gebhart/patrepeval huggingface dataset:
Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus (2010)

Agarose gel electrophoresis, circular dichroism and differential scanning calorimetry showed that single-stranded RNA from satellite tobacco mosaic virus transforms from a conformationally ‘closed state’ at 4°C to a more conformationally ‘open state’ at 65°C. The transition is reversible and shows no hysteresis. Atomic force microscopy (AFM) allowed visualization of the two states and indicated that the conformationally ‘closed state’ probably corresponds to the native encapsidated conformation, and that the ‘open state’ represents a conformation, characterized as short, thick chains of domains, as a consequence of the loss of tertiary interactions. Heating from 75°C to 85°C in the presence of EDTA was necessary to further unravel the ‘open’ conformation RNA into extended chains of lengths &amp;gt;280 nm. Virus exposed to low concentrations of phenol at 65°C, extruded RNA as distinctive ‘pigtails’ in a synchronous fashion, and these ‘pigtails’ then elongated, as the RNA was further discharged by the particles. Moderate concentrations of phenol at 65°C produced complete disruption of virions and only remains of decomposed particles and disordered RNA were evident. AFM images of RNA emerging from disrupted virions appear most consistent with linear arrangements of structural domains.
Modeling of laser planarization of thin metal films (1989)

The differences between excimer (≊30 ns pulse duration) and flashlamp-pumped dye (≊500 ns pulse duration) laser planarization are examined for 1.5–2 μm thick gold films over SiO2 layers. Test structures containing bar patterns (square waves) of 5000 Å peak-to-trough amplitude with spatial periods ranging from 10 to 100 μm were prepared and laser irradiated. A linear model is presented which described the time evolution of the film’s surface topography when melted with a dye laser pulse. Excimer laser planarization is found to be susceptible to evaporative recoil effects which may cause undesired pattern amplification.
Massively parallel layout generation in real time (2019)

Conceiving an artwork requires designers to create assets and organize (or layout) them in a harmonious, self-orating story. While creativity is fundamental to both aspects, the latter can be bolstered with automated techniques. We present a first true SIMD formulation for the layout generation and leverage CUDA-enabled GPU to scan through millions of possible permutations and rank them on aesthetic appeal using weighted parameters such as symmetry, alignment, density, size balance, etc. The entire process happens in real-time using a GPU-accelerated implementation of replica exchange Monte Carlo Markov Chain method. The exploration of design space is rapidly narrowed by performing distant jumps from poorly ranked layouts, and fine tuning the highly ranked ones. Several iterations are carried out until desired rank or system convergence is achieved. In contrast to existing approaches, our technique generates aesthetically better layouts and runs more than two orders of magnitude faster.
Classification of Network Traffic via Packet-Level Hidden Markov Models (2008)

Traffic classification and identification is a fertile research area. Beyond Quality of Service, service differentiation, and billing, one of the most important applications of traffic classification is in the field of network security. This paper proposes a packet-level traffic classification approach based on Hidden Markov Model (HMM). Classification is performed by using real network traffic and estimating - in a combined fashion - Packet Size (PS) and Inter Packet Time (IPT) characteristics, thus remaining applicable to encrypted traffic too. The effectiveness of the proposed approach is evaluated by considering several traffic typologies: we applied our model to real traffic traces of Age of Mythology and Counter Strike (two Multi Player Network Games), HTTP, SMTP, Edonkey, PPlive (a peer-to-peer IPTV application), and MSN Messenger. An analytical basis and the mathematical details regarding the model are given. Results show how the proposed approach is able to classify network traffic by using packet-level statistical properties and therefore it is a good candidate as a component for a multi-classification framework.
Donor graft adenoviral iNOS gene transfer ameliorates rat liver transplant preservation injury and improves survival (2006)

