Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative ‘Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids

Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. ‘Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the ‘Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining the monomer composition of mcl-PHA polymers. Understanding the relationships between genome content, gene and gene product expression, and how these factors influence polymer synthesis, will aid in optimization of mcl-PHA production by P. putida LS46 using biodiesel waste streams.
Physical Education Increases Daily Moderate to Vigorous Physical Activity and Reduces Sedentary Time.

BACKGROUND Physical activity (PA) is important to mental and physical health. Physical education (PE) lessons have the potential to increase daily moderate to vigorous PA (MVPA) and reduce sedentary time (SED). We measured MVPA and SED in primary school PE, determined the contribution of PE to daily MVPA and SED, and compared PA on days with and without PE. METHODS PA was measured in 504 first (ages 7-9) and second (ages 10-12) school level children for 1 school week, with inclusion criteria of at least 10 hours of valid data. Linear mixed methods were used for data analysis. RESULTS In PE, students spent 28.6 ± 16.5% in MVPA and 29.3 ± 19.8% in SED. Each additional MVPA minute in PE was associated with 1.4 more daily MVPA minutes. On days with PE, students had 12.8 (95% CI 10.5; 15.0) minutes more MVPA and 9.7 (95% CI 16.3; 3.1) minutes less SED compared with days without PE. CONCLUSIONS Although MVPA in PE was relatively low and SED high, PE significantly increased daily MVPA and reduced SED, confirming the important role of PE in supporting the healthy development of children.
Analysis of Immune Response Markers in Jorge Lobo's Disease Lesions Suggests the Occurrence of Mixed T Helper Responses with the Dominance of Regulatory T Cell Activity

Jorge Lobo’s disease (JLD) is a chronic infection that affects the skin and subcutaneous tissues. Its etiologic agent is the fungus Lacazia loboi. Lesions are classified as localized, multifocal, or disseminated, depending on their location. Early diagnosis and the surgical removal of lesions are the best therapeutic options currently available for JLD. The few studies that evaluate the immunological response of JLD patients show a predominance of Th2 response, as well as a high frequency of TGF-β and IL-10 positive cells in the lesions; however, the overall immunological status of the lesions in terms of their T cell phenotype has yet to be determined. Therefore, the objective of this study was to evaluate the pattern of Th1, Th2, Th17 and regulatory T cell (Treg) markers mRNA in JLD patients by means of real-time PCR. Biopsies of JLD lesions (N = 102) were classified according to their clinical and histopathological features and then analyzed using real-time PCR in order to determine the expression levels of TGF-β1, FoxP3, CTLA4, IKZF2, IL-10, T-bet, IFN-γ, GATA3, IL-4, IL-5, IL-13, IL-33, RORC, IL-17A, IL-17F, and IL-22 and to compare these levels to those of healthy control skin (N = 12). The results showed an increased expression of FoxP3, CTLA4, TGF-β1, IL-10, T-bet, IL-17F, and IL-17A in lesions, while GATA3 and IL-4 levels were found to be lower in diseased skin than in the control group. When the clinical forms were compared, TGF-β1 was found to be highly expressed in patients with a single localized lesion while IL-5 and IL-17A levels were higher in patients with multiple/disseminated lesions. These results demonstrate the occurrence of mixed T helper responses and suggest the dominance of regulatory T cell activity, which could inhibit Th-dependent protective responses to intracellular fungi such as L. loboi. Therefore, Tregs may play a key role in JLD pathogenesis.
Effect of Nonthermal Electrons and Ions on Longitudinal Dust Acoustic Solitary Waves in a Strongly Coupled Dusty Plasma

The propagation properties of longitudinal dust acoustic waves (LDAWs) have been investigated in a strongly coupled dusty plasma containing negatively charged dust fluid, and nonthermal electrons and ions using the generalized hydrodynamic model in “kinetic regime. ” The nonlinear dynamics of the system are shown to be governed by a modified KdV equation in the presence of viscoelastic forces. The modified KdV equation so obtained is found to possess a nonlinear force term and a linear damping term. The effects of various physical parameters on the phase velocity and coefficients of modified KdV equation have been analyzed. Furthermore, the effect of nonthermality of electrons and ions is realized in the numerical solution of the equation so obtained to study the time evolution of LDAWs under the influence of dust correlation forces.
Data assimilation for identification of cardiovascular network characteristics

