gebhart/patrepeval huggingface dataset:
An approach to identify microRNAs involved in neuropathic pain following a peripheral nerve injury (2014)

Peripheral nerve injury alters the expression of hundreds of proteins in dorsal root ganglia (DRG). Targeting some of these proteins has led to successful treatments for acute pain, but not for sustained post-operative neuropathic pain. The latter may require targeting multiple proteins. Since a single microRNA (miR) can affect the expression of multiple proteins, here, we describe an approach to identify chronic neuropathic pain-relevant miRs. We used two variants of the spared nerve injury (SNI): Sural-SNI and Tibial-SNI and found distinct pain phenotypes between the two. Both models induced strong mechanical allodynia, but only Sural-SNI rats maintained strong mechanical and cold allodynia, as previously reported. In contrast, we found that Tibial-SNI rats recovered from mechanical allodynia and never developed cold allodynia. Since both models involve nerve injury, we increased the probability of identifying differentially regulated miRs that correlated with the quality and magnitude of neuropathic pain and decreased the probability of detecting miRs that are solely involved in neuronal regeneration. We found seven such miRs in L3-L5 DRG. The expression of these miRs increased in Tibial-SNI. These miRs displayed a lower level of expression in Sural-SNI, with four having levels lower than those in sham animals. Bioinformatic analysis of how these miRs could affect the expression of some ion channels supports the view that, following a peripheral nerve injury, the increase of the seven miRs may contribute to the recovery from neuropathic pain while the decrease of four of them may contribute to the development of chronic neuropathic pain. The approach used resulted in the identification of a small number of potentially neuropathic pain relevant miRs. Additional studies are required to investigate whether manipulating the expression of the identified miRs in primary sensory neurons can prevent or ameliorate chronic neuropathic pain following peripheral nerve injuries.
A metal-free and all-organic redox flow battery with polythiophene as the electroactive species (2014)

A metal-free and all-organic redox flow battery is proposed and investigated. It employs polythiophene microparticles dispersed in electrolyte solutions as the redox couple and does not depend on limited metal resources. It shows a high cell potential and stable charge/discharge performance with a high energy efficiency of 60.9%.
Digital polarization-encoding technique for optical logic operations (1996)

We implement optical logic operations, using a polarization-encoding architecture based on digital speckle pattern interferometry (DSPI). The method is based on the intensity dependence of DSPI on the rotation of the polarization direction in the paths of the interferometer between acquisition of frames. The 16 two-input logic operations can be achieved and stored in a host computer. This scheme also offers the possibility of creating dynamic logic gates.
Toward Reagent-free Clinical Analysis: Quantitation of Urine Urea, Creatinine, and Total Protein from the Mid-Infrared Spectra of Dried Urine Films (2000)

Infrared (IR) spectroscopy offers an approach to clinical analysis that is conceptually very appealing. Whereas countless assays rely on the use of chemical agents to “recognize” the analyte of interest and to react with the analyte to produce specific color changes, IR-based analysis is founded on the rich IR absorption patterns that characterize the analytes themselves. These absorption patterns provide the basis to distinguish among the constituents and to separately quantify them. The most obvious distinguishing feature is that no reagents are required. In addition, IR-based analytical methods require very small sample volumes (typically microliters), show good precision over the entire physiological range, and are well suited for automation.
Viewpoint: Global order - Enlightenment or Confucian values? (2010)

Extract: Books with titles such as When China Rules the World by Martin Jacques, In the Jaws of the Dragon: Americaâs Fate in the Coming Era of Chinese Hegemony by Eamonn Fingleton and China's New Confucianism: Politics and Everyday Life in a Changing Society by Daniel A. Bell already pose the question that is the title of this piece. Moreover, articles like Complexity and Collapse by Harvard Historian Niall Ferguson in the March/April 2010 edition of the authoritative American journal Foreign Affairs, with its focus on the abrupt collapse of empires, give the question an additional immediacy.
Algorithms for Fast Back- and Re-Projection in Computed Tomography (1981)

While the computation time for reconstructing images in C.T. is not a problem in commercial systems, there are many experimental and developmental applications where resources are limited and image reconstruction places a heavy burden on the computer system. This paper describes a very efficient back-projection algorithm which results in large time savings when implemented in machine code. Also described is a minor modification to this algorithm which converts it to a re-projection procedure with comparable efficiency.
THE USE OF DISSEMINATION ENVIRONMENTS IN COMPETITIVE INTELLIGENCE (2010)

