gebhart/patrepeval huggingface dataset:
Transgenic Mice Expressing Human Interleukin-10 in the Antigen-Presenting Cell Compartment Show Increased Susceptibility to Infection withMycobacterium aviumAssociated with Decreased Macrophage Effector Function and Apoptosis (2002)

Interleukin-10 (IL-10) is thought to play an important role in the regulation of microbial immunity. While T-cell-derived IL-10 has been shown to suppress cell-mediated immunity, there has been debate as to whether antigen presenting cell (APC)-derived cytokine can perform the same function in vivo. To assess the influence of APC-produced IL-10 on host resistance to mycobacterial infection, transgenic mice expressing human IL-10 under the control of the major histocompatibility complex class II promoter (hu10Tg) were infected with Mycobacterium avium, and bacterial burdens and immune responses were compared with those observed in wild-type (wt) animals. Hu10Tg mice harbored substantially higher numbers of M. avium and succumbed 16 to 18 weeks postinfection. The granulomas in infected hu10Tg mice showed marked increases in both acid-fast bacilli and host macrophages. In addition, these animals displayed a dramatic increase in hepatic fibrosis. The increased susceptibility of the hu10Tg mice to M. avium infection is independent of T-cell-produced endogenous murine IL-10, since bacterial burdens in mice derived by crossing hu10Tg mice with murine IL-10-deficient mice were not significantly different from those in hu10Tg mice. Importantly, gamma interferon (IFN-gamma) responses were not decreased in the infected transgenic animals from those in wt animals, suggesting the normal development of Th1 effector cells. In contrast, mycobacterium-induced macrophage apoptosis as well as production of TNF, nitric oxide, and IL-12p40 were strongly inhibited in hu10Tg mice. Together, these data indicate that APC-derived IL-10 can exert a major inhibitory effect on control of mycobacterial infection by a mechanism involving the suppression of macrophage effector function and apoptosis.
Photodarkening in Upconversion Pumped Thulium Doped Fluorozirconate Fibre Lasers (1995)

Upconversion pumped lasing in rare earth doped fluorozirconate optical fibre offers the potential for compact blue green laser sources pumped by commercially available infrared laser diodes. A promising candidate for such a source is the thulium system first demonstrated by Steve Grubb and co-workers [1], which lases in the blue at 482 nm with a single pump source at about 1130 nm. Figure 1 illustrates the relevant energy levels of the trivalent thulium ion, and the upconversion mechanism. Ions excited to the short lived H 5 and F 23 levels decay rapidly by phonon emission to the metastable H 4 and F 4 levels from which further upconversion transitions occur. The centre wavelengths of the three transitions are respectively 1220 nm (H 6 to H s ), 1130 nm (H 4 to F 2 ), and 1150 nm (F 4 to G 4 ), but because of the broadening of the transitions in glass it is possible to excite all three with a single wavelength pump in the range 1110 nm to 1160 nm. The next energy level above G 4 in thulium is D 2 with a transition of 1480 nm separating the two, so that further upconversion above G 4 should not occur, or only very weakly. A low phonon energy host material such as ZBLAN fluorozirconate glass is necessary so that the metastable levels do not decay rapidly by phonon emission.
ChemInform Abstract: Architecture at the Nanoscale‐Self‐Pillared Zeolite Nanosheets (2013)

Abstract Review: 10 refs.
Toward simulating quantum field theories with controlled phonon-ion dynamics: A hybrid analog-digital approach (2021)

Quantum field theories are the cornerstones of modern physics, providing relativistic and quantum mechanical descriptions of physical systems at the most fundamental level. Simulating real-time dynamics within these theories remains elusive in classical computing. This provides a unique opportunity for quantum simulators, which hold the promise of revolutionizing our simulation capabilities. Trapped-ion systems are successful quantum-simulator platforms for quantum many-body physics and can operate in digital, or gate-based, and analog modes. Inspired by the progress in proposing and realizing quantum simulations of a number of relativistic quantum field theories using trapped-ion systems, and by the hybrid analog-digital proposals for simulating interacting boson-fermion models, we propose hybrid analog-digital quantum simulations of selected quantum field theories, taking recent developments to the next level. On one hand, the semi-digital nature of this proposal offers more flexibility in engineering generic model interactions compared with a fully-analog approach. On the other hand, encoding the bosonic fields onto the phonon degrees of freedom of the trapped-ion system allows a more efficient usage of simulator resources, and a more natural implementation of intrinsic quantum operations in such platforms. This opens up new ways for simulating complex dynamics of e.g., Abelian and non-Abelian gauge theories, by combining the benefits of digital and analog schemes.
Application-aware aggregations in a columnar in-memory database (2011)

