gebhart/patrepeval huggingface dataset:
HIV, Cytokines and Programmed Cell Death: A Subtle Interplay (2000)

HIV infection is marked by the progressive destruction of the CD4 T lymphocyte subset, an essential component of the immune system and a vital source of cytokines required for differentiation of natural killer (NK) and gamma delta T cells, for maturation of B lymphocytes into plasmocytes, and for differentiation of CD8+ T cells into virus-specific cytotoxic T lymphocytes. CD4 T lymphocytes are also a source of chemokines which control migration of lymphocytes to the site of infection and which also inhibit HIV entry into CD4-expressing targets. Continuous production of viral proteins leads to an unbalanced immune activation and to the triggering of apoptotic programs, turning mononuclear cells, including CD4 T cells, CD8 T cells and APC, into effectors of apoptosis, leading to fratricidal destruction of healthy uninfected cells expressing the death receptors. Inappropriate PCD is also responsible for the disappearance of T helper cells primed for type-1 cytokine synthesis, thus contributing to the lack of survival factors which could prevent spontaneous lymphocyte apoptosis. Under potent anti-retroviral therapies, a significant decrease in spontaneous, TCR- and CD95-induced lymphocyte apoptosis is observed, concomitant with a partial quantitative and qualitative restoration of the immune system in treated patients. However, owing to the suppressive effect of anti-retroviral drugs on physiological apoptosis, these therapies are associated with alteration of TNF-alpha-regulated T cell homeostasis, leading to an accumulation in the blood of T cells primed for TNF-alpha synthesis, and contributing to the development of a new syndrome associated with these treatments, the lipodystrophy syndrome.
Realistic and Intelligent Management of Connected Storage Devices in Future Smart Homes Considering Energy Price Tag (2019)

Coordinated energy management plays a main role in increasing the performance and economic benefits of future smart homes. This article focuses on the energy management of a smart home equipped with a plug-in electric vehicle (PEV), household battery storage, and photovoltaics (PV), and it proposes an energy price tag (EPT) for all energy storage devices connected to the smart home system. A hybrid approach that consists of optimization and a rule-based prioritization is presented. The proposed algorithm establishes a priority order between the PEV, the household battery, and the imported power from the grid based on the EPT of energy sources. The proposed energy management algorithm seeks for the minimum overall energy cost for the smart home and PEV owner while satisfying household power demand and charging requirements of the storage devices. The performance of the energy management algorithm is examined on a typical smart home over a 24-h period based on time-varying grid electricity price.
Ultra broadband waveguide coupler using an anisotropic sub-wavelength metamaterial (2016)

Multimode interference couplers are a fundamental building block in many integrated photonic systems, ranging from high-speed coherent receivers to quantum splitters. However, their basic structure has remained fundamentally unchanged for almost four decades, limiting their size and operation bandwidth. Using sub-wavelength metamaterials, photonic devices with break-through size and performance have been recently reported. Leveraging the inherent anisotropy of these structures, here we derive a semi-analytic expression that enables the design of compact and ultra broadband multimode interference couplers. We experimentally demonstrate virtually perfect operation over a bandwidth in excess of 300nm (500nm in simulation), for a device three times shorter than its conventional counterpart, making this the most broadband multimode interference coupler reported to date. These results will enable ultra broadband integrated systems for applications in communications and sensing.
Identification of a bona-fide biomarker of microRNA in serum exosomes to predict recurrence of hepatocellular carcinoma after liver transplantation. (2013)

