gebhart/patrepeval huggingface dataset:
Quantitative imaging using genetically encoded sensors for small molecules in plants (2012)

Quantitative imaging in live cells is a powerful method for monitoring the dynamics of biomolecules at an excellent spatio-temporal resolution. Such an approach, initially limited to a small number of substrates for which specific dyes were available, has become possible for a large number of biomolecules due to the development of genetically encoded, protein-based sensors. These sensors, which can be introduced into live cells through a transgenic approach, offer the benefits of quantitative imaging, with an extra advantage of non-invasiveness. In the past decade there has been a drastic expansion in the number of biomolecules for which genetically encoded sensors are available, and the functional properties of existing sensors are being improved at a dramatic pace. A number of technical improvements have now made the application of genetically encoded sensors in plants rather straightforward, and some of the sensors such as calcium indicator proteins have become standard analytical tools in many plant laboratories. The use of a handful of probes has already revealed an amazing specificity of cellular biomolecule dynamics in plants, which leads us to believe that there are many more discoveries to be made using genetically encoded sensors. In this short review, we will summarize the progress made in the past 15 years in the development in genetically encoded sensors, and highlight significant discoveries made in plant biology.
Antisense Oligonucleotides with Alternating Phosphodiester-"Amide-3" Linkages (1994)

The synthesis of the building blocks required for the preparation of all the "amide-3" dimers is reported. Five representative dimers are described, as well as the melting temperatures (Tm) of the duplexes formed between an oligonucleotide containing alternating phosphodiester-"amide-3" linkages with its complementary DNA and RNA strand.
Synthesis and Characterization of a Type of Gemini Surfactant (2013)

A type of Gemini surfactants was synthesized by dipheny ether.The synthesis process included alkyl reaction,sulfonic reaction and neutralization reaction.In the alkylation reaction,anhydrous AlCl3 was used as catalyst,and anhydrous cyclohexane was used as a reaction solvent,wherein the catalyst with the reaction reagent with a ratio of 1:1.Fuming sulfuric acid and chlorosulfonic acid were used respectively as sulfonating agent in the sulfonation reaction.Taking into account the yield and other factors,fuming sulfuric acid as the sulfonating agent preferably was the best.
Mapping of a gene for autosomal dominant juvenile-onset open-angle glaucoma to chromosome Iq. (1994)

A large Caucasian family is presented, in which a juvenile-onset form of open-angle glaucoma is transmitted in an autosomal dominant fashion. Sixteen affected family members were identified from 31 at-risk individuals descended from the affected founder. Affected patients developed high intraocular pressures (sometimes > 40 mm Hg) within the first 2 decades of life. Linkage analysis between the disease phenotype and 12 microsatellite repeat markers located on chromosome 1q gave a maximum lod score of 8.38 at a recombination fraction of zero for marker D1S210. Analysis of recombinant haplotypes suggests a total inclusion region of about 14 cM between markers D1S194 and D1S218 at 1q21-q31. This represents the second juvenile-glaucoma family, in which the disease has been mapped to the long arm of chromosome 1.
Risk factors for endometrial cancer: An umbrella review of the literature (2018)

