gebhart/patrepeval huggingface dataset:
A Small Angle Neutron Scattering Study of the Adsorbed Asphaltene Layer in Water-in-Hydrocarbon Emulsions:  Structural Description Related to Stability (2007)

We have developed a specific protocol to study with SANS measurements, the structure of the interfacial film layer in water-in-oil emulsions stabilized by asphaltene. Using the contrast matching technique available for neutron scattering, we have access to both the composition and the quantity of interface. The results obtained give us a view of the asphaltene aggregates in the interfacial film, which are structured as a monolayer and show a direct correlation between the size of asphaltene aggregates in solution and the thickness of the film layer. The organization of the interface has been studied as a function of several parameters such as the quantity of resins, i.e., the size of aggregates, the pH of the aqueous phase, and the aging time of the emulsions and the consequences of these variations on the macroscopic stability of these emulsions. We show that the key parameter for the stability is the inter-asphaltene aggregate interaction inside the film layer. Changing the attractive/repulsive balance between the aggregates in the film at the microscopic scale, by changing the aggregate's size or the aggregate's ionization, has a direct incidence on the quantity of water recovered after centrifugation: the stronger the attraction between aggregates in the film, the more stable the emulsion is.
A Novel Naturally Sampled Space Vector Pulse Width Modulation Algorithm (2009)

A novel algorithm for the naturally sampled SVPWM in overmodulation region is proposed in this paper, the comparison between naturally sampled SVPWM and conventional SVPWM in overmodulation region is carried out. It was proved that naturally sampled SVPWM could be used not only in under modulation but also in overmodulation region by the results of analysis and simulation. The work was done by this paper shows a promising use of the naturally sampled SVPWM. The obviously advantage is that it could be implemented by using DSP with only simplified computation and short time of on line calculation, or just by using analog circuits without the help of microprocessor at all. All the work did by this paper provide a platform for the implementation of naturally sampled SVPWM operating in under modulation and over modulation region.
Viability of Cryptosporidium parvum oocysts: correlation of in vitro excystation with inclusion or exclusion of fluorogenic vital dyes (1992)

A viability assay for oocysts of Cryptosporidium parvum based on the inclusion or exclusion of two fluorogenic vital dyes, 4',6-diamidino-2-phenylindole (DAPI) and propidium iodide, was developed by using several different isolates of oocysts. Correlation of this assay with viability measured by in vitro excystation was highly statistically significant, with a calculated correlation coefficient of 0.997. In this research, two similar excystation protocols were utilized, and no significant difference between excystation protocols was detected. Percent excystation of oocyst suspensions could be increased or reduced by inclusion of a preincubation treatment in either excystation protocol, and this alteration was also demonstrated in the viability assay. Oocysts which excluded both dyes would not excyst in vitro unless a further trigger was provided and were more resistant to acid or alkali treatment. The results of this research provide a reproducible, user-friendly assay which is applicable to individual oocysts and also provides a useful adjunct for identification of oocysts in water and environmental samples.
Response to retreatment with interferon-α plus ribavirin in chronic hepatitis C patients is independent of the NS5A gene nucleotide sequence (1999)

Therapy with interferon-alpha-2b plus ribavirin was well tolerated, achieving an end-of-treatment response in 25 (40.3%) patients. Response did not correlate with the presence of mutations in the NS5A gene analyzed, including the interferon sensitivity determining region (ISDR) and its flanking sequences.
Starched Carbon Nanotubes (2002)

Common-or-garden starch can render single-walled carbon nanotubes (SWNTs) readily soluble in water. The secret is to preorganize the linear amylose component in the starch into a helix with iodine prior to bringing the SWNTs on the scene. The SWNTs displace the iodine molecules in a “pea-shooting” type of mechanism (see scheme). After some physical cajoling of the aqueous solution containing the starch–SWNT complex, a fine “bucky paper” is formed. Spitting in the aqueous solution, followed by sitting around for a few hours, also enables equally fine “bucky paper” to be harvested.
Effect of Ritonavir on<sup>99m</sup>Technetium–Mebrofenin Disposition in Humans: A Semi‐PBPK Modeling and<i>In Vitro</i>Approach to Predict Transporter‐Mediated DDIs (2013)