The exact role of inducible NOS (iNOS) in liver ischemia/reperfusion (I/R) injury is controversial. This study was designed to investigate whether donor liver pretreatment with adenovirus encoding iNOS (AdiNOS) ameliorates I/R injury associated with liver transplantation. Orthotopic syngeneic LEW rat liver transplantation (OLT) was performed after 18 or 24 hours' preservation in cold UW. AdiNOS or control gene vector (AdLacZ) was delivered to the liver by donor intravenous pretreatment 4 days before graft harvesting. Uninfected grafts also served as control. Recipients were sacrificed 1 to 48 hours posttransplantation. An abundant hepatic iNOS protein expression and marked serum NO elevation was observed in the AdiNOS-treated group, without affecting endothelial nitric oxide synthase (eNOS) expression, before harvesting and after OLT. AdiNOS pretreatment markedly improved liver function assessed by serum aspartate aminotransferase/alanine aminotransferase levels and reduced liver necrosis formation. AdiNOS treatment also was associated with reduced ICAM-1 mRNA expression and neutrophil accumulation in the liver graft after OLT compared with untransfected or AdLacZ-treated group. Furthermore, AdiNOS delivery significantly improved transplant survival, compared with AdLacZ or saline controls. AdiNOS pretreatment did not attenuate I/R-induced apoptotic cell death in the liver graft. Administration of a selective inhibitor for iNOS abrogated the protection afforded by AdiNOS pretreatment. In conclusion, donor pretreatment with AdiNOS led to improved liver graft injury and posttransplantation survival. Downregulation of ICAM-1 mRNA and neutrophil infiltration may be associated with the mechanisms by which AdiNOS pretreatment confer the protection against transplant-associated hepatic I/R injury.
Enhanced Performance Love Wave Magnetic Field Sensors With Temperature Compensation (2020)

Temperature compensation is critical and important for surface acoustic wave (SAW) magnetic field sensors. In this study, a Love wave mode based SAW device is investigated as a magnetic field sensor. The considered structure is composed of a CoFeB magnetostrictive film as sensitive layer, SiO2, and ZnO film as insulating and temperature compensation layers and ST+90°-cut quartz as substrate. A theoretical model is proposed to study the magnetic field sensitivity and temperature coefficient of frequency (TCF) variations. Optimized structures by calculation were fabricated and characterized and obtained results show a good agreement between experiments and our model simulation. We clearly shown that signal performances as well as the flexibility of the resonator design were improved by adding the isolating SiO2 layer. Thus, a sensor showing a near zero TCF (0.1 ppm/°C) and a magnetic field sensitivity of -420 ppm/mT was achieved with the structure CoFeB(100 nm)/SiO2(250 nm)/ZnO(300 nm)/Quartz(ST-X+90°). This multi-layered structure is beneficial to design reliable SAW magnetic field sensors.
A Black-Box Approach to Query Cardinality Estimation (2007)

We present a “black-box” approach to estimating query cardinality that has no knowledge of query execution plans and data distribution, yet provides accurate estimates. It does so by grouping queries into syntactic families and learning the cardinality distribution of that group directly from points in a high-dimensional input space constructed from the query’s attributes, operators, function arguments, aggregates, and constants. We envision an increasing need for such an approach in applications in which query cardinality is required for resource optimization and decision-making at locations that are remote from the data sources. Our primary case study is the Open SkyQuery federation of Astronomy archives, which uses a scheduling and caching mechanism at the mediator for execution of federated queries at remote sources. Experiments using real workloads show that the black-box approach produces accurate estimates and is frugal in its use of space and in computation resources. Also, the black-box approach provides dramatic improvements in the performance of caching in Open SkyQuery.
THE EFFECT OF CARCASS ELECTRICAL STIMULATION ON MEAT OBTAINED FROM BOS INDICUS AND BOS TAURUS CATTLE1 (1988)

ABSTRACT Sides of 30 carcasses obtained from steers of Hereford and Angus (HA), Braham (Br) or Sahiwal (Sh) crossbreds were electrically stimulated (ES) by high voltage or remained as controls (CN). Longissimus muscle at the 12th rib of carcasses from the Br and Sh crossbreds was darker (P &lt; 0.05) in color and possessed greater (P &lt; 0.05) degrees of dark coarse band formation than muscle from the HA crossbreds. Broiled steaks from carcasses of Br and Sh crossbreds were less tender than steaks from HA. Electrical stimulation markedly improved (P &lt; 0.05) dark coarse band formation, color and tenderness of steaks within the Bos indicus breed groups. Improved tenderness was associated with better (P &lt; 0.05) sensory panel scores for ease of fragmentation of the myofibrillar portion and less (P &lt; 0.05) connective tissue.
Effect of trace iron levels and iron withdrawal by chelation on the growth of Candida albicans and Candida vini (2010)