Although many risk factors could have causal association with endometrial cancer, they are also prone to residual confounding or other biases which could lead to over- or underestimation. This umbrella review evaluates the strength and validity of evidence pertaining risk factors for endometrial cancer. Systematic reviews or meta-analyses of observational studies evaluating the association between non-genetic risk factors and risk of developing or dying from endometrial cancer were identified from inception to April 2018 using PubMed, the Cochrane database and manual reference screening. Evidence was graded strong, highly suggestive, suggestive or weak based on statistical significance of random-effects summary estimate, largest study included, number of cases, between-study heterogeneity, 95% prediction intervals, small study effects, excess significance bias and sensitivity analysis with credibility ceilings. We identified 171 meta-analyses investigating associations between 53 risk factors and endometrial cancer incidence and mortality. Risk factors were categorised: anthropometric indices, dietary intake, physical activity, medical conditions, hormonal therapy use, biochemical markers, gynaecological history and smoking. Of 127 meta-analyses including cohort studies, three associations were graded with strong evidence. Body mass index and waist-to-hip ratio were associated with increased cancer risk in premenopausal women (RR per 5 kg/m<sup>2</sup> 1.49; CI 1.39-1.61) and for total endometrial cancer (RR per 0.1unit 1.21; CI 1.13-1.29), respectively. Parity reduced risk of disease (RR 0.66, CI 0.60-0.74). Of many proposed risk factors, only three had strong association without hints of bias. Identification of genuine risk factors associated with endometrial cancer may assist in developing targeted prevention strategies for women at high risk.
Proteomic analysis of Nrf2 deficient transgenic mice reveals cellular defence and lipid metabolism as primary Nrf2-dependent pathways in the liver (2010)

The transcription factor Nrf2 regulates expression of multiple cellular defence proteins through the antioxidant response element (ARE). Nrf2-deficient mice (Nrf2(-/-)) are highly susceptible to xenobiotic-mediated toxicity, but the precise molecular basis of enhanced toxicity is unknown. Oligonucleotide array studies suggest that a wide range of gene products is altered constitutively, however no equivalent proteomics analyses have been conducted. To define the range of Nrf2-regulated proteins at the constitutive level, protein expression profiling of livers from Nrf2(-/-) and wild type mice was conducted using both stable isotope labelling (iTRAQ) and gel electrophoresis methods. To establish a robust reproducible list of Nrf2-dependent proteins, three independent groups of mice were analysed. Correlative network analysis (MetaCore) identified two predominant groups of Nrf2-regulated proteins. As expected, one group comprised proteins involved in phase II drug metabolism, which were down-regulated in the absence of Nrf2. Surprisingly, the most profound changes were observed amongst proteins involved in the synthesis and metabolism of fatty acids and other lipids. Importantly, we show here for the first time, that the enzyme ATP-citrate lyase, responsible for acetyl-CoA production, is negatively regulated by Nrf2. This latter finding suggests that Nrf2 is a major regulator of cellular lipid disposition in the liver.
Binding of human virus oncoproteins to hDlg/SAP97, a mammalian homolog of the <i>Drosophila</i> discs large tumor suppressor protein (1997)

The 9ORF1 gene encodes an adenovirus E4 region oncoprotein that requires a C-terminal region for transforming activity. Screening a lambdagt11 cDNA expression library with a 9ORF1 protein probe yielded a novel cellular PDZ domain-containing protein, 9BP-1, which binds to wild-type, but not a transformation-defective, C-terminal, mutant 9ORF1 protein. The fact that PDZ domains complex with specific sequences at the free C-terminal end of some proteins led to the recognition that the 9ORF1 C-terminal region contained such a consensus-binding motif. This discovery prompted investigations into whether the 9ORF1 protein associates with additional cellular proteins having PDZ domains. It was found that the 9ORF1 protein interacts directly, in vitro and in vivo, with the PDZ domain-containing protein hDlg/SAP97 (DLG), which is a mammalian homolog of the Drosophila discs large tumor suppressor protein and which also binds the adenomatous polyposis coli tumor suppressor protein. Of interest, in forming complexes, the 9ORF1 protein preferentially associated with the second PDZ domain of DLG, similar to adenomatous polyposis coli protein. Human T cell leukemia virus type 1 Tax and most oncogenic human papillomavirus E6 oncoproteins also possessed PDZ domain-binding motifs at their C termini and, significantly, human T cell leukemia virus type 1 Tax and human papillomavirus 18 E6 proteins bound DLG in vitro. Considering the requirement of the 9ORF1 C-terminal region in transformation, these findings suggest that interactions with the cellular factor DLG may contribute to the tumorigenic potentials of several different human virus oncoproteins.
LabPET II, an APD-based Detector Module with PET and Counting CT Imaging Capabilities (2015)

