gebhart/patrepeval huggingface dataset:
Isolation and characterization of the mouse acetylcholine receptor delta subunit gene: identification of a 148-bp cis-acting region that confers myotube-specific expression. (1988)

We have isolated the gene encoding the delta subunit of the mouse skeletal muscle acetylcholine receptor (AChR) and have identified a 148-bp cis-acting region that controls cell type-specific and differentiation-dependent gene expression. The 5' flanking region of the delta subunit gene was fused to the protein-coding region of the chloramphenicol acetyltransferase (CAT) gene and gene fusions were transfected into C2 mouse skeletal muscle cells. Both transiently and stably transfected cells were assayed for CAT gene expression. Deletions from the 5' end of the mouse delta gene demonstrate that 148 bp of 5' flanking DNA is sufficient to confer cell type-specific and differentiation-dependent expression: CAT activity is present in transfected myotubes, but not in transfected 3T3 cells or 10T1/2 cells. Moreover, the level of CAT expression in myotubes transfected with constructs containing 148 bp of 5' flanking DNA from the delta subunit gene is identical to that in myotubes transfected with constructs containing 3.2 kb of 5' flanking DNA and similar to expression from the SV-40 early promoter. Increased CAT activity in myotubes is a result of an increased rate of transcription from the delta subunit promoter, since CAT RNA levels are also 35-fold more abundant in myotubes than myoblasts. In contrast, the SV-40 early promoter is similarly active in all cell types. Thus, 148 bp of 5' flanking DNA from the delta subunit gene contains all the information required for cell type-specific and differentiation-dependent expression of the AChR delta subunit.
Efficient Modification and Preparation of Circular DNA for Expression in Cell Culture (2022)

Abstract DNA plasmids are an essential tool for delivery and expression of RNAs and proteins in cell culture experiments. The preparation of plasmids typically involves a laborious process of bacterial cloning, validation, and purification. While the expression plasmids can be designed and ordered from the contract manufacturers, the cost may be prohibitive when a large number of plasmids is required. We have developed an efficient fully synthetic method and protocol that enables the production of circularized DNA containing expression elements ready for transfection in as little as 3 hours, thereby eliminating the bacterial cloning steps. The protocol describes how to take a linear double-stranded DNA fragment and efficiently circularize and purify this DNA fragment with minimal hands-on time. As proof of the principle, we applied Circular Vector expressing engineered prime editing guide RNA (epegRNA) in cell culture, and demonstrated matching and even exceeding performance of this method as compared to guides expressed by plasmids. The method is not limited to gene editing and its speed of preparation, low cost, and ease of use will make it a useful tool in a variety of applications requiring the expression of short RNAs and proteins.
Industrial contribution in design, manufacturing, and erection of large ground-based telescopes (2003)

Industry is a bridge which links scientific thought with its concrete possibility to realize something operative and functional. In the last fifteen years, Astronomy has undergone a total revolution: telescopes are getting bigger and bigger and even more efficient. Enclosures are being more and more integrated into scientific performances. From NTT to VLT, from LBT to ALMA, to VST and to VISTA: there is always an industrial contribution in the development of the biggest astronomic projects. A comparison between scientific and technological research, a synergy that leads to the future.
Eggs and Health Promotion (2002)

Introduction Composition of hen's eggs Dietary cholesterol from eggs Role of eggs in the diet Nutritional and functional significance of designer eggs Eggs and saturated fat Meta analysis of dietary cholesterol Raw eggs and bacterial infection causation Antibodies produced in eggs for medical use Iodine supplemented chickens Home preparation of eggs Effects of enriched hen eggs The new area of antibodies in eggs Veterinary drug residues Functional use of eggs Egg safety Eggs and health myths and misconceptions Nutritional benefits of eggs Salmonella enteritidis in eggs Dietary changes in the diet of hens Conclusions.
Normative Adolescent Baseline SCAT5 Scores with Groupwise Comparisons (2020)

Anderson, Aaron; Goldberg, Zachary; Flannell, John; Tarr, Adam; Arnold, Paul M MD; Wszalek, Tracey; Zimmerman, Jerrad Author Information
A Novel Role for Tissue Factor Pathway Inhibitor-2 in the Therapy of Human Esophageal Carcinoma (2009)

