Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Heterogeneity within Cultured Cells on Bacterial Invasion: Analysis of Pseudomonas aeruginosa andSalmonella enterica Serovar Typhi Entry into MDCK cells by Using a Green Fluorescent Protein-Labelled Cystic Fibrosis Transmembrane Conductance Regulator Receptor

ABSTRACT The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride ion channel that also serves as a receptor for entry ofPseudomonas aeruginosa and Salmonella entericaserovar Typhi into epithelial cells. To evaluate heterogeneity in CFTR protein expression in cultured cells and the effect of heterogeneity on internalization of different P. aeruginosa and serovar Typhi strains, we used two-color flow cytometry and confocal laser microscopy to study bacterial uptake by Madin-Darby canine kidney (MDCK) type I epithelial cells stably expressing a green fluorescent protein (GFP)-CFTR fusion construct (MDCK–GFP-CFTR cells). We found a strong correlation between cell size and GFP-CFTR protein expression, with 60 to 70% of cells expressing low levels of GFP-CFTR protein, 20 to 30% expressing intermediate levels, and <10% expressing high levels. The cells were sorted into low-, intermediate-, or high-level producers of CFTR protein; in vitro growth of each sorted population yielded the same distribution of CFTR protein expression as that in the original population. Cells expressing either low or high levels of CFTR protein internalized bacteria poorly; maximal bacterial uptake occurred in the cells expressing intermediate levels of CFTR protein. Treatment of MDCK cells with sodium butyrate markedly enhanced the production of CFTR protein without increasing cell size; butyrate treatment also increased the proportion of cells with internalized bacteria. However, there were fewer bacteria per butyrate-treated cell and, for P. aeruginosa, there was an overall decrease in the total level of bacterial uptake. The most highly ingested bacterial strains were internalized by fewer total MDCK–GFP-CFTR cells, indicating preferential bacterial uptake by a minority of epithelial cells within a given culture. Confocal fluorescence microscopy showed that P. aeruginosa and serovar Typhi induced cytoplasmic accumulation of CFTR protein close to the plasma membrane where the bacteria were adherent. These results show that within a population of MDCK–GFP-CFTR cells, there are cells with markedly different abilities to ingest bacteria via CFTR, the majority of the P. aeruginosa and serovar Typhi cells are ingested by the one-fourth to one-third of the cells that exhibit an intermediate size and level of CFTR protein expression, and overexpression of the CFTR receptor does not increase total bacterial uptake but rather allows more epithelial cells to ingest fewer total bacteria.
Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species‐level diversity. Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure. Here, I present a meta‐analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta‐analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts. Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community‐ and ecosystem‐level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively. There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation. Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful.
Temporal lobe and “default” hemodynamic brain modes discriminate between schizophrenia and bipolar disorder

Schizophrenia and bipolar disorder are currently diagnosed on the basis of psychiatric symptoms and longitudinal course. The determination of a reliable, biologically‐based diagnostic indicator of these diseases (a biomarker) could provide the groundwork for developing more rigorous tools for differential diagnosis and treatment assignment. Recently, methods have been used to identify distinct sets of brain regions or “spatial modes” exhibiting temporally coherent brain activity. Using functional magnetic resonance imaging (fMRI) data and a multivariate analysis method, independent component analysis, we combined the temporal lobe and the default modes to discriminate subjects with bipolar disorder, chronic schizophrenia, and healthy controls. Temporal lobe and default mode networks were reliably identified in all participants. Classification results on an independent set of individuals revealed an average sensitivity and specificity of 90 and 95%, respectively. The use of coherent brain networks such as the temporal lobe and default mode networks may provide a more reliable measure of disease state than task‐correlated fMRI activity. A combination of two such hemodynamic brain networks shows promise as a biomarker for schizophrenia and bipolar disorder. Hum Brain Mapp 2008. © 2007 Wiley‐Liss, Inc.
Real time quaking‐induced conversion analysis of cerebrospinal fluid in sporadic Creutzfeldt–Jakob disease

Current cerebrospinal fluid (CSF) tests for sporadic Creutzfeldt–Jakob disease (sCJD) are based on the detection of surrogate markers of neuronal damage such as CSF 14‐3‐3, which are not specific for sCJD. A number of prion protein conversion assays have been developed, including real time quaking‐induced conversion (RT‐QuIC). The objective of this study is to investigate whether CSF RT‐QuIC analysis could be used as a diagnostic test in sCJD.
Antigenic cross-reactions among herpes simplex virus types 1 and 2, Epstein-Barr virus, and cytomegalovirus

