gebhart/patrepeval huggingface dataset:
Paving the Way for Future Research in Autologous Chondrocyte Implantation: Response (2014)

which suggested that graft maturation after autol-ogous chondrocyte implantation (ACI) in the knee jointneeds at least 1 year, with ongoing adjustment of the T2relaxation time values compared with native surroundingcartilage, and found no correlation between increasingACI graft maturation and clinical outcomes (InternationalKnee Documentation Committee [IKDC] score).This is a very important study, adding to the studies onevaluating ACI graft maturation in osteochondral lesions.It would have been interesting if the authors—because ofobvious heterogeneity of defect locations as well as seriousmethodological limitations inherent in case series studies(eg, lack of comparative cohort or control group)—couldhave improved their study assessment tools (such as alsousing histological findings or the Short Form–36 [SF-36]questionnaire as secondary outcomes) to determine thecontributing factors that affected clinical outcomes. Mentalfactors, which could be assessed by the SF-36 question-naire, or other variables that are not visible on magneticresonance imaging (MRI), such as inflammation, increasedvascular penetration, and nerve growth, may influenceclinical outcomes. Moreover, the complexity of the kneeinjury and the patient history can make it difficult forany of the used outcome questionnaires to reflect the exactareas that are important to patients.
Molecular dynamics simulation of cytotoxicity of graphene nanosheets to blood-coagulation protein (2017)

Graphene is a nanomaterial that is widely used in electronics, biomedicine, and drug-delivery systems. Although it has many industrial applications, the cytotoxicity of graphene has not been sufficiently studied. In this study, the authors used molecular dynamics simulation to investigate how a graphene nanosheet affects a blood-coagulation protein, namely, a tissue factor/FVIIa binary complex bound to a lipid bilayer membrane, in a 4:1 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine lipid bilayer mixture. Based on the results, the authors suggest a mechanism for the cytotoxicity of graphene nanosheets to blood-coagulation protein at the molecular level.
Pseudouridine and <i>N</i><sup>6</sup>-methyladenosine modifications weaken PUF protein/RNA interactions (2017)

RNA modifications are ubiquitous in biology, with over 100 distinct modifications. While the vast majority were identified and characterized on abundant noncoding RNA such as tRNA and rRNA, the advent of sensitive sequencing-based approaches has led to the discovery of extensive and regulated modification of eukaryotic messenger RNAs as well. The two most abundant mRNA modifications-pseudouridine (Ψ) and <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A)-affect diverse cellular processes including mRNA splicing, localization, translation, and decay and modulate RNA structure. Here, we test the hypothesis that RNA modifications directly affect interactions between RNA-binding proteins and target RNA. We show that Ψ and m<sup>6</sup>A weaken the binding of the human single-stranded RNA binding protein Pumilio 2 (hPUM2) to its consensus motif, with individual modifications having effects up to approximately threefold and multiple modifications giving larger effects. While there are likely to be some cases where RNA modifications essentially fully ablate protein binding, here we see modest responses that may be more common. Such modest effects could nevertheless profoundly alter the complex landscape of RNA:protein interactions, and the quantitative rather than qualitative nature of these effects underscores the need for quantitative, systems-level accounting of RNA:protein interactions to understand post-transcriptional regulation.
Simulations of Silicon-on-Insulator Channel-Waveguide Electrooptical 2 × 2 Switches and 1 × 1 Modulators Using a ${\bf Ge_2}{\bf Sb_2}{\bf Te_5}$ Self-Holding Layer (2015)

This paper reports theoretical designs and simulations of electrooptical 2 × 2 switches and 1 × 1 loss modulators based upon GST-embedded SOI channel waveguides. It is assumed that the amorphous and crystalline phases of GST can be triggered electrically by Joule heating current applied to a 10-nm GST film sandwiched between doped-Si waveguide strips. TEo and TMo mode effective indices are calculated over 1.3 to 2.1-μm wavelength range. For 2 × 2 Mach-Zehnder and directional coupler switches, low insertion loss, low crosstalk, and short device lengths are predicted for 2.1 μm, although a decreased performance is projected for 1.55 μm. For 1.3-2.1 μm, the 1 × 1 EO waveguide has application as a variable optical attenuator and as a digital modulator, albeit with ≤100-ns state-transition time. Because the active material has two “stable” phases, the device holds itself in either state, and voltage needs to be applied only during transition.
Current noise of trimmed thick‐film resistors: measurement and simulation (1998)

