gebhart/patrepeval huggingface dataset:
Muscle-specific Overexpression Of Sirt1 Results In Incomplete Mitochondrial Biogenesis In Skeletal Muscle (2011)

The protein deacetylase, sirtuin 1 (SIRT1), has been proposed as a central mediator of exercise-induced mitochondrial biogenesis in skeletal muscle, due in part to its ability to regulate PGC-1α transcriptional activity. However, while acute and chronic endurance exercise increases the expression, activity and protein abundance of SIRT1, all in conjunction with increased mitochondrial biogenesis, transient over-expression of SIRT1 has been shown to reduce skeletal muscle oxidative capacity and PGC-1α expression. Thus, the precise role of SIRT1 in regulating skeletal muscle mitochondrial biogenesis, in vivo, remains unclear. PURPOSE: To determine the effect of SIRT1 overexpression in murine skeletal muscle on mitochondrial biogenesis and oxidative capacity. METHODS: Mice with a transcriptional stop cassette flanked by lox-P sites upstream of a constitutively-driven SIRT promoter were crossed with MCK-Cre mice, thus generating mice with muscle-specific over-expression of SIRT1 (mTgSIRT1). To assess mitochondrial adaptation and function, we analyzed protein and gene expression of key mitochondrial enzymes, as well as mitochondrial state III respiration in isolated mitochondria in skeletal muscle from mTgSIRT1 and floxed (CON) mice. RESULTS: SIRT1 gene and protein expression were increased ∼10 fold in mTgSIRT1 vs. CON mice (p<0.05). In line with this, PGC-1α gene and protein expression was significantly increased in mTgSIRT1 vs. CON mice, as was the gene expression of cytochrome-c (p<0.05). Despite the increase in SIRT1 and PGC-1α in mTgSIRT1 muscle, the gene expression of PGC-1α target genes, NRF1, NRF2, ERRα, PPARα, PPARδ, Tfam and mitofusin-2 were similar between groups. There was also no difference in state III respiration of isolated mitochondria between groups. CONCLUSIONS: These data demonstrate that induction of SIRT1 (and PGC-1α), per se, is not sufficient to induce complete mitochondrial biogenesis in skeletal muscle.
Synthesis and antitumor activity of spergualin analogues. II. Chemical modification of the spermidine moiety. (1987)

Chemical modifications of the spermidine moiety of an antitumor antibiotic, spergualin (Ia), and the structure-activity relationship are described. Replacement of spermidine with other polyamines decreased the antitumor activity against mouse leukemia L1210. Analogues containing an oxidized spermidine moiety that probably formed during oxidation with amine oxidase were inactive. Spermidine is indispensable for the antitumor activity. A facile method for the synthesis of glyoxyloyl polyamine, a key intermediate of spergualin-related compounds, is also reported.
Host Defense Peptide LL-37, in Synergy with Inflammatory Mediator IL-1β, Augments Immune Responses by Multiple Pathways (2007)

The human cathelicidin LL-37 is a cationic host defense peptide and serves as an important component of innate immunity. It has been demonstrated to be a multifunctional modulator of innate immune responses, although the mechanism(s) underlying this have not been well characterized. In this study, it was demonstrated that LL-37 synergistically enhanced the IL-1beta-induced production of cytokines (IL-6, IL-10) and chemokines such as macrophage chemoattractant proteins (MCP-1, MCP-3) in human PBMC, indicating a role in enhancing certain innate immune responses. Similarly, LL-37 synergistically enhanced chemokine production in the presence of GM-CSF, but IFN-gamma, IL-4, or IL-12 addition led to antagonism, indicating that the role of LL-37 in reinforcing specific immune responses is selective and restricted to particular endogenous immune mediators. The inhibition of G protein-coupled receptors and PI3K substantially suppressed the ability of IL-1beta and LL-37 to synergistically enhance the production of chemokine MCP-3. Consistent with this, the combination of IL-1beta and LL-37 enhanced the activation/phosphorylation of kinase Akt and the transcription factor CREB. The role of transcription factor NF-kappaB was revealed through the demonstration of enhanced phosphorylation of IkappaBalpha and the consequent nuclear translocation of NF-kappaB subunits p50 and p65, as well as the antagonistic effects of an inhibitor of IkappaBalpha phosphorylation. These results together indicate that the human host defense peptide LL-37 can work in synergy with the endogenous inflammatory mediator IL-1beta to enhance the induction of specific inflammatory effectors by a complex mechanism involving multiple pathways, thus reinforcing certain innate immune responses.
Regional lung perfusion estimated by electrical impedance tomography in a piglet model of lung collapse (2011)

