gebhart/patrepeval huggingface dataset:
External marker-based automatic congruencing: A new method of 3D reconstruction from serial sections (1997)

Implemented on a low-cost hardware platform, EMAC provides a fast and efficient tool that largely facilitates the use of computer-based 3D visualization for the analysis of complex structural, molecular, and genetic information in morphological research. Due to its conceptual versatility, EMAC can be easily adapted for a broad range of tasks, including all modern molecular-staining techniques, such as immunohistochemistry and in situ hybridization.
Generating private recommendations in a social trust network (2011)

Recommender systems have become increasingly important in e-commerce as they can guide customers with finding personalized services and products. A variant of recommender systems that generates recommendations from a set of trusted people is recently getting more attention in social networks. However, people are concerned about their privacy as the information revealed in recommender systems, particularly in social networks, can be misused easily. A way to eliminate the privacy risks is to make the privacy-sensitive data inaccessible by means of encryption. While the private data is inaccessible to any outsiders and the server, the same functionality of the system can be achieved by processing the encrypted data. Unfortunately, the efficiency of processing encrypted data constitutes a big challenge. In this paper, we present a privacy-enhanced recommender system in a social trust network, which is designed to be highly efficient. The cryptographic protocol for generating recommendations is based on homomorphic encryption and secure multi-party computation techniques. The additional overhead with regard to computation and communication is minimized by packing data. The experimental results show that our proposal is promising to be deployed in real world.
Activation of the xylDLEGF promoter of the TOL toluene-xylene degradation pathway by overproduction of the xylS regulatory gene product (1987)

The xylS regulatory gene of the Pseudomonas putida TOL plasmid (pWWO) has been cloned under the transcriptional control of the Escherichia coli tac promoter in a broad-host-range controlled-expression vector. Induction with isopropylthiogalactoside allowed overproduction and characterization of the xylS product by specific interaction with the TOL meta-cleavage pathway operator-promoter region (OP2) in vivo in E. coli. Examination of plasmid-specified polypeptides in E. coli maxicells led to identification of the xylS product as a 36-kilodalton polypeptide. The operator sequences required for xylS interactions lay upstream of the OP2 transcriptional start, and the xylS gene product recognized this region even in the absence of known coinducers.
Best-match querying in general database systems-a language approach (2005)

We reason in this paper that many queries in general database systems are best-match in nature: to a user, some records are more useful than others, and when the best records cannot be found or when there are not a sufficient number of them, the next best records should be retrieved. The heterogeneity of general databases will require different treatment on such queries than that in some special-purpose systems where the concept of best-match has been exploited. Language features are proposed to augment typical query languages in order to accommodate best-match querying. This is intended as another effort toward the design of convenient, expressive user interface to facilitate decision making via database systems.
Proteomic Characterization of the Interstitial Fluid Perfusing the Breast Tumor Microenvironment (2004)

Clinical cancer proteomics aims at the identification of markers for early detection and predictive purposes, as well as to provide novel targets for drug discovery and therapeutic intervention. Proteomics-based analysis of traditional sources of biomarkers, such as serum, plasma, or tissue lyzates, has resulted in a wealth of information and the finding of several potential tumor biomarkers. However, many of these markers have shown limited usefulness in a clinical setting, underscoring the need for new clinically relevant sources. Here we present a novel and highly promising source of biomarkers, the tumor interstitial fluid (TIF) that perfuses the breast tumor microenvironment. We collected TIFs from small pieces of freshly dissected invasive breast carcinomas and analyzed them by two-dimensional polyacrylamide gel electrophoresis in combination with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Western immunoblotting, as well as by cytokine-specific antibody arrays. This approach provided for the first time a snapshot of the protein components of the TIF, which we show consists of more than one thousand proteins--either secreted, shed by membrane vesicles, or externalized due to cell death--produced by the complex network of cell types that make up the tumor microenvironment. So far, we have identified 267 primary translation products including, but not limited to, proteins involved in cell proliferation, invasion, angiogenesis, metastasis, inflammation, protein synthesis, energy metabolism, oxidative stress, the actin cytoskeleton assembly, protein folding, and transport. As expected, the TIF contained several classical serum proteins. Considering that the protein composition of the TIF reflects the physiological and pathological state of the tissue, it should provide a new and potentially rich resource for diagnostic biomarker discovery and for identifying more selective targets for therapeutic intervention.
An Improved Tomlinson-Harashima Precoder Reducing Transmission Power (2008)

