gebhart/patrepeval huggingface dataset:
The Expression of Phosphorylated mTOR in Breast Cancer from BRCA1-Mutation Carriers. (2009)

Abstract Background: The mammalian target of rapamycin (mTOR) is a serine-threonine kinase coupling growth stimuli and metabolic signals to cell cycle progression and protein synthesis. mTOR represents also a novel therapeutic target in various types of cancer. The role of mTOR in development and progression of breast cancer is not fully understood. There are studies suggesting that mTOR is responsible for the resistance of breast cancer to tamoxifen, trastuzumab and various chemotherapeutic agents. Since there are no studies evaluating the activation (phosphorylation) of mTOR in breast cancer cells carrying a germinal mutation of BRCA1, we have decided to assess activation of this kinase in tumor specimens in BRCA1-mutation carriers.Materials and methods: Formalin fixed paraffin-embedded tumor samples were obtained from 19 patients carrying BRCA1 germinal mutation and 24 patients with intact BRCA1 gene. All patients have been treated in the Great Poland Cancer Center between 2000-2008. The blocks were retrieved from the archives of the Department of Pathology and immunostained for phospho mTOR (Phospho-mTOR (Ser 2448), rabbit antibody, Cell Signaling).Results: Phosphorylation of mTOR was not detected in any of 19 patients carrying the mutated BRCA1 gene. Most of the BRCA1-mutated cancers were ER and HER2 negative (18 (95%) and 16 (94%), respectively). In the tumors with a wildtype BRCA1 gene, mTOR activation was detected in 12 samples (50%). Lack of mTOR phosphorylation was again observed mostly in ER and HER2 negative tissue samples (10 (83%) and 11 (92%), respectively).Discussion: Our findings have demonstrated differential activation of mTOR between tumors carrying a wild-type and mutated BRCA1 gene. We have also observed a negative correlation between ER and HER2 status and phosphorylation of mTOR. Although our study included a relatively low number of cases, the results indicate that activation of mTOR and probably also of its upstream targets do not play a crucial role in biology of tumors with a BRCA1 mutation or with the triple-negative phenotype. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3144.
Dimerization of A-α-[SiNb3W9O40]7- by pH-Controlled Formation of Individual Nb−μ-O−Nb Linkages (2003)

The reversible, stepwise formation of individual Nb-mu-O-Nb linkages during acid condensation of 2 equiv of A-alpha-[SiNb(3)W(9)O(40)](7-) (1) to the tri-mu-oxo-bridged structure A-alpha-[Si(2)Nb(6)W(18)O(77)](8-) (4) is demonstrated by a combination of X-ray crystallography and variable-pD solution (183)W and (29)Si NMR spectroscopy. Addition of DCl to a pD 8.4 solution of 1 (Li(+) salt in D(2)O) results in formation of a mono-Nb-mu-O-Nb-linked dimer, A-alpha-[Si(2)Nb(6)W(18)O(79)](12-) (2; pD = 3.0-1.3). At pD values between 1.6 and 0.3, two isomers (syn and anti) of the di-mu-oxo-bridged dimer, A-alpha-[Si(2)Nb(6)W(18)O(78)](10-) (3), are observed by (183)W NMR (C(2v) and C(2h) symmetry for the syn and anti isomers, respectively; 5 (183)W NMR signals for each isomer in the ratio 2:2:2:2:1). X-ray-quality crystals of syn-3 were isolated in 53% yield (syn-A-alpha-Cs(8)H(2)[Si(2)Nb(6)W(18)O(78)].18H(2)O, orthorhombic, Cmcm, a = 40.847(2), b = 13.2130(7), and c = 16.8179(9) A at 173K, Z = 4, final R(1) = 0.0685). At the low-pD limit of -0.08 (1.2 M DCl), 4 alone is observed. Additional supporting data are provided by variable-pD (29)Si NMR spectroscopy. Reversibility of the above processes was subsequently demonstrated by acquisition of (183)W NMR spectra after incremental additions of LiOH to D(2)O solutions of 4 to effect its stepwise hydrolysis to 2 equiv of 1.
Immunomodulatory Effect ofRhaphidophora korthalsiion Natural Killer Cell Cytotoxicity (2011)