The use of dissemination environments in competitive intelligence (CI) is a big step forward in a friendlier way to distribute information to specific publics. In this paper, we approach the innovations used in Sistema de Inteligencia Setorial (SIS), a project designed to offer CI to small enterprises. The CI concepts and theory are explained, as well as the idea of Arranjos Produtivos Locais (APLs), wich are similar to the American concept of sector clusters. We also bring some light to the development model used in the SIS dissemination environment and the way users browse it. Techniques were used to make the browsing more friendly, making it possible that the environment and the project itself gained success, providing CI to entrepreneurs individually and in groups with great quality, accordingly to the results show in this paper.
INDICATIONS FOR NONOPERATIVE MANAGEMENT OF URETEROCELES (2005)

Furosemide renography can identify a select subgroup of patients with ureteroceles who are candidates for nonoperative management. Ureteroceles with nonobstructed duplex systems have better preservation of renal function and a high rate of natural resolution of hydronephrosis and reflux. Ureteroceles associated with MCD or completely nonfunctioning upper pole moieties may never require surgical management.
Long-term treatment of hypertrophic cardiomyopathy with verapamil or propranolol in matched pairs of patients: Results of a multicenter study (1988)

The effects of a 2-year treatment with high-dose propranolol (mean, 340 +/- 135 mg/day) and verapamil (mean, 493 +/- 136 mg/day) were compared in two groups of patients with hypertrophic cardiomyopathy. Both groups were broadly identical at the beginning of the trial and were formed of matched pairs. Out of 137 patients entering the study, 37 pairs completed the 2 year follow-up. The mean group symptomatology (NYHA-classification) improved significantly only following verapamil treatment. Individual improvement was seen more often following verapamil (V), but deterioration was almost exclusively seen during propranolol (P) treatment. Reduction of the Sokolow-index was significant in the V group only. Reduction in the resting heart rate and maximum gradient was more pronounced following P. No correlation could be found between the change in clinical symptoms and electrocardiographic, echocardiographic or hemodynamic data, nor to the dosage of V or P administered. From clinical and echocardiographic findings and in respect of side effects, V is advantageous over P in the treatment of hypertrophic cardiomyopathy, although a considerable number of patients improve after P. Objective data do not allow one to anticipate responders or non-responders to either treatment.
White Matter Abnormalities in Obsessive-compulsive Disorder (2005)

These preliminary findings provide evidence of an abnormality that involves the anterior cingulate white matter in the pathogenesis of OCD and are consistent with neurobiological models that posit a defect in connectivity in the anterior cingulate basal ganglia-thalamocortical circuit. White matter abnormalities in other brain regions may also be implicated in the neurobiology of OCD.
Low Power Energy Harvesting with Piezoelectric Generator (2002)

Energy harvesting using piezoelectric material is not a new concept, but its generation capability has not been attractive for mass energy generation. For this reason, little research has been done on the topic. Recently, concepts such as wearable computers, as well as small portable electrical devices have re-ignited the study of piezoelectric energy harvesting. The theory behind cantilever type piezoelectric elements is well known, but transverse moving diaphragm elements, which can be used in pressure type energy generation have not been yet fully developed. Power generation in a diaphragm depends on several factors. Among them, the thickness of each layer, the poling direction, and stress distribution are most important. In this thesis, unimorph and triple-morph diaphragm structures with various poling configurations were considered. Their energy generation was calculated with varying thickness ratios and poling directions at various locations using piezoelectric constitutive equations. The results of this analysis are presented, along with experimental results that indicate that an optimal electrode pattern will result in maximum electrical energy generation.
Morphology and stability of water condensation structures on a series of self-similar micropatterned substrates (2012)

In this work, we report on the morphology and stability of water domains growing by condensation on flat chemically micropatterned substrates. The surface pattern consists of hydrophobic hexagonal domains that are distributed following a hexagonal lattice in a hydrophilic continuum. The size and spacing of the hexagons are varied from one sample to the other in such a way as to produce a series of self-similar surface patterns. The size and stability of the water condensation structures growing on these surfaces are investigated in relation to the pattern size and the chemical contrast between the wetted continuum and the non-wetted hydrophobic domains. The water structures that initially grow and spread over the hydrophilic continuum are found to be unstable, collapsing on the hydrophobic domains at a characteristic (normalized) size, which is shown to be independent of the patterns, for a given chemical contrast. This scale invariance of the condensation structures is discussed on the basis of the self-similar variation of the characteristic sizes of the patterns that drive their instability and collapse. Finally, we show that for a high enough chemical contrast, the condensation structure could be tuned into a stable continuum water film that surrounds “dry” spots of non-wetted hydrophobic hexagons.
Giant magnetoresistance in La1−<i>x</i>Sr<i>x</i>MnO<i>z</i> films near room temperature (1994)