183 Background: The predictive biomarker for the recurrence of hepatocellular carcinoma (HCC) has great benefit on the selection of treatment options including liver transplantation (LT) for HCC. Micro RNA (miR), a class of small non-coding RNA molecule, affect crucial processes in cancer development and offer great potential as biomarkers for cancer due to their remarkable stability in blood. The objective of this study is to identify specific miRs in exosomes of HCC recurrence from the serum and bone marrow of the patients and validate these molecules as novel biomarkers for HCC recurrence. Methods: We employed microarray-based profiling of miR expression from exosome in serum and bone marrow of the patient with HCC to define a biomarker that distinguishes between patients with and without HCC recurrence after liver transplantation or hepatic resection. This was followed by a real-time semi-quantitative PCR validation in a separate cohort of 63 HCC patients who underwent living related LT. Results: We found that 4 miRs which were differentialy (&gt;2 folds) expressed in the serum exosome with HCC cases that had recurrence after LT compared to those without recurrence. They were associated with tumor aggressiveness of HCC in the validated cohort series. To disclose the original cell fraction of each identified miR in bone marrow, we divided bone marrow cells into 3 fractions by cell surface markers, such as CD14+ (macrophage), CD14-/CD45- (lymphocyte) and CD14-/CD45-/EpCAM+ (epithelial cell), then we performed microRNA microarray in each fraction. The increased expression of miR-150, miR-135a, and miR-1225-5p were observed in the CD14-/CD45+ fraction of bone marrow of HCC cases with recurrence, which suggested the association of CD4+ lymphocyte impairment and tumor recurrence. Conclusions: Circulating miR in serum exosome has potential as a novel biomarker to predict recurrence of HCC. MiR profiling of serum and bone marrow may help to clarify the mechanism of recurrence of HCC. The identified miR/gene axis indicated that the disruption of the immune systems after LT should provoke the recurrence of HCC in the future.
Quantitative LC–MS Provides No Evidence for m6dA or m4dC in the Genome of Mouse Embryonic Stem Cells and Tissues (2017)

Until recently, it was believed that the genomes of higher organisms contain, in addition to the four canonical DNA bases, only 5-methyl-dC (m<sup>5</sup> dC) as a modified base to control epigenetic processes. In recent years, this view has changed dramatically with the discovery of 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC) in DNA from stem cells and brain tissue. N<sup>6</sup> -methyldeoxyadenosine (m<sup>6</sup> dA) is the most recent base reported to be present in the genome of various eukaryotic organisms. This base, together with N<sup>4</sup> -methyldeoxycytidine (m<sup>4</sup> dC), was first reported to be a component of bacterial genomes. In this work, we investigated the levels and distribution of these potentially epigenetically relevant DNA bases by using a novel ultrasensitive UHPLC-MS method. We further report quantitative data for m<sup>5</sup> dC, hmdC, fdC, and cadC, but we were unable to detect either m<sup>4</sup> dC or m<sup>6</sup> dA in DNA isolated from mouse embryonic stem cells or brain and liver tissue, which calls into question their epigenetic relevance.
US Military Engagement in Humanitarian Surgery (2017)

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Abstract 3549: RUNX3 is a biomarker for determining sensitivity to pheophorbide a-photodynamic therapy in human oral squamous cell carcinoma. (2013)

Abstract Background &amp; Objective: Photodynamic therapy (PDT) with photosensitizer is one of the promising modalities for cancer treatment. For clinical use of PDT, the screening process for sensitive cancers to PDT should be preceded. For this, we investigated a molecular biomarker to determine the sensitivity to Pa-PDT in immortalized human oral keratinocytes (IHOK) and OSCC cell lines. Methods: For this study, two immortalized oral keratinocytes (IHOK-p, IHOK-s) and 8 oral squamous cell carcinoma (OSCC) cell lines were used. After cells were treated with Pa-PDT, phototoxicity and the level of reactive oxygen species (ROS) were measured. Apoptosis was measured using annexin V/PI staining and western blotting. mRNA and proteins of apoptotic genes were investigated by RT-PCR, real-time PCR, and western blotting. Transfection was performed using RUNX3-small interfering RNA. Results: After Pa-PDT, cell viability was more than 50% reduced and ROS generated in IHOK and OSCC. In addition, apoptosis occurred in all cell lines. Among apoptosis-related genes, Bim expression was altered following Pa-PDT. Therefore, mRNA and protein expression of RUNX3, a gene upstream of Bim were examined by Pa-PDT. We found that RUNX3 was highly responsive to Pa-PDT. Furthermore, knockdown of RUNX3 expression reduced cytotoxicity by Pa-PDT. In addition, we found that the cytotoxicity by Pa-PDT was proportional to RUNX3 expression in OSCC cell lines. Conclusion: This is the first study to find a new target molecule that enhances Pa-PDT effects in IHOK and OSCC cell lines. These results should be further proven by animal studies to apply to clinical trials. Nevertheless, the development of a PDT-dependent biomarker could provide a novel approach to improve the effects of PDT in oral precancerous and cancerous lesions. Acknowledgments This study was supported by a grant of the Korean Health Technology R&amp;D Project, Ministry for Health, Welfare &amp; Family Affairs, Republic of Korea (No. A100490). Citation Format: Sook Moon, Jung Yoon Bae, Doo Young Lee, Gyeong Ju Park, Hyun Yoo, Hyo jin Ko, Yong Chul Kim, Jin Kim. RUNX3 is a biomarker for determining sensitivity to pheophorbide a-photodynamic therapy in human oral squamous cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3549. doi:10.1158/1538-7445.AM2013-3549
A novel class of microbial phosphocholine‐specific phospholipases C (2002)