The in vivo immunomodulatory effect of ethanolic extracts from leaves of Rhaphidophora korthalsii was determined via immune cell proliferation, T/NK cell phenotyping, and splenocyte cytotoxicity of BALB/c mice after 5 consecutive days of i.p. administration at various concentrations. Splenocyte proliferation index, cytotoxicity, peripheral blood T/NK cell population, and plasma cytokine (IL-2 and IFN-γ) in mice were assessed on day 5 and day 15. High concentration of extract (350 μg/mice/day for 5 consecutive days) was able to stimulate immune cell proliferation, peripheral blood NK cell population, IL-2, and IFN- γ cytokines, as well as splenocyte cytotoxicity against Yac-1 cell line. Unlike rIL-2 which degraded rapidly, the stimulatory effect from the extract managed to last until day 15. These results suggested the potential of this extract as an alternative immunostimulator, and they encourage further study on guided fractionation and purification to identify the active ingredients that contribute to this in vitro and in vivo immunomodulatory activity.
Flat-shaped microfluidic optical cell for in situ ellipsometry using glass slide as optical window component (2018)

The design and optics of a microfluidic optical cell for in situ ellipsometry are described. The cell employs a typical glass slide serving as both its cover and window. The glass slide is mounted parallel to the specimen with a small gap spacing, which allows the internal volume of the cell to significantly decrease, consequently, increasing the line velocity of the fluid.
Comparative Study of Bioactivity and Safety Evaluation of Ethanolic Extracts of Zanthoxylum schinifolium Fruit and Pericarp (2021)

The fruit and pericarp of <i>Zanthoxylum schinifolium</i> (ZS) have been used in traditional medicine; however, few studies have characterized ZS fruit and pericarp. Therefore, in the present study, we evaluated the safety of ZS fruit (ZSF) and pericarp (ZSP) extracts and compared their bioactivity. To evaluate the safety of ZSF and ZSP, mutagenicity, cytotoxicity, and oxidative stress assays were performed and nontoxic concentration ranges were obtained. ZSP was found to be superior to ZSF in terms of its antimutagenic, antioxidant, and anti-inflammatory activities. In the S9 mix, the mutation inhibition rate of ZSP was close to 100% at concentrations exceeding 625 µg·plate<sup>-1</sup> for both the TA98 and TA100 strains. ZSP exhibited efficient DPPH (IC<sub>50</sub> = 75.6 ± 6.1 µg·mL<sup>-1</sup>) and ABTS (IC<sub>50</sub> = 57.4 ± 6 µg·mL<sup>-1</sup>) scavenging activities. ZSP inhibited the release of cytokines, involved in IL-1β (IC<sub>50</sub> = 134.4 ± 7.8), IL-6 (IC<sub>50</sub> = 262.8 ± 11.2), and TNF-α (IC<sub>50</sub> = 223.8 ± 5.8). These results indicate that ZSP contains a higher amount of biochemicals than ZSF, or that ZSP contains unique biochemicals. In conclusion, for certain physiological activities, the use of ZSP alone may be more beneficial than the combined use of ZSF and ZSP.
Centralized and distributed LTE uplink scheduling in a distributed base station scenario (2009)

The distributed base station concept is treated in the LTE scenario. Uplink scheduling in LTE systems with distributed base stations is considered. In the proposed model, users are connected to remote radio heads deployed throughout the cell and connected to a central base station. Centralized and distributed scheduling with a distributed base station are compared to centralized scheduling with a central base station. Monte carlo simulation results showed that LTE systems with distributed base stations achieve better throughput than systems with conventional base stations while allowing edge users better chances of accessing the resources.
Experiments with Language Models for Known-Item Finding of E-mail Messages. (2005)

