Nanoflows through disordered media: a joint Lattice Boltzmann and Molecular Dynamics investigation

We investigate nanoflows through dilute disordered media by means of joint lattice Boltzmann (LB) and molecular dynamics (MD) simulations -- when the size of the obstacles is comparable to the size of the flowing particles -- for randomly located spheres and for a correlated particle-gel. In both cases at sufficiently low solid fraction, $\Phi<0.01$, LB and MD provide similar values of the permeability. However, for $\Phi > 0.01$, MD shows that molecular size effects lead to a decrease of the permeability, as compared to the Navier-Stokes predictions. For gels, the simulations highlights a surplus of permeability, which can be accommodated within a rescaling of the effective radius of the gel monomers.Comment: 4 pages, 4 figure

“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?

The traditional classification of fungal and oomycete phytopathogens into three classes – biotrophs, hemibiotrophs, or necrotrophs – is unsustainable. This study highlights multiple phytopathogen species for which these labels have been inappropriately applied. We propose a novel and reproducible classification based solely on genome-derived analysis of carbohydrate-active enzyme (CAZyme) gene content called CAZyme-Assisted Training And Sorting of -trophy (CATAStrophy). CATAStrophy defines four major divisions for species associated with living plants. These are monomertrophs (Mo) (corresponding to biotrophs), polymertrophs (P) (corresponding to necrotrophs), mesotrophs (Me) (corresponding to hemibiotrophs), and vasculartrophs (including species commonly described as wilts, rots, or anthracnoses). The Mo class encompasses symbiont, haustorial, and non-haustorial species. Me are divided into the subclasses intracellular and extracellular Me, and the P into broad and narrow host sub-classes. This gives a total of seven discrete plant-pathogenic classes. The classification provides insight into the properties of these species and offers a facile route to develop control measures for newly recognized diseases. Software for CATAStrophy is available online at https://github.com/ccdmb/catastrophy. We present the CATAStrophy method for the prediction of trophic phenotypes based on CAZyme gene content, as a complementary method to the traditional tripartite “biotroph–hemibiotroph–necrotroph” classifications that may encourage renewed investigation and revision within the fungal biology community.</p

Characterization of Knots and Links Arising From Site-specific Recombination on Twist Knots

We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three well-understood families of knots and links, and prove that given a positive integer $n$, the number of product knots and links with minimal crossing number equal to $n$ grows proportionally to $n^5$. In the (common) case of twist knot substrates whose products have minimal crossing number one more than the substrate, we prove that the types of products are tightly prescribed. Finally, we give two simple examples to illustrate how this model can help determine previously uncharacterized experimental data.Comment: 32 pages, 7 tables, 27 figures, revised: figures re-arranged, and minor corrections. To appear in Journal of Physics

Jean-Baptiste Bélanger, hydraulic engineer, researcher and academic

Jean-Baptiste BÉLANGER (1790-1874) worked as a hydraulic engineer at the beginning of his career. He developed the backwater equation to calculate gradually-varied open channel flow properties for steady flow conditions. Later, as an academic at the leading French engineering schools (Ecole Centrale des Arts et Manufactures, Ecole des Ponts et Chaussées, and Ecole Polytechnique), he developed a new university curriculum in mechanics and several textbooks including a seminal text in hydraulic engineering. His influence on his contemporaries was considerable, and his name is written on the border of one of the four facades of the Eiffel Tower. BÉLANGER's leading role demonstrated the dynamism of practicing engineers at the time, and his contributions paved the way to many significant works in hydraulics

Central Coherence in Eating Disorders: A Synthesis of Studies Using the Rey Osterrieth Complex Figure Test

Background: Large variability in tests and differences in scoring systems used to study central coherence in eating disorders may lead to different interpretations, inconsistent findings and between study discrepancies. This study aimed to address inconsistencies by collating data from several studies from the same research group that used the Rey Osterrieth Complex Figure Test (Rey Figure) in order to produce norms to provide benchmark data for future studies. Method: Data was collated from 984 participants in total. Anorexia Nervosa, Bulimia Nervosa, recovered Anorexia Nervosa, unaffected family members and healthy controls were compared using the Rey Figure. Results: Poor global processing was observed across all current eating disorder sub-groups and in unaffected relatives. There was no difference in performance between recovered AN and HC groups. Conclusions: This is the largest dataset reported in the literature and supports previous studies implicating poor global processing across eating disorders using the Rey Figure. It provides robust normative data useful for future studies