The iron requirements of the opportunistic pathogenic yeast, Candida albicans, and the related nonpathogenic spoilage yeast Candida vini were investigated along with their responses to various exogenous iron chelators. The influence of iron as well as the exogenous chelating agents lactoferrin, EDTA, deferiprone, desferrioxamine, bathophenanthroline sulphonate and a novel carried chelator with a hydroxypyridinone-like Fe-ligand functionality, DIBI, on fungal growth was studied in a chemically defined medium deferrated to trace iron levels (<1.2 microg L(-1) or 0.02 microM of Fe). Candida albicans competed better at low iron levels compared with C. vini, which was also more susceptible to most added chelators. Candida albicans was resistant to lactoferrin at physiologically relevant concentrations, but was inhibited by low concentrations of DIBI. Candida vini was sensitive to lactoferrin as well as to DIBI, whose inhibitory activity was shown to be Fe reversible. The pathogenic potential of C. albicans and the nonpathogenic nature of C. vini were consistent with their differing abilities to grow under iron-limiting conditions and in the presence of exogenous iron chelators. Both yeasts could be controlled by appropriately strong chelators. This work provides the first evidence of the iron requirements of the spoilage organism C. vini and its response to exogenous chelators. Efficient iron withdrawal has the potential to provide the basis for new fungal growth control strategies.
Hollow Plasma Acceleration Driven by a Relativistic Reflected Hollow Laser (2020)

In order to address the present difficulty in experimentally generating the relativistic Laguerre-Gaussian laser, primarily due to damage caused to optical modulators, a high-reflectivity phase mirror is applied in the femtosecond petawatt laser system to generate a relativistic hollow laser at the highest intensity of 6.3×10^{19} W/cm^{2} for the first time. A simple optical model is used to verify that the vortex laser may be generated in this new scheme; using such a relativistic vortex laser, the hollow plasma drill and acceleration are achieved experimentally and proven by particle-in-cell simulations. With the development of the petawatt laser, this scheme opens up possibilities for the convenient production of the relativistic hollow laser at high repetition and possible hollow plasma acceleration, which is important for a wide range of applications such as the generation of radiation sources with orbital angular momentum, fast ignition for inertial confinement fusion, and jet research in the astrophysical environment.
Determination of 105 antibiotic, anti-inflammatory, antiparasitic agents and tranquilizers by LC-MS/MS based on an acidic QuEChERS-like extraction (2018)

A procedure for screening 105 veterinary drugs in foods by liquid chromatography tandem mass-spectrometry (LC-MS/MS) is presented. Its scope encompasses raw materials of animal origin (milk, meat, fish, egg and fat) but also related processed ingredients and finished products commonly used and manufactured by food business operators. Due to the complexity of the matrices considered and to efficiently deal with losses during extraction and matrix effects during MS source ionisation, each sample was analysed twice, that is 'unspiked' and 'spiked at the screening target concentration' using a QuEChERS-like extraction. The entire procedure was validated according to the European Community Reference Laboratories Residues Guidelines. False-negative and false-positive rates were below 5% for all veterinary drugs whatever the food matrix. Effectiveness of the procedure was further demonstrated through participation to five proficiency tests and its ruggedness demonstrated in quality control operations by a second laboratory.
Mimotope/anti-mimotope probing of structural relationships in platelet glycoprotein Ib alpha. (1996)

