Miracle-dz/UniFAR-FTUs huggingface dataset:
Mathematical modelling of fungal growth and function

This contribution is based on the six presentations given at the Special Interest Group meeting on Mathematical modelling of fungal growth and function held during IMC9. The topics covered aspects of fungal growth ranging across several orders of magnitude of spatial and temporal scales from the bio-mechanics of spore ejection, vesicle trafficking and hyphal tip growth to the form and function of mycelial networks. Each contribution demonstrated an interdisciplinary approach to questions at specific scales. Collectively, they represented a significant advance in the multi-scale understanding of fungal biology.
The Arabidopsis thaliana Myo-Inositol 1-Phosphate Synthase1 Gene Is Required for Myo-inositol Synthesis and Suppression of Cell Death[W]

This work uses functional genomics to delineate the role of the inositol synthesis genes in regulating growth, development, and cell death and reveals a connection between inositol, phosphatidylinositol, and sphingolipids. l-myo-inositol 1-phosphate synthase (MIPS; EC 5.5.1.4) catalyzes the rate-limiting step in the synthesis of myo-inositol, a critical compound in the cell. Plants contain multiple MIPS genes, which encode highly similar enzymes. We characterized the expression patterns of the three MIPS genes in Arabidopsis thaliana and found that MIPS1 is expressed in most cell types and developmental stages, while MIPS2 and MIPS3 are mainly restricted to vascular or related tissues. MIPS1, but not MIPS2 or MIPS3, is required for seed development, for physiological responses to salt and abscisic acid, and to suppress cell death. Specifically, a loss in MIPS1 resulted in smaller plants with curly leaves and spontaneous production of lesions. The mips1 mutants have lower myo-inositol, ascorbic acid, and phosphatidylinositol levels, while basal levels of inositol (1,4,5)P3 are not altered in mips1 mutants. Furthermore, mips1 mutants exhibited elevated levels of ceramides, sphingolipid precursors associated with cell death, and were complemented by a MIPS1-green fluorescent protein (GFP) fusion construct. MIPS1-, MIPS2-, and MIPS3-GFP each localized to the cytoplasm. Thus, MIPS1 has a significant impact on myo-inositol levels that is critical for maintaining levels of ascorbic acid, phosphatidylinositol, and ceramides that regulate growth, development, and cell death.
Prairie Dogs: An Ecological Review and Current Biopolitics

Abstract In recent years, people have interpreted scientific information about the black-tailed prairie dog (Cynomys ludovicianus) in various, and sometimes conflicting, ways. Political complexity around the relationship among black-tailed prairie dogs, agricultural interests, and wildlife has increased in recent years, particularly when prairie dogs occur on publicly owned lands leased to private entities for livestock grazing. Some have proposed that estimates of prairie dog (Cynomys spp.) numbers from 1900 are inflated, that prairie dog grazing is not unique (other grazers have similar affects on vegetation), and that prairie dogs significantly reduce carrying capacity for livestock and wildlife. We address all these issues but concentrate on the degree of competition between prairie dogs and ungulates because this motivates most prairie dog control actions. We conclude that the available information does not justify holding distribution and numbers of prairie dogs at a level that is too low to perform their keystone ecological function. We further conclude that it is especially important that prairie dogs be sufficiently abundant on public lands to perform this function.
AMPA Receptor-Mediated, Calcium-Dependent CREB Phosphorylation in a Subpopulation of Auditory Neurons Surviving Activity Deprivation

