Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing novel applications of mycelium based bio-composite materials for design and architecture

The growing need of the industry for alternative materials and products that are biodegradable and derived from renewable resources has recently led researchers from varied fields to search for more sustainable alternatives, and develop natural biocomposites to replace varied petroleum-based products in order to reduce the intolerable stress on the planet environment. In this research, the natural ability of saprophytic fungi to bind and digest lingo-cellulose, is utilized to develop natural bio-composite materials for novel applications in design and architecture. Previous research has shown a potential to develop products such as packaging, building and insulation materials, leather-like, textile and transparent edible films. However, no research has been found in which all the significant variables were systematically tested. In this work, several fungi species were grown on varied local agricultural-growth wastes to evaluate which pair of fungi-plant material features the most suitable combination for future applications. The fungi; Pleurotus pulmonarius, Pleurotus ostreatus, Pleurotus salmoneostramineus and Aaegerita agrocibe where grown on woodchips of Eucalyptus, Oak, Pine, Apple and vine. The samples were tested for selected properties, including chemical changes in organic matter (pH, electric conductivity, water, carbon and nitrogen contents), mycelium growth rate, density and quality impression. By examining these fundamental materials characteristics, we aim to achieve a thorough understanding of the structural and aesthetic opportunities that this novel bio-material should offer. The current stage of the research shows that the most efficient integrations where the samples of P. ostreatus grown on Apple or Vine woodchips. Future work will focus on using suitable analytical methods for further understanding of the changes in mycelium and plant structures during the digestion process, and locating essential variable parameters of previous and post processing, to achieve desired material properties and introduce innovative characteristics and functions over existing industrial products and applications.
Leptin and Leptin Resistance in the Pathogenesis of Obstructive Sleep Apnea: A Possible Link to Oxidative Stress and Cardiovascular Complications

Obesity-related sleep breathing disorders such as obstructive sleep apnea (OSA) and obesity hypoventilation syndrome (OHS) cause intermittent hypoxia (IH) during sleep, a powerful trigger of oxidative stress. Obesity also leads to dramatic increases in circulating levels of leptin, a hormone produced in adipose tissue. Leptin acts in the hypothalamus to suppress food intake and increase metabolic rate. However, obese individuals are resistant to metabolic effects of leptin. Leptin also activates the sympathetic nervous system without any evidence of resistance, possibly because these effects occur peripherally without a need to penetrate the blood-brain barrier. IH is a potent stimulator of leptin expression and release from adipose tissue. Hyperleptinemia and leptin resistance may upregulate generation of reactive oxygen species, increasing oxidative stress and promoting inflammation. The current review summarizes recent data on a possible link between leptin and oxidative stress in the pathogenesis of sleep breathing disorders.
A matching approach to business services and software services

Recent studies have shown that service-oriented architecture (SOA) has the potential to revive enterprise legacy systems (Cai et al., 2011; Gasevic and Hatala, 2010; De Castro et al., 2011; Chengjun, 2008; Elgedawy, 2009; Tian et al., 2007; Chen et al., 2009; Zhang et al., 2006; Sindhgatta and Ponnalagu, 2008; Khadka, 2011), making their continued service in the corporate world viable. In the process of reengineering legacy systems to service-oriented architecture, some software services extracted in legacy systems can be reused to implement business services in target systems. In order to achieve efficient reuse to software services, a matching approach is proposed to extract the software services related to specified business services, where service semantics and structure similarity measures are integrated to evaluate the similarity degree between business service and software services. Experiments indicate that the approach can efficiently map business services to relevant software services, and then legacy systems can be reused as much as possible.
Shortened therapy of eight weeks with paritaprevir/ritonavir/ombitasvir and dasabuvir is highly effective in people with recent HCV genotype 1 infection

