gebhart/patrepeval huggingface dataset:
Spectral based tissue classification and ultrastructural characterization using ISOCT (Conference Presentation) (2019)

Alterations to nanoscale structures, lymphatics, and microvasculature are early hallmarks of neoplasia as well as a variety of other diseases. Unfortunately, nanoscale alterations and microvasculature function, such as oxygen saturation, cannot be probed by histology. Furthermore, properly evaluating lymphatic and microvasculature organization can be challenging with histological slices. Optical Coherence Tomography (OCT) offers a promising noninvasive solution to evaluating these biomarkers in 3D in vivo. OCT has shown the ability to provide 3D maps of vasculature with flow rate and blood oxygenation, as well as, lymphatic organization with a resolution on the order of 1-10 microns. Our group has established Inverse Spectroscopic OCT (ISOCT), which measures nanoscale mass density tissue fluctuations and can distinguish between histologically normal cancerous and noncancerous tissue. However, the most influential underlying assumption that allows the distinction between subdiffractional structural alterations in tissue is that the region of interest (ROI) includes a homogenous tissue type with similar scattering and absorption properties. Therefore, the highly absorbing blood and low scattering lymphatics must be excluded from analysis. Traditional OCT techniques to isolate vasculature and its spectra require timely repetitive scanning protocols, and the commonly utilized near infrared operating bandwidths require vessel-like filters to locate lymphatics. Herein we show how vasculature location and spectra can be extracted with a single visible OCT scan. Additionally, we demonstrate the high image contrast from visible OCT allows lymphatic location to be well defined. Finally, we show ultrastructural metrics fall within physiologically reasonable ranges after excluding vasculature and lymphatics from the ROI.
A Distance-Adaptive Refueling Recommendation Algorithm for Self-Driving Travel (2018)

Taking the maximum vehicle driving distance, the distances from gas stations, the route length, and the number of refueling gas stations as the decision conditions, recommendation rules and an early refueling service warning mechanism for gas stations along a self-driving travel route were constructed by using the algorithm presented in this research, based on the spatial clustering characteristics of gas stations and the urgency of refueling. Meanwhile, by combining ArcEngine and Matlab capabilities, a scenario simulation system of refueling for self-driving travel was developed by using c#.net in order to validate and test the accuracy and applicability of the algorithm. A total of nine testing schemes with four simulation scenarios were designed and executed using this algorithm, and all of the simulation results were consistent with expectations. The refueling recommendation algorithm proposed in this study can automatically adapt to changes in the route length of self-driving travel, the maximum driving distance of the vehicle, and the distance from gas stations, which could provide variable refueling recommendation strategies according to differing gas station layouts along the route. Therefore, the results of this study could provide a scientific reference for the reasonable planning and timely supply of vehicle refueling during self-driving travel.
Sediment diagenesis (2007)

Diagenesis is the set of processes by which sediments evolve after they are deposited and begin to be buried. Diagenesis includes physical effects such as compaction and the deformation of grains in the sediment (or sedimentary rock), as well as chemical reactions such as the dissolution of grains and the precipitation of minerals to form cements in the sediment's pore space. The chemical aspects of diagenesis are of special interest here.
Importance of research on peptidylarginine deiminase and citrullinated proteins in age‐related disease (2010)

Peptidylarginine deiminases (PAD) are a group of post-translational modification enzymes that citrullinate (deiminate) protein arginine residues in a calcium ion-dependent manner. Enzymatic citrullination abolishes positive charges of native protein molecules, inevitably causing significant alterations in their structure and functions. Citrullinated protein has an important physiological purpose; the formation of a cornified layer of skin that covers the human body. Despite this beneficial function, citrullinated protein also has a negative side, because this protein's accumulation in the brain is a possible cause of Alzheimer's disease. In the present review, we introduce PAD and their protein citrullination function, now considered critical for advancing research on aging and disease.
Antimalarial Drug Resistance: Clinical Perspectives (2009)