Islet amyloidosis is characterized by the deposition and accumulation of amylin in pancreatic beta-cells and is observed in 90% of patients with type 2 diabetes. Previous studies have also revealed the presence of the specific heparan sulfate proteoglycan, perlecan, colocalized to islet amyloid deposits, similar to perlecan's known involvement with other amyloid proteins. In the present study, perlecan purified from the Engelbreth-Holm-Swarm (EHS) tumor was used to define perlecan's interactions with amylin (i.e., islet amyloid polypeptide) and its effects on amylin fibril formation. Using a solid phase-binding immunoassay, human amylin, but not rat amylin, bound immobilized EHS perlecan with a single dissociation constant (Kd) = 2.75 x 10(-6) mol/l. The binding of human amylin to perlecan was similarly observed using perlecan heparan sulfate glycosaminoglycans (GAGs), and was completely abolished by 10 micromol/l heparin. Using thioflavin T fluorometry, Congo red staining, and electron microscopy methodology, intact perlecan was found to enhance amylin fibril formation in a dosage-dependent manner, with the majority of these effects attributed to the heparan sulfate GAG chains of perlecan. Other sulfated GAGs and related macromolecules were also effective in the enhancement of amylin fibril formation in the order of heparin > heparan sulfate > chondroitin-4-sulfate = dermatan sulfate = dextran sulfate > pentosan polysulfate, implicating the importance of the specific GAG/carbohydrate backbone. The sulfate content of heparin/heparan sulfate was also important for the enhancement of amylin fibril formation in the order of heparin > N-desulfated N-acetylated heparin > completely desulfated N-sulfated heparin > completely desulfated N-acetylated heparin. These studies suggest that the enhancement effects of perlecan on amylin fibril formation are mediated primarily by both specific GAG chain backbone and GAG sulfate content, and implicate perlecan as an important macromolecule that is likely involved in the pathogenesis of islet amyloidosis.
A Mechanistic Model for Wettability Alteration by Chemically Tuned Water Flooding in Carbonate Reservoirs (2014)

Abstract Injection of chemically tuned brines into carbonate reservoirs has been reported to enhance oil recovery by 5% to 30% OOIP in core flooding experiments and field tests. One proposed mechanism for this improved oil recovery (IOR) is wettability alteration of rock from oil wet or mixed-wet to more water wet conditions. Modeling of wettability alteration experiments, however, are challenging due to the complex interactions among ions in the brine and crude oil on the solid surface. In this research, we developed a multiphase multicomponent reactive transport model that explicitly takes into account wettability alteration from these geochemical interactions in carbonate reservoirs. Published experimental data suggests that desorption of acidic oil components from rock surfaces make carbonate rocks more water wet. One widely accepted mechanism is that sulfate (SO42−) replaces the adsorbed carboxylic group from the rock surface while cations (Ca2+, Mg2+) decrease the oil surface potential. In the proposed mechanistic model, we used a reaction network that captures the competitive surface reactions among carboxylic groups, cations, and sulfate. These reactions control the wetting fractions and contact angles, which subsequently determine the capillary pressure, relative permeabilities, and residual oil saturations. The developed model was first tuned with experimental data from the Stevns Klint chalk and then used to predict oil recovery for additional un-tuned experiments under a variety of conditions where IOR increased by as much as 30% OOIP, depending on salinity and oil acidity. The numerical results showed that an increase in sulfate concentration can lead to an IOR of over 40% OOIP, while cations such as Ca2+ have a relatively minor effect on recovery (about 5% OOIP). Other physical parameters, including the total surface area of the rock and the diffusion coefficient, control the rate of recovery, however not the final oil recovery. The simulation results further demonstrate that the optimum brine formulation for chalk are those with relatively abundant SO42− (0.096 mol/kg water), moderate concentrations of cations, and low salinity (total ionic strength less than 0.2 mol/kg water). These findings are consistent with the experimental data reported in the literature. The new model provides a powerful tool to predict the IOR potential of chemically tuned waterflooding in carbonate reservoirs under different scenarios.
Design and Application of Microsatellite Marker Panels for Semiautomated Genotyping of Rice (Oryza sativa L.) (2002)