Although dependence on afferent synaptic activity has been shown for central neurons in every sensory system, the mechanisms of afferent maintenance of target sensory neurons are not understood. Neurons in the cochlear nucleus (CN) require afferent activity for maintenance and survival. One of the earliest changes seen after activity deprivation is an increase in intracellular calcium that leads to the death of 30% of the neuronal population. Sixty minutes after deafferentation, the surviving neurons show increased phosphorylation of the transcription factor calcium/cAMP response element-binding protein (CREB). CREB phosphorylation in activity-deprived CN neurons is dependent on increased intracellular calcium resulting from influx through AMPA receptors and is mediated by calcium/calmodulin-dependent kinases and protein kinase A. We conclude that in CN neurons, the deafferentation-induced increase in calcium activates at least two kinase pathways that phosphorylate CREB in surviving neurons. We hypothesize that this phosphorylation results in the transcription of genes containing the calcium/cAMP response element within their promoter regions, and these genes code for proteins that allow the neurons to compensate for their hypercalcemic, activity-deprived state.
High-Dose Versus Conventional-Dose Continuous Venovenous Hemodiafiltration and Patient and Kidney Survival and Cytokine Removal in Sepsis-Associated Acute Kidney Injury: A Randomized Controlled Trial.

BACKGROUND Soluble inflammatory mediators are known to exacerbate sepsis-induced acute kidney injury (AKI). Continuous renal replacement therapy (CRRT) has been suggested to play a part in immunomodulation by cytokine removal. However, the effect of continuous venovenous hemodiafiltration (CVVHDF) dose on inflammatory cytokine removal and its influence on patient outcomes are not yet clear. STUDY DESIGN Prospective, randomized, controlled, open-label trial. SETTING & PARTICIPANTS Septic patients with AKI receiving CVVHDF for AKI. INTERVENTION Conventional (40mL/kg/h) and high (80mL/kg/h) doses of CVVHDF for the duration of CRRT. OUTCOMES Patient and kidney survival at 28 and 90 days, circulating cytokine levels. RESULTS 212 patients were randomly assigned into 2 groups. Mean age was 62.1 years, and 138 (65.1%) were men. Mean intervention durations were 5.4 and 6.2 days for the conventional- and high-dose groups, respectively. There were no differences in 28-day mortality (HR, 1.02; 95% CI, 0.73-1.43; P=0.9) or 28-day kidney survival (HR, 0.96; 95% CI, 0.48-1.93; P=0.9) between groups. High-dose CVVHDF, but not the conventional dose, significantly reduced interleukin 6 (IL-6), IL-8, IL-1b, and IL-10 levels. There were no differences in the development of electrolyte disturbances between the conventional- and high-dose groups. LIMITATIONS Small sample size. Only the predilution CVVHDF method was used and initiation criteria were not controlled. CONCLUSIONS High CVVHDF dose did not improve patient outcomes despite its significant influence on inflammatory cytokine removal. CRRT-induced immunomodulation may not be sufficient to influence clinical end points.
White matter fractional anisotrophy differences and correlates of diagnostic symptoms in autism.

BACKGROUND Individuals with autism have impairments in 3 domains: communication, social interaction and repetitive behaviours. Our previous work suggested early structural and connectivity abnormalities in prefrontal-striato-temporal-cerebellar networks but it is not clear how these are linked to diagnostic indices. METHOD Children with autism (IQ > 70) aged 6 to 14 years old and matched typically developing controls were studied using diffusion tensor imaging. Voxel-based methods were used to compare fractional anisotrophy (FA) measures in each group and to correlate FA measures in the autism group with the diagnostic phenotype described by the Autism Diagnostic Interview - Revised (ADI-R) algorithm for ICD-10. RESULTS After controlling for the effects of age and white matter volume, we found that FA in the autism group was significantly lower than controls in bilateral prefrontal and temporal regions, especially in the right ventral temporal lobe adjacent to the fusiform gyrus. FA was greater in autism in the right inferior frontal gyrus and left occipital lobe. We observed a tight correlation between lower FA and higher ADI-R diagnostic algorithm scores across white matter tracts extending from these focal regions of group difference. Communication and social reciprocity impairments correlated with lower FA throughout fronto-striato-temporal pathways. Repetitive behaviours correlated with white matter indices in more posterior brain pathways, including splenium of the corpus callosum and cerebellum. CONCLUSIONS Our data support the position that diagnostic symptoms of autism are associated with a core disruption of white matter development.
Label-free colorimetric detection of trace cholesterol based on molecularly imprinted photonic hydrogels