The reunification of online transactional processing and online analytical processing in one single database has been proposed recently as the advent of columnar in-memory databases makes this both viable and feasible. Compared to traditional row-based databases, resource-intensive operations such as the aggregation can now be executed with high performance. This has emerged to the radical approach of eliminating materialized aggregate tables and calculate all aggregations on the fly. This paper contributes by investigating application and data characteristics that have an influence on the aggregation performance in columnar in-memory databases. In particular, we have examined the Availability-to-Promise application that calculates if a desired order can be fulfilled on the requested date and in the requested quantity. We have implemented a prototype that incorporates our identified characteristics and backed up our findings with relevant experiments and real-life customer data.
346 PRECURSORS OF SYSTEM II ETHYLENE SYNTHESIS IN SENESCING CARNATION PETALS (1994)

Methionine (MET) is considered the first committed precursor of ethylene (C 2 H 4 ), and the pathway has been established as MET → S-adenosylmethionine (SAM) → 1-aminocyclopropane-1-carboxylic acid (ACC) → C 2 H 4 . It has been suggested that another pathway to C 2 H 4 may exist, and this pathway has been labeled System II. Our objective was to evaluate several compounds as possible precursors of System II C 2 H 4 production. `White Sim' carnations were placed continuously in 20 mM solutions of MET, ACC, δ-aminolevulinic acid, glutamic acid, α-ketoglutarate, or homocysteine. Deionized water was the control. C 2 H 4 production from the entire flower was measured, and ACC in the basal portion of the petals was quantified. Flowers treated with ACC exhibited the greatest C 2 H 4 production and accumulation of ACC. Homocysteine caused greater production of C 2 H 4 and accumulated more ACC than MET and the other possible precursors. These results suggest that homocysteine may be involved in System II C 2 H 4 production in senescing carnation petals.
System model of an inertial navigation system using SystemC-AMS. (2005)

This paper presents an approach for modeling an inertial navigation system. This system consists of a 3D acceleration and rotation sensor array, analog and digital error correction, gravitation compensation, supporting point extraction, serial interface and software application. Analogue interfaces are described on lowest abstraction level to allow easy exchange and refinement of components. Modeling is achieved using SystemC-AMS for analogue parts and SystemC for digital and software components. The SystemC extension library SVE is used allowing high abstraction levels for communication between main components. The model is simulated and verificated by stimulating with different accelerations and rotations representing sensor movements.
A sensor network for non-intrusive and efficient leak detection in long pipelines (2011)

Our society relies on extensive pipeline networks to transfer and deliver water, oil, etc. In many cases the pipeline extends over hundreds of miles and run through inhospitable environments. The pipes are often subject to erosion over time due to the parametric conditions. In addition, pipes carrying valuable commodity may be subject to theft, sabotage, etc. Leakage not only would waste resources, but also can be harm and hazardous. Therefore detecting leakage and containing its negative effect is very important. Current pipeline monitoring systems are inefficient and costly. They lack responsiveness and often report the problem after significant fluid is spilled. Furthermore, current systems involve mobile equipment and significant manpower. This paper describes the design of a wireless sensor networks that continuously monitor a pipeline and provide an early warning when leakage starts. The proposed leak detection system employs non-intrusive methods to track the flow speed and interprets the drop of flow volume as indication of liquid loss through a crack in a pipe. The system is composed of a set of ultrasonic transducers that are mounted around the pipe in multiple locations. The system combines the transit-time and Doppler based flow speed measurements in order to deal with various liquid characteristics. The data collected by the individual components are sent over multi-hop routes to a base-station over radio links for further analysis. The simulation results have confirmed the effectiveness of the proposed system.
Recent Research in Chronicles (2009)