Tomlinson-Harashima precoder (THP) is an efficient interference pre-canceler, however, the transmission power is increased over the symbol power due to the modulo operation. In this paper, we propose an improved THP that reduces the transmission power of the conventional THP by tilting a group of symbols by an angle toward minimizing the transmission power. The tilted angle can be either estimated by the receiver or notified by the transmitter using a feed-forward information. Assuming a large interference, the average transmission power of the proposed THP is derived by the central limit theorem and Gumbel extreme value distribution. The symbol error rate (SER) and its asymptotic behavior is also derived and compared. The more tilted angles or the smaller size of groups are used, the more power the proposed THP saves. The transmission power can even be less than the symbol power. Accordingly, in an environment that the power gain overwhelms the other losses, the SER can be less than the SER of AWGN channel.
Direct Blood Dry LAMP: A Rapid, Stable, and Easy Diagnostic Tool for Human African Trypanosomiasis (2015)

Loop-mediated isothermal amplification (LAMP) is a rapid and sensitive tool used for the diagnosis of a variety of infectious diseases. One of the advantages of this method over the polymerase chain reaction is that DNA amplification occurs at a constant temperature, usually between 60-65°C; therefore, expensive devices are unnecessary for this step. However, LAMP still requires complicated sample preparation steps and a well-equipped laboratory to produce reliable and reproducible results, which limits its use in resource-poor laboratories in most developing countries. In this study, we made several substantial modifications to the technique to carry out on-site diagnosis of Human African Trypanosomiasis (HAT) in remote areas using LAMP. The first essential improvement was that LAMP reagents were dried and stabilized in a single tube by incorporating trehalose as a cryoprotectant to prolong shelf life at ambient temperature. The second technical improvement was achieved by simplifying the sample preparation step so that DNA or RNA could be amplified directly from detergent-lysed blood samples. With these modifications, diagnosis of HAT in local clinics or villages in endemic areas becomes a reality, which could greatly impact on the application of diagnosis not only for HAT but also for other tropical diseases.
Effects of Hypothermia on the Rate of Excitatory Amino Acid Release After Ischemic Depolarization (1996)

These results suggest that effects of hypothermia on EAA concentrations during cerebral ischemia may be the result of both a delay until initial EAA release as well as a direct effect of temperature on the rate of amino acid release. The observed temperature effects are more consistent with carrier-mediated processes controlling EAA release.
Molecular, functional and structural properties of the prolyl oligopeptidase of<i>Trypanosoma cruzi</i>(POP Tc80), which is required for parasite entry into mammalian cells (2005)

We have demonstrated that the 80 kDa POP Tc80 (prolyl oligopeptidase of Trypanosoma cruzi) is involved in the process of cell invasion, since specific inhibitors block parasite entry into non-phagocytic mammalian host cells. In contrast with other POPs, POP Tc80 is capable of hydrolysing large substrates, such as fibronectin and native collagen. In this study, we present the cloning of the POPTc80 gene, whose deduced amino acid sequence shares considerable identity with other members of the POP family, mainly within its C-terminal portion that forms the catalytic domain. Southern-blot analysis indicated that POPTc80 is present as a single copy in the genome of the parasite. These results are consistent with mapping of POPTc80 to a single chromosome. The active recombinant protein (rPOP Tc80) displayed kinetic properties comparable with those of the native enzyme. Novel inhibitors were assayed with rPOP Tc80, and the most efficient ones presented values of inhibition coefficient Ki < or = 1.52 nM. Infective parasites treated with these specific POP Tc80 inhibitors attached to the surface of mammalian host cells, but were incapable of infecting them. Structural modelling of POP Tc80, based on the crystallized porcine POP, suggested that POP Tc80 is composed of an alpha/beta-hydrolase domain containing the catalytic triad Ser548-Asp631-His667 and a seven-bladed beta-propeller non-catalytic domain. Docking analysis suggests that triple-helical collagen access to the catalytic site of POP Tc80 occurs in the vicinity of the interface between the two domains.
Genomics in Neurological Disorders (2014)

