gebhart/patrepeval huggingface dataset:
Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets (2010)

Primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) share a frequent constitutive activation of JAK (Janus kinase)/STAT signaling pathway. Because of complex, nonlinear relations within the pathway, key dynamic properties remained to be identified to predict possible strategies for intervention. We report the development of dynamic pathway models based on quantitative data collected on signaling components of JAK/STAT pathway in two lymphoma-derived cell lines, MedB-1 and L1236, representative of PMBL and cHL, respectively. We show that the amounts of STAT5 and STAT6 are higher whereas those of SHP1 are lower in the two lymphoma cell lines than in normal B cells. Distinctively, L1236 cells harbor more JAK2 and less SHP1 molecules per cell than MedB-1 or control cells. In both lymphoma cell lines, we observe interleukin-13 (IL13)-induced activation of IL4 receptor α, JAK2, and STAT5, but not of STAT6. Genome-wide, 11 early and 16 sustained genes are upregulated by IL13 in both lymphoma cell lines. Specifically, the known STAT-inducible negative regulators CISH and SOCS3 are upregulated within 2 hours in MedB-1 but not in L1236 cells. On the basis of this detailed quantitative information, we established two mathematical models, MedB-1 and L1236 model, able to describe the respective experimental data. Most of the model parameters are identifiable and therefore the models are predictive. Sensitivity analysis of the model identifies six possible therapeutic targets able to reduce gene expression levels in L1236 cells and three in MedB-1. We experimentally confirm reduction in target gene expression in response to inhibition of STAT5 phosphorylation, thereby validating one of the predicted targets.
Origin of Autocatalysis in the Biphasic Alkaline Hydrolysis of C-4 to C-8 Ethyl Alkanoates (1998)

The alkaline hydrolysis of C-4 to C-8 (butanoate to octanoate) ethyl esters shows autocatalytic kinetics when performed under two-phase conditions without any mixing solvent. Alkanoate anions and ethanol are the products of the reaction. A dynamic model is proposed that describes quantitatively this kinetic behavior. The model includes the main processes occurring in the biphasic medium and the corresponding thermodynamic calculations of the average size and stoichiometry of the molecular aggregates. Modeling indicates that salting-in and solvent effects caused by the alkanoate anions and ethanol determine the autocatalytic kinetics in the hydrolysis of C-4 ethyl ester where no aggregation occurs. In the C-5 to C-8 experiments, ester-containing micelles (ECM) are mainly formed by cooperative aggregation of alkanoate anions with ester molecules. ECM is formed only after a threshold concentration of the alkanoate anion has been reached. In a phase-transfer-like process, ECM carries ester molecules into the aqueous phase, where hydrolysis takes place yielding alkanoate anions. Additionally, in C-6 and C-7 ethyl ester hydrolysis, autocatalysis appears to be delayed, since acceleration only starts after the extent of hydrolysis has reached a certain level. A transient storage of alkanoate anions in a reservoir has been assumed to explain this delay. Collective adsorption of alkanoate anions at the oil−water interface, which occurs without any threshold concentration, could play the role of such a transient storage. The model also shows that empty micelles are without any kinetic importance, since they are formed at the end of reaction after the ester is completely depleted.
Towards a living earth simulator (2013)

The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to real-world questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
High Frequency of Fusion Gene Transcript Resulting From t(10;11)(p12;q23) Translocation in Pediatric Acute Myeloid Leukemia in Poland (2020)

11q23/<i>MLL</i> rearrangements are frequently detected in pediatric acute myeloid leukemia. The analysis of their clinical significance is difficult because of the multitude of translocation fusion partners and their low frequency. The presence of t(10;11)(p12;q23) translocation was previously identified in pediatric acute myelogenous leukemia (AML). It is considered as the second most common translocation detected in pediatric 11q23/<i>MLL</i>-rearranged (present <i>KMT2A</i>) AML, after t(9;11)(p22;q23). The presence of the above translocation was previously identified as an unfavorable prognostic factor. Since June 2015, the Polish Pediatric Leukemia/Lymphoma Study Group has applied the therapeutic protocol requiring extensive diagnostics of genetic changes in pediatric AML. Until November 2019, molecular genetic studies were performed in 195 children with diagnosed AML to identify carriers of fusion gene transcripts for 28 most common chromosomal translocations in acute leukemia. The fusion gene transcript for translocation t(10;11)(p12;q23) involving <i>MLL</i> gene was detected with unexpectedly high frequency (8.9%) in our research. It was the highest frequency of all detected <i>MLL</i> rearrangements, as well as other detected fusion gene transcripts from chromosomal aberrations characteristic for AML. It seems that chromosomal aberration between chromosomes 10 and 11 can be relatively frequent in some populations. Paying attention to this fact and ensuring proper genetic diagnosis seem to be important for appropriate allocation of patients to risk groups of pediatric AML treatment protocols.
Multitimescale Mitigation for Performance Variability Improvement in Time-Critical Systems (2022)