This article surveys trends in Chronicles scholarship from 1994 to 2007. Most of the trends established by 1993 have continued with more depth and focus, although with a few challenges. These trends include: refining the distinctions between Chronicles and Ezra-Nehemia as coming from separate authors/editors; recognizing the integral role of the genealogies; and examining the literary artistry of the Chronicler. Newer trends include: pursuing the interplay between orality, on the one hand, and textuality and literacy, on the other; and bringing insights from an increasing sociological understanding of the Persian and Hellenistic periods in general. Recent years have also seen a wealth of new commentaries.
Cooperation between soluble factors and integrin‐mediated cell anchorage in the control of cell growth and differentiation (1996)

Recently it has become clear that integrins and other adhesive receptors play an important role in the control of cell growth and differentiation. In various cell types, anchorage to the extracellular matrix via integrins strongly influences the ability of the cell to respond to soluble mitogens or to differentiation factors. Thus adhesive receptors must generate signals that influence cell behavior. Some of the pathways of adhesion receptor signaling are now beginning to be worked out, but there is still much to learn. In particular, the mechanistic basis for the cooperation between anchorage signals and signals from soluble growth and differentiation factors remains ill-defined. This review will examine some of the current information linking adhesion receptors to control of mitogenesis and differentiation.
Activation of gene expression by human herpesvirus 6 is reporter gene-dependent (1991)

Infection with human herpesvirus 6 (HHV-6) was found to up-regulate expression of human immunodeficiency virus and human T cell leukaemia virus type I (HTLV-I) long terminal repeat sequence (LTR), and herpes simplex virus type 1 (HSV-1) gD chloramphenicol acetyltransferase (CAT) constructs transfected into the T cell line, J. Jhan. Activation by HHV-6 was due to one or more viral proteins produced early in infection and, in the case of the HTLV-I LTR, was synergistic to induction mediated by the HTLV-I tax gene product. Neither the HTLV-I enhancer nor basal promoter elements of the HSV-1 gD gene were essential for activation and no increase in accumulated HTLV-I mRNA was observed due to HHV-6 infection. Induction by HHV-6 was found to be dependent on the reporter construct used, because the CAT gene and, to a lesser extent, the HSV-1 thymidine kinase gene were responsive to HHV-6 infection although no significant activation of growth hormone constructs was observed. Our results bear a strong resemblance to those obtained for the Epstein-Barr virus BMLF1 gene, indicating that the major HHV-6 trans-activator may be a homologue of this gene.
Synthesis, spectroscopic, thermal, antimicrobial and electrochemical characterization of some novel Ru(iii), Pt(iv) and Ir(iii) complexes of pipemidic acid (2018)

Three new solid complexes of pipemidic acid (Pip-H) with Ru<sup>3+</sup>, Pt<sup>4+</sup> and Ir<sup>3+</sup> were synthesized and characterized. Pipemidic acid acts as a uni-dentate chelator through the nitrogen atom of the -NH piperazyl ring. The spectroscopic data revealed that the general formulas of Pip-H complexes are [M(L) <sub><i>n</i></sub> (Cl) <sub><i>x</i></sub> ]·<i>y</i>H<sub>2</sub>O ((1) M = Ru<sup>3+</sup>, L: Pip-H, <i>n</i> = 3, <i>x</i> = 3, <i>y</i> = 6; (2) M = Pt<sup>4+</sup>, L: Pip-NH<sub>4</sub>, <i>n</i> = 2, <i>x</i> = 4, <i>y</i> = 0 and (3) M = Ir<sup>3+</sup>, L: Pip-H, <i>n</i> = 3, <i>x</i> = 3, <i>y</i> = 6). The number of water molecules with their locations inside or outside the coordination sphere were assigned <i>via</i> thermal analyses (TG, DTG). The DTG curves refer to 2-3 thermal decomposition steps where the first decomposition step at a lower temperature corresponds to the loss of uncoordinated water molecules followed by the decomposition of Pip-H molecules at higher temperatures. Thermodynamic parameters (<i>E</i>*, Δ<i>S</i>*, Δ<i>H</i>* and Δ<i>G</i>*) were calculated from the TG curves using Coats-Redfern and Horowitz-Metzeger non-isothermal models. X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) techniques were carefully used to assign properly the particle sizes of the prepared Pip-H complexes. The biological enhancement of Pip-H complexes rather than free chelate were assessed <i>in vitro</i> against four kinds of bacteria G(+) (<i>Staphylococcus epidermidis</i> and <i>Staphylococcus aureus</i>) and G(-) (<i>Klebsiella</i> and <i>Escherichia coli</i>) as well as against the human breast cancer (MCF-7) tumor cell line.
Comment on: Methotrexate pharmacogenomics in rheumatoid arthritis: introducing false positive report probability: reply (2009)

