gebhart/patrepeval huggingface dataset:
Fully Distributed Cooperative Charging for Plug-in Electric Vehicles in\n Constrained Power Networks (2018)

Plug-in Electric Vehicles (PEVs) play a pivotal role in transportation\nelectrification. The flexible nature of PEVs' charging demand can be utilized\nfor reducing charging cost as well as optimizing the operating cost of power\nand transportation networks. Utilizing charging flexibilities of geographically\nspread PEVs requires design and implementation of efficient optimization\nalgorithms. To this end, we propose a fully distributed algorithm to solve the\nPEVs' Cooperative Charging with Power constraints (PEV-CCP). Our solution\nconsiders the electric power limits that originate from physical\ncharacteristics of charging station, such as on-site transformer capacity\nlimit, and allows for containing charging burden of PEVs on the electric\ndistribution network. Our approach is also motivated by the increasing load\ndemand at the distribution level due to additional PEV charging demand. Our\nproposed approach distributes computation among agents (PEVs) to solve the\nPEV-CCP problem in a distributed fashion through an iterative interaction\nbetween neighboring agents. The structure of each agent's update functions\nensures an agreement on a price signal while enforcing individual PEV\nconstraints. In addition to converging towards the globally-optimum solution,\nour algorithm ensures the feasibility of each PEV's decision at each iteration.\nWe have tested performance of the proposed approach using a fleet of PEVs.\n
Immunotherapy with VGX-3100 (HPV16 and HPV18 plasmids) + INO-9012 (DNA encoding IL-12) in human papillomavirus (HPV) associated head and neck squamous cell carcinoma (HNSCCa): interim safety and immunogenicity results (2015)

Meeting abstracts Oropharyngeal HNSCCa is frequently associated with HPV infection. DNA-based Immunotherapy with plasmids encoding HPV16 and HPV18 E6/E7 antigens has been shown to generate robust immune responses in women with HPV-driven high-grade cervical dysplasia. We hypothesize that HPV-
Minimizing the Contribution of Enterohepatic Recirculation to Clearance in Rat for the NCINI Class of Inhibitors of HIV (2014)

A scaffold replacement approach was used to identifying the pyridine series of noncatalytic site integrase inhibitors. These molecules bind with higher affinity to a tetrameric form compared to a dimeric form of integrase. Optimization of the C6 and C4 positions revealed that viruses harboring T124 or A124 amino acid substitutions are highly susceptible to these inhibitors, but viruses having the N124 amino acid substitution are about 100-fold less susceptible. Compound 20 had EC50 values <10 nM against viruses having T124 or A124 substitutions in IN and >800 nM in viruses having N124 substitions. Compound 20 had an excellent in vitro ADME profile and demonstrated reduced contribution of biliary excretion to in vivo clearance compared to BI 224436, the lead compound from the quinoline series of NCINIs.
Specific T cells targeting Staphylococcus aureus fibronectin‐binding protein 1 induce a type 2/type 1 inflammatory response in sensitized atopic dermatitis patients (2021)

We demonstrate that FBP1 contains immunodominant peptides that induce a specific pro-inflammatory T helper cell response with increased Th2 levels that can drive an allergic inflammation in sensitized AD patients.
OP019 In faecal microbiota transplantation (FMT) for ulcerative colitis, fusobacterium is associated with lack of remission, while metabolic shifts to starch degradation and short-chain fatty acid production are associated with remission (FOCUS study) (2018)

