241 research outputs found
Deep spatial context: when attention-based models meet spatial regression
We propose 'Deep spatial context' (DSCon) method, which serves for
investigation of the attention-based vision models using the concept of spatial
context. It was inspired by histopathologists, however, the method can be
applied to various domains. The DSCon allows for a quantitative measure of the
spatial context's role using three Spatial Context Measures: ,
, to distinguish whether the spatial context
is observable within the features of neighboring regions, their target values
(attention scores) or residuals, respectively. It is achieved by integrating
spatial regression into the pipeline. The DSCon helps to verify research
questions. The experiments reveal that spatial relationships are much bigger in
the case of the classification of tumor lesions than normal tissues. Moreover,
it turns out that the larger the size of the neighborhood taken into account
within spatial regression, the less valuable contextual information is.
Furthermore, it is observed that the spatial context measure is the largest
when considered within the feature space as opposed to the targets and
residuals
Microwave-assisted automated glycan assembly
Automated synthesis of DNA, RNA, and peptides provides quickly and reliably important tools for biomedical research. Automated glycan assembly (AGA) is significantly more challenging as highly branched carbohydrates require strict regio- and stereocontrol during synthesis. A new AGA synthesizer enables rapid temperature adjustment from -40 °C to +100 °C to control glycosylations at low temperature and accelerates capping, protecting group removal, and glycan modifications by using elevated temperatures. Thereby, the temporary protecting group portfolio is extended from two to four orthogonal groups that give rise to oligosaccharides with up to four branches. In addition, sulfated glycans and unprotected glycans can be prepared. The new design reduces the typical coupling cycles from 100 min to 60 min while expanding the range of accessible glycans. The instrument drastically shorten and generalizes the synthesis of carbohydrates for use in biomedical and material science
VaporSPOT : parallel synthesis of oligosaccharides on membranes
Automated chemical synthesis has revolutionized synthetic access to biopolymers in terms of simplicity and speed. While automated oligosaccharide synthesis has become faster and more versatile, the parallel synthesis of oligosaccharides is not yet possible. Here, a chemical vapor glycosylation strategy (VaporSPOT) is described that enables the simultaneous synthesis of oligosaccharides on a cellulose membrane solid support. Different linkers allow for flexible and straightforward cleavage, purification, and characterization of the target oligosaccharides. This method is the basis for the development of parallel automated glycan synthesis platforms
STABILIZATION OF NON ISOTHERMAL CHEMICAL REACTORS USING TWO THERMODYNAMIC LYAPUNOV FUNCTIONS
The main goal of this paper is to introduce a link between the thermodynamics and control systems theory. More precisely, the paper focuses on Lyapunov based control of process systems, specially the non isothermal Continuous Stirred Tank Reactors in a thermodynamic framework, using either the jacket temperature or the inlet molar flow rate as the only control input. As soon as the constraint on the total mass is considered and the reaction kinetics is a Lipschitz continuous function with respect to the temperature, it shows that the stabilization of thermal solicitations reciprocally entails the one of matter using La Salle’s invariance principle. As a consequence, these control problems can be solved if the closed loop Lyapunov functions are chosen to be proportional to the thermal part or material part of the so called thermodynamic availability function. Some numerical simulations for a first order chemical reaction with multiple steady states are given to validate our theoretical developments. The performance of the obtained nonlinear controllers with regard to the conversion rate is also discussed.The main goal of this paper is to introduce a link between the thermodynamics and control systems theory. More precisely, the paper focuses on Lyapunov based control of process systems, specially the non isothermal Continuous Stirred Tank Reactors in a thermodynamic framework, using either the jacket temperature or the inlet molar flow rate as the only control input. As soon as the constraint on the total mass is considered and the reaction kinetics is a Lipschitz continuous function with respect to the temperature, it shows that the stabilization of thermal solicitations reciprocally entails the one of matter using La Salle’s invariance principle. As a consequence, these control problems can be solved if the closed loop Lyapunov functions are chosen to be proportional to the thermal part or material part of the so called thermodynamic availability function. Some numerical simulations for a first order chemical reaction with multiple steady states are given to validate our theoretical developments. The performance of the obtained nonlinear controllers with regard to the conversion rate is also discussed
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A 25-Year-Old Male with Orogenital Ulcers, Rash, and Difficulty Swallowing
A 25-year-old otherwise healthy male presented with new-onset odynophagia, rash, and orogenital ulcers. Despite treatment with antibiotics for presumed bacterial pharyngitis, the patient remained symptomatic, with abnormal vital signs and laboratory values. Upon dermatology consultation and histopathologic correlation, he was diagnosed with Behçet disease. Behçet disease is a rare rheumatologic condition that presents with recurrent oral ulcers and varying degrees of ophthalmic, neurologic, cardiac, and vascular disease. Given its protean nature, the treatment of Behçet disease is tailored to the patient's presentation and severity of organ involvement. Following treatment with colchicine and prednisone, the patient's symptoms improved rapidly
Dynamical chaos and power spectra in toy models of heteropolymers and proteins
The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied
by molecular dynamics simulations. It is shown that two nearby trajectories
quickly diverge from each other if the heteropolymer corresponds to a random
sequence. For good folders, on the other hand, two nearby trajectories may
initially move apart but eventually they come together. Thus good folders are
intrinsically non-chaotic. A choice of a distance of the initial conformation
from the native state affects the way in which a separation between the twin
trajectories behaves in time. This observation allows one to determine the size
of a folding funnel in good folders. We study the energy landscapes of the toy
models by determining the power spectra and fractal characteristics of the
dependence of the potential energy on time. For good folders, folding and
unfolding trajectories have distinctly different correlated behaviors at low
frequencies.Comment: 8 pages, 9 EPS figures, Phys. Rev. E (in press
Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi
Microbial glycan degradation is essential to global carbon cycling. The marine bacterium Salegentibacter sp. Hel_I_6 (Bacteroidota) isolated from seawater off Helgoland island (North Sea) contains an α-mannan inducible gene cluster with a GH76 family endo-α-1,6-mannanase (ShGH76). This cluster is related to genetic loci employed by human gut bacteria to digest fungal α-mannan. Metagenomes from the Hel_I_6 isolation site revealed increasing GH76 gene frequencies in free-living bacteria during microalgae blooms, suggesting degradation of α-1,6-mannans from fungi. Recombinant ShGH76 protein activity assays with yeast α-mannan and synthetic oligomannans showed endo-α-1,6-mannanase activity. Resolved structures of apo-ShGH76 (2.0 Å) and of mutants co-crystalized with fungal mannan-mimicking α-1,6-mannotetrose (1.90 Å) and α-1,6-mannotriose (1.47 Å) retained the canonical (α/α)6 fold, despite low identities with sequences of known GH76 structures (GH76s from gut bacteria: <27%). The apo-form active site differed from those known from gut bacteria, and co-crystallizations revealed a kinked oligomannan conformation. Co-crystallizations also revealed precise molecular-scale interactions of ShGH76 with fungal mannan-mimicking oligomannans, indicating adaptation to this particular type of substrate. Our data hence suggest presence of yet unknown fungal α-1,6-mannans in marine ecosystems, in particular during microalgal blooms
Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam
Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development
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