Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular epidemiology of KPC-producing Klebsiella pneumoniae from invasive infections in Italy: increasing diversity with predominance of the ST512 clade II sublineage.

OBJECTIVES The spread of carbapenem-resistant Enterobacteriaceae (CRE) represents one of the most worrisome problems for clinical medicine worldwide. In Italy, the Antibiotic-Resistance-Istituto Superiore di Sanità surveillance network, in collaboration with the Committee for Antimicrobial Agents of the Italian Society of Clinical Microbiologists, promoted a study to investigate the carbapenem-resistance mechanisms, clonal relatedness and capsular typing of a recent collection of carbapenem-resistant Klebsiella pneumoniae (CR-KP). METHODS A total of 17 laboratories distributed across Italy collected all consecutive non-replicate CR-KP isolated from invasive infections during two different study periods (2011-12 and 2013). Carbapenemase genes were searched for by filter hybridization and confirmed by PCR and sequencing. KPC-producing K. pneumoniae (KPC-KP) were typed by PFGE and MLST. Capsular types were identified by wzi gene typing. RESULTS Of the collected K. pneumoniae isolates (n = 461), the overall proportion of CR-KP was 36.2% (n = 167). The majority (97%) of the CR-KP were positive for the blaKPC gene. Among the KPC-KP population, nine different STs were detected with the majority of isolates (94%) belonging to the clonal group (CG) 258. A subpopulation that belonged to ST512 and showed an identical PFGE profile represented the majority (57%) of KPC-KP strains, with a countrywide distribution. Capsular characterization showed the predominance of the wzi154, cps-2 capsular type (88.8% of all CG258 strains). ST258 strains were associated with both cps-1 and cps-2 capsular types, while ST512 was associated with cps-2 only. CONCLUSIONS Although a trend to a polyclonal evolution of the Italian KPC-KP was noted, this study showed that the KPC-KP population remained largely oligoclonal with the wide diffusion of an ST512 lineage carrying cps-2 capsular type and producing the KPC-3 enzyme.
Free-flight responses of Drosophila melanogaster to attractive odors

SUMMARY Many motile organisms localize the source of attractive odorants by following plumes upwind. In the case of D. melanogaster, little is known of how individuals alter their flight trajectories after encountering and losing a plume of an attractive odorant. We have characterized the three-dimensional flight behavior of D. melanogaster in a wind tunnel under a variety of odor conditions. In the absence of olfactory cues, hungry flies initiate flight and display anemotactic orientation. Following contact with a narrow ribbon plume of an attractive odor, flies reduce their crosswind velocity while flying faster upwind, resulting in a surge directed toward the odor source. Following loss of odor contact due to plume truncation, flies frequently initiate a stereotyped crosswind casting response, a behavior rarely observed in a continuous odor plume. Similarly, within a homogeneous odor cloud, flies move fast while maintaining an upwind heading. These results indicate both similarities and differences between the behavior of D. melanogaster and the responses of male moths to pheromone plumes, suggesting possible differences in underlying neural mechanisms.
The C-Terminal Domain of CENP-C Displays Multiple and Critical Functions for Mammalian Centromere Formation

CENP-C is a fundamental component of functional centromeres. The elucidation of its structure-function relationship with centromeric DNA and other kinetochore proteins is critical to the understanding of centromere assembly. CENP-C carries two regions, the central and the C-terminal domains, both of which are important for the ability of CENP-C to associate with the centromeric DNA. However, while the central region is largely divergent in CENP-C homologues, the C-terminal moiety contains two regions that are highly conserved from yeast to humans, named Mif2p homology domains (blocks II and III). The activity of these two domains in human CENP-C is not well defined. In this study we performed a functional dissection of C-terminal CENP-C region analyzing the role of single Mif2p homology domains through in vivo and in vitro assays. By immunofluorescence and Chromatin immunoprecipitation assay (ChIP) we were able to elucidate the ability of the Mif2p homology domain II to target centromere and contact alpha satellite DNA. We also investigate the interactions with other conserved inner kinetochore proteins by means of coimmunoprecipitation and bimolecular fluorescence complementation on cell nuclei. We found that the C-terminal region of CENP-C (Mif2p homology domain III) displays multiple activities ranging from the ability to form higher order structures like homo-dimers and homo-oligomers, to mediate interaction with CENP-A and histone H3. Overall, our findings support a model in which the Mif2p homology domains of CENP-C, by virtue of their ability to establish multiple contacts with DNA and centromere proteins, play a critical role in the structuring of kinethocore chromatin.
Artifacts in KPFM in FM, AM and Heterodyne AM Modes