Computed tomography (CT) is currently the standard modality to provide anatomical reference for positron emission tomography (PET) in molecular imaging applications. Since both PET and CT rely on detecting radiation to generate images, using the same detection system for data acquisition is a compelling idea even though merging PET and CT hardware imposes stringent requirements on detectors. These requirements include large signal dynamic range with high signal-to-noise ratio for good energy resolution in PET and energy-resolved photon-counting CT, high pixelization for suitable spatial resolution in CT, and high count rate capability for reasonable CT acquisition time. To meet these criteria, the avalanche photodiode (APD)-based LabPET II module is proposed as the building block for a truly combined PET/CT scanner. The module is made of two monolithic 4×8 APD pixel arrays mounted side-by-side on a custom ceramic holder. Individual APD pixels have an active area of 1.1×1.1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at a 1.2 mm pitch. The APD arrays are coupled to a 12-mm high, 8 ×8 LYSO scintillator array made of 1.12 ×1.12 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> pixels also at a pitch of 1.2 mm to ensure direct one-to-one coupling to individual APD pixels. The scintillator array was designed with unbound specular reflective material between pixels to maximize the difference between refractive indices and enhance total internal reflection at the crystal side surfaces for better light collection, and the APD quantum efficiency was improved to ~ 60% at 420 nm to optimize intrinsic detector performance. Mean energy resolution was 20 ±1% at 511 keV and 41±4% at 60 keV. The measured intrinsic spatial and time resolution for PET were respectively 0.81 ±0.04 mm FWHM/1.57 ±0.04 mm FWTM and 3.6±0.3 ns FWHM with an energy threshold of 400 keV. Initial phantom images obtained using a CT test bench demonstrated excellent contrast linearity as a function of material density. With a magnification factor of 2, a CT spatial resolution of 0.66 mm FWHM/1.2 mm FWTM, corresponding to 1.18 lp/mm at MTF10%/0.67 lp/mm at MTF50%, was measured, allowing 0.75 mm air holes in an Ultra-Micro Hot Spot resolution phantom to be clearly distinguished.
Production evaluation of automated reticle defect printability prediction application (2007)

The growing complexity of reticles and continual tightening of defect specifications causes the reticle defect disposition function to become increasingly difficult. No longer can defect specifications be distilled to a single number, nor can past simple classification rules be employed due to the effects of MEEF on actual printing behavior. The mask maker now requires lithography-based rules and capabilities for making these go/no-go decisions at the reticle inspection step. We have evaluated an automated system that predicts the lithographic significance of reticle defects using PROLITHTM technology. This printability prediction tool was evaluated and tested in a production environment using both standard test reticles and production samples in an advanced reticle manufacturing environment. Reference measurements on Zeiss AIMSTM systems were used to assess the accuracy of predicted results. The application, called the Automated Mask Defect Disposition System, or AMDD, models defective and non-defective test and reference images generated by a high-resolution inspection system. The results were calculated according to the wafer exposure conditions given at setup such that the reticle could be judged for its 'fitness-for-use' from a lithographic standpoint rather than from a simple physical measurement of the film materials. We present the methods and empirical results comparing 1D and 2D Intensity Difference Metrics (IDMs) with respect to AIMS and discuss the results of usability and productivity studies as they apply to manufacturing environments.
Anti-histaminic Activity of<i>Desmostachya bipinnata</i> (2014)

Desmostachya bipinnata, Gramineae (Poaceae) family, has been traditionally used in treatment of various disorders like asthma, kidney stone, diarrhoea, wound healing etc. Several extracts of Desmostachya bipinnata were prepared. Ex-vivo estimation of contractile responses of guinea pig ileum were measured for prepared extracts against histamine and compared with chlorphenirame. All the extracts were able to contract guinea pig ileum while alcoholic extract was superior among all. Such results indicated that prepared extract possess good anti-histaminic activity, which was further confirmed with histamine induced lethality test. Histamine induced lethality in guinea pigs was prevented when the extracts were administered prior to histamine injection in guinea pigs. Hence, it is concluded that the extracts possess anti-histaminic activity and may possess anti-asthmatic potential.
Rapid prototyping of electronic systems (2002)