The assessment of the regional match between alveolar ventilation and perfusion in critically ill patients requires simultaneous measurements of both parameters. Ideally, assessment of lung perfusion should be performed in real-time with an imaging technology that provides, through fast acquisition of sequential images, information about the regional dynamics or regional kinetics of an appropriate tracer. We present a novel electrical impedance tomography (EIT)-based method that quantitatively estimates regional lung perfusion based on first-pass kinetics of a bolus of hypertonic saline contrast. Pulmonary blood flow was measured in six piglets during control and unilateral or bilateral lung collapse conditions. The first-pass kinetics method showed good agreement with the estimates obtained by single-photon-emission computerized tomography (SPECT). The mean difference (SPECT minus EIT) between fractional blood flow to lung areas suffering atelectasis was -0.6%, with a SD of 2.9%. This method outperformed the estimates of lung perfusion based on impedance pulsatility. In conclusion, we describe a novel method based on EIT for estimating regional lung perfusion at the bedside. In both healthy and injured lung conditions, the distribution of pulmonary blood flow as assessed by EIT agreed well with the one obtained by SPECT. The method proposed in this study has the potential to contribute to a better understanding of the behavior of regional perfusion under different lung and therapeutic conditions.
A Mathematical Formula to Determine the Minimum Continuous Glucose Monitoring Duration to Assess Time-in-ranges: Sensitivity Analysis Over the Parameters (2021)

In diabetes management, the fraction of time spent with glucose concentration within the physiological range of [70-180] mg/dL, namely time in range (TIR) is often computed by clinicians to assess glycemic control using a continuous glucose monitoring sensor. However, a sufficiently long monitoring period is required to reliably estimate this index. A mathematical equation derived by our group provides the minimum trial duration granting a desired uncertainty around the estimated TIR. The equation involves two parameters, p<sub>r</sub> and α, related to the population under analysis, which should be set based on the clinician's experience. In this work, we evaluated the sensitivity of the formula to the parameters.Considering two independent datasets, we predicted the uncertainty of TIR estimate for a population, using the parameters of the formula estimated for a different population. We also stressed the robustness of the formula by testing wider ranges of parameters, thus assessing the impact of large errors in the parameters' estimates.Plausible errors on the α estimate impact very slightly on the prediction (relative discrepancy < 5%), thus we suggest using a fixed value for α independently on the population being analyzed. Instead, p<sub>r</sub> should be adjusted to the TIR expected in the population, considering that errors around 20% result in a relative discrepancy of ~10%.In conclusion, the proposed formula is sufficiently robust to parameters setting and can be used by investigators to determine a suitable duration of the study.
Sulfonated hollow sphere carbon as an efficient catalyst for acetalisation of glycerol (2013)

Sulfonated hollow sphere carbon (HSC-SO3H) was synthesized from carbonization of a SiO2–polymer core–shell structure, followed by removal of the SiO2 core and sulfonation with chlorosulfonic acid. HSC-SO3H shows superior performances in acetalisation of glycerol, which is related to the hollow sphere carbon shell with rich microporosity for good mass transfer in the reaction.
Quantum noise locking (2005)

