gebhart/patrepeval huggingface dataset:
Quantitative Trait Locus Mapping Methods for Diversity Outbred Mice (2014)

Genetic mapping studies in the mouse and other model organisms are used to search for genes underlying complex phenotypes. Traditional genetic mapping studies that employ single-generation crosses have poor mapping resolution and limit discovery to loci that are polymorphic between the two parental strains. Multiparent outbreeding populations address these shortcomings by increasing the density of recombination events and introducing allelic variants from multiple founder strains. However, multiparent crosses present new analytical challenges and require specialized software to take full advantage of these benefits. Each animal in an outbreeding population is genetically unique and must be genotyped using a high-density marker set; regression models for mapping must accommodate multiple founder alleles, and complex breeding designs give rise to polygenic covariance among related animals that must be accounted for in mapping analysis. The Diversity Outbred (DO) mice combine the genetic diversity of eight founder strains in a multigenerational breeding design that has been maintained for >16 generations. The large population size and randomized mating ensure the long-term genetic stability of this population. We present a complete analytical pipeline for genetic mapping in DO mice, including algorithms for probabilistic reconstruction of founder haplotypes from genotyping array intensity data, and mapping methods that accommodate multiple founder haplotypes and account for relatedness among animals. Power analysis suggests that studies with as few as 200 DO mice can detect loci with large effects, but loci that account for <5% of trait variance may require a sample size of up to 1000 animals. The methods described here are implemented in the freely available R package DOQTL.
Performance enhancement of signaling compression in IP Multimedia Subsystem (2009)

In this paper, multiple compression algorithms have been compared and in accordance with the characteristics of the session initiation protocol (SIP), empel-ziv-storer-szymanski (LZSS) is selected as the basic algorithm for the SIP signaling compression (SigComp) in IP multimedia subsystem (IMS). In order to further enhance the SIP SigComp ratio, the LZSS with Huffman coding compression algorithm as well as the detailed implementation procedure is proposed in this paper. With the aid of Huffman coding, a shorter code is utilized to indicate high probability symbol in SIP message and a longer code for the symbol with low probability. And hence, the average code length can be reduced and the message compression ratio can be enhanced. Simulation results showed that with proposed algorithm the message compression ratio can be greatly reduced which results into a reduction of session delay.
Antioxidants: Positive or Negative Actors? (2018)

The term "antioxidant" is one of the most confusing definitions in biological/medical sciences. In chemistry, "antioxidant" is simply conceived "a compound that removes reactive species, mainly those oxygen-derived", while in a cell context, the conceptual definition of an antioxidant is poorly understood. Indeed, non-clinically recommended antioxidants are often consumed in large amounts by the global population, based on the belief that cancer, inflammation and degenerative diseases are triggered by high oxygen levels (or reactive oxygen species) and that through blocking reactive species production, organic unbalances/disorders can be prevented and/or even treated. The popularity of these chemicals arises in part from the widespread public mistrust of allopathic medicine. In fact, reactive oxygen species play a dual role in dealing with different disorders, since they may contribute to disease onset and/or progression but may also play a key role in disease prevention. Further, the ability of the most commonly used supplements, such as vitamins C, E, selenium, and herbal supplements to decrease pathologic reactive oxygen species is not clearly established. Hence, the present review aims to provide a nuanced understanding of where current knowledge is and where it should go.
Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases (2007)

The binding of diatomic ligands, such as O(2), NO, and CO, to heme proteins is a process intimately related with their function. In this work, we analyzed by means of a combination of classical Molecular Dynamics (MD) and Hybrid Quantum-Classical (QM/MM) techniques the existence of multiple conformations in the distal site of heme proteins and their influence on oxygen affinity regulation. We considered two representative examples: soybean leghemoglobin (Lba) and Paramecium caudatum truncated hemoglobin (PcHb). The results presented in this work provide a molecular interpretation for the kinetic, structural, and mutational data that cannot be obtained by assuming a single distal conformation.
Encapsulation of metallic iron magnetic nanoparticles by polyacrylamide in water suspensions (2017)

