A finite-volume scheme for gradient-flow equations with non-homogeneous diffusion

We develop a first- and second-order finite-volume scheme to solve gradient flow equations with non-homogeneous properties, obtained in the framework of dynamical-density functional theory. The scheme takes advantage of an upwind approach for the space discretization to ensure positivity of the density under a CFL condition and decay of the discrete free energy. Our computational approach is used to study several one- and two-dimensional systems, with a general free-energy functional accounting for external fields and inter-particle potentials, and placed in non-homogeneous thermal baths characterized by anisotropic, space-dependent and time-dependent properties

Preseason Training Improves Perception of Fatigue and Recovery From a Futsal Training Session.

Purpose: To compare the posttraining recovery timeline of elite Brazilian futsal athletes before (Pre-PS) and after 10 weeks of the preseason (Post-PS) period of high-intensity technical–tactical training. Methods: At the start (n = 13) and at the end of the preseason (n = 7), under-20 male futsal players undertook fitness testing for maximal aerobic power, the countermovement jump (CMJ), and the 10-m sprint with change of direction. Furthermore, at both Pre-PS and Post-PS, the players participated in a training session where performance and psychophysiological measures were recorded before, immediately, 3, 24, and 48 hours postsession. The measures included CMJ, 10-m sprint, creatine kinase, Total Quality Recovery Scale, and Brunel Mood Scale. Effect size (ES) analyses compared fitness and posttraining recovery values for each parameter at Pre-PS versus Post-PS. Results: Only trivial ES (−0.02 to 0.11) was evident in maximal aerobic power, CMJ, and 10-m sprint at Post-PS compared with Pre-PS. For the timeline of recovery, only trivial and small ESs were evident for the 10-m sprint (−0.12 to 0.49), though CMJ recovery was improved at 3 hours (0.87) and 48 hours (1.27) at Post-PS and creatine kinase was lower at 48 hours (−1.33) at Post-PS. Perception of recovery was improved in Post-PS at 3 hours (1.50) and 24 hours postsession (0.92). Furthermore, perception of effort was lower immediately after the session (−0.29), fatigue was lower at 3 hours (−0.63), and vigor responses were improved in all postseason assessments (0.59 to 1.13). Conclusion: Despite minimal changes in fitness, preseason training attenuated players' perception of effort and fatigue and improved their recovery profile following a high-intensity technical–tactical training session

Lower Left Ventricular Ejection Fraction Relates to Cerebrospinal Fluid Biomarker Evidence of Neurodegeneration in Older Adults

BACKGROUND: Subclinical cardiac dysfunction is associated with decreased cerebral blood flow, placing the aging brain at risk for Alzheimer's disease (AD) pathology and neurodegeneration. OBJECTIVE: This study investigates the association between subclinical cardiac dysfunction, measured by left ventricular ejection fraction (LVEF), and cerebrospinal fluid (CSF) biomarkers of AD and neurodegeneration. METHODS: Vanderbilt Memory & Aging Project participants free of dementia, stroke, and heart failure (n = 152, 72±6 years, 68% male) underwent echocardiogram to quantify LVEF and lumbar puncture to measure CSF levels of amyloid-β42 (Aβ42), phosphorylated tau (p-tau), and total tau (t-tau). Linear regressions related LVEF to CSF biomarkers, adjusting for age, sex, race/ethnicity, education, Framingham Stroke Risk Profile, cognitive diagnosis, and apolipoprotein E ɛ4 status. Secondary models tested an LVEF x cognitive diagnosis interaction and then stratified by diagnosis (normal cognitive (NC), mild cognitive impairment (MCI)). RESULTS: Higher LVEF related to decreased CSF Aβ42 levels (β= -6.50, p = 0.04) reflecting greater cerebral amyloid accumulation, but this counterintuitive result was attenuated after excluding participants with cardiovascular disease and atrial fibrillation (p = 0.07). We observed an interaction between LVEF and cognitive diagnosis on CSF t-tau (p = 0.004) and p-tau levels (p = 0.002), whereas lower LVEF was associated with increased CSF t-tau (β= -9.74, p = 0.01) and p-tau in the NC (β= -1.41, p = 0.003) but not MCI participants (p-values>0.13). CONCLUSIONS: Among cognitively normal older adults, subclinically lower LVEF relates to greater molecular evidence of tau phosphorylation and neurodegeneration. Modest age-related changes in cardiovascular function may have implications for pathophysiological changes in the brain later in life

Management of a South African family with retinitis pigmentosa—should potential therapy influence translational research protocols?

Mutation analysis of retinal candidate genes is performed as part of an ongoing research to identify the causative genetic defect in South African families with retinal degenerative disorders (RDDs). A translational research protocol has been established whereby probands are counseled and given their molecular genetic results to take back to other family members, who can then request individual diagnostic testing. A Thr17Met mutation of the rhodopsin gene was identified in a Caucasian South African family with autosomal dominant retinitis pigmentosa. Patients with this mutation appear to benefit from treatment using oral vitamin A supplementation. This family has been informed that a molecular diagnosis is available; however, one individual has refused testing and none of the younger generation has shown interest in receiving molecular results or genetic counseling. Adapting the established protocol for the translation of RDD research results and contacting mutation positive individuals may be justifiable in light of the potential benefit of therapy

Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison

In vivo performance of hierarchical HRP-crosslinked silk fibroin/β-TCP scaffolds for osteochondral tissue regeneration

