Miracle-dz/UniFAR-FTUs huggingface dataset:
Indians in Aotearoa New Zealand: A study of migrant social networks and integration through an assemblage lens

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Evaluation of E-Test for determination of antimicrobial MICs for Pseudomonas aeruginosa isolates from cystic fibrosis patients

We determined the E-Test and National Committee for Clinical Laboratory Standards standardized agar dilution MICs of ceftazidime, ciprofloxacin, piperacillin, and tobramycin for Pseudomonas aeruginosa during tests of 100 rough and mucoid P. aeruginosa isolates from cystic fibrosis patients. The levels of agreement (+/- 1 log2 dilution) between quantitative E-Test and agar dilution MIC results were 80, 97, 73, and 89% for ceftazidime, ciprofloxacin, piperacillin, and tobramycin, respectively. Comparison of the results after converting the MIC data to qualitative categories (susceptible, intermediate, and resistant) yielded levels of agreement of 84, 96, 88, and 93% for the same agents, respectively. Of the 39 qualitative discrepancies, 36 were minor and 3 were very major. We conclude that use of the E-Test is easier and more practical than use of the agar dilution method for most laboratories and that the E-Test furnishes results which are at least as accurate as those obtained by the agar dilution method. However, the higher cost of the E-Test method would likely discourage most laboratories from selecting it over disk diffusion for routine antimicrobial susceptibility testing of P. aeruginosa isolates from cystic fibrosis patients.
Molecular Dissection of a Protein SopB Essential for Escherichia coli F Plasmid Partition*

Biochemical and genetic experiments were carried out to deduce the structural and functional domains of SopB protein involved in the equipartition of F plasmid. The protein is dimeric. Proteolytic and chemical footprinting studies support earlier genetic analyses that the binding of SopB to specific sites within the F plasmid sopC locus involves mainly the C-terminal region. In vivo, the expression of a high level of SopB protein is known to repress sopC-linked genes. This silencing activity is shown to be unaffected by the deletion of 35 N-terminal residues, but abolished when 71 or more were removed from the N terminus. An excess of SopB protein does not extend its in vitro binding outside sopC, implicating participation of a host factor(s) in SopB-mediated gene silencing. A data base search identified a number of SopB homologues, including both chromosomally encoded bacterial proteins and phage- and plasmid-encoded proteins known to be involved in partition. Sequence homology is limited to the N-terminal half, suggesting that the N-terminal regions of these proteins are conserved to interact with a conserved cellular structure(s), whereas the C-terminal regions have diverged to bind different nucleotide sequences.
White Matter Hyperintensities Are an Independent Predictor of Physical Decline in Community-Dwelling Older People

Background: Ageing is associated with physical disability, but little is known about the influence of white matter hyperintensities (WMHs) on physical function decline in older people. Objective: To investigate the role of WMHs as a predictor of decline in physical function in cognitively intact older people. Methods: 287 community-dwelling people aged 70–90 years underwent the Physiological Profile Assessment (PPA) and assessments of total and regional WMH volumes, cognitive function and comorbidities. Participants underwent reassessment of the PPA 12 months later, and those in the top quartile for increases in PPA scores over the year were regarded as having declined physically. Results: Multivariate logistic regression analyses revealed that people with WMH volumes in the 4th quartile showed greater physical decline (odds ratio 3.02, 95% confidence interval 1.02–8.95) while controlling for age, baseline physical function, general health, physical activity and cognitive function. Subsequent univariate analyses indicated that WMHs in the deep fronto-parietal and periventricular parieto-occipital regions had the strongest associations with physical decline. Conclusions: These findings indicate that WMHs are an independent predictor of decline in physical function and suggest that interventions that focus on preventing the development or progression of white matter lesions may help preserve physical function in older people.
Understanding the development of inter-monsoon convective storms over the western Peninsular Malaysia

