gebhart/patrepeval huggingface dataset:
Maxizymes, Novel Allosterically Controllable Ribozymes, Can Be Designed To Cleave Various Substrates (2000)

We demonstrated previously that an allosterically controllable novel ribozyme, designated the maxizyme, is a powerful tool for disruption of an abnormal chimeric RNA target [BCR-ABL (b2a2) mRNA], and we proposed that it might provide the basis for future gene therapy for the treatment of chronic myelogenous leukemia (Kuwabara et al. Mol. Cell 1998, 2, 617-627). The maxizyme has sensor arms that can recognize a specific sequence and, in the presence exclusively of such a specific sequence, it can form a cavity for capture of catalytically indispensable Mg2+ ions. Cleavage of the target RNA then occurs at a site distant from the specific sequence. Clearly, the specific sequences recognized by sensor arms should not be limited to those of the above mentioned abnormal chimeric target. Thus, to demonstrate the general applicability of maxizyme technology, we constructed maxizymes targeted to other mRNAs, such as PML-RAR alpha mRNA, sDLST mRNA, and BCR-ABL (b1a2) mRNA, that are not cleaved with high specificity by the wild-type hammerhead ribozyme. Specific and efficient cleavage in vitro of these mRNAs by the custom-designed maxizymes demonstrated clearly that maxizyme technology is not limited to a specific case but may have broad general applicability in molecular biology and, also, in a clinical setting.
Real-Time Field Monitoring To Optimize Microbe Control (2012)

Technology Update Microbial growth in oil and gas systems can cause numerous problems that result in production downtime, lost revenue, and safety concerns. Unfortunately, microbial populations are ubiquitous in many oil and gas production zones and minimizing their impact is challenging. The most common effects of microbial growth are corrosion, hydrogen sulfide (H2S) production, and biofouling. The ability to minimize the negative impact of microbes is confounded by the current field monitoring technology, which is unable to detect many of the organisms. These monitoring technologies are culture-based, meaning that organisms must be grown in culture to be detected and quantified. It is well documented in many systems that less than 1% of the total organisms present are culturable. In addition, the culture-based methods commonly take days or weeks to produce a result. Thus, operators must wait a considerable time before taking control measures, and the impact of microbial populations can increase during the long period of undetection. New Development in Monitoring Method Two essential parameters for any new field monitoring technology are the ability to obtain a result in real time and the ability to detect all organisms, not just the ones that can be grown in culture. The industry has evaluated several of these technologies over the years, including a first-generation adenosine triphosphate (ATP) assay in which the level of ATP is used to measure the number of actively growing microbes in a sample. ATP is the molecule used by cells to drive any process that requires energy. This includes metabolism, protein translation, DNA repair, and cell division. Although there are differences in the absolute quantity of ATP in different species or organisms, it is assumed that actively growing bacterial cells hold relatively similar amounts of ATP, and a calculation has been determined to quantify microbial cell numbers based on a measurement of ATP. The major challenge of using this technology in oilfield systems is that the enzymatic assay used to quantify ATP is very sensitive to the quality of the fluids tested. This means that many oilfield fluids such as oil, emulsions, produced water with significant solids, high-salinity fluids, and fluids contaminated with certain chemicals would not yield meaningful results. As an example, the first-generation ATP test was not generally accepted by oilfield operators and has been little used. However, a second-generation ATP test that addresses the concerns has been developed recently. Specifically, additional steps were developed to enable accurate testing of fluids that contain oil, high salinity, residual chemicals, and solids. This technology also meets the other necessary criteria—real-time results and detection of all microbes, not only those that grow in culture.
An adaptive multi-objective evolutionary algorithm with human-like reasoning for enhanced decision-making in building design (2011)

An adaptive multi-objective genetic algorithm is presented, where a fuzzy system is used for the fitness evaluation. The adaptivity of the evolutionary algorithm refers to modifying in a measured way the degree of relaxation of the conventional Pareto dominance concept that is used to grade solutions in multi-objective space. The aim of the adaptive relaxation is to retain adequate selection pressure during the search process. The fuzzy system models human-like reasoning that is used to evaluate the suitability of candidate solutions. This way vagueness and imprecision inherent to criteria is taken care of. Next to that, due to the use of fuzzy information processing, the resulting Pareto optimal solutions may be distinguished regarding their suitability for the ultimate goal, although from the Pareto dominance viewpoint the solutions are equivalent. This yields relevant information for a decision maker, so that some of the difficulties to select among the Pareto optimal solutions are alleviated. The algorithm is implemented for a decision making problem from the domain of architecture, where an optimal spatial arrangement of a multi-functional building is sought that satisfies three soft objectives.
Zephyr: efficient incremental reprogramming of sensor nodes using function call indirections and difference computation (2009)

