaneously injectable drug delivery implant.
Artificial Immune System for Protein Folding Model (2011)

To improve protein folding simulations, artificial immune system (AIS) was investigated on a 2D lattice model. AIS is a novel intelligent problem solving technique inspired from vertebrate immune system. Compared with stand genetic algorithm (SGA), AIS contains four new operators such as cloning selection, inverse mutation, pairwise interchange mutation, and receptor editing. In the experiments, we compared AIS with the immune genetic algorithm (IGA) for 4 chains of different lengths of 20, 36, 48, and 64. The results show that AIS has a higher success rate but costs more time. Keyword: Artificial Immune System, Protein Folding Model, Immune Genetic Algorithm
Real-time on a "standard" UNIX workstation? (1992)

This is a report of an ongoing R&D project which is investigating the use of standard UNIX workstations for the real-time data acquisition from a major new experimental initiative, the SLAC B Factory (PEP II). For this work an IBM RS/6000 workstation running the AIX operating system is used. Real-time extensions to the UNIX operating system are explored and performance measured. These extensions comprise a set of AIX-specific and POSIX-compliant system services. Benchmark comparisons are made with embedded processor technologies. Results are presented for a simple prototype on-line system for laboratory-testing of a new prototype drift chamber.
Accurate Modeling of the Intrinsic Brillouin Linewidth via Finite-Element Analysis (2010)

We present a finite-element analysis of the Brillouin gain spectrum of a highly Ge-doped azimuthally symmetric nonuniform fiber treating the heterogeneous viscosity profile in detail. Measured Stokes' frequencies and spectral widths for the acoustic modes, and the peak Brillouin gain coefficient are found to be in excellent agreement with the model. An approximate expression for the Brillouin spectral width in azimuthally symmetric, nonuniform fibers is presented and verified for estimating this quantity using simplified boundary-value models.
Minimum oil analysis for reliable WAT modelling[Wax appearance temperature] (2000)

The development of a waxy of a crude oil or condensate field may face serious problems because of crystallisation of the paraffinic components of the fluid. One of the first fluid data to be obtained in order to determine if wax deposit may occur during production and as a consequence, if the field development requires specific consideration for wax management is the WAT Appearance Temperature (WAT). WAT is generally measured on stock tank crude oils, at the time of the evaluation phase of future development. Lighter ends of the live oil have to be accounted for through thermodynamic modelling. Thermodynamic modelling may also be used to foresee production issues due to changes in the oil composition during the field life. It may as well evaluate the benefit of an eventual fluxing of produced fluids. It is well understood that the description of the oil composition in the thermodynamic modelling cannot be endlessly extensive, because of technical limits and cost efficiency of laboratory analyses. The CRYSPAR thermodynamic model was published in 1996, together with recommendations for the lab analyses of the oil and their processing for data input. Were set forth the following features: separation between C{sub 20+} (light) and C{sub 20-} (heavy) components, GC analysis to lump the light fraction in 5 components, molecular weight measurement of the heavy fraction, GC analysis and LC distribution of the heavy fraction to identify its normal-paraffin content and lump the whole into 4 components. These recommendations were used satisfactorily up to now but the need to make the best use of eventual more limited analytical data was evidenced. The aim of this study was to evaluate the accuracy of the WAT calculations, when only very few data are available. Correlations from literature were used to calculate the distribution between the different chemical families when only the specific gravity and the molecular weight of the heavy fraction were known. Comparisons of measured and modelled WAT, calculated from more or less limited chemical analyses are discussed. Satisfactory results were obtained, in relationship with the expected result accuracy. The quantity of crystallised fraction were also calculated through the model, but the comparison shows that the results are not satisfactory. (au)
Supplementary Figure 1 from Histone Deacetylase Inhibitors Influence Chemotherapy Transport by Modulating Expression and Trafficking of a Common Polymorphic Variant of the ABCG2 Efflux Transporter (2023)

&lt;p&gt;PDF file - 47K, Effect of inhibition of autophagy on ABCG2 expression&lt;/p&gt;
Synthesis and Ring-Opening Polymerization of Poly(alkylene 2,6-naphthalenedicarboxylate) Cyclic Oligomers (1996)

