gebhart/patrepeval huggingface dataset:
The dynamics of avian influenza in Lesser Snow Geese: implications for annual and migratory infection patterns (2015)

Wild water birds are the natural reservoir for low-pathogenic avian influenza viruses (AIV). However, our ability to investigate the epizootiology of AIV in these migratory populations is challenging and, despite intensive worldwide surveillance, remains poorly understood. We conducted a cross-sectional, retrospective analysis in Pacific Flyway Lesser Snow Geese, Chen caerulescens, to investigate AIV serology and infection patterns. We collected nearly 3000 sera samples from Snow Geese at two breeding colonies in Russia and Canada during 1993-1996 and swab samples from >4000 birds at wintering and migration areas in the United States during 2006-2011. We found seroprevalence and annual seroconversion varied considerably among years. Seroconversion and infection rates also differed between Snow Goose breeding colonies and wintering areas, suggesting that AIV exposure in this gregarious waterfowl species is likely occurring during several phases (migration, wintering, and potentially breeding areas) of the annual cycle. We estimated AIV antibody persistence was longer (14 months) in female geese compared to males (6 months). This relatively long period of AIV antibody persistence suggests that subtype-specific serology may be an effective tool for detection of exposure to subtypes associated with highly pathogenic AIV. Our study provides further evidence of high seroprevalence in Arctic goose populations, and estimates of annual AIV seroconversion and antibody persistence for North American waterfowl. We suggest future AIV studies include serology to help elucidate the epizootiological dynamics of AIV in wild bird populations.
Automating power system fault diagnosis through multi-agent system technology (2004)

Fault diagnosis within electrical power systems is a time consuming and complex task. SCADA systems, digital fault recorders, travelling wave fault locators and other monitoring devices are drawn upon to inform the engineers of incidents, problems and faults. Extensive research by the authors has led to the conclusion that there are two issues which must be overcome. Firstly, the data capture and analysis activity is unmanageable in terms of time. Secondly, the data volume leads to engineers being overloaded with data to interpret. This paper describes how multi-agent system technology, combined with intelligent systems, can be used to automate the fault diagnosis activity. Within the multi-agent system, knowledge-based and model-based reasoning are employed to automatically interpret SCADA system data and fault records. These techniques and the design of the multi-agent system architecture that integrates them are described. Consequently, the use of engineering assistant agents as a means of providing engineers with decision support, in terms of timely and summarised diagnostic information tailored to meet their personal requirements, is discussed.
Profiling of primary peripheral blood‐ and monocyte‐derived dendritic cells using monoclonal antibodies from the HLDA10 Workshop in Wollongong, Australia (2015)

Dendritic cells (DCs) arise from hematopoietic stem cells and develop into a discrete cellular lineage distinct from other leucocytes. Mainly three phenotypically and functionally distinct DC subsets are described in the human peripheral blood (PB): plasmacytoid DCs (pDCs), which express the key marker CD303 (BDCA-2), and two myeloid DC subsets (CD1c(+) DC (mDC1) and CD141(+) DC (mDC2)), which express the key markers CD1c (BDCA-1) and CD141 (BDCA-3), respectively. In addition to these primary cell subsets, DCs can also be generated in vitro from either CD34(+) stem/progenitor cells in the presence of Flt3 (Fms-related tyrosine kinase 3) ligand or from CD14(+) monocytes (monocyte-derived DCs (mo-DCs)) in the presence of granulocyte-macrophage colony-stimulating factor+interleukin-4 (GM-CSF+IL-4). Here we compare the reactivity patterns of HLDA10 antibodies (monoclonal antibody (mAb)) with pDCs, CD1c(+) DCs and CD141(+) DCs, as well as with CD14(+)-derived mo-DCs cultured for 7 days in the presence of 100 ng/ml GM-CSF plus 20 ng/ml IL-4. A detailed profiling of these DC subsets based on immunophenotyping and multicolour flow cytometry analysis is presented. Using the panel of HLDA10 Workshop mAb, we could verify known targets selectively expressed on discrete DC subsets including CD370 as a selective marker for CD141(+) DCs and CD366 as a marker for both myeloid subsets. In addition, vimentin and other markers are heterogeneously expressed on all three subsets, suggesting the existence of so far not identified DC subsets.
Numerical modeling of a spherical array of monopoles using FDTD method (2006)