A novel colorimetric sensor for cholesterol assay was constructed by combining a molecular imprinting technique with photonic crystals. The molecularly imprinted photonic hydrogel (MIPH) film was prepared by a non-covalent, self-assembly approach using cholesterol as a template molecule, and exhibited a highly ordered three-dimensional macroporous structure characterized by scanning electron microscopy under the optimized imprinting conditions. Various factors affecting rebinding of cholesterol are discussed along with recognition specificity studies on its analogues of stigmasterol and ergosterol through estimation of UV-Vis and electrochemical impedance spectroscopy. The MIPH film generated a significantly readable optical signal directly self-reporting within less than 2 min upon binding cholesterol. The colorimetric measurement of cholesterol concentration strongly relies on the fact that the blue shift effect of the Bragg diffraction peak of the MIPH is gradually enlarged with the increase of cholesterol amounts. The detection level approached 10−13 g mL−1, which is comparable to that of fluorescence measurements. The simultaneous possession of high selectivity, high sensitivity, high stability, easy operation and being label-free enables this sensor to be potentially applicable for rapid on-site detection of trace cholesterol.
Persistent Cohomology and Circular Coordinates

Nonlinear dimensionality reduction (NLDR) algorithms such as Isomap, LLE, and Laplacian Eigenmaps address the problem of representing high-dimensional nonlinear data in terms of low-dimensional coordinates which represent the intrinsic structure of the data. This paradigm incorporates the assumption that real-valued coordinates provide a rich enough class of functions to represent the data faithfully and efficiently. On the other hand, there are simple structures which challenge this assumption: the circle, for example, is one-dimensional, but its faithful representation requires two real coordinates. In this work, we present a strategy for constructing circle-valued functions on a statistical data set. We develop a machinery of persistent cohomology to identify candidates for significant circle-structures in the data, and we use harmonic smoothing and integration to obtain the circle-valued coordinate functions themselves. We suggest that this enriched class of coordinate functions permits a precise NLDR analysis of a broader range of realistic data sets.
Characterization and applications of new electrochromic devices: comparison with other electrically controllable transmittance technologies

Electrochromic (EC) materials are able to change their optical properties, such as color, in a persistent and reversible way under the action of a voltage pulse or a small constant value. Nowadays, electrochromic devices (ECD) are, with suspended particle devices (SPD), polymer dispersed liquid crystals (PDLC) and micro-blinds, the four electrically controllable smart windows technologies. Not only used for optical appearance purposes, the use of such technologies could reduce the cost of heating, air-conditioning and lighting by the energy savings that can be accomplished in buildings and vehicles, places where modern people use to spend around 90% of their time. These variable transmittance technologies allow the optical switching from a transparent or bleached state to a colored, darken or in another case to translucent state by different operation principles. In all the cases these technologies require the use of transparent conductors. Other applications of these technologies, besides windows are found on mirrors and displays. ECDs for architectural applications incorporate solid EC films and consist of a thin multi-layer assembly that is typically sandwiched between two panes of glass. Coloration of solid anodic films rely on upon electrochemical oxidation or cathodic films upon electrochemical reduction, involving transfer of ions into and out of the EC films, which requires a component where ions can be stored. Among the materials showing electrochromism effect it can be found transition metal oxides (TMOs), Prussian Blue (PB) systems, viologens, conductive polymers and rare earth metals. Regarding the 2nd smart windows technology in the list, SPD incorporates an active layer that contains needle-shaped dipole particles that are uniformly distributed in an organic fluid or film. The active layer is laminated of filled between two transparent conductors on polyester. The change in the optical properties is caused by the motion and orientation of dispersed particles relative to a fluid under the application of an AC electrical potential of high amplitude. Smart windows LC technology has already been used in buildings and several LC glass products are available in the market. PDLC, the LC glazing, consists of two outer layers of polyester that are coated with a transparent conductor and a polyester matrix that contains the LCs. When no voltage is applied, the LC molecule chains are randomly scattered and LC system is translucent opal white, showing a milky appearance. When a voltage is applied, the molecules align with the lines of the electric field and the film appears almost transparent. In this work, different samples of new ECDs, SPDs and PDLCs were electro-optically characterized. ECD and PDLC samples were developed by CIDETEC, the Center of Electrochemical Research and Development of San Sebastian (Spain). -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
LTE under the High-Speed-Train Channel Model

Long Term Evolution (LTE) is considered as a future technology for railway communications. In this work we provide an overview of the main channel models developed during the last years, including the High-Speed Train (HST) channel model defined for LTE conformance tests. A standard-compliant implementation of the transmitter, the HST channel model, and the receiver of a single-antenna LTE downlink physical layer was developed to evaluate its performance under the HST channel model. Results show that Doppler shifts dramatically impact on the receiver for speeds as low as 15 km/h, demanding for fast Doppler compensation methods. Additionally, more realistic channel models considering viaducts, tunnels, hilly terrain, and urban scenarios are also required.
Electroless Deposition of Palladium and Platinum

Much effort has been invested in the development ofmethods for electroless plating of palladium and platinum alongside the rapid technological growth in the electronics industry. In particular, it is the communication industry that requires electroless palladium plating, since it yields uniform deposits on minute integrated circuitry made of intricate design and provides stable contact surfaces for conductors which operate at elevated temperatures. Palladium coating is useful as a substitute for gold coating and also as diffusion barrier layers between gold coating and copper or silver substrate in the electronics industry. The utility of palladium coating is attributable to its good corrosion resistance, low contact resistance, and last but not least relatively lower price. It was recognized by Brenner [1] that electroless deposition of palladium is possible but also that the progress toward homogeneous deposition of palladium results in a high degree of instability of the deposition bath. Fortunately, today the instability of electroless palladium baths can be controlled by a proper selection of additives. On the other hand, there are only a small number of reports available about the electroless plating of platinum as compared to electroless palladium plating at least up to the 1990s. Since that time there has been significant progress in the field of fuel cell technology (particularly during the late 1990s); many studies have been reported regarding the electroless deposition of nanoscale particles of platinum or platinum alloys on special materials, for example, carbon powder, carbon paper, carbon nanotubes, and Nafion (perfluorosulfonic acid polymer), as well as the deposition of palladiumon porous electrodes of fuel cells. Recently Rao and Trivedi [2] reviewed past studies of the electroless and electrochemical deposition of platinum group metals and their applications. In this chapter, electroless palladium and platinum plating baths and thematerials used as substrate are briefly reviewed.
Epidemiology of seasonal and perennial rhinitis: clinical presentation and medical history.

BACKGROUND: Little is known about the epidemiology of rhinitis, particularly the perennial and non-allergic forms. The aim of this study was to compare the symptoms, atopic state, and medical history of individuals with seasonal and perennial rhinitis. DESIGN: Of 7702 adults aged 16-65 years registered with a London general practice, 2969 (30%) were screened by postal questionnaire. Samples of 113 subjects without rhinitis, 51 with seasonal symptoms alone, 128 with perennial symptoms and seasonal exacerbations were then interviewed. Atopic and non-atopic subjects were distinguished by skinprick testing with five common allergens. RESULTS: The estimated minimum prevalence of rhinitis was 24%: 3% had seasonal symptoms only, of whom 78% were atopic; 13% had perennial symptoms only, of whom 50% were atopic; and 8% had perennial symptoms with seasonal exacerbations, of whom 68% were atopic. Seasonal rhinitis was characterised by sneezing, itching, and a high prevalence of diurnal variation in symptoms. The most common provoking factors were dust, pollens, and infections. By comparison, perennial rhinitis was characterised by a higher prevalence of nasal blockage and catarrh, and a lower prevalence of diurnal variation and provocation by pollen. There were no significant differences among the groups in the sociodemographic characteristics examined. Subjects with seasonal rhinitis were more likely to be atopic and to have eczema and a family history of hayfever than those without rhinitis. Those with perennial rhinitis were more likely to have past or current eczema or migraine, be wheezy or labelled asthmatic, or have a family history of nose trouble other than hayfever. Subjects with both seasonal and perennial symptoms presented an intermediate clinical picture. CONCLUSIONS: Seasonal and perennial rhinitis differ in their atopic state, clinical presentation, and medical history. The extent to which these differences are genetically or environmentally determined requires further investigation.
High-Q and wide dynamic range inertial MEMS for north-finding and tracking applications

