gebhart/patrepeval huggingface dataset:
Electrical Current Signatures of DNA Base Modifications in Single Molecules Immobilized in the α‐Hemolysin Ion Channel (2013)

Nanopore technology holds high potential for next-generation DNA sequencing. This method operates by drawing an individual single-stranded DNA molecule through a nanoscale pore while monitoring the current deflections that occur as the DNA passes through. Individual current levels for the four DNA nucleotides have been established by immobilization of an end biotinylated strand in the pore in which the nucleotide of interest is suspended at the most sensitive region of the ion channel. Due to the inherent reactivity of the DNA bases, many modified nucleotides in the genome exist resulting from oxidative and UV insults, among others. Herein, the current levels for the common DNA damages 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), uridine (U), abasic sites (AP), thymine dimers (T=T), thymine glycol (Tg) and 5-iodocytosine (5-I-C) were assessed via immobilization experiments. In some cases, the current difference between the damaged and canonical nucleotides was not well resolved; therefore, we took advantage of the chemical reactivity of the new functional groups present to make amine adducts that shifted the current levels outside the range of the native nucleotides. Among adducts studied, only the 2-aminomethyl-18-crown-6 adduct was able to give a large current shift in the immobilization experiment, as well as to be observed in a translocation experiment. The results show potential in providing current level modulators for identification of some types of DNA damage. In principle, any DNA base modification that can be converted chemically or enzymatically to an abasic site could be identified in this way.
MITAP-compliant characterization of human regulatory macrophages (2017)

This article provides a transparent description of Mreg_UKR cell products, including manufacture and quality-control processes, using the structure and vocabulary of the 'Minimum Information about Tolerogenic Antigen-presenting Cells' reporting guidelines. This information is intended as a resource for those in the field, as well as a stimulus to develop a new wave of immunoregulatory and tissue-reparative monocyte-derived cell therapies.
The SemEval-2007 WePS evaluation (2007)

This paper presents the task definition, resources, participation, and comparative results for the Web People Search task, which was organized as part of the SemEval-2007 evaluation exercise. This task consists of clustering a set of documents that mention an ambiguous person name according to the actual entities referred to using that name.
Surface modification of polyethylene and polypropylene in atmospheric pressure glow discharge (2005)

An atmospheric pressure glow discharge (APGD) was used for surface modification of polyethylene (PE) and polypropylene (PP). The discharge was generated between two planar metal electrodes, with the top electrode covered by a glass and the bottom electrode covered by the treated polymer sample. The discharge burned in pure nitrogen or in nitrogen–hydrogen or nitrogen–ammonia mixtures. The surface properties of both treated and untreated polymers were characterized by scanning electron microscopy, atomic force microscopy, surface free energy measurements and x-ray photoelectron spectroscopy. The influence of treatment time and power input to the discharge on the surface properties of the polymers was studied. The ageing of the treated samples was investigated as well. The surface of polymers treated in an APGD was homogeneous and it had less roughness in comparison with polymer surfaces treated in a filamentary discharge. The surface free energy of treated PE obtained under optimum conditions was 54 mJ m−2 and the corresponding contact angle of water was 40°; the surface free energy of treated PP obtained under optimum conditions was 53 mJ m−2 and the contact angle of water 42°. The maximum decrease in the surface free energy during the ageing was about 10%.
An Intersubunit Disulfide Bond Prevents in Vitro Aggregation of a Superoxide Dismutase-1 Mutant Linked to Familial Amytrophic Lateral Sclerosis (2004)