Background: Osteochondral defects (OCD) can affect the articular cartilage and subchondral bone tissues, which requires superior therapies for the simultaneous and full restoration of such structurally and biologically different tissues. Methods: Tissue engineered OC grafts were prepared using a horseradish peroxidase (HRP) approach to crosslink silk fibroin (HRP-SF) as the articular cartilage-like layer and an underlying HRP-SF/ZnSrTCP subchondral bone-like layer (HRP-SF/dTCP), through salt-leaching/freeze-drying methodologies. In vivo OC regeneration was assessed by implantating the hierarchical scaffolds in rabbit critical size OC defects, during 8 weeks. A comparative analysis was performed using hierarchical OC grafts made of pure β-TCP (HRP-SF/TCP). Results: The hierarchical scaffolds showed good integration into the host tissue and no signs of acute inflammatory reaction, after 8 weeks of implantation. The histological analyses revealed positive collagen type II and glycosaminoglycansâ formation in the articular cartilage-like layer. New bone ingrowthâ s and blood vessels infiltration were detected in the subchondral bone-like layers. Conclusions: The proposed hierarchical scaffolds presented an adequate in vivo response with cartilage tissue regeneration and calcified tissue formation specially promoted by the ionic incorporation into the subchondral bone layer, confirming the hierarchical structures as suitable for OCD regeneration.Portuguese Foundation for Science and Technology for the Hierarchitech project (M-era-Net/0001/2014), for the fellowships (SFRH/BD/99555/2014) and (SFRH/BPD/101952/2014), and for the distinctions attributed to JMO (IF/01285/2015) and SP (CEECIND/03673/2017). Also, financial support from FCT/MCTES (Fundação para a Ciência e a Tecnologia/ Ministério Da Ciência, Tecnologia, e Ensino Superior) and fundo social europeu através do programa operacional do capital humano (FSE/POCH), PD/59/2013, PD/BD/113806/201

Inactivation of VCP/ter94 Suppresses Retinal Pathology Caused by Misfolded Rhodopsin in Drosophila

The most common Rhodopsin (Rh) mutation associated with autosomal dominant retinitis pigmentosa (ADRP) in North America is the substitution of proline 23 by histidine (RhP23H). Unlike the wild-type Rh, mutant RhP23H exhibits folding defects and forms intracellular aggregates. The mechanisms responsible for the recognition and clearance of misfolded RhP23H and their relevance to photoreceptor neuron (PN) degeneration are poorly understood. Folding-deficient membrane proteins are subjected to Endoplasmic Reticulum (ER) quality control, and we have recently shown that RhP23H is a substrate of the ER–associated degradation (ERAD) effector VCP/ter94, a chaperone that extracts misfolded proteins from the ER (a process called retrotranslocation) and facilitates their proteasomal degradation. Here, we used Drosophila, in which Rh1P37H (the equivalent of mammalian RhP23H) is expressed in PNs, and found that the endogenous Rh1 is required for Rh1P37H toxicity. Genetic inactivation of VCP increased the levels of misfolded Rh1P37H and further activated the Ire1/Xbp1 ER stress pathway in the Rh1P37H retina. Despite this, Rh1P37H flies with decreased VCP function displayed a potent suppression of retinal degeneration and blindness, indicating that VCP activity promotes neurodegeneration in the Rh1P37H retina. Pharmacological treatment of Rh1P37H flies with the VCP/ERAD inhibitor Eeyarestatin I or with the proteasome inhibitor MG132 also led to a strong suppression of retinal degeneration. Collectively, our findings raise the possibility that excessive retrotranslocation and/or degradation of visual pigment is a primary cause of PN degeneration

Emergence of Collective Territorial Defense in Bacterial Communities: Horizontal Gene Transfer Can Stabilize Microbiomes

Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment

To be or not to be a pseudogene: a molecular epidemiological approach to the mclx genes and its impact in tuberculosis

Tuberculosis presents a myriad of symptoms, progression routes and propagation patterns not yet fully understood. Whereas for a long time research has focused solely on the patient immunity and overall susceptibility, it is nowadays widely accepted that the genetic diversity of its causative agent, Mycobacterium tuberculosis, plays a key role in this dynamic. This study focuses on a particular family of genes, the mclxs (Mycobacterium cyclase/LuxR-like genes), which codify for a particular and nearly mycobacterial-exclusive combination of protein domains. mclxs genes were found to be pseudogenized by frameshift-causing insertion(s)/deletion(s) in a considerable number of M. tuberculosis complex strains and clinical isolates. To discern the functional implications of the pseudogenization, we have analysed the pattern of frameshift-causing mutations in a group of M. tuberculosis isolates while taking into account their microbial-, patient- and disease-related traits. Our logistic regression-based analyses have revealed disparate effects associated with the transcriptional inactivation of two mclx genes. In fact, mclx2 (Rv1358) pseudogenization appears to be primarily driven by the microbial phylogenetic background, being mainly related to the Euro-American (EAm) lineage; on the other hand, mclx3 (Rv2488c) presents a higher tendency for pseudogenization among isolates from patients born on the Western Pacific area, and from isolates causing extra-pulmonary infections. These results contribute to the overall knowledge on the biology of M. tuberculosis infection, whereas at the same time launch the necessary basis for the functional assessment of these so far overlooked genes.This work was supported by Fundacao para a Ciencia e Tecnologia (FCT), Portugal, and cofunded by Programa Operacional Regional do Norte (ON.2-O Novo Norte), Quadro de Referencia Estrategico Nacional (QREN), through the Fundo Europeu de Desenvolvimento Regional (FEDER), and from Projeto Estrategico - LA 26 - 2013-2014 (PEst-C/SAU/LA0026/2013). H.N.-G. received a personal FCT Grant (SFRH/BD/33902/2209). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript