gebhart/patrepeval huggingface dataset:
TRPV1 Gene Knockout Impairs Postischemic Recovery in Isolated Perfused Heart in Mice (2005)

Thus, our data show that (1) TRPV1 gene deletion decreases injury-induced SP release and impairs cardiac recovery function after ischemia/reperfusion injury; (2) TRPV1 gene deletion leads to reconditioning of the heart with improved postischemic recovery compared with that induced by acute TRPV1 blockade and in terms of cardiac response to exogenous SP; and (3) blockade of the NK1 but not CGRP receptors worsens postischemic recovery of hearts in both genotypes. Taken together, these data indicate that TRPV1 plays a role in protecting the heart from injury possibly via increasing SP release and that deletion of this receptor reconditions the heart for escaping, at least in part, from injury possibly via enhancing NK1 receptor function.
Optimisation of squalene from palm oil mesocarp using supercritical carbon dioxide (2015)

A promising technique of Green Supercritical Carbon Dioxide (SC-CO2) process was developed for the extraction of squalene from palm oil mesocarp. In this study, the green SC-CO2 was compared with the conventional Soxhlet extraction for quantify the best extraction method. The independent variables in SC-CO2 were selected as follows: temperature (45–75 °C), pressure (16–30 MPa) and CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> flow rate (2–5 ml/min). The responses are oil yield and the concentration of squalene. On the other hands, the conventional soxhlet extraction condition was type of solvents. Furthermore, the conditions of SC-CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> extraction for squalene and oil yield were optimized by response surface methodology (RSM) following Box-Behnken Design (BBD). The optimum conditions were at pressure (16 MPa), temperature (45.01 °C) and CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> flow rate (2 ml/min) and the concentration of squalene was 0.506%. Meanwhile for soxhlet extraction method showed the concentration of squalene was 0.143% with chloroform. In overall, the results indicated the green SC-CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> was the best an alternative technique.
Neural-Network Based Self-Initializing Algorithm for Multi-Parameter Optimization of High-Speed ADCs (2020)

This brief proposes a new automatic model parameter selection approach for determining the optimal configuration of high-speed analog-to-digital converters (ADCs) using a combination of particle swarm optimization (PSO) and stochastic gradient descent (SGD) algorithm. The proposed hybrid method first initializes the PSO algorithm to search for optimal neural-network configuration via the particles moving in finite search space with coarse quantization. Using the PSO estimates, the SGD algorithm then finds the global optimum solution. The global search ability of the PSO algorithm and the local search ability of the SGD are thus exploited to determine an optimal solution that is close to the global optimum with reduced latency. Several experiments were constructed to optimize the non-linearities in Nyquist flash and pipeline ADC datasets to show that the neural networks trained by the PSO-SGD algorithm outperform the random search-based performance optimization. Comparative resource analysis of the proposed algorithm is also conducted against the state-of-the-art that highlights improved latencies and performance with similar area and implementation complexity.
Xenobiotic‐Metabolizing gene polymorphisms and ovarian cancer risk (2010)

Because selected xenobiotic-metabolizing enzymes process pro-carcinogens that could initiate ovarian carcinogenesis, we hypothesized that single nucleotide polymorphisms (SNPs) in the genes encoding xenobiotic-metabolizing enzymes are associated with risk of ovarian cancer. Cases with invasive epithelial ovarian cancer (N = 1571 including 956 of serous sub-type) and controls (N = 2046) from three studies were genotyped at 11 SNPs in EPHX1, ADH4, ADH1A, NQO2, NAT2, GSTP1, CYP1A1, and NQO1, following an initial SNP screen in a subset of participants. Logistic regression analysis of genotypes obtained via Illumina GoldenGate and Sequenom iPlex technologies revealed the following age- and study-adjusted associations: EPHX1 rs1051740 with increased serous ovarian cancer risk [per-allele odds ratio (OR) 1.17, 95% confidence interval (95% CI) 1.04-1.32, P = 0.01), ADH4 r1042364 with decreased ovarian cancer risk (OR 0.90, 95% CI: 0.81-1.00, P = 0.05), and NQO1 rs291766 with increased ovarian cancer risk (OR 1.11, 95% CI: 1.00-1.23, P = 0.04). These findings are consistent with prior studies implicating these genes in carcinogenesis and suggest that this collection of variants is worthy of follow-up in additional studies.
Electronically Reconfigurable Reflective Phase Shifter for Circularly Polarized Reflectarray Systems (2016)