Esophageal cancer is characterized by rapid clinical progression and poor prognosis, due to early-stage invasion of adjacent tissues and metastasis. Tissue factor pathway inhibitor-2 (TFPI-2) has been implicated as a metastasis-associated gene in many types of tumors. Here we describe the potential involvement of TFPI-2 in the development of esophageal carcinoma. Western blotting revealed that TFPI-2 was downregulated in 75% of esophageal carcinomas and in most esophageal carcinoma cell lines. Immunohistochemistry revealed that TFPI-2 was significantly downregulated in tumor tissues and in lymph node metastases. Experimental overexpression of TFPI-2 in KYSE450, KYSE510, YES2, and EC9706 cells significantly inhibited their invasive ability. Overexpression of TFPI-2 in EC9706 cells inhibited xenograft tumor growth and invasion into surrounding tissues, as well as reduced lung metastasis. Further studies demonstrated that recombinant TFPI-2 protein significantly inhibited the activity of matrix metalloproteinases and tumor-related angiogenesis. Parenteral treatment with recombinant TFPI-2 protein significantly suppressed xenograft growth and metastasis. Together, these data indicate that TFPI-2 inhibits tumor invasion and angiogenesis both in vitro and in vivo, and suggest a potentially important therapeutic role for recombinant TFPI-2 in the treatment of malignant esophageal carcinomas.
Automated compound management evolves to meet the drug discovery demands of the future (2013)

The development of new drugs involves testing hundreds of thousands of compounds, from high throughput screening through to subsequent lead optimization. Recognizing the importance of a compound bank in supporting drug discovery activities and to accommodate the change from standardized HTS to integrated lead finding the Novartis Institutes for Biomedical Research (NIBR)’s Compound Management group embarked on an innovative compound bank initiative – the implementation of an advanced automated tube store and dose-response plate module – to meet the demands of today’s research.
Genetics of Type 2 Diabetes in U.S. Hispanic/Latino Individuals: Results From the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) (2017)

Few genome-wide association studies (GWAS) of type 2 diabetes (T2D) have been conducted in U.S. Hispanics/Latinos of diverse backgrounds who are disproportionately affected by diabetes. We conducted a GWAS in 2,499 T2D case subjects and 5,247 control subjects from six Hispanic/Latino background groups in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Our GWAS identified two known loci (<i>TCF7L2</i> and <i>KCNQ1)</i> reaching genome-wide significance levels. Conditional analysis on known index single nucleotide polymorphisms (SNPs) indicated an additional independent signal at <i>KCNQ1</i>, represented by an African ancestry-specific variant, rs1049549 (odds ratio 1.49 [95% CI 1.27-1.75]). This association was consistent across Hispanic/Latino background groups and replicated in the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium. Among 80 previously known index SNPs at T2D loci, 66 SNPs showed consistency with the reported direction of associations and 14 SNPs significantly generalized to the HCHS/SOL. A genetic risk score based on these 80 index SNPs was significantly associated with T2D (odds ratio 1.07 [1.06-1.09] per risk allele), with a stronger effect observed in nonobese than in obese individuals. Our study identified a novel independent signal suggesting an African ancestry-specific allele at <i>KCNQ1</i> for T2D. Associations between previously identified loci and T2D were generally shown in a large cohort of U.S. Hispanics/Latinos.
Physics of magnetic flux ropes (1989)

Magnetic flux ropes are tubes of magnetic flux that contain field lines twisted about the axis of the rope. Such tubes may occur in isolation, as in the ionosphere of Venus, or surrounded by equally strong magnetic fields, as in the terrestrial magentosphere. Magnetic flux ropes appear to play a critical role in solar physics, magnetospheric physics, in the Venusian ionosphere, and in interplanetary space. More than 100 scientists gathered the week of March 27 at an AGU Chapman Conference held at the Princess Hotel, Hamilton, Bermuda, to discuss the physics of magnetic flux ropes. Conference convenors were E. R. Priest, L. C. Lee and C. T. Russell.
Purification, characterization and gene cloning of 6‐hydroxynicotinate  3‐monooxygenase from Pseudomonas fluorescens TN5 (1999)