In this paper, the crosstalk in potential measurements caused by the topographic feedback and the resonance frequency in Kelvin probe force microscopy (KPFM) was investigated in frequency modulation (FM), amplitude modulation (AM) and heterodyne amplitude modulation (heterodyne AM) modes. We showed theoretically that the distance-dependence of the modulated electrostatic force in AM-KPFM is significantly weaker than in FM-and heterodyne AM-KPFMs. We experimentally confirmed that the crosstalk in FM-KPFM and heterodyne AM-KPFM is weak than that in AM-KPFM due to the bigger difference of the modulated frequencies in topographic and potential measurements in FM and heterodyne AM-KPFMs. We also compared the corrugations in the local contact potential difference (LCPD) on the surface of Si (001) show that difference on topographic (potential) images is approximately 15 pm (10 mV) between the faulted and unfaulted parts using heterodyne AM-KPFM, on the other hand, this difference cannot be observed using AM-KPFM mode. Original of this was attributed to the low crosstalk between the topographic and the LCPD measurements in heterodyne AM-KPFM.
Paralytic shellfish poison outbreaks in the Penzé estuary: Environmental factors affecting toxin uptake in the oyster, Crassostrea gigas

Several experiments using a self-regulated system were conducted to define the factors likely to influence the uptake of paralytic shellfish poison (PSP) by oysters in the Penze estuary (France, Brittany). Each 4-day experiment was carried out in a recirculated sea water system using 15 Pacific oysters (Crassostrea gigas) separated from each other and supplied with unfiltered natural seawater containing alternatively toxic (Alexandrium minutum) or non-toxic (Skeletonema costatum) algal diets. The food supply and exposure times to toxic diets were determined according to field studies of the upstream and downstream movement of patches containing A. minutum. The experimental parame- ters corresponded roughly to the hydrological conditions generally observed in June when tidal coefficients are lowest and blooms occur: (i) A. minutum concentrations in sea water of 200, 5000 and 10 000 cell ml −1 ; (ii) inorganic matter consisting of 5 and 15 mg L −1 of calcinated muddy sediments; and (iii) low and high tide salinities of 25 and 35%� , respectively. Significant experimental contamination (greater than the 80 µg STX equiv. 100 g −1 sanitary threshold) oc- curred after 4 days of exposure for the monospecific A. minutum diet (20−200 cell ml −1 ) and alternated A. minutum and S. costatum diets (5000 and 20 000 cell ml −1 , respectively). Contamination levels were less than the sanitary threshold for alternated A. minutum/S. costatum diets of 200 and 20 000 cell ml −1 , respectively, and for a monospecific A. minutum diet (1000−10 000 cell ml −1 ). In the last case, the accumulation rate was quite low, possibly because of inhibition of the filtration rate related to a lower biodeposit production rate and decreased feeding time activity. The addition of inorganic matter appeared to play a significant role in the observed increase of toxin uptake, whereas salinity was not a determining factor for toxin accumulation rates. These last observations were corroborated by statistical analysis and stepwise multiple linear regressions integrating all or some of the experimental parameters.
UAV-Borne Profiling Radar for Forest Research