Quantum optical states which have no coherent amplitude, such as squeezed vacuum states, cannot rely on standard readout techniques to generate error signals for control of the quadrature phase. Here we investigate the use of asymmetry in the quadrature variances to obtain a phase-sensitive readout and to lock the phase of a squeezed vacuum state, a technique which we call noise locking (NL). We carry out a theoretical derivation of the NL error signal and the associated stability of the squeezed and anti-squeezed lock points. Experimental data for the NL technique both in the presence and absence of coherent fields are shown, including a comparison with coherent locking techniques. Finally, we use NL to enable a stable readout of the squeezed vacuum state on a homodyne detector.
Amphiphilic particle-stabilized nanoliter droplet reactors with a multi-modal portable reader for distributive biomarker quantification (2023)

Abstract Compartmentalization, leveraging microfluidics, enables highly sensitive assays; but the requirement for significant infrastructure for their design, build, and operation limits access. Newer multi-material particle-based technologies thermodynamically stabilize monodisperse droplets as individual reaction compartments with simple liquid handling steps, precluding the need for expensive microfluidic equipment. Here, we further improve the accessibility of this lab on a particle technology to resource-limited settings by combining this assay system with a portable multi-modal reader, thus enabling nanoliter droplet assays in an accessible platform. We show the utility of this platform in measuring N-terminal propeptide B-type natriuretic peptide (NT-proBNP), a heart failure biomarker, in complex medium and patient samples. We report a limit of detection of ∼0.05 ng/ml and a linear response between 0.2 – 2 ng/ml in spiked plasma samples. We also show that, owing to the plurality of measurements per sample, “swarm” sensing acquires better statistical quantitation with a portable reader. Monte Carlo simulations show the increasing capability of this platform to differentiate between negative and positive samples, i.e. below or above the clinical cut-off for acute heart failure (∼0.1ng/ml), as a function of the number of particles measured. Our platform measurements correlate with gold standard ELISA measurement in cardiac patient samples, and achieve lower variation in measurement across samples compared to the standard well plate-based ELISA. Thus, we show the capabilities of a cost-effective droplet-reader system in accurately measuring biomarkers in nanoliter droplets for diseases that disproportionally affect underserved communities in resource-limited settings.
Acupuncture for post-stroke depression: a systematic review and network meta-analysis (2023)

This study was registered in the International Prospective Register of Systematic Reviews (PROSPERO) database in November 2020 and updated in July 2021. The registration number is CRD42020218752.
WE‐D‐17A‐03: Improvement of Accuracy of Spot‐Scanning Proton Beam Delivery for Liver Tumor by Real‐Time Tumor‐Monitoring and Gating System: A Simulation Study (2014)

Purpose: To improve the accuracy of spot‐scanning proton beam delivery for target in motion, a real‐time tumor‐monitoring and gating system using fluoroscopy images was developed. This study investigates the efficacy of this method for treatment of liver tumors using simulation. Methods: Three‐dimensional position of a fiducial marker inserted close to the tumor is calculated in real time and proton beam is gated according to the marker's distance from the planned position (Shirato, 2012). The efficient beam delivery is realized even for the irregular and sporadic motion signals, by employing the multiple‐gated irradiations per operation cycle (Umezawa, 2012). For each of two breath‐hold CTs (CTV=14.6cc, 63.1cc), dose distributions were calculated with internal margins corresponding to freebreathing (FB) and real‐time gating (RG) with a 2‐mm gating window. We applied 8 trajectories of liver tumor recorded during the treatment of RTRT in X‐ray therapy and 6 initial timings. Dmax/Dmin in CTV, mean liver dose (MLD), and irradiation time to administer 3 Gy (RBE) dose were estimated assuming rigid motion of targets by using in‐house simulation tools and VQA treatment planning system (Hitachi, Ltd., Tokyo). Results: Dmax/Dmin was degraded by less than 5% compared to the prescribed dose with all motion parameters for smaller CTV and less than 7% for larger CTV with one exception. Irradiation time showed only a modest increase if RG was used instead of FB; the average value over motion parameters was 113 (FB) and 138 s (RG) for smaller CTV and 120 (FB) and 207 s (RG) for larger CTV. In RG, it was within 5 min for all but one trajectory. MLD was markedly decreased by 14% and 5–6% for smaller and larger CTVs respectively, if RG was applied. Conclusions: Spot‐scanning proton beam was shown to be delivered successfully to liver tumor without much lengthening of treatment time. This research was supported by the Cabinet Office, Government of Japan and the Japan Society for the Promotion of Science (JSPS) through the Funding Program for World‐Leading Innovative R&amp;D on Science and Technology (FIRST Program), initiated by the Council for Science and Technology Policy (CSTP).
Random transparency targets for modulation transfer function measurement in the visible and infrared regions (1995)