Ensuring a timing guarantee is crucial for time-critical applications. However, this task becomes more challenging with the increasing performance variability generated by complicated modern hardware and software. A widespread solution to the problem is real-time scheduling, which depends on worst-case execution time (WCET) and dynamic voltage frequency scaling (DVFS). Although these techniques provide the necessary guarantees, they also exhibit important limitations from the long switching time of DVFS and the overly pessimistic execution time model of WCET. In this work, a multitimescale mitigation methodology is proposed to improve the way of tackling performance variability in both timing guarantee and energy saving. By using both the DVFS and heterogeneous datapath (HDP) knobs, this methodology can push the timescale of mitigation down to the submillisecond level. Moreover, this methodology can calculate a tight upper bound of execution time at run-time using dynamic scenarios (DSs). Simulation shows that the proposed methodology can ensure zero deadline misses with a smaller safety time margin than the method using only DVFS and WCET. This advantage can translate into an energy reduction by half compared to the conventional WCET-based method with a single DVFS knob.
Tools for Molecular Epidemiology of Streptococcus suis (2020)

Diseases caused by <i>Streptococcus suis</i> are a significant economic and welfare concern in pigs as well as in humans. Several molecular methods have been applied to investigate S. suis strain diversity and identify phylogenetic groups. Multilocus sequence typing (MLST), commonly used to differentiate between <i>S. suis</i> strains, has been instrumental in identifying that the species is genetically highly diverse. Recent advances in whole-genome analysis have resulted in schemes permitting the classification of S. suis populations as pathogenic or non-pathogenic, or disease-associated or non-disease associated. Here, we review these and other molecular approaches that can be used for surveillance, outbreak tracking, preventative health management, effective treatment and control, as well as vaccine development, including PCR based-assays that are easy to apply in modest diagnostic settings and which allow for the rapid screening of a large number of isolates at relatively low cost, granting the identification of several major clonal complexes of the <i>S. suis</i> population.
STUDY EVALUATING AQUAPORIN-1 GENE THERAPY FOR THE TREATMENT OF IRRADIATION-INDUCED SALIVARY HYPOFUNCTION. (2019)

Introduction:Therapy for head and neck cancer commonly includes ionizing radiation (IR). IR irreversibly damages the salivary glands causing decrements in quality-of-life and oral health. There are no therapies to correct this disorder or its sequelae. Previously, proof-of-concept studies have demonstrated the effectiveness of adenovirus (Ad) vector gene transfer of human aquaporin-1 (hAQP1) to the parotid gland and correction of salivary hypofunction (NCT00372320). We aimed to develop and test adeno-associated virus serotype 2 (AAV2) for gene transfer of hAQP1 to correction of IR-induced xerostomia in humans.Methods:Using well-established preclinical models (e.g., mice and minipigs), we tested the safety, kinetics, and effectiveness of AAV2-hAQP1 to recover IR-induced salivary hypofunction. Using this data, we developed a Phase 1 human clinical trial to test the safety of AAV2-hAQP1 and some measures of biological activity.Results:In our first Ad-AQP1 trial, all subjects tolerated vector delivery and study procedures well and positive objective and subjective responses were seen in five patients, all at doses &lt;5.8x10^9vector particles (vp)/gland. These findings encouraged us to pursue preclinical studies with AAV2-based vectors, which have demonstrated lower immunogenicity and more stable expression than Ad vectors.Conclusions:Preclinical data on the safety and efficacy of AAV2 based vectors will be presented. A Phase 1 study (NCT02446249) using AAV2-hAQP1 vector is actively enrolling.
Exposure to long-term evolution radiofrequency electromagnetic fields decreases neuroblastoma cell proliferation via Akt/mTOR-mediated cellular senescence (2021)