In the FOCUS study, multidonor FMT was effective in the treatment of active ulcerative colitis (UC).1 Here we characterise the bacterial taxonomic and functional changes associated with outcome. A total of 314 fecal and 160 colonic biopsy samples were collected at specific intervals from 70 patients. A total of 113 fecal samples were collected from the 14 individual donors and 21 multidonor batches. DNA and RNA were extracted, RNA converted to cDNA, then 16S rRNA gene sequencing performed using 2x300 bp Illumina MiSeq chemistry. Sequences were analysed using MOTHUR. Shotgun metagenomics was performed on 285 fecal samples using 2x250bp HiSeq 2500 chemistry, with samples analysed using MetaPhlAn2 and HUMANn2 for taxonomic and functional inferences, respectively. Patients: α-Diversity consistently increased following FMT across all datasets (fecal 16S DNA and RNA/cDNA, colonic mucosa 16S DNA and RNA/cDNA, shotgun metagenomics—taxonomic; p < 0.005). α-Diversity saturated by Week 4 with trends to greater α-diversity with remission. β-Diversity across all datasets showed FMT significantly shifted global microbial composition (t = 2.85, p = 0.001, df=104; Figure 1), from Bacteroides to Prevotella dominance. Fusobacterium was most consistently associated with lack of remission (LDA=3.34, p = 0.028), as were Sutterella, Veillonella, and Haemophilus. There was less consistency in taxa associated with remission (most commonly Firmicutes members, e.g. Clostridium XVIII, Ruminococcus, Lachnospiraceae). High concordance was observed between fecal and colonic mucosal microbiota. Donors: The presence of a Streptococcus OTU was associated with ineffective batches. Metabolic function: Fecal shotgun metagenomics demonstrated FMT-associated shifts in bacterial metabolic function—remission was associated with starch degradation pathways and SCFA production, while lack of remission was associated with heme biosynthesis. Biopsy PICRUSt data corroborated the association of SCFA production with remission. Taxa contributing to beneficial pathways included Eubacterium, Ruminococcus, Lachnospiraceae, and Roseburia. PCA of transformed relative abundances inferred from shotgun metagenomics. FMT treatment consistently increased diversity and changed microbial composition. Fusobacterium appears critical in relation to outcomes of FMT for UC. Changes in bacterial metabolic activity may also play a key role in FMT success or failure. These specific bacterial findings may have important aetiological relevance, help identify suitable donors and patients for treatment, and guide refinement of future bacterial therapy. 1. Paramsothy S. Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet, 2017;389:1218–28.
Impact of Substituents in Tumor Uptake and Fluorescence Imaging Ability of Near‐Infrared Cyanine‐like Dyes (2015)

This report presents a simple strategy to introduce various functionalities in a cyanine dye (bis-indole-N-butylsulfonate-polymethine bearing a fused cyclic chloro-cyclohexene ring structure), and assess the impact of these substitutions in tumor uptake, retention and imaging. The results obtained from the structural activity relationship (SAR) study demonstrate that certain structural features introduced in the cyanine dye moiety make a remarkable difference in tumor avidity. Among the compounds investigated, the symmetrical CDs containing an amino-phenyl thioether group attached to a cyclohexene ring system and the two N-butyl linkers with terminal sulfonate groups in benzoindole moieties exhibited excellent tumor imaging ability in BALB/c mice bearing Colon26 tumors. Compared to indocyanine green (ICG), approved by FDA as a blood pooling agent, which has also been investigated for the use in tumor imaging, the modified CD selected on the basis of SAR study produced enhanced uptake and longer retention in tumor(s). A facile approach reported herein for introducing a variety of functionalities in tumor-avid CD provides an opportunity to create multi-imaging modality agent(s). Using a combination of mass spectrometry and absorbance techniques, the photobleaching of one of the CDs was analyzed and significant regioselective photooxidation was observed.
Pseudo‐random Gaussian distribution through optimised LFSR permutations (2015)

Efficient hardware solutions to generate Gaussian‐distributed random numbers are required in many applications. Linear feedback shift registers (LFSRs) are a low‐complexity implementation of an approximated uniform pseudo‐random distribution: multiple LFSRs can be used in combination to approximate a Gaussian distribution with a low complexity cost. The technique proposed in this work exploits the same principle but relies on a single LFSR and ad‐hoc permutations of its bits to obtain an accurate approximation of a Gaussian distribution with low maximum autocorrelation, leading to a very low complexity implementation of a Gaussian pseudo‐random number generator.
10 Gbit/s clock recovery circuit using temperaturecompensated dielectric resonator filter (1995)

A clock recovery circuit using a dielectric resonator filter (DRF) for 10 Gbit/s data regeneration is presented, where a temperature compensation technique was for the first time employed to keep the relative phase between the input data and clock to the decision circuit as constant as possible. The experimental results showed an output clock phase variation of &lt;±6 deg over the operating temperature range from 0 – 75°C and the measured maximum RMS jitters of &lt;2 ps with the resonance detunings of up to ±10 MHz.
Meta‐analysis of clinical trials as a scientific discipline. I: Control of bias and comparison with large co‐operative trials (1987)