This letter presents the design of a two-port electronically reconfigurable phase shifter for circularly polarized reflectarray systems at microwave frequencies. The phase shifter is based on 3 dB/90° couplers combined with reflective circuits that introduce sequentially the phase variation. Each reflective circuit, formed by printed elements (L) and tunable varactors, produces the phase variation due to the variable capacity value of the varactor. The phase shifting process includes three different stages of phase shifting for the signal in its way from the input port towards the output port through the phase shifter. Both ports are interchangeable, acting either as input or output ports. This fulfils the reflection requirements of circularly polarized reflectarrays, being especially suitable for this purpose. The complete design, together with its circuital behavior and performance results, are depicted in this document.
IFN gamma regulates proliferation and neuronal differentiation by STAT1 in adult SVZ niche (2015)

The adult subventricular zone (SVZ) is the main neurogenic niche in normal adult brains of mice and rats. Interferon gamma (IFNγ) has somewhat controversially been associated with SVZ progenitor proliferation and neurogenesis. The in vivo involvement of IFNγ in the physiology of the adult SVZ niche is not fully understood and its intracellular mediators are unknown. Here we show that IFNγ, through activation of its canonical signal transducer and activator of transcription 1 (STAT1) pathway, acts specifically on Nestin+ progenitors by decreasing both progenitor proliferation and the number of cycling cells. In addition, IFNγ increases the number of neuroblasts generated without shifting glial fate determination. The final result is deficient recruitment of newborn neurons to the olfactory bulb (OB), indicating that IFNγ-induced stimulation of neuronal differentiation does not compensate for its antiproliferative effect. We conclude that IFNγ signaling via STAT1 in the SVZ acts dually as an antiproliferative and proneurogenic factor, and thereby regulates neurogenesis in normal adult brains.
Planetary gearbox fault feature enhancement based on combined adaptive filter method (2015)

The reliability of vibration signals acquired from a planetary gear system (the indispensable part of wind turbine gearbox) is directly related to the accuracy of fault diagnosis. The complex operation environment leads to lots of interference signals which are included in the vibration signals. Furthermore, both multiple gears meshing with each other and the differences in transmission rout produce strong nonlinearity in the vibration signals, which makes it difficult to eliminate the noise. This article presents a combined adaptive filter method by taking a delayed signal as reference signal, the Self-Adaptive Noise Cancellation method is adopted to eliminate the white noise. In the meanwhile, by applying Gaussian function to transform the input signal into high-dimension feature-space signal, the kernel least mean square algorithm is used to cancel the nonlinear interference. Effectiveness of the method has been verified by simulation signals and test rig signals. By dealing with simulation signal, the signal-to-noise ratio can be improved around 30 dB (white noise) and the amplitude of nonlinear interference signal can be depressed up to 50%. Experimental results show remarkable improvements and enhance gear fault features.
Transient nanobubbles in short-time electrolysis (2013)

Water electrolysis in a microsystem is observed and analyzed on a short-time scale of ∼10 μs. The very unusual properties of the process are stressed. An extremely high current density is observed because the process is not limited by the diffusion of electroactive species. The high current is accompanied by a high relative supersaturation, S > 1000, that results in homogeneous nucleation of bubbles. On the short-time scale only nanobubbles can be formed. These nanobubbles densely cover the electrodes and aggregate at a later time to microbubbles. The effect is significantly intensified with a small increase of temperature. Application of alternating polarity voltage pulses produces bubbles containing a mixture of hydrogen and oxygen. Spontaneous reaction between gases is observed for stoichiometric bubbles with sizes smaller than ∼150 nm. Such bubbles disintegrate violently affecting the surfaces of the electrodes.
Dielectric function of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">CaF</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>between 10 and 35 eV (1990)

