gebhart/patrepeval huggingface dataset:
Developing a method for vitellogenin quantification to investigate the reproductive investment in Gammarids (2010)

Reproductive success of organisms is related to the quantity and quality of eggs produced by females. Vitellogenin (Vtg), precursor molecule of vitellin that is the energy available for embryonic development in oviparous organisms, could be proposed as an indicator of maternal reproductive investment. Numerous strategies, such as enzyme-linked immunosorbent assays have been developed to characterise and quantify this protein particularly in vertebrates. On contrary, in invertebrates as non-decapod crustaceans few methods are available. These gaps mainly result from the low between-species cross-reactivity of antibodies in relation to phylogenetic distance and molecular divergence accumulated by proteins through animal evolution. This poster presents the development of a quantitative assay of vitellogenin in a widespread amphipod, Gammarus fossarum, using liquid chromatography tandem mass spectrometry (LC/MS/MS). This method offers the possibility to identify and quantify Vtg, based only on the quantification of specific peptides containing from 5 to 15 amino-acids. Our results show that LC/MS/MS is a robust and sensitive method for Vtg measurement in G. fossarum. Vtg changes in oocytes and embryos, in relation to the reproductive cycle and the development, have been characterized. Moreover, partial conservation between homologuous proteins in different evolutive lineages can persist. Therefore it should be possible to take advantage of peptidic motifs conservation to propose a transferable method across species. The present study showed that some peptides selected for Vtg measurement in G. fossarum could be equally used in other gammarid species, currently found in French aquatic ecosystems.
Small Caliber Compliant Vascular Grafts Based on Elastin-Like Recombinamers for in situ Tissue Engineering (2019)

Vascular disease is a leading cause of death worldwide, but surgical options are restricted by the limited availability of autologous vessels, and the suboptimal performance of prosthetic vascular grafts. This is especially evident for coronary artery by-pass grafts, whose small caliber is associated with a high occlusion propensity. Despite the potential of tissue-engineered grafts, compliance mismatch, dilatation, thrombus formation, and the lack of functional elastin are still major limitations leading to graft failure. This calls for advanced materials and fabrication schemes to achieve improved control on the grafts' properties and performance. Here, bioinspired materials and technical textile components are combined to create biohybrid cell-free implants for endogenous tissue regeneration. Clickable elastin-like recombinamers are processed to form an open macroporous 3D architecture to favor cell ingrowth, while being endowed with the non-thrombogenicity and the elastic behavior of the native elastin. The textile components (i.e., warp-knitted and electrospun meshes) are designed to confer suture retention, long-term structural stability, burst strength, and compliance. Notably, by controlling the electrospun layer's thickness, the compliance can be modulated over a wide range of values encompassing those of native vessels. The grafts support cell ingrowth, extracellular matrix deposition and endothelium development <i>in vitro</i>. Overall, the fabrication strategy results in promising off-the-shelf hemocompatible vascular implants for <i>in situ</i> tissue engineering by addressing the known limitations of bioartificial vessel substitutes.
CHARACTERISATION, RECOMBINANT EXPRESSION AND IMMUNOGENICITY OF BHLP29.7, AN OUTER MEMBRANE LIPOPROTEIN OF BRACHYSPIRA HYODYSENTERIAE (2006)