Familial amyotrophic lateral sclerosis (FALS) is linked to over 90 point mutations in superoxide dismutase-1 (SOD1), a dimeric metalloenzyme. The postmortem FALS brain is characterized by SOD1 inclusions in the motor neurons of regions in which neuronal loss is most significant. These findings, together with animal modeling studies, suggest that aggregation of mutant SOD1 produces a pathogenic species. We demonstrate here that a mutant form of SOD1 (A4V) that is linked to a particularly aggressive form of FALS aggregates in vitro, while wild-type SOD1 (WT) is stable. Some A4V aggregates resemble amyloid pores formed by other disease-associated proteins. The WT dimer is significantly more stable than the A4V dimer, suggesting that dimer dissociation may be the required first step of aggregation. To test this hypothesis, an intersubunit disulfide bond between symmetry-related residues at the A4V dimer interface was introduced. The resultant disulfide bond (V148C-V148C') eliminated the concentration-dependent loss of enzymatic activity of A4V, stabilized the A4V dimer, and completely abolished aggregation. A drug-like molecule that could stabilize the A4V dimer could slow the onset and progression of FALS.
A comparison study on the efficacy of SpinoMed® and soft lumbar orthosis for osteoporotic vertebral fracture (2014)

In this study, SpinoMed® could not provide additional treatment benefits to patients with osteoporotic vertebral fracture regarding pain relief and functional independence improvement at the subacute stage. The effects of SpinoMed® in muscle-strengthening and thoracic kyphotic angle reduction for patients with osteoporotic vertebral fracture need to be further verified in a more intensive and longer-term training program.
Advances in H<sub>1</sub>-Antihistamines (2004)

Histamine has an important role as a chemical messenger in physiologic responses, neurotransmission, allergic inflammation, and immunomodulation by way of the H1-receptor. Most H1-antihistamines, which are useful in treating these effects, possess similar efficacy in allergic rhinoconjunctivitis and chronic urticaria. However, there are clinically relevant differences among them in their pharmacology and safety profiles.
Novel toxicology challenges in the era of chimeric antigen receptor T-cells therapies (2016)

T-lymphocytes are fine executioners of adaptive immune-responses, however, quantitative and qualitative immunological defects in patients with cancer (1), together with tumor immune-evasion strategies can result in inefficient anti-tumor surveillance (2). Genetically engineered T-cells, redirected towards the CD19 antigen with chimeric antigen receptors (CARs), have proven successful in treating patients with relapsed/refractory acute lymphoblastic leukemia (ALL). In addition, CAR T-cells redirected towards tumor associated antigens are actively being investigated in a variety of malignancies, including solid cancers (3).
System architecture for implementing multiuser detector within an ad-hoc network (2002)

The near-far problem for direct-sequence spread-spectrum (DS-SS) can be alleviated by the use of low-complexity multiuser receiver implementations, such as successive interference cancellation (SIC) and parallel interference cancellation (PIC) receivers. Ironically, multiuser detection (MUD) has received more research attention for its potential application to 3rd generation commercial cellular systems which employ tight power control than for its application to ad-hoc military networks that might benefit from the near-far resistance of MUD techniques. Some previous research has demonstrated the feasibility of simple MUD techniques for improving the performance and capacity of ad-hoc peer-to-peer packet radio networks (Howlader and Woerner 1998, 1999). This paper presents an architecture for DS-SS packet radio networks exploiting MUD. Issues to be considered include: the performance of fixed complexity PIC and SIC receivers in peer-to-peer environments with AWGN and fading channels, the formulation of signal amplitude estimation for the MUD, and packet acquisition using receiver-oriented spreading codes.
Java servlet technology for analogue module generation (2003)

A World Wide Web (WWW) based client/server system has been developed which uses Java servlet technology. The system allows a server-side, process-independent layout generator servlet to generate active messages, which create design rule correct geometry of analogue components such as resistors, capacitors and transistors within a design system on the local workstation. This combination of server based servlets and active messages is a very powerful technique for developing remote applications which run in cooperation with a local design system, leading to real increases in system availability, functionality and performance.
Nanomechanotransduction and Interphase Nuclear Organization influence on genomic control (2007)