Paritaprevir/ritonavir/ombitasvir and dasabuvir with or without ribavirin for 12 weeks are approved for treatment of chronic HCV genotype 1 infection. This study assessed the efficacy of shortened duration paritaprevir/ritonavir/ombitasvir and dasabuvir with or without ribavirin for 8 weeks among people with recent HCV infection. In this open‐label single‐arm trial conducted in Australia, England and New Zealand, adults with recent HCV (duration of infection <12 months) received paritaprevir/ritonavir/ombitasvir and dasabuvir (with weight‐based ribavirin for genotypes 1a and 1, no subtype) for 8 weeks. The primary endpoint was sustained virological response at 12 weeks post‐treatment (SVR12) in the intention‐to‐treat (ITT) population. Thirty people (median age 38 years, male 93%) commenced treatment (with ribavirin, 97%), of whom 77% (n = 23) were HIV‐positive, 93% (n = 28) had genotype 1a infection and 53% (n = 16) had ever injected drugs. Median maximum ALT in the preceding 12 months was 433 IU/L (IQR 321, 1012). Acute clinical hepatitis with ALT > 10 x ULN was documented in 83% (n = 25); one participant (3%) had jaundice. At baseline, median estimated duration of infection was 30 weeks (range 11, 51), and median HCV RNA was 5.7 log10 IU/mL (range 2.7, 7.3). SVR12 was achieved in 97% (29/30; early discontinuation at week 2, n = 1; per protocol 100%, 29/29). No relapse or reinfection was observed. In conclusion, paritaprevir/ritonavir/ombitasvir and dasabuvir (with ribavirin) for eight weeks were highly effective among HIV‐positive and HIV‐negative individuals with recent HCV infection. These data support the use of this shortened duration direct‐acting antiviral regimen in this population.
A BCMP network approach to modeling and controlling autonomous mobility-on-demand systems

In this paper we present a queuing network approach to the problem of routing and rebalancing a fleet of self-driving vehicles providing on-demand mobility within a capacitated road network. We refer to such systems as autonomous mobility-on-demand (AMoD) systems. We first cast an AMoD system into a closed, multi-class Baskett–Chandy–Muntz–Palacios (BCMP) queuing network model capable of capturing the passenger arrival process, traffic, the state-of-charge of electric vehicles, and the availability of vehicles at the stations. Second, we propose a scalable method for the synthesis of routing and charging policies, with performance guarantees in the limit of large fleet sizes. Third, we explore the applicability of our theoretical results on a case study of Manhattan. Collectively, this paper provides a unifying framework for the analysis and control of AMoD systems, which provides a large set of modeling options (e.g. the inclusion of road capacities and charging constraints), and subsumes earlier Jackson and network flow models.
Residual Recurrent Neural Networks for Learning Sequential Representations

Recurrent neural networks (RNN) are efficient in modeling sequences for generation and classification, but their training is obstructed by the vanishing and exploding gradient issues. In this paper, we reformulate the RNN unit to learn the residual functions with reference to the hidden state instead of conventional gated mechanisms such as long short-term memory (LSTM) and the gated recurrent unit (GRU). The residual structure has two main highlights: firstly, it solves the gradient vanishing and exploding issues for large time-distributed scales; secondly, the residual structure promotes the optimizations for backward updates. In the experiments, we apply language modeling, emotion classification and polyphonic modeling to evaluate our layer compared with LSTM and GRU layers. The results show that our layer gives state-of-the-art performance, outperforms LSTM and GRU layers in terms of speed, and supports an accuracy competitive with that of the other methods.
The Spatial and Temporal Variability of Air-Sea CO2 Fluxes and the Effect of Net Coral Reef Calcification in the Indonesian Seas: A Numerical Sensitivity Study