We report the observation of giant magnetoresistance near room temperature in ferromagnetic films of La1−xSrxMnOz for 0.16≤x≤0.33. For B=5 T, the maximum magnetoresistance ratio [R(0)−R(B)]/R(0) of an annealed film is 60% at 260 K for x=0.2, and 35% at 330 K for x=0.33. Annealed films have higher Curie temperature (Tc), a larger saturation moment and a larger magnetoresistance effect near Tc than do as-grown films. The temperature dependence of resistivity for all the samples investigated is unusual, activated above Tc and metallic below Tc. This and the giant magnetoresistance are possibly explained by scattering from magnetic polarons which dominate the transport near Tc.
Isolation‐based anomaly detection using nearest‐neighbor ensembles (2018)

Abstract The first successful isolation‐based anomaly detector, ie, iForest, uses trees as a means to perform isolation. Although it has been shown to have advantages over existing anomaly detectors, we have identified 4 weaknesses, ie, its inability to detect local anomalies, anomalies with a high percentage of irrelevant attributes, anomalies that are masked by axis‐parallel clusters, and anomalies in multimodal data sets. To overcome these weaknesses, this paper shows that an alternative isolation mechanism is required and thus presents iNNE or isolation using Nearest Neighbor Ensemble. Although relying on nearest neighbors, iNNE runs significantly faster than the existing nearest neighbor–based methods such as the local outlier factor, especially in data sets having thousands of dimensions or millions of instances. This is because the proposed method has linear time complexity and constant space complexity.
Alzheimer′s disease: the silver tsunami of the 21<sup>st</sup>century (2016)

Alzheimer's disease (AD), a fatal progressive neurodegenerative disorder, has no cure to date. One of the causes of AD is the accumulation of amyloid-beta 42 (Aβ42) plaques, which result in the onset of neurodegeneration. It is not known how these plaques trigger the onset of neurodegeneration. There are several animal models developed to (i) study etiology of disease, (ii) look for genetic modifiers, and (iii) identify chemical inhibitors that can block neurodegeneration and help to find cure for this disease. An insect model of Drosophila melanogaster has also provided new insights into the disease. Here we will discuss the utility of the Drosophila eye model to study Alzheimer's disease.
Comprehensive lipid analysis: a powerful metanomic tool for predictive and diagnostic medicine. (2000)

The power and accuracy of predictive diagnostics stand to improve dramatically as a result of lipid metanomics. The high definition of data obtained with this approach allows multiple rather than single metabolites to be used in markers for a group. Since as many as 40 fatty acids are quantified from each lipid class, and up to 15 lipid classes can be quantified easily, more than 600 individual lipid metabolites can be measured routinely for each sample. Because these analyses are comprehensive, only the most appropriate and unique metabolites are selected for their predictive value. Thus, comprehensive lipid analysis promises to greatly improve predictive diagnostics for phenotypes that directly or peripherally involve lipids. A broader and possibly more exciting aspect of this technology is the generation of metabolic profiles that are not simply markers for disease, but metabolic maps that can be used to identify specific genes or activities that cause or influence the disease state. Metanomics is, in essence, functional genomics from metabolite analysis. By defining the metabolic basis for phenotype, researchers and clinicians will have an extraordinary opportunity to understand and treat disease. Much in the same way that gene chips allow researchers to observe the complex expression response to a stimulus, metanomics will enable researchers to observe the complex metabolic interplay responsible for defining phenotype. By extending this approach beyond the observation of individual dysregulations, medicine will begin to profile not single diseases, but health. As health is the proper balance of all vital metabolic pathways, comprehensive or metanomic analysis lends itself very well to identifying the metabolite distributions necessary for optimum health. Comprehensive and quantitative analysis of lipids would provide this degree of diagnostic power to researchers and clinicians interested in mining metabolic profiles for biological meaning.
Conversion of the Coenzyme Specificity of Isocitrate Dehydrogenase by Module Replacement (1996)

The coenzyme specificity of isocitrate dehydrogenase from an extreme thermophilic bacterium was converted from NADP-dependent to NAD-dependent by replacing a "module" involved in the coenzyme binding site. The conversion was not possible with the replacement of a few residues that interact with the coenzyme. In addition, the module-replaced mutant dehydrogenase was as stable as the original, wild type enzyme. The results support a previous hypothesis that a module is a structural and functional unit of a protein.
Performance Evaluation and Field Application of Porous Vegetation Concrete Made with By-Product Materials for Ecological Restoration Projects (2016)