The aim of this study was to examine the potential effects of long-term evolution (LTE) radiofrequency electromagnetic fields (RF-EMF) on cell proliferation using SH-SY5Y neuronal cells. The growth rate and proliferation of SH-SY5Y cells were significantly decreased upon exposure to 1760 MHz RF-EMF at 4 W/kg specific absorption rate (SAR) for 4 hr/day for 4 days. Cell cycle analysis indicated that the cell cycle was delayed in the G0/G1 phase after RF-EMF exposure. However, DNA damage or apoptosis was not involved in the reduced cellular proliferation following RF-EMF exposure because the expression levels of histone H2A.X at Ser139 (γH2AX) were not markedly altered and the apoptotic pathway was not activated. However, SH-SY5Y cells exposed to RF-EMF exhibited a significant elevation in Akt and mTOR phosphorylation levels. In addition, the total amount of p53 and phosphorylated-p53 was significantly increased. Data suggested that Akt/mTOR-mediated cellular senescence led to p53 activation via stimulation of the mTOR pathway in SH-SY5Y cells. The transcriptional activation of p53 led to a rise in expression of cyclin-dependent kinase (CDK) inhibitors p21 and p27. Further, subsequent inhibition of CDK2 and CDK4 produced a fall in phosphorylated retinoblastoma (pRb at Ser807/811), which decreased cell proliferation. Taken together, these data suggest that exposure to RF-EMF might induce Akt/mTOR-mediated cellular senescence, which may delay the cell cycle without triggering DNA damage in SH-SY5Y neuroblastoma cells.
Leukotriene B4 mediates shear rate-dependent leukocyte adhesion in mesenteric venules. (1992)

Previous studies have demonstrated that low shear rates promote leukocyte adherence to microvascular endothelium in postcapillary venules. The objective of this study was to determine whether an accumulation of inflammatory mediators such as platelet activating factor and leukotriene B4 is responsible for shear rate-dependent leukocyte-endothelial cell adhesion. Postcapillary venules (25-39 microns in diameter) in cat mesentery were studied by intravital microscopy. Venular wall shear rate was varied over a wide range by graded occlusion of the mesenteric artery. Red blood cell velocity, vessel diameter, leukocyte rolling velocity, and the numbers of rolling and adherent leukocytes were measured at each shear rate. In one series of experiments, shear rate-dependent leukocyte adherence was monitored at different superfusion rates (1.0 and 2.5 ml/min). At the lower superfusion rate, the number of adherent leukocytes was significantly higher at any given shear rate when compared with results obtained at the higher superfusion rate. This suggests that reduced washout of inflammatory mediators contributes to shear rate-dependent leukocyte adhesion. Pretreatment with different platelet activating factor receptor antagonists (WEB 2086 or WEB 2170) had no effect on the number of adherent leukocytes normally observed at lower shear rates, suggesting that platelet activating factor does not play a major role in this process. However, shear rate-dependent leukocyte adhesion was largely prevented by pretreatment with either a leukotriene B4 receptor antagonist (SC-41930) or a leukotriene synthesis inhibitor (L663,536). The results of this study indicate that a reduced washout of leukotriene B4 is responsible for the enhanced leukocyte adherence that occurs at low venular wall shear rates.
Nonlinear Dynamic Neural Network for Text-Independent Speaker Identification using Information Theoretic Learning Technology (2006)

In this paper we present a novel design for a nonlinear dynamic neural network to implement text-independent speaker recognition without the benefit of exact voice signatures. The dynamic properties between the input neuron and the output neuron make use of a nonlinear high-order synaptic neural model with memory of previous input signals. The dynamic neural network is realized in the short-term-frequency long-term-temporal domain. Informatics metric is used to overcome the challenge of performing blind learning for the nonlinear network. The goal of this study is not only to improve the recognition performance but also to amplify the distinctiveness among different speakers.
Simulation of Cycle-to-Cycle Variation in Dual-Fuel Engines (2017)

Standard practices of internal combustion (IC) engine experiments are to conduct the measurements of quantities averaged over a large number of cycles. Depending on the operating conditions, the cycle-to-cycle variation (CCV) of quantities, such as the indicated mean effective pressure (IMEP) are observed at different levels. Accurate prediction of CCV in IC engines is an important but challenging task. Computational fluid dynamics (CFD) simulations using high performance computing (HPC) can be used effectively to visualize such 3D spatial distributions. In the present study, a dual fuel large engine is considered, with natural gas injected into the manifold accompanied with direct injection of diesel pilot fuel to trigger ignition. Multiple engine cycles in 3D are simulated in series as in the experiments to investigate the potential of HPC based high fidelity simulations to accurately capture the cycle to cycle variation in dual fuel engines. Open cycle simulations are conducted to predict the combined effect of the stratification of fuel-air mixture, temperature and turbulence on the CCV of pressure. The predicted coefficient of variation (COV) of pressure compared to the results from closed cycle simulations and the experiments.
Localization in the quantum sawtooth map emulated on a quantum-information processor (2006)

