gebhart/patrepeval huggingface dataset:
pH-Sensitive Fluorescent Dyes: Are They Really pH-Sensitive in Cells? (2013)

Chemically synthesized near-infrared aza-BODIPY dyes displayed off-on fluorescence at acidic pH (pKa = 6.2-6.6) through the suppression of the photoinduced electron transfer and/or internal charge transfer process. The apparent pKas of the dyes were shifted well above physiological pH in a hydrophobic microenvironment, which led to "turned-on" fluorescence in micelles and liposomes at neutral and basic pH. Bovine serum albumin also activated the fluorescence, though to a much lesser extent. When these small molecular dyes entered cells, instead of being fluorescent only in acidic organelles, the whole cytoplasm exhibited fluorescence, with a signal/background ratio as high as ∼10 in no-wash live-cell imaging. The dye 1-labeled cells remained highly fluorescent even after 3 days. Moreover, slight variations of the dye structure resulted in significantly different intracellular fluorescence behaviors, possibly because of their different cellular uptake and intracellular activation capabilities. After the separation of cellular components, the fraction of plasma membrane and endoplasmic reticulum showed the highest fluorescence, further confirming the fluorescence activation by membrane structures. The fluorescence intensity of these dyes at different intracellular pHs (6.80 and 8.00) did not differ significantly, indicating that intracellular pH did not play a critical role. Altogether, we showed here for the first time that the fluorescence of pH-sensitive aza-BODIPY dyes was switched intracellularly not by acidic pH, but by intracellular membranes (and proteins as well). The excellent membrane permeability, ultrahigh fluorescence contrast ratio, persistent fluorescent signal, and minimal biological interference of dye 1 make it an ideal choice for live-cell imaging and in vivo cell tracking. These findings also imply that the intracellular fluorescence properties of pH-sensitive dyes should be carefully examined before they are used as pH indicators.
Reliability and validity of a new fingertip-shaped pressure algometer for assessing pressure pain thresholds in the temporomandibular joint and masticatory muscles. (2007)

Both the PAP and the Somedic algometer showed high reliability. Concurrent validity was demonstrated by statistically significant correlations between the devices. Both showed equally high capacity for differentiating TMD cases from controls. The PAP yielded significantly higher PPTs than the Somedic algometer.
Ocean One: A Robotic Avatar for Oceanic Discovery (2016)

The promise of oceanic discovery has long intrigued scientists and explorers, whether with the idea of studying underwater ecology and climate change or with the hope of uncovering natural resources and historic secrets buried deep in archaeological sites. This quest to explore the oceans requires skilled human access, yet much of the oceans are inaccessible to human divers; nearly ninetenths of the ocean floor is at 1 km or deeper [1]. Accessing these depths is imperative since factors such as pollution and deep-sea trawling threaten ecology and archaeological sites. While remotely operated vehicles (ROVs) are inadequate for the task, a robotic avatar could go where humans cannot and still embody human intelligence and intentions through immersive interfaces.
Virus-induced loss of class I MHC antigens from the surface of cells infected with myxoma virus and malignant rabbit fibroma virus (1992)

