Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a New Variant of IS257 That Has Displaced the Capsule Genes within Bovine Isolates of Staphylococcus aureus

ABSTRACT Many bovine Staphylococcus aureus isolates from Argentina are nontypeable (NT), i.e., they do not produce serotype 5 or 8 capsular polysaccharides (CPs). Some of these NT strains have a deletion of the cap5(8) gene cluster mediated by a variant of IS257, now designated IScap. IScap showed 93% amino acid identity to S. aureus ORF49 but only 85% identity to IS431 from S. aureus N315 and 88% identity to an IS257-like element from bovine strain RF122. Thirty-six (53%) of 68 bovine isolates, drawn from a previously described S. aureus strain collection, carried some variant of IS257, including IScap. Of these 36 IS+ isolates, 6 were CP5+, 1 was CP8+, and 29 were NT. Forty-four of the 68 isolates were NT, and 24 of these 44 NT isolates (55%) exhibited IScap-mediated deletion of the cap5(8) gene cluster. IScap was not found among 20 human NT S. aureus isolates bearing the cap5HIJK genes, which suggests that IScap-mediated deletion of the capsule locus is restricted to bovine strains of S. aureus. We were unable to identify a precursor strain in which IScap flanked the cap5(8) capsule locus, nor were we able to select for deletion of the cap5(8) locus in vitro. Our results support the hypothesis that deletion of the cap5 locus occurred in the distant past and that the relative abundance of these NT strains may be a result of their ability to persist in subclinical mastitis infection in cows.
Energy-Efficient Optimization for Physical Layer Security in Multi-Antenna Downlink Networks with QoS Guarantee

In this letter, we consider a multi-antenna downlink network where a secure user (SU) coexists with a passive eavesdropper. There are two design requirements for such a network. First, the information should be transferred in a secret and efficient manner. Second, the quality of service (QoS), i.e. delay sensitivity, should be take into consideration to satisfy the demands of real-time wireless services. In order to fulfill the two requirements, we combine the physical layer security technique based on switched beam beamforming with an energy-efficient power allocation. The problem is formulated as the maximization of the secrecy energy efficiency subject to delay and power constraints. By solving the optimization problem, we derive an energy-efficient power allocation scheme. Numerical results validate the effectiveness of the proposed scheme.
Morphology Development in Novel Composition of Thermoplastic Vulcanizates Based on PA12/PDMS Reactive Blends

The main objective of the present work was to tailor a new thermoplastic vulcanisate (TPV) composed of PA 12 as the thermoplastic phase and PDMS as the rubber phase. The PDMS was crosslinked by dicumyl peroxide (DCP). Interestingly, addition of 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) to the TPV provided the compatibilization of the PA12/PDMS blend in the dynamic process and gave a new material with control structure and morphology. The electron microscopy (SEM and TEM) studies revealed that adding silica nanoparticles and Lotader in PA12 and PDMS phases, respectively, led to a drastic reduction in R(v) of the PDMS particles from 16.5 mu m(virgin blend) to nearly 0.6 mu m for the PA12/PDMS reactive blend. Therefore, a stable co-continuous morphology was obtained for the new TPV based on 60-40 wt. -% of PDMS-PA12 blend.
Tobacco and alcohol use in lung transplant candidates and recipients

Abstract: Tobacco and alcohol use among lung transplant candidates and recipients is unknown. Our first goal was to describe tobacco and alcohol use before and after lung transplant in patients with cystic fibrosis (CF) and other pulmonary diseases (non‐CF). Our second goal was to determine whether demographic variables, depression, anxiety and social support predicted tobacco and alcohol use. Self‐report data from transplant candidates and recipients, and transplant nurse coordinator ratings of post‐transplant smoking and drinking were utilized. Data from two samples were analyzed. Sample 1 comprised 219 patients being evaluated for lung transplant, and sample 2 comprised 45 transplant recipients who were 1–7 yrs post‐transplant. The results from analyzing sample 1 indicated that 72% of non‐CF patients and 16% of CF patients had a history of smoking cigarettes, and the majority of patients in both groups had consumed alcohol in the past. For CF patients, past smoking was related to higher depression scores, and past drinking was related to higher education and lower social support. For non‐CF patients, a history of smoking was associated with being Caucasian and older. For CF patients, a history of drinking was associated with being older and less depressed, and for non‐CF patients a history of drinking was associated with higher education and lower social support. Post‐transplant 100% of recipients reported abstinence from tobacco, and over 60% reported abstinence from alcohol. Transplant coordinator ratings corroborated that no transplant recipients were using tobacco products or consuming alcohol in an excessive or problematic manner. For both groups, consuming alcohol after transplant was related to lower levels of social support. In conclusion, lung recipients remain abstinent from tobacco, and although over 30% of patients consume alcohol after transplant, it is not at problematic levels. Smoking and drinking behaviors were related to demographic variables, depression, and low social support.
Occupational health literacy and work-related injury among US adolescents