Polyvalent rabbit antisera against herpes simplex virus type 1 and 2 (HSV-1 and HSV-2), cytomegalovirus (CMV), and Epstein-Barr virus (EBV), monospecific antisera against affinity-purified HSV-2 glycoproteins gB and gG, and a panel of monoclonal antibodies against HSV and EBV proteins were used to analyze cross-reactive molecules in cells infected with the four herpesviruses. A combination of immunoprecipitation and Western blotting with these reagents was used to determine that all four viruses coded for a glycoprotein that cross-reacted with HSV-1 gB. CMV coded for proteins that cross-reacted with HSV-2 gC, gD, and gE. Both CMV and EBV coded for proteins that cross-reacted with HSV-2 gG. Antigenic counterparts to the p45 nucleocapsid protein of HSV-2 were present in HSV-1 and CMV, and counterparts of the major DNA-binding protein and the ribonucleotide reductase of HSV-1 were present in all the viruses. The EBV virion glycoprotein gp85 was immunoprecipitated by antisera to HSV-1, HSV-2, and CMV. Antisera to CMV and EBV neutralized the infectivity of both HSV-1 and HSV-2 at high concentrations. This suggests that cross-reactivity between these four human herpesviruses may have pathogenic as well as evolutionary significance.
Postmenopausal therapy reduces catalase activity and attenuates cardiovascular risk.

BACKGROUND Menopause can lead to alterations in women's health, with changes in the oxidative status of postmenopausal women in whom information regarding the influence of hormone therapy (HT) on antioxidant enzyme activities is limited. OBJECTIVE To evaluate the influence of HT on catalase activity; concentrations of lipids and lipoprotein, cholesteryl ester transfer protein, thiobarbituric acid-reactive substances, nitrates, high-sensitivity C-reactive protein and carotid thickness in postmenopausal women. METHODS Ninety-four consecutive women were allocated to one of four groups, without HT and with HT. The latter group was subdivided into women using estrogen and those using estrogen plus progestogen therapy. Plasma biochemical parameters and common carotid intima-media thickness measurements were performed. RESULTS HT antagonized the decrease in catalase activity after menopause, but had no effect on the levels of cholesteryl ester transfer protein, thiobarbituric acid-reactive substances, lipid peroxide, nitrate, high-sensitivity C-reactive protein, or on the common carotid intima-media thickness. Multivariate analysis showed that estrogen-based HT attenuated the relationship between cardiovascular risk factors and the intima-media thickness of the common carotid. CONCLUSION This study indicates that HT in postmenopausal women produces beneficial antioxidant and anti-atherosclerotic effects by ameliorating the plasma lipid and lipoprotein profiles, increasing plasma catalase activity and attenuating the association between cardiovascular risk factors and early atherosclerosis.
Adaptive minimum bit error rate beamforming assisted QPSK receiver

A novel adaptive beamforming technique is proposed for wireless communication with quadrature phase shift keying signalling based on the minimum bit error rate (MBER) criterion. It is shown that the MBER approach provides significant performance gain in terms of smaller bit error rate over the standard minimum mean square error approach. Using the classical Parzen window estimate of probability density function, both the block-data and sample-by-sample adaptive implementations of the MBER solution are developed.
Canonical Orderings on Grids

Jump Point Search, an algorithm developed for fast search on uniform cost grids, has successfully improved the performance of grid-based search. But, the approach itself is actually a set of diverse ideas applied together. This paper decomposes the algorithm and gradually re-constructs it, showing the component pieces from which the algorithm is constructed. In this process, we are able to define a spectrum of new algorithms that borrow and repurpose ideas from Jump Point Search. This decomposition opens the door for applying the ideas from Jump Point Search in other grid domains with significantly different characteristics from two dimensional grids.
Friction modeling and identification for industrial manipulators

The paper is focused on the development of an adequate model of the friction acting on the joints of an industrial manipulator, suitable to be used for simulation and control purposes. The experimental tests required for the identification are executable via the standard interface for the robot programming, without any change in the path planning procedure or in the robot control. The proposed friction model is developed and validated for the six-dof Comau SMART NS12 manipulator.
Vascular remodeling underlies rebleeding in hemophilic arthropathy