Quantum computers will be unique tools for understanding complex quantum systems. We report an experimental implementation of a sensitive, quantum coherence-dependent localization phenomenon on a quantum information processor (QIP). The localization effect was studied by emulating the dynamics of the quantum sawtooth map in the perturbative regime on a three-qubit QIP. Our results show that the width of the probability distribution in momentum space remained essentially unchanged with successive iterations of the sawtooth map, a result that is consistent with localization. The height of the peak relative to the baseline of the probability distribution did change, a result that is consistent with our QIP being an ensemble of quantum systems with a distribution of errors over the ensemble. We further show that the previously measured distributions of control errors correctly account for the observed changes in the probability distribution.
Knowledge Graph Completion Models are Few-shot Learners: An Empirical Study of Relation Labeling in E-commerce with LLMs (2023)

Knowledge Graphs (KGs) play a crucial role in enhancing e-commerce system performance by providing structured information about entities and their relationships, such as complementary or substitutable relations between products or product types, which can be utilized in recommender systems. However, relation labeling in KGs remains a challenging task due to the dynamic nature of e-commerce domains and the associated cost of human labor. Recently, breakthroughs in Large Language Models (LLMs) have shown surprising results in numerous natural language processing tasks. In this paper, we conduct an empirical study of LLMs for relation labeling in e-commerce KGs, investigating their powerful learning capabilities in natural language and effectiveness in predicting relations between product types with limited labeled data. We evaluate various LLMs, including PaLM and GPT-3.5, on benchmark datasets, demonstrating their ability to achieve competitive performance compared to humans on relation labeling tasks using just 1 to 5 labeled examples per relation. Additionally, we experiment with different prompt engineering techniques to examine their impact on model performance. Our results show that LLMs significantly outperform existing KG completion models in relation labeling for e-commerce KGs and exhibit performance strong enough to replace human labeling.
Kinetics of an Air- and Water-Stable Ruthenium(IV) Catalyst for the Deprotection of Allyl Alcohol in Water (2010)

Kynurenic allyl ester reacts readily with [CpRu(NCCH3)3]PF6 in dry acetone to yield the RuIV allyl. The complex is an effective catalyst for the hydrolysis of methyl allyl carbonate in aqueous solution in air yet decomposes rapidly in aerobic solutions of methanol. Kinetic studies are consistent with rate-limiting attack of water (or methanol) on the RuIV allyl as a key step. A polystyrene-supported version of the catalyst was active for the catalytic hydrolysis of methylallyl carbonate, but kinetic studies indicate that the Ru leaches from polystyrene upon repeated catalytic cycles.
CD82 (KAI1), a member of the tetraspan family, is expressed on early haemopoietic progenitor cells and up‐regulated in distinct human leukaemias (1999)

CD82 (KAI1) is a member of the tetraspan transmembrane protein family which has been cloned from lymphoblastoid variant cell lines. However, a role for CD82 in early normal and malignant haemopoiesis has not yet been characterized. We studied the CD82 expression in 33 normal donor samples and 98 leukaemias by fluorescence activated cell sorting (FACS) and reverse transcriptase polymerase chain reaction (RT‐PCR). We demonstrated that CD82 was moderately expressed in the vast majority of normal granulocytes and monocytes. In contrast, only about one third of the peripheral blood lymphocytes were weakly CD82 positive (CD82 + ). Interestingly, judgement of the CD82 transcription and expression in various leukaemias revealed that CD82 was overexpressed in chronic myeloid leukaemia (CML) patients in accelerated or blastic phase (CML‐AP/BP) as well as in acute myeloid leukaemia (AML) and chronic lymphocytic leukaemia (CLL) patients. Analysis of AML patients with CD34 + /CD82 + blasts prompted us to expand our studies on haemopoietic CD34 + progenitor cells. Intriguingly, 84–95% of the CD34 + cells isolated from healthy bone marrow, cord blood or peripheral blood were highly CD82 + . CD82 was abundantly expressed on primitive as well as on committed haemopoietic progenitor cells. After in vitro induction of myeloid differentiation in CD34 + peripheral blood progenitor cells (PBPC), the expression of CD82 decreased to levels similar to those found on peripheral blood granulocytes. These observations suggest for the first time a role for CD82 in normal and malignant haemopoiesis.
Optocoupler Effect on In-Vivo Measurements Characterization for Human Body Communication (2018)

Body Area Network (BAN) has found intuitive applications in healthcare and medical monitoring, where interconnected electronic terminals are used around a user. In this contest, Human Body Communication (HBC) is a promising technique which uses the human body as a communication medium. Almost measures targeting the HBC channel characterization, the balun has been used to separate the grounds between transceivers. In this work, optocoupler was used for the first time, to decouple transceiver ports from each other and prevent the parasitic return path. Optocoupler's effect on the measured results was analyzed for both capacitive and galvanic HBC coupling.