Building on the concept of ‘health literacy’ used in the US, we developed an analogous measure specific to safety in the workplace labeled ‘occupational health literacy’ (OHL) and investigated whether OHL is a protective factor against work-related injury (WRI) among adolescents. Using cross-sectional survey data from 2262 14 to 18-year olds in five high schools across the US, we found that OHL (level of occupational safety and health (OSH) information and training received combined with knowledge and awareness of OSH information and concepts) is positively associated with WRI prevalence. This association appears to be largely driven by the OHL subscale on respondents’ receipt of safety training, which likely represents job hazardousness and may be overwhelming any protective effect of OHL on work injury. This exploratory study has shown that more precise measurement of OHL and confounding variables (job hazardousness) will be crucial in further studies exploring a OHL–WRI relationship.
Triglyceride-rich lipoproteins and high-density lipoprotein cholesterol in patients at high risk of cardiovascular disease: evidence and guidance for management

Even at low-density lipoprotein cholesterol (LDL-C) goal, patients with cardiometabolic abnormalities remain at high risk of cardiovascular events. This paper aims (i) to critically appraise evidence for elevated levels of triglyceride-rich lipoproteins (TRLs) and low levels of high-density lipoprotein cholesterol (HDL-C) as cardiovascular risk factors, and (ii) to advise on therapeutic strategies for management. Current evidence supports a causal association between elevated TRL and their remnants, low HDL-C, and cardiovascular risk. This interpretation is based on mechanistic and genetic studies for TRL and remnants, together with the epidemiological data suggestive of the association for circulating triglycerides and cardiovascular disease. For HDL, epidemiological, mechanistic, and clinical intervention data are consistent with the view that low HDL-C contributes to elevated cardiovascular risk; genetic evidence is unclear however, potentially reflecting the complexity of HDL metabolism. The Panel believes that therapeutic targeting of elevated triglycerides (≥1.7 mmol/L or 150 mg/dL), a marker of TRL and their remnants, and/or low HDL-C (<1.0 mmol/L or 40 mg/dL) may provide further benefit. The first step should be lifestyle interventions together with consideration of compliance with pharmacotherapy and secondary causes of dyslipidaemia. If inadequately corrected, adding niacin or a fibrate, or intensifying LDL-C lowering therapy may be considered. Treatment decisions regarding statin combination therapy should take into account relevant safety concerns, i.e. the risk of elevation of blood glucose, uric acid or liver enzymes with niacin, and myopathy, increased serum creatinine and cholelithiasis with fibrates. These recommendations will facilitate reduction in the substantial cardiovascular risk that persists in patients with cardiometabolic abnormalities at LDL-C goal.
Micropatterning of 3D Microenvironments for Living Biosensor Applications

