Hi-gMISnet: generalized medical image segmentation using DWT based multilayer fusion and dual mode attention into high resolutionpGAN

Objective.Automatic medical image segmentation is crucial for accurately isolating target tissue areas in the image from background tissues, facilitating precise diagnoses and procedures. While the proliferation of publicly available clinical datasets led to the development of deep learning-based medical image segmentation methods, a generalized, accurate, robust, and reliable approach across diverse imaging modalities remains elusive.Approach.This paper proposes a novel high-resolution parallel generative adversarial network (pGAN)-based generalized deep learning method for automatic segmentation of medical images from diverse imaging modalities. The proposed method showcases better performance and generalizability by incorporating novel components such as partial hybrid transfer learning, discrete wavelet transform (DWT)-based multilayer and multiresolution feature fusion in the encoder, and a dual mode attention gate in the decoder of the multi-resolution U-Net-based GAN. With multi-objective adversarial training loss functions including a unique reciprocal loss for enforcing cooperative learning inpGANs, it further enhances the robustness and accuracy of the segmentation map.Main results.Experimental evaluations conducted on nine diverse publicly available medical image segmentation datasets, including PhysioNet ICH, BUSI, CVC-ClinicDB, MoNuSeg, GLAS, ISIC-2018, DRIVE, Montgomery, and PROMISE12, demonstrate the proposed method's superior performance. The proposed method achieves mean F1 scores of 79.53%, 88.68%, 82.50%, 93.25%, 90.40%, 94.19%, 81.65%, 98.48%, and 90.79%, respectively, on the above datasets, surpass state-of-the-art segmentation methods. Furthermore, our proposed method demonstrates robust multi-domain segmentation capabilities, exhibiting consistent and reliable performance. The assessment of the model's proficiency in accurately identifying small details indicates that the high-resolution generalized medical image segmentation network (Hi-gMISnet) is more precise in segmenting even when the target area is very small.Significance.The proposed method provides robust and reliable segmentation performance on medical images, and thus it has the potential to be used in a clinical setting for the diagnosis of patients.

MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.

Role of SEC14-like phosphatidylinositol transfer proteins in membrane identity and dynamics

Membrane identity and dynamic processes, that act at membrane sites, provide important cues for regulating transport, signal transduction and communication across membranes. There are still numerous open questions as to how membrane identity changes and the dynamic processes acting at the surface of membranes are regulated in diverse eukaryotes in particular plants and which roles are being played by protein interaction complexes composed of peripheral and integral membrane proteins. One class of peripheral membrane proteins conserved across eukaryotes comprises the SEC14-like phosphatidylinositol transfer proteins (SEC14L-PITPs). These proteins share a SEC14 domain that contributes to membrane identity and fulfills regulatory functions in membrane trafficking by its ability to sense, bind, transport and exchange lipophilic substances between membranes, such as phosphoinositides and diverse other lipophilic substances. SEC14L-PITPs can occur as single-domain SEC14-only proteins in all investigated organisms or with a modular domain structure as multi-domain proteins in animals and streptophytes (comprising charales and land plants). Here, we present an overview on the functional roles of SEC14L-PITPs, with a special focus on the multi-domain SEC14L-PITPs of the SEC14-nodulin and SEC14-GOLD group (PATELLINs, PATLs in plants). This indicates that SEC14L-PITPs play diverse roles from membrane trafficking to organism fitness in plants. We concentrate on the structure of SEC14L-PITPs, their ability to not only bind phospholipids but also other lipophilic ligands, and their ability to regulate complex cellular responses through interacting with proteins at membrane sites.

Quantifying dementia prevention potential in the FINGER randomized controlled trial using the LIBRA prevention index

INTRODUCTION

Individuals in early dementia prevention trials may differ in how much they benefit from interventions depending on their initial risk level. Additionally, modifiable dementia risk scores might be used as surrogate/intermediate outcomes.

METHODS

In the Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER), we investigated in post hoc analyses (N = 1207) whether the cognitive benefits of the 2-year multi-domain lifestyle intervention differed by baseline dementia risk measured with the "LIfestyle for BRAin Health" (LIBRA) score. We also investigated intervention effects on change in LIBRA score over time.

RESULTS

Overall, higher baseline LIBRA was related to less cognitive improvement over time. This association did not differ between the intervention and control groups. The intervention was effective in decreasing LIBRA scores over time, regardless of baseline demographics or cognition.

DISCUSSION

The cognitive benefit of the FINGER intervention was similar across individuals with different LIBRA scores at baseline. Furthermore, LIBRA may be useful as a surrogate/intermediate endpoint and surveillance tool to monitor intervention success during trial execution.

Prodromal clinical, demographic, and socio-ecological correlates of asthma in adults: a 10-year statewide big data multi-domain analysis

Objectives: To identify prodromal correlates of asthma as compared to chronic obstructive pulmonary disease and allied-conditions (COPDAC) using a multi domain analysis of socio-ecological, clinical, and demographic domains.Methods: This is a retrospective case-risk-control study using data from Florida's statewide Healthcare Cost and Utilization Project (HCUP). Patients were grouped into three groups: asthma, COPDAC (without asthma), and neither asthma nor COPDAC. To identify socio-ecological, clinical, demographic, and clinical predictors of asthma and COPDAC, we used univariate analysis, feature ranking by bootstrapped information gain ratio, multivariable logistic regression with LogitBoost selection, decision trees, and random forests.Results: A total of 141,729 patients met inclusion criteria, of whom 56,052 were diagnosed with asthma, 85,677 with COPDAC, and 84,737 with neither asthma nor COPDAC. The multi-domain approach proved superior in distinguishing asthma versus COPDAC and non-asthma/non-COPDAC controls (area under the curve (AUROC) 84%). The best domain to distinguish asthma from COPDAC without controls was prior clinical diagnoses (AUROC 82%). Ranking variables from all the domains found the most important predictors for the asthma versus COPDAC and controls were primarily socio-ecological variables, while for asthma versus COPDAC without controls, demographic and clinical variables such as age, CCI, and prior clinical diagnoses, scored better.Conclusions: In this large statewide study using a machine learning approach, we found that a multi-domain approach with demographics, clinical, and socio-ecological variables best predicted an asthma diagnosis. Future work should focus on integrating machine learning-generated predictive models into clinical practice to improve early detection of those common respiratory diseases.

Reproducing Patient-Specific Hemodynamics in the Blalock-Taussig Circulation Using a Flexible Multi-Domain Simulation Framework: Applications for Optimal Shunt Design

For babies born with hypoplastic left heart syndrome, several open-heart surgeries are required. During Stage I, a Norwood procedure is performed to construct an appropriate circulation to both the systemic and the pulmonary arteries. The pulmonary arteries receive flow from the systemic circulation, often using a Blalock-Taussig (BT) shunt between the innominate artery and the right pulmonary artery. This procedure causes significantly disturbed flow in the pulmonary arteries. In this study, we use computational hemodynamic simulations to demonstrate its capacity for examining the properties of the flow through and near the BT shunt. Initially, we construct a computational model which produces blood flow and pressure measurements matching the clinical magnetic resonance imaging (MRI) and catheterization data. Achieving this required us to determine the level of BT shunt occlusion; because the occlusion is below the MRI resolution, this information is difficult to recover without the aid of computational simulations. We determined that the shunt had undergone an effective diameter reduction of 22% since the time of surgery. Using the resulting geometric model, we show that we can computationally reproduce the clinical data. We, then, replace the BT shunt with a hypothetical alternative shunt design with a flare at the distal end. Investigation of the impact of the shunt design reveals that the flare can increase pulmonary pressure by as much as 7% and flow by as much as 9% in the main pulmonary branches, which may be beneficial to the pulmonary circulation.

Cortical Thickness Changes Correlate with Cognition Changes after Cognitive Training: Evidence from a Chinese Community Study

The aim of this study was to investigate whether changes in cortical thickness correlated with cognitive function changes in healthy older adults after receiving cognitive training interventions. Moreover, it also aimed to examine the differential impacts of a multi-domain and a single-domain cognitive training interventions. Longitudinal magnetic resonance imaging (MRI) scanning was performed on participants 65–75 years of age using the Siemens 3.0 T Trio Tim with the Magnetization Prepared Rapid Gradient Echo (MPRAGE) sequence. The cortical thickness was determined using FreeSurfer Software. Cognitive functioning was evaluated using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). There were significant group × time interaction effects on the left supramarginal, the left frontal pole cortical regions; and a marginal significant group × time interaction effects on visuospatial/constructional and delayed memory scores. In a multi-domain cognitive training group, a number of cortical region changes were significantly positively correlated with changes in attention, delayed memory, and the total score, but significantly negatively correlated with changes in immediate memory and language scores. In the single-domain cognitive training group, some cortical region changes were significantly positively associated with changes in immediate memory, delayed memory, and the total score, while they were significantly negatively associated with changes in visuospatial/constructional, language, and attention scores. Overall, multi-domain cognitive training offered more advantages in visuospatial/constructional, attention, and delayed memory abilities, while single-domain cognitive training benefited immediate memory ability more effectively. These findings suggest that healthy older adults benefit more from the multi-domain cognitive training than single-domain cognitive training. Cognitive training has impacted on cortical thickness changes in healthy elderly.

An Evaluation of the Pedestrian Classification in a Multi-Domain Multi-Modality Setup

The objective of this article is to study the problem of pedestrian classification across different light spectrum domains (visible and far-infrared (FIR)) and modalities (intensity, depth and motion). In recent years, there has been a number of approaches for classifying and detecting pedestrians in both FIR and visible images, but the methods are difficult to compare, because either the datasets are not publicly available or they do not offer a comparison between the two domains. Our two primary contributions are the following: (1) we propose a public dataset, named RIFIR , containing both FIR and visible images collected in an urban environment from a moving vehicle during daytime; and (2) we compare the state-of-the-art features in a multi-modality setup: intensity, depth and flow, in far-infrared over visible domains. The experiments show that features families, intensity self-similarity (ISS), local binary patterns (LBP), local gradient patterns (LGP) and histogram of oriented gradients (HOG), computed from FIR and visible domains are highly complementary, but their relative performance varies across different modalities. In our experiments, the FIR domain has proven superior to the visible one for the task of pedestrian classification, but the overall best results are obtained by a multi-domain multi-modality multi-feature fusion.

Unfolding study of a trimeric membrane protein AcrB

The folding of a multi-domain trimeric α-helical membrane protein, Escherichia coli inner membrane protein AcrB, was investigated. AcrB contains