Neurological disorders comprise a variety of complex diseases in the central nervous system, which can be roughly classified as neurodegenerative diseases and psychiatric disorders.The basic and translational research of neurological disorders has been hindered by the difficulty in accessing the pathological center(i.e., the brain) in live patients. The rapid advancement of sequencing and array technologies has made it possible to investigate the disease mechanism and biomarkers from a systems perspective. In this review, recent progresses in the discovery of novel risk genes, treatment targets and peripheral biomarkers employing genomic technologies will be discussed. Our major focus will be on two of the most heavily investigated neurological disorders,namely Alzheimer's disease and autism spectrum disorder.
Electrogenerated Chemiluminescence Sensors Using Ru(bpy)<sub>3</sub><sup>2+</sup> Doped in Silica Nanoparticles (2006)

A novel electrogenerated chemiluminescence (ECL) sensor based on Ru(bpy)3(2+)-doped silica (RuDS) nanoparticles conjugated with a biopolymer chitosan membrane was developed. These uniform RuDS nanoparticles (approximately 40 nm) were prepared by a water-in-oil microemulsion method and were characterized by electrochemical and transmission electron microscopy technology. The Ru(bpy)3(2+)-doped interior maintained its high ECL efficiency, while the exterior nanosilica prevented the luminophor from leaching out into the aqueous solution due to the electrostatic interaction. This is the first attempt to branch out the application of RuDS nanoparticles into the field of ECL, and since a large amount of Ru(bpy)3(2+) was immobilized three-dimensionally on the electrode, the Ru(bpy)3(2+) ECL signal could be enhanced greatly, which finally resulted in the increased sensitivity. This sensor shows a detection limit of 2.8 nM for tripropylamine, which is 3 orders of magnitude lower than that observed at a Nafion-based ECL sensor. Furthermore, the present ECL sensor displays outstanding long-term stability.
Kinetic Studies on the Fragmentation of the Third Component of Complement (C3) by Trypsin (1977)

The kinetics of cleavage of C3 by trypsin was analyzed by electrophoresis in agarose and in polyacrylamide gels containing sodium dodecyl sulfate and the data obtained were used to construct an anatomical model for C3 showing the sites of tryptic attack, the fragments generated, and their composition. Trypsin was shown to cleave C3 in a stepwise fashion. The attack was initially directed at the alpha-polypeptide chain and resulted in the generation of C3a and C3b. Further cleavage of the alpha-chain of C3b, converted it into C3b1 and then into C3d and C3c. Cleavage of the beta-chain by trypsin occurred only at the C3c stage with the release of a small peptide (m.w. 12,000) from C3c and the formation of C3c'. On immunoelectrophoresis, C3c' had a less anodal mobility compared to the beta1A mobility of C3c. C3a, once formed could be further cleaved to give residual fragments with decreasing net positive charge. Exposure of C3 to acid conditions, pH 5.0 or below, rendered the molecule exceedingly susceptible to tryptic degradation.
Design of shaped-beam antennas through minimax gain optimization (1984)

An essential part of realizing a shaped beam by using a multiple-beam antenna is determining the excitation coefficient for each individual port. An algorithm which optimizes the power gain in a minimax sense is described. This criterion, although not as mathematically tractable as least squares, is necessary when the specifications prescribe that the worst case be as good as possible. It will be shown how the basic algorithm is very efficient and how it permits simple modifications to allow the specification of one-sided errors for the pattern, and direct optimization of gain slopes. A design of a C-band shaped-beam satellite antenna provides an example.
Protective Effect of Resveratrol Against Renal Oxidative Stress in Cholestasis (2005)