Micro-scale printing and patterning of living cells has multiple applications including tissue engineering, cell signaling assays, and the fabrication of cell-based biosensors. In this work, a molecular printing instrument, the Bioforce Nano eNabler, was modified to enable micron-scale “quill-pen” based printing of mammalian cells in a 3D hyaluronan/gelatin based hydrogel. Specifically, photo-initiated “thiol-ene” click chemistry was used to couple the thiol groups of thiolated hyaluronan/thiolated gelatin to the alkene groups of 4-arm polyethylene glycol (PEG)-norbornene molecules. Rapid photopolymerization enabled direct printing and controlled curing of living cells within the hydrogel matrix. The resulting hydrogels were biocompatible with human adipose-derived stem cells, NIH-3T3 cells, and mouse embryonic stem cells. The utility of this printing approach was also explored for cell-based biosensors. Micro-printed cells expressing a redox sensitive variant of the green fluorescent protein (roGFP-R12) showed a measurable fluorescent response to addition of oxidizing and then reducing agents. This work represents a novel approach to micron-scale cell patterning, and its potential for living, cell-based biosensors.
Integrin α6β1-laminin interactions regulate early myotome formation in the mouse embryo

We addressed the potential role of cell-laminin interactions during epaxial myotome formation in the mouse embryo. Assembly of the myotomal laminin matrix occurs as epaxial myogenic precursor cells enter the myotome. Most Myf5-positive and myogenin-negative myogenic precursor cells localise near assembled laminin, while myogenin-expressing cells are located either away from this matrix or in areas where it is being assembled. In Myf5nlacZ/nlacZ (Myf5-null) embryos, laminin, collagen type IV and perlecan are present extracellularly near myogenic precursor cells, but do not form a basement membrane and cells are not contained in the myotomal compartment. Unlike wild-type myogenic precursor cells, Myf5-null cells do not express the α6β1 integrin, a laminin receptor, suggesting that integrin α6β1-laminin interactions are required for myotomal laminin matrix assembly. Blockingα 6β1-laminin binding in cultured wild-type mouse embryo explants resulted in dispersion of Myf5-positive cells, a phenotype also seen in Myf5nlacZ/nlacZ embryos. Furthermore, inhibition ofα 6β1 resulted in an increase in Myf5 protein and ectopic myogenin expression in dermomyotomal cells, suggesting that α6β1-laminin interactions normally repress myogenesis in the dermomyotome. We conclude that Myf5 is required for maintaining α6β1 expression on myogenic precursor cells, and that α6β1 is necessary for myotomal laminin matrix assembly and cell guidance into the myotome. Engagement of laminin byα 6β1 also plays a role in maintaining the undifferentiated state of cells in the dermomyotome prior to their entry into the myotome.
Snake based unsupervised texture segmentation using Gaussian Markov Random Field Models

A functional for unsupervised texture segmentation is investigated in this paper. An auto-normal model based on Markov Random Fields is employed here to represent textures. The functional investigated here is optimized with respect to the auto-normal model parameters and the evolving contour to simultaneously estimate auto-normal model parameters and find the evolving contour. Experimental results applied on the textures of the Brodatz album demonstrate the higher speed of convergence of this algorithm in comparison with a traditional stochastic algorithm in the literature.
Multi-material, multi-technology stereolithography

For more than a decade, our group has been developing the methods and systems required to have spatial control over material placement and structure creation, leading to, for example, the realisation of complex three-dimensional (3D) devices that integrate electronics and thus intelligence within mechanical structures as well as 3D spatially complex bioactive, implantable, tissue engineered constructs. There are myriad issues associated with combining multiple materials to create functional products, ranging from the deposition and processing of different materials to the combined performance of the materials in the resulting product. Stereolithography (SL) has been the primary technology focus of this work because it offers high quality surface finish, dimensional accuracy, and a variety of material options that includes implantable materials. Moreover, SL builds in essentially ambient, minimally controlled environmental conditions that provide easy access to the build chamber and enable straightforward conversion of existing single material SL systems to multiple material and hybrid manufacturing systems. This paper describes the development of multiple material and multiple technology (hybrid) stereolithography systems capable of manufacturing multiple material structures with mechanical, electrical, and biochemical functionality.
Comparing Families of Dynamic Causal Models