Hemophilic arthropathy is a debilitating condition that can develop as a consequence of frequent joint bleeding despite adequate clotting factor replacement. The mechanisms leading to repeated spontaneous bleeding are unknown. We investigated synovial, vascular, stromal, and cartilage changes in response to a single induced hemarthrosis in the FVIII‐deficient mouse. We found soft‐tissue hyperproliferation with marked induction of neoangiogenesis and evolving abnormal vascular architecture. While soft‐tissue changes were rapidly reversible, abnormal vascularity persisted for months and, surprisingly, was also seen in uninjured joints. Vascular changes in FVIII‐deficient mice involved pronounced remodeling with expression of α‐Smooth Muscle Actin (SMA), Endoglin (CD105), and vascular endothelial growth factor, as well as alterations of joint perfusion as determined by in vivo imaging. Vascular architecture changes and pronounced expression of α‐SMA appeared unique to hemophilia, as these were not found in joint tissue obtained from mouse models of rheumatoid arthritis and osteoarthritis and from patients with the same conditions. Evidence that vascular changes in hemophilia were significantly associated with bleeding and joint deterioration was obtained prospectively by dynamic in vivo imaging with musculoskeletal ultrasound and power Doppler of 156 joints (elbows, knees, and ankles) in a cohort of 26 patients with hemophilia at baseline and during painful episodes. These observations support the hypothesis that vascular remodeling contributes significantly to bleed propagation and development of hemophilic arthropathy. Based on these findings, the development of molecular targets for angiogenesis inhibition may be considered in this disease. Am. J. Hematol. 90:1027–1035, 2015. © 2015 Wiley Periodicals, Inc.
THE USE OF A SUBSTRATE CASSETTE STRATEGY TO IMPROVE THE CAPACITY AND THROUGHPUT OF CYTOCHROME P450 INDUCTION STUDIES IN HUMAN HEPATOCYTES

The gold standard for estimating the ability of a new chemical entity to induce the human cytochromes P450 (P450s) is to determine the increase in catalytic activity of these enzymes after treatment of primary cultures of human hepatocytes with the potential inducer. The limited availability of fresh human hepatocytes makes these studies impossible to perform on demand. A substrate cassette strategy in which probe substrates for three different P450s were simultaneously added to hepatocyte preparations was studied to determine whether this would be a viable method to increase the capacity of induction studies. The biotransformations of phenacetin (CYP1A2), diclofenac (CYP2C9), and midazolam (CYP3A) were compared when administered to four different hepatocyte preparations (±inducer) individually or simultaneously as a cassette. The determinations of fold-induction in response to known inducers were not significantly affected, although slight differences were occasionally observed between the various P450 activities, whether determined individually or in the cassette. In total, for three P450 activities in the four hepatocyte preparations with and without inducer, no trend demonstrating a drug-drug interaction among any of the three probes was detected. The lack of interactions between the probe substrates demonstrates that this cassette strategy may be used in primary human hepatocyte induction studies without concern that the interactions between the substrates may be affecting the results, as has been seen in other cassette dosing experiments. Therefore, this substrate cassette is an excellent method for increasing the capacity and throughput of human hepatocyte induction studies by combining three experiments into one.
Pharmacokinetics and disposition of recombinant human osteoprotegerin (rhOPG) after intravenous administration in female fischer rats

Osteoprotegerin (OPG) is a secreted member of the tumour necrosis factor receptor (TNFR) family that leads to the suppression of the differentiation, activation and survival of osteoclasts. The objective was to investigate the in vivo pharmacokinetics and tissue distribution of full-length recombinant human OPG (rhOPG) as well as its clearance mechanism using 125I-labelled protein (125I-rhOPG) after intravenous administration to female Fischer rats. 2. 125I-rhOPG was rapidly and predominantly distributed to the liver after dosing (3 mg kg−1). Immunohistochemical analysis indicated that rhOPG was located in the sinusoids of the liver. The hepatic uptake of 125I-rhOPG (0.01 mg kg−1) was partly regulated under a saturable process. Pre-dosing of some sulfated glycans (20 mg kg−1), especially dextran sulfate, heparin and fucoidan, markedly inhibited the hepatic uptake of 125I-rhOPG. The clearance of 125I-rhOPG was markedly reduced by the conjugation of dextran sulfate. The results suggested that the hepatic clearance of 125I-rhOPG was mainly mediated by the interaction with glycosaminoglycans.
The complex refractive indices of the liquid crystal mixture E7 in the terahertz frequency range