The present study demonstrates that intraperitoneal administration of resveratrol in bile duct ligated rats maintains antioxidant defenses and reduces kidney oxidative damage. This effect of resveratrol may be useful in the preservation of renal oxidative stress in cholestasis.
On the sensitivity of IMRT dose optimization to the mathematical form of a biological imaging-based prescription function (2009)

Voxel-based prescriptions of deliberately non-uniform dose distributions based on molecular imaging, so-called dose painting or theragnostic radiation therapy, require specification of a transformation that maps the image data intensities to prescribed doses. However, the functional form of this transformation is currently unknown. An investigation into the sensitivity of optimized dose distributions resulting from several possible prescription functions was conducted. Transformations between the radiotracer activity concentrations from Cu-ATSM PET images, as a surrogate of tumour hypoxia, and dose prescriptions were implemented to yield weighted distributions of prescribed dose boosts in high uptake regions. Dose escalation was constrained to reflect clinically realistic whole tumour doses and constant normal tissue doses. Optimized heterogeneous dose distributions were found by minimizing a voxel-by-voxel quadratic objective function in which all tumour voxels were given equal weight. Prescriptions based on a polynomial mapping function were found to be least constraining on their optimized plans, while prescriptions based on a sigmoid mapping function were the most demanding to deliver. A prescription formalism that fixed integral dose was less sensitive to errors in the choice of the mapping function than one that boosted integral dose. Integral doses to normal tissue and critical structures were insensitive to the shape of the prescription function. Planned target dose conformity improved with smaller beamlet dimensions until the inherent spatial resolution of the functional image was matched. Clinical implementation of dose painting depends on advances in absolute quantification of functional images and improvements in delivery techniques over smaller spatial scales.
A Review of Pre-Chamber Initiated Jet Ignition Combustion Systems (2010)

<div class="section abstract"><div class="htmlview paragraph">This paper reviews progress on turbulent jet ignition systems for otherwise standard spark ignition engines, with focus on small prechamber systems (≺3% of clearance volume) with auxiliary pre-chamber fueling. The review covers a range of systems including early designs such as those by Gussak and Oppenheim and more recent designs proposed by General Motors Corporation, FEV, Bosch and MAHLE Powertrain. A major advantage of jet ignition systems is that they enable very fast burn rates due to the ignition system producing multiple, distributed ignition sites, which consume the main charge rapidly and with minimal combustion variability. The locally distributed ignition sites allow for increased levels of dilution (lean burn/EGR) when compared to conventional spark ignition combustion. Dilution levels are comparable to those reported in recent homogeneous charge compression ignition (HCCI) systems. In addition, jet ignition systems have the potential for combustion phasing control and hence speed/load range benefits when compared to HCCI, without the need for SI-HCCI combustion mode switching. The faster burn rates also allow for a base compression ratio increase (1-2 points) when compared to spark ignition and when combined with diluted mixture combustion, provide increased engine efficiency.</div></div>
Cumulus (2009)

Cumulus is a system for efficiently implementing filesystem backups over the Internet, specifically designed under a thin cloud assumption—that the remote datacenter storing the backups does not provide any special backup services, but only a least-common-denominator storage interface. Cumulus aggregates data from small files for storage and uses LFS-inspired segment cleaning to maintain storage efficiency. While Cumulus can use virtually any storage service, we show its efficiency is comparable to integrated approaches.
Electrokinetic Energy Conversion Efficiency in Nanofluidic Channels (2006)

We theoretically evaluate the prospect of using electrokinetic phenomena to convert hydrostatic energy to electrical power. An expression is derived for the energy conversion efficiency of a two-terminal fluidic device in terms of its linear electrokinetic response properties. For a slitlike nanochannel of constant surface charge density, we predict that the maximum energy conversion efficiency occurs at low salt concentrations. An analytic expression for the regime of strong double-layer overlap reveals that the efficiency depends only on the ratio of the channel height to the Gouy-Chapman length, and the product of the viscosity and the counterion mobility. We estimate that an electrokinetic energy conversion device could achieve a maximum efficiency of 12% for simple monovalent ions in aqueous solution.
Agent based intelligent decluttering enhancements (2011)