6-Hydroxynicotinate 3-monooxygenase, a membrane-bound, 42-kDa monomeric enzyme from Pseudomonas fluorescens TN5 was purified and characterized. The enzyme catalyzes the oxidative decarboxylation of 6-hydroxynicotinate and depends on O2, NADH and FAD with the holoenzyme containing 1 M of FAD per 1 M of enzyme. The isolated enzyme was used for the synthesis of 2,5-dihydroxypyridine, a precursor for the chemical synthesis of 5-aminolevulinic acid, which is applied as a plant growth hormone, a herbicide and in cancer therapy. A 1.8-kbp DNA fragment, which contains the ORF encoding 6-hydroxynicotinic acid 3-monooxygenase, was cloned, sequenced and expressed in Escherichia coli. The deduced 385 amino acid sequence of the cloned ORF is in agreement with the enzyme molecular mass, amino acid sequence of an internal peptide, contains a putative FAD-binding site and is homologous to similar flavoproteins such as salicylate 1-monoxygenase.
Effect of the antibacterial agents octenidine and chlorhexidine on the plaque flora in primates (1981)

The effect of the antibacterial substance octenidine on plaque formation and on oral microflora in eight monkeys fed a sucrose diet was studied. Plaque was obtained from buccal tooth surfaces of premolars and first molars in two quadrants using a swab and a dental carver and examined using culture and fluorescent antibody procedures. A significant reduction in plaque score was observed on the buccal tooth surfaces after daily topical application of 1% solutions of octenidine and chlorhexidine for 7 d; octenidine was more effective than chlorhexidine. Placebo treatment with water was without significant effect. Octenidine and chlorahexidine affected the plaque flora in a similar manner; the proportion of S sanguis increased in relation to baseline levels while the population of Actinomyces, especially the group A. viscous and A. naeslundii, was markedly reduced. S. sanguis showed an inverse relationship to members of actinomyces in response to the action of the antimicrobial agents. Both plaque sampling methods revealed similar changes in bacterial composition as a result of treatment. The data show that octenidine is an effective inhibitor of dental plaque and its antimicrobial and antiplaque properties make it worthy of further studies.
Residual stress reconstruction for large-Eddy simulation (2014)

A modelling technique for Large-Eddy Simulation is presented, in which the residual-stress tensor is reconstructed by applying an optimal convolution operator to the resolved stresses. This convolution operator is defined as a Taylor-series expansion in which the coefficients are determined using a dynamic procedure. The method is evaluated for the 1D Burger’s equation as proof of concept. Promising results are obtained.
Asynchronous In Situ Connected-Components Analysis for Complex Fluid flows (2016)

The simulation of multiscale physics is an important challenge for scientific computing. For this class of problem, large three-dimensional simulations are performed to advance scientific inquiry. On massively parallel computing systems, the volume of data generated by such approaches can become a productivity bottleneck if the raw data generated from the simulation is analyzed in a post-processing step. To address this, we present a physics-based framework for in situ data reduction that is theoretically grounded in multiscale averaging theory. We show how task parallelism can be exploited to concurrently perform a variety of analysis tasks with data-dependent costs, including the generation of iso-surfaces, morphological analyses, and connected components analysis. All analyses are performed in parallel using distributed memory and use the same domain decomposition as the simulation. A task management framework is constructed to leverage available parallelism within a node for analysis. The capabilities of the framework are to launch asynchronous analysis threads, manage dependencies between different tasks, promote data locality and minimize the impact of data transfers. The framework is applied to analyze GPU-based simulations of two-fluid-phase flow in porous media, generating a set of averaged measures that represents the overall system behavior. We demonstrate how the approach can be applied to perform physically-consistent analysis over fluid sub-regions determined from connected components analysis. Simulations performed on Oak Ridge National Lab's Titan supercomputer are profiled to demonstrate the performance of the associated multi-threaded in situ analysis approach for typical production simulation of two-fluid-phase flow.
Proteomic signatures of the serological response to flu vaccination in a large human cohort study (2022)