The western Peninsular Malaysia experiences biannual maxima in total rainfall. The first maximum is between October and December and the second is between March and May. During these periods, localised severe rainfall events are common. They are usually short, intense and sometime cause flash floods and landslides. Forecasting these local events is difficult, and continuous study to understand the mechanism of the rainfall events is important for the advancement of tropical weather forecasting in the future. This study focuses on inter-monsoons, which are April-May and September-October. Heavy rainfall days (daily total rainfall ≥ the 90th percentile value) are determined by the average regional mean of three Peninsular Malaysia regions (northwest coast, west coast and inland). The analysis shows that a stronger easterly wind anomaly is common during these heavy rainfall days. Another common feature is a stronger ascending motion over the peninsula and also a high amount of moisture in the mid troposphere ( around 700hPa pressure level) over the east side of the peninsula. To investigate the mechanisms responsible for severe inter-monsoon convection in greater detail, two case studies were selected and simulated using the limitedarea high-resolution UK MetOffice Unified Model. The Peninsular Malaysia and Sumatra Island influence the development of overnight rainfall over the Malacca Strait by constraining land-sea breezes and low-level flow. The Titiwangsa mountains over the Peninsular Malaysia then induce rainfall development at noon. The combination of these two events influences the development of severe convective storms of 2 May 2012 over the western Peninsular Malaysia. Sensitivity studies were carried out to investigate the influence of the local orography on this event. The flattened Peninsular Malaysia orography causes a lack of rainfall over the inland part of the Peninsular Malaysia and Sumatra Island yet still produces overnight rainfall over Malacca Strait but weaker. By removing Sumatra Island, it can be seen that the western and inland parts of the Peninsular Malaysia receive more rainfall, as it is influenced by the westerly wind and the Indian Ocean. The second case study of 24 September 2014 was inaccurately simulated thus further analysis on the mechanism of the convective storm development is rather impossible. However, the sensitivity experiments were still conducted and the results showed a significant difference in the rainfall pattern as the local orography was modified and Sumatra Island was removed. These results suggest the importance of the interaction between land masses, orography, low level flow and the diurnal cycle on the development of the severe rainfall events.
MeCP2-Mediated Transcription Repression in the Basolateral Amygdala May Underlie Heightened Anxiety in a Mouse Model of Rett Syndrome

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder that results from loss of function mutations in the methyl-CpG binding protein 2 (MECP2) gene. Using viral-mediated basolateral amygdala (BLA)-specific deletion of Mecp2 in mice, we show that intact Mecp2 function is required for normal anxiety behavior as well as some types of learning and memory. To examine whether these behavioral deficits are the result of impaired transcriptional repression, because Mecp2 is believed to act as a transcriptional repressor in complex with histone deacetylases (HDACs), we infused a HDAC inhibitor chronically into the BLA of wild-type mice. We found that HDAC inhibition produces behavioral deficits similar to those observed after the deletion of Mecp2 in the BLA. These results suggest a key role for Mecp2 as a transcriptional repressor in the BLA in mediating behavioral features of RTT.
Development of a Parsimonious Urban Landscape Nutrient Model using Representations of Terrestrial Denitrification Controls

Watershed models often estimate annual nitrogen (N) or phosphorus (P) pollutant loads in rural areas with export coefficients (EC) (kg/ha/yr) values based on land cover, and in urban areas as the product of spatially uniform event mean concentration (EMC) (mg/L) values and runoff volume. Actual N and P nonpoint source (NPS) pollutant loading has more spatial complexity due to watershed variation in runoff likelihood and buffering likelihood along surface and subsurface pathways, which can be represented in a contributing area dispersal area (CADA) NPS model. This research develops a CADA NPS model to simulate how watershed properties of elevation, land cover, and soils upslope and downslope of each watershed pixel influence nutrient loading. The model uses both surface and subsurface runoff indices (RI), and surface and subsurface buffer indices (BI), to quantify the runoff and buffering likelihood for each watershed pixel, and generate maps of weighted EC and EMC values that identify NPS pollutant loading hotspots. The research illustrates how CADA NPS model maps and pixel loading values are sensitive to the spatial resolution and accuracy of elevation and land cover data, and model predictions can represent the lower and upper bounds of NPS loading. The model provides managers with a tool to rapidly visualize, rank, and investigate likely areas of high nutrient export. KEY TERMS: nonpoint source pollution, watershed management, nutrients, runoff, land use/land cover change, urbanization
Nonparametric method for estimating the effects of climatic and catchment characteristics on mean annual evapotranspiration