Swine dysentery (SD) is an important endemic infection in many piggeries, and control can be problematic. In this study, the gene encoding a 29.7 kDa outer membrane lipoprotein of the causative intestinal spirochaete Brachyspira hyodysenteriae, was identified and sequenced. An 816 bp hypothetical open reading frame (ORF) was identified, with a potential ribosome binding site, and putative -10 and -35 promoter regions upstream from the start of the ORF. The 29.7 kDa outer membrane lipoprotein was designated Bhlp29.7 and the encoding gene named bhlp29.7.&#13;\n&#13;\nThe amino acid sequence of Bhlp29.7 included a 19 residue hydrophobic signal peptide, incorporating a potential signal peptidase cleavage site and membrane lipoprotein lipid attachment site. In silico analysis of this protein together with lipidation studies further supported its probable outer membrane localisation. Comparison of the Bhlp29.7 sequence with public sequence databases showed that it had up to 40% similarity with the D-methionine substrate-binding outer membrane lipoprotein (MetQ) of a number of bacterial pathogens. The Bhlp29.7 gene was detected in all 48 strains of B. hyodysenteriae examined, and in Brachyspira innocens strain B256T, but not in 10 other strains of B. innocens or in 42 strains of other Brachyspira spp. The gene was sequenced from B. innocens strain B256T and from 11 strains of B. hyodysenteriae. The B. hyodysenteriae genes shared 97.9-100% nucleotide sequence identity and had 97.5-99.5% identity with the gene of B. innocens strain B256T. The Bhlp29.7 gene was subsequently cloned and expressed as a histidine fusion protein in an Escherichia coli expression system.&#13;\n&#13;\nAn ELISA test using recombinant his-tagged Bhlp29.7 (His6-Bhlp29.7) as the detecting antigen was developed and evaluated. The threshold value of the test was chosen to provide a highly stringent assessment of the disease status of a herd. The sensitivity and specificity of the test was 100%. When the test was applied to sera from eight herds with suspected SD, four gave ELISA values indicating that the herds were diseased. The remaining four herds gave ELISA values below the threshold value. These results indicated that the Bhlp29.7-ELISA was useful as an indirect test for exposure of a herd to B. hyodysenteriae and may be a helpful complement to current methods of SD diagnosis.&#13;\n&#13;\nRecombinant His6-Bhlp29.7 was evaluated as a vaccine subunit for prevention of SD. The His6-Bhlp29.7 was shown to be immunogenic in mice following two intramuscular injections. Vaccination of mice with His6-Bhlp29.7 provided full protection after oral challenge with B. hyodysenteriae. In two experiments, intramuscular and oral vaccination of pigs with the His6-Bhlp29.7 resulted in a 50% reduction in incidence of SD compared to unvaccinated control pigs (P=0.047). This is the first subunit vaccine shown to provide pigs with protection from SD. Further work is needed to optimise delivery routes and adjuvants for commercial development of the vaccine.
The Cognitive Agents Toolbox (CAT) - programmingautonomous vehicles (2009)

Maple syrup urine disease is a rare inborn error of amino acid metabolism involving catabolic pathway of the branched-chain amino acids. This disease, if left untreated, may cause damage to the brain and may even cause death. These patients typically present with distinctive maple syrup odour of sweat and urine. Patients typically present with skin and urine smelling like maple syrup. Here we describe a case with relevant magnetic resonance imaging findings and confirmatory biochemical findings.
Muscarinic receptors: their distribution and function in body systems, and the implications for treating overactive bladder (2006)

1. The effectiveness of antimuscarinic agents in the treatment of the overactive bladder (OAB) syndrome is thought to arise through blockade of bladder muscarinic receptors located on detrusor smooth muscle cells, as well as on nondetrusor structures. 2. Muscarinic M3 receptors are primarily responsible for detrusor contraction. Limited evidence exists to suggest that M2 receptors may have a role in mediating indirect contractions and/or inhibition of detrusor relaxation. In addition, there is evidence that muscarinic receptors located in the urothelium/suburothelium and on afferent nerves may contribute to the pathophysiology of OAB. Blockade of these receptors may also contribute to the clinical efficacy of antimuscarinic agents. 3. Although the role of muscarinic receptors in the bladder, other than M3 receptors, remains unclear, their role in other body systems is becoming increasingly well established, with emerging evidence supporting a wide range of diverse functions. Blockade of these functions by muscarinic receptor antagonists can lead to similarly diverse adverse effects associated with antimuscarinic treatment, with the range of effects observed varying according to the different receptor subtypes affected. 4. This review explores the evolving understanding of muscarinic receptor functions throughout the body, with particular focus on the bladder, gastrointestinal tract, eye, heart, brain and salivary glands, and the implications for drugs used to treat OAB. The key factors that might determine the ideal antimuscarinic drug for treatment of OAB are also discussed. Further research is needed to show whether the M3 selective receptor antagonists have any advantage over less selective drugs, in leading to fewer adverse events.
Enriching Search and Retrieval of Multimedia Information with DRM Services and Context-Based Content Adaptation (2008)