ABSTRACT The objective of this study was to develop a systematic and flexible method for assembling multiplex simple sequence repeat (SSR) marker panels for high throughput genome analysis in rice, Oryza sativa , and to test these panels on a set of cultivated rice germplasm. To do this, 159 microsatellite markers were fluorescently labeled and assembled into 21 multiplex panels for semiautomated genotyping, providing genome‐wide coverage of the 12 rice chromosomes. Panels are comprised of an average of eight markers each, occurring at approximately 11‐centimorgan (cM) intervals throughout the genome. On a standard set of 13 genetically diverse cultivars of Oryza , these markers detected an average of five alleles per locus and had a mean polymorphism information content (P.I.C. value) of 0.67. Polymerase chain reactions (PCR) were optimized on a per marker basis to generate a uniform amount of PCR product and each primer pair was assessed in replicated trials for reliability of allele size estimates. T4 DNA polymerase was used to treat PCR products where the standard deviation of allele molecular weight was greater than 0.5 base pairs (bp). This treatment minimized the variance so that, in the multiplex set reported here, the average std. dev./marker was 0.24 bp, allowing accurate discrimination of alleles that differed by a single nucleotide. The resulting data on allele sizes were then entered into GeneFlow analysis software for the evaluation of polymorphism patterns among diverse rice cultivars. The use of an automated software tool for designing multiplex panels on the basis of both highly polymorphic and more conservative SSR markers resulted in the development of a highly informative semiautomated genotyping system for applications in rice genetics and breeding.
Methotrexate Concentrations in Biological Fluids: Comparison of Results Obtained by Radioimmunoassay and Direct Ligand Binding Radioassay (1979)

A sensitive (sensitivity 2.2 X 10(-9) mol/l) and specific (practically no cross-reaction with circulating folates) radioimmunoassay for the determination of methotrexate concentrations in biological fluids in described and compared with a commercial competitive protein binding assay. Antiserum with high titer was produced in rabbits immunized with MTX-human serum albumin conjugate. Fitness for use in pharmacokinetic drug level determinations was shown in three patients, who received both low doses and high dose therapy combined with citrovorum factor rescue. An excellent correlation was found between plasma and urine MTX concentrations obtained by RIA and competitive protein binding assay. A two-compartment pharmacokinetic model was found adequately describing the serum decay curves, but there was a great interindividual variability in the calculated pharmacokinetic parameters.
Flow-Design and Event-Based Components: A New Approach in Designing Software Compared to Established Procedures (2012)

Flow-Design is a new approach in developing software architectures. Flow-Design focuses on data processing function
units and the communication among them. Event-Based Components represent a programming language independent
methodology for implementing Flow-Design and can also be considered as a resulting software architecture. The Event-
Based Components software architecture is structured by components that communicate via events. Therefore it is
compared to the concept of service-oriented architecture and event-driven architecture which aim to create independent
components as well. In conclusion Flow-Design and Event-Based Components provide a platform and programming
language independent concept to develop software components. The resulting components are reusable, maintainable
and testable. Although it can lead to a more complex coding.
Kinetic Model Evaluation of the Resilience of Plasmonic Nanoantennas for Laser-Induced Fusion (2022)

A kinetic model of the plasmonic response and stability of gold nanorods under high-intensity laser irradiation is used to evaluate their suitability as amplifiers for laser-induced inertial confinement fusion.
Performance Characterization of the Smartphone Video Guidance Sensor as Vision-Based Positioning System (2020)

The Smartphone Video Guidance Sensor (SVGS) is a vision-based sensor that computes the six-state position and orientation vector of a target relative to a coordinate system attached to a smartphone. This paper presents accuracy-characterization measurements of the Smartphone Video Guidance Sensor (SVGS) to assess its performance as a position and attitude estimator, evaluating its accuracy in linear and angular motion for different velocities and various types of targets based on the mean and standard deviation errors between SVGS estimates and known motion profiles, in both linear and angular motions. The study also examines the effects of target velocity and sampling rate on the overall performance of SVGS and provides an overall assessment of SVGS' performance as a position/attitude estimator. While the error metrics are dependent on range and camera resolution, the results of this paper can be scaled to other operational conditions by scaling the blob size in pixels (the light markers identified in the images) relative to the total resolution (number of pixels) of the image. The error statistics of SVGS enable its incorporation (by synthesis of a Kalman estimator) in advanced motion-control systems for navigation and guidance.
Energy transfer and enhanced 154 μm emission in Erbium-Ytterbium disilicate thin films (2011)