We report high-Q and wide dynamic range MEMS gyroscopes and accelerometers for development of an IMU capable of north finding and tracking. The vacuum sealed SOI gyroscope utilizes symmetric quadruple mass architecture with measured quality factors of 1.2 million and proven sub-°/hr Allan deviation of bias. The true north detection was accomplished in conventional amplitude modulated (AM) rate mode and showed 3 milliradian measurement uncertainty. The north (azimuth) tracking necessitates a wide dynamic range, for which the same QMG transducer is switched to a frequency modulated (FM) modality. The test results for FM operation experimentally demonstrated a wide linear input rate range of 18,000 °/s and inherent self-calibration against temperature changes. Vertical alignment is possible using resonant accelerometers with a projected bias error of 5 μg and self-calibration against temperature variations, enabled by differential frequency measurements. We believe the developed low dissipation inertial MEMS with interchangeable AM/FM modalities may enable wide dynamic range IMUs for north-finding and inertial guidance applications previously limited to optical and quartz systems.
A New Performance Index for the Repetitive Motion of Mobile Manipulators

A mobile manipulator is a robotic device composed of a mobile platform and a stationary manipulator fixed to the platform. To achieve the repetitive motion control of mobile manipulators, the mobile platform and the manipulator have to realize the repetitive motion simultaneously. To do so, a novel quadratic performance index is, for the first time, designed and presented in this paper, of which the effectiveness is analyzed by following a neural dynamics method. Then, a repetitive motion scheme is proposed by combining the criterion, physical constraints, and integrated kinematical equations of mobile manipulators, which is further reformulated as a quadratic programming (QP) subject to equality and bound constraints. In addition, two important Bridge theorems are established to prove that such a QP can be converted equivalently into a linear variational inequality, and then equivalently into a piecewise-linear projection equation (PLPE). A real-time numerical algorithm based on PLPE is thus developed and applied for the online solution of the resultant QP. Two tracking-path tasks demonstrate the effectiveness and accuracy of the repetitive motion scheme. In addition, comparisons between the nonrepetitive and repetitive motion further validate the superiority and novelty of the proposed scheme.
Weight Change Is Associated With Change in Arterial Stiffness Among Healthy Young Adults

Risk factors for arterial stiffness progression have not been well characterized. We examined the relationship between arterial stiffness progression and body weight and weight gain in a group of healthy young adults. Aortic pulse-wave velocity was assessed at 2 time points approximately 2 years apart in 152 white and black adults aged 20 to 40 years, and was standardized by the time between visits to obtain annualized pulse-wave velocity changes. Blacks had 15.5 cm/s per year larger annual pulse-wave velocity increases compared with whites (P=0.02), even after multivariable adjustment for weight and blood pressure changes. Larger annual pulse-wave velocity increases were also associated with larger baseline body weight (P=0.02), waist girth (P=0.003), and body mass index (P<0.001), and greater annual weight gain (P=0.02), after adjustment for baseline pulse-wave velocity. After multivariable adjustment that included blood pressure changes, larger baseline waist girth (P=0.009), baseline body mass index (P=0.001), body mass index increase (P=0.037), and weight gain (P=0.017) remained significantly associated with larger annual pulse-wave velocity progression. Weight change showed a direct relationship with pulse-wave velocity change; mean annual pulse-wave velocity changes were −29.9 cm/s per year (regression) for those with ≥4.5 kg annual weight loss and 18.2 cm/s per year (progression) for those with ≥4.5 kg annual weight gain. These data show strong associations between weight gain and arterial stiffness progression, as well as between weight loss and arterial stiffness regression. These data greatly underscore the vascular benefit of weight loss. Successful weight loss programs in young adults, particularly blacks, are needed.