This paper presents a standards-based architecture for a complex and generic distributed multimedia scenario, which combines content search and retrieval, DRM, and context-based content adaptation together. The most innovative part of the proposed work comes from the integration of a flexible language for multimedia search based on MPEG Query Format (MPQF) standard with the application of video analysis algorithms for the automatic extraction of low-level features.
Decomposition techniques for optimal design-space exploration of streaming applications (2013)

Streaming data programs are an important class of applications, for which queueing network models are frequently available. While the design space can be large, decomposition techniques can be effective at design space reduction. We introduce two decomposition techniques called convex decomposition and unchaining and present implications for a biosequence search application.
Early Divergence in Neutrophil Apoptosis between Pathogenic and Nonpathogenic Simian Immunodeficiency Virus Infections of Nonhuman Primates (2008)

We used pathogenic and nonpathogenic simian models of SIV infection of Chinese and Indian rhesus macaque (RMs) and African green monkeys (AGMs), respectively, to investigate the relationship between polymorphonuclear neutrophil (PMN) death and the extent of viral replication and disease outcome. In this study, we showed that PMN death increased early during the acute phase of SIV infection in Chinese RMs and coincided with the peak of viral replication on day 14. The level of PMN death was significantly more severe in RMs that progressed more rapidly to AIDS and coincided with neutropenia. Neutropenia was also observed in Indian RMs and was higher in non-Mamu-A*01 compared with Mamu-A*01 animals. In stark contrast, no changes in the levels of PMN death were observed in the nonpathogenic model of SIVagm-sab (sabaeus) infection of AGMs despite similarly high viral replication. PMN death was a Bax and Bak-independent mitochondrial insult, which is prevented by inhibiting calpain activation but not caspases. We found that BOB/GPR15, a SIV coreceptor, is expressed on the PMN surface of RMs at a much higher levels than AGMs and its ligation induced PMN death, suggesting that SIV particle binding to the cell surface is sufficient to induce PMN death. Taken together, our results suggest that species-specific differences in BOB/GPR15 receptor expression on PMN can lead to increased acute phase PMN death. This may account for the decline in PMN numbers that occurs during primary SIV infection in pathogenic SIV infection and may have important implications for subsequent viral replication and disease progression.
A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. (2014)

Synthetic genetic systems share resources with the host, including machinery for transcription and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors and activators) that enable switching between different promoters and modulation of activity. Here, we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be co-expressed to function. The DNA-binding loop is encoded in a C-terminal 285-aa 'σ fragment', and fragments with different specificity can direct the remaining 601-aa 'core fragment' to different promoters. Using these parts, we have built a resource allocator that sets the core fragment concentration, which is then shared by multiple σ fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional capacity available to a synthetic system. Further, positive and negative regulation is implemented using a 67-aa N-terminal 'α fragment' and a null (inactivated) σ fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via different schemes, which we demonstrate by building a system which adjusts promoter activity to compensate for the difference in copy number of two plasmids.
Differential presentation of hepatitis B S-preS(2) particles and peptides by macrophages and B-cell like antigen-presenting cells. (1991)

Different cell types, including dendritic cells, macrophages and Ia+ B cells, have been described to present soluble antigen (Ag) to T-cell hybridomas. However, it is still not clear whether these different cell types can act as antigen-presenting cells (APC) for complex and insoluble Ag such as viral particles. Using yeast recombinant hepatitis B S-preS(2)-containing particles, T-cell hybridomas were generated and used as a tool to study processing and presentation of antigen. Different types of APC were compared in regard to their capacity to process and present the protein-lipid composed S-preS(2) particles and the thereof derived T-cell epitope containing peptides by different types of APC. While a S-preS(2)-derived T-cell epitope containing peptide, which does not require processing, could be presented both by macrophage and B-cell like APC, the presentation of S-preS(2) particles required the presence of macrophages. The fact that B-cell like APC and macrophages behave differently with regard to the presentation of S-preS(2) particles suggest that the uptake and/or processing of this type of Ag by B-cell like APC and macrophages is different.
An accelerated BEM formulation for the forward problem solution of ESI using realistic head models (2004)