A semiphysiologically based pharmacokinetic (semi-PBPK) model was developed to describe a unique blood, liver, and bile clinical data set for the hepatobiliary imaging agent (99m)Technetium-mebrofenin ((99m)Tc-mebrofenin), and to simulate sites/mechanisms of a (99m)Tc-mebrofenin-ritonavir drug-drug interaction (DDI). The transport inhibitor ritonavir (multiple-dose: 2 × 300 mg) significantly increased systemic (99m)Tc-mebrofenin exposure as compared with control (4,464 ± 1,861 vs. 1,970 ± 311 nCi min/ml; mean ± SD), without affecting overall hepatic exposure or biliary recovery. A novel extrahepatic distribution compartment was required to characterize (99m)Tc-mebrofenin disposition. Ritonavir inhibited (99m)Tc-mebrofenin accumulation in human sandwich-cultured hepatocytes (SCH) (half maximal inhibitory concentration (IC50) = 3.46 ± 1.53 µmol/l). Despite ritonavir accumulation in hepatocytes, intracellular binding was extensive (97. 6%), which limited interactions with multidrug resistance protein 2 (MRP2)-mediated biliary excretion. These in vitro data supported conclusions from modeling/simulation that ritonavir inhibited (99m)Tc-mebrofenin hepatic uptake, but not biliary excretion, at clinically relevant concentrations. This integrated approach, utilizing modeling, clinical, and in vitro data, emphasizes the importance of hepatic and extrahepatic distribution, assessment of inhibitory potential in relevant in vitro systems, and intracellular unbound concentrations to assess transporter-mediated hepatic DDIs.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e20; doi:10.1038/psp.2012.21; advance online publication 2 January 2013.
Ultrasound calibration framework for the image-guided surgery toolkit (IGSTK) (2011)

Registration is a key technology in image-guided navigation systems. By aligning pre-operative images with the intra-operative setting these systems provide visual feedback that improves the physician's understanding of the spatial relationships between anatomical structures and surgical tools. Most often the alignment is obtained using fiducials. Another option is to replace the use of fiducials with intra-operative imaging. Two dimensional ultrasound (US) is a widely available intra-operative non-ionizing imaging modality. To utilize this modality for registration one must first perform spatial calibration of the US. In this work we describe the implementation of three spatial calibration methods as part of the image-guided surgery toolkit (IGSTK). The implementation follows the IGSTK calibration framework, separating algorithmic aspects from user interaction aspects of the calibration. Our calibration framework includes three methods. The first is a phantom-less method using a tracked pointer tool in addition to the tracked US, the second method uses a cross-wire phantom, and the third method is based on the use of a plane phantom.
Occupancy of dipeptidyl peptidase IV activates an associated tyrosine kinase and triggers an apoptotic signal in human hepatocarcinoma cells (1998)

Dipeptidyl peptidase IV (CD26/DPP-IV) is an ectoenzyme expressed on different cell types. Signaling properties and functional consequences of the CD26 triggering have been elucidated mostly on T cells, where the molecule delivers a costimulatory signal that potentiates T-cell activation through the T-cell receptor. We conducted studies in the human hepatocarcinoma-derived PLC/PRF/5 cell line to examine the signal transduction through CD26 and its functional properties in the absence of other T-cell-specific membrane molecules. Engagement of CD26 in PLC/PRF/5 cells through a specific antibody induces tyrosine phosphorylation of several proteins with maximal intensity 15 minutes after the stimulation. This effect was under the negative regulatory control of CD45 tyrosine phosphatase, in that the addition of orthovanadate clearly enhanced the phosphorylation events. Using in vitro kinase assays with CD26 immunoprecipitates, we observed that a protein or proteins with kinase activity are coprecipitated with the CD26 molecule. In addition, unlike Jurkat T cells, in which CD26 expression exerts a protective effect against apoptosis, in PLC/PRF/5 cells CD26 occupancy delivers a potent apoptotic signal. This effect was also observed in HepG2 cells, thus indicating that it represents a more general phenomenon occurring in different liver neoplastic cell lines.
Alpha/Beta Interferons Potentiate Virus-Induced Apoptosis through Activation of the FADD/Caspase-8 Death Signaling Pathway (2000)