The dielectric function of ${\mathrm{CaF}}_{2}$ over the photon energy region 10--35 eV has been determined by spectroscopic ellipsometry. Close to the fundamental absorption edge the data agree fairly well with band-structure calculations. A sharp exciton at the Ca 3p threshold (27.9 eV) is immediately followed by structures which can be attributed to variations in the conduction-band density of states. The strong transitions observed at higher energies cannot be explained in the one-electron band-structure model. Detailed theoretical calculations are required.
Transthoracic Pulmonary Artery Denervation for Pulmonary Arterial Hypertension (2019)

Objective- Pulmonary arterial hypertension is characterized by progressive pulmonary vascular remodeling and persistently elevated mean pulmonary artery pressures and pulmonary vascular resistance. We aimed to investigate whether transthoracic pulmonary artery denervation (TPADN) attenuated pulmonary artery (PA) remodeling, improved right ventricular (RV) function, and affected underlying mechanisms. We also explored the distributions of sympathetic nerves (SNs) around human PAs for clinical translation. Approach and Results- We identified numerous SNs in adipose and connective tissues around the main PA trunks and bifurcations in male Sprague Dawley rats, which were verified in samples from human heart transplant patients. Pulmonary arterial hypertensive rats were randomized into TPADN and sham groups. In the TPADN group, SNs around the PA trunk and bifurcation were completely and accurately removed under direct visualization. The sham group underwent thoracotomy. Hemodynamics, RV function, and pathological changes in PA and RV tissues were measured via right heart catheterization, cardiac magnetic resonance imaging, and pathological staining, respectively. Compared with the sham group, the TPADN group had lower mean pulmonary arterial pressures, less PA and RV remodeling, and improved RV function. Furthermore, TPADN inhibited neurohormonal overactivation of the sympathetic nervous system and renin-angiotensin-aldosterone system and regulated abnormal expressions and signaling of neurohormone receptors in local tissues. Conclusions- There are numerous SNs around the rat and human main PA trunks and bifurcations. TPADN completely and accurately removed the main SNs around PAs and attenuated pulmonary arterial hypertensive progression by inhibiting excessive activation of the sympathetic nervous system and renin-angiotensin-aldosterone system neurohormone-receptor axes.
Prolyl endopeptidase purified from granulomatous inflammation in mice (1992)

Activity of prolyl endopeptidase (EC 3.4.21.26) which hydrolyses the Pro7-Phe8 bond in angiotensin II has been found to elevate in experimentally produced granulomatous inflammation in liver and skin. We purified the enzyme 1,536-fold by 6 steps from murine hepatic granulomas. The purified enzyme has a molecular weight of 79 kDa and physicochemical properties equivalent to those previously reported for prolyl endopeptidase purified from other sources. By HPLC analysis, the cleavage of Phe8-Leu10 and Phe8 from angiotensin I and II, respectively, was detected and quantified. Monospecific IgG was prepared from serum of rabbits injected with purified enzyme. Concentration of the enzyme was immunohistochemically detected in cells which form granulomatous organization, but not in inflammatory cells surrounding the foci. The antibody, however, cross reacted with the enzyme in adjacent liver cells and weakly stained their cytoplasm. The findings indicate that this enzyme, in addition to angiotensin converting enzyme, may serve as a useful biochemical marker for granulomatous tissue reactions.
Embedded Model Predictive Control for Enhancing Tracking Performance of a Ball-and-Plate System (2019)

Implementing model predictive control (MPC) on a limited-performance microcontroller has always been a great challenge. In this paper, we propose an MPC implementation method that can run on a microcontroller by improving the calculation efficiency and address applied to the ball-and-plate system to enhance tracking performance. First, we convert the MPC quadratic programming problem, which causes difficulties in implementing MPC, into an equivalent nonnegative least-squares problem so that we can build the solver in a C program easily. Subsequently, we separate the offline calculation from the online process, which drastically reduces the calculation time. Finally, we implement the proposed MPC in a C program to run it on a Nucleo-32 microcontroller, apply it to a tracking control problem using a laboratory-built ball-and-plate system, and then explain the improved tracking performance compared with the conventional control methods.
Transverse Mode Control and Reduction of Threshold Current in (GaAl)As Buried-Heterostructure Lasers with a Buried Optical Guide (1980)