Malaria is one of the most important infectious diseases in the world, and the problem appears to be worsening. An important contributor to our continued inability to control malaria is the increasing resistance of malaria parasites to available drugs. New drugs are greatly needed, but the continued use of some agents against which resistance has already developed is inevitable. As we attempt to improve methods for malaria surveillance and control, it is important to standardize methods for the assessment of antimalarial drug resistance. Such efforts include the establishment of standard means of assessing responses to antimalarial treatment, the discrimination of recrudescence due to drug resistance from reinfection after treatment, the characterization of molecular mediators of drug resistance in fi eld isolates, and the establishment of improved systems for the in vitro analysis of the drug susceptibility of fi eld isolates.
Investigation of Partially Premixed Combustion Characteristics in Low Load Range with Regards to Fuel Octane Number in a Light-Duty Diesel Engine (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The impact of ignition quality and chemical properties on engine performance and emissions during low load partially premixed combustion (PPC) in a light-duty diesel engine were investigated. Four fuels in the gasoline boiling range, together with Swedish diesel (MK1), were operated at loads between 2 and 8 bar IMEP&lt;sub&gt;g&lt;/sub&gt; at 1500 rpm, with 50% heat released located at 6 crank angle degrees (CAD) after top dead center (TDC). A single injection strategy was used, wherein the start of injection (SOI) and the injection duration were adjusted to achieve desired loads with maintained CA50, as the injection pressure was kept constant at 1000 bar. The objective of this work was to examine the low-load limit for PPC at approximately 50% EGR and λ=1.5, since these levels had been suggested as optimal in earlier studies. The low-load limits with stable combustion were between 5 and 7 bar gross IMEP for the gasoline fuels, higher limit for higher RON values. MK1 had the lowest low-load limit, 3 bar gross IMEP. By increasing λ with the kept EGR ratio, with extended boosting, all the fuels could be operated down to 2 bar IMEP&lt;sub&gt;g&lt;/sub&gt;. The main difference in engine-out emissions between the fuels was the filtered smoke number (FSN), as the gasoline fuels produced much lower smoke than MK1. Higher RON value gave higher levels of carbon monoxide (CO) and unburned hydrocarbon (HC) for the gasoline fuels, while MK1 had the lowest levels of these emissions.&lt;/div&gt;&lt;/div&gt;
The Potential of Solar Energy in Saudi Arabia: The Residential Sector (2018)

Journal of Anthropology and Archaeology is a peer-reviewed international journal, which publishes original papers promoting theoretical, methodological and empirical developments in the discipline of socio-cultural anthropology.
Taurine uptake in apical membrane vesicles from the bovine retinal pigment epithelium. (1991)

Characteristics of taurine uptake were investigated in apical membrane vesicles isolated from bovine retinal pigment epithelium. Uptake of taurine into these vesicles was stimulated markedly by the presence of an inwardly directed NaCl gradient across the membrane. The time course of the NaCl gradient-dependent uptake showed an overshoot, indicating a transient accumulation of taurine in the vesicles against a concentration gradient. Monovalent cations other than Na+ did not support taurine uptake. There was also an anion requirement for the uptake system, and Cl- was the most potent among several monovalent anions tested. The NaCl-dependent taurine uptake was stimulated by inside-negative, K+, and H+ diffusion potentials, demonstrating the electrogenic nature of the system. Stoichiometric analysis revealed that two Na+ and one Cl- ions were involved in the translocation of one taurine molecule. The system had an apparent dissociation constant (Kt) of 96 +/- 17 microM and a maximal velocity of 267 +/- 24 pmol/mg of protein over 15 sec. Uptake of radiolabeled taurine was inhibited by excess amounts of unlabeled taurine, hypotaurine, beta-alanine, and gamma-aminobutyric acid. The relative potencies of the amino acids to inhibit taurine uptake were compared in three tissues, the bovine retinal pigment epithelium, the rat kidney, and the human placenta. In the apical membrane vesicles of the pigment epithelium, gamma-aminobutyric acid was many times more potent than taurine itself in inhibiting radiolabeled taurine uptake. However, in the brush border membrane vesicles of the kidney and the placenta, taurine was many times more potent than gamma-aminobutyric acid.(ABSTRACT TRUNCATED AT 250 WORDS)
A Globally Convergent Stochastic Pairwise Conjugate Gradient-Based Algorithm for Adaptive Filtering (2008)

It is well known that, for the deterministic optimization problem, the method of conjugate gradient has superior convergence rates compared to ordinary gradient methods. For quadratic problems, the conjugate gradient method has finite termination property which makes it one of the most favorable iterative methods. However, the fast convergence and the finite termination property can easily break down when the function to be optimized is noisy since conjugacy among search directions can no longer be maintained over the course of the iterations. In this letter, a conjugation procedure is applied in an adaptive filtering algorithm, where, instead of producing a set of conjugate search directions, only pairwise conjugation of gradients is produced during each system update. Simulations show that the algorithm provides superior convergence compared to the stochastic gradient descent algorithm, and comparable to existing conjugate gradient-based adaptive filtering algorithms, but at a lower computational cost.
Volume Regulation in Liver: Further Characterization by Inhibitors and Ionic Substitutions (1990)

The present study has been performed to elucidate the mechanisms of volume regulation in isolated perfused liver. Reduction of extracellular osmolarity by 80 mOsm/L leads to a release of potassium and a sustained alkalinization of effluent. Reexposure to isotonic perfusate leads to reuptake of potassium by the liver and acidification of effluent. Part of the alkalinization could be due to release of bicarbonate parallel to potassium release. Carboanhydrase inhibition and replacement of bicarbonate/CO2 by HEPES buffer, however, do not significantly modify volume regulatory potassium release or reuptake. Reduction of perfusate chloride to 37 mmol/L by replacement of NaCl with raffinose leads to a decrease of liver weight indicative of shrinkage of liver cells. Subsequent omission of 180 mmol/L raffinose leads to potassium and chloride release and to alkalinization of effluent. Volume regulatory release of potassium is impaired in 1 mmol/L quinidine, 1 mmol/L SITS and 5 mmol/L barium. Volume regulatory reuptake of potassium is impaired by 1 mmol/L amiloride. Volume regulatory release of potassium is not appreciably affected by either; 1 mmol/L furosemide, 1 mumol/L verapamil, 1 mmol/L amiloride or 1 mmol/L barium and volume regulatory potassium reuptake proved insensitive to 1 mmol/L furosemide or 1 mmol/L barium. The data suggest that the cells release potassium and chloride during regulatory volume decrease by quinidine, SITS and weakly barium-sensitive transport systems and that regulatory volume increase is accomplished by activation of Na/H exchange.
Screening for trisomy 21 in monochorionic twins by measurement of fetal nuchal translucency thickness (2005)

In monochorionic twins, effective screening for trisomy 21 is best provided by using the average NT measured in the two fetuses.
Impact of Node Architecture in the Power Consumption and Footprint Requirements of Optical Transport Networks (2013)

We evaluate and compare the power consumption and the number of required slots (footprint) of fixed and flexible transport nodes. The node architecture is assumed to comprise a grooming structure, and a reconfigurable optical add/drop multiplexer (ROADM). Fixed grooming is achieved using cascades of muxponders. Alternatively, flexible grooming is achieved with electrical switches. Fixed frequency and fixed direction ROADM, and colorless and directionless ROADM are considered. For all the architectures, we present an accurate dimensioning model that allows computation of the required modules. Results show that to optimize the total power consumption and footprint of the network, the architecture of each node has to be selected according to the amount and pattern of the add/drop and regenerated traffic and the number of pairs of fibers convergent to the node. An optimization method based on simple rules for node type selection is proposed.
Efficacy of biofeedback therapy via a mini wireless device on sleep bruxism contrasted with occlusal splint：a pilot study (2015)

bruxism 的通常认为的原因是 multifactorial，为 bruxism 管理没有明确的措施。这研究的目的是在睡觉 bruxism 上评估生物反馈治疗的功效，与 occlusal 藤条相比。有睡觉 bruxism 的 24 个志愿者被划分成二个组：与生物反馈治疗被对待的 GTB 组(n &#x0200a； =&#x0200a； 12 ) 并且与 occlusal 藤条被对待的 GTO 组(n &#x0200a； =&#x0200a； 12 ) 。与由一根颚的生物反馈藤条的使用的一个监视电路综合的一个微型压力传感器被制作。促进咀嚼的肌肉和神经系统的松驰，无线设备从 bruxism 事件收到了信号，当阀值被超过时，颤动警告了 bruxer。全部的事件和 bruxism 事件的平均持续时间用监视程序(TRMY1.0 ) 在 8 小时睡觉期间被分析。在 6 和 12 个星期以后，事件(P &#x0200a； =&#x0200a；0.001 ) 并且持续时间(P &#x0003c；0.05 ) 在 GTB，组戏剧性地拒绝了。相反，在在处理以后的 GTO 组没有重要差别(P &#x0003e；0.05 ) 。而且，事件在处理的一样的时期以后有 GTB 组和 GTO 组之间的重要差别(P &#x0200a； =&#x0200a；0.000 ) 。结果建议那生物反馈治疗可以是为温和 bruxers 的一项有效、方便的措施，当时与 occlusal 相比藤条治疗。无线生物反馈方法以后可能具有为 bruxism 的诊断和管理的价值的微型。
Author Correction: A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis (2019)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Extension of the Virasoro and Neveu-Schwartz algebras and generalized Sturm-Liouville operators (1996)