Model-driven visualization (MDV) is a novel framework that supports more effective, intelligent user interfaces to improve decision making in complex environments by coupling cognitive and perceptual theories of information processing with advanced artificial intelligence methods. It embeds empirical and theory driven approaches for identifying and prioritizing data based on the information requirements and needs of the human decision maker within intelligent agents. The agents automatically deliver and present information based on its likely value using visualizations that best convey that information to the user(s) of the system. Agents also reason about the context and constraints of the user, environment, and display to enable a higher degree of personalization within an interactive user interface (e.g., by drawing a user‟s attention to interesting aspects of the data such as trends, anomalies, and patterns). We apply cognitive systems engineering processes to help identify the information available to individuals and/or teams, where it resides, where it is needed, and ultimately how to create the mappings required in connecting critical information to those who need it with innovative visualizations that most effectively support the end user. This paper describes the application of MDV to intelligently deliver timely, mission-critical information by adapting a Common Tactical Picture (CTP) display used by Undersea Warfare (USW) commanders for situation awareness, threat assessment, and decision support.
PREVALENCE AND SOME RELATED FACTORS OF IRRITABLE BOWEL SYNDROME AMONG MEDICAL STUDENTS IN HUE UNIVERSITY OF MEDICINE AND PHARMACY, HUE UNIVERSITY (2020)

Background: Irritable bowel syndrome (IBS) is considered as a common functional bowel disorder. The prevalence of IBS vary in different communities and has been related to multifactorial mechanisms. Objective: To investigate the prevalence and some related factors about irritable bowel syndrome among medical students in Hue University of Medicine and Pharmacy, Vietnam. Methods: A cross-sectional study was carried out among medical students of first to sixth year enrolled in Hue University of Medicine and Pharmacy during the academic year 2018 to 2019. Participants were asked to complete a comprehensive anonymous questionnaire which detailed characteristics on socio-demographic, health-related, lifestyle factors (according to DASS-21, ISS) and Rome IV Diagnostic Questionnaires & Tables for Investigators and Clinicians. Results: 299 medical students completed the survey. The prevalence of IBS was 14.4% (43/299) according to ROME IV criteria, female are higher than male (60.5% vs 39.5%). Among the IBS subjects, IBS-M accounted for 44.2%, IBS-D with 32.6%, IBS-C and IBS-U with the same 11.6%. Live-alone status, exercise habits, depression, anxiety, stress (according to DASS-21) are factors related to IBS. Conclusion: IBS among medical students are with a quite high prevalence. Screening of these IBS students for psychological problems and stress need to consider. Keywords: Irritable bowel syndrome, IBS , Prevalence, Medical students, ROME IV criteria
Super-Helix Formation Induced by Cyanine J-Aggregates onto Random-Coil Carboxymethyl Amylose as Template (2005)

The J-aggregation of Cyanine-1dye in the presence of carboxymethyl amylose (CMA) is described. The J-aggregation requires a large excess CMA concentration; the J-band maximum appears in the concentration range, [CMA]/[dye] = 10-50, depending on the degree of substitution (DS) of carboxylation, where [CMA] is the concentration of polymer repeat units. An extraordinarily large induced circular dichroism (CD) is observed from J-aggregates of the achiral cyanine dye in association with a random coil CMA, suggesting that the CMA is transformed into a helix. The magnitude of CD intensity increases with increasing DS of CMA and pH up to neutral (where a maximum J-aggregation occurs), while the CMA-bound dye monomer and H-aggregates (occurring at pH > or = 9) exhibit no induced CD. The trend in the CD intensity (of the J-aggregates) is in parallel with the fluorescence intensity of the J-aggregates. This suggests that binding of the J-aggregates onto the template CMA is sterically controlled by the asymmetric environment of glucose residues (of CMA) so that more twisting power is exerted with increasing DS (of CMA), rendering the cyanine dye/CMA complex a more rigid (a high fluorescence intensity) super-helix. This is also revealed by the AFM image of a long strand.