Wireless reprogramming of sensor nodes is an essential requirement for long-lived networks since the software functionality changes over time. The amount of information that needs to be wirelessly transmitted during reprogramming should be minimized since reprogramming time and energy depend chiefly on the amount of radio transmissions. In this paper, we present a multihop incremental reprogramming protocol called Zephyr that transfers the delta between the old and the new software and lets the sensor nodes rebuild the new software using the received delta and the old software. It reduces the delta size by using application-level modifications to mitigate the effects of function shifts. Then it compares the binary images at the byte-level with a novel method to create small delta, that is then sent over the wireless network to all the nodes. For a wide range of software change cases that we experimented with, we find that Zephyr transfers 1.83 to 1987 times less traffic through the network than Deluge, the standard reprogramming protocol for TinyOS, and 1.14 to 49 times less than an existing incremental reprogramming protocol by Jeong and Culler. 1
Investigating influences on the strain – axle load relationship in asphalt pavement using Finite Element Modelling (2019)

Current pavement maintenance strategies are reliant on invasive measurements or visual inspection. Fibre- WIM sensors can improve this by measuring strain, which can be used to calculate axle loads. However, this process is not simple. Finite Element Modelling is used to study several circumstantial influences on the strain – axle load relationship. These factors are combined into a predicting function, which can be refined so that it can be used to calculate axle loads. This allows for more insight in pavement deterioration. Other than describing the results of the Finite Element Model, the implications for sustainable pavement maintenance are discussed.
Effect of Vitamin E Eye Drops on Naphthalene-Induced Cataract in Rats (1999)

The effect of vitamin E acetate (VEA) eye drops on naphthalene-induced cataract in rats was investigated by Scheimpflug image analysis. The control group was administered only naphthalene (1 g/kg), while the other group was additionally given 1% VEA eye drops into both eyes 5 times a day every day for 9 weeks from the start of naphthalene treatment. During those 9 weeks, the changes of the crystalline lens were documented by an anterior eye segment analysis system (EAS-1000, NIDEK) once a week in mydriasis (Mydrin-P, Santen Pharmaceutical Co., Ltd.). The characteristic density values of the anterior deeper cortex regions were measured. The light scattering intensity of lenses from VEA eye drop-treated animals was significantly lower than that of animals without VEA treatment. This difference was found 1 week, 4 weeks, and from 7 to 9 weeks after the start of naphthalene application. VEA eye drops may have the potential to delay the progression of naphthalene-induced cataract in rats.
Ionically Conducting Ceramics as Active Catalyst Supports (2013)

AIR
Synthesis and Characterization of New 3,5-Dinaphthyl Substituted 2-Pyrazolines and Study of Their Antimicrobial Activity (2002)

A number of chalcones were prepared by condensing either 1-acetylnaphthalene or substituted 1-acetylnaphthalenes with 1-naphthaldehyde or 4-dimethylamino-1-naphthaldehyde in ethanolic NaOH solutions. These chalcones were immediately reacted with hydrazine hydrochloride, phenyl hydrazine and semicarbazide hydrochloride in the presence of dry acetic acid to obtain the corresponding 2-pyrazolines. The synthesised heterocycles were characterized on the basis of their chemical properties and spectroscopic data. These compounds were tested for antimicrobial activity against a variety of test organisms: Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Proteus mirabillis, Shigella dysentry and Salmonella typhii. The compounds containing chloro, hydroxo and dimethylamino - N(CH3)2 group as substituents on the naphthalene rings have been found to be very effective antimicrobial agents. In addition, the presence of a carboxamido -CONH2 substituent group at the N-1 position of the 2-pyrazoline rings is shown to contribute substantially to the antimicrobial activity.
Analysis of the skin of mice humanized for the immune system (2017)

Development of new immunotherapeutic strategies relies on the ability to activate the right cells at the right place and at the right moment and on the capacity of these cells to home to the right organ(s). Skin delivery has shown high potency for immunotherapeutic administration. However, an adequate in vivo model of human skin immunity is still a critical bottleneck. We demonstrated here that the skin of human immune system mice is colonized by human hematopoietic cells, mainly human T cells and that complementation with human antigen-presenting cells at the vaccination site allowed the induction of an immune response.
Synthesis and biological activity of highly potent heptapeptide analogs of somatostatin with C-terminal modifications. (2001)

New heptapeptide analogs of somatostatin with C-terminal modifications were more potent and longer acting than the native hormone.
Efficacy and safety of xaliproden in amyotrophic lateral sclerosis: results of two phase III trials (2004)

Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive and fatal motor neuron disease. We carried out two randomized, double-blind, placebo-controlled, multi-centre, multi-national studies with xaliproden ( a drug with neurotrophic effect) to assess drug efficacy and safety at two doses. Patients with clinically probable or definite ALS of more than 6 months and less than 5 years duration were randomly assigned to placebo, 1 mg or 2 mg xaliproden orally once daily as monotherapy in Study 1 (n = 867); or to the same regimen with addition of riluzole 50 mg bid background therapy in Study 2 (n = 1210 patients). The two primary endpoints were defined as: 1. Time to death, tracheostomy, or permanent assisted ventilation (DTP), and 2. Time to vital capacity ( VC), 50% or DTP before (log-rank test) and after adjustment using a Cox proportional hazard model for prespecified prognostic factors. Secondary endpoints were rates of change of various functional measures. In Study 1, primary outcome measures did not reach statistical significance. For the 2 mg group, for time to VC 50%; RRR 12% [CI: -6.27, ns] for time to VC
Polycytosine regions contained in DNA hairpin loops interact via a four-stranded, parallel structure similar to the i-motif (1994)

Thermal denaturation profiles of an oligodeoxynucleotide that forms a hairpin structure with a cytidine-rich loop show an unexpected transition at 60 degrees C at pH 5.0 but not at pH 8.0. Analytical ultracentrifugation shows that this transition reflects dimer formation via the interaction of loops from two molecules to form a novel structure termed the h-dimer. The dependence of this structure on low pH implies the formation of cytosine-protonated cytosine base pairs. NMR spectroscopy, thermal denaturation and ultraviolet absorption spectral analysis suggest a similarity to the i-motif structure recently proposed for the interaction of deoxycytidine oligomers. The use of hairpin loops to form i-motif-like structures may prove useful in searches for cognate proteins and possibly in the production of antibodies.
Aldosterone and end-organ damage (2005)

Aldosterone induces oxidative stress, endothelial dysfunction, inflammation and fibrosis in the vasculature, heart and kidney. While most of these effects appear to be mediated via the mineralocorticoid receptor, better understanding of the mineralocorticoid receptor-independent effects of aldosterone, the role of nonaldosterone mineralocorticoid receptor agonists, and the mechanisms involved in the progression from inflammation to fibrosis and remodeling would enable the development of new strategies to slow the progression of cardiovascular and renal disease.
Is CO{sub 2} disposal possible? (1996)

Recently, Moore and Braswell have reviewed the present state of knowledge of the carbon cycle. As they state: {open_quotes}the carbon cycle is still not adequately understood or quantified globally. Using averages for the 1980`s, sources of atmospheric CO{sub 2} exceed identified sinks by 1.8 - 1.2 PgC per year{close_quotes}. It is interesting to examine their diagram of the global carbon cycle, and to note that there is essentially no attention given to processes deep in the earth`s crust. One of the most interesting recent observations on the nature of the biosphere has been the discovery of thriving colonies of microorganisms at depth. While workers on the alteration of seafloor basalts had suggested the actions of deep organisms, problems related to possible deep bio-corrosion of nuclear waste containers have stimulated more careful observations. Pedersen has reviewed the present state of knowledge, and reported the present record of microorganisms at depths of 4.2 km below the surface, at temperatures up to 110{degrees}C.
Representing the O/R Address hierarchy in the X.500 Directory Information Tree (1998)

This document defines a representation of the O/R Address hierarchy in the Directory Information Tree [6, 1]. This is useful for a range of purposes, including:
Structural Similarity-Based Object Tracking in Video Sequences (2006)

This paper addresses the problem of object tracking in video sequences. The use of a structural similarity measure for tracking is proposed. The measure reflects the distance between two images by comparing their structural and spatial characteristics and has shown to be robust to illumination and contrast changes. As a result it guarantees robustness of the tracking process under changes in the environment. The previously used Bhattacharyya distance is not robust to such changes. Additionally, when a tracker is run with the Bhattacharyya distance, histograms should be calculated in order to find the likelihood function of the measurements. With the new function there is no need to calculate histograms. A particle filter (PF) is implemented where this measure is used for computing the distance between the reference and current frame. The algorithm performance has been tested and evaluated over real-world video sequences, and has been shown to outperform methods based on colour and edge histograms
Perceived fitness and responses to laboratory induced stress (2000)