We consider the universal central extension of the Lie algebra $\Vect (S^1)${\math \s}$ C^{\infty}(S^1)$. The coadjoint representation of this Lie algebra has a natural geometric interpretation by matrix analogues of the Sturm-Liouville operators. This approach leads to new Lie superalgebras generalizing the well-known Neveu-Schwartz algebra.
Identification and Validation of a 3-Gene Methylation Classifier for HPV-Based Cervical Screening on Self-Samples (2018)

<b>Purpose:</b> Offering self-sampling of cervico-vaginal material for high-risk human papillomavirus (hrHPV) testing is an effective method to increase the coverage in cervical screening programs. Molecular triage directly on hrHPV-positive self-samples for colposcopy referral opens the way to full molecular cervical screening. Here, we set out to identify a DNA methylation classifier for detection of cervical precancer (CIN3) and cancer, applicable to lavage and brush self-samples.<b>Experimental Design:</b> We determined genome-wide DNA methylation profiles of 72 hrHPV-positive self-samples, using the Infinium Methylation 450K Array. The selected DNA methylation markers were evaluated by multiplex quantitative methylation-specific PCR (qMSP) in both hrHPV-positive lavage (<i>n</i> = 245) and brush (<i>n</i> = 246) self-samples from screening cohorts. Subsequently, logistic regression analysis was performed to build a DNA methylation classifier for CIN3 detection applicable to self-samples of both devices. For validation, an independent set of hrHPV-positive lavage (<i>n</i> = 199) and brush (<i>n</i> = 287) self-samples was analyzed.<b>Results:</b> Genome-wide DNA methylation profiling revealed 12 DNA methylation markers for CIN3 detection. Multiplex qMSP analysis of these markers in large series of lavage and brush self-samples yielded a 3-gene methylation classifier (<i>ASCL1, LHX8,</i> and <i>ST6GALNAC5</i>). This classifier showed a very good clinical performance for CIN3 detection in both lavage (AUC = 0.88; sensitivity = 74%; specificity = 79%) and brush (AUC = 0.90; sensitivity = 88%; specificity = 81%) self-samples in the validation set. Importantly, all self-samples from women with cervical cancer scored DNA methylation-positive.<b>Conclusions:</b> By genome-wide DNA methylation profiling on self-samples, we identified a highly effective 3-gene methylation classifier for direct triage on hrHPV-positive self-samples, which is superior to currently available methods. <i>Clin Cancer Res; 24(14); 3456-64. ©2018 AACR</i>.
Preparation and Thermal Radiation Properties of ZnO Thin Films (2010)

ZnO thin films with different thickness were prepared on glass substrates by using a sol-gel method.The effect of different sol ratio and concentration on the thermal radiation properties of the ZnO thin films was analyzed.The ZnO thin film had the best thermal radiation property and best absorption ability when its sol ratio was 1:1 and its concentration is 0.8%.The structure and morphology of the ZnO thin film were characterized by using both X-ray diffraction(XRD) and Scanning Electron Microscope (SEM) technologies.The results showed that the prepared ZnO thin film exhibited its hexagonal wurtzite structure with preferred orientation at(002) and had good crystallization behavior.
Salvianolic acid B attenuates VCAM‐1 and ICAM‐1 expression in TNF‐α‐treated human aortic endothelial cells (2001)