Measurements of modulation transfer function (MTF), particularly for staring imager systems, are affected by the position of the test target with respect to the rows and columns of the detector array. We demonstrate that random transparency targets of known spatial-frequency content allow shift-invariant MTF measurement in the visible, 3- to 5-μm, and 8- to 12-μm bands. Design criteria and verification procedures for the targets are presented.
Different role of oxidative stress in paraventricular nucleus and rostral ventrolateral medulla in cardiovascular regulation in awake spontaneously hypertensive rats (2012)

These findings indicate that inhibition of oxidative stress in the PVN decreases HR, but not BP in SHR, and elicits a further decrease in HR, but not BP, by interacting with the RVLM. Taken together, the oxidative stress in the PVN and RVLM plays a different role for cardiovascular regulation in SHR.
A carbon nanotube immunosensor for Salmonella (2011)

Antibody-functionalized carbon nanotube devices have been suggested for use as bacterial detectors for monitoring of food purity in transit from the farm to the kitchen. Here we report progress towards that goal by demonstrating specific detection of Salmonella in complex nutrient broth solutions using nanotube transistors functionalized with covalently-bound anti-Salmonella antibodies. The small size of the active device region makes them compatible with integration in large-scale arrays. We find that the on-state current of the transistor is sensitive specifically to the Salmonella concentration and saturates at low concentration (&amp;lt;1000 cfu/ml). In contrast, the carrier mobility is affected comparably by Salmonella and other bacteria types, with no sign of saturation even at much larger concentrations (108 cfu/ml).
Effect of Salt Concentration on Ion Clustering and Transport in Polymer Solid Electrolytes: A Molecular Dynamics Study of PEO–LiTFSI (2018)

Currently available solid polymer electrolytes for Li-ion cells require deeper understanding and significant improvement in ionic transport properties to enable their use in high-power batteries. We use molecular dynamics simulations to model the solid amorphous polymer electrolyte system comprising poly(ethylene) oxide (PEO), lithium, and bis(trifluoromethane)sulfonimide anion (TFSI), exploring effects of high salt concentrations relevant for battery applications. Using statistical analysis of ion distribution and transport, we investigate the significant effect that salt concentration has on ion mobility. At practical salt concentrations, a previously undetected ensemble of Li–TFSI clusters emerges where Li ions have significantly lower coordination by the polymer, and this results in their significantly lower mobility as compared to Li ions coordinated by the polymer. We also find the tendency for cation–anion clusters to be asymmetrical, with the anions in greater number than Li cations, which may further affect the transport properties of this material. The existence of such negatively charged clusters has been recently speculated to explain the experimentally observed negative transference number at high LiTFSI concentrations in PEO. Our methodology enables us to suggest strategies for improvement of transport properties and can be generalized to other polymer–Li–salt combinations.
Ordering of guarded and unguarded stores for no-sync I/O (2023)

A parallel computing system processes at least one store instruction. A first processor core issues a store instruction. A first queue, associated with the first processor core, stores the store instruction. A second queue, associated with a first local cache memory device of the first processor core, stores the store instruction. The first processor core updates first data in the first local cache memory device according to the store instruction. The third queue, associated with at least one shared cache memory device, stores the store instruction. The first processor core invalidates second data, associated with the store instruction, in the at least one shared cache memory. The first processor core invalidates third data, associated with the store instruction, in other local cache memory devices of other processor cores. The first processor core flushing only the first queue.
The role of the direct wave and Green's theorem in seismic interferometry and spurious multiples (2007)