Development of the Bélanger Equation and Backwater Equation by Jean-Baptiste Bélanger (1828)

A hydraulic jump is the sudden transition from a high-velocity to a low-velocity open channel flow. The application of the momentum principle to the hydraulic jump is commonly called the Bélanger equation, but few know that Bélanger's (1828) treatise was focused on the study of gradually varied open channel flows. Further, although Bélanger understood the rapidly-varied nature of the jump flow, he applied incorrectly the Bernoulli principle in 1828, and corrected his approach 10 years later. In 1828, his true originality lay in the successful development of the backwater equation for steady, one-dimensional gradually-varied flows in an open channel, together with the introduction of the step method, distance calculated from depth, and the concept of critical flow conditions

RAS/MAPK activation is associated with reduced Tumor-infiltrating lymphocytes in Triple-Negative Breast Cancer: Therapeutic Cooperation Between MEK and PD-1/PD-L1 Immune Checkpoint Inhibitors

PURPOSE: Tumor-infiltrating lymphocytes (TIL) in the residual disease (RD) of triple-negative breast cancers (TNBC) after neoadjuvant chemotherapy (NAC) are associated with improved survival, but insight into tumor cell-autonomous molecular pathways affecting these features are lacking. EXPERIMENTAL DESIGN: We analyzed TILs in the RD of clinically and molecularly characterized TNBCs after NAC and explored therapeutic strategies targeting combinations of MEK inhibitors with PD-1/PD-L1-targeted immunotherapy in mouse models of breast cancer. RESULTS: Presence of TILs in the RD was significantly associated with improved prognosis. Genetic or transcriptomic alterations in Ras-MAPK signaling were significantly correlated with lower TILs. MEK inhibition upregulated cell surface MHC expression and PD-L1 in TNBC cells both in vivo and in vitro. Moreover, combined MEK and PD-L1/PD-1 inhibition enhanced antitumor immune responses in mouse models of breast cancer. CONCLUSIONS: These data suggest the possibility that Ras-MAPK pathway activation promotes immune-evasion in TNBC, and support clinical trials combining MEK- and PD-L1-targeted therapies. Furthermore, Ras/MAPK activation and MHC expression may be predictive biomarkers of response to immune checkpoint inhibitors

Exploring and Exploiting Disease Interactions from Multi-Relational Gene and Phenotype Networks

The availability of electronic health care records is unlocking the potential for novel studies on understanding and modeling disease co-morbidities based on both phenotypic and genetic data. Moreover, the insurgence of increasingly reliable phenotypic data can aid further studies on investigating the potential genetic links among diseases. The goal is to create a feedback loop where computational tools guide and facilitate research, leading to improved biological knowledge and clinical standards, which in turn should generate better data. We build and analyze disease interaction networks based on data collected from previous genetic association studies and patient medical histories, spanning over 12 years, acquired from a regional hospital. By exploring both individual and combined interactions among these two levels of disease data, we provide novel insight into the interplay between genetics and clinical realities. Our results show a marked difference between the well defined structure of genetic relationships and the chaotic co-morbidity network, but also highlight clear interdependencies. We demonstrate the power of these dependencies by proposing a novel multi-relational link prediction method, showing that disease co-morbidity can enhance our currently limited knowledge of genetic association. Furthermore, our methods for integrated networks of diverse data are widely applicable and can provide novel advances for many problems in systems biology and personalized medicine

Vaccines against toxoplasma gondii : challenges and opportunities

Development of vaccines against Toxoplasma gondii infection in humans is of high priority, given the high burden of disease in some areas of the world like South America, and the lack of effective drugs with few adverse effects. Rodent models have been used in research on vaccines against T. gondii over the past decades. However, regardless of the vaccine construct, the vaccines have not been able to induce protective immunity when the organism is challenged with T. gondii, either directly or via a vector. Only a few live, attenuated T. gondii strains used for immunization have been able to confer protective immunity, which is measured by a lack of tissue cysts after challenge. Furthermore, challenge with low virulence strains, especially strains with genotype II, will probably be insufficient to provide protection against the more virulent T. gondii strains, such as those with genotypes I or II, or those genotypes from South America not belonging to genotype I, II or III. Future studies should use animal models besides rodents, and challenges should be performed with at least one genotype II T. gondii and one of the more virulent genotypes. Endpoints like maternal-foetal transmission and prevention of eye disease are important in addition to the traditional endpoint of survival or reduction in numbers of brain cysts after challenge