Describes a system for the rapid prototyping, testing and debugging of DSP designs. The DSP algorithm is first coded in a high level algorithmic language. This description is translated by the synthesis software into a structural specification suitable for HDI fabrication. The synthesis process includes the insertion of test capabilities into the hardware to allow for debugging the design. The rapid turnaround of HDI fabrication means that the user can have a prototype HDI module (DSP accelerator) in his hands ready for testing within at most a day or two, and at moderate cost. The DSP accelerator is then placed in a socket on a specially designed board (called the mother-board), connected to a Sun or other workstation, where it may be thoroughly tested and debugged. The debugging capabilities include structural verification, debugging and in-system test. Structural verification is testing the DSP accelerator to see that it is connected together correctly and that all the parts are working. Debugging involves sending test vectors through the chip, stepping, observing internal node values and limited reconfigurability with the purpose of debugging the algorithm. In-system test is done by connecting the DSP accelerator via a cable into the target system. This allows the system to be run at full speed (up to 20 MHz) with the DSP accelerator in place, but still retaining full observability of internal nodes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ionic liquid stationary phases for gas chromatography (2011)

Abstract This article provides a summary of the development of ionic liquids as stationary phases for gas chromatography beginning with early work on packed columns that established details of the retention mechanism and established working methods to characterize selectivity differences compared with molecular stationary phases through the modern development of multi‐centered cation and cross‐linked ionic liquids for high‐temperature applications in capillary gas chromatography. Since there are many reviews on ionic liquids dealing with all aspects of their chemical and physical properties, the emphasis in this article is placed on the role of gas chromatography played in the design of ionic liquids of low melting point, high thermal stability, high viscosity, and variable selectivity for separations. Ionic liquids provide unprecedented opportunities for extending the selectivity range and temperature‐operating range of columns for gas chromatography, an area of separation science that has otherwise been almost stagnant for over a decade.
Development of real-time reverse transcriptase qPCR assays for the detection of Punta Toro virus and Pichinde virus (2016)

PTV and PICV Taq-man MGB based real-time RT-qPCR assays developed here showed relevant sensitivity and reproducibility in samples extracted from a variety of clinical matrices. These assays will be useful as a standard by researchers for future experiments utilizing PTV and PICV as infection models, offering the ability to track infection and viral replication kinetics during research studies.
siRNA Knockdown of RRM2 Effectively Suppressed Pancreatic Tumor Growth Alone or Synergistically with Doxorubicin (2018)

Pancreatic cancer is currently one of the deadliest of the solid malignancies, whose incidence and death rates are increasing consistently during the past 30 years. Ribonucleotide reductase (RR) is a rate-limiting enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides, which are essential for DNA synthesis and replication. In this study, 23 small interfering RNAs (siRNAs) against RRM2, the second subunit of RR, were designed and screened, and one of them (termed siRRM2), with high potency and good RNase-resistant capability, was selected. Transfection of siRRM2 into PANC-1, a pancreatic cell line, dramatically repressed the formation of cell colonies by inducing remarkable cell-cycle arrest at S-phase. When combining with doxorubicin (DOX), siRRM2 improved the efficacy 4 times more than applying DOX alone, suggesting a synergistic effect of siRRM2 and DOX. Moreover, the combined application of siRRM2-loaded lipid nanoparticle and DOX significantly suppressed the tumor growth on the PANC-1 xenografted murine model. The inhibition efficiency revealed by tumor weight at the endpoint of the treatment reached more than 40%. Hence, siRRM2 effectively suppressed pancreatic tumor growth alone or synergistically with DOX. This study provides a feasible target gene, a drug-viable siRNA, and a promising therapeutic potential for the treatment of pancreatic cancer.
One‐pot synthesis of (3‐sulfopropyl methacrylate potassium)‐silica hybrid monolith via thiol‐ene click chemistry for <scp>CEC</scp> (2012)