Transverse modes of (GaAl)As buried-heterostructure (BH) lasers with a buried optical guide (BOG) are experimentally analyzed in terms of the physical parameters of lasers. A reproducible fundamental transverse mode is obtained by controlling active layer thickness, width and cross sectional geometry. A remarkable reduction in the threshold current is achieved in BH lasers with a BOG using a highly resistive (GaAl)As layer as the burying layer. A threshold current as low as 9 mA and a power conversion efficiency as high as 55% at an output of 15 mW per facet are obtained.
Structural Changes in the Carboxyl Terminus of the Gap Junction Protein Connexin43 Indicates Signaling between Binding Domains for c-Src and Zonula Occludens-1 (2004)

Regulation of cell-cell communication by the gap junction protein connexin43 can be modulated by a variety of connexin-associating proteins. In particular, c-Src can disrupt the connexin43 (Cx43)-zonula occludens-1 (ZO-1) interaction, leading to down-regulation of gap junction intercellular communication. The binding sites for ZO-1 and c-Src correspond to widely separated Cx43 domains (approximately 100 residues apart); however, little is known about the structural modifications that may allow information to be transferred over this distance. Here, we have characterized the structure of the connexin43 carboxyl-terminal domain (Cx43CT) to assess its ability to interact with domains from ZO-1 and c-Src. NMR data indicate that the Cx43CT exists primarily as an elongated random coil, with two regions of alpha-helical structure. NMR titration experiments determined that the ZO-1 PDZ-2 domain affected the last 19 Cx43CT residues, a region larger than that reported to be required for Cx43CT-ZO-1 binding. The c-Src SH3 domain affected Cx43CT residues Lys-264-Lys-287, Ser-306-Glu-316, His-331-Phe-337, Leu-356-Val-359, and Ala-367-Ser-372. Only region Lys-264-Lys-287 contains the residues previously reported to act as an SH3 binding domain. The specificity of these interactions was verified by peptide competition experiments. Finally, we demonstrated that the SH3 domain could partially displace the Cx43CT-PDZ-2 complex. These studies represent the first structural characterization of a connexin domain when integrated in a multimolecular complex. Furthermore, we demonstrate that the structural characteristics of a disordered Cx43CT are advantageous for signaling between different binding partners that may be important in describing the mechanism of channel closure or internalization in response to pathophysiological stimuli.
MolDock:  A New Technique for High-Accuracy Molecular Docking (2006)

In this article we introduce a molecular docking algorithm called MolDock. MolDock is based on a new heuristic search algorithm that combines differential evolution with a cavity prediction algorithm. The docking scoring function of MolDock is an extension of the piecewise linear potential (PLP) including new hydrogen bonding and electrostatic terms. To further improve docking accuracy, a re-ranking scoring function is introduced, which identifies the most promising docking solution from the solutions obtained by the docking algorithm. The docking accuracy of MolDock has been evaluated by docking flexible ligands to 77 protein targets. MolDock was able to identify the correct binding mode of 87% of the complexes. In comparison, the accuracy of Glide and Surflex is 82% and 75%, respectively. FlexX obtained 58% and GOLD 78% on subsets containing 76 and 55 cases, respectively.
Development of Mesophase Pitch Derived Mesoporous Carbons through a Commercially Nanosized Template (2006)

Mesoporous carbons (MCs) with a high surface area (up to 900 m2/g), large pore volume (up to 2.1 cm3/g), high mesopore ratio (94%), and high yield (70%) were successfully prepared from an AR mesophase pitch, using a commercially nanosized silica template. The removal of the template provided some larger mesopores of 25-50 nm (pore I) with a surface area of ca. 300 m2/g, while the successive carbonization opened the closed pores within the carbon body to give smaller mesopores of 2-10 nm (pore II) with a similar surface area. During the carbonization of pitch precursor, the evaporation of volatile components swells the carbon to introduce the second mesopores among the domains and even microdomain units because of their rearrangements and overlappings in the process. The addition of iron salt with the silica template resulted in a remarkable increase of the surface area (ca. 300 m2/g) by introducing mesopores of 3-5 nm. The resultant MCs maintained some graphitizable natures derived from the anisotropic precursor. Their graphitization at 2400 degrees C provided the graphitic structure with large surface areas (270-460 m2/g) and mesoporosity.
Overcoming the effects of false positives and threshold bias in graph theoretical analyses of neuroimaging data (2015)