The ability of cells to alter their genomic regulation in response to mechanical conditioning or through changes in morphology and the organization of the interphase nuclei are key questions in cell biology. Here, two nanotopographies have been used as a model surfaces to change cell morphology in order to investigate spatial genomic changes within the nuclei of fibroblasts. Initially, centromeres for chromosome pairs were labeled and the average distance on different substrates calculated. Further to this, Affymetrix whole genome GeneChips were used to rank genomic changes in response to topography and plot the whereabouts on the chromosomes these changes were occurring. It was seen that as cell spreading was changed, so were the positions along the chromosomes that gene regulations were being observed. We hypothesize that as changes in cell and thus nuclear morphology occur, that this may alter the probability of transcription through opening or closing areas of the chromosomes to transcription factors.
Thin film Palladium-Ytrium membranes for hydrogen separation (2010)

The permeability of hydrogen in thin film Pd-Y composite membranes has been investigated for the first time. Thin (5 µm) Pd-Y films were deposited onto macroporous 316L stainless steel substrates by magnetron sputtering. Prior to deposition, a novel laser melting technique was employed in an attempt to reduce the surface roughness and pore size, thus facilitating the deposition of defect-free films. The active hydrogen transport mechanisms of each layer have been determined and the observed hydrogen permeability was analysed using a series resistance type model. The porous substrate was found to contribute significantly to the total transport resistance, and was the predominant source of the non diffusion limited permeation. After correcting for the substrate effects, the permeability of thin film Pd-Y closely matched that in bulk Pd-Y alloys.
Landscape factors associated with exotic plant invasion in Western Riverside County, California (2015)

This study used a combination of spatial analysis and multiple regression to examine the relationship between various environmental and proximate factors affecting exotic vegetation cover in Western Riverside County, California.The study sought to answer two main questions:1) is exotic cover spatially clustered within the study area, and 2) which landscape factors are most associated with high levels of exotic cover?Data on exotic vegetation percent cover was obtained from a vegetation GIS dataset adhering to the National Vegetation Classification System.Data on several landscape attributes, which included slope, elevation, distance to urban areas, distance to roads, distance to agriculture, number of fires, distance to habitat edge, and vegetation community type were obtained from a variety of sources.A random sample of 5,000 points was generated, and data on exotic cover and all landscape attributes were processed in ArcMap 10.2 and then spatially joined to each random point.A Global Moran's I (Test for Spatial Autocorrelation) was performed on all sample points.Two ordinal logistic regression analyses were then performed in IBM SPSS 22. ixThe first regression analysis examined all points throughout the study area, and the second examined points within protected areas only.Results from the Global Moran's I showed exotic cover to be highly clustered throughout the study area.Results from the first ordinal logistic regression showed sites in grassland communities, sites that experienced multiple fires, and unprotected areas to be the most associated with high exotic cover, whereas sites in chaparral and open woodland communities were the least associated with high exotic cover.Results from the second regression, which considered protected areas only, showed sites in grassland and sage scrub communities to be the most associated with high exotic cover, whereas sites in chaparral communities and sites further away from highly invaded areas were the least associated with high exotic cover.
Drying of Ethanol/Water Droplets Containing Silica Nanoparticles (2019)

The evaporation of colloidal drop on a substrate with a pinned contact line usually results in a ring stain (the so-called coffee-ring effect). In this paper, we present an investigation of the evaporation of sessile picoliter droplets of binary solvent mixtures containing fumed silica nanoparticles (NPs). The internal flows in ethanol/water droplets are suppressed, and a uniform deposit morphology is achieved with a low loading (0.2-0.5 vol %) of hydrophobic fumed silica NPs. The effective control of the particle deposit morphology is based on a rapid sol-gel transition assisted by preferential evaporation of ethanol. For droplets of dilute suspensions, the fumed silica NPs tend to agglomerate and form an elastic network quickly, starting from the region close to the three-phase contact line and below the gas-liquid interface and growing toward the interior of the droplet as the solvents evaporate and the surface descends. Higher silica particle concentrations, lower ethanol concentrations, and weaker Marangoni flows all contribute to the sol-gel transition and hence to the suppression of the coffee-ring effect.
Privacy Preserving & Access Control to IntrusionDetection in Cloud System (2013)

As Cloud Computing becomes common, more and more responsive information are being centralized into the cloud. For the protection of data privacy, sensitive data usually have to be encrypted before outsourcing, which makes effectual data utilization, a very challenging task. We propose a new model for data storage and access in clouds. Our scheme avoids storing multiple encrypted copies of same data. In our framework for secure data storage, cloud stores encrypted data (without being able to decrypt them). The main innovation of our model is addition of key distribution centers (KDCs). In this paper, we propose a solution which removes the trusted central authority, and protects the users privacy by preventing the authorities from pooling their information on particular users, thus making ABE more usable in practice. To handle large scale network access traffic and administrative control of data and application in cloud, a new multi-threaded distributed cloud IDS model has been proposed. Our proposed cloud IDS handles large flow of data packets, analyze them and generate reports efficiently by integrating knowledge and behavior analysis to detect intrusions.
Apolipoprotein A-IV stimulates duodenal vagal afferent activity to inhibit gastric motility via a CCK<sub>1</sub> pathway (2004)

Apolipoprotein A-IV (apo A-IV), a peptide expressed by enterocytes in the mammalian small intestine and released in response to long-chain triglyceride absorption, may be involved in the regulation of gastric acid secretion and gastric motility. The specific aim of the present study was to determine the pathway involved in mediating inhibition of gastric motility produced by apo A-IV. Gastric motility was measured manometrically in response to injections of either recombinant purified apo A-IV (200 microg) or apo A-I, the structurally similar intestinal apolipoprotein not regulated by triglyceride absorption, close to the upper gastrointestinal tract in urethane-anesthetized rats. Injection of apo A-IV significantly inhibited gastric motility compared with apo A-I or vehicle injections. The response to exogenous apo A-IV injections was significantly reduced by 77 and 55%, respectively, in rats treated with the CCK(1) receptor blocker devazepide or after functional vagal deafferentation by perineural capsaicin treatment. In electrophysiological experiments, isolated proximal duodenal vagal afferent fibers were recorded in vitro in response to close-arterial injection of vehicle, apo A-IV (200 microg), or CCK (10 pmol). Apo A-IV stimulated the discharge of duodenal vagal afferent fibers, significantly increasing the discharge in 4/7 CCK-responsive units, and the response was abolished by CCK(1) receptor blockade with devazepide. These data suggest that apo A-IV released from the intestinal mucosa during lipid absorption stimulates the release of endogenous CCK that activates CCK(1) receptors on vagal afferent nerve terminals initiating feedback inhibition of gastric motility.
Multi-Scale PIIFD for Registration of Multi-Source Remote Sensing Images (2021)

This paper aims at providing multi-source remote sensing images registered in geometric space for image fusion. Focusing on the characteristics and differences of multi-source remote sensing images, a feature-based registration algorithm is implemented. The key technologies include image scale-space for implementing multi-scale properties, Harris corner detection for keypoints extraction, and partial intensity invariant feature descriptor (PIIFD) for keypoints description. Eventually, a multi-scale Harris-PIIFD image registration algorithm framework is proposed. The experimental results of fifteen sets of representative real data show that the algorithm has excellent, stable performance in multi-source remote sensing image registration, and can achieve accurate spatial alignment, which has strong practical application value and certain generalization ability.
Abstract CT104: Evaluation of peripheral T cell subset proliferation as a pharmacodynamic assay to guide the development of anti-CTLA-4 and PD-1 antibody combinations in patients with solid tumors (2018)