A method to estimate the hemodynamics parameters of a network of vessels using an Ensemble Kalman filter is presented. The elastic moduli (Young's modulus) of blood vessels and the terminal boundary parameters are estimated as the solution of an inverse problem. Two synthetic test cases and a configuration where experimental data are available are presented. The sensitivity analysis confirms that the proposed method is quite robust even with a few numbers of observations. The simulations with the estimated parameters recovers target pressure or flow rate waveforms at given specific locations, improving the state‐of‐the‐art predictions available in the literature. This shows the effectiveness and efficiency of both the parameter estimation algorithm and the blood flow model.
When Ontogeny Matters: A New Japanese Species of Brittle Star Illustrates the Importance of Considering both Adult and Juvenile Characters in Taxonomic Practice

Current taxonomy offers numerous approaches and methods for species delimitation and description. However, most of them are based on the adult characters and rarely suggest a dynamic representation of developmental transformations of taxonomically important features. Here we show how the underestimation of ontogenetic changes may result in long term lack of recognition of a new species of one of the most common ophiacanthid brittle stars (Echinodermata: Ophiuroidea) from the North Pacific. Based on vast material collected predominantly by various Japanese expeditions in the course of more than 50 years, and thorough study of appropriate type material, we revise the complex of three common species of the ophiuroid genus Ophiacantha which have been persistently confused with each other. The present study thus reveals the previously unrecognized new species Ophiacantha kokusai sp.nov. which is commonly distributed off the Pacific coast of Japan. The new species shows developmental differentiation from the closely related species Ophiacantha rhachophora H. L. Clark, 1911 and retains clearly expressed early juvenile features in the adult morphology. Another species, Ophiacantha clypeata Kyte, 1977, which had been separated from O. rhachophora, is in turn shown to be just a juvenile stage of another North Pacific species, Ophiacantha trachybactra H.L. Clark, 1911. For every species, detailed morphological data from both adult and juvenile specimens based on scanning electron microscopy are presented. A special grinding method showing complex internal features has been utilized for the first time. For all three species in this complex, a clear bathymetric differentiation is revealed: O. rhachophora predominantly inhabits shallow waters, 0–250 m, the new species O. kokusai lives deeper, at 250–600 m, and the third species, O. trachybactra, is found at 500–2,000 m. The present case clearly highlights the importance of considering developmental transformations, not only for a limited number of model organisms, but as part of the taxonomic process.
Carbon Nanotube Arrays for Intracellular Delivery and Biological Applications

iii Acknowledgement. v CHAPTER 1: Introduction. 1 1.1. Motivation. 2 1.1.1. CRISPR/Cas9-Mediated Genome Engineering. 2 1.1.2. Cancer Immunotherapy. 3 1.2. Carbon Nanotubes and Carbon Nanostructures. 5 1.3. CNT Properties. 7 1.4. Biomedical Applications of CNTs. 8 1.5. Research Objectives. 8 1.6. Dissertation Overview. 10 CHAPTER 2: Background. 12 2.1. CNT and CNF-Based Devices. 13 2.1.1. Devices with Randomly Ordered CNTs. 13 2.1.2. Devices with Vertically Aligned CNTs and CNFs. 15 2.1.3. Carbon Nanostructure-Tipped Devices. 18 2.1.4. Enhancement and Selectivity. 21 2.2. CNT Fabrication. 23 2.3. Template-Based Manufacturing of CNTs. 24 2.4. AAO Membranes. 27 2.5. Detection of Biomolecules Using CNTs. 33
Myogenic temporomandibular disorders: Clinical systemic comorbidities in a female population sample

Background Myogenic temporomandibular disorders (MTMD) frequently coexist with other clinical conditions in the same individual. In the last decades, several authors have analyzed these comorbidities looking for the origin of this overlapping. Objetives The aim of this study was to perform a comparative anaylisis between a group of patients with MTMD and a control group of dental patients without dysfunctional pathology to assess whether there are significant differences in the presence of systemic medical comorbidities between the two groups. Material and Methods Restrospective epidemiological analysis, based on medical questionnaires in a group of 31 patients, women, aged from 24 to 58 (average 39.96 years), diagnosed with MTMD (Masticatory Myofascial Pain), with a control group with the same number of individuals, gender and age range to evaluate if there is a significant statistical difference in the presence of medical comorbidities in this group of patients with MTMD and if they are in a higher risk of suffering different pathological conditions. Results It was found that the group affected by MTMD presented many more associated medical conditions than the control group: health changes during the last year, medical evaluations and treatments, presence of pain, sinus disease, tinnitus, headache, joint pain, ocular disorders, fatigue, dizziness, genitourinary disorders and xerostomia among others; and they were also in a higher risk to suffer other pathological entities as headaches and articular pain. Conclusions These results reinforce our hypothesis that MTMD belong to a group of medical conditions triggered by a loss of equilibrium of the individual’s Psycho-Neuro-Endocrine-Immune (PNEI) Axis that produces alterations in the response against external stimuli in some genetically predisposed individuals. It is, therefore, necessary to change the way of diagnosing and managing these individual’s medical conditions, being mandatory to look from a more multidisciplinary perspective than the one we are currently offering. Key words:Temporomandibular joint disorders, myofascial pain syndromes, comorbidity, chronic pain, health status, health questionnaire, self report.
Pricing for enabling forwarding in self-configuring ad hoc networks