Interferon (IFN) mediates its antiviral effects by inducing a number of responsive genes, including the double-stranded RNA (dsRNA)-dependent protein kinase, PKR. Here we report that inducible overexpression of functional PKR in murine fibroblasts sensitized cells to apoptosis induced by influenza virus, while in contrast, cells expressing a dominant-negative variant of PKR were completely resistant. We determined that the mechanism of influenza virus-induced apoptosis involved death signaling through FADD/caspase-8 activation, while other viruses such as vesicular stomatitis virus (VSV) and Sindbis virus (SNV) did not significantly provoke PKR-mediated apoptosis but did induce cytolysis of fibroblasts via activation of caspase-9. Significantly, treatment with IFN-alpha/beta greatly sensitized the fibroblasts to FADD-dependent apoptosis in response to dsRNA treatment or influenza virus infection but completely protected the cells against VSV and SNV replication in the absence of any cellular destruction. The mechanism by which IFN increases the cells' susceptibility to lysis by dsRNA or certain virus infection is by priming cells to FADD-dependent apoptosis, possibly by regulating the activity of the death-induced signaling complex (DISC). Conversely, IFN is also able to prevent the replication of viruses such as VSV that avoid triggering FADD-mediated DISC activity, by noncytopathic mechanisms, thus preventing destruction of the cell.
Gravitational wave detection: Principles and practice (2013)

The technology of gravitational wave detection has been developed to a high degree. I review the basic principles of interferometric detectors, and give an account of the current state of the art, and plans for the near-term future.
Non-dominated sorting genetic filter a multi-objective evolutionary particle filter (2014)

In this paper, the problem of nonlinear state estimation converted to a multi-objective optimization problem, and based on Non-dominated Genetic Algorithm II (NSGA-II) and Particle Filter (PF), a multi-objective evolutionary particle filter, namely Non-dominated Genetic Filter (NSGF) is proposed. Search and optimization abilities of NSGA-II are incorporated into standard particle filtering framework to improve the estimation performance. Classic filtering approaches define a single criterion to evaluate an estimated state vector, however in this paper, two criteria are defined to evaluate and rate estimated state vectors. Conversion of the state estimation problem into a multi-objective optimization problem, improves diversity of promising solutions, and finally improves the estimation performance. Simulation results are given for an example and NSGF is compared to other types of particle filters. Efficiency and applicability of NSGF is confirmed according to the obtained results.
The type IV secretion system affects the expression of Omp25/Omp31 and the outer membrane properties of<i>Brucella melitensis</i> (2009)

The type IV secretion system (T4SS) contributes to Brucella intracellular survival through its effector proteins. Comparative proteomic analysis showed that intracellular survival proteins are expressed differentially in a virB mutant. Interestingly, several outer membrane proteins (OMPs) are also differentially expressed, implying that T4SS might affect the OM properties of Brucella. To further evaluate the impact of T4SS on OM, in the present study, the OM proteomes were isolated and compared. Many more products of OMPs, particularly different products of the Omp25/Omp31 family, were found to be altered in the virB mutant. The transcription profiles of Omp25/Omp31 were different from those of their protein products, implying their regulation by virB at both transcriptional and post-transcriptional levels. The virB mutant aggregates at a high cell density and produces exopolysaccharide, a phenotype resembling that of the vjbR mutant. The virB mutant showed increased sensitivity to polymyxin B and decreased survival under oxidative, high-salt and high-osmolarity stresses, indicating drastic membrane alterations. These results indicated that in addition to being an effector protein secretion system, T4SS affects OM properties that might be important for the adaptation of Brucella to both in vitro and in vivo hostile environments.
Strain‐dependent effects of the histamine H<sub>4</sub>receptor antagonist JNJ7777120 in a murine model of acute skin inflammation (2011)