Theoretical consideration of the factors of the stability of metallic iron magnetic nanoparticles (MNPs) in water suspensions was done using extended DLVO (Derjaguin-Landau-Verwey-Overbeek) approach based on the balance among Van der Waals, electrostatic, magnetic and steric interactions . Magnetic and steric interactions dominate over other in suspensions of Fe MNPs. To test the theory Fe MNPs with average diameter 84 nm were synthesized by electrical explosion of wire and encapsulated by polyacrylamide in water suspension to provide steric repulsion. It was shown that encapsulation resulted in the efficient diminishing of the aggregation of metallic iron MNPs in water.
Preoperative Multiparametric Prostate Magnetic Resonance Imaging Structured Report Informs Risk for Positive Apical Surgical Margins During Radical Prostatectomy (2022)

Multiparametric MRI is able to identify patients at increased risk for aPSM, and this information can be conveyed in a structured report to urologists, facilitating patient counseling and treatment decisions.
The treatment of advanced chronic lower limb ischaemia with marrow stem cell autotransplantation. (2005)

Marrow stem cell autotransplantation into the ischaemic lower limb seems to be a potentially effective method of peripheral perfusion enhancement. Further studies are needed to clarify the underlying mechanisms of such improvement.
Bioluminescence tomography with Gaussian prior (2010)

Parameterizing the bioluminescent source globally in Gaussians provides several advantages over voxel representation in bioluminescence tomography. It is mathematically unique to recover Gaussians [Med. Phys. 31(8), 2289 (2004)] and practically sufficient to approximate various shapes by Gaussians in diffusive medium. The computational burden is significantly reduced since much fewer unknowns are required. Besides, there are physiological evidences that the source can be modeled by Gaussians. The simulations show that the proposed model and algorithm significantly improves accuracy and stability in the presence of Gaussian or non- Gaussian sources, noisy data or the optical background mismatch. It is also validated through in vivo experimental data.
<title>Optical fiber grating sensor network for monitoring refractive index and temperature distributions in fluids</title> (1999)

In a fiber-optic multi-point sensor network basing on optical fiber Bragg gratings, simultaneous measurements of refractive indices and of temperature are performed. The Bragg wavelength of a side-polished fiber grating is determined by the refractive index of the surrounding fluid, and is measured using a high-resolving low-cost compact spectrometer. The influence of temperature is separated considering the temperature-induced Bragg wavelength shift in an adjacent non-polished part of the fiber grating. The sensor network can be applied for on-line process control in chemical, biochemical and petrol technologies, and for environmental and geotechnical monitoring, especially in flammable or corrosive surroundings, and in electromagnetic fields. A buffer layer between fiber core and analyte allows to adjust the sensor characteristic to appear with high sensitivity in the refractive index range of the interesting fluids.
Relay Node Deployment Based Small World Effect in Hierarchical Industrial Wireless Sensor Networks (2013)

The industrial wireless sensor networks (IWSNs) brings several advantages over traditional wired industrial monitoring and control systems. The communication reliability of IWSNs has to be guaranteed as the real-time field data need to be transmitted to the control system. The specific requirements of IWSNs have brought challenges to the deployment strategy of sensors in industrial environments. Obviously the network architecture has a significant influence on the performance of IWSNs. Therefore, in this paper, we place three types of nodes in a manufacturing shop to monitor equipment situation, production status and environment. We construct an IWSN with small world characteristics through the random additions of efficient relay nodes and short-cuts at a certain probability. The sensor data will be transmitted in multi-hop to the server quickly and exactly through the small world IWSN. In addition, the proposed deployment strategy will ensure balanced energy-usage among the nodes in the network. Simulation results show that the built network topology possesses the property of rapid transmission to reduce the transmission relay drastically and has good robustness. Compared to the flat single-tier network structure of homogeneous sensor nodes, the small world networks utilizing heterogeneous elements will be preferred in IWSNs.
Tertiarybutylarsine as a substitute for AsH<sub>3</sub>: application to InGaAs/InP photonic integrated circuits (1990)