Techniques to estimate the Green's function between two measured points using wavefield correlations and/or crosscorrelations are classified as seismic interferometry. In this paper we provide a unifying framework for understanding a broad class of interferometric techniques using Green's theorem. This framework and foundation allows spurious multiples that occur in certain interferometric approaches to be anticipated and fully explain as a consequence of approximations and compromises made within Green's theorem. We also develop a set of more effective seismic interferometry methods, where fewer compromises effect in a better result. Standard seismic interferometry is based on far‐field and one‐way approximations of the Green's theorem relating two wavefield measurements in the same volume. This method, when applied to surface seismic data, reconstructs the wavefield with a squared source signature and adds spurious multiples, whose amplitudes are comparable to the reconstructed primaries. The artefacts introduced, reduce the method's value. The spurious multiples come from the approximations made to avoid the need of the wavefield's normal derivative. We propose and examine various alternative approaches to seismic interferometry which overcome the appearance of spurious multiples and provides an improvement over traditional methods. One method uses Green's theorem relating a reference Green's function with the measured wavefield. The data are reconstructed without spurious multiples and with a wavelet due to a single source. A synthesized wavefield ought to have a single factor of the wavelet. Using an analytic reference Green's function, data can be extrapolated to positions where no receivers or sources were located. In addition, we provide another form of Green's theorem by imposing a two‐surface Dirichlet boundary condition to the reference Green's function; this method only requires the total wavefield. The normal derivative of the field is not needed.
Artifacts-reduced 2D cine SSFP with flow compensation for myocardial BOLD imaging (2010)

Robust image quality is critical for reliable detection and evaluation of myocardial oxygenation changes with blood-oxygen-level-dependent (BOLD) imaging. Recently, balanced SSFP methods have been employed to overcome image quality limitations associated with myocardial BOLD methods. However, the long TRs required for BOLD contrast, can lead to unwanted flow/motion artifacts, ultimately compromising image quality.
Annealing of Cobaht-Ferrous Ferrite Films on Glass Substrates in the Remanent State (1973)

It is well known that when a cobalt‐ferrous ferrite crystal is annealed in a magnetic field below its Curie temperature, a uniaxial anisotropy will be induced in addition to its normal cubic anisotropy. The magnetic field applied during the annealing has no direct contribution to the induction of the uniaxial anisotropy. Its only function is to align the magnetization in the field direction. It is the direction of the magnetization which determines the direction of the uniaxial anisotropy. Based on this principle, one should be able to induce a magnetic easy axis in cobalt‐ferrous ferrite by magnetizing it at room temperature, followed by a heat treatment in its remanent state. This was done on cobalt‐iron oxide films on glass substrates. Results on films having different Co/Fe ratios will be discussed.
Characteristics of deep-well 4.8-μm emitting quantum-cascade lasers grown by MOCVD (2009)

In this work we present the characteristics of a novel type of quantum-cascade (QC) laser: the deep-well (DW) QC device, which, unlike conventional QC lasers, contains a superlattice of quantum wells and barriers of different composition, respectively. The fabrication of DW-QC devices is made possible by the use of metal-organic chemical vapor deposition (MOCVD), a crystal growth technique which allows one to easily vary the composition of wells and barriers within QC structures, thus providing significantly increased flexibility in optimizing the device design. We have designed such varying-composition QC structures to have deep quantum wells in and tall barriers in and around the active region. DW- QC laser structures have fabricated into 19 &mu;m-wide ridges and 3 mm-long chips. Threshold-current densities as low as 1.5 kA/cm<sup>2</sup> are obtained at room temperature in the 4.6-4.8 &mu;m wavelength region. In conventional QC lasers emitting in the 4.5-5.5&mu;m range there is substantial thermionic carrier leakage from the upper laser level to the continuum, as evidenced by a significant decrease in the slope efficiency above 250 K, which is understandable given the relatively small (i.e., ~ 200 meV) energy differential, &delta;E, between the upper lasing level and the top of the exit barrier. For the DW design carrier leakage is suppressed due to deep active wells and tall barriers, such that &delta;E reaches values in excess of 400 meV. Preliminary results include a threshold-current characteristic temperature, T<sub>0</sub>, value of 218 K over the temperature range: 250- 340 K.