Cyclic oligomers of poly(ethylene 2,6-naphthalenedicarboxylate) (PEN) and poly(butylene 2,6-naphthalenedicarboxylate) (PBN) were prepared by reaction of 2,6-naphthalenedicarbonyl dichloride with the corresponding diol. The structures of the cyclic oligomers were confirmed by a combination of GPC, mass spectrometry, and NMR analysis. The PEN cyclics were obtained in 57% yield with a preponderance of the cyclic trimer. The PBN cyclics were obtained in 75% yield with a preponderance of the cyclic dimer. Ring-opening polymerization of either cyclic material was performed in the melt using either a tin or titanium catalyst. The inherent viscosity of PBN or PEN prepared via ring-opening polymerization was lower than that of commercial samples.
Setting research priorities to improve global newborn health and prevent stillbirths by 2025 (2020)

BackgroundIn 2013, an estimated 2.8 million newborns died and 2.7 million were stillborn. A much greater number suffer from long term impairment associated with preterm birth, intrauterine growth restriction, congenital anomalies, and perinatal or infectious causes. With the approaching deadline for the achievement of the Millennium Development Goals (MDGs) in 2015, there was a need to set the new research priorities on newborns and stillbirth with a focus not only on survival but also on health, growth and development. We therefore carried out a systematic exercise to set newborn health research priorities for 2013–2025.MethodsWe used adapted Child Health and Nutrition Research Initiative (CHNRI) methods for this prioritization exercise. We identified and approached the 200 most productive researchers and 400 program experts, and 132 of them submitted research questions online. These were collated into a set of 205 research questions, sent for scoring to the 600 identified experts, and were assessed and scored by 91 experts.ResultsNine out of top ten identified priorities were in the domain of research on improving delivery of known interventions, with simplified neonatal resuscitation program and clinical algorithms and improved skills of community health workers leading the list. The top 10 priorities in the domain of development were led by ideas on improved Kangaroo Mother Care at community level, how to improve the accuracy of diagnosis by community health workers, and perinatal audits. The 10 leading priorities for discovery research focused on stable surfactant with novel modes of administration for preterm babies, ability to diagnose fetal distress and novel tocolytic agents to delay or stop preterm labour.ConclusionThese findings will assist both donors and researchers in supporting and conducting research to close the knowledge gaps for reducing neonatal mortality, morbidity and long term impairment. WHO, SNL and other partners will work to generate interest among key national stakeholders, governments, NGOs, and research institutes in these priorities, while encouraging research funders to support them. We will track research funding, relevant requests for proposals and trial registers to monitor if the priorities identified by this exercise are being addressed.
The Technology of Helianthus Tuberosus Agricultural Residues Processing to Obtain Activated Carbons (2015)

Today the issue of straw processing into fuel bricks is being widely discussed, for thermal capacity of such bricks made of straw of various agricultural crops is not lower, but even higher than that one of timber (timber produces usually up to 17,5–19,0 megajoule/kg). In order to obtain active carbons from straw of various oil Brassica crops (Camelina sativa) have been chosen as raw material. The technique was as follows.The straw was milled, loaded into a steel retort, which was capped and placed in the electric furnace, feeding nitrogen into the vessel to create an inert atmosphere. The retort was heated at a rate of temperature rise 1–20°C/min to 450–500°C and maintained at the final carbonization temperature for 30–60 min. After completing the process of carbonization the retort was switched to the mode of steam activation at 850–870 °C. Powder activated carbons, obtained from Camelina sativa, false flax, barley and wheat straw according to this technology has a product yield of 5.7%. The obtained powder activated carbon was analyzed in accordance with the accepted state standards and the following characteristics have been determined: Ac = 15.6% by weight; Δ = 140 g/dm3; VΣ = 2.43 cm 3 /g; Ws = 0.69 cm 3 /g, the adsorption capacity for iodine and methylene blue (MB) was 43 and 82 mg/g. As a result, during activation process a vast sorption space Ws is being developed, which leads to a high iodine adsorption. The active carbons adsorption isotherm of nitrogen, measured on the device ASAP- 2020, made possible calculating the parameters of its microporous structure: micropore volume (Vmi) – 0.135 cm 3 /g, micropore size (full width of the gap) – 1.66 nm the total pore surface area (Sud – 380 m 2 / g), the adsorption energy Ea – 19.8 kJ/mol. We have developed and studied polyfunctional, environmentally safe (nano) chips based on oligo-, polysaccharides and activated carbon derivatives, obtained from waste vegetable matter (straw of various oil Brassica crops). Their influence on growth, development, seed yield and quality of various crops (corn crops, legumes, oil crops and etc.) has been determined. Extending target properties of various agricultural (nano)polymerous materials provides optimal level of gradual consumption of physiologically active substances, decreasing chemical load and increasing plant resistance to unfavorable environmental factors.
Shear-driven modelling of thrombus formation in type B aortic dissection (2022)