A novel (3-sulfopropyl methacrylate potassium)-silica hybrid monolithic column for CEC has been prepared by a simple one-pot approach based on efficient thiol-ene click chemistry. In this process, the polycondensation of hydrolyzed alkoxysilanes and in situ click reaction of vinyl groups on 3-sulfopropyl methacrylate potassium and thiol groups on the precondensed siloxanes simultaneously occurred in a pretreated capillary. Homogeneous monolithic matrix with large through-pores tightly bonded to the inner wall of the capillary was shown by optical microscope and SEM. The minimum plate height of this hybrid monolithic column was determined as 3.9 μm for thiourea. Anilines, alkylbenzenes, and phenols were well separated on this hybrid monolithic column by CEC, which indicated typical reversed-phase and cation-exchange chromatographic retention mechanisms of the column.
Performance of dynamic channel allocation in the DECT system (2002)

The authors present the results of computer simulations of an indoor wireless PABX system conforming to the Digital European Cordless Telecommunications (DECT) standard. Of particular interest is the evaluation of the dynamic channel allocation algorithm proposed by the DECT standard. It is shown that this system is capable of meeting the expected capacity requirements for high-density indoor applications as long as there are a sufficient number of base stations on each floor of the building. System performance has been measured in terms of setup blocking, handover blocking, lost calls, cleared traffic, and carrier-to-interference ratios.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Neuroprotective Effects of an Erythropoietin-Derived Peptide in PC1 2 Cells under Oxidative Stress (2016)

Erythropoietin (EPO) has been shown to be a key cytokine in the production of erythrocytes from erythroblasts. Recently, attempts have been made to adopt EPO as a drug target for neuroprotection in selected neurological pathologies. In the current study, a novel EPO-derived peptide which mimics the weak binding site of EPO to its receptor (MK-X) was generated. Experimental results demonstrated that MK-X was able to ameliorate neuronal death due to reactive oxygen species and conditions of oxidative stress similar to EPO. In addition, MK-X induced long-lasting Extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) and Akt activation. Furthermore, treatment with inhibitors of ERK1/2 and Akt abolished the neuroprotective effect of MK-X. Unlike EPO, however, MK-X did not induce cellular proliferation. Collectively, the results of the current study suggested that MK-X may be useful as a novel neuroprotective reagent.
An analysis of the learning curve and its application to industry (2016)

This paper studies The Learning curve and how it can be applied to industry. The “Learning Effect” was being firstly noted in connection with the production of Aircrafts. It explains that the time required to make a product decreases as the number of times it is made by the same person or group, who is working and relates the manufacturing cost to cumulative production. The learning process helps to improve the quality and stock of knowledge, technological abilities and estimate the labor hours of the firm.
Finding Satisfactory Transparency (2015)

This paper focuses on designing an affective user interface for public transparent displays in a shop context. In order to maintain harmonious view and satisfactory experience, the relationship between the information and transparency needs to be considered. Therefore, in this paper, we investigate different levels of transparency for determining their appropriateness with regard to user's proximity. Two user studies show that 25% transparency is more satisfactory in closer proximity while 50% transparency offers more harmonious view in a distant context. Our findings on satisfactory transparency can be applied to a basis of further investigation for public transparent displays, especially in a shop context.
GENERIC DETECTION AND CLASSIFICATION OF POLYMORPHIC MALWARE USING NEURAL PATTERN RECOGNITION (2006)

Additionally to the AP and PP, a delayed phase should be performed when cirrhosis is present. Even though AP and DP depicted all HCC's in this study, the PP provides undispensable additional information, so that, in our opinion, a THCT should be given preference when HCC is suspected.