It is now well known that forested catchments have higher evapotranspiration than grassed catchments. Models for mean annual evapotranspiration have been developed to quantify catchment scale differences in mean annual evapotranspiration. Zhang et al. (2001) developed a simple, one parameter, model for the relationships between evapotranspiration and vegetation cover by evaluating the differences of model parameter values for different vegetation covers. However, other factors such as climate and catchment topography may also affect evapotranspiration and therefore the model parameter. Simple models acknowledging only categorical vegetation cover (forested, mixed, and grassed) may introduce some uncertainty, and more seriously, lead to inconsistent conclusions regarding relationships between vegetation cover and evapotranspiration. Zhang et al. (2004) investigated possible inclusion of climatic factors and catchment characteristics to improve the estimation of mean annual evapotranspiration by modeling the residuals of the model parameter via a stepwise linear regression. In this paper we propose the use of a multivariate adaptive regression spline (MARS) model for estimating the model parameter. In contrast to a simple stepwise regression, the MARS model provides not only insight into the interactions between explanatory factors but also a potential for prediction for ungauged basins as long as the values of explanatory factors are within the domain of calibration catchments. The MARS model is able to determine statistically significant factors and therefore is a powerful tool to identify important factors and their interactions. Using 241 Australian catchments where climate factors and catchment characteristics are available, we found the following significant terms affecting the mean annual evapotranspiration. (1) The functional relationship with the number of months that peak precipitation follows peak potential evapotranspiration (PfE) states that closer phase between precipitation and potential evapotranspiration results in less streamflow. (2) The interactions between coefficient of variation of precipitation and average storm depth shows that the value of the model parameter is smaller when the coefficient of variance of precipitation is larger than 2.24 and the average storm depth is less than 8.70 mm d−1. (3) The interaction between relief ratio and average storm depth term shows that both larger average storm depth in flat catchments and smaller average storm depth in hilly catchments result in more streamflow. (4) The interaction between relief ratio and forest coverage reveals that for flat catchments with reasonable forest cover, increasing forest cover generally results in more mean annual evapotranspiration and less mean annual streamflow. The performance of the MARS model was assessed by a calibration‐testing procedure to support its usage for prediction for ungauged basins.
Relationship between oxidant and antioxidant activity in hyperemesis gravidarum

Abstract Objective: To evaluate oxidant and antioxidant activity in patients with hyperemesis gravidarum (HG) by using serum total antioxidant activity (TAO), total free sulfhydryl (–SH), ceruloplasmin and lipid hydroperoxide (LOOH) levels. Materials and methods: In a cross-sectional trial, blood samples were collected from patients with HG (n = 25) and healthy pregnant women (n = 25) as control group. Serum TAO activities, –SH levels and LOOH levels and ceruloplasmin levels were measured. Results: Serum TAO activity was found to be significantly lower (p = 0.003) in patients with HG compared with controls. However, serum –SH levels, LOOH levels and ceruloplasmin levels did not change significantly in patients with HG compared to controls. Conclusion: Presence of oxidative stress in HG patients depends more on reduced antioxidant activities than increased oxidative stress.
Balance impairment not predictive of falls in geriatric rehabilitation wards.

