gebhart/patrepeval huggingface dataset:
Higher polymerase activity of a human influenza virus enhances activation of the hemagglutinin-induced Raf/MEK/ERK signal cascade (2007)

Influenza viruses replicate within the nucleus of infected cells. Viral genomic RNA, three polymerase subunits (PB2, PB1, and PA), and the nucleoprotein (NP) form ribonucleoprotein complexes (RNPs) that are exported from the nucleus late during the infectious cycle. The virus-induced Raf/MEK/ERK (MAPK) signal cascade is crucial for efficient virus replication. Blockade of this pathway retards RNP export and reduces virus titers. Hemagglutinin (HA) accumulation and its tight association with lipid rafts activate ERK and enhance localization of cytoplasmic RNPs. We studied the induction of MAPK signal cascade by two seasonal human influenza A viruses A/HK/218449/06 (H3N2) and A/HK/218847/06 (H1N1) that differed substantially in their replication efficiency in tissue culture. Infection with H3N2 virus, which replicates efficiently, resulted in higher HA expression and its accumulation on the cell membrane, leading to substantially increased activation of MAPK signaling compared to that caused by H1N1 subtype. More H3N2-HAs were expressed and accumulated on the cell membrane than did H1N1-HAs. Viral polymerase genes, particularly H3N2-PB1 and H3N2-PB2, were observed to contribute to increased viral polymerase activity. Applying plasmid-based reverse genetics to analyze the role of PB1 protein in activating HA-induced MAPK cascade showed that recombinant H1N1 virus possessing the H3N2-PB1 (rgH1N1/H3N2-PB1) induced greater ERK activation, resulting in increased nuclear export of the viral genome and higr virus titers. We conclude that enhanced viral polymerase activity promotes the replication and transcription of viral RNA leading to increased accumulation of HA on the cell surface and thereby resulting in an upregulation of the MAPK cascade and more efficient nuclear RNP-export as well as virus production.
Dynamic Reserve and Transmission Capacity Allocation in Wind-Dominated\n Power Systems (2020)

The large shares of wind power generation in electricity markets motivate\nhigher levels of operating reserves. However, current reserve sizing practices\nfail to account for important topological aspects that might hinder their\ndeployment, thus resulting in high operating costs. Zonal reserve procurement\nmitigates such inefficiencies, however, the way the zones are defined is still\nopen to interpretation. This paper challenges the efficiency of predetermined\nzonal setups that neglect the location of stochastic power production in the\nsystem, as well as the availability, cost and accessibility of flexible\ngenerating units. To this end, we propose a novel reserve procurement approach,\nformulated as a two-stage stochastic bilevel model, in which the upper level\nidentifies a number of contiguous reserve zones using dynamic grid partitioning\nand sets zonal requirements based on the total expected operating costs. Using\ntwo standard IEEE reliability test cases, we show how the efficient\npartitioning of reserve zones can reduce expected system cost and promote the\nintegration of stochastic renewables.\n
Scalable polylithic on-package integratable apparatus and method (2023)

Described is an apparatus which comprises: a first die including: a processing core; a crossbar switch coupled to the processing core; and a first edge interface coupled to the crossbar switch; and a second die including: a first edge interface positioned at a periphery of the second die and coupled to the first edge interface of the first die, wherein the first edge interface of the first die and the first edge interface of the second die are positioned across each other; a clock synchronization circuit coupled to the second edge interface; and a memory interface coupled to the clock synchronization circuit.
PMMA-Fe3O4 for internal mechanical support and magnetic thermal ablation of bone tumors (2022)