A numerical model system was developed and applied to simulate air-sea fluxes of CO2 and coral reef calcification in the Indonesian Seas and adjacent ocean basin for the period 1960 to 2014 on a fine resolution grid (ca. 11 km) in order to study their response to rising sea water temperatures and CO2 concentrations in the atmosphere. Results were analyzed for different sub-regions on the Sunda Shelf (Gulf of Thailand, Malacca Strait, Java Sea) and show realistic and different levels, signs and pronounced temporal variability in air-sea CO2 flux. The Gulf of Thailand changes from an atmospheric CO2 sink during the boreal winter to a CO2 source in summer due to higher water temperatures, while other sub-regions as well as the entire averaged Sunda Shelf act as a continuous source of CO2 for the atmosphere. However, increasing atmospheric CO2 concentrations weakened this source function during the simulation period. In 2007, the model simulations showed even a first flux inversion, in course of which the Java Sea took up CO2 . The simulated trends suggest that the entire Sunda Shelf will turn into a permanent sink for atmospheric CO2 within the next 30 to 35 years if current trends remain constant. Considering the period between 2010 and 2014, coral reef calcification enhanced the average CO2 emission of the Sunda Shelf by more than 10 % from 15 to 17 Tg C yr−1 due to lowering the pH and increasing the partial pressure of CO2 in surface water. During the entire period of simulation, net reef calcification decreased although increasing seawater temperature mitigated effects of reduced CO2 emission and the resulting decrease of the pH values on reef calcification. Our realistic simulation results already without consideration of any biological processes suggest that biological processes taking up and releasing CO 2 are currently well balanced in these tropical regions. However, the counteracting effects of climate change on the reef calcification, on other biological processes and the carbonate system need to be investigated in more detail. SST ◦increased by about 0.6 C during the last 55 years, while SSS decreased by about 0.7 psu.
Physiologic benefits of mechanical insufflation-exsufflation in children with neuromuscular diseases.

STUDY OBJECTIVES To analyze the physiologic effects and tolerance of mechanical insufflation-exsufflation (MI-E) by means of mechanical cough assistance (Cough Assist; JH Emerson Company; Cambridge, MA) for children with neuromuscular disease. DESIGN Prospective clinical trial. SETTING Physiology laboratory of a pediatric pulmonary department of a university hospital. PATIENTS Seventeen children with Duchenne muscular dystrophy (n = 4), spinal muscular atrophy (n = 4), or other congenital myopathy (n = 9) who were in a stable state. INTERVENTIONS Pressures of 15, 30, and 40 cm H(2)O were cycled to each patient, with 2 s for insufflation and 3 s for exsufflation. One application consisted of six cycles at each pressure for a total of three applications. MEASUREMENTS AND RESULTS Airway pressure and airflow were measured during every application. Breathing pattern, vital capacity (VC), sniff nasal inspiratory pressure (SNIP), peak expiratory flow (PEF), and respiratory comfort were evaluated at baseline and after each application. The tolerance of the patients was excellent, with a significant increase in the respiratory comfort score in all of the patients (p = 0.02). Expired volume during the MI-E application increased significantly to reach twice the VC at 40 cm H(2)O. Mean and maximal inspiratory and expiratory flows increased in a pressure-dependent manner. Breathing pattern did not change after the MI-E applications and pulse oximetric saturation remained stable within normal values, but the mean end-tidal carbon dioxide pressure decreased significantly. VC did not change, but the mean SNIP and PEF improved significantly after MI-E applications. CONCLUSIONS Our results confirm the good tolerance and physiologic short-term benefit of the MI-E in children with neuromuscular disease who were in a stable state.
Numerical simulation of the geometrical-optics reduction of CE2 and comparisons to quasilinear dynamics.

Zonal flows have been observed to appear spontaneously from turbulence in a number of physical settings. A complete theory for their behavior is still lacking. Recently, a number of studies have investigated the dynamics of zonal flows using quasilinear theories and the statistical framework of a second-order cumulant expansion (CE2). A geometrical-optics (GO) reduction of CE2, derived under an assumption of separation of scales between the fluctuations and the zonal flow, is studied here numerically. The reduced model, CE2-GO, has a similar phase-space mathematical structure to the traditional wave-kinetic equation, but that wave-kinetic equation has been shown to fail to preserve enstrophy conservation and to exhibit an ultraviolet catastrophe. CE2-GO, in contrast, preserves nonlinear conservation of both energy and enstrophy. We show here how to retain these conservation properties in a pseudospectral simulation of CE2-GO. We then present nonlinear simulations of CE2-GO and compare with direct simulations of quasilinear (QL) dynamics. We find that CE2-GO retains some similarities to QL. The partitioning of energy that resides in the zonal flow is in good quantitative agreement between CE2-GO and QL. On the other hand, the length scale of the zonal flow does not follow the same qualitative trend in the two models. Overall, these simulations indicate that CE2-GO provides a simpler and more tractable statistical paradigm than CE2, but CE2-GO is missing important physics.
Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions

The growth plate mediates bone growth where SOX9 and GLI factors control chondrocyte proliferation, differentiation and entry into hypertrophy. FOXA factors regulate hypertrophic chondrocyte maturation. How these factors integrate into a Gene Regulatory Network (GRN) controlling these differentiation transitions is incompletely understood. We adopted a genome-wide whole tissue approach to establish a Growth Plate Differential Gene Expression Library (GP-DGEL) for fractionated proliferating, pre-hypertrophic, early and late hypertrophic chondrocytes, as an overarching resource for discovery of pathways and disease candidates. De novo motif discovery revealed the enrichment of SOX9 and GLI binding sites in the genes preferentially expressed in proliferating and prehypertrophic chondrocytes, suggesting the potential cooperation between SOX9 and GLI proteins. We integrated the analyses of the transcriptome, SOX9, GLI1 and GLI3 ChIP-seq datasets, with functional validation by transactivation assays and mouse mutants. We identified new SOX9 targets and showed SOX9-GLI directly and cooperatively regulate many genes such as Trps1, Sox9, Sox5, Sox6, Col2a1, Ptch1, Gli1 and Gli2. Further, FOXA2 competes with SOX9 for the transactivation of target genes. The data support a model of SOX9-GLI-FOXA phasic GRN in chondrocyte development. Together, SOX9-GLI auto-regulate and cooperate to activate and repress genes in proliferating chondrocytes. Upon hypertrophy, FOXA competes with SOX9, and control toward terminal differentiation passes to FOXA, RUNX, AP1 and MEF2 factors.
Prolonged life span among endemic Gasterosteus populations

Throughout their circumboreal coastal distribution, the threespine stickleback (Gasterosteus aculeatus L., 1758) typically reproduce at 1 or 2 years of age (second or third summer) and die during the year of the reproductive cycle. Extending from a previous study on the Haida Gwaii archipelago, western Canada, that identified an exceptionally long life span (8 years) in a population of large-bodied threespine stickleback, we use pelvic spine annuli to examine age of the five largest adult stickleback of 12 additional populations comprising five populations with average-sized adults (45–60 mm standard length (SL)) and seven populations with large-bodied adult stickleback (>75 mm SL). Each of the small-bodied populations had a maximum age of 1 or 2 years typical for the taxon. Among the large-bodied populations, which also reached adult size in the 2nd year, adult stickleback in the populations ranged from 3 to 6 years, indicating extended longevity. Low productivity habitats and refuge against gape-limited piscivores, each of which theoretically predicts reduced rate of senescence, are associated with the greatest longevity among these populations. These data combined with the recent full genome sequence for stickleback provide opportunities for locating genetic markers for extended longevity. Resume : Dans l’ensemble de leur repartition cotiere circumboreale, les epinoches a trois epines (Gasterosteus aculeatus L., 1758) se reproduisent typiquement a l’âge de 1 ou 2 ans (deuxieme ou troisieme ete) et meurent durant l’annee de leur cycle reproductif. En prolongement d’une etude anterieure sur l’archipel Haida Gwaii, dans l’Ouest canadien, qui a decouvert des durees de vie exceptionnellement longues (8 ans) chez une population de grande taille d’epinoche a trois epines, nous utilisons les annulus de l’epine pelvienne pour determiner l’âge des cinq epinoches adultes les plus grandes de 12 populations additionnelles, dont cinq populations avec des adultes de taille moyenne (longueur standard (SL) 45–60 mm) et sept populations a adultes de grande taille (SL >75 mm). Chacune des populations de petite taille a l’âge maximal de 1 ou 2 ans typique du taxon. Parmi les populations de grande taille, qui atteignent aussi leur taille adulte la seconde annee, l’âge des epinoches adultes dans la population varie de 3 a 6 ans, ce qui represente une extension de la longevite. Il y a une association entre les habitats de faible productivite et les refuges contre les predateurs a ouverture de bouche limitee, des facteurs qui tous deux peuvent theoriquement predire un taux reduit de senescence, et les longevites maximales dans ces populations. Ces donnees combinees au sequencage complet recent de l’epinoche fournissent des occasions pour identifier les marqueurs genetiques de la longevite prolongee. [Traduit par la Redaction]
A general prediction model for the detection of ADHD and Autism using structural and functional MRI