In this study, the forward problem of electrical source imaging (ESI) is solved using the boundary element method (BEM) with realistic head models. The realistic model consists of scalp, skull, CSF, brain and eyes. To get more accurate results quadratic elements are used in the meshes and a new method is proposed for the generation of the quadratic mesh. An accelerated method is proposed for the solution of the potential field.
Abstract 4545: Positron emission tomography (PET) of TSPO expression in preclinical models of human cancer (2012)

Abstract There is a critical need to develop and rigorously validate molecular imaging biomarkers to aid diagnosis and characterization of human cancer. Elevated expression of translocator protein (TSPO) has been shown to predict disease progression and aggressive, invasive behavior in a variety of solid tumors. Thus, noninvasive molecular imaging of TSPO expression could form the basis of a novel, predictive cancer imaging biomarker. In quantitative preclinical PET studies, we have evaluated a high-affinity pyrazolopyrimidinyl TSPO imaging ligand ([18F]DPA-714) and an aryloxyanilide-based TSPO imaging ligand ([18F]PBR06), as translational probes for quantification of TSPO levels in glioma, breast cancer, and colorectal cancer. In these studies, glioma-bearing rats or genetically engineered mice bearing spontaneously arrising breast or colorectal cancers were imaged with TSPO PET ligands in a microPET system. Dynamic images were acquired simultaneously upon injection of radioactive TSPO PET ligands. Arterial blood was collected to derive the input function (AIF), with HPLC radiometabolite analysis performed upon select samples for AIF correction. Compartmental modeling was performed using the corrected AIF. Immediately following imaging, tumor and healthy surrounding tissues were harvested for validation by western blotting and immunohistochemistry. Our results illustrate the feasibility of using TSPO PET ligands for visualization of TSPO-expressing tumors of the brain, breast and colon. Importantly, both [18F]DPA-714 and [18F]PBR06 appear suitable for quantitative assay of tumor TSPO levels in vivo. Given the relationship between elevated TSPO levels and poor outcome in oncology, these studies suggest the potential of these imaging agents to serve as a novel predictive cancer imaging biomarkers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4545. doi:1538-7445.AM2012-4545
Topological Properties (2006)

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On the Feasibility of Remote Driving Application over Dense 5G Roadside Networks (2019)

Remote driving (RD) is a critical backup option for an autonomous vehicle when it faces an unexpected situation on the road. Fifth generation (5G) mobile communication is a key enabler of RD providing link between the remote operator and the vehicle. There are stringent requirements in terms of coverage, data rate and latency for RD application. In this paper, a feasibility study at the radio access network level for the radio coverage conditions that are required for RD application is carried out. The study considers RD over three carriers including 2.6 GHz, 5 GHz and 28 GHz. A ray tracing software is used for the channel pathloss computation. The RD provision in terms of coverage and rate statistics is analysed for these frequency carriers. The role of interference is also investigated. The performance statistics are aggregated using a large number of realistic vehicular routes created using Google Directions APIs. It is shown that the provision of RD can not be guaranteed over a wide network area especially in high-load/high-interference conditions and it is more feasible to define the RD application for specific roads.
[Immunology in medical practice. XXV. Use of dendritic cells in the immunotherapy of cancer]. (1999)