&lt;p&gt;Background: Minimally invasive modalities are of great interest in the field of treating bone tumors. However, providing reliable mechanical support and fast killing of tumor cells to achieve rapid recovery of physical function is still challenging in clinical works. &lt;/p&gt; &lt;p&gt;Methods: A material with two functions, mechanical support and magnetic thermal ablation, was developed from Fe3O4 nanoparticles (NPs) distributed in a polymethylmethacrylate (PMMA) bone cement. The mechanical properties and efficiency of magnetic field-induced thermal ablation were systematically and successfully evaluated in vitro and ex vivo. CT images and pathological examination were successfully applied to evaluate therapeutic efficacy with a rabbit bone tumor model. Biosafety evaluation was performed with a rabbit in vivo, and a cytotoxicity test was performed in vitro. &lt;/p&gt; &lt;p&gt;Results: An NP content of 6% Fe3O4 (PMMA-6% Fe3O4, mFe: 0.01 g) gave the most suitable performance for in vivo study. At the 56-day follow-up after treatment, bone tumors were ablated without obvious side effects. The pathological examination and new bone formation in CT images clearly illustrate that the bone tumors were completely eliminated. Correspondingly, after treatment, the tendency of bone tumors toward metastasis significantly decreased. Moreover, with well-designed mechanical properties, PMMA-6�3O4 implantation endowed tumor-bearing rabbit legs with excellent bio-mimic bone structure and internal support. Biosafety evaluation did not induce an increase or decrease in the immune response, and major functional parameters were all at normal levels. &lt;/p&gt; &lt;p&gt;Conclusion: We have presented a novel, highly efficient and minimally invasive approach for complete bone tumor regression and bone defect repair by magnetic thermal ablation based on PMMA containing Fe3O4 NPs; this approach shows excellent heating ability for rabbit VX2 tibial plateau tumor ablation upon exposure to an alternating magnetic field (AMF) and provides mechanical support for bone repair. The new and powerful dual-function implant is a promising minimally invasive agent for the treatment of bone tumors and has good clinical translation potential.&lt;/p&gt;
Research and Successful Field Application of Nanosilica System for Gas Shutoff in Horizontal Well (2022)

Abstract Innovative and cost-effective gas shutoff technologies are required to improve the oil recovery and avoid the problems associated with the unwanted gas production. A novel strong and stable material with controlled gelation time was developed to isolate gas production zones over a wide range of parameters including the temperature, pressure, injectivity duration, and flow rate. This paper details the nanosilica for gas shutoff from laboratory development to successful field treatment. The nanosilica technology is composed of modified nanosilica and an activator which is used to trigger the viscosity of the system. The gelation time and gel strength of the nanosilica in presence of different concentrations of the activator have been investigated. In addition, the impact of the temperature on the gelation time was examined. The gas shutoff field treatment was designed to prevent the gas production from horizontal oil well based on the results obtained in the laboratory at comparable conditions. Laboratory results revealed that the two-component system namely the modified nanosilica and the activator exhibits low viscosity i.e. 6 cp prior to the exposure to high temperature. Once the temperature is increased to certain values, the viscosity of the mixture will increase depending on the concentration of the activator such that the start point of colloid-gelling ranged from a few minutes to several hours at a given temperature. Thus, this fluid system can be placed as a single phase, low-viscosity solution into the targeted formation zones and subsequently gelled inside the formation resulting in complete plugging. For the job design, production logging tools were run on the E-coil string to detect the gas source and measure the bottomhole temperature required for the formulation of gas shutoff nanosilica, and also to measure the injection pressure to monitor the injectivity. The objective of this job is to isolate the 980 ft. of stand-alone screens. Results unveiled the great potential of nanosilica as a gas-shutoff approach to mitigate gas intrusion with a sustainable 65% gas reduction compared to pre-treatment results. The new trend of using eco-friendly and nanoscale particles in gas control applications is a breakthrough in the oil industry. Laboratory results and field data revealed that the nanosilica for gas shutoff was effective over a wide range of parameters including the temperature, pressure and permeability.
Synchronization Constraints for Interconnect Synthesis (2017)