It has been shown that bulk layers of InGaAs and InGaAsP grown using tertiarybutylarsine (TBA) have nearly as good electrical and optical properties as AsH/sub 3/-grown layers. As a consequence conventional InGaAsP lasers at 1.3 mu m were grown by TBA and were found to have properties as good as those of AsH/sub 3/ lasers. Investigations into other components of PIC circuits grown by using TBA as substitute for AsH/sub 3/ are presented. Studies of multi-quantum-well (MQW) and strained-layer MQW lasers, a four-port directional coupler optical switch, and quantum-confined Stark effect modulator structures grown by this technique are reported. The components are intended for use in photonic integrated circuits. In all cases satisfactory performance is demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Three-Phase Hydraulic Conductances in Angular Capillaries (2002)

Abstract In this paper, we extend to three fluid phases a prior finite-element study of hydraulic conductance of two-phase creeping flow in angular capillaries. Previously, we obtained analytic expressions for the hydraulic conductance of water in corner filaments. Here we present the results of a large numerical study with a high-resolution finite element method that solves the three-phase creeping flow approximation of the Navier-Stokes equation. Using the projection-pursuit regression approach, we provide simple analytic expressions for the hydraulic conductance of an intermediate layer of oil sandwiched between water in the corners of the capillary and gas in the center. Our correlations are derived for the oil layers bounded by the concave or convex interfaces that are rigid or allow perfect slip. Therefore, our correlations are applicable to drainage, spontaneous imbibition, and forced imbibition with maximum feasible hysteresis of each contact angle, oil/water and gas/oil. These correlations should be useful in porenetwork calculations of three-phase relative permeabilities of spreading oils. Finally, we compare our results with the existing correlations by Zhou et al., and Hui &amp; Blunt, who assumed thin-film flow with an effective film thickness proportional to the ratio of the average, our correlations are two-four times closer to the numerical results than the corresponding correlations by Zhou et al., and Hui &amp; Blunt.
High co-expression of IL-34 and M-CSF correlates with tumor progression and poor survival in lung cancers (2018)

Despite recent advances in diagnosis and treatment of lung cancers, the 5-year survival rate remains unsatisfactory, which necessitates the identification of novel factors that associates with disease progression and malignant degree for improving diagnostic and therapeutic strategies. Recent progress in cancer immunology research has unveiled critical roles for colony stimulating factor 1 receptor (CSF1R) in multiple aspects of the tumor microenvironment. CSF1R is expressed on tumor-associated macrophages (TAMs), and mediates important pro-tumorigenic functions. CSF1R also provides critical autocrine signals that promote cancer cell survival and proliferation. Activation of CSF1R can be achieved by two independent ligands; macrophage colony-stimulating factor (M-CSF) and interleukin 34 (IL-34). Accordingly, the expression of these ligands in cancer is expected to result in poor prognosis. In this study, we show that IL-34 and M-CSF expression correlates with poor survival in a cohort of lung cancer patients. Importantly, high co-expression of IL-34 and M-CSF associates with the poorest survival compared to cancers that show weak or absent expression of the two ligands. Furthermore, high expression of IL-34 and M-CSF associates with advanced stages of lung cancers. Together, these results indicate a correlation between IL-34/M-CSF expression with poor survival and disease progression in lung cancer patients.
Pseudotumour of the tongue caused by herpes simplex virus type 2 in an HIV-1 infected immunosuppressed patient (1998)