The effects of the histamine H(4) receptor antagonist JNJ7777120 were evaluated in a model of acute skin inflammation induced by local application of croton oil. The influence of strain on the effect of JNJ7777120 was investigated in four different mouse strains (CD-1, NMRI, BALB/c and C57BL/6J). In CD-1 mice, JNJ777720 (30-100 mg/kg subcutaneously, s.c.) exerted a dose-dependent inhibition of croton oil-induced ear inflammation and polymorphonuclear leucocyte infiltration, as confirmed by histological evaluation of ear tissues. JNJ7777120 (30-100 mg/kg) did not reduce ear oedema in NMRI, BALB/c or C57BL/6J mice. The positive control, dexamethasone (2 mg/kg s.c.) induced significant anti-inflammatory effects only in CD-1 and NMRI mice. In these strains, also the histamine H(1) -receptor blocker pyrilamine (30 mg/kg s.c.) significantly reduced ear oedema at 2 h after croton oil challenge, being as effective as JNJ7777120 in CD-1 mice. Taken together, these data demonstrate that the H(4) receptor antagonist JNJ7777120 may reduce acute croton oil-induced skin inflammation as effectively as H(1) receptor blockade. However, present experiments evidenced for the first time marked strain-related differences in the JNJ7777120 pharmacological activity, which have to be carefully considered when using this ligand to characterize histamine H(4) receptor functions in murine models and translating preclinical data to clinical human settings.
The Effect of Pregnancy on Thyroid Nodule Formation (2002)

Epidemiology data have revealed a higher prevalence of nodular goiters in women than men in both iodine-sufficient and iodine-deficient areas. Increased prevalence of thyroid nodules has also been reported in women with higher gravidity. However, the association between pregnancy and thyroid nodule formation has never been studied. The aim of our study was to evaluate the incidence of thyroid nodules during pregnancy and determine whether pregnancy will induce thyroid nodule formation. Two hundred twenty-one healthy southern Chinese women in the first trimester of their pregnancy were studied prospectively. Thyroid ultrasonography, thyroid function tests, and urinary iodine excretion were measured at first, second, and third trimesters of pregnancy as well as 6 wk and 3 months postpartum. Thyroid nodules (>2 mm in any dimension on ultrasonography) were detected in 34 (15.3%) subjects at first trimester, with 12 (5.4%) subjects having more than one nodule. Eight subjects had clinically palpable nodules. Women with thyroid nodules were older (P < 0.01) and had higher gravidity (P < 0.02) than those women without thyroid nodules. The volume of the single/dominant nodules increased from 60 (14--344) mm(3), median (interquartile range) at first trimester to 65 (26-472) mm(3) at third trimester (P < 0.02). These nodules remained enlarged at 103 (25-461) mm(3) 6 wk postpartum (P < 0.005) and 73 (22-344) mm(3) at 3 months postpartum (P < 0.05). Patients with thyroid nodules had lower serum TSH values (P < 0.03) and higher Tg levels (P < 0.05) throughout pregnancy. Appearance of new nodules was detected in 25 (11.3%) women as pregnancy advanced so that by 3 months postpartum, the incidence of thyroid nodular disease was 24.4% (P < 0.02 vs. first trimester). Compared with those with no detectable nodules throughout pregnancy, subjects with new nodule formation had higher urinary iodine excretion from second trimester onward (P all < 0.05). However, no difference could be detected in their TSH and Tg levels throughout pregnancy. Fine-needle aspiration on nodules greater than 5 mm in any dimension after delivery (n = 21) confirmed the majority having histological features consistent with nodular hyperplasia. No thyroid malignancy was detected. In conclusion, pregnancy is associated with an increase in the size of preexisting thyroid nodules as well as new thyroid nodule formation. This may predispose to multinodular goiter in later life.
Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects (2016)