In this paper, the spherical-coordinate finite-difference time-domain method is applied to numerical analysis of phased array of monopoles distributed over a sphere. Outer boundary of the given problem is modeled by accurate spherical- coordinate anisotropic perfectly matched layer. The problem of increased cell aspect ratio near the sphere poles causing degradation of results is solved by dispersion optimization through artificial anisotropy. The accuracy of the approach is verified by comparing a model case with an exact solution. Finally, radiation patterns obtained by frequency-domain near-to-far-field transform and s-parameters of the array elements are presented and validated by comparing with measurement data.
A reactive motion planner to maintain visibility of unpredictable targets (2003)

This paper deals with the problem of computing the motions of one or more robot observers in order to maintain visibility of one or several moving targets. The targets are assumed to move unpredictably, and the distribution of obstacles in the workspace is assumed to be known in advance. Our algorithm computes a motion strategy by maximizing the shortest distance to escape $the shortest distance the target needs to move in order to escape the observer's visibility region. Three main points are discussed: 1) the design and implementation of a reactive planner; 2) the integration and testing of such a planner in a robot system which includes perceptual and control capabilities; and 3) the design and simulation of a motion planner for the task of maintaining visibility of two targets using two mobile observers.
Verification of MA-T Safety and Efficacy Against Pathogens Including SARS-CoV-2 (2021)

Matching transformation system (MA-T) is an on-demand aqueous chlorine dioxide solution. It is a disinfectant developed to maximize the safety of chlorine dioxide radical in water and its effectiveness against various microorganisms. In this study, we examined the safety and effectiveness of MA-T for its use in various infectious disease countermeasures, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and consider if MA-T can be implemented in society. To validate the safety of MA-T, we conducted safety tests and efficacy tests in accordance with GLP-based reliability criteria. To evaluate the efficacy, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) confirmation tests against various bacteria, and virus inactivation test against various viruses including SARS-CoV-2 by TCID50 method were performed. The results of safety tests showed that MA-T was at least as safe as Japanese tap water. As a result of efficacy tests for microorganisms, MA-T was effective against many bacteria. Efficacy tests for virus showed that MA-T inactivates SARS-CoV-1, Middle East respiratory syndrome coronavirus (MERS-CoV), rotavirus A (RV-A), hepatitis C virus (HCV), dengue virus (DENV), and hepatitis B virus (HBV). MA-T also inactivated 99.98% of SARS-CoV-2, which is equivalent to ethanol for disinfection. MA-T has proven to be a safe and effective disinfectant. MA-T is a next-generation disinfectant that has the potential to be safer and more effective than conventional chlorine disinfectants and other disinfectants. It also proved to be an effective disinfectant against SARS-CoV-2, which is currently causing pandemic all over the world.
Application Layer Protocol Negotiation (ALPN) for Session Traversal Utilities for NAT (STUN) (2014)

An Application Layer Protocol Negotiation (ALPN) label for the Session
Traversal Utilities for NAT (STUN) protocol is defined in this
document to allow the application layer to negotiate STUN within the
Transport Layer Security (TLS) connection. The STUN ALPN protocol
identifier applies to both TLS and Datagram Transport Layer Security
(DTLS).
Energy-Aware Cooperative Content Distribution over Wireless Networks: Design Alternatives and Implementation Aspects (2013)

This paper presents a comprehensive overview on the area of energy-aware common content distribution over wireless networks with mobile-to-mobile cooperation. It is assumed that a number of mobile terminals (MTs) that are geographically close to each other are interested in downloading the same content from a server via a base station using a long-range wireless technology. Selected MTs download the content directly from the base station and transmit it to other MTs using a short-range wireless technology. This cooperation can lead to significant performance gains since short-range wireless technologies are energy efficient and provide higher data rates due to the geographical proximity among the MTs. In this paper, we highlight the main alternatives that shape the design of cooperative content distribution architectures with focus on energy efficiency. These include content segmentation, long-range and short-range distribution strategies, grouping of the MTs into cooperating clusters, single hop and multihop communications among the MTs, resource allocation, fairness considerations, and network dynamics. We also discuss various methods commonly utilized for developing content distribution algorithms and evaluating network performance. Finally, we present sample results for selected network scenarios, discuss related standardization activities, and highlight future research directions.
Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines (2017)

The response of cancer cells to drugs is determined by various factors, including the cells’ mutations and gene expression levels. These factors can be assessed using next-generation sequencing. Their integration with vast prior knowledge on signaling pathways is, however, limited by the availability of mathematical models and scalable computational methods. Here, we present a computational framework for the parameterization of large-scale mechanistic models and its application to the prediction of drug response of cancer cell lines from exome and transcriptome sequencing data. With this framework, we parameterized a mechanistic model describing major cancer-associated signaling pathways (&gt;1200 species and &gt;2600 reactions) using drug response data. For the parameterized mechanistic model, we found a prediction accuracy, which exceeds that of the considered statistical approaches. Our results demonstrate for the first time the massive integration of heterogeneous datasets using large-scale mechanistic models, and how these models facilitate individualized predictions of drug response. We anticipate our parameterized model to be a starting point for the development of more comprehensive, curated models of signaling pathways, accounting for additional pathways and drugs.
Maternal overnutrition programs hedonic and metabolic phenotypes across generations through sperm tsRNAs (2019)

There is a growing body of evidence linking maternal overnutrition to obesity and psychopathology that can be conserved across multiple generations. Recently, we demonstrated in a maternal high-fat diet (HFD; MHFD) mouse model that MHFD induced enhanced hedonic behaviors and obesogenic phenotypes that were conserved across three generations via the paternal lineage, which was independent of sperm methylome changes. Here, we show that sperm tRNA-derived small RNAs (tsRNAs) partly contribute to the transmission of such phenotypes. We observe increased expression of sperm tsRNAs in the F1 male offspring born to HFD-exposed dams. Microinjection of sperm tsRNAs from the F1-HFD male into normal zygotes reproduces obesogenic phenotypes and addictive-like behaviors, such as increased preference of palatable foods and enhanced sensitivity to drugs of abuse in the resultant offspring. The expression of several of the differentially expressed sperm tsRNAs predicted targets such as <i>CHRNA2</i> and GRIN3A, which have been implicated in addiction pathology, are altered in the mesolimbic reward brain regions of the F1-HFD father and the resultant HFD-tsRNA offspring. Together, our findings demonstrate that sperm tsRNA is a potential vector that contributes to the transmission of MHFD-induced addictive-like behaviors and obesogenic phenotypes across generations, thereby emphasizing its role in diverse pathological outcomes.
Progress in stem cell‐based therapy for liver disease (2016)

Liver transplantation has been accepted as a useful therapeutic approach for patients with end-stage liver disease. However, the mismatch between the great demand for liver transplants and the number of available donor organs underscores the urgent need for alternative therapeutic strategies for patients with acute and chronic liver failure. The rapidly growing knowledge on stem cell biology has opened new avenues toward stem cell-based therapy for liver disease. As stem cells have capacity for high proliferation and multipotent differentiation, the characteristics of stem cells fit the cell therapy. Several types of cells have been investigated as possible sources of liver regeneration: mesenchymal stem cells, hematopoietic stem cells, liver progenitor cells, induced pluripotent stem cells, and bone marrow mononuclear cells. In vitro and in vivo experiments revealed that these cells have great potential as candidates of stem cell therapy. We reviewed the reports on clinical trials of cell therapy for liver disease that have been recently undertaken using mesenchymal stem cells, hematopoietic stem cells, bone marrow mononuclear cells, and liver progenitor cells. These reports have heterogeneity of description of trial design, types of infused cells, patient population, and efficacy of therapies. We addressed these reports from these viewpoints and clarified their significance. We hope that this review article will provide a perspective on the available approaches based on stem cell-based therapy for liver disease.
The defect in mu heavy chain disease protein GLI. (1976)