An HIV-1 infected immunosuppressed patient (CD4+ cell counts: 382 cells/microL; viral load 94,000 copies/mL) with recurrent perianal herpes simplex virus type 2 (HSV-2) infections is described, showing an unusual exophytic tumour resembling a squamous cell carcinoma in the lateral part of the tongue. He also had persistent facial herpes infection, oral candidosis, oral hairy leukoplakia and lymphadenopathy. The presence of HSV-2 was detected by polymerase chain reaction both in smears and in a tissue biopsy taken from the involved tongue area. Treatment with brivudin, a new oral virustatic drug, led to rapid regression of the tumour.
A First Course in Differential Equations, Modeling, and Simulation (2011)

Emphasizing a practical approach for engineers and scientists, A First Course in Differential Equations, Modeling, and Simulation avoids overly theoretical explanations and shows readers how differential equations arise from applying basic physical principles and experimental observations to engineering systems. It also covers classical methods for
A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert (2019)

Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.
Exploring the Current Landscape of Intravenous Infusion Practices and Errors (ECLIPSE): protocol for a mixed-methods observational study (2016)

Ethical approval has been obtained from an NHS Research Ethics Committee (14/SC/0290); local approvals will be sought from each participating organisation. Findings will be published in peer-reviewed journals and presented at conferences for academic and health professional audiences. Results will also be fed back to participating organisations to inform local policy, training and procurement. Aggregated findings will inform the debate on costs and benefits of the NHS investing in smart pump technology, and what other changes may need to be made to ensure effectiveness of such an investment.
General Resource Revenue Sharing between the Government of Alberta and Indigenous Peoples in Alberta: Policy Options, Implications, and Considerations (2017)

For any jurisdiction, having the option, some would say opportunity, to share significant resource wealth is in many ways, “a good problem to have”. Significant comparative research has been conducted with specific reference to the wide variety of models in Canada and internationally that enable Indigenous communities to benefit from resource development through revenue sharing agreements. This Capstone is a response to the lack of a jurisdictionally-focussed analysis for Alberta, where the concept is not currently applied but where the debate continues. The goal of this Capstone is to equip policymakers with both context and data needed to ensure a constructive and informed dialogue around the important and complex issue of sharing Alberta's general resource revenues with indigenous communities in the province. It explores the historical and legal context of the issue, as well as the context of Indigenous Peoples in Alberta. Its Literature Review covers the sources of Alberta's significant but volatile resource revenues, the vastly different financial capacities of Alberta's indigenous communities, the current distribution of Alberta's resource revenues, and the positions of relevant parties. The Analysis component evaluates models for revenue sharing from across Canada and around the world, as well as estimating the potential costs of revenue sharing if those models were applied to the Alberta context. These indicate an annual cost to the Government of Alberta of anywhere from $66 million to $2.5 billion per year by 2019-20. Finally, it provides an overview of several key considerations for policymakers. The Capstone's primary recommendation is the development of an inclusive and politically arms-length process involving all relevant parties to study various policy options and make recommendations. This process would be focussed not only on the “how” of revenue sharing, but also on the “why”. This would allow the Government of Alberta and the province's indigenous communities to better ensure that the ultimate outcome will best reflect their available resources and preferences, and build a stronger and more durable foundation for future cooperation.
Action sequencing in the spontaneous swimming behavior of zebrafish larvae - implications for drug development (2017)

All motile organisms need to organize their motor output to obtain functional goals. In vertebrates, natural behaviors are generally composed of a relatively large set of motor components which in turn are combined into a rich repertoire of complex actions. It is therefore an experimental challenge to investigate the organizational principles of natural behaviors. Using the relatively simple locomotion pattern of 10 days old zebrafish larvae we have here characterized the basic organizational principles governing the swimming behavior. Our results show that transitions between different behavioral states can be described by a model combining a stochastic component with a control signal. By dividing swimming bouts into a limited number of categories, we show that similar types of swimming behavior as well as stand-stills between bouts were temporally clustered, indicating a basic level of action sequencing. Finally, we show that pharmacological manipulations known to induce alterations in the organization of motor behavior in mammals, mainly through basal ganglia interactions, have related effects in zebrafish larvae. This latter finding may be of specific relevance to the field of drug development given the growing importance of zebrafish larvae in phenotypic screening for novel drug candidates acting on central nervous system targets.
Treatment of Hepatocellular Carcinoma by Multimodal In Situ Vaccination Using Cryoablation and a Plant Virus Immunostimulant (2023)