Advances in genomic technology have enabled the faithful detection and measurement of mutations and the gene expression profile of cancer cells at the single-cell level. Recently, several single-cell sequencing methods have been developed that permit the comprehensive and precise analysis of the cancer-cell genome, transcriptome, and epigenome. The use of these methods to analyze cancer cells has led to a series of unanticipated discoveries, such as the high heterogeneity and stochastic changes in cancer-cell populations, the new driver mutations and the complicated clonal evolution mechanisms, and the novel identification of biomarkers of variant tumors. These methods and the knowledge gained from their utilization could potentially improve the early detection and monitoring of rare cancer cells, such as circulating tumor cells and disseminated tumor cells, and promote the development of personalized and highly precise cancer therapy. Here, we discuss the current methods for single cancer-cell sequencing, with a strong focus on those practically used or potentially valuable in cancer research, including single-cell isolation, whole genome and transcriptome amplification, epigenome profiling, multi-dimensional sequencing, and next-generation sequencing and analysis. We also examine the current applications, challenges, and prospects of single cancer-cell sequencing.
Saturation in Phosphene Size with Increasing Current Levels Delivered to Human Visual Cortex (2017)

Electrically stimulating early visual cortex results in a visual percept known as a phosphene. Although phosphenes can be evoked by a wide range of electrode sizes and current amplitudes, they are invariably described as small. To better understand this observation, we electrically stimulated 93 electrodes implanted in the visual cortex of 13 human subjects who reported phosphene size while stimulation current was varied. Phosphene size increased as the stimulation current was initially raised above threshold, but then rapidly reached saturation. Phosphene size also depended on the location of the stimulated site, with size increasing with distance from the foveal representation. We developed a model relating phosphene size to the amount of activated cortex and its location within the retinotopic map. First, a sigmoidal curve was used to predict the amount of activated cortex at a given current. Second, the amount of active cortex was converted to degrees of visual angle by multiplying by the inverse cortical magnification factor for that retinotopic location. This simple model accurately predicted phosphene size for a broad range of stimulation currents and cortical locations. The unexpected saturation in phosphene sizes suggests that the functional architecture of cerebral cortex may impose fundamental restrictions on the spread of artificially evoked activity and this may be an important consideration in the design of cortical prosthetic devices.<b>SIGNIFICANCE STATEMENT</b> Understanding the neural basis for phosphenes, the visual percepts created by electrical stimulation of visual cortex, is fundamental to the development of a visual cortical prosthetic. Our experiments in human subjects implanted with electrodes over visual cortex show that it is the activity of a large population of cells spread out across several millimeters of tissue that supports the perception of a phosphene. In addition, we describe an important feature of the production of phosphenes by electrical stimulation: phosphene size saturates at a relatively low current level. This finding implies that, with current methods, visual prosthetics will have a limited dynamic range available to control the production of spatial forms and that more advanced stimulation methods may be required.
The effects of age on the response of rabbit periosteal osteoprogenitor cells to exogenous transforming growth factor-β2 (1994)

Additional bone and cartilage are formed if transforming growth factor-beta is injected into the periosteum of calvariae or long bones. To investigate this further, transforming growth factor-beta 2 was injected into the periosteum of the tibia of 3-day-old, 3-month-old and 2-year-old rabbits. In all instances, there was an increase in proliferation of the cells of the cambial layer of the periosteum, that is, the osteoprogenitor cells, and breakdown of the fibrous layer. Oedema was induced in the surrounding connective tissues. Over the experimental period the normal neonatal tibia is undergoing rapid growth; there is periosteal bone formation and endosteal resorption. In the experimental neonatal tibiae, an increase in periosteal bone formation is seen after three injections of 20 ng of transforming growth factor-beta 2, which is accompanied by cartilage after five injections; the amounts of induced bone and cartilage increase with the number of injections. The chondrocytes hypertrophy after 4 days and the cartilage is replaced by bone endochondrally. In contrast, after seven injections of 20 ng transforming growth factor-beta 2, there is only a small amount of new bone on the 3-month-old tibia and none on the 2-year-old tibia. One day after seven injections of 200 ng transforming growth factor-beta 2, there is a small amount of bone formation, while seven days after cartilage is found as small discrete nodules on the 3-month-old tibia, but as small areas within the bone on the 2-year-old tibia. It is concluded that the primary effect of transforming growth factor-beta 2 in this experimental model is to increase the proliferative rate of the osteoprogenitor cells in the periosteum. It is argued that transforming growth factor-beta 2 does not initiate osteoblastic or chondrocytic differentiation of osteoprogenitor cells. It is suggested that their differentiation is controlled by the local environment, in particular, the vascularity and locally circulating growth factors.