gebhart/patrepeval huggingface dataset:
CCAAT/Enhancer Binding Protein δ in Macrophages Contributes to Immunosuppression and Inhibits Phagocytosis in Nasopharyngeal Carcinoma (2013)

Although tumors tend to be associated with immune cells and inflammation, this immune response often fails to eliminate the cancer and instead promotes cancer progression. Tumor-associated macrophages (TAMs) fail to phagocytose tumor cells, and they also produce signals that suppress the adaptive immune response. We showed that immunosuppressive prostaglandin E₂ (PGE₂) led to the production and activity of the transcription factor CCAAT/enhancer binding protein δ (C/EBPδ) by stimulating the nucleocytoplasmic shuttling of the RNA binding protein Hu antigen R (HuR), which bound to and stabilized CEBPD mRNA in macrophages. An increase in C/EBPδ abundance in macrophages in response to PGE₂ resulted in enhanced production of the immunosuppressive cytokine interleukin-10 (IL-10) and of pentraxin 3 (PTX3), which suppresses the ability of macrophages to phagocytose tumor cells. Furthermore, conditioned medium from C/EBPδ-replete, but not C/EBPδ-deficient, macrophages inhibited the phagocytosis of tumor cells by macrophages, suggesting an autocrine mode of regulation. Immunohistochemical analysis demonstrated that the amount of cytosolic HuR protein correlated with increased C/EBPδ abundance in TAMs in malignant nasopharyngeal carcinoma. Together, these data suggest that the inflammatory PGE₂-HuR-C/EBPδ axis in macrophages promotes tumor progression by preventing the phagocytosis of tumor cells and inducing immunosuppressive cytokine production.
Antenna selection diversity for IEEE 802.11p (2013)

Dependable vehicular communications systems are a key requirement for the implementation of intelligent transportation systems (ITS). Multiple antenna receivers enable the utilization of spatial diversity to increase the reliability as well as improve the availability. The cost of a multiple antenna receiver is the increased hardware complexity due to multiple receive chains. In this paper we demonstrate that antenna selection for IEEE 802.11p allows to connect the antenna with the best instantaneous signal to noise ratio (SNR) to a single receive chain while maintaining the diversity gain. We extend the IEEE 802.11p frame structure by two short preambles to estimate the SNR for each receive branch. The numerical simulation results from our standard compliant link level simulation show a bit error ratio reduction from 8.159 · 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> to 6.681 · 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> at an SNR of 8 dB and from 4.688 · 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> to 1.063 · 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> at an SNR of 12 dB with antenna selection.
Economic Power Schedule and Transactive Energy through Intelligent Centralized Energy Management System for DC Residential Distribution System (2017)

DC residential distribution system (RDS) consisted by DC living home will be a significant integral part in the future green transmission. Meanwhile, the increasing number of distributed resources and intelligent devices will change the power flow between main grid and demand sides. The utilization of distributed generations (DGs) requires an economic operation, stability, environmentally friendly in the whole DC system. This paper not only presents an optimization schedule and transactive energy (TE) approach through centralized energy management system (CEMS), but a control approach to implement and ensure DG output voltages to various DC buses in DC RDS. Based on data collection, prediction and a certain objection, the expert system in CEMS can work out the optimization schedule, after this, the voltage droop control for steady voltage is aligned with the command of unit power schedule. In this work, a DC RDS is as a case study to demonstrate the process, the RDS is associated with unit economic models, cost minimization objective is proposed to achieve based on real-time electrical price. The results show that the proposed framework and methods will help the targeted DC residential system to reduce the total cost and reach stability and efficiency.
Safe Backstepping with Control Barrier Functions (2022)