Meta-analysis is an important method of bridging the gap between undersized randomized control trials and the treatment of patients. However, as in any retrospective study, the opportunities for bias to distort the results are widespread. Attempts must be made to introduce the controls found in prospective studies by blinding the selection of papers and extraction of data and making blinded duplicate determinations. Informal and personalized methods of obtaining data are probably more liable to error and bias than employing only published data. Publication bias is a serious problem requiring further research. There also need to be more comparisons of meta-analysed small studies with large co-operative trials.
Semiparallel deep neural network hybrid architecture: first application on depth from monocular camera (2018)

Deep neural networks have been applied to a wide range of problems in recent years. Convolutional neural network is applied to the problem of determining the depth from a single camera image (monocular depth). Eight different networks are designed to perform depth estimation, each of them suitable for a feature level. Networks with different pooling sizes determine different feature levels. After designing a set of networks, these models may be combined into a single network topology using graph optimization techniques. This “semiparallel deep neural network (SPDNN)” eliminates duplicated common network layers and can be further optimized by retraining to achieve an improved model compared to the individual topologies. Four SPDNN models are trained and have been evaluated at two stages on the KITTI dataset. The ground truth images in the first part of the experiment are provided by the benchmark, and for the second part, the ground truth images are the depth map results from applying a state-of-the-art stereo matching method. The results of this evaluation demonstrate that using postprocessing techniques to refine the target of the network increases the accuracy of depth estimation on individual mono images. The second evaluation shows that using segmentation data alongside the original data as the input can improve the depth estimation results to a point where performance is comparable with stereo depth estimation. The computational time is also discussed in this study.
Observations of Λ b 0  → ΛK +π− and Λ b 0  → ΛK + K − decays and searches for other Λ b 0 and Ξ b 0 decays to Λh + h′− final states (2016)

A search is performed for the charmless three-body decays of the 0 b and 0 b baryons to the final states h + h -, where h ( ) = or K. The analysis is based on a data sample, corresponding to an integrated luminosity of 3 fb -1 of pp collisions, collected by the LHCb experiment. The 0 b K + -and 0 b K + K -decays are observed for the first time and their branching fractions and CP asymmetry parameters are measured. Evidence is seen for the 0 b + -decay and limits are set on the branching fractions of 0 b baryon decays to the h + h -final states.
CCR6 and NK1.1 distinguish between IL‐17A and IFN‐γ‐producing γδ effector T cells (2009)

Gammadelta T cells are a potent source of innate IL-17A and IFN-gamma, and they acquire the capacity to produce these cytokines within the thymus. However, the precise stages and required signals that guide this differentiation are unclear. Here we show that the CD24(low) CD44(high) effector gammadelta T cells of the adult thymus are segregated into two lineages by the mutually exclusive expression of CCR6 and NK1.1. Only CCR6+ gammadelta T cells produced IL-17A, while NK1.1+ gammadelta T cells were efficient producers of IFN-gamma but not of IL-17A. Their effector phenotype correlated with loss of CCR9 expression, particularly among the NK1.1+ gammadelta T cells. Accordingly, both gammadelta T-cell subsets were rare in gut-associated lymphoid tissues, but abundant in peripheral lymphoid tissues. There, they provided IL-17A and IFN-gamma in response to TCR-specific and TCR-independent stimuli. IL-12 and IL-18 induced IFN-gamma and IL-23 induced IL-17A production by NK1.1+ or CCR6+ gammadelta T cells, respectively. Importantly, we show that CCR6+ gammadelta T cells are more responsive to TCR stimulation than their NK1.1+ counterparts. In conclusion, our findings support the hypothesis that CCR6+ IL-17A-producing gammadelta T cells derive from less TCR-dependent selection events than IFN-gamma-producing NK1.1+ gammadelta T cells.
Control design, simulation and validation of a turbo-machinery auxiliary plant (2016)