A bacteriophage library displaying random decapeptides was used to characterize the binding preference of C-34, a monoclonal antibody originally raised against platelet-type von Willebrand disease platelets heterozygous for the mutation 23OWKQ (G --> V)233V234 in the alpha chain of glycoprotein Ib (GPIb alpha). Three rounds of biopanning C-34 against the library resulted in striking convergence upon the sequence WNWRYREYV. Since no portion of this sequence corresponds to a recognizable peptide sequence within human platelet GPIb alpha, it may be considered a "mimotope" of the naturally occurring C-34 epitope, presumably bearing similarity to it in three-dimensional structure. Synthetic AWNWRYREYV peptide preincubated with C-34 fully neutralized the ability of C-34 to inhibit platelet aggregation, with an IC50 of approximately 6 microg/ml. When biotinylated AWNWRYREYV was subsequently bioparmed against the original decapeptide library, the sole clone demonstrating inhibitory activity above background level in a functional platelet assay displayed the sequence RHVAWWRQGV, and chemically synthesized peptide fully inhibited ristocetin-induced aggregation, with an IC50 of 200-400 microg/ml. Synthesized RHVAWWKQGV peptide exerted only slight inhibition, whereas RHVAWWKQVV peptide showed potent inhibitory activity. Moreover, whereas synthesized wild-type 228YVWKQGVDVK237 GPIb alpha peptide was virtually without inhibitory activity, the 228YVWKQ(G -->V) 233VDVK237 peptide fully inhibited ristocetin-induced aggregation, with an IC50 of approximately 400 microg/ml. These studies raise the possibility of an intramolecular association of peptide regions within GPIb alpha that may play a role in the regulation of von Willebrand factor-dependent platelet aggregation.
Residual Viraemia in HIV‐1‐Infected Patients with Plasma Viral Load ≤20 copies/ml is Associated with Increased Blood Levels of Soluble Immune Activation Markers (2008)

Abstract Despite undetectable viral load in conventional assays, probably all human immunodeficiency virus (HIV)‐1 infected patients have residual viraemia (RV) detectable by ultra‐sensitive assays. To study this issue, this study investigated virologic and immunologic consequences of RV in highly active antiretroviral therapy (HAART)‐treated HIV‐1‐infected patients with plasma HIV‐1 RNA ≤20 copies/ml. The study included 32 HAART‐treated HIV‐1‐infected patients with HIV‐1 RNA ≤20 copies/ml followed prospectively 6‐monthly for 24 months. RV was detected by transcription‐mediated amplification (TMA‐RV) technique (Procleix ® HIV‐1 Discriminatory Assay; Chiron) and by PCR (PCR‐RV, Amplicor HIV‐1 Monitor Assay; Roche Diagnostics). The association between RV and proviral‐HIV‐1‐DNA, CD4‐count, CD8‐count, soluble [soluble tumour necrosis factor receptor (TNFr)‐II, β 2 ‐microglobulin, immunoglobulins] and cellular (HLA‐DR, CD38, CD45RO, CD45RA, CD62L) T‐cell markers of immune activation was investigated. In the 24‐months study‐period, 23 patients had ≥1 episode with TMA‐RV whereas 9 patients had undetectable TMA‐RV throughout the study‐period. Time‐points with TMA‐RV and PCR‐RV were associated with higher circulating sTNFrII (+0.234 ng/ml, P = 0.030) and β 2 ‐microglobulin (+22 nmol/l, P = 0.016) and time‐points with PCR‐RV were also associated with higher IgA (+0.82 μmol/l, P = 0.035) and CD8‐count (+1.18‐fold, P = 0.001). Patients with TMA‐RV in the study‐period had higher HIV‐1 RNA pre‐HAART ( P = 0.032). RV was not associated with proviral‐HIV‐1‐DNA, CD4‐count, CD4+HLA‐DR+, CD8+HLA‐DR+CD38+, CD4+CD45RA−CD45RO+, CD8+CD45RA−CD45RO+, CD4+CD45RA+CD62L+, CD8+CD45RA+CD62L+ T cells, IgG or IgM. In conclusion, RV was associated with increased blood levels of soluble immune activation markers in HAART‐treated HIV‐1‐infected patients. The finding that RV was associated with higher pre‐HAART plasma viral load suggests that RV is linked to pre‐HAART disease progression.
Faculty Opinions recommendation of Small molecules that induce cardiomyogenesis in embryonic stem cells. (2004)

A phenotypic cell-based screen of a large combinatorial chemical library led to the identification of a class of diaminopyrimidine compounds (cardiogenol A-D) which can selectively and efficiently induce mouse embryonic stem cells (ESCs) to differentiate into cardiomyocytes. ESC-derived cardiomyocytes were shown to express multiple cardiac muscle markers, including myosin heavy chain, GATA-4, MEF2, and Nkx2.5, and spontaneously form beating regions. Such small molecules will serve as useful chemical probes to study cardiac muscle differentiation and may ultimately facilitate the therapeutic application of ESCs for cardiac repair. PMID: 14871063
Group mobility: Detection, tracking and characterization (2016)