Shope fibroma virus (SFV) is a leporipoxvirus that causes localized benign fibromas in immunocompetent adult rabbits that spontaneously regress due, in part, to a cell-mediated immune response. Myxoma virus (MYX) and malignant rabbit fibroma virus (MRV) are related leporipoxviruses that induce rapidly lethal generalized infections accompanied by tumors and immunosuppression. Because only these latter two viruses are known to compromise cell-mediated antiviral responses, cell surface levels of class I MHC molecules in SFV-, MRV-, and MYX-infected cells were investigated by fluorescent activated cell sorting analysis using a variety of different anti-HLA mAb. After infection with MYX or MRV there is a rapid decrease in the levels of detectable surface class I epitopes as detected by each antibody and by 24 h postinfection class I MHC Ag levels at the cell surface approach the level of background fluorescence observed with control antibodies. In contrast, only a moderate class I decrease is seen during infection with either SFV or vaccinia virus, an orthopoxvirus that is neither tumorigenic nor immunosuppressive. Surface class I marker loss induced by MYX and MRV is not simply due to nonspecific inhibition of total cellular protein synthesis by the viruses because class I levels decrease much further than the extent measured by estimating surface marker turnover in the presence of the protein synthesis inhibitor cycloheximide. Thus the loss of cellular surface class I molecules greatly exceeds the drop in level caused by complete blockage of host cell gene expression, and must involve removal or masking of preexisting class I epitopes from the cell surface by MRV/MYX. Cell surface levels of the transferrin receptor are unaffected by MYX and MRV infection, suggesting the observed class I decrease is not a nonspecific effect on total cell surface glycoproteins. Analysis of cells infected with MRV/MYX in the presence of cycloheximide or of cytosine arabinoside, an inhibitor of poxviral DNA replication, indicates that the class I marker loss is mediated in part by one or more viral late gene products. A probable explanation is that MRV/MYX late protein(s) interact with the class I MHC complex to either physically sequester these away from the cell surface and inhibit their recycling or else induce a conformational change that precludes recognition by all class I antibodies tested. In either event, we propose that such a major perturbation of the class I MHC complex would likely downregulate the class I-mediated presentation of viral Ag required to initiate cell-mediated immunity to these viruses.
DNA Is Packaged within Membrane-Derived Vesicles of Gram-Negative but Not Gram-Positive Bacteria (1990)

Recently, DNA packaged within nuclease-resistant membrane vesicles of Neisseria gonorrhoeae and Borrelia burgdorferi was described. This study assayed 18 species of gram-negative and gram-positive eubacteria for nuclease-protected DNA associated with extracellular membrane vesicles. Vesicles from only the gram-negative bacteria contained nuclease-protected linear or supercoiled DNAs or both.
Compact dual‐band MIMO antenna for 4G USB dongle applications (2012)

Abstract An extremely compact dual‐band MIMO antenna for 4G USB dongle applications is proposed for operation in the long term evolution (LTE) band 13 (0.746–0.787 GHz) and the M‐WiMAX band (2.5–2.69 GHz).The proposed multiple‐input multiple‐output (MIMO) antenna consists of two identical elements, each of which is 15 × 13.25 mm 2 . The minimum separation between the two elements is 0.5 mm (about 0.13% of the wavelength in free space at 0.765 GHz). Each antenna element of the proposed MIMO system is composed of a feeding strip, a spiral‐like radiating strip, and an L‐shaped parasitic strip. The radiating and L‐shaped strips are short‐circuited to the ground plane. The radiating and parasitic strips, which are capacitively coupled to the feeding strip, operate not only as radiators but also work as resonators to reduce the coupling between the two closely packed input ports. The proposed MIMO antenna has a measured port‐to‐port isolation performance of more than 13 dB over the frequency bands of interest. In addition, the ECCs are maintained below 0.3. © 2012 Wiley Periodicals, Inc. Microwave Opt Technol Lett 54:744–748, 2012; View this article online at wileyonlinelibrary.com. DOI 10.1002/mop.26612
Vacant-Site Octahedral Tilings on<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>SrTiO</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:math>(001), the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mo stretchy="false">(</mml:mo><mml:msqrt><mml:mn>13</mml:mn></mml:msqrt><mml:mo>×</mml:mo><mml:msqrt><mml:mn>13</mml:mn></mml:msqrt><mml:mo stretchy="false">)</mml:mo><mml:mi>R</mml:mi><mml:mn>33.7</mml:mn><mml:mo>°</mml:mo></mml:math>Surface, and Related Structures (2011)

The structure of the SrTiO(3) (001) (sqrt[13]×sqrt[13])R33.7° surface reconstruction has been determined using transmission electron diffraction combined with direct methods and density functional theory. It has a TiO(2)-rich surface with a 2D tiling of edge or corner-sharing TiO(5)□ octahedra. Additionally, different arrangements of these octahedral units at the surface, dictated by local bond-valence sums, form 2D networks that can account for many ordered surface reconstructions as well as disordered glasslike structures consistent with the multitude of structures observed experimentally, and potentially other materials and interfaces.
EŞİT ÇIKAN RİSK ÖNCELİK SAYILARININ FARKLILAŞMASINI SAĞLAYACAK ALTERNATİF BİR MODEL ÖNERİSİ (2013)