In this report we describe the 1,500-fold purification and characterization of the haemolytic phospholipase C (PLC) of Pseudomonas aeruginosa, the paradigm member of a novel PLC/phosphatase superfamily. Members include proteins from Mycobacterium tuberculosis, Bordetella spp., Francisella tularensis and Burkholderia pseudomallei. Purification involved overexpression of the plcHR1,2 operon, ion exchange chromatography and native preparative polyacrylamide gel electrophoresis. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry confirmed the presence of two proteins in the purified sample with sizes of 17,117.2 Da (PlcR2) and 78,417 Da (PlcH). Additionally, liquid chromatography electrospray mass spectrometry (LCMS) revealed that PlcH and PlcR2 are at a stoichiometry of 1 : 1. Western blot analysis demonstrated that the enzyme purifies as a heterodimeric complex, PlcHR2. PlcHR2 is only active on choline-containing phospholipids. It is equally active on phosphatidylcholine (PC) and sphingomyelin (SM) and is able to hydrolyse plasmenylcholine phospholipids (plasmalogens). Neither PlcHR2 nor the M. tuberculosis homologues are inhibited by D609 a widely used, competitive inhibitor of the Bacillus cereus PLC. PlcH, PlcR2, and the PlcHR2 complex bind calcium. While calcium has no detectable effect on enzymatic activity, it inhibits the haemolytic activity of PlcHR2. In addition to being required for the secretion of PlcH, the chaperone PlcR2 affects both the enzymatic and haemolytic properties of PlcH. Inclusive in these data is the conclusion that the members of this PC-PLC and phosphatase family possess a novel mechanism for the recognition and hydrolysis of their respective substrates.
Identifying Metrical and Temporal Structure With an Autocorrelation Phase Matrix (2006)

This article introduces a new method for detecting long-timescale structure in music. We describe a way to compute autocorrelation such that the distribution of energy in phase space is preserved in a matrix. The resulting Autocorrelation Phase Matrix (APM) is useful for several tasks involving metrical structure. In this article we describe the details of calculating the APM. We then show how phase-related regularities from music are stored in the APM and present two ways to recover these regularities. The simpler approach uses variance or entropy calculated on the distribution of information in the APM. The more complex approach explicitly searches through the phase and lag space of the APM to predict meter and tempo in parallel. We compare these approaches against standard autocorrelation for the task of tempo prediction on a relatively large database of annotated digital audio files. We demonstrate that better tempo prediction is achieved by exploiting the phase-related information in the APM.We argue that the APM is an effective data structure for tempo prediction and related applications, such as real-time beat induction and music analysis.
Bacterial and archaeal diversity in high altitude wetlands of the Chilean Altiplano (2013)