An investigation of laser‐trimmed thick‐film resistors’ current noise was carried out. A large number of samples from two pastes with different P‐ and L‐cuts were prepared. The noise spectrum of the trimmed resistors was measured to obtain a relationship between the current noise and the cut parameters. A simple but comprehensive electrical model for the simulation of the current noise of trimmed resistors is also presented. The results from the noise simulation agree with the measured data.
A new optical cell switching paradigm (2003)

Most of the existing all-optical switching paradigms assume different wavelengths are switched independently, and hence require W switching planes at each core switch, where W is the number of wavelengths that an optical fiber can carry. As W is becoming as large as a few hundreds in the near future, the above requirement limits the scalability of core switches. In this paper, we present a novel all-optical switching paradigm, called optical cell switching (OCS), for the next-generation optical network. By time-division multiplexing (TDM), time in OCS is divided into time slots of fixed size, and every F consecutive time slots constitute a frame. Fine bandwidth granularity can be achieved by increasing F. The wavelengths in a time slot are all bundled, and each time slot is called an optical composite cell (OCC). The OCC is the switching unit in the OCS network. Therefore, each OCS core switch (OCX) requires only one switching plane and performs mere time-space switching, thus simplifying the management and reducing the implementation complexity of the OCX. Nevertheless, traffic can be aggregated at edge routers and groomed in the wavelength domain before entering the OCS core network. The OCS network can support both guaranteed and best-effort services. Optical time-slot interchangers (OTSIs) can be employed to further improve the performance of OCS. We provide simulation results to show that the OCS network can achieve low call-blocking rate for guaranteed services, and low cell-loss rate for besteffort services.
Ag Nano-composite Glasses Synthesized By Swift Heavy Ion Irradiation (2015)

In the present work, we have used swift heavy ions (SHI) irradiation and post irradiation annealing to synthesize Ag nanoparticles in fused silica. Fused silica samples deposited with 15 nm of Ag film were irradiated using SHI beam of 120 MeV Ag 9+ ions at different fluences and post irradiation annealing was done at 500 °C in air for 30 min. The samples were characterized using UV-vis absorption spectroscopy, Rutherford Backscattering Spectrometry (RBS), GAXRD, Transmission Electron Microscopy (TEM), and open aperture z-scan measurements. The signature of Ag nanoparticles was observed in optical absorption spectra and the average size of the Ag nanoparticles was estimated using Mie’s theory. The size of the nanoparticles (~3 nm) was also confirmed from the GAXRD and TEM measurements. RBS results for Ag/SiO2 irradiated with the fluence of 5 x10 13 ions/cm 2 shows the decrease in slope at the interface of the Ag profile, indicating a partial mixing at a fluence of 5 x10 13 ions/cm 2 . Open aperture z-scan measurement of Ag/SiO2 SHI irradiated sample after annealing shows a saturation behavior, indicating that the sample is optically non-linear. The sample shows saturation behavior but does not show optical limiting behavior, which indicates that the size and number density of nanoparticles are low. The ability to control the particle size using ion beam technique as a function of fluence and observed nonlinearity results provide concrete evidence that Ag nano composite glasses can be used in nonlinear and optical limiting application.
The influence of frusemide formulation on diuretic effect and efficiency (1999)

Controlled release formulations of frusemide with a low and extended rate of dissolution lead to a more prolonged absorption and subsequent diuresis, but still maintain a similar cumulative response, due to their higher diuretic efficiency.
Fine needle aspiration cytology, with immediate reporting, in the outpatient diagnosis of breast disease. (1987)