Mathematical models of scientific data can be formally compared using Bayesian model evidence. Previous applications in the biological sciences have mainly focussed on model selection in which one first selects the model with the highest evidence and then makes inferences based on the parameters of that model. This “best model” approach is very useful but can become brittle if there are a large number of models to compare, and if different subjects use different models. To overcome this shortcoming we propose the combination of two further approaches: (i) family level inference and (ii) Bayesian model averaging within families. Family level inference removes uncertainty about aspects of model structure other than the characteristic of interest. For example: What are the inputs to the system? Is processing serial or parallel? Is it linear or nonlinear? Is it mediated by a single, crucial connection? We apply Bayesian model averaging within families to provide inferences about parameters that are independent of further assumptions about model structure. We illustrate the methods using Dynamic Causal Models of brain imaging data.
Bioactivity and Surface Reactivity of RF-sputtered Calcium Phosphate Thin Films

Calcium phosphates (CaP) are known to be bioactive, i.e. able to bond to bone. This makes CaPs very suitable to be aplied as thin coatings on bone-implants. In this work we studied the physicochemical behaviour of CaP coatings applied with radio frequency (RF) magnetron sputtering, a deposition technique that can produce thin (~100 nm), homogeneous, and well-adhereing coatings. As-deposited CaP coatings are amorphous and can be crystallized by a heat-treatment of 30 minutes at 650C, resulting in a mainly apatitic structure. Firstly, we have studied the behaviour of these CaP coatings in so-called simulated body fluid (SBF or SBF1), an anorganic equivalent of human blood plasma. Amorphous CaP coatings dissolve in SBF and even in SBF with twice the Ca and PO4 concentrations (SBF2). After a heat-treatment CaP coatings remain inert in SBF for days, i.e. coatings do not dissolve and no crystals are formed from the solution on the coating surface. However, formation of crystals is possible in SBF2. At room temperature, the formation of crystals is preceeded by an induction time, in which rod-shaped sediments can be found on the coating surface, but no significant growth is observed. Only after completion of the induction period growth of CaP crystals is allowed. Growth can proceed in solutions with lower concentrations like SBF1. Only within a limited range of Ca over PO4 ratio of the coatings, formation of CaP crystals from SBF2 is possible. In a rat bone marrow (RBM) cell-culture CaP was compared to RF-sputtered coatings of other bioceramics like alumina (Al2O3) and titania (TiO2). Alumina is a known bioinert material. However, there is still discussion on the biocompatibility of titania. It was found that cell behavior on CaP coatings significantly differed from alumina. CaP coatings showed decreased early proliferation, increased differentiation, and increased mature osteoblast activity compared to alumina. Results for titania were intermediate compared to CaP and alumina. That is, early proliferation followed the alumina results, whereas the mature osteoblast activity and the matrix production confirmed the CaP findings. Coinciding with the differentiation of cells towards mature, extracellular matrix forming osteoblasts, both the CaP and titania coatings showed the formation of a directly bonded CaP layer (~1 micron after 16 days), quite similar to the precipitate grown in simulated body fluids. The directly bonded CaP layer is thought to be indicative of bone-bonding bioactivity. In simulated body fluids we showed that the presence of CaP nuclei, obtained by 40-60 minutes pre-immersion in SBF2, is required to allow growth in SBF1. Therefore, we also studied the effect of pre-immersion in a RBM cell-model. The coatings that were not pre-immersed showed the formation of a directly bonded \cap layer, again after the start of osteoblast-differentiation. However, the pre-immersed samples allowed the growth of a this layer without an offset. Thus by applying CaP nuclei, the formation of the directly bonded CaP layer has been decoupled from the ECM calcifications.
Joint frequency and 2-D DOA recovery with sub-Nyquist difference space-time array

In this paper, joint frequency and 2-D direction of arrival (DOA) estimation at sub-Nyquist sampling rates of a multi-band signal (MBS) comprising of P disjoint narrowband signals is considered. Beginning with a standard uniform rectangular array (URA) consisting of M = Mx × My sensors, this paper proposes a simpler modification by adding a N — 1 delay channel network to only one of the sensor. A larger array is then formed by combining the sub-Nyquist sampled outputs of URA and the delay channel network, referred to as the difference space-time (DST) array. Towards estimating the joint frequency and 2-D DOA on this DST array, a new method utilizing the 3-D spatial smoothing for rank enhancement and a subspace algorithm based on ESPRIT is presented. Furthermore, it is shown that an ADC sampling frequency of fs ≥ B suffices, where B is the bandwidth of the narrow-band signal. With the proposed approach, it is shown that O(MN/4) frequencies and their 2-D DOAs can be estimated even when all frequencies alias to the same frequency due to sub-Nyquist sampling. Appropriate simulation results are also presented to corroborate these findings.
Common themes in PrP signaling: the Src remains the same