The microbial diversity of five unconnected high altitude (≥ 3800 m a.s.l.) wetlands from the Chilean Altiplano was analyzed by a culture-independent approach, using 16 S rRNA gene sequences of different microbial groups. The wetlands (Chungara Lake, Parinacota wetland, Piacota Lake, Salar de Huasco and Salar de Ascotan) differed in terms of habitat type and physicochemical properties. The bacterial communities of these systems were dominated by Bacteroidetes (24-94 % of the clones) and Proteobacteria (Alpha, Beta, Gamma and Delta subgroups) with smaller contributions by the Firmicutes, Actinobacteria, Planctomycetes, Verrucomicrobia, Chloroflexi, Cyanobacteria, Acidobacteria, Deinococcus-Thermus and Candidate Division WS3. Fourteen phylotypes matching Alphaproteobacteria were part of the marine Roseobacter clade, representing new clusters of this group. Archaeal diversity was much lower than that seen for bacteria, and was dominated by Euryarchaeota; however Crenarchaeota were also present. Considering the large differences in microbial community composition between sites and samples, the presence of eleven phylotypes common to two or more habitats is highlighted. The frequent presence of new taxa in different phylogenetic groups in the altiplanic wetlands studied here revealed the unique characteristics of Bacteria and Archaea in these fragile Andean ecosystems.
Modification of rapeseed oil with free fatty acids (2011)

Presently strickt World and European environ mental requirements made force on research, manufacture and use of environmentally friendly lubricants. Scientists lucking for the ways to reduce harm of lubricants to envi ronment and the cost of lubricants too. Both these prob lems can be solved using efficient natural lubricating materials. In current study the natural free fatty acid additive ADX 18 was used to reduce friction and wear lubricating&nbsp;with rapeseed oil. Tests were performed with standard four ball tribometer. The load was 150 N and 300 N. The results show positive influence of free fatty acid additive. How ever the effect in different loads is not equal. In the low loads (150 N) the wear reduction effect of additive is supe rior in comparison with reference oil. In the high loads (300 N) the wear reduction ability is not sufficient. Never theless the friction in both loads is less in comparison with the reference. The use of free fatty acid loaded rapeseed oil can reduce friction and wear in mechanisms with low load condition.http://dx.doi.org/10.5755/j01.mech.17.2.341
Effect of mitral valve replacement on left ventricular function in mitral regurgitation. (1983)

To evaluate the effect of mitral valve replacement on left ventricular function in mitral regurgitation, we measured (1) the end-systolic stress/volume ratio, which is practically independent of changes in loading conditions, and (2) the left ventricular contractile reserves upon isometric exercise, both before and one year after mitral valve replacement in 11 patients with mitral regurgitation. The end-systolic stress/volume ratio increased, though the ejection fraction decreased after mitral valve replacement. The ejection fraction decreased and the end-systolic stress/volume ratio remained unchanged during isometric exercise before operation, whereas afterwards the ejection fraction remained unchanged and the end-systolic stress/volume ratio increased during exercise. Ventricular function improves after mitral valve replacement in patients with mitral regurgitation, though the ejection fraction, which is affected by altered loading conditions, deteriorates. The left ventricular response to stress caused by isometric exercise is also improved after surgery.
A novel suicide shuttle plasmid for Streptococcus suis serotype 2 and Streptococcus equi ssp. zooepidemicus gene mutation (2016)

The mariner-based Himar1 system has been utilized for creating mutant libraries of many Gram-positive bacteria. Streptococcus suis serotype 2 (SS2) and Streptococcus equi ssp. zooepidemicus (SEZ) are primary pathogens of swine that threaten the swine industry in China. To provide a forward-genetics technology for finding virulent phenotype-related genes in these two pathogens, we constructed a novel temperature-sensitive suicide shuttle plasmid, pMar4s, which contains the Himar1 system transposon, TnYLB-1, and the Himar1 C9 transposase from pMarA and the repTAs temperature-sensitive fragment from pSET4s. The kanamycin (Kan) resistance gene was in the TnYLB-1 transposon. Temperature sensitivity and Kan resistance allowed the selection of mutant strains and construction of the mutant library. The SS2 and SEZ mutant libraries were successfully constructed using the pMar4s plasmid. Inverse-Polymerase Chain Reaction (Inverse-PCR) results revealed large variability in transposon insertion sites and that the library could be used for phenotype alteration screening. The thiamine biosynthesis gene apbE was screened for its influence on SS2 anti-phagocytosis; likewise, the sagF gene was identified to be a hemolytic activity-related gene in SEZ. pMar4s was suitable for mutant library construction, providing more information regarding SS2 and SEZ virulence factors and illustrating the pathogenesis of swine streptococcosis.
Key‐layered normal distributions transform for point cloud registration (2015)