Cryoablation and intratumoral CPMV, alone or combined, demonstrated potent efficacy against treated HCC tumors; however, only cryoablation combined with CPMV slowed the growth of untreated tumors, consistent with an abscopal effect.
Transmutation of minor actinides in PWRs: preparation of the ``Actineau`` experiment (1993)

This paper deals with the experimental work that is performed at the CEA to study the metallurgical problems that need to be overcome in order to transmute neptunium and americium in PWRs. After recalling the experience gained on transmutation under thermal flux, the preparation of the experimental irradiation ACTINEAU is described. This experiment, to be carried out in the OSIRIS reactor, will test both homogeneous and heterogeneous recycling with different inert matrices and different mass fractions of actinide in the rods. According to prediction, a transmutation rate of over 50% is expected after 600 days of irradiation. 2 refs., 4 tabs., 3 figs.
Tobacco mosaic virus rods and spheres as supramolecular high-relaxivity MRI contrast agents (2013)

To compensate for the low sensitivity of magnetic resonance imaging (MRI), nanoparticles have been developed to deliver high payloads of contrast agents to sites of disease. Here, we report the development of supramolecular MRI contrast agents using the plant viral nanoparticle tobacco mosaic virus (TMV). Rod-shaped TMV nanoparticles measuring 300×18 nm were loaded with up to 3,500 or 2,000 chelated paramagnetic gadolinium (III) ions selectively at the interior (iGd-TMV) or exterior (eGd-TMV) surface, respectively. Spatial control is achieved through targeting either tyrosine or carboxylic acid side chains on the solvent exposed exterior or interior TMV surface. The ionic T<sub>1</sub> relaxivity per Gd ion (at 60 MHz) increases from 4.9 mM<sup>-1</sup>s<sup>-1</sup> for free Gd(DOTA) to 18.4 mM<sup>-1</sup>s<sup>-1</sup> for eGd-TMV and 10.7 mM<sup>-1</sup>s<sup>-1</sup> for iGd-TMV. This equates to T<sub>1</sub> values of ~ 30,000 mM<sup>-1</sup>s<sup>-1</sup> and ~ 35,000 mM<sup>-1</sup>s<sup>-1</sup> per eGd-TMV and iGd-TMV nanoparticle. Further, we show that interior-labeled TMV rods can undergo thermal transition to form 170 nm-sized spherical nanoparticles containing ~ 25,000 Gd chelates and a per particle relaxivity of almost 400,000 mM<sup>-1</sup>s<sup>-1</sup> (15.2 mM<sup>-1</sup>s<sup>-1</sup> per Gd). This work lays the foundation for the use of TMV as a contrast agent for MRI.
Towards defending connected vehicles against attacks (2017)

Connected vehicles utilize various communication types that take place between different entities such as vehicle, infrastructure, cloud, and mobile. Connected vehicles have sensors and Electronic Control Units (ECUs) that perform in-vehicle communications, and they communicate with the other entities using cellular, vehicular, and wireless networks. These communications may be compromised through different attacks including Man-In-The-Middle (MITM) and Man-At-The-End (MATE) attacks. Existing security solutions are not suitable for this complex integration between different technologies. In this paper, we provide a taxonomy of connected vehicle attacks that can be classified into four main categories. We identify the relations between these attacks and connected vehicle attributes and security requirements. We also present a trust model that contains various countermeasures to secure connected vehicles against different attacks. This trust model consists of four components: integrity, access control, availability, and privacy. The proposed trust model will ensure the achievement of the security requirements against common MITM and MATE attacks.