Bu calismada, bir firmada gerceklestirilmis Hata Turu ve Etkileri Analizi (HTEA) calismasi sonucu esit cikan risk oncelik sayilarinin farklilasmasini saglayacak modelin Excel Premium Solver Platform yardimiyla cozumlenmesi ve gelistirilen alternatif cozumun cozume kavusturulan model ile olan iliskisi uzerinde durulmustur. Farklilasmayi saglayacak model olusturulurken ilkin; maksimize edilecek hucre isiginda degismesi muhtemel hucrelere kukla degiskenler atanmis, daha sonra “Yeni ROS Degerlendirme Yontemi”, Excel’deki fonksiyonlar yardimiyla modele eklenmistir. Modelin cozumlenmesi sirasinda ise, ilgili yontem ile olusturulmus sayisal degerler arasindaki fark, modelde maksimize edilecek deger olarak secilmis ve ilgili modele ait kisitlar olusturulmustur. Kisitlarin olusturulmasinda ise, uygulamada gerceklesen durumun gostergesi niteliginde olan ve esit cikan ROS toplamlarina ait alt bilesenler dikkate alinmistir.
Demonstration of all-optical Mach-Zehnder demultiplexer (1995)

A new type of ultrafast all-optical switch based on a Mach-Zehnder configuration has been demonstrated using the same wavelength and polarisation for both clock and data signals. A 10 ps switching window was measured with a 0.65 pJ clock pulse at 1.313 µm.
Allergen‐specific immunotherapy in horses with insect bite hypersensitivity: a double‐blind, randomized, placebo‐controlled study (2013)

Using commercially available extracts and tests, we could not demonstrate a beneficial effect of 1 year multiple ASIT in nonstabled horses with IBH.
Use of Antisense Oligomers to Study the Role of c‐<i>jun</i> in G<sub>1</sub> Progressiona (1992)

In actively proliferating Swiss 3T3 fibroblasts, expression of the protooncogene c-jun is maximally induced early in G1, immediately after completion of mitosis. Within 2 hours, c-jun mRNA levels drop to a basal amount that is approximately 30% of the maximum. This is maintained throughout the remainder of G1. To access the functional implications of this pattern of c-jun expression, antisense oligomers specific to c-jun were added to either actively proliferating or synchronized Swiss 3T3 cells, and their ability to inhibit DNA synthesis and division was determined. Our results show that if Swiss 3T3 cells are treated with anti-c-jun while actively growing or at any time during G1 after completion of mitosis, they exhibit a reduced ability to enter S-phase and subsequently divide. These results demonstrate that the regulation of G1 progression following mitosis depends on the expression and function of the protooncogene c-jun.
Resource management in wireless heterogeneous networks (WHNs) (2009)

Resources, especially in wireless networking context, are considered to be scarce and deficient. Appropriate management of resources is crucial for efficient networks' usage and users' satisfaction. This paper elaborates on the resource management issues in Wireless Heterogeneous Networks (WHNs). It explains the market and business cases for wireless heterogeneity and reflects on the most common radio resource management frameworks envisioned today. Furthermore, the paper pinpoints and explains two network architectures, i.e. the RIWCoS and the ARAGORN architecture, designed to deal with resource management under various access technologies possible. The former one is specifically tailored to meet the demands of emergency situations, whereas the latter one introduces the notion of cognitive resource management and policy regulated networking. Finally, some ideas regarding the future work in this vibrant area will be elaborated.
Three of Four Cysteines, Including That Responsible for Substrate Activation, Are Ionized at pH 6.0 in Yeast Pyruvate Decarboxylase:  Evidence from Fourier Transform Infrared and Isoelectric Focusing Studies (1996)

Oligonucleotide-directed site-specific mutagenesis was carried out on pyruvate decarboxylase (EC 4.1.1.1) from Saccharomyces cerevisiae at three of the four cysteines (152, 221, and 222), the fourth (69) being buried according to X-ray crystallographic results [Arjunan et al. (1996) J. Mol. Biol. 256, 590-600]. All of the variants still retained significant activity, and all could be purified to homogeneity. FT-IR experiments were run on the C221S, C222S, C221S/C222S and C152A variants, as well as on the wild-type enzyme. There is a band present at 2557 cm-1 in the spectra of all variants and the wild-type enzyme, except in the spectrum of the C152A variant. This frequency is appropriate to a cysteine S-H stretching mode. It was therefore concluded that C152 is the only undissociated cysteine on the enzyme at pH 6.0, the pH optimum of this enzyme, whereas C221, C222, and C69 are all ionized. Isoelectric focusing experiments were carried out on all of these variants, as well as on the H92A variant (H92 is across the domain divide on the alpha domain, from C221 located on the beta domain). The variation in isoelectric points deduced from the data was consistent with removal of negative charges concomitant with the C221S, C222S, and C221S/C222S substitutions and removal of a positive charge with the H92A substitution when compared to that of the wild-type enzyme. The results of these two types of experiments are in good accord and suggest that the site of substrate activation at C221 [Baburina et al. (1994) Biochemistry 33, 5630-5635] is comprised of a Cys221S- +HHis92 ion pair, not unlike that found in papain and glyceraldehyde-3-phosphate dehydrogenase. This finding suggests that the regulatory site of this enzyme has been optimized for nucleophilic reactivity between the thiolate of C221 and the keto carbon of the 2-oxoacid.
A simplified method for deriving shunt and reduced V<sub>A</sub>/Q in infants (2009)

The slide-rule method was reliable for deriving shunt and right shift (reduced V(A)/Q) of the P(I)O(2) versus SpO(2) curve when compared with the more complex algorithm. The new method should enable wider clinical application of these measurements of oxygen exchange.
Sendust Sheet-Processing Techniques and Magnetic Properties (1964)

A procedure has been developed whereby the brittle magnetic alloy of silicon, aluminum, and iron (Sendust) can be produced in sheet from through metal powder rolling techniques. Ring laminations stamped from this sheet at 0.014 in. thickness have the following dc properties: μ20=16 130; μmax=36 625; Hc=0.062 Oe; Br=3450 G; Bm=8960 G. High frequency (&lt;1 Mc/sec) loss values were lower than in laminated molybdenum Permalloy cores of the same thickness. The nominal Sendust composition is 9.5% silicon, 5.7% aluminum, and balance iron. This new process should make possible more extensive use of Sendust in applications that can take advantage of its remarkable intrinsic characteristics such as high initial permeability, high resistivity, low magnetostriction, and low magnetocrystalline anisotropy.
Prediction of human protein–protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk (2010)

Protein–protein interaction (PPI) prediction method has provided an opportunity for elucidating potential biological processes and disease mechanisms. We integrated eight features involving proteomic, genomic, phenotype and functional annotation datasets by a mixed model consisting of full connected Bayesian (FCB) model and naive Bayesian model to predict human PPIs, resulting in 40 447 PPIs which contain 2740 common PPIs with the human protein reference database (HPRD) by a likelihood ratio cutoff of 512. Then we applied them to exploring underlying pathway crosstalk where pathways were derived from the pathway interaction database. Two pathway crosstalk networks (PCNs) were constructed based on PPI sets. The PPI sets were derived from two different sources. One source was strictly the HPRD database while the other source was a combination of HPRD and PPIs predicted by our mixed Bayesian method. We demonstrated that PCNs based on the mixed PPI set showed much more underlying pathway interactions than the HPRD PPI set. Furthermore, we mapped cancer-causing mutated somatic genes to PPIs between significant pathway crosstalk pairs. We extracted highly connected clusters from over-represented subnetworks of PCNs, which were enriched for mutated gene interactions that acted as crosstalk links. Most of the pathways in top ranking clusters were shown to play important roles in cancer. The clusters themselves showed coherent function categories pertaining to cancer development.
ChR2 Mutants at L132 and T159 with Improved Operational Light Sensitivity for Vision Restoration (2014)