A new scan matching algorithm is proposed using the concept of key layers. In the conventional multi‐layered normal distributions transform (MLNDT), the number of layers and iterations per layer are fixed and mismatches in point clouds occur due to the limited number of optimising iterations per layer. Moreover, the accuracy of registration is low and the number of layers is heuristically determined in MLNDT. The proposed key‐layered normal distributions transform (KLNDT) works well with both enhanced success rate and accuracy. It is also possible for KLNDT to register in higher layers than the traditional MLNDT.
Basic physics of gaseous dielectrics (1990)

Basic physical processes involved in the prebreakdown stages of gaseous dielectrics are discussed, with particular emphasis on electron attachment, electron-molecule scattering, and electron impact ionization. Particular emphasis is placed on the dielectric properties of gases at moderately high pressures (few kilopascals to few atmospheres) and under uniform DC conditions for which the electrons generated in the gas quickly reach a steady state, and thus electron-molecule interactions leading to electrical breakdown can be addressed assuming steady-state conditions even though the breakdown itself is a transient, nonequilibrium phenomenon. Utilization of the understanding of these basic processes for tailoring gases/mixtures with optimum dielectric strengths is indicated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Influence de l'hydrogène sur le frottement intérieur du titane (1978)

Le spectre de frottement intérieur d'un titane de pureté 5 N a été déterminé entre −190 °C et la température ambiante, après écrouissage à la température ambiante suivi d'un chargement en hydrogène. Les pics observés et leur évolution sont reliés à l'action de l'hydrogène, selon deux mécanismes: le désépinglage thermiquement activé des dislocations épinglées par les atomes d'hydrogène, et à plus haute température, le draǐnage par les dislocations des atomes d'hydrogène ayant segrégé dans leur voisinage. Les énergies d'activation correspondant à ces deux mécanismes sont respectivement de 0,28 et 0,40 eV et les facteurs de fréquence de l'ordre de quelques 1010 s−1. L'utilisation d'un métal très pur permet de dissocier ces deux mécanismes, qui existent toujours simultanément sur un métal de moindre pureté. Des expériences de dégazage à haute température sous ultra vide ont également été effectuées sur du titane de pureté commerciale et l'évolution du spectre après écrouissage a montré que l'on pouvait utiliser le frottement intérieur comme moyen de détection de l'hydrogène dans le titane. The internal friction spectra of a very pure titanium (5N) sample are studied in the temperature range −190 to +30 °C after cold-working at room temperature followed by hydrogenation. The observed relaxation peaks and their evolution are attributed to the action of hydrogen; two kinds of mechanism are considered: a thermally activated depinning of dislocations pinned by hydrogen atoms and, in a higher temperature range, a dragging by the dislocations of hydrogen atoms situated in their vicinity. The activation energies associated with these mechanisms are found to be 0.28 and 0.40 eV, respectively, the frequency factors being of the order of 1010 s−1. The use of this well purified metal permits a dissociation of these two mechanisms, which are always simultaneously present in a metal in which impurities are existent in a larger extent. Commercialy pure titanium is degasified in high vacuum at elevated temperature and the evolution of the damping spectra got after cold-working shows the possible use of internal friction as a means of hydrogen detection in titanium.
Cyclisierungsreaktionen von o‐Acylamino‐benzhydroxamsäure‐O‐alkylestern (1973)

Abstract o ‐Acylamino‐benzhydroxamsäure‐ O ‐alkylester ( 1 ) cyclisieren leicht zu den entsprechenden 2‐substituierten 3‐Alkoxy‐chinazolinonen 2 , wobei der Ringschluß möglicherweise über die tautomere Imid‐Form 4′ erfolgt. Da die Verwendung von basischen Katalysatoren für die Cyclisierung nicht erforderlich ist, sind die 2‐Halogenalkyl‐chinazolinone 5 somit gut zugänglich.