BACKGROUND Falls are common among hospital inpatients, particularly in rehabilitation wards. Standing balance impairment is widely held to be a contributing factor to falls, is a component of several falls risk screening tools, and has motivated the development of balance retraining programs for the reduction of in-hospital falls. Little rigorous investigation of the link between standing balance impairment and in-hospital falls has been undertaken. METHODS We identified optimal cut-off points of four commonly used balance measures (functional reach, Timed Up and Go, step test, and timed static stance) in a prospective multicenter cohort study. Admission data (n = 1373) were clustered and matched by center then randomly allocated to development and validation data sets. RESULTS Optimal cut-off points for each test were identified from the development data set. The predictive accuracy of all four balance tests was poor when the optimal cut-off was applied to the validation data set (Youden Index scores ranged between 0.02 and 0.15). CONCLUSIONS These findings do not support an association between admission standing balance and falls in a geriatric rehabilitation setting. This result has implications for content of falls risk screening tools and interventions to prevent falls in a geriatric rehabilitation population.
An endogenous processing pathway in vaccinia virus-infected cells for presentation of cytoplasmic antigens to class II-restricted T cells

The recognition of virus-infected cells by class I MHC-restricted cytotoxic T cells requires endogenous processing of antigen for presentation. It is still unclear whether endogenous processing of antigen can be utilized by class II MHC molecules for presentation. To test this possibility, a human B cell line expressing HLA-A2 and HLA- DR1 was infected with a recombinant vaccinia virus expressing the Influenza A virus M1 matrix protein (VAC-M1) and was assayed for lysis by different M1-specific cytolytic T cell lines, restricted by either HLA-A2 or by HLA-DR1. Class II-restricted lysis of VAC-M1-infected cells did occur. This lysis required de novo M1 synthesis and was not due to exogenous antigen. Several properties of the endogenous processing pathway for class II-restricted presentation were different from those of the pathway utilized by class I molecules. First, class II-mediated recognition of VAC-M1 infected cells was less efficient, requiring higher doses of virus and longer infection times, than the class I-mediated recognition. Second, chloroquine completely blocked presentation of endogenous M1 to class II-restricted T cells but had no effect on the class I-restricted presentation. Third, the class II- restricted presentation of M1 was only mildly affected by Brefeldin A, a drug that prevents transport from the endoplasmic reticulum to the Golgi, whereas the class I-restricted presentation of M1 was completely abrogated by this drug. These data demonstrate the existence of an endogenous processing pathway for the presentation of cytosolic antigen by class II molecules and show that this pathway is distinct from the one used for presentation by class I molecules.
Double-diffusive convection and baroclinic instability in a differentially heated and initially stratified rotating system: the barostrat instability

A water-filled differentially heated rotating annulus with initially prepared stable vertical salinity profiles is studied in the laboratory. Based on two-dimensional horizontal particle image velocimetry data and infrared camera visualizations, we describe the appearance and the characteristics of the baroclinic instability in this original configuration. First, we show that when the salinity profile is linear and confined between two non-stratified layers at top and bottom, only two separate shallow fluid layers can be destabilized. These unstable layers appear nearby the top and the bottom of the tank with a stratified motionless zone between them. This laboratory arrangement is thus particularly interesting to model geophysical or astrophysical situations where stratified regions are often juxtaposed to convective ones. Then, for more general but stable initial density profiles, statistical measures are introduced to quantify the extent of the baroclinic instability at given depths and to analyze the connections between this depth-dependence and the vertical salinity profiles. We find that, although the presence of stable stratification generally hinders full-depth overturning, double-diffusive convection can lead to development of multicellular sideways convection in shallow layers and subsequently to a multilayered baroclinic instability. Therefore we conclude that by decreasing the characteristic vertical scale of the flow, stratification may even enhance the formation of cyclonic and anticyclonic eddies (and thus, mixing) in a local sense.
THE RESPONSE OF PLANT TISSUES TO MAGNETIC FLUID AND ELECTROMAGNETIC EXPOSURE