Using a microeconomic framework based on game theory, we design and analyze a pricing algorithm that encourages forwarding among autonomous (selfish) nodes by reimbursing forwarding. Taking a joint network-centric and user-centric approach, the revenue maximizing network and utility maximizing nodes interact through prices for channel use, reimbursements for forwarding, transmitter power control as well as forwarding and destination preferences. In a three-node (two sources, one access point) network, the network converges to an architecture that induces forwarding only when the network geometries are such that forwarding is likely to bring higher network efficiency. For other geometries, the network converges to architectures that do not favor forwarding. We characterize the Nash equilibria for each geometry and design specific game implementations to achieve the most Pareto superior Nash equilibrium. In a general multi-node network, our results indicate that the nodes' willingness to forward decrease for large values of the ratio of the average internodal distance to the average distance between the access point and nodes with direct connections to it.
Matrix completability analysis via graph k-connectivity

The problem of low-rank matrix completion is continually attracting attention for its applicability to many real-world problems. Still, the large size, extreme sparsity, and nonuniformity of these matrices pose a challenge. In this paper, we make the observation that even when the observed matrix is not suitable for accurate completion there may be portions of the data where completion is still possible. We propose the CompleteID algorithm, which exploits the non-uniformity of the observation, to analyze the completability of the input instead of blindly applying completion. Balancing statistical accuracy with computational efficiency, we relate completability to edge-connectivity of the graph associated with the input partially-observed matrix. We develop the MaxKCD algorithm for finding maximally k-edge-connected components efficiently. Experiments across datasets from a variety of applications demonstrate not only the success of CompleteID but also the importance of completability analysis.
Host Genetics and Environment Drive Divergent Responses of Two Resource Sharing Gall-Formers on Norway Spruce: A Common Garden Analysis

A central issue in the field of community genetics is the expectation that trait variation among genotypes play a defining role in structuring associated species and in forming community phenotypes. Quantifying the existence of such community phenotypes in two common garden environments also has important consequences for our understanding of gene-by-environment interactions at the community level. The existence of community phenotypes has not been evaluated in the crowns of boreal forest trees. In this study we address the influence of tree genetics on needle chemistry and genetic x environment interactions on two gall-inducing adelgid aphids (Adelges spp. and Sacchiphantes spp.) that share the same elongating bud/shoot niche. We examine the hypothesis that the canopies of different genotypes of Norway spruce (Picea abies L.) support different community phenotypes. Three patterns emerged. First, the two gallers show clear differences in their response to host genetics and environment. Whereas genetics significantly affected the abundance of Adelges spp. galls, Sacchiphantes spp. was predominately affected by the environment suggesting that the genetic influence is stronger in Adelges spp. Second, the among family variation in genetically controlled resistance was large, i.e. fullsib families differed as much as 10 fold in susceptibility towards Adelges spp. (0.57 to 6.2 galls/branch). Also, the distribution of chemical profiles was continuous, showing both overlap as well as examples of significant differences among fullsib families. Third, despite the predicted effects of host chemistry on galls, principal component analyses using 31 different phenolic substances showed only limited association with galls and a similarity test showed that trees with similar phenolic chemical characteristics, did not host more similar communities of gallers. Nonetheless, the large genetic variation in trait expression and clear differences in how community members respond to host genetics supports our hypothesis that the canopies of Norway spruce differ in their community phenotypes.
Culture Change in a Professional Sports Team: Shaping Environmental Contexts and Regulating Power: A commentary

INTRODUCTION Cruickshank et al. provide an interesting account of elite sporting culture, having chosen professional rugby union club Leeds Carnegie as the site for their investigation. In their article, they promote a perspective on cultural change that is very different from the majority of top-down processes described in sport management and sport psychology domains. Theirs is a more textured analysis of cultural change in a professional sport environment that, in a number of ways, serves to advance the empirical research base in this area.
Interaction of two shallow non-circular tunnels with imperfect interfaces subjected to shear waves

The dynamic interaction of two non-circular shallow tunnels with imperfect interfaces subjected to anti-plane waves is investigated, and the semi-analytical solution of dynamic stress with the half-plane boundary effect is presented. The spring model is adopted to analyse the effect of imperfect interfaces between the tunnel and the rock mass on the dynamic stress. The half-plane boundary is modelled by an arc with a large radius to satisfy the traction-free boundary condition. Combining the wave function expansion method and conformal transformation method, the analytical solutions of stresses and displacements are expanded in terms of wave functions. The expanded coefficients are determined by satisfying the imperfect boundary conditions around the tunnels and the traction-free boundary condition at the surface. Some numerical examples are provided to discuss the imperfect interface effects on the dynamic stress under different depths of tunnels and different distances between the two tunnels. Comparison with existing numerical results validates this present dynamic model.
On a Non-Reflecting Boundary Condition for Hyperbolic Conservation Laws

AbstractA non-reﬂectingboundarycondition(NRBC) for practicalcomputationsin ﬂuid dynamicsand aeroacousticsis presented. The technique is based on the ﬁrst principle of non-reﬂecting, plane wave propagation [1] andthe hyperbolicity of the Euler equation system. The NRBC is simple and effective, provided the numericalscheme maintains locally a C 1 continuous solution at the boundary. Several numerical examples in 1D, 2Dand 3D space are illustrated to demonstrate its robustness in practical computations.1 IntroductionIt is well-known that non-reﬂecting boundary conditions (NRBCs) play an important role in ﬂuid ﬂow and aeroa-coustics computations. The need for artiﬁcial boundary conditions arises when the domain of the problem is un-bounded and extends to inﬁnity. In order to treat the problem numerically, a domain of ﬁnite size is required andartiﬁcial boundaries are imposed. At these artiﬁcial boundaries, NRBCs are sought for to minimize their inﬂuenceson the ﬂow. A spurious reﬂection resulting from an inappropriate numerical boundary condition will contaminate theﬂow ﬁeld and may entirely spoil the ﬂow computation. Research on NRBC is a challenging topic in engineering andapplied mathematics. For decades, a vast number of papers on NRBC have been published, e.g. see [3-6], the reviewpaper by Givoli [2], and the references cited there.In one-dimensional ﬂow, at an artiﬁcial boundary, Enquist and Majda [3], and Hedstrom [7] proved that a bound-ary condition is non-reﬂecting is equivalent to saying that the characteristic variables corresponding to the incomingcharacteristic curve remain constant across the artiﬁcial boundary (see also Hirsch [8], p. 370). For multi-dimensionalﬂow, this 1-D technique is combined with dimension splitting and applied in the practical NRBC treatment. Such acombined treatment has been the topic of many papers on the characteristics based NRBCs (see e.g. [4] and referencesin [2]).
Cicatricial pemphigoid.

UNLABELLED Cicatricial pemphigoid (CP) is a heterogeneous group of rare, chronic, subepithelial blistering disorders of the mucous membranes and, occasionally, the skin, which can have serious and rarely fatal consequences. The most common clinical features are desquamative gingivitis, oral erosions, and conjunctival fibrosis. Skin lesions occur less frequently and may present as widespread vesicles and bullae, as in bullous pemphigoid (BP). In some patients, the scarring can be a source of significant morbidity because it can result in odynophagia, strictures of the upper aerodigestive tract, or corneal opacities leading to eventual blindness. This article is a comprehensive review and discusses clinical, pathologic, and pathophysiologic aspects of this group of disorders collectively known as CP. (J Am Acad Dermatol 2000;43:571-91.) LEARNING OBJECTIVE At the conclusion of this learning activity, participants should be familiar with the clinical spectrum of CP, the histopathologic and immunopathologic characteristics, the differential diagnosis, the treatment, and the natural history of the disease. Furthermore, this learning activity should facilitate early diagnosis of CP and should promote the idea that the involvement of other specialists, including ophthalmologists, otolaryngologists, gastroenterologists, and oral medicine specialists, as appropriate, will aid in providing these patients with the highest quality of care.