This work presents a novel method for learning a model that can diagnose Attention Deficit Hyperactivity Disorder (ADHD), as well as Autism, using structural texture and functional connectivity features obtained from 3-dimensional structural magnetic resonance imaging (MRI) and 4-dimensional resting-state functional magnetic resonance imaging (fMRI) scans of subjects. We explore a series of three learners: (1) The LeFMS learner first extracts features from the structural MRI images using the texture-based filters produced by a sparse autoencoder. These filters are then convolved with the original MRI image using an unsupervised convolutional network. The resulting features are used as input to a linear support vector machine (SVM) classifier. (2) The LeFMF learner produces a diagnostic model by first computing spatial non-stationary independent components of the fMRI scans, which it uses to decompose each subject’s fMRI scan into the time courses of these common spatial components. These features can then be used with a learner by themselves or in combination with other features to produce the model. Regardless of which approach is used, the final set of features are input to a linear support vector machine (SVM) classifier. (3) Finally, the overall LeFMSF learner uses the combined features obtained from the two feature extraction processes in (1) and (2) above as input to an SVM classifier, achieving an accuracy of 0.673 on the ADHD-200 holdout data and 0.643 on the ABIDE holdout data. Both of these results, obtained with the same LeFMSF framework, are the best known, over all hold-out accuracies on these datasets when only using imaging data—exceeding previously-published results by 0.012 for ADHD and 0.042 for Autism. Our results show that combining multi-modal features can yield good classification accuracy for diagnosis of ADHD and Autism, which is an important step towards computer-aided diagnosis of these psychiatric diseases and perhaps others as well.
Detection of Periodic Orbits in Hamiltonian Systems Using Lagrangian Descriptors

The purpose of this paper is to apply Lagrangian Descriptors, a concept used to describe phase space structure, to autonomous Hamiltonian systems with two degrees of freedom in order to detect periodic solutions. We propose a method for Hamiltonian systems with saddle-center equilibrium and apply this approach to the classical Henon–Heiles system. The method was successful in locating the unstable Lyapunov orbits in phase space.
The Physical Behavior of Stabilised Soft Clay by Electrokinetic Stabilisation Technology

Electrokinetic Stabilisation (EKS) technology is the combination processes of electroosmosis and chemical grouting. This technique is most effective in silty and clayey soils where the hydraulic conductivity is very low. Stabilising agents will assist the EKS treatment by inducing it into soil under direct current. The movement of stabilising agents into soil is governed by the principle of electrokinetics. The aim of this study is to evaluate the physical behavior of soft soil using the EKS technology as an effective method to strengthen soft clay soils with calcium chloride (CaCl2) as the stabilising agent. Stainless steel plates were used as the electrodes, while 1.0 mol/l of CaCl2 was used as the electrolyte that fed at the anode compartment. Soft marine clay at Universiti Tun Hussein Onn Malaysia was used as the soil sample. The EKS treatment was developed at Research Centre for Soft Soil (RECESS), UTHM with a constant voltage gradient (50 V/m) in 21 days. The result shows that the shear strength of treated soil was increased across the soil sample. The treated soil near the cathode showed the highest value of shear strength (24.5 – 33 kPa) compared with the anode and in the middle of the soil sample.
A review of methods to study hydration effects on cartilage friction

The mechanical and tribological responses of cartilage depend strongly on its hydration state, which is a function of the mechanical and tribological conditions of the contact. The interdependencies between stresses and water content make controlled studies of cartilage function difficult. This paper reviews some of the experimental challenges in cartilage tribology and the methods we have used to help address them. For example, we demonstrate a simple method to eliminate the frictional errors associated with sample curvature in the migrating contact area and show how in situ measurements can be used to assess hydration and its effect on friction. Finally, we demonstrate a new explant testing configuration, the convergent stationary contact area (cSCA), in which cartilage loses, maintains and recovers interstitial water in response to loading and sliding in a manner consistent with in vivo joint mechanics. We propose that the cSCA provides an ideal test bed for studying cartilage tribology, while maximising experimental control and physiological relevance.