α-(Yb1-xErx)2Si2O7 thin films on Si substrates were synthesized by magnetron co-sputtering. The optical emission from Er3+ ions has been extensively investigated, evidencing the very efficient role of Yb-Er coupling. The energy-transfer coefficient was evaluated for an extended range of Er content (between 0.2 and 16.5 at.%) reaching a maximum value of 2 × 10⁻¹⁶ cm⁻³s⁻¹. The highest photoluminescence emission at 1535 nm is obtained as a result of the best compromise between the number of Yb donors (16.4 at.%) and Er acceptors (1.6 at.%), for which a high population of the first excited state is reached. These results are very promising for the realization of 1.54 μm optical amplifiers on a Si platform.
Evaluation of Hospital Floors as a Potential Source of Pathogen Dissemination Using a Nonpathogenic Virus as a Surrogate Marker (2016)

Hospital floors are frequently contaminated with pathogens, but it is not known whether floors are a potential source of transmission. We demonstrated that a nonpathogenic virus inoculated onto floors in hospital rooms disseminated rapidly to the hands of patients and to high-touch surfaces inside and outside the room. Infect Control Hosp Epidemiol 2016;1-4.
Environmentally Friendly Catalysis using Supported Reagents: Enhanced Selectivity without Loss in Activity in the Alkylation of Benzene using Hexagonal Mesoporous Silica (HMS)-supported Aluminium Chloride†,1 (1997)

Substantial increases in selectivity towards monoalkylation of benzene with alkenes can be achieved through the use of mesoporous HMS as support for immobilised aluminium chloride and through the use of external site poisons while maintaining activities comparable to homogeneous AlCl3.
Effect of kernel type on hardness and interrelationship with endosperm chemical components of Malawian local maize (Zea mays L.) varieties during storage (2020)

The aim of this study was to establish the attributes of kernel type based on kernel hardness and its interrelationship with maize endosperm chemical components, which are essential during storage. Three local varieties and one hybrid variety commonly grown by smallholder farmers in central Malawi were used. For storage experiment, the maize samples were infested with Prostephanus truncatus, larger grain borer (LGB) for eight weeks. Due to the high propensity of maize to cross-pollinate, the kernels were classified into flint and dent kernels to establish the physicochemical properties of the kernel type and variety independently. Local variety (L-3) exhibited the lowest number and weight of damaged grains and the highest adult LGB cadavers. Local variety, L-1 and L-3 had significantly the highest proportion of flint kernels type. Moreover, flint kernels of local varieties showed significantly the highest hardness, and the highest content of protein, total zein, &alpha;-zein and zinc (p &lt; 0.05). Furthermore, hardness was significantly and positively correlated with total zein and 14 kDa &beta;-zein content (p &lt; 0.05). Zein in the endosperm, particularly 19 and 22 kDa &alpha;-zein mainly contributed to distinct hardness of the local varieties hence may contribute to physical barrier of the kernels against storage pests. Key words: Maize, local variety, kernel type, hardness, chemical properties, larger grain borer. &nbsp;
Strain-Specific Biostimulant Effects of Chlorella and Chlamydomonas Green Microalgae on Medicago truncatula (2021)

Microalgae have been identified to produce a plethora of bioactive compounds exerting growth stimulating effects on plants. The objective of this study was to investigate the plant-growth-promoting effects of three selected strains of eukaryotic green microalgae. The biostimulatory effects of two <i>Chlorella</i> species (MACC-360 and MACC-38) and a <i>Chlamydomonas reinhardtii</i> strain (cc124) were investigated in a <i>Medicago truncatula</i> model plant grown under controlled greenhouse conditions. The physiological responses of the <i>M. truncatula</i> A17 ecotype to algal biomass addition were characterized thoroughly. The plants were cultivated in pots containing a mixture of vermiculite and soil (1:3) layered with clay at the bottom. The application of live algae cells using the soil drench method significantly increased the plants' shoot length, leaf size, fresh weight, number of flowers and pigment content. For most of the parameters analyzed, the effects of treatment proved to be specific for the applied algae strains. Overall, <i>Chlorella</i> application led to more robust plants with increased fresh biomass, bigger leaves and more flowers/pods compared to the control and <i>Chlamydomonas</i>-treated samples receiving identical total nutrients.