The ability of the cellular prion protein (PrPC) to trigger intracellular signals appears central to neurodegeneration pathways, yet the physiological significance of such signals is rather puzzling. For instance, PrPC deregulation disrupts phenomena as diverse as synaptic transmission in mammals and cell adhesion in zebrafish. Although unrelated, the key proteins in these events -the NMDA receptor (NMDAR) and E-cadherin, respectively- are similarly modulated by the Src family kinase (SFK) Fyn. These observations highlight the importance of PrPC-mediated Fyn activation, a finding reported nearly two decades ago. Given their complex functions and regulation, SFKs may hold the key to intriguing aspects of PrP biology such as its seemingly promiscuous functions and the lack of strong phenotypes in knockout mice. Here we provide a mechanistic perspective on how SFKs might contribute to the uncertain molecular basis of neuronal PrP phenotypes affecting ion channel activity, axon myelination and olfactory function. In particular, we discuss SFK target proteins involved in these processes and the role of tyrosine phosphorylation in the regulation of their activity and cell surface expression.
In-situ high-resolution electron microscopy study on a surface reconstruction of Au-deposited Si at very high temperatures

Abstract In-situ high-temperature high-resolution electron microscopy was applied to a study of the surface modification of Au-deposited Si. The experiment was carried out above the melting points of small particles of Au (approximately several nanometres in diameter) in a 300 kV high-resolution analytical transmission electron microscope equipped with a direct-heating-type specimen-heating holder in a vacuum of 4–6 × 10−6 Pa. Facet-unfacet transformation and reconstruction of the Si{111}, {001}, {211} and {311} surfaces induced by wetting of molten Au atoms have been observed at near-atomic resolution. It is concluded that molten Au atoms remove a surface amorphous layer on the Si surface, making the surface clean even in a non ultra-high vacuum.
Effect of different reconstruction algorithms on the dynamics and modeling parameters of 18F-Galacto-RGD in mice

So far FBP (filtered back projection) is still the standard reconstruction method for kinetic modeling of PET data. Iterative reconstruction algorithms, such as OSEM (ordered subsets expectation maximization) or MAP (maximum a posteriori) create images with better signal-to-noise ratios and less streak artifacts. This is of special interest in the short-time frames with low statistics at the beginning of a dynamic acquisition. To determine if iteratively reconstructed PET data could be used for kinetic modeling of pre-clinical data, we compared OSEM2D and OSEM3D/MAP data with FBP data using microPET data. Nude mice (n=6) bearing a human melanoma tumor were imaged over 90 minutes with a FOCUS 120 microPET. We applied 18F-Galacto-RGD via a tail vein catheter into the animal (9-19 MBq). 18F-Galacto-RGD is used for imaging the alphanubeta3 expression during angiogenesis and on specific tumor cells. Each list mode dataset was binned into 19 frames and reconstructed with FBP, OSEM2D and OSEM3D/MAP. The data was not corrected for scatter and attenuation. Volumes of interest (VOIs) were drawn on the heart and tumor tissue. No corrections for spillover and partial volume effect were applied. For the kinetic modeling of the tumor data a standard 2-tissue-compartment model with reversible binding was used (fitting parameters: K1, k2, k3, k4 (rate constants) and Dnu (vascular blood fraction)). The input function TACs of the iteratively reconstructed data showed no considerable difference to the FBP data. Only the OSEM3D/MAP TACs for the tumor VOIs were clearly and consistently higher for all datasets than the corresponding FBP and OSEM2D TACs. Kinetic modeling shows negligible parameter changes for K1, k2, k3 and k4 for all reconstruction algorithms. The higher OSEM3D/MAP tumor values are compensated only with an overestimated Dnu (Dnu(FBP)=2.2%, Dnu(OSEM3D/MAP)=3.3%). Further work needs to be done on optimizing the iteration settings for the OSEM3D/MAP.