One hundred and fifty one new patients attending a breast clinic over a 6 month period underwent fine needle aspiration cytology (FNAC), with immediate reporting of the smears in the clinic. Thirty nine smears (25.8%) were classified as unequivocally malignant, 10 (6.6%) as being suspicious of malignancy, 61 (40.3%) as benign and 41 (27.1%) were acellular. There were no false positive diagnoses and only one false negative cytological diagnosis of breast cancer [corrected]. Immediate reporting of results enabled the diagnosis to be discussed with the patient at the first attendance and allowed improved surgical management of both benign as well as malignant breast disease.
Association Between Hypertensive Disorders of Pregnancy and Later Risk of Cardiomyopathy (2016)

( JAMA 2016;315(10):1026–1033) Hypertensive disorders of pregnancy (HDP), including preeclampsia and gestational hypertension, are common, occurring in approximately 10% of parturients worldwide. Women with preeclampsia have been shown to be at increased risk for peripartum cardiomyopathy as well as cardiovascular disease later in life. It has not yet been determined if these women are also at greater risk for developing cardiomyopathy beyond the peripartum period. However, recent research has suggested women with preeclampsia may undergo some degree of cardiac remodeling that results in persistent cardiac dysfunction. The aim of this study was to investigate the association between HDP and cardiomyopathy after the peripartum period.
Colchicine may assist in reducing granulation tissue in junctional epidermolysis bullosa (2016)

Epidermolysis bullosa (EB) is a rare, inherited blistering genodermatosis. Patients with junctional EB (JEB) due to LAMB3 mutations have widespread blisters and erosions of skin, mucosae, and nails, creating significant physical, emotional, and psychosocial burdens. Here we report the use of colchicine for ameliorating hypergranulating wounds in a 41-year-old female with JEB generalized intermediate. Her skin wounds and granulation tissue gradually exacerbated under silicone dressings such that she became profoundly anemic. Subsequently, she was commenced on colchicine 500 μg daily on the basis that it may inhibit cell proliferation and be anti-inflammatory. After a 6-month trial of colchicine, she had an objective and subjective improvement in her validated EB Disease Activity and Scarring Index activity and damage scores and Quality Of Life in EB score with less skin erosions, granulation tissue, and erythema. In addition, her anemia resolved. She denied any gastrointestinal side effects. The exact mechanism of colchicine in assisting reduction of the blistering, erosions, and granulation in JEB is unclear, but the anti-inflammatory and antimitotic properties of colchicine may be partially responsible for this process.
A three-dimensional stochastic spatio-temporal model of cell spreading (2007)

Cell motility is important for many physiological processes and the underlyingbiochemical reactions motility have been well characterized. Mathematical models, usingthe biochemical reactions and focused on different types of spreading behavior have beenconstructed and analyzed. In this study, we build on these previous models to develop athree-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell spreading behavior. We analyzed the effects of varying branching reaction rates, membrane resistance forces and capping protein concentrations on the dynamics of isotropic spreading. The simulations allowed us to identify the range within which branching reaction rates and membrane force values cooperate to yield isotropic spreading behavior. The model predicts increasing capping protein concentration would lead to a linear decrease in average peripheral velocity. We tested this prediction experimentally using varying concentrations of a pharmacologic agent (Cytochalasin D) that caps growing actin filaments. We find that the experimental results agree with the numerical simulations. Thus, a spatio-temporally complex model made up of a simple set of stochastic reactions near the cell surface, when constrained by membrane forces, can yield deterministic behavior as characterized by isotropic cell spreading.
Golgi Complex Function in the Excretion of Renal Kallikrein (1982)

A Golgi complex rich-fraction containing both N-acetylglucosamine galactosyltransferase and kallikrein activity has been isolated from kidney of rats previously treated with colchicine, a secretion inhibitor, followed by the administration of high-sodium solutions, to stimulate biosynthesis or activation of renal kallikrein. After the treatment, N-acetylglucosamine galactosyltransferase and kallikrein activities were increased in the Golgi complex, about 18- and 24-fold, respectively, as compared to the homogenate. Low kallikrein activity was found in the crude light mitochondrial fraction from treated animals, whereas a high level of activity was observed in the microsomal fraction. The inverse situation was found in rats treated only with high-sodium solution. Results suggest that kallikrein is probably transported by microsomal elements, particularly by the Golgi complex. Furthermore, the evidence seems to indicate that the kallikrein activity reported in the plasma membrane and/or in the lysosomal fraction is due to kallikrein secretion, in the form of intact granules, which have sedimented with these two fractions.
Multiple-View Spectral Clustering for Group-wise Functional Community\n Detection (2016)