We have used terahertz time-domain spectroscopy to investigate the complex optical constants and birefringence of a widely used liquid crystal mixture E7 in both nematic and isotropic phases (26°C–70°C). The extinction coefficient of E7 at room temperature is less than 0.035 and without sharp absorption features in the frequency range of 0.2–2.0 THz. The extraordinary (ne) and ordinary (no) indices of refraction at 26°C are 1.690–1.704 and 1.557–1.581, respectively, giving rise to a birefringence of 0.130–0.148 in this frequency range. The temperature-dependent (26°C–70°C) order parameter extracted from the birefringence data agrees with that in the visible region quite well. Further, the temperature gradients of the terahertz optical constants of E7 are also determined. The optical constants of E7 in the terahertz or sub-millimeter wave range are found to deviate significantly from values predicated by the usual extended Cauchy equations used in the visible and near-infrared.
Structure of the Pion from Full Lattice QCD

Moments of generalised parton distributions can be related to off-forward matrix elements of local operators. We calculate a few of the leading twist matrix elements for the pion on the lattice. The simulations are performed using two flavours of dynamical fe rmions and a range of pion masses from 550 to 1090 MeV. Our lattice spacings and spatial volumes lie in the range 0.07‐0.12 fm and (1.6‐2.2 fm) 3 , respectively. Key features of our investigation are the us e of O(a) improved Wilson fermions and non-perturbative renormalisation. We present first results for the two lowest moments of the gene ralised parton distributions of the pion and compare the pion electromagnetic form factor Fπ to experimental data. Good agreement is found between lattice data and experiment.
Cloudoscopy: services discovery and topology mapping

We define and study cloudoscopy, i.e., exposing sensitive information about the location of (victim) cloud services and/or about the internal organisation of the cloud network, in spite of location-hiding efforts by cloud providers. A typical cloudoscopy attack is composed of a number of steps: first expose the internal IP address of a victim instance, then measure its hop-count distance from adversarial cloud instances, and finally test to find a specific instance which is close enough to the victim (e.g., co-resident) to allow (denial of service or side-channel) attacks. We refer to the three steps/modules involved in such cloudoscopy attack by the terms IP address deanonymisation, hop-count measuring, and co-residence testing. We present specific methods for these three cloudoscopy modules, and report on results of our experimental validation on popular cloud platform providers. Our techniques can be used for attacking (victim) servers, as well as for benign goals, e.g., optimisation of instances placement and communication, or comparing clouds and validating cloud-provider placement guarantees.
ARTHROPOD MANAGEMENT Impact of Bollworms (Helicoverpa zea (Boddie)) on Maturity and Yield of Bollgard Cotton

A large percentage of Bollgard cotton is treated for bollworms [Helicoverpa zea (Boddie)] with little information about economic losses from these infestations. The impact of bollworm infestations on maturity and yield of Bollgard cotton was determined. Infestations of 1-d-old bollworm larvae were established on non-Bollgard and Bollgard cottons in large field cages. Treatments included three and five levels of infestation for 1 to 4 wk in 2002 and 2003, respectively. Bollworms significantly delayed maturity of Bollgard cotton when 100% of white flowers were infested for 1 to 4 wk or when 50% of white flowers were infested for 2 to 4 wk in 2002. When averaged across weeks, bollworms delayed maturity of Bollgard cotton when 100% of white flowers were infested in 2003. Yield responses of Bollgard cotton varied between years, but yields tended to decline as the level of infestation increased each year. There was a significant negative relationship between the cumulative numbers of white flowers infested and seedcotton yields in Bollgard cottons. The resulting regression equation from this relationship had a slope of -1.69, indicating a 1.69 g reduction in yield for every white flower infested. Results of this study will be important for refining action thresholds for bollworms on Bollgard cotton and suggested controls should be initiated before infestation levels reach greater than 25% of white flowers. These data also provide a base of information for predicting yield reductions caused by bollworm infestations in white flowers of Bollgard cotton.
Robust tracking control of an IPMC actuator using nonsingular terminal sliding mode

Ionic polymer metal composite (IPMC) is a highly innovative material that has recently gained attention in many fields such as medical, biomimetic, and micro/nano underwater applications. The main characteristic of IPMC lies in its ability to achieve a large deflection under a fairly low driving voltage. Moreover, its agile, light weight, noiseless and flexible features render it well suited for certain specific applications. Like other smart materials, such as piezoelectric ceramics, IPMC could be used in actuators or sensors. In this paper, we study the application of IPMC as an actuator for underwater use. The goal is to develop a robust feedback controller for the IPMC actuator to track a desired reference whilst dealing with the uncertainties due to the inherent actuator nonlinearity, external disturbance or the variations of working environment. To this end, we first present a nominal model of the IPMC actuator through experimental identification. Next, a nonsingular terminal sliding mode controller is proposed. Lastly, experimental studies are conducted to verify the tracking accuracy and robustness of the designed controller.