<b>Background:</b> Type B aortic dissection (TBAD) is a dangerous pathological condition with a high mortality rate. TBAD is initiated by an intimal tear that allows blood to flow between the aortic wall layers, causing them to separate. As a result, alongside the original aorta (true lumen), a false lumen (FL) develops. TBAD compromises the whole cardiovascular system, in the worst case resulting in complete aortic rupture. Clinical studies have shown that dilation and rupture of the FL are related to the failure of the FL to thrombose. Complete FL thrombosis has been found to improve the clinical outcomes of patients with chronic TBAD and is the desired outcome of any treatment. Partial FL thrombosis has been associated with late dissection-related deaths and the requirement for re-intervention, thus the level of FL thrombosis is dominant in classifying the risk of TBAD patients. Therefore, it is important to investigate and understand under which conditions complete thrombosis of the FL occurs. <b>Method:</b> Local FL hemodynamics play an essential role in thrombus formation and growth. In this study, we developed a simplified phenomenological model to predict FL thrombosis in TBAD under physiological flow conditions. Based on an existing shear-driven thrombosis model, a comprehensive model reduction study was performed to improve computational efficiency. The reduced model has been implemented in Ansys CFX and applied to a TBAD case following thoracic endovascular aortic repair (TEVAR) to test the model. Predicted thrombus formation based on post-TEVAR geometry at 1-month was compared to actual thrombus formation observed on a 3-year follow-up CT scan. <b>Results:</b> The predicted FL status is in excellent agreement with the 3-year follow-up scan, both in terms of thrombus location and total volume, thus validating the new model. The computational cost of the new model is significantly lower than the previous thrombus model, with an approximate 65% reduction in computational time. Such improvement means the new model is a significant step towards clinical applicability. <b>Conclusion:</b> The thrombosis model developed in this study is accurate and efficient at predicting FL thrombosis based on patient-specific data, and may assist clinicians in choosing individualized treatments in the future.
Lamellar ordering in computer-simulated block copolymer melts by a variety of thermal treatments (2003)

A lattice computer simulation of a symmetric A–B–A triblock copolymer melt is reported. This melt is quenched, in simulation, from an athermal state to 39 different temperatures using cooperative motion algorithm. Energy, specific heat, copolymer end-to-end distance, bridging fraction, lamellar spacing, concentration profiles, and microstructure visualizations are reported. The quenching simulation results are compared with those obtained by alternative thermal treatments, that is by slow heating and slow cooling. Quenches yield data consistent with theory and experiment, whereas slow cooling and slow heating results do not capture the expected behavior for the lamellar spacing and the bridging fraction. Finally, at very low temperatures, below the conventional order–disorder transition temperature, an additional ordering is recorded, from a conventional lamellar phase to a lamellar structure showing copolymer junction points condensed into a two-dimensional plane.
Embedded Single-Inductor Bipolar-Output DC–DC Converter in Class-D Amplifier for Low Common Noise (2015)

This paper proposes a high efficiency class-D amplifier (CDA) with embedded single-inductor bipolar output (SIBO) power module. The characteristics of SIBO converter's bipolar outputs not only suppress equivalent common-mode noise but also remove several large external bulky components in conventional boost supply CDA systems. Since bipolar outputs in the SIBO provide independent driving capability, CDA is capable of operating in both single-ended and bridge-tide load configurations. Furthermore, the proposed dynamic voltage boosting technique adjusts the SIBO output voltage level according to the CDA's output level with 5% power efficiency improvement. Peak total harmonic distortion plus noise performance is 0.012%. Peak power efficiency of SIBO and CDA is 89% and 93.2%, respectively.
Epidermal growth factor (EGF)-like repeats of human tenascin-C as ligands for EGF receptor (2001)