Functional connectivity analysis yields powerful insights into our\nunderstanding of the human brain. Group-wise functional community detection\naims to partition the brain into clusters, or communities, in which functional\nactivity is inter-regionally correlated in a common manner across a group of\nsubjects. In this article, we show how to use multiple-view spectral clustering\nto perform group-wise functional community detection. In a series of\nexperiments on 291 subjects from the Human Connectome Project, we compare three\nversions of multiple-view spectral clustering: MVSC (uniform weights), MVSCW\n(weights based on subject-specific embedding quality), and AASC (weights\noptimized along with the embedding) with the competing technique of Joint\nDiagonalization of Laplacians (JDL). Results show that multiple-view spectral\nclustering not only yields group-wise functional communities that are more\nconsistent than JDL when using randomly selected subsets of individual brains,\nbut it is several orders of magnitude faster than JDL.\n
The Photosensitivity of Rhodopsin Bleaching and Light-Induced Increases of Fundus Reflectance in Mice Measured In Vivo With Scanning Laser Ophthalmoscopy (2016)

The elevated photosensitivity of rhodopsin bleaching in vivo is explained by waveguide condensing of light in propagation from rod inner segment (RIS) to rod outer segment (ROS). The similar photosensitivity of rhodopsin in the two strains reveals that little light backscattered from the sclera can enter the ROS. The bleaching-induced increases in reflectance at the IS/OS junctions and OS tips resemble results previously reported in human cones, but are ascribed to rods due to their 30/1 predominance over cones in mice and to the relatively minor amount of cone M-opsin in the regions scanned.
A nonsense mutation in Exon 3 results in the HLA‐B null allele B*5127N (2002)

A new HLA-B null allele has been identified within the B*51 group by combined serological and molecular typing of an Italian Caucasoid family. Serological data indicated that the proband typed homozygous for A2 and B60. Confirmatory typing using sequence specific oligonucleotide hybridization (SSPOH) detected a second B allele within the B*51 group. Allele specific typing (SSP) for B*51 subtypes, including the known B*5111N allele, was performed, and typing results were consistent with B*5101, suggesting the presence of a new null variant. Cloning and sequencing of this allele identified a B*5101 variant with a nonsense mutation in exon 3. This new null allele has been designated B*5127N. The combined use of serologic and DNA-based typing methods facilitates the identification of null and low-expression alleles. An overview of null alleles of class I HLA is presented.
ChemInform Abstract: Considered Stable Carbocations. Part 267. Pagodane Dication, a Unique Zn‐Aromatic Cyclobutanoid System. (1986)

Abstract Under superacidic conditions pagodane (I) forms a remarkably stable dication instead of its expected isomerization.
Role of cytokines in human B lymphocyte growth and differentiation. (1993)

B lymphocytes express at their surface the CD40 antigen which belongs to the NGF receptor superfamily. The crosslinking of the CD40 antigen using a mouse fibroblastic cell line expressing the human Fc receptor (Fc gamma RII/CDw32) and anti-CD40 monoclonal antibody induces resting B lymphocytes to enter a state of sustained proliferation. Addition of IL-4 to such cultures results in the generation of factor dependent long-term normal human B cell lines and in the secretion of IgE following isotype switching. Addition of IL-10 results in limited cell proliferation but most importantly in very high immunoglobulin production which results from the differentiation of B cells into plasma cells. The combination of IL-10 and TGF beta induces naive sIgD+ sIgM+ B cells to secrete IgA1 and IgA2 as a consequence of isotype switching. The extracellular domain of CD40 binds with high affinity and high specificity to a 32 kDa glycoprotein transiently expressed on activated T cells. This interaction of the CD40 antigen on B cells with its ligand on T cells represents a key step in T cell dependent B cell activation.
New pH-Sensitive Vesicles. Release Control of Trapped Materials from the Inner Aqueous Phase of Vesicles Made from Triple-Chain Amphiphiles Bearing Two Carboxylate Groups (2001)