The ectopic expression of microbial opsin-based optogenetic sensors, such as channelrhodopsin-2 (ChR2) in surviving inner retinal neurons, is a promising approach to restoring vision after retinal degeneration. However, a major limitation in using native ChR2 as a light sensor for vision restoration is the low light sensitivity of its expressing cells. Recently, two ChR2 mutations, T159C and L132C, were reported to produce higher photocurrents or have ultra light sensitivity. In this study, we created additional ChR2 mutants at these two sites to search for more light responsive ChR2 forms and evaluate their suitability for vision restoration by examining their light responsive properties in HEK cells and mouse retinal ganglion cells. We found additional ChR2 mutants at these two sites that showed a further increase in current amplitude at low light levels in the cells expressing these mutants, or operational light sensitivity. However, the increase in the operational light sensitivity was correlated with a decrease in temporal kinetics. Therefore, there is a trade-off between operational light sensitivity and temporal resolution for these more light responsive ChR2 mutants. Our results showed that for the two most light responsive mutants, L132C/T159C and L132C/T159S, the required light intensities for generating the threshold spiking activity in retinal ganglion cells were 1.5 and nearly 2 log units lower than wild-type ChR2 (wt-ChR2), respectively. Additionally, their ChR2-mediated spiking activities could follow flicker frequencies up to 20 and 10 Hz, respectively, at light intensities up to 1.5 log units above their threshold levels. Thus, the use of these more light responsive ChR2 mutants could make the optogenetic approach to restoring vision more feasible.
Differentiated Data Persistence with Priority Random Linear Codes (2007)

Both peer-to-peer and sensor networks have the fundamental characteristics of node churn and failures. Peers in P2P networks are highly dynamic, whereas sensors are not dependable. As such, maintaining the persistence of periodically measured data in a scalable fashion has become a critical challenge in such systems, without the use of centralized servers. To better cope with node dynamics and failures, we propose priority random linear codes, as well as their affiliated pre-distribution protocols, to maintain measurement data in different priorities, such that critical data have a higher opportunity to survive node failures than data of less importance. A salient feature of priority random linear codes is the ability to partially recover more important subsets of the original data with higher priorities, when it is not feasible to recover all of them due to node dynamics. We present extensive analytical and experimental results to show the effectiveness of priority random linear codes.
Sensing ambient oxygen using a W/Cu<inf>x</inf>O/Cu memristor (2015)

Three memristive devices were fabricated and investigated for sensing oxygen in ambient air. The device design was as follows: Deposition of copper (Cu) bottom electrodes, copper oxide (Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> O) switching layers, and W top electrodes in a crossbar array structure. The Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> O layer was deposited via reactive sputtering of a Cu target with Ar/O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> mixture. A portion of this layer was left exposed for sensing. Atomic composition was confirmed via energy-dispersive X-ray spectroscopy (EDS), and current-voltage characteristics were measured using a picoammeter. Results demonstrate an increase in resistance states (24-31% for low resistance states) upon prolonged exposure to ambient air.
miR-135b mediates NPM-ALK–driven oncogenicity and renders IL-17–producing immunophenotype to anaplastic large cell lymphoma (2011)

Many transformed lymphoma cells show immune-phenotypes resembling the corresponding normal lymphocytes; thus, they provide a guide for proper diagnosis and present promising routes to improve their pathophysiologic understanding and to identify novel therapeutic targets. However, the underlying molecular mechanism(s) of these aberrant immune-phenotypes is largely unknown. Here, we report that microRNA-135b (miR-135b) mediates nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)-driven oncogenicity and empowers IL-17-producing immunophenotype in anaplastic large cell lymphoma (ALCL). NPM-ALK oncogene strongly promoted the expression of miR-135b and its host gene LEMD1 through activation of signal transducer and activator of transcription (STAT) 3. In turn, elevated miR-135b targeted FOXO1 in ALCL cells. miR-135b introduction also decreased chemosensitivity in Jurkat cells, suggesting its contribution to oncogenic activities of NPM-ALK. Interestingly, miR-135b suppressed T-helper (Th) 2 master regulators STAT6 and GATA3, and miR-135b blockade attenuated IL-17 production and paracrine inflammatory response by ALCL cells, indicating that miR-135b-mediated Th2 suppression may lead to the skewing to ALCL immunophenotype overlapping with Th17 cells. Furthermore, antisense-based miR-135b inhibition reduced tumor angiogenesis and growth in vivo, demonstrating significance of this "Th17 mimic" pathway as a therapeutic target. These results collectively illuminated unique contribution of oncogenic kinase-linked microRNA to tumorigenesis through modulation of tumor immune-phenotype and microenvironment.