In the oil and gas industry, the testing of auxiliary lubrication plants represents an important preliminary activity before the whole turbo machinery train (including the auxiliary lubrication plant) can be put in operation. Therefore, the employment of both efficient and accurate plant models becomes mandatory to synthesize satisfactory control strategies both for testing and normal operation purposes. For this reason, this paper focuses on the development of innovative real-time models and control architectures to describe and regulate auxiliary lubrication plants. In particular, according to the Bond-Graph modelling strategy, a novel lumped parameter model of the lube oil unit has been developed to properly optimize the behaviour of this unit if it is controlled. The code has been compiled and uploaded on a commercial real-time platform, employed to control the pressure control valve of the physical plant, for which a new controller has been developed. The comparison between the data obtained from the simulated system and acquired from the physical plant shows good agreement and the good performance and reliability of the proposed model and control strategy. The modelling approach and the control strategy have been developed in collaboration with GE Nuovo Pignone S.p.a. while the experimental data were acquired in a plant located in Ptuj (Slovenia).
Abstract PR5: Treatment of ovarian cancer with targeted tumor-penetrating siRNA nanocomplexes (2012)

Abstract Whole-genome analysis of cancer samples is identifying many potential therapeutic targets, by virtue of their being frequently mutated or functionally essential in specific types of cancer. However, we lack efficient ways to test the therapeutic benefit of modulating targets in vivo. RNAi offers one potential solution; however, approaches to deliver siRNA in vivo have been challenging due to their susceptibility to serum nucleases, endosomal entrapment, and stimulation of innate immunity. Furthermore, nanoparticle- and antibody-based siRNA delivery approaches have historically suffered from limited tumor penetration and low transvascular transit, thereby limiting the applicability of parenchymal siRNA targets. Here we describe a tumor penetrating nanocomplex (TPN) comprised of siRNA complexed to a tandem tumor-penetrating and membrane-translocating peptide, which enables the homing of siRNA deep into tumor parenchyma. Upon complexation with siRNA, the resulting nanocomplex is stable, non-immunostimulatory, displays homing peptides in a multivalent fashion that increases their binding avidity and delivers siRNA to the cytosol of tumor cells through receptor-specific interactions and membrane translocation. Upon systemic administration into mice, this nanocomplex penetrates into the parenchyma of metastatic peritoneal tumors and silences target genes in cells of interest in a receptor-specific manner. We employed TPNs in vivo to evaluate ID4, a novel candidate oncogene in ovarian cancer, which we identified by combining genome-scale RNAi screening of cancer cell lines with genome-scale sequence analysis of patient tumors. We show that treatment of tumor-bearing mice with ID4-specific TPNs suppresses tumor growth and significantly improved survival. These findings provide a framework for the identification, credentialing, and understanding of novel cancer targets as well as validating a specific therapeutic target in ovarian cancer. This abstract is also presented as Poster B2. Citation Format: Yin Ren, Hiu Wing Cheung, Ronny Drapkin, David Root, Justin Lo, Valentina Fogal, Erkki Ruoslahti, William Hahn, Sangeeta Bhatia, Geoffrey von Maltzahn, Amit Agrawal, Glenn Cowley, Barbara Weir, Jesse Boehm, Pablo Tamayo, Jill Mesirov, Alison Karst. Treatment of ovarian cancer with targeted tumor-penetrating siRNA nanocomplexes [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr PR5.
ChemInform Abstract: Efficient Synthetic Routes to Fluorinated Isosteres of Inositol and Their Effects on Cellular Growth. (1990)

Abstract As reported in a previous work, quebrachitol can be transformed in a two‐step sequence to the monofluoro product (I).
Improved Data-Aided Channel Estimation in LTE PUCCH Using a Tensor Modeling Approach (2010)