Microwave Radar is an attractive solution for forest mapping and inventories because microwave signals penetrates into the forest canopy and the backscattering signal can provide information regarding the whole forest structure. Satellite-borne and airborne imaging radars have been used in forest resources mapping for many decades. However, their accuracy with respect to the main forest inventory attributes substantially varies depending on the wavelength and techniques used in the estimation. Systems providing canopy backscatter as a function of canopy height are, practically speaking, missing. Therefore, there is a need for a radar system that would enable the scientific community to better understand the radar backscatter response from the forest canopy. Consequently, we undertook a research study to develop an unmanned aerial vehicle (UAV)-borne profiling (i.e., waveform) radar that could be used to improve the understanding of the radar backscatter response for forestry mapping and inventories. A frequency modulation continuous waveform (FMCW) profiling radar, termed FGI-Tomoradar, was introduced, designed and tested. One goal is the total weight of the whole system is less than 7 kg, including the radar system and georeferencing system, with centimetre-level positioning accuracy. Achieving this weight goal would enable the FGI-Tomoradar system to be installed on the Mini-UAV platform. The prototype system had all four linear polarization measuring capabilities, with bistatic configuration in Ku-band. In system performance tests in this study, FGI-Tomoradar was mounted on a manned helicopter together with a Riegl VQ-480-U laser scanner and tested in several flight campaigns performed at the Evo site, Finland. Airborne laser scanning data was simultaneously collected to investigate the differences and similarities of the outputs for the same target area for better understanding the penetration of the microwave signal into the forest canopy. Preliminary analysis confirmed that the profiling radar measures a clear signal from the canopy structure and has substantial potential to improve our understanding of radar forest mapping using the UAV platform.
Enhanced second-harmonic generation from magnetic resonance in AlGaAs nanoantennas

We designed cylindrical AlGaAs-on-aluminium-oxide all-dielectric nanoantennas with magnetic dipole resonance at near-infrared wavelengths. Our choice of material system offers a few crucial advantages with respect to the silicon-oninsulator platform for operation around 1. 55μm wavelength: absence of two-photon absorption, high χ(2) nonlinearity, and the perspective of a monolithic integration with a laser. We analyzed volume second-harmonic generation associated to a magnetic dipole resonance in these nanoantennas, and we predict a conversion efficiency exceeding 10-3 with 1GW/cm2 of pump intensity.
Infrared–red cores in nearby elliptical galaxies

We present the Spitzer Space Telescope Infrared Array Camera observations for a sample of local elliptical galaxies to study later stages of active galactic nucleus (AGN) activity. A sample of 36 elliptical galaxies is selected from the Palomar spectroscopic survey. We detect nuclear non-stellar infrared emission in nine of them. There is unambiguous evidence of circumnuclear dust in these nine galaxies in their optical images. We also find a remarkable correlation between the infrared excess emission and the nuclear radio/X-ray emission, suggesting that infrared excess emission is tightly related to nuclear activity. The possible origin of infrared excess emission from hot dust heated by the central AGN is supported by the spectral indices of the infrared excess emission.
Microbial mineral colonization across a subsurface redox transition zone

This study employed 16S rRNA gene amplicon pyrosequencing to examine the hypothesis that chemolithotrophic Fe(II)-oxidizing bacteria (FeOB) would preferentially colonize the Fe(II)-bearing mineral biotite compared to quartz sand when the minerals were incubated in situ within a subsurface redox transition zone (RTZ) at the Hanford 300 Area site in Richland, WA, USA. The work was motivated by the recently documented presence of neutral-pH chemolithotrophic FeOB capable of oxidizing structural Fe(II) in primary silicate and secondary phyllosilicate minerals in 300 Area sediments and groundwater (Benzine et al., 2013). Sterilized portions of sand+biotite or sand alone were incubated in situ for 5 months within a multilevel sampling (MLS) apparatus that spanned a ca. 2-m interval across the RTZ in two separate groundwater wells. Parallel MLS measurements of aqueous geochemical species were performed prior to deployment of the minerals. Contrary to expectations, the 16S rRNA gene libraries showed no significant difference in microbial communities that colonized the sand+biotite vs. sand-only deployments. Both mineral-associated and groundwater communities were dominated by heterotrophic taxa, with organisms from the Pseudomonadaceae accounting for up to 70% of all reads from the colonized minerals. These results are consistent with previous results indicating the capacity for heterotrophic metabolism (including anaerobic metabolism below the RTZ) as well as the predominance of heterotrophic taxa within 300 Area sediments and groundwater. Although heterotrophic organisms clearly dominated the colonized minerals, several putative lithotrophic (NH4+, H2, Fe(II), and HS- oxidizing) taxa were detected in significant abundance above and within the RTZ. Such organisms may play a role in the coupling of anaerobic microbial metabolism to oxidative pathways with attendant impacts on elemental cycling and redox-sensitive contaminant behavior in the vicinity of the RTZ.
How the Social Ecology and Social Situation Shape Individuals’ Affect Valence and Arousal