SIR, We should thank Barretta and colleagues [1] for bringing to our attention the recent and somewhat severe criticism of the false positive report probability (FPRP) method developed by Wacholder et al. [2] in their comment [3] on our recently published editorial [4]. Obviously, biostatisticians are not able to reach a consensus on the methods that best control for false positives in genetic association studies. We are all faced with the multiple comparison issue, and Bonferroni adjustments are the most commonly employed methods to minimize type I error. However, Bonferroni adjustments have serious limitations and biases, they are overly conservative and do not make much sense in exploratory candidate gene approaches because the level of significance of a candidate single nucleotide polymorphism (SNP) depends on the number of other SNPs measured. Alternatives to the sacrosanct, ‘P-values’ are needed and the concept of FPRP that uses Bayesian statistics has been extensively discussed and used in the literature. What is appealing with the FPRP is its flexibility and the assignment of a prior probability that is really the choice of the reader, reviewer and/or editors. If it is true that FPRP promotes false positives, it is also true that Bonferroni adjustment promotes false negatives. A compromise is needed and perhaps a more stringent prior probability should be used with FPRP. It should be noted that Lucke’s criticism of the FPRP is followed by a proposed alternative, the conditional error probability. Furthermore, another Bayesian method has been recently proposed by Wakefield [5] (Bayesian False Discovery probability). It will be important for biostatisticians to reach a consensus and provide us with the most appropriate guidelines to adjust for multiple testing in pharmacogenetic studies.
A Review on the Extraction Methods Use in Medicinal Plants, Principle, Strength and Limitation (2015)

Medicinal plants are gaining much interest recently because their use in ethno medicine treating common disease such as cold, fever and other medicinal claims are now supported with sound scientific evidences. The study on medicinal plants started with extraction procedures that play a critical role to the extraction outcomes (e.g. yield and phytochemicals content) and also to the consequent assays performed. A wide range of technologies with different methods of extraction is available nowadays. Hence, this review aim to describe and compare the most commonly used methods based on their principle, strength and limitation to help evaluating the suitability and economic feasibility of the methods.
Survival by Depth of Response and Efficacy by International Metastatic Renal Cell Carcinoma Database Consortium Subgroup with Lenvatinib Plus Pembrolizumab Versus Sunitinib in Advanced Renal Cell Carcinoma: Analysis of the Phase 3 Randomized CLEAR Study (2023)

In this report of the CLEAR trial, we explored the survival of patients with advanced renal cell carcinoma by assessing how well they initially responded to treatment. We also explored how certain groups of patients responded to treatment overall. Patients were assigned to cycles of either lenvatinib 20 mg daily plus pembrolizumab 200 mg every 3 wk or sunitinib 50 mg daily for 4 wk (followed by a 2-wk break). Patients who either had a "complete response" or had their tumors shrunk by >75% within 6 mo after starting treatment with lenvatinib plus pembrolizumab had better survival than those with less tumor reduction by 6 mo. Additionally, patients who had more severe disease (as per the International Metastatic Renal Cell Carcinoma Database Consortium) at the start of study treatment survived for longer without disease progression with lenvatinib plus pembrolizumab than with sunitinib.
starmapVR: immersive visualisation of single cell spatial omic data (2020)