Interconnect synthesis tools ease the burden on the designer by automatically generating and optimizing communication hardware. In this paper we propose a novel capability for FPGA interconnect synthesis tools that further simplifies the designer's effort: automatic cycle-level synchronization of data delivery. This capability enables the creation of interconnect with significantly reduced hardware cost, provided that communicating modules have fixed latency and do not apply upstream backpressure. To do so, the designer specifies constraints on the lengths, in clock cycles, of multi-hop logical communication paths. The tool then uses an integer programming-based method to insert balancing registers into optimal locations, satisfying the designer's constraints while minimizing register usage. On an example convolutional neural network application, the new approach uses 43% less area than a FIFO-based synchronization scheme.
AAV Based Ex Vivo Gene Therapy in Rabbit Adipose-derived Mesenchymal Stem/Progenitor Cells for Osteogenesis (2009)

To explore a new source of adult derived stem cells for musculoskeletal tissue repair and regeneration, we isolated rabbit adipose-derived mesenchymal stem/progenitor cells (rAMSCs) from adult rabbit adipose tissue. In vitro, the isolated cells were shown to possess the potential to differentiate into cells of mesenchymal lineages that include osteoblasts. The isolated cells were transduced with AAV2 vectors encoding eGFP, human BMP-2, and human TGF-￻ 1 genes prior to implantation into hind limb muscles of SCID mice to assess osteogenesis in vivo. The results showed that rAMSCs were more efficiently transduced with GFP by AAV2 than by AAV6. The AAV2-BMP2- and AAV-TGF-￻ 1- transduced rAMSCs showed efficient expression of BMP-2 and TGF-￻ 1 proteins in vitro. When the combination of AAV2-BMP2- and AAV-TGF-￻ 1-transduced rAMSCs were implanted into the thigh muscles of SCID mice, the cells osteogenically differentiated toward new bone formation at the implanted sites 15 days after implantation. This study demonstrates that rabbit adipose tissue contains cells with the potential to give rise to osteoblasts, and that the combination of AAV2-BMP-2- and AAV2-TGF-￻ 1-transduced rAMSCs may provide a novel strategy to enhance new bone formation in vivo in less than 3 weeks. In addition, the data suggest that the AAV2 vector is suitable for genetic engineering of rAMSCs.
Mixed Differential Privacy in Computer Vision (2022)

We introduce AdaMix, an adaptive differentially private algorithm for training deep neural network classifiers using both private and public image data. While pre-training language models on large public datasets has enabled strong differential privacy (DP) guarantees with minor loss of accuracy, a similar practice yields punishing trade-offs in vision tasks. A few-shot or even zero-shot learning baseline that ignores private data can outperform fine-tuning on a large private dataset. AdaMix incorporates few-shot training, or cross-modal zero-shot learning, on public data prior to private fine-tuning, to improve the trade-off. AdaMix reduces the error increase from the non-private upper bound from the 167-311\% of the baseline, on average across 6 datasets, to 68-92\% depending on the desired privacy level selected by the user. AdaMix tackles the trade-off arising in visual classification, whereby the most privacy sensitive data, corresponding to isolated points in representation space, are also critical for high classification accuracy. In addition, AdaMix comes with strong theoretical privacy guarantees and convergence analysis.
The Impact of Point-To-Point VSC-HVDC Protection on Short-Term AC System Voltage (2018)

Whilst point-to-point HVDC systems are presently protected from DC-side faults using circuit breakers at the AC-side of the converter stations, converters are unable to provide reactive power support to the AC system during the fault clearance. Implementing DC circuit breakers within the HVDC system could result in several benefits, including the near- continuous provision of reactive power to the AC systems. This paper compares HVDC system protection sequences using AC- side and DC-side protection, and evaluates the impact of these protection strategies on the AC voltage under varying AC-system configurations and varying power flow conditions.
A Context-aware Time Model for Web Search (2016)

In web search, information about times between user actions has been shown to be a good indicator of users' satisfaction with the search results. Existing work uses the mean values of the observed times, or fits probability distributions to the observed times. This implies a context-independence assumption that the time elapsed between a pair of user actions does not depend on the context, in which the first action takes place. We validate this assumption using logs of a commercial web search engine and discover that it does not always hold. For between 37% to 80% of query-result pairs, depending on the number of observations, the distributions of click dwell times have statistically significant differences in query sessions for which a given result (i) is the first item to be clicked and (ii) is not the first. To account for this context bias effect, we propose a context-aware time model (CATM). The CATM allows us (i) to predict times between user actions in contexts, in which these actions were not observed, and (ii) to compute context-independent estimates of the times by predicting them in predefined contexts. Our experimental results show that the CATM provides better means than existing methods to predict and interpret times between user actions.
Incentives for a Softwarization of Wind Park Communication Networks (2019)