Many theories highlight the role social contexts play in shaping affective experience. However, little is known about how individuals’ social environments influence core affect on short time-scales (e.g., hours). Using experience sampling data from the iSAHIB, wherein 150 adults aged 18 to 89 years reported on 64,213 social interactions (average 6.92 per day, SD = 2.85) across 9 weeks of daily life, we examined how 4 features of individuals’ social ecology (between-person differences) and immediate social situations (within-person changes) were associated with core affect—valence and arousal—and how those associations differ with age. Results from multilevel models revealed that familiarity, importance, type of social partner, and gender composition of the social context were associated with affect valence and/or affect arousal. Higher familiarity, higher importance, and same-gender composition were associated with more positive affect valence and higher arousal. Interactions with family and friends were linked to more positive valence whereas nonfamily social partners were linked to higher arousal. Age moderated the associations between importance and affect arousal, and between type of social partner and both dimensions of core affect. Findings align with theoretical propositions, contributing to but also suggesting need for further precision regarding how development shapes the interplay between social context and moment-to-moment affective experience.
Some Notes on the Control of Attention, its Modeling and Anticipatory Cognitive Computing

This paper is aimed at furthering discussions about the properties which computational cognitive models of attentional control should have if they are meant to be applied in interactive human-computer systems, namely for predicting human attention shifts across control levels. The paper discusses a number of issues of attentional control and implications that follow for computational modeling. It concludes by proposing the term anticipatory cognitive computing for those computational approaches that incorporate cognitive processing mechanisms found to exist in humans and that employ these mechanisms to generate hypothesis about imminent human cognitive and external actions.
Effects of fire and grazing on grasshopper sparrow nest survival

Patch-burn grazing is a management framework designed to promote heterogeneity in grasslands, creating more diverse grassland structure to accommodate the habitat requirements of many grassland species, particularly grassland birds. Published studies on the effects of patch-burn grazing on passerines have been conducted on relatively large (430–980 ha pastures), contiguous grasslands, and only 1 of these studies has investigated the reproductive success of grassland birds. We assessed the effects of the patch-burn grazing and a more traditional treatment on the nesting ecology of grasshopper sparrows (Ammodramus savannarum) in small (<37 ha pastures) grasslands located in southern Iowa from May to August of 2008 and 2009. The study pastures were grazed from May to September and prescribed burns were conducted in the spring. We investigated the effects of treatments on clutch size and modeled grasshopper sparrow nest survival as a function of multiple biological and ecological factors. We found no difference in clutch size between treatments; however, we did find a reduction in clutch size for nests that were parasitized by brown-headed cowbirds (Molothrus ater). Constant daily survival rates were greater in patch-burn grazed pastures than in grazed-and-burned pastures (patch-burn grazed rate and grazed-and-burned rate ). Competitive survival models included year, stage of nest, nest age, and cool-season grass (csg) abundance within 5 m of the nest. Overall, csg abundance had the greatest effect on survival and had a negative influence. Although survival rates were highest in patch-burn grazed pastures, multiple factors influenced grasshopper sparrow survival. Nest survival rates for both treatments were relatively low, and variables other than treatment were more instrumental in predicting grasshopper sparrow survival. We recommend decreasing overall vegetation cover if increasing nesting habitat for grasshopper sparrows is a management goal. In addition, we recommend further investigation of heterogeneity management in fragmented landscapes to better understand how it affects biodiversity in relatively small management units that typify grassland habitats in the Midwest. © 2011 The Wildlife Society.
Lead-Related Genetic Loci, Cumulative Lead Exposure and Incident Coronary Heart Disease: The Normative Aging Study