Abstract The serological response to the influenza virus vaccine is highly heterogeneous for reasons that are not entirely clear. While the impact of demographic factors such as age, body mass index (BMI), sex, prior vaccination and titer levels are known to impact seroconversion, they only explain a fraction of the response. To identify signatures of the vaccine response, we quantified 273 proteins from serum samples of 160 flu vaccine recipients (2019-2020 season). We found that levels of proteins functioning in cholesterol transport were positively associated with seroconversion, likely linking to the known impact of BMI. When adjusting seroconversion for the demographic factors, we identified additional, unexpected signatures: proteins regulating actin cytoskeleton dynamics were significantly elevated in participants with high adjusted seroconversion. Viral strain specific analysis showed that this trend was largely driven by the H3N2 strain. Further, we identified complex associations between adjusted seroconversion and other factors: levels of proteins of the complement system associated positively with adjusted seroconversion in younger participants, while they were associated negatively in the older population. We observed the opposite trends for proteins of high density lipoprotein remodeling, transcription, and hemostasis. In sum, careful integrative modeling can extract new signatures of seroconversion from highly variable data that suggest links between the humoral response as well as immune cell communication and migration.
MicroMHiDe: A Multispectral Sub-Meter Resolution Payload for SmallSats (2020)

The Earth Observation market has been going through a complete mutation during the last decade with the deployment of constellations of nano- and smallsats. These can offer shorter revisit time and capture relevant information for specific applications, and this for a significantly lower cost.
The Impacts of Single-use Plastics - A Life Cycle Assessment (2020)

The objective of this study is to compare some examples of plastic and compostable single use eating and drinking utensils in terms of their environmental degradation. We use Life Cycle Assessment (LCA) to quantitatively compare these products’ impacts on the environment throughout their life cycle. Specifically, we quantify and compare the global warming potential (GWP) of each single use eating and drinking utensil/container. The results of this study were that product weight, and that the material products are made from have a significant impact on GWP. This study outlined similar studies that have been done on this topic to better understand the environmental effects of single-use products, and efforts to minimize their impacts as use continues to grow.
The Biomechanical Effects of 1.0 to 1.2 Mrad of Gamma Irradiation on Human Bone–Patellar Tendon–Bone Allografts (2013)

Aside from graft stiffness during load to failure testing, low-dose (1.0-1.2 Mrad) gamma irradiation of central-third human BTB allografts is not deleterious to preimplantation biomechanical properties.
Mechanism of serpin action: evidence that C1 inhibitor functions as a suicide substrate (1991)

Serpins form a family of structurally related proteins, many of which function in plasma as inhibitors of serine proteases involved in inflammation, blood coagulation, fibrinolysis, and complement activation. To further characterize the mechanism by which serpins inhibit their target enzymes, we have studied the effect of temperature on the reaction of C1 inhibitor and the serine protease plasma kallikrein. At both 38 and 4 degrees C, C1 inhibitor (Mr 105,000) is cleaved by alpha-kallikrein (Mr 85,000 and 88,000) at position P1 (Arg444) of the reactive center, a reaction that leads to the formation of a covalent bimolecular enzyme-serpin complex (Mr 195,000) and cleaved but uncomplexed serpin (Mr 95,000). Between 38 and 4 degrees C, the product distribution is temperature-dependent, with more cleaved C1 inhibitor (Mr 95,000) formed at lower temperatures and correspondingly less Mr 195,000 complex. Studies employing intrinsic tryptophan fluorescence and 1H NMR spectroscopy show that this behavior is not caused by temperature-dependent conformational changes of kallikrein or C1 inhibitor. C1 inhibitor also behaves in this manner with the light chain of kallikrein and, to a lesser extent, with plasmin and C1s. These data are best explained by a branched reaction pathway, identical with the scheme describing the mechanism of action of suicide substrates. This scheme involves the formation of an enzyme-inhibitor intermediate, which can be stabilized into a covalent complex and/or dissociate into free enzyme and cleaved inhibitor, depending on the reaction conditions.
Randomised trial of 0.2% chlorhexidine gluconate and 2.5% natamycin for fungal keratitis in Bangladesh (1998)

Chlorhexidine may have potential as an inexpensive topical agent for fungal keratitis and warrants further assessment as a first line treatment in situations where microbiological facilities and a range of antifungal agents are not available.
Thermal Destruction Behavior of Selected Waste Compounds Under Short-Time, High Quench Rate Conditions (1997)