In 3rd. Generation Partnership Project (3GPP) Long Term Evolution (LTE) systems, when no resources has been assigned in the uplink to a given user, the control information associated with Layers 1 and 2 in the protocol stack is conveyed back to the LTE base station (also known as eNodeB) through the so-called Physical Uplink Control Channel (PUCCH). In this work we consider the Format 2 of LTE PUCCH which conveys information about the channel status. At the eNodeB, conventional receivers generally resort to reference signals (RS), or pilot symbols, to perform channel estimation prior to symbol detection. In this paper, we propose a tensor modeling approach for a Data-Aided (DA) channel estimation in PUCCH. First, we formulate the practical channel estimation problem in PUCCH using the Parallel Factor (PARAFAC) tensor model. Based in this model, we resort to the Alternating Least Squares (ALS) algorithm as a DA-based channel estimator. Contrary to conventional RS-based channel estimation operating only on reference signals, the proposed algorithm also simultaneously exploits the energy of the data symbols of all the users, which is contained in PUCCH slots in order to iteratively estimate the user channel coefficients. As will be shown in our simulation results, improved channel estimation accuracy is obtained.
Differential IL-17 Production and Mannan Recognition Contribute to Fungal Pathogenicity and Commensalism (2010)

In this study, we present evidence of differential Th17 responses in human monocyte-derived dendritic cells exposed to the pathogenic Candida albicans or the nonpathogenic Saccharomyces cerevisiae. We use different forms of the microorganisms, cells, hyphae, and spores, as a toolbox to dissect the role of surface mannan in the fungal immune response. In contrast to the S. cerevisiae yeast cell-induced Th1 response, dendritic cells stimulated with spores or C. albicans hyphae induce cellular responses shifted toward Th17 differentiation. The differential recognition of specific mannan structures is the master regulator of the discrimination between harmful and harmless fungi. The switch between spores and yeast is crucial for the commensalism of S. cerevisiae and depends on the use of a different receptor repertoire. Understanding the role of cell wall recognition during infection might lead to understanding the boundaries between safety and pathogenicity.
Silencing of the tRNA Modification Enzyme Cdkal1 Effects Functional Insulin Synthesis in NIT-1 Cells: tRNALys3 Lacking ms2- (ms2t6A37) is Unable to Establish Sufficient Anticodon:Codon Interactions to Decode the Wobble Codon AAG (2021)

Human Genome Wide Association Studies found a significant risk of Type 2 Diabetes Mellitus (T2DM) in single nucleotide polymorphisms in the <i>cdkal1</i> gene. The <i>cdkal1</i> gene is remote from the insulin gene and with the surprising function of a specific tRNA modification. Population studies and case control studies acquired evidences of the connection between Cdkal1 protein and insulin production over the years. To obtain biochemical proofs directly linking potential SNPs to their roles in insulin production and availability is challenging, but the development of Cdkal1 knock out mice and knock out cell lines made it possible to extend our knowledge towards therapeutic field of diabetic research. Supporting the evidences, here we show that knock down of the <i>cdkal1</i> gene using small interfering and short hairpin RNA in the NIT-1 cell line, a β-cell line inducible for insulin resulted in reduced levels of <i>cdkal1</i> and mature insulin mRNAs, increased the level of precursor insulin mRNA, decreased Cdkal1 and insulin proteins, and diminished modification of tRNA<sup>Lys3</sup> from t<sup>6</sup>A<sub>37</sub> to ms<sup>2</sup>t<sup>6</sup>A<sub>37</sub>, the specified function of Cdkal1. tRNA<sup>Lys3</sup> lacking ms<sup>2</sup>- is incapable of establishing sufficient hydrogen bonding energy and hydrophobic stabilization to decode the wobble codon AAG.
Isolation of a Protein Containing Covalently Linked Large and Small Subunits of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase from Botryococcus braunii (1996)

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and a 66-kD protein were co-purified from solubilized microsomal preparations of the green alga Botryococcus braunii by Green A agarose, sucrose density gradient, MonoQ, and gel filtration. The 66-kD protein remained intact after 6 M urea treatment and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It could be detected in the soluble fraction of the cell-free extract but appeared to be more abundant in the microsomal preparations. It cross-reacted with antibodies raised against Rubisco holoenzyme, large and small subunits, indicating that the 66-kD protein contains both the large and the small subunits of Rubisco. The N-terminal amino acid sequence of this protein and that of a proteolytic fragment showed high homology with the mature Rubisco small subunits, and the sequence of another proteolytic fragment showed high homology with that of the Rubisco large subunit. It is concluded that the 66-kD protein is produced by cross-linking of large and small sub-units of Rubisco in the cell.