Background Cumulative exposure to lead is associated with cardiovascular outcomes. Polymorphisms in the δ-aminolevulinic acid dehydratase (ALAD), hemochromatosis (HFE), heme oxygenase-1 (HMOX1), vitamin D receptor (VDR), glutathione S-transferase (GST) supergene family (GSTP1, GSTT1, GSTM1), apolipoprotein E (APOE),angiotensin II receptor-1 (AGTR1) and angiotensinogen (AGT) genes, are believed to alter toxicokinetics and/or toxicodynamics of lead. Objectives We assessed possible effect modification by genetic polymorphisms in ALAD, HFE, HMOX1, VDR, GSTP1, GSTT1, GSTM1, APOE, AGTR1 and AGT individually and as the genetic risk score (GRS) on the association between cumulative lead exposure and incident coronary heart disease (CHD) events. Methods We used K-shell-X-ray fluorescence to measure bone lead levels. GRS was calculated on the basis of 22 lead-related loci. We constructed Cox proportional hazard models to compute adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for incident CHD. We applied inverse probability weighting to account for potential selection bias due to recruitment into the bone lead sub-study. Results Significant effect modification was found by VDR, HMOX1, GSTP1, APOE, and AGT genetic polymorphisms when evaluated individually. Further, the bone lead-CHD associations became larger as GRS increases. After adjusting for potential confounders, a HR of CHD was 2.27 (95%CI: 1.50–3.42) with 2-fold increase in patella lead levels, among participants in the top tertile of GRS. We also detected an increasing trend in HRs across tertiles of GRS (p-trend = 0.0063). Conclusions Our findings suggest that lead-related loci as a whole may play an important role in susceptibility to lead-related CHD risk. These findings need to be validated in a separate cohort containing bone lead, lead-related genetic loci and incident CHD data.
Stretchable gold conductors embedded in PDMS and patterned by photolithography: fabrication and electromechanical characterization

Stretchable gold conductors embedded in polydimethylsiloxane (PDMS) films were successfully prepared using standard photolithography. The minimum feature sizes patterned in the metal film and PDMS encapsulation are 10 µm and 20 µm, respectively. The micro-patterned conductors are robust to uni-axial (1D) and radial (2D) stretching with applied strains of tens of percent. The electrical response of the conductors follows a nonlinear increase with strain, and is reversible. The extensive stretchability of the conductors relies on a randomly and independently distributed network of micro-cracks (∼100 nm long) in the metal film on PDMS. The micro-cracks elongate to a few microns length both in the stretching and normal directions in 1D stretching but during 2D stretching, the micro-cracks grow and form ‘dry mud’ islands leaving the gold microstructure inside the islands intact. Patterning metallic thin films directly onto elastomeric substrates opens a promising route for microelectrodes and interconnects for soft and ultra-compliant MEMS and electronic devices.
Gene Expression Profiling of H9c2 Myoblast Differentiation towards a Cardiac-Like Phenotype

H9c2 myoblasts are a cell model used as an alternative for cardiomyocytes. H9c2 cells have the ability to differentiate towards a cardiac phenotype when the media serum is reduced in the presence of all-trans-retinoic acid (RA), creating multinucleated cells with low proliferative capacity. In the present study, we performed for the first time a transcriptional analysis of the H9c2 cell line in two differentiation states, i.e. embryonic cells and differentiated cardiac-like cells. The results show that RA-induced H9c2 differentiation increased the expression of genes encoding for cardiac sarcomeric proteins such as troponin T, or calcium transporters and associated machinery, including SERCA2, ryanodine receptor and phospholamban as well as genes associated with mitochondrial energy production including respiratory chain complexes subunits, mitochondrial creatine kinase, carnitine palmitoyltransferase I and uncoupling proteins. Undifferentiated myoblasts showed increased gene expression of pro-survival proteins such as Bcl-2 as well as cell cycle-regulating proteins. The results indicate that the differentiation of H9c2 cells lead to an increase of transcripts and protein levels involved in calcium handling, glycolytic and mitochondrial metabolism, confirming that H9c2 cell differentiation induced by RA towards a more cardiac-like phenotype involves remodeled mitochondrial function. PI3K, PDK1 and p-CREB also appear to be involved on H9c2 differentiation. Furthermore, complex analysis of differently expressed transcripts revealed significant up-regulation of gene expression related to cardiac muscle contraction, dilated cardiomyopathy and other pathways specific for the cardiac tissue. Metabolic and gene expression remodeling impacts cell responses to different stimuli and determine how these cells are used for biochemical assays.