Wind energy is one of the most attractive and one of the fastest growing sources of green energy in the world. With the expansion of wind parks, there is a growing need for an efficient coordination of the diverse energy production systems, as well as a tighter coupling between the production and the consumer side of the grid. Current grid operators have unnecessarily high costs due to the lack of an integrated management system toward a diverse set of proprietary network protocols, complex and error prone operation of the networks, as well as rigid security mechanisms. Network softwarization concepts, that is, SDN and NFV, offer great potential for reducing capital and operational expenditures by providing simplified network management and automated control. Recent works have demonstrated the feasibility of achieving stringent industrial-grade quality of service and fine grain security control with SDN and NFV. In this article, we provide an insight into wind park communication network requirements, analyze the technological benefits of the network softwarization, and demonstrate the economic profits in a case study of a typical Northwestern Europe wind park.
Phase I adoptive cellular therapy trial with ex-vivo stimulated autologous CD8+ T-cells against multiple targets (ACTolog IMA101) in patients with relapsed and/or refractory solid cancers. (2018)

TPS3106 Background: Adoptive cellular therapy (ACT) has demonstrated substantial clinical progresses in hematologic cancers; however, only a small proportion of solid tumor patients have benefited from these advances due to i) lack of suitable immunotherapy targets with high specificity in solid tumors, ii) frequent relapse following immunotherapy to single targets often associated with loss of target expression in the tumor. The ACTolog® concept, utilizing antigen specific T cells (IMA101) against targets identified by the Immatics’ proprietary XPRESIDENT® technology, is intended to overcome these limitations by addressing multiple novel tumor antigens per patient. One key defining feature in this trial is the generation of robust T cells, where autologous T cells are primed against the expressed ACTolog targets in the presence of IL-21 followed by HLA tetramer-guided cell sorting and rapid expansion. This process has been shown to result in higher frequencies of central memory T cells, extended in vivo persistence, and a more robust clinical response. Methods: This study is a first-in-human phase I trial in patients with relapsed or refractory solid tumors expressing up to 4 targets from a warehouse of 8 cancer targets in which autologous T-cell products are manufactured against the most relevant tumor target peptides for individual patients. Key eligibility criteria include: HLA-A*02:01 phenotype, qPCR biomarker positive from a tumor biopsy, RECIST v1.1 measurable lesions, and ECOG status 0 or 1. At baseline, patients will undergo leukapheresis to collect mononuclear cells for manufacturing of IMA101 cells. Patients will receive anti-cancer therapy during the production phase. IMA101 will be infused after lymphodepletion regimen followed by low dose IL2. The primary objective is to assess safety and tolerability of IMA101. Secondary endpoints include overall response rate, PFS and OS. The translational objective includes the assessment of in vivo persistence and ex vivo characterization of transferred T cells in addition to evaluation of target expression in tumors. Enrollment in the study is currently ongoing. Clinical trial information: NCT02876510.
Innovative High Performance Steel Bridge Girders (2001)

High performance steels (HPS) are providing new opportunities to design cost-effective steel bridges by exploiting the high strength, corrosion resistance, fracture toughness, and weldability of HPS. Under certain conditions, however, steel bridge designs may be controlled by design limits that are not influenced by steel strength, and the use of HPS may not be economical. Innovative bridge girders have been proposed to overcome these design limits. This paper focuses on I-shaped girders with corrugated webs and I-shaped girders with tubular flanges. Design criteria for these girders are proposed and limited design studies are presented.
Volatil organic compounds : a way to detect fungal development in indoor environments (2013)