Signaling through growth factor receptors controls such diverse cell functions as proliferation, migration, and differentiation. A critical question has been how the activation of these receptors is regulated. Most, if not all, of the known ligands for these receptors are soluble factors. However, as matrix components are highly tissue-specific and change during development and pathology, it has been suggested that select growth factor receptors might be stimulated by binding to matrix components. Herein, we describe a new class of ligand for the epidermal growth factor (EGF) receptor (EGFR) found within the EGF-like repeats of tenascin-C, an antiadhesive matrix component present during organogenesis, development, and wound repair. Select EGF-like repeats of tenascin-C elicited mitogenesis and EGFR autophosphorylation in an EGFR-dependent manner. Micromolar concentrations of EGF-like repeats induced EGFR autophosphorylation and activated extracellular signal-regulated, mitogen-activated protein kinase to levels comparable to those induced by subsaturating levels of known EGFR ligands. EGFR-dependent adhesion was noted when the ligands were tethered to inert beads, simulating the physiologically relevant presentation of tenascin-C as hexabrachion, and suggesting an increase in avidity similar to that seen for integrin ligands upon surface binding. Specific binding to EGFR was further established by immunofluorescence detection of EGF-like repeats bound to cells and cross-linking of EGFR with the repeats. Both of these interactions were abolished upon competition by EGF and enhanced by dimerization of the EGF-like repeat. Such low affinity behavior would be expected for a matrix-"tethered" ligand; i.e., a ligand which acts from the matrix, presented continuously to cell surface EGF receptors, because it can neither diffuse away nor be internalized and degraded. These data identify a new class of "insoluble" growth factor ligands and a novel mode of activation for growth factor receptors.
Optical tweezers for single molecule force spectroscopy on bacterial adhesion organelles (2006)

Instrumentation and methodologies for single molecule force spectroscopy on bacterial adhesion organelles by the use of force measuring optical tweezers have been developed. A thorough study of the biomechanical properties of fimbrial adhesion organelles expressed by uropathogenic <i>E. coli</i>, so-called pili, is presented. Steady-state as well as dynamic force measurements on P pili, expressed by <i>E. coli</i> causing pyelonephritis, have revealed, among other things, various unfolding and refolding properties of the helical structure of P pili, the PapA rod. Based on these properties an energy landscape model has been constructed by which specific biophysical properties of the PapA rod have been extracted, e.g. the number of subunits, the length of a single pilus, bond lengths and activation energies for bond opening and closure. Moreover, long time repetitive measurements have shown that the rod can be unfolded and refolded repetitive times without losing its intrinsic properties. These properties are believed to be of importance for the bacteria's ability to maintain close contact with host cells during initial infections. The results presented are considered to be of importance for the field of biopolymers in general and the development of new pharmaceuticals towards urinary tract infections in particular. The results show furthermore that the methodology can be used to gain knowledge of the intrinsic biomechanical function of adhesion organelles. The instrumentation is currently used for characterization of type 1 pili, expressed by <i>E. coli</i> causing cystitis, i.e. infections in the bladder. The first force spectrometry investigations of these pili will be presented.
Evaluation of Pressure Drop and Particle Sphericity for an Air-rock Bed Thermal Energy Storage System (2014)

The pressure drop of a packed bed thermal energy storage system with irregular shaped solid pellets and tank-to-particle diameter ratio of 10.4 is investigated. The bed height to diameter ratio is 2. The particle sphericity is calculated and used to compare pressure drop correlations to the measured values in the particle Reynolds number range of 353 ≤ Rep ≤ 5206.
Exocrine pancreatic response to the venom of the scorpion, Tityus trinitatis. (1977)

This paper records for the first time the exocrine pancreatic response to scorpion venom, in this case that of Tityus trinitatis, a scorpion endemic in Trinidad. The crude venom injected intravenously into fasting anaesthetised dogs induced a secretion of the exocrine pancreas. The secretion evoked was rich in enzymes.
Asymmetric Palladium-Catalyzed Allylic Alkylation of Indoles (2011)

The authors exploit the intrinsic chirality of a sulfur donor atom in their sulfur-MOP ligand to increase the stereocontrol of the catalyst system in their alkylation of indoles. Optically ­active indoles are common in biologically active compounds, and good yields and enantioselectivities can be achieved for these types of molecules with this methodology.
Influence of Gamma-ray irradiation on the spectral properties of Bi-doped silica fibers (2014)

After Bi-doped silica fiber is irradiated, its absorption peaks intensity at 520, 700, and 800 nm increase, and the fluorescence intensity at 950-1650 nm increases with 980 nm pumping, while decreases with 532 nm pumping.