The purpose of this study was to evaluate the performance of porous vegetation concrete block made from blast furnace slag cement containing industrial by-products such as blast furnace slag aggregate and powder. The blocks were tested for void ratio, compressive strength and freeze-thaw resistance to determine the optimal mixing ratio for the porous vegetation block. An economic analysis of the mixing ratio showed that the economic efficiency increased when blast furnace slag aggregate and cement were used. Porous vegetation concrete blocks for river applications were designed and produced. Hydraulic safety, heavy metal elution and vegetation tests were completed after the blocks were applied in the field. The measured tractive force ranged between 7.0 kg/m2 for fascine revetment (vegetation revetment) and 16.0 kg/m2 for stone pitching (hard revetment), which ensured sufficient hydraulic stability in the field. Plant growth was measured after the porous vegetation concrete block was placed in the field. Seeds began to sprout one week after seeding; after six weeks, the plant length exceeded 300 mm. The average coverage ratio reached as high as 90% after six weeks of vegetation. These results clearly indicated that the porous vegetation concrete block was suitable for environmental restoration projects.
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms (2015)

Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.
Curli Loci of <i>Shigella</i> spp (2000)

An unstable chromosomal element encoding multiple antibiotic resistance in Shigella flexneri serotype 2a was found to include sequences homologous to the csg genes encoding curli in Escherichia coli and Salmonella enterica serovar Typhimurium. As curli have been implicated in the virulence of serovar Typhimurium, we investigated the csg loci in all four species of Shigella. DNA sequencing and PCR analysis showed that the csg loci of a wide range of Shigella strains, of diverse serotypes and different geographical distributions, were almost universally disrupted by deletions or insertions, indicating the existence of a strong selective pressure against the expression of curli. Strains of enteroinvasive E. coli (EIEC), which share virulence traits with Shigella spp. and cause similar diseases in humans, also possessed insertions or deletions in the csg locus or were otherwise unable to produce curli. Since the production of curli is a widespread trait in environmental isolates of E. coli, our results suggest that genetic lesions that abolish curli production in the closely related genus Shigella and in EIEC are pathoadaptive mutations.
Extracting Exact Answers using a Meta Question Answering System (2005)

This work concerns a question answering tool that uses multiple Web search engines and Web question answering systems to retrieve snippets of text that may contain an exact answer for a natural language question. The method described here treats each Web information retrieval system in a unique manner in order to extract the best results they can provide. The results obtained suggest that our method is comparable with some of today’s state-of-the-art systems.
Multigigahertz voltage-controlled oscillators in advanced silicon bipolar technology (1992)

Relaxation-type monolithic silicon bipolar voltage-controlled oscillators (VCOs) with center frequencies ranging from 1.5 to 5 GHz are described. The maximum oscillating frequency achieved is 7.4 GHz. The VCOs dissipate about 70 mW from a 3.6-V supply, including the output buffer and voltage-to-current converter stages. Two types of on-chip timing capacitor structure and various configurations used in achieving these results are described. A wide tuning range sufficient for covering the normal process tolerances and supply variations expected in a practical environment was achieved. The circuits were fabricated in an advanced 0.8- mu m double-poly self-aligned bipolar technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>Large-scale logic array computation</title> (1996)

For a number of years, we have studied the large-scale fine-grained limit of cellular-logic-array calculations and computers-with particular emphasis on applications to physical simulation. Perhaps the most relevant lessons of this work for the FPGA community have to do with the applicability of virtual-processor techniques to these logic-array computations-and by extension to the design of FPGA's themselves. These techniques allow us to tradeoff speed against size, to balance resources devoted to data storage with those devoted to processing, and to time-share communication resources as we share processors. An application area of particular interest to the FPGA community is in logic emulation, where a virtual processing approach lets us maximize useful processor cycles by having processing hardware follow computational wavefronts through arrays of virtual logic ("temporal pipelining"). This technique is of direct relevance to FPGA design. Our virtual processor approach is embodied in our indefinitely scalable cAM-8 cellular automata (CA) machine. Personal-computer-scale prototypes, designed and built at MIT using 1988 technology, are still about as fast as any conventional computer for most large-scale physical CA applications. Using today's high-bandwidth DRAM'S, machine's with the same number of memory chips could be built that run 100 times faster. Rather than build a new dedicated CA machine processor, it is attractive to instead add appropriate DRAM I/O and data-buffering circuitry to an FPGA design, to create a general-purpose class of FPGA's optimized for large-scale virtualprocessor applications.