Emission of waste compounds and byproducts from thermal treatment systems is generally recognized to be due to limitations in the transport processes. A relatively small fraction of the feed material experiences an environment in which complete waste destruction cannot occur within the time available. These environments involve low temperatures, short times (i.e., high quench rates), oxygen-starved conditions, and possibly combinations of these. The research reported here examines waste compound destruction under the short reaction times that are representative of flame zone extinction processes. An externally fired stirred reactor system is used to study the behavior of toluene, chlorobenzene, 1,2-dichloroethane, 1,1,1-trichloroethane, and chloroform. Each of these is added to the reactor at a rate equivalent to a concentration of 10,000 ppm of carbon atoms. Major byproducts include the light paraffin and olefin hydrocarbons and species that are specific to the individual parent compounds. Tests also evaluated the influence of reactor residence time and initial concentration on toluene behavior, and a published mechanism for toluene destruction was compared with the data. Additional tests focused on mixture effects (toluene and 1,1,1-trichloroethane fired together). At 1200–1350 K, 1,1,1-trichloroethane fired alone results in no measurable emissions. In a mixture, however, the presence of toluene prevents the complete destruction of the more reactive 1,1,1-trichloroethane under these same conditions. Kinetic analysis shows that the additional free radicals generated by the toluene act in a complex way to increase 1,1,1-trichloroethane concentrations in the reactor, illustrating the difficulties encountered in predicting the behavior of complex waste mixtures. Key words: Incineration; toluene; byproducts; DRE; wastes; thermal oxidation
Low Adiponectin Levels Are an Independent Predictor of Mixed and Non-Calcified Coronary Atherosclerotic Plaques (2009)

Adiponectin levels predict mixed and non-calcified coronary atherosclerotic plaque burden. Low adiponectin levels may contribute to coronary plaque vulnerability and may thus play a role in the pathophysiology of ACS.
Fabrication of quasi-random photonic crystals for ultrathin solar cells (2021)

Quasi-random structures for light management present an intermediate ordering between a completely random rough surface and a perfect ordered photonic crystal. They are attractive for broadband applications due to their power spectral density. This makes them excellent candidates for photovoltaic applications. Here we present preliminary fabrication results creating quasi-random structures using a self-assembly approach based on polymer blends and wet etching. We are able to create patterns with average lattice constant of five to two microns. This structure is proposed to be used as a rear patterning layer for ultrathin GaAs cells for better sustainability and radiation- hard devices.
Heritability and family-based GWAS analyses of the N -acyl ethanolamine and ceramide plasma lipidome (2021)

Signalling lipids of the N-acyl ethanolamine (NAE) and ceramide (CER) classes have emerged as potential biomarkers of cardiovascular disease (CVD). We sought to establish the heritability of plasma NAEs (including the endocannabinoid anandamide) and CERs, to identify common DNA variants influencing the circulating concentrations of the heritable lipids, and assess causality of these lipids in CVD using 2-sample Mendelian randomization (2SMR). Nine NAEs and 16 CERs were analyzed in plasma samples from 999 members of 196 British Caucasian families, using targeted ultra-performance liquid chromatography with tandem mass spectrometry. All lipids were significantly heritable (h2 = 36-62%). A missense variant (rs324420) in the gene encoding the enzyme fatty acid amide hydrolase (FAAH), which degrades NAEs, associated at genome-wide association study (GWAS) significance (P < 5 × 10-8) with four NAEs (DHEA, PEA, LEA and VEA). For CERs, rs680379 in the SPTLC3 gene, which encodes a subunit of the rate-limiting enzyme in CER biosynthesis, associated with a range of species (e.g. CER[N(24)S(19)]; P = 4.82 × 10-27). We observed three novel associations between SNPs at the CD83, SGPP1 and DEGS1 loci, and plasma CER traits (P < 5 × 10-8). 2SMR in the CARDIoGRAMplusC4D cohorts (60 801 cases; 123 504 controls) and in the DIAGRAM cohort (26 488 cases; 83 964 controls), using the genetic instruments from our family-based GWAS, did not reveal association between genetically determined differences in CER levels and CVD or diabetes. Two of the novel GWAS loci, SGPP1 and DEGS1, suggested a casual association between CERs and a range of haematological phenotypes, through 2SMR in the UK Biobank, INTERVAL and UKBiLEVE cohorts (n = 110 000-350 000).