Dendritic cells are among the most efficient antigen-presenting cells of our immune system and they play a crucial role in immunity reactions such as the activation of T and B cells and the induction or maintenance of tolerance. New culture methods allow us to generate dendritic cells in sufficient numbers for further studies and for the preparation of antigen-loaded dendritic cells for clinical application in cancer patients. In animal studies immunization with antigen-loaded dendritic cells offered protection from growth of injected tumour cells. In experimental clinical studies in cancer patients with e.g. metastatic renal carcinoma, melanoma and B cell lymphoma some lasting remissions were observed after administration of antigen-loaded dendritic cells. Side effects were minor. Unanswered questions on tumour vaccines with antigen-loaded dendritic cells concern specific matters, such as optimal culture methods and antigen loading, and general matters, such as dose, frequency, duration and route of administration. Also, no method is currently available by which the in vivo immune response can be measured accurately.
Motion-Copying System Using FPGA-based Friction-Free Disturbance Observer (2014)

A motion-copying system is characterized by its ability to preserve and reproduce the motions of a human operator. The performance of a motion-copying system based on bilateral control is affected by friction and harmonic disturbances. To improve the performance of this system, we propose a friction-free disturbance observer with a dither signal for both motion-saving and motion-loading systems. The dither signal reduces the effect of friction, while the friction-free disturbance observer suppresses oscillatory disturbances in force estimation. Moreover, the friction-free disturbance observer achieves effective harmonic disturbance suppression in force estimation. All control algorithms are implemented in a field-programmable gate array to achieve a short sampling period that reduces the controller execution time and enables a wider force-sensing bandwidth. The effectiveness of the proposed method is verified by experimental results.
Nucleobase Modified Adefovir (PMEA) Analogues as Potent and Selective Inhibitors of Adenylate Cyclases from Bordetella pertussis and Bacillus anthracis (2018)

A series of 13 acyclic nucleoside phosphonates (ANPs) as bisamidate prodrugs was prepared. Five compounds were found to be non-cytotoxic and selective inhibitors of Bordetella pertussis adenylate cyclase toxin (ACT) in J774A.1 macrophage cell-based assays. The 8-aza-7-deazapurine derivative of adefovir (PMEA) was found to be the most potent ACT inhibitor in the series (IC<sub>50</sub> =16 nm) with substantial selectivity over mammalian adenylate cyclases (mACs). AC inhibitory properties of the most potent analogues were confirmed by direct evaluation of the corresponding phosphonodiphosphates in cell-free assays and were found to be potent inhibitors of both ACT and edema factor (EF) from Bacillus anthracis (IC<sub>50</sub> values ranging from 0.5 to 21 nm). Moreover, 7-halo-7-deazapurine analogues of PMEA were discovered to be potent and selective mammalian AC1 inhibitors (no inhibition of AC2 and AC5) with IC<sub>50</sub> values ranging from 4.1 to 5.6 μm in HEK293 cell-based assays.
Flow Fairness With Core-Stateless Resource Sharing in Arbitrary Topology (2022)

Resource sharing is of utmost importance in networking environments where substantial overprovisioning is economically infeasible. Different centralized solutions have recently been proposed for Wide Area Networks, Access Aggregation Networks and other closed networking domains, relying on different ideas from exploiting the capabilities of Software Defined Networking for dynamically allocating bandwidth among flows or other traffic aggregates, to moving bottlenecks from the network to a single location (e.g., a gateway node). In contrast to centralized solutions, core-stateless resource sharing proposals have also emerged, solving the resource allocation problem in a distributed way. In this paper, we focus on the network-wide behavior of a recent core-stateless resource sharing proposal called Per Packet Value (PPV). In PPV, each traffic aggregate is represented by a distribution of values carried by the packets. The distribution is used to express the resource sharing policy. We provide a theoretical analysis of PPV and show that it solves the generalized max-min fair allocation problem in arbitrary topology. PPV has provable convergence in case of both scalable and non-scalable congestion control behaviors. To validate the theoretical results under various network conditions, thorough simulations have been carried out in networks with real-world topology. The method assumes congestion controlled sources since non-responsive UDP flows can generate dead packets taking bandwidth away from well-behaving flows. To remedy the problem of dead packets, we propose a lightweight core-stateless policer method that can autonomously rule the resource usage of unfriendly flows, reducing the effect of dead packets in the system.