Amino acid sequence studies of muHCD protein GLI reveal the absence of the amino terminal 130 residues. The molecule starts at Ala 131 and contains Cys 140, normally involved in the H-L disulfide bridges. Except for the deletion and presumably an extra H-H disulfide bridge involving Cys 140, the remainder of the mu-chain appears normal.
Ultrahigh-performance transparent conductive films of carbon-welded isolated single-wall carbon nanotubes (2018)

Single-wall carbon nanotubes (SWCNTs) are ideal for fabricating transparent conductive films because of their small diameter, good optical and electrical properties, and excellent flexibility. However, a high intertube Schottky junction resistance, together with the existence of aggregated bundles of SWCNTs, leads to a degraded optoelectronic performance of the films. We report a network of isolated SWCNTs prepared by an injection floating catalyst chemical vapor deposition method, in which crossed SWCNTs are welded together by graphitic carbon. Pristine SWCNT films show a record low sheet resistance of 41 ohm □<sup>-1</sup> at 90% transmittance for 550-nm light. After HNO<sub>3</sub> treatment, the sheet resistance further decreases to 25 ohm □<sup>-1</sup>. Organic light-emitting diodes using this SWCNT film as anodes demonstrate a low turn-on voltage of 2.5 V, a high current efficiency of 75 cd A<sup>-1</sup>, and excellent flexibility. Investigation of isolated SWCNT-based field-effect transistors shows that the carbon-welded joints convert the Schottky contacts between metallic and semiconducting SWCNTs into near-ohmic ones, which significantly improves the conductivity of the transparent SWCNT network. Our work provides a new avenue of assembling individual SWCNTs into macroscopic thin films, which demonstrate great potential for use as transparent electrodes in various flexible electronics.
High reliability polyoxide fabricated by using TEOS oxide deposited on disilane polysilicon film (2001)

This paper reports the TEOS oxide deposited on the polysilicon film which was prepared by using the disilane chemical vapor deposition. Compared to the thermally grown oxide or TEOS (tetra-ethyl-ortho-silicate) oxide deposited on the conventional silane polysilicon film, it had symmetrical J-E characteristics that had lower leakage currents but much higher breakdown field, a lower electron trapping rate, and a much larger charge to breakdown. These good properties are attributed to the smoother surface of the deposited disilane poly-I film and the more incorporation of nitrogen during the rapid thermal annealing (RTA) in N/sub 2/O ambient. It is suitable to be as the inter-polyoxide of the electrically-erasable programmable read only memory (EEPROM).
Three stage sample preparation for purification of proteins from complex biological samples (2013)

In this manuscript we present a three-component sample preparation platform for delivering proteins, with controlled orientation, purified from a complex biological sample to a sensor surface. The presented platform depletes highly abundant proteins and cells from complex biological samples, and then is capable of immobilizing the target analyte on the surface with controlled immobilization. A herringbone structure is used to mix the test sample with beads coated with antibodies against the highly abundant proteins, which is then fed into a second component, consisting of a filter trench with interdigitated electrodes above for applying dielectrophoretic force. The beads and cells are pushed down into the filter trench, thus allowing only the serum to pass through. In a third step, protein orientation and immobilization is controlled with electric field. In this manuscript we discuss the proof of concept for each of these three components separately.
Assessment of The Clinical Impact of Postponing Endoscopic Procedures Using Risk Stratification During Covid-19 Pandemic: a Prospective Systematic Multicentric Study (2021)

Aims During the COVID-19 outbreak, we adopted in March 2020 our own risk stratification triage policy facing massive cancellation/postponing of all endoscopic procedures not considered urgent or immediately necessary. At the end of the first wave endoscopy activity resumed progressively. We aimed to assess the impact of procedure postponing on patient outcome.
Ethernet-Tree (E-Tree) Support in Virtual Private LAN Service (VPLS) (2016)