Graph theory (GT) is a powerful framework for quantifying topological features of neuroimaging-derived functional and structural networks. However, false positive (FP) connections arise frequently and influence the inferred topology of networks. Thresholding is often used to overcome this problem, but an appropriate threshold often relies on a priori assumptions, which will alter inferred network topologies. Four common network metrics (global efficiency, mean clustering coefficient, mean betweenness and smallworldness) were tested using a model tractography dataset. It was found that all four network metrics were significantly affected even by just one FP. Results also show that thresholding effectively dampens the impact of FPs, but at the expense of adding significant bias to network metrics. In a larger number (n=248) of tractography datasets, statistics were computed across random group permutations for a range of thresholds, revealing that statistics for network metrics varied significantly more than for non-network metrics (i.e., number of streamlines and number of edges). Varying degrees of network atrophy were introduced artificially to half the datasets, to test sensitivity to genuine group differences. For some network metrics, this atrophy was detected as significant (p<0.05, determined using permutation testing) only across a limited range of thresholds. We propose a multi-threshold permutation correction (MTPC) method, based on the cluster-enhanced permutation correction approach, to identify sustained significant effects across clusters of thresholds. This approach minimises requirements to determine a single threshold a priori. We demonstrate improved sensitivity of MTPC-corrected metrics to genuine group effects compared to an existing approach and demonstrate the use of MTPC on a previously published network analysis of tractography data derived from a clinical population. In conclusion, we show that there are large biases and instability induced by thresholding, making statistical comparisons of network metrics difficult. However, by testing for effects across multiple thresholds using MTPC, true group differences can be robustly identified.
Diagnostic tests for Niemann-Pick disease type C (NP-C): A critical review (2016)

Niemann-Pick disease type C (NP-C) is a neurovisceral lysosomal cholesterol trafficking and lipid storage disorder caused by mutations in one of the two genes, NPC1 or NPC2. Diagnosis has often been a difficult task, due to the wide range in age of onset of NP-C and clinical presentation of the disease, combined with the complexity of the cell biology (filipin) laboratory testing, even in combination with genetic testing. This has led to substantial delays in diagnosis, largely depending on the access to specialist centres and the level of knowledge about NP-C of the physician in the area. In recent years, advances in mass spectrometry has allowed identification of several sensitive plasma biomarkers elevated in NP-C (e.g. cholestane-3β,5α,6β-triol, lysosphingomyelin isoforms and bile acid metabolites), which, together with the concomitant progress in molecular genetic technology, have greatly impacted the strategy of laboratory testing. Specificity of the biomarkers is currently under investigation and other pathologies are being found to also result in elevations. Molecular genetic testing also has its limitations, notably with unidentified mutations and the classification of new variants. This review is intended to increase awareness on the currently available approaches to laboratory diagnosis of NP-C, to provide an up to date, comprehensive and critical evaluation of the various techniques (cell biology, biochemical biomarkers and molecular genetics), and to briefly discuss ongoing/future developments. The use of current tests in proper combination enables a rapid and correct diagnosis in a large majority of cases. However, even with recent progress, definitive diagnosis remains challenging in some patients, for whom combined genetic/biochemical/cytochemical markers do not provide a clear answer. Expertise and reference laboratories thus remain essential, and further work is still required to fulfill unmet needs.
Optical tweezers-based immunosensor detects femtomolar concentrations of antigens. (1997)

We used optical tweezers (optical trapping technology) to measure the force required to separate antigen-antibody bonds. Under competitive-binding conditions, we used the force determination to detect and measure protein antigen concentrations as small as 1 fmol/L (10(-15) mol/L).