In the era of mobile computing, understanding human mobility patterns is crucial in order to better design protocols and applications. Many studies focus on different aspects of human mobility such as people's points of interests, routes, traffic, individual mobility patterns, among others. In this work, we propose to look at human mobility through a social perspective, i.e., analyze the impact of social groups in mobility patterns. We use the MIT Reality Mining proximity trace to detect, track and investigate group's evolution throughout time. Our results show that group meetings happen in a periodical fashion and present daily and weekly periodicity. We analyze how groups' dynamics change over day hours and find that group meetings lasting longer are those with less changes in members composition and with members having stronger social bonds with each other. Our findings can be used to propose meeting prediction algorithms, opportunistic routing and information diffusion protocols, taking advantage of those revealed properties.
A Local/Global Approach to Mesh Parameterization (2008)

Abstract We present a novel approach to parameterize a mesh with disk topology to the plane in a shape‐preserving manner. Our key contribution is a local/global algorithm, which combines a local mapping of each 3D triangle to the plane, using transformations taken from a restricted set, with a global “stitch” operation of all triangles, involving a sparse linear system. The local transformations can be taken from a variety of families, e.g. similarities or rotations, generating different types of parameterizations. In the first case, the parameterization tries to force each 2D triangle to be an as‐similar‐as‐possible version of its 3D counterpart. This is shown to yield results identical to those of the LSCM algorithm. In the second case, the parameterization tries to force each 2D triangle to be an as‐rigid‐as‐possible version of its 3D counterpart. This approach preserves shape as much as possible. It is simple, effective, and fast, due to pre‐factoring of the linear system involved in the global phase. Experimental results show that our approach provides almost isometric parameterizations and obtains more shape‐preserving results than other state‐of‐the‐art approaches. We present also a more general “hybrid” parameterization model which provides a continuous spectrum of possibilities, controlled by a single parameter. The two cases described above lie at the two ends of the spectrum. We generalize our local/global algorithm to compute these parameterizations. The local phase may also be accelerated by parallelizing the independent computations per triangle.
Underwater Pipe and Valve 3D Recognition Using Deep Learning Segmentation (2020)

During the past few decades, the need to intervene in underwater scenarios has grown due to the increasing necessity to perform tasks like underwater infrastructure inspection and maintenance or archaeology and geology exploration. In the last few years, the usage of Autonomous Underwater Vehicles (AUVs) has eased the workload and risks of such interventions. To automate these tasks, the AUVs have to gather the information of their surroundings, interpret it and make decisions based on it. The two main perception modalities used at close range are laser and video. In this paper, we propose the usage of a deep neural network to recognise pipes and valves in multiple underwater scenarios, using 3D RGB point cloud information provided by a stereo camera. We generate a diverse and rich dataset for the network training and testing, assessing the effect of a broad selection of hyperparameters and values. Results show F1-scores of up to 97.2% for a test set containing images with similar characteristics to the training set and up to 89.3% for a secondary test set containing images taken at different environments and with distinct characteristics from the training set. This work demonstrates the validity and robust training of the PointNet neural in underwater scenarios and its applicability for AUV intervention tasks.
Preliminary examination of time‐resolved fluorometry for protein array applications (2000)

The advantages of time-resolved fluorometry over conventional fluorometric analysis are well known. However, time-resolved fluorescence has not as yet found wide applications in protein microarray or other multiparametric methods of analysis. Here we describe a general method which is suitable for multiparametric and microarray analysis, based on time-resolved fluorometry. A polystyrene surface is coated with different monoclonal antibodies, specific for certain analytes. The analyte mixtures are then universally biotinylated, using an active biotin ester. After removing excess biotin, the biotinylated samples are applied on the polystyrene surface, incubated and the excess is washed away. The bound moieties are then quantified by adding a universal detection reagent containing streptavidin, labelled with a fluorescent europium chelate. After washing and drying of the solid surface, the immobilized moieties are detected by using solid-phase, laser-excited time-resolved fluorometric analysis. In a preliminary examination of this principle, we have demonstrated that we can correctly identify upregulation of three secreted proteins, following stimulation of a breast carcinoma cell line with various steroids. Our method should be suitable for high-density microarray analysis of proteins, captured by specific monoclonal antibodies or other binding reagents. Copyright © 2000 John Wiley & Sons, Ltd.