Background : Fungi are common biocontaminants in closed environments able to induce respiratory diseases and degradation of substrates they colonize.However, as soon as they start to grow, fungi emit VOCs which arise from their metabolism or from the degradation of materials. Unlike spores, VOCs are dispersed in the environment and are not retained by substrates. Consequently, measuring these specific compounds should enable both the detection of early and hidden proliferations. However, until now, the use of VOCs as a fungal tracer has been limited by their low levels compared with those from materials and also by the lack of specificity of most of the VOCs emitted. Aims :The aim of this study consists on determining if there are specific chemical emissions of fungal growth. To achieve this, chemical emissions from sterile products and those contaminated artificially by molds were analyzed using a descriptive statistical method. Methods :Three fungal strains frequently isolated in indoor environments were employed.Two types of products were used as growth substrates: a control substrate consists on fiberglass and five commercial materials frequently encountered in indoor environments. The VOC are sampled on adsorbent tube and analyzed by GC/MS. Results : The statistical analysis used, Principal Component Analysis, considers the chromatograms of each type of substrate without prejudging compounds. This analysis, applied to each product’s emissions, enabled to differentiate contaminated substrates from sterile ones. Furthermore comparison of ion fragments from chemical emissions between contaminated and sterile products enabled to determinate 59 ion fragments responsible of the discrimination.This VOC fingerprint of fungal growth has been tested on samples from 12 dwellings and permitted to detect the 7 contaminated ones. Conclusions :Despite the low emission rates, this study proves that the emission of specific VOC enables to detect the presence of an active fungal development in indoor environments even in the case of hidden contamination.
The Ability of Protein Tyrosine Phosphatase SHP-1 to Suppress NF κ B Can Be Inhibited by Dominant Negative Mutant of SIRP α (2004)

In contrast with hematopoietic cells and fibroblasts, which express mainly one form of protein tyrosine phosphatase (PTP) SHP-1 or SHP-2, epithelial cells like A431, HeLa, and 293 express both forms of PTP. These two PTP regulate NFkappaB activity differently; SHP-1 inhibits and SHP-2 stimulates NFkappaB activation. In epithelial cells the process of NFkappaB activation depends on the combination of two PTP activities. The activity of PTP SHP-1 dominates in this tandem according to our data. The signal regulatory protein (SIRPalpha) is the adapter and the substrate of PTP SHP-1 and SHP-2. We investigated the role of SIRPalpha and its dominant negative mutant in PTP activities in 293 cells. The overexpression of wild-type SIRPalpha suppresses the activities of both PTP, but has a stronger effect on PTP SHP-2, especially when this protein is overexpressed in 293 cells. In contrast with wild-type SIRPalpha, its dominant negative mutant acts predominantly against PTP SHP-1, and can be detected in the complex with PTP SHP-1. The expression of dominant negative mutant of SIRPalpha has an effect similar to the expression of dominant negative PTP SHP-1 in the process of NFkappaB activation.
Increasing the Speed of EELS/EDS Mapping Through Dynamic/Adaptive Sampling Methodologies (2018)

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GPU implementations of deflate encoding and decoding (2022)

Summary Deflate coding is a very popular lossless data compression method used in zlib, gzip (GNU zip), and zip, which performs the LZSS compression algorithm with Huffman coding. Deflate encoding and decoding involve sequential operations and their parallel acceleration using a GPU is quite hard. The main purpose of this paper is to present GPU implementations for encoding and decoding of Deflate coding. For efficient GPU implementations of Deflate coding, we have used multiple small hash tables for finding matching subsequences in the dictionary by multiple threads in parallel and applied the Single Kernel Soft Synchronization (SKSS) technique to fully utilize GPU computing resources. We have also adopted Huffman coding with gap arrays to accelerate parallel Huffman decoding. We have evaluated the performance of our GPU implementations using an NVIDIA A100 GPU and compared them with parallel/sequential Deflate encoding and decoding on the Intel X86 multicore CPUs using multiple threads/a single thread. Our GPU implementation of Deflate decoding is 1.66x–8.33x faster than the multiple thread implementation and 4.13x–36.56x faster than the single thread implementation.