This document specifies a generic Virtual Private LAN Service (VPLS)
solution, which uses VLANs to indicate root or leaf traffic to support
Ethernet-Tree (E-Tree) services. A VPLS Provider Edge (PE) model is
illustrated as an example for the solution. In the solution, E-Tree
VPLS PEs are interconnected by Pseudowires (PWs), which carry the VLAN
indicating the E-Tree attribute. The MAC address-based Ethernet
forwarding engine and the PW work in the same way as specified in RFC
4762 and RFC 4448, respectively. A signaling mechanism is described to
support E-Tree capability and VLAN mapping negotiation.
Funtional and applied studies on the adenovirus minor capsid protein IX (2006)

&lt;p&gt;The adenoviral vector is one of the most used viral vectors for gene therapy applications. The specificity towards its primary receptor is a limitation of the use of HAdV as therapeutical vector, as not all cells have these primary receptors on their surface. To overcome this problem scientists have started to change the receptor specificity of the HAdV vectors by introducing heterologous polypeptides. One of the most promising candidates to function as anchor for these heterologous polypeptides is the minor capsid protein IX (pIX). Alpha-helical spacers of different lengths have been inserted between pIX and a polypeptide ligand. The results showed that an increase in spacer length positively correlated with the accessibility of the peptide on the capsid surface for antibodies and cellular membrane proteins. Next, a hyper stable scFv directed against __-galactosidase was incorporated in the virion via fusion to pIX. These data were the first to show incorporation of a hyper-stable scFv into the HAdV, and that was functional on the capsid surface. Beside the technical approach to use pIX as anchor for heterologous polypeptides here also the function of pIX in the capsid has been studied. This study has led to the model in which the capsid stability mediated by pIX might not be the result of homo-multimerization of this molecule.&lt;/p&gt;
An unusual agent for an unusual localization of infective endocarditis (2017)

We report on a 32-year-old male patient with acute left-hemispheric stroke caused by embolism due to infective endocarditis affected from the HACEK group. Additionally, atypical findings from the transesophageal echocardiography (TEE) which showed fluttering structures belonging to the papillary muscle could be proven as infectious agents with the help of a glucose positron emission tomography (PET) scan. TEE controls showed increasing vegetation involving the mitral valve so that surgery became necessary. The current work reflects, in detail, the emergent clinical course of this young patient, suffering from both an unusual localization and an infrequent cause of endocarditis and focuses on an actual view to the literature.
Multi-core design automation challenges (2007)

The trend to multi-core chip designs presents new challenges for design automation, while the increased reuse of components may offer solutions. This paper describes some of the key challenges with attention paid to three enablers: a physical architecture to streamline chip integration, the linking of early analysis tools around shared data and an updated verification approach for multi-core designs.
Follicular dendritic cells and B cell chemotaxis (1995)

B cells isolated from germinal centers (GC) of immune mice 2-5 days after antigen (Ag) challenge migrate in response to chemotactic signals, whereas GC B cells isolated at other times and resting B cells do not. Since B cells are in direct contact with follicular dendritic cells (FDC) in GC we reasoned that FDC might play a role in enabling B cells to become chemotactically active. Resting B cells were co-cultured with FDC either with or without anti-mu-dextran (anti-mu-dex) as an Ag surrogate and/or recombinant interleukin (rIL)-4 as a T cell surrogate. After 3 days, the B cells were isolated and their migration to chemotactic factors contained in zymosan-activated serum assessed in microchemotaxis chambers. B cells incubated alone or with anti-mu-dex or rIL-4 showed minimal migration, which could be increased if both anti-mu-dex or rIL-4 were present. However, maximal migration was obtained when B cells were cultured with FDC, and this was not increased by addition of anti-mu-dex and/or rIL-4, indicating that the FDC signal was a primary signal and did not require pre-activation of the B cells. Checkerboard analysis using variation in concentration and location of the chemoattractant in chemotaxis chambers indicated that both chemotaxis and chemokinesis occurred. B cell migration began within 6 h of culture, peaked by 48 h and decreased thereafter. Removal of FDC or interference with FDC-B cell contact ablated or significantly decreased induction of B cell migration. Furthermore, induction did not require functional T cells. These data indicate that FDC can induce resting B cells to become responsive to chemotactic signals.