This experimental study was dedicated to the possible oxidative stress induced by magnetic fluid accumulation in the living tissues. The aqueous magnetic fluid was prepared by dispersing iron oxide particles coated with perchloric acid in water, characterized by physical diameter average value of 10.55 nm as revealed by electron microscopy and 18.3 kA/m value for saturation magnetization. Electromagnetic exposure was accomplished during the seeds germination, within transverse electromagnetic cell at 20 mW power level and 300 kHz frequency for 30 minutes while diluted magnetic fluid was supplied both during germination and plant development. The biochemical investigations, i.e. the assay of photo-assimilatory pigments and nucleic acids contents, after 12 days of plants growth were performed. Chlorophylls ratio was diminished up to 30% while plant lengths were shorter with about 40% in the samples exposed to electromagnetic field; however, nucleic acid biosynthesis seems to be remarkably stimulated following the electromagnetic exposure.
Marine and Terrestrial Organic Ice‐Nucleating Particles in Pristine Marine to Continentally Influenced Northeast Atlantic Air Masses

Sea spray aerosol (SSA) generated by bubble bursting at the ocean surface is an important component of aerosol‐cloud interactions over remote oceans, providing the atmosphere with ice‐nucleating particles (INPs) or particles required for heterogeneous ice nucleation. Studies have shown that organic INPs are emitted during phytoplankton blooms, but changes in INP number concentrations (nINPs) due to ocean biological activity have not been directly demonstrated in natural SSA. In this study, a clean sector sampler was used to differentiate ice nucleation and composition of pristine SSA from terrestrial aerosol at the Mace Head Research Station in August 2015. Average nINPs active at −15 °C (nINPs,−15 °C) were 0.0011 L−1, and large variability (up to a factor of 200) was observed for INPs active warmer than −22 °C. Highest nINPs in the clean sector occurred during a period of elevated marine organic aerosol from offshore biological activity (M1, nINPs,−15 °C = 0.0077 L−1). A peak in nINPs was also observed in terrestrial organic aerosol (T1, nINPs,−15 °C = 0.0076 L−1). The impacts of heating and hydrogen peroxide digestion on nINPs indicate that INPs at Mace Head Research Station were largely organic and that INPs observed during M1 and T1 were biological (i.e., protein containing). Complexities of predicting increases in nINPs due to offshore biological activity are explored. A parameterization for pristine SSA INPs over the North Atlantic Ocean was developed, illustrating that SSA is associated with a factor of 1,000 fewer ice‐nucleating sites per surface area of aerosol compared to mineral dust.
Enlarging the scope: grasping brain complexity

To further advance our understanding of the brain, new concepts and theories are needed. In particular, the ability of the brain to create information flows must be reconciled with its propensity for synchronization and mass action. The theoretical and empirical framework of Coordination Dynamics, a key aspect of which is metastability, are presented as a starting point to study the interplay of integrative and segregative tendencies that are expressed in space and time during the normal course of brain and behavioral function. Some recent shifts in perspective are emphasized, that may ultimately lead to a better understanding of brain complexity.
PP2A/B55 and Fcp1 Regulate Greatwall and Ensa Dephosphorylation during Mitotic Exit

Entry into mitosis is triggered by activation of Cdk1 and inactivation of its counteracting phosphatase PP2A/B55. Greatwall kinase inactivates PP2A/B55 via its substrates Ensa and ARPP19. Both Greatwall and Ensa/ARPP19 are regulated by phosphorylation, but the dynamic regulation of Greatwall activity and the phosphatases that control Greatwall kinase and its substrates are poorly understood. To address these questions we applied a combination of mathematical modelling and experiments using phospho-specific antibodies to monitor Greatwall, Ensa/ARPP19 and Cdk substrate phosphorylation during mitotic entry and exit. We demonstrate that PP2A/B55 is required for Gwl dephosphorylation at the essential Cdk site Thr194. Ensa/ARPP19 dephosphorylation is mediated by the RNA Polymerase II carboxy terminal domain phosphatase Fcp1. Surprisingly, inhibition or depletion of neither Fcp1 nor PP2A appears to block dephosphorylation of the bulk of mitotic Cdk1 substrates during mitotic exit. Taken together our results suggest a hierarchy of phosphatases coordinating Greatwall, Ensa/ARPP19 and Cdk substrate dephosphorylation during mitotic exit.