The pH-induced release of trapped materials from the inner aqueous phase of vesicles made from the synthetic triple-chain amphiphile 1 bearing two carboxyl groups was investigated. While a particular pH-dependence of the release of trapped materials from the inside of vesicles made from distearoylphosphatidylcholine (DSPC) was not observed, vesicles made from compound 1 showed unique pH-sensitive character toward the pH of the outer bulk phase as follows: it released less than 10% of 5(6)-carboxyfluorescein (CF) as a water-soluble marker at pH 7.5 after 1 year. But the vesicular assemblies were broken below pH 3.5−4.0, resulting in the liberation of the trapped CF into the bulk phase. The latter result is associated with a full-protonation of the carboxylate groups of compound 1. In the case of vesicles made from a mixture of DSPC and compound 1, the addition of cholesterol into the vesicle membranes was effective in providing clear pH-sensitive character for this type of vesicle. The ζ potentials of a series of vesicles containing compound 1 at various pH synchronized well with the pKa1 value of vesicles made from compound 1 and the pH-dependence of the release of trapped CF from these vesicles.
Transient Silenes and Their Dimethyl-<i>d</i><sub>6</sub> Ether Donor Complexes from the Gas-Phase Pyrolysis of Siletanes<sup>,</sup> (2000)

The silenes H2SiCH2 (2), MeHSiCH2 (7), and Me2SiCH2 (8) have been prepared by low-pressure flow pyrolysis from the corresponding siletanes (1), (5), and (6). 2, 7, and 8 were identified by residual gas analysis of the pyrolysis stream and by low-temperature NMR spectroscopy of their complexes 2·O(CD3)2 (16), 7·O(CD3)2 (17), and 8·O(CD3)2 (18). The complexes 16−18 are stable to temperatures between −140 and −100 °C. Above these temperatures rapid polymerization occurs. The complexation with dimethyl ether obviously stabilizes the silenes and allows their spectroscopic investigation. The 29Si chemical shifts of the complexes are −25.2 (16), −1.8 (17) and 16.8 ppm (18). The experimental results are supported by ab initio and density functional calculations of geometries and magnetic properties of the silenes 2, 7, and 8 and the dimethyl ether complexes 16−18. The calculations predict a relatively short Si−O separation of about 1.7 Å in the corresponding silene−ether adducts. Natural bond analysis of the donor−acceptor complex 16 reveals that the interaction between the ether molecule and the silene is predominantly ionic, despite the relatively short Si−O distance.
Effect of carrier heating on the wavelength chirp of ultrashort laser pulses in semiconductor traveling wave amplifiers (1994)

The effect of the carrier heating is numerically studied. It is shown that the spectrum of the optical pulses is blue shifted when the duration of the pulse tail is comparable to or shorter than the relaxation time of heated carriers. The results are in good agreement with the experimental data on an AlGaAs/GaAs traveling wave amplifier.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Bacterial Immobilization for Imaging by Atomic Force Microscopy (2011)

AFM is a high-resolution (nm scale) imaging tool that mechanically probes a surface. It has the ability to image cells and biomolecules, in a liquid environment, without the need to chemically treat the sample. In order to accomplish this goal, the sample must sufficiently adhere to the mounting surface to prevent removal by forces exerted by the scanning AFM cantilever tip. In many instances, successful imaging depends on immobilization of the sample to the mounting surface. Optimally, immobilization should be minimally invasive to the sample such that metabolic processes and functional attributes are not compromised. By coating freshly cleaved mica surfaces with porcine (pig) gelatin, negatively charged bacteria can be immobilized on the surface and imaged in liquid by AFM. Immobilization of bacterial cells on gelatin-coated mica is most likely due to electrostatic interaction between the negatively charged bacteria and the positively charged gelatin. Several factors can interfere with bacterial immobilization, including chemical constituents of the liquid in which the bacteria are suspended, the incubation time of the bacteria on the gelatin coated mica, surface characteristics of the bacterial strain and the medium in which the bacteria are imaged. Overall, the use of gelatin-coated mica is found to be generally applicable for imaging microbial cells.