This study sought to evaluate the contribution of perceived physical fitness beyond the contributions of gender, body mass index (BMI), and estimated actual physical fitness on both physiological and self-reported stress responsivity to laboratory induced stress. Seventy-two nonsymptomatic participants participated in the experiment. Participants completed a laboratory procedure measuring cardiovascular responses and self-reported rating of calmness while performing stressful laboratory tasks. Estimated aerobic fitness (VO2 max) as well as perceived fitness were also determined. Perceived fitness significantly contributed to the variance associated with self-reported responses to laboratory stress as well as with some of the physiological measures. Perceived fitness significantly added to the variance beyond that attributed to gender, body mass, and estimated actual physical fitness while assessing systolic blood pressure and calmness. Overall, the results support the view that perception of fitness may be an important factor above and beyond aerobic fitness in its association with responses to stress.
Modulation of native chondroitin sulphate structure in tissue development and in disease (1990)

Chondroitin sulphate proteoglycans are synthesised by different tissues and cell types, and the chondroitin sulphate chains are variably sulphated. Three monoclonal antibodies 3B3, 7D4 and 6C3 that recognise different native chondroitin sulphate epitopes have been used to investigate changes in structure during embryonic tissue development in the chick and in the response of mature canine articular cartilage during experimental osteoarthritis. Strong focal expression of the epitopes was seen during development of chick bursa, which was different for the three epitopes and which changed during 5 days of development. In embryonic chick limb, although chondroitin sulphate is present throughout the cartilage, the 3B3 epitope, which is at the non-reducing terminus of chains, was only expressed on chondroitin sulphate within one region of the sub-articular cartilage. In mature canine articular cartilage the expression of this epitope on proteoglycans was very low, but when determined 3 or 6 months after induction of experimental osteoarthritis the level was greatly increased in all joints tested (23/23). The abundance of the other two native chondroitin sulphate epitopes was also increased in this experimental disease. The results show that expression of the chondroitin sulphate epitopes detected by the monoclonal antibodies changes during cellular differentiation and development and suggests that it is closely controlled by the cells synthesising chondroitin sulphate chains.
Accelerated A  Deposition in APPswe/PS1 E9 Mice with Hemizygous Deletions of TTR (Transthyretin) (2007)

A cardinal pathological lesion of Alzheimer's disease (AD) is the deposition of amyloid beta (Abeta) in the brain. We previously reported that exposing transgenic mice harboring APPswe/PS1deltaE9 transgenes to an enriched environment resulted in reduced levels of Abeta peptides and deposition, findings that were correlated with an increase in the expression of TTR, encoding transthyretin (TTR). TTR is expressed at high levels in the choroid plexus and known to bind Abeta peptides and modulate their aggregation in vitro and in vivo. To explore the impact of TTR expression on Abeta levels and deposition in vivo, we crossed ceAPPswe/PS1deltaE9 transgenic mice to mice with genetic ablations of TTR. We now report that the levels of detergent-soluble and formic acid-soluble levels of Abeta and deposition are elevated in the brains of ceAPPswe/PS1deltaE9/TTR+/- mice compared with age-matched ceAPPswe/PS1deltaE9/TTR+/+ mice. Moreover, Abeta deposition is significantly accelerated in the hippocampus and cortex of ceAPPswe/PS1deltaE9/TTR+/- mice. Our results strongly suggest that TTR plays a critical role in modulating Abeta deposition in vivo.
Identification of an ovulation rate QTL in cattle on BTA14 using selective DNA pooling and interval mapping<sup>1</sup> (2004)

Increased twinning incidence in beef cattle has the potential to improve production efficiency. However, phenotypic selection for twinning rate is difficult because of the trait's low heritability and the long time interval necessary to collect phenotypic records. Therefore, this trait and the correlated trait of ovulation rate are ideal candidates for marker-assisted selection. The objective of this study was to complete a genome-wide search for ovulation rate quantitative trait loci (QTL) in two related sire families. The families (paternal halfsib sires 839802 and 839803) were from a population of cattle selected for ovulation rate at the USDA Meat Animal Research Center, Clay Center, Nebraska. Putative ovulation rate QTL have previously been identified in the 839802 family on chromosomes 7 and 19; however, marker coverage in the original scan was not complete. This study fills the gaps in marker coverage of the earlier study by adding approximately 60 informative microsatellites to each sire family. Each family was genotyped using selective DNA pooling. Sons and daughters were included in either the high or low pool based on their estimated breeding value deviations from the mid-parent average (EBVMD) for ovulation rate. Approximately 40% (839802) and 26% (839803) of available progeny comprised the high and low pools combined. Pooled typing revealed possible associations (nominal P < 0.05) between ovulation rate and marker genotype for 11 and 15 microsatellites in the 839802 and 839803 families, respectively. Subsequent interval mapping strengthened support for the presence of an ovulation rate QTL on BTA14 (chromosome-wise P < 0.02).