Abstract Motivation Advances in high throughput single-cell and spatial omic technologies have enabled the profiling of molecular expression and phenotypic properties of hundreds of thousands of individual cells in the context of their two dimensional (2D) or three dimensional (3D) spatial endogenous arrangement. However, current visualisation techniques do not allow for effective display and exploration of the single cell data in their spatial context. With the widespread availability of low-cost virtual reality (VR) gadgets, such as Google Cardboard, we propose that an immersive visualisation strategy is useful. Results We present starmapVR, a light-weight, cross-platform, web-based tool for visualising single-cell and spatial omic data. starmapVR supports a number of interaction methods, such as keyboard, mouse, wireless controller and voice control. The tool visualises single cells in a 3D space and each cell can be represented by a star plot (for molecular expression, phenotypic properties) or image (for single cell imaging). For spatial transcriptomic data, the 2D single cell expression data can be visualised alongside the histological image in a 2.5D format. The application of starmapVR is demonstrated through a series of case studies. Its scalability has been carefully evaluated across different platforms. Availability and implementation starmapVR is freely accessible at https://holab-hku.github.io/starmapVR , with the corresponding source code available at https://github.com/holab-hku/starmapVR under the open source MIT license. Supplementary Information Supplementary data are available at Bioinformatics online.
Buckled graphene-like materials in ultrashort and strong optical fields (2016)

This paper investigates the interaction of buckled Dirac materials (silicene and germanene) with ultrashort and ultrastrong optical pulses. Highly intensive few-cycle pulses strongly modify the electronic and optical properties of these two dimensional materials. Electron dynamics in such a short optical pulse is coherent and can be robustly controlled by altering the propagation direction, as well as the polarization angle of the pulse. The strong nonlinearity of the system for fields applied (~ V/Å) causes the violation of the charge (C) and parity (P) symmetries, effectively reducing the system’s symmetry from hexagonal to triangular. Such symmetry violations are related to the electron transfer between the sublattices caused by the normal field component and result in nonreciprocity, optical rectification and the appearance of a cross current.
Protein and DNA Reactions Stimulated by Electromagnetic Fields (2008)

The stimulation of protein and DNA by electromagnetic fields (EMF) has been problematic because the fields do not appear to have sufficient energy to directly affect such large molecules. Studies with electric and magnetic fields in the extremely low-frequency range have shown that weak fields can cause charge movement. It has also been known for some time that redistribution of charges in large molecules can trigger conformational changes that are driven by large hydration energies. This review considers examples of direct effects of electric and magnetic fields on charge transfer, and structural changes driven by such changes. Conformational changes that arise from alterations in charge distribution play a key role in membrane transport proteins, including ion channels, and probably account for DNA stimulation to initiate protein synthesis. It appears likely that weak EMF can control and amplify biological processes through their effects on charge distribution.
Ultra Trace Determination Scheme for26Al by High-Resolution Resonance Ionization Mass Spectrometry using a Pulsed Ti:Sapphire Laser (2008)

We propose an ultra trace analysis approach for 26Al by high-resolution Resonance Ionization Mass Spectrometry (RIMS) using a pulsed narrow band-width Ti:Sapphire laser. For ensuring efficient ionization and high isotopic selectivity in RIMS of Al, we developed an injection seeded pulsed Ti:Sapphire laser with high repetition rate operation at up to 10 kHz. The laser produced an output power of 2 W and a spectral band-width of ~20 MHz with a repetition rate of 7 kHz. A first demonstration of its performance was done by detecting stable 27Al using RIMS.
A 0.1–2-GHz Quadrature Correction Loop for Digital Multiphase Clock Generation Circuits in 130-nm CMOS (2016)

A 100-MHz-2-GHz closed-loop analog in-phase/ quadrature correction circuit for digital clocks is presented. The proposed circuit consists of a phase-locked looptype architecture for quadrature error correction. The circuit corrects the phase error to within a 1.5° up to 1 GHz and to within 3° at 2 GHz. It consumes 5.4 mA from a 1.2 V supply at 2 GHz. The circuit was designed in UMC 0.13-μm mixed-mode CMOS with an active area of 102 μm×95 μm. The impact of duty cycle distortion has been analyzed. High-frequency quadrature measurement related issues have been discussed. The proposed circuit was used in two different applications for which the functionality has been verified.
Response to ‘Comment on “A critical assessment on two predictive models of binary vapor–liquid equilibrium”’ by A. Klamt, Phys. Chem. Chem. Phys., 2004,6, DOI: 10.1039/b411213j (2004)

The first page of this article is displayed as the abstract.