Attachment to, and migration of leukocytes into the vessel wall is an early event in atherogenesis. Expression of cell adhesion molecules by the arterial endothelium may play a major role in atherosclerosis. It has been suggested that antioxidants inhibit the expression of adhesion molecules and may thus attenuate the processes leading to atherosclerosis. In the present study, the effects of a potent water-soluble antioxidant, salvianolic acid B (Sal B), and an aqueous ethanolic extract (SME), both derived from a Chinese herb, Salvia miltiorrhiza, on the expression of endothelial-leukocyte adhesion molecules by tumor necrosis factor-alpha (TNF-alpha)-treated human aortic endothelial cells (HAECs) were investigated. When pretreated with SME (50 and 100 microg/ml), the TNF-alpha-induced expression of vascular adhesion molecule-1 (VCAM-1) was notably attenuated (77.2 +/- 3.2% and 80.0 +/- 2.2%, respectively); and with Sal B (1, 2.5, 5, 10, and 20 microg/ml), 84.5 +/- 1.9%, 78.8 +/- 1.2%, 58.9 +/- 0.4%, 58.7 +/- 0.9%, and 57.4 +/- 0.3%, respectively. Dose-dependent lowering of expression of intercellular cell adhesion molecule-1 (ICAM-1) was also seen with SME or Sal B. In contrast, the expression of endothelial cell selectin (E-selectin) was not affected. SME (50 microg/ml) or Sal B (5 microg/ml) significantly reduced the binding of the human monocytic cell line, U937, to TNF-alpha-stimulated HAECs (45.7 +/- 2.5% and 55.8 +/- 1.2%, respectively). SME or Sal B significantly inhibited TNF-alpha-induced activation of nuclear factor kappa B (NF-kappaB) in HAECs (0.36- and 0.48-fold, respectively). These results demonstrate that SME and Sal B have anti-inflammatory properties and may explain their anti-atherosclerotic properties. This new mechanism of action of Sal B and SME, in addition to their previously reported inhibition of LDL, may help explain their efficacy in the treatment of atherosclerosis.
High pretreatment serum gamma-glutamyl transpeptidase predicts an inferior outcome in nasopharyngeal carcinoma (2017)

Pretreatment GGT can be a novel and independent prognostic biomarker for patients with NPC.
Effects of termination networks on signal-induced EMI from the shields of Fibre Channel cables operating in the Gb/s regime (2002)

Differential transmission lines support both odd (differential) and even (common) modes of excitation. Imbalance in the differential signal creates a common-mode signal resulting in EMI. A common practice in differential signaling is to match terminate the differential pair with a single resistor. A termination network that provides a good match to both the differential and common-mode impedances should reduce common-mode reflections and therefore common-mode shield currents and radiated electric fields. Three different termination networks (differential, Pi and Tee) were built and studied with a network analyzer. In addition, the networks were shielded and driven through a shielded cable using a battery-powered transceiver that was placed in a shielded enclosure. The radiated electric field was measured at a 3 meter distance in a fully anechoic chamber. The radiated electric field below 500 MHz was found to be more than 4 dB higher for a purely differential termination, when compared to either the Pi or Tee. Above 500 MHz, parasitics appear to dominate the common-mode impedance of the termination network, degrading the impedance match.
The Matrix Protein of Nipah Virus Targets the E3-Ubiquitin Ligase TRIM6 to Inhibit the IKKε Kinase-Mediated Type-I IFN Antiviral Response (2016)

For efficient replication, viruses have developed mechanisms to evade innate immune responses, including the antiviral type-I interferon (IFN-I) system. Nipah virus (NiV), a highly pathogenic member of the Paramyxoviridae family (genus Henipavirus), is known to encode for four P gene-derived viral proteins (P/C/W/V) with IFN-I antagonist functions. Here we report that NiV matrix protein (NiV-M), which is important for virus assembly and budding, can also inhibit IFN-I responses. IFN-I production requires activation of multiple signaling components including the IκB kinase epsilon (IKKε). We previously showed that the E3-ubiquitin ligase TRIM6 catalyzes the synthesis of unanchored K48-linked polyubiquitin chains, which are not covalently attached to any protein, and activate IKKε for induction of IFN-I mediated antiviral responses. Using co-immunoprecipitation assays and confocal microscopy we show here that the NiV-M protein interacts with TRIM6 and promotes TRIM6 degradation. Consequently, NiV-M expression results in reduced levels of unanchored K48-linked polyubiquitin chains associated with IKKε leading to impaired IKKε oligomerization, IKKε autophosphorylation and reduced IFN-mediated responses. This IFN antagonist function of NiV-M requires a conserved lysine residue (K258) in the bipartite nuclear localization signal that is found in divergent henipaviruses. Consistent with this, the matrix proteins of Ghana, Hendra and Cedar viruses were also able to inhibit IFNβ induction. Live NiV infection, but not a recombinant NiV lacking the M protein, reduced the levels of endogenous TRIM6 protein expression. To our knowledge, matrix proteins of paramyxoviruses have never been reported to be involved in innate immune antagonism. We report here a novel mechanism of viral innate immune evasion by targeting TRIM6, IKKε and unanchored polyubiquitin chains. These findings expand the universe of viral IFN antagonism strategies and provide a new potential target for development of therapeutic interventions against NiV infections.