Abstract The combination of anti-CTLA-4 and anti-PD-1 antibodies has demonstrated significant clinical efficacy in metastatic melanoma, but also significant toxicities. Pharmacodynamic (PD) markers are important tools in optimizing the safety and efficacy of anti-CTLA-4/anti-PD-1 combinations, but have remained elusive to date. To test the hypothesis that blockade of both CTLA-4 and PD-1 together results in increased expression of the proliferation marker Ki67 in CD4+ T cells, we studied two dose regimens of ipilimumab in combination with nivolumab in patients with advanced or metastatic solid tumors, using a validated assay. Subjects received either 1.0 mg or 0.3 mg /kg of ipilimumab every 6 weeks in combination with nivolumab 3mg/kg every 2 weeks for a maximum of 12 weeks (2 cycles). A total of 9 subjects were enrolled at the 1.0 mg/kg of ipilimumab cohort and 12 subjects in the 0.3 mg/kg cohort. Highly statistically significant increases of 4.56 fold (range 3.35-6.20) from baseline at cycle 1 day 8 post-treatment (p &lt; 0.001) in cohort 1, and 3.13 fold (range 2.31-4.33) from baseline at cycle 1 day 8 post-treatment (p &lt; 0.001) in cohort 2, in Ki67 expression were observed in CD4+ T cells. The absolute increase in Ki67 expression was also observed to be dose dependent numerically. Significant increases in Ki67 expression were also observed in CD8+ T cells, regulatory T cells, and natural killer T (NKT) cells following treatment. These results identify and support Ki67 expression as a PD biomarker in the context of CTLA-4 and PD-1 blockade. More work is required to correlate these finding with clinical outcomes in order to establish a benchmark biomarker assay for anti-CTLA-4 and anti-PD-1 combinations. (ACTRN12617001059358) Citation Format: Paul De Souza, Agnieszka Malczewski, Igor Proscurshim, Guojun Yuan, Elisabeth Coart, Christopher Dupont, Mariana Manrique, Elise Drouin, Ana Gonzalez, Meg Carini, Olga Shebanova, Jean-Marie Cuillerot. Evaluation of peripheral T cell subset proliferation as a pharmacodynamic assay to guide the development of anti-CTLA-4 and PD-1 antibody combinations in patients with solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT104.
Self-Assembly and Magnetic Properties of FePt, FeRh Nanoparticles, and FePt/FeRh Nanocomposite Particles (2007)

FeRh nanoparticles with the composition of Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">75</sub> Rh <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">25</sub> and Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">36</sub> Rh <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">64</sub> have been fabricated by a solution phase chemical method. After refining and size selection, a particle size is about 2 to 5 nm by HRTEM observation. From XRD results, as-deposited FeRh nanopaticles reveal a typical chemically disordered fcc structure which can be transformed into CsCl-type structure through thermal annealing. In the case of annealed Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">64</sub> Pt <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">36</sub> nanoparticles, the perpendicular coercivity increases comparing with that of as-deposited particles. It may be the results of the crystal orientation of fct-phase
On the error statistics of Viterbi decoding and the performance of concatenated codes (1981)

Computer simulation results are presented on the performance of convolutional codes of constraint lengths 7 and 10 concatenated with the (255, 223) Reed-Solomon code (a proposed NASA standard). These results indicate that as much as 0.8 dB can be gained by concatenating this Reed-Solomon code with a (10, 1/3) convolutional code, instead of the (7, 1/2) code currently used by the DSN. A mathematical model of Viterbi decoder burst-error statistics is developed and is validated through additional computer simulations.
Prognostic Factors and Outcome of Human Herpesvirus 8–Associated Primary Effusion Lymphoma in Patients With AIDS (2005)

Based on a retrospective series of 28 patients, two prognostic factors were identified as being independently associated with impaired clinical outcome in HIV-related PEL--(1) a poor performance status and (2) the absence of HAART before PEL diagnosis.
Agile risk management using software agents (2017)

Risk management is an important process in Software Engineering. However, it can be perceived as somewhat contrary to the more lightweight processes used in Agile methods. Thus an appropriate and realistic risk management model is required as well as tool support that minimizes human effort. We propose the use of software agents to carry out risk management tasks and make use of the data collected from the project environment to detect risks. This paper describes the underlying risk management model in an Agile risk tool where software agents are used to support identification, assessment and monitoring of risk. It demonstrates the interaction between agents, agents’ compliance with designated rules and how agents can react to changes in project environment data. The results, demonstrated using case studies, show that agents are of use for detecting risk and reacting dynamically to changes in project environment thus, help to minimize the human effort in managing risk.