Complex control systems are often described in a layered fashion, represented as higher-order systems where the inputs appear after a chain of integrators. While Control Barrier Functions (CBFs) have proven to be powerful tools for safety-critical controller design of nonlinear systems, their application to higher-order systems adds complexity to the controller synthesis process -- it necessitates dynamically extending the CBF to include higher order terms, which consequently modifies the safe set in complex ways. We propose an alternative approach for addressing safety of higher-order systems through Control Barrier Function Backstepping. Drawing inspiration from the method of Lyapunov backstepping, we provide a constructive framework for synthesizing safety-critical controllers and CBFs for higher-order systems from a top-level dynamics safety specification and controller design. Furthermore, we integrate the proposed method with Lyapunov backstepping, allowing the tasks of stability and safety to be expressed individually but achieved jointly. We demonstrate the efficacy of this approach in simulation.
Inulin-grown Faecalibacterium prausnitzii cross-feeds fructose to the human intestinal epithelium (2021)

Many chronic diseases are associated with decreased abundance of the gut commensal <i>Faecalibacterium prausnitzii</i>. This strict anaerobe can grow on dietary fibers, e.g., prebiotics, and produce high levels of butyrate, often associated to epithelial metabolism and health. However, little is known about other <i>F. prausnitzii</i> metabolites that may affect the colonic epithelium. Here, we analyzed prebiotic cross-feeding between <i>F. prausnitzii</i> and intestinal epithelial (Caco-2) cells in a "Human-oxygen Bacteria-anaerobic" coculture system. Inulin-grown <i>F. prausnitzii</i> enhanced Caco-2 viability and suppressed inflammation- and oxidative stress-marker expression. Inulin-grown <i>F. prausnitzii</i> produced excess butyrate and fructose, but only fructose efficiently promoted Caco-2 growth. Finally, fecal microbial taxonomy analysis (16S sequencing) from healthy volunteers (n = 255) showed the strongest positive correlation for <i>F. prausnitzii</i> abundance and stool fructose levels. We show that fructose, produced and accumulated in a fiber-rich colonic environment, supports colonic epithelium growth, while butyrate does not.
Enhanced Supercritical Fluid Carbon Dioxide Extraction of Pesticides from Foods using Pelletized Diatomaceous Earth (1991)

Supercritical fluid carbon dioxide (SC-CO2), when used with an extraction enhancer, comprises a supercritical fluid extraction (SFE) system for extraction of pesticides and matrix components from fatty and nonfatty foods. After being mixed with the enhancer, samples ranging from 95% water to pure lipophilic oils can be extracted efficiently with SC-CO2. This extraction technique yields analyte recoveries in excess of 85% for over 30 types of pesticides at incurred levels ranging from 0.005 to 2 ppm in such diverse matrixes as carrots, lettuce, peanut butter, hamburger, and fortified butter fat and fortified potatoes. SC-CO2 provides a solvent medium that is nontoxic, nonflammable, and inexpensive while also eliminating the use and disposal of potentially carcinogenic organic solvents.
Knockdown of HPRT for Selection of Genetically Modified Human Hematopoietic Progenitor Cells (2013)

The inability to obtain sufficient numbers of transduced cells remains a limitation in gene therapy. One strategy to address this limitation is in vivo pharmacologic selection of transduced cells. We have previously shown that knockdown of HPRT using lentiviral delivered shRNA facilitates efficient selection of transduced murine hematopoietic progenitor cells (HPC) using 6-thioguanine (6TG). Herein, we now extend these studies to human HPC. We tested multiple shRNA constructs in human derived cell lines and identified the optimal shRNA sequence for knockdown of HPRT and 6TG resistance. We then tested this vector in human umbilical cord blood derived HPC in vitro and in NOD/SCID recipients. Knockdown of HPRT effectively provided resistance to 6TG in vitro. 6TG treatment of mice resulted in increased percentages of transduced human CD45(+) cells in the peripheral blood and in the spleen in particular, in both myeloid and lymphoid compartments. 6TG treatment of secondary recipients resulted in higher percentages of transduced human cells in the bone marrow, confirming selection from the progeny of long-term repopulating HPCs. However, the extent of selection of cells in the bone marrow at the doses of 6TG tested and the toxicity of higher doses, suggest that this strategy may be limited to selection of more committed progenitor cells. Together, these data suggest that human HPC can be programmed to be resistant to purine analogs, but that HPRT knockdown/6TG-based selection may not be robust enough for in vivo selection.
TheSchizosaccharomyces pombe rhp3+gene required for DNA repair and cell viability is functionally interchangeable with theRAD3gene ofSaccharomyces cerevisiae (1992)

The RAD3 gene of Saccharomyces cerevisiae is required for excision repair and is essential for cell viability. RAD3 encoded protein possesses a single stranded DNA-dependent ATPase and DNA and DNA.RNA helicase activities. Mutational studies have indicated a requirement for the RAD3 helicase activities in excision repair. To examine the extent of conservation of structure and function of RAD3 during eukaryotic evolution, we have cloned the RAD3 homolog, rhp3+, from the distantly related yeast Schizosaccharomyces pombe. RAD3 and rhp3+ encoded proteins are highly similar, sharing 67% identical amino acids. We show that like RAD3, rhp3+ is indispensable for excision repair and cell viability, and our studies indicate a requirement of the putative rhp3+ DNA helicase activity in DNA repair. We find that the RAD3 and rhp3+ genes can functionally substitute for one another. The level of complementation provided by the rhp3+ gene in S.cerevisiae rad3 mutants or by the RAD3 gene in S.pombe rhp3 mutants is remarkable in that both the excision repair and viability defects in both yeasts are restored to wild type levels. These observations suggest a parallel evolutionary conservation of other protein components with which RAD3 interacts in mediating its DNA repair and viability functions.
Figure S2 from Orchestration and Prognostic Significance of Immune Checkpoints in the Microenvironment of Primary and Metastatic Renal Cell Cancer (2023)

&lt;p&gt;Figure S2. CD8+ and PD1+ cell density and Furhman Grade in primary ccRCC&lt;/p&gt;
Greater antioxidant and respiratory metabolism in field‐grown soybean exposed to elevated O3under both ambient and elevated CO2 (2011)

Antioxidant metabolism is responsive to environmental conditions, and is proposed to be a key component of ozone (O(3)) tolerance in plants. Tropospheric O(3) concentration ([O(3)]) has doubled since the Industrial Revolution and will increase further if precursor emissions rise as expected over this century. Additionally, atmospheric CO(2) concentration ([CO(2)]) is increasing at an unprecedented rate and will surpass 550 ppm by 2050. This study investigated the molecular, biochemical and physiological changes in soybean exposed to elevated [O(3) ] in a background of ambient [CO(2)] and elevated [CO(2)] in the field. Previously, it has been difficult to demonstrate any link between antioxidant defences and O(3) stress under field conditions. However, this study used principle components analysis to separate variability in [O(3)] from variability in other environmental conditions (temperature, light and relative humidity). Subsequent analysis of covariance determined that soybean antioxidant metabolism increased with increasing [O(3)], in both ambient and elevated [CO(2)]. The transcriptional response was dampened at elevated [CO(2)], consistent with lower stomatal conductance and lower O(3) flux into leaves. Energetically expensive increases in antioxidant metabolism and tetrapyrrole synthesis at elevated [O(3)] were associated with greater transcript levels of enzymes involved in respiratory metabolism.
Erratum: Impact parameter dependent parton distributions and off-forward parton distributions forζ→0[Phys. Rev. D62, 071503(R) (2000)] (2002)

Throughout the paper, a sign error occurred in the exponents of Fourier transforms. Specifically, Eq. 2.
Practical Experiences with Purenet, a Self-Learning Malware Prevention System (2011)

This paper introduces Purenet, which is a self-learning malware detection system aimed at avoiding zero-day attacks and other delays in patching application systems when attacks are identified. The concept and architecture of Purenet are described, specifically positioning anomaly detection as the system enabler. Deployment of the system in an operational environment is discussed, and associated recommendations and findings are presented based on this. Findings from the prototype include various considerations which should influence the design of such security software including latency considerations, multi protocol support, cloud anti-malware integration, resource requirement issues, reporting, base platform hardening and SIEM integration.
Study on the High Efficiency Closed Cycle Gas Turbine System (2001)

In WE-NET project Phase I Program, the power generation system with more than 60%(HHV) thermal efficiency had been designed. However, because this system must be fueled by pure hydrogen, commercialization of this system in early stage is thought to be difficult. Therefore, the new project, in which the natural gas fueled system is targeted, has been started since FY1999. In this project, the power generation efficiency is aimed to be 60%(HHV) or higher, with turbine inlet maximum temperature of 1973K. In this report, the feature of the target system is explained at first. Then, the sensitivities of many parameters are examined in detail.
Learning Effect on Wrist Guidance Using Multiple Vibrotactile Cues (2019)

In this paper, we present a paradigm to improve the followability on a path-following task for the wrist by practicing repeatedly using vibrotactile cues. Vibrotactile cues were provided as a direction to modify the wrist’s path when the wrist’s position deviates from the desired path. The experiment was conducted to test the learning effect of the vibrotactile feedback on a participants’ wrist motion during three days. We found that the root mean squared error of the participants wrist’s trajectory decreased when provided with vibrotactile feedback. Additionally, most participants could reproduce the desired path in a more accurate way after removing the feedback immediately after training. This effect continued slightly over three days and the performance gradually improved after training.
On a generalization of the proper orthogonal decomposition and optimal construction of reduced order models (2012)

In this paper, the popular proper orthogonal decomposition (POD) without the usual integral or inner product constraints is extended to general Hilbert spaces, such as Sobolev spaces, using functional analytic methods. It is shown that a particular tensor product space is dense in the Hilbert space where the partial differential equation (PDE) solution lives. This allows approximating the PDE solution by tensors to any desired accuracy. Optimal approximation by these tensors is shown to result in the POD using operator theoretic arguments. This is achieved by solving a nonlinear optimization problem where the PDE solution is approximated by operators of a prescribed finite rank in the corresponding trace class 2 norm. POD modes can then be computed by solving an infinite dimensional eigenvalue problem using Hilbert-Schmidt theory. Moreover, an optimal method in constructing reduced order models for the two-dimensional Burgers' equation subject to boundary control is presented and compared to the POD reduced models. A closed-loop feedback controller then designed using the reduced order model and then applied to the full order model.
Manufacture and utilization of palatinose. (1988)

A pure preparation of a-glucosyltransferase, prepared from sucrose-grown cells of Protaininobacter rubrum CBS 574. 77, produces simultaneously about 80 parts of palatinose and about 10 parts of trehalulose (a-glucopyranosyl-1, 1-fructof uranose) from 100 parts of sucrose. In order to utilize the enzyme of P. rubrum for the large scale production of palatinose, a method for immobilizing whole cells has been developed. The latter comprises a cell entrapping process involving alginate and a cross-linking process involving polyethyleneimine absorbed in the alginate-gel with glutaraldehyde. The composition of the products produced from sucrose by the immobilized enzyme is the same as that in the case of the free enzyme. A commercial palatinose production process gives two kinds of products, i. e., crystals and a syrup. The former consists of palatinose monohydrate, above 99.0% in purity, and the latter is a liquid product with a solid content of 71%. About 60% of the total solid in the syrup is occupied by trehalulose and palatinose. Both products are now used as bulky foodstuffs with sweetening power and as sugar substitutes in the food industry in Japan. The main advantage in using palatinose products is the reduced cariogenicity of the food, because many experiments have shown that pure palatinose is non-cariogenic and that the palatinose syrup is low-cariogenic. Palatinose and trehalulose are hydrolyzed by isomaltase in the small intestine. Palatinose is absorbed so slowly that it only causes smalll increases in the levels of blood glucose and insulin. This suggests the feasibility of its novel use for special foods for diabetics.
Evaluation of CD4+ T cells proliferating to grass pollen in seasonal allergic subjects by flow cytometry (2003)

Our objective was to characterize T-cell responses to Phleum pratense in grass pollen allergic individuals and healthy controls using the fluorescent dye PKH26. Peripheral blood mononuclear cells were stimulated with P. pratense, or with recall antigens, and CD3+/CD4+ and CD3+/CD8+ T-cells that had proliferated were analysed by flow cytometry. In the presence of P. pratense CD4+/CD3+ T-cells proliferated more in grass pollen sensitive atopic patients than in nonallergic controls or in nongrass pollen sensitive atopic subjects. PPD and TT recall antigens elicited uniformly high proliferation in all T-cell subsets. Only half of pollen sensitive patients also had an increased proliferation of CD3+/CD8+ T-cells in response to P. pratense. We determined precursor frequency of CD4+ T cells in the original population that responded to P. pratense and found values ranging from 1 x 10-3 to 0.6 x 10-1, in the same range as those measured for PPD and TT. In conclusion, grass pollen sensitive atopic patients show enhanced CD4+ T-cell reactivity to P. pratense, and this could be related to the presence of elevated numbers of circulating allergen-specific CD4+ T cells. This flow cytometric method should allow the identification of other phenotypic markers such as intracellular cytokines in allergen specific responding CD4+ T cells.
X-MAC: A Short Preamble MAC Protocol for Duty-Cycled Wireless Sensor Networks ; CU-CS-1008-06 (2006)

In this paper we present X-MAC, a low power MAC protocol for wireless sensor networks (WSNs). Standard MAC protocols developed for duty-cycled WSNs such as BMAC, which is the default MAC protocol for TinyOS, employ an extended preamble and preamble sampling. While this “low power listening” approach is simple, asynchronous, and energy-efficient, the long preamble introduces excess latency at each hop, is suboptimal in terms of energy consumption, and suffers from excess energy consumption at nontarget receivers. X-MAC proposes solutions to each of these problems by employing a shortened preamble approach that retains the advantages of low power listening, namely low power communication, simplicity and a decoupling of transmitter and receiver sleep schedules. We demonstrate through implementation and evaluation in a wireless sensor testbed that X-MAC’s shortened preamble approach significantly reduces energy usage at both the transmitter and receiver, reduces per-hop latency, and offers additional advantages such as flexible adaptation to both bursty and periodic sensor data sources.
An in silico analysis of effective siRNAs against COVID‐19 by targeting the leader sequence of SARS‐CoV‐2 (2021)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a retrovirus having genome size of around 30 kb. Its genome contains a highly conserved leader sequence at its 5' end, which is added to all subgenomic mRNAs at their 5' terminus by a discontinuous transcription mechanism and regulates their translation. Targeting the leader sequence by RNA interference can be an effective approach to inhibit the viral replication. In the present study an in-silico prediction of highly effective siRNAs was performed to target the leader sequence using the online software siDirect version 2.0. Low seed-duplex stability, exact complementarity with target, at least three mismatches with any off-target and least number of off-targets, were considered as effective criteria for highly specific siRNA. Further validation of siRNA affinity for the target was accomplished by molecular docking by HNADOCK online server. Our results revealed four potential siRNAs, of which siRNA having guide strand sequence 5'GUUUAGAGAACAGAUCUACAA3' met almost all specificity criteria with no off-targets for guide strand. Molecular docking of all predicted siRNAs (guide strand) with the target leader sequence depicted highest binding score of -327.45 for above-mentioned siRNA. Furthermore, molecular docking of the passenger strand of the best candidate with off-target sequences gave significantly low binding scores. Hence, 5'GUUUAGAGAACAGAUCUACAA3' siRNA possess great potential to silence the leader sequence of SARS-CoV-2 with least off-target effect. Present study provides great scope for development of gene therapy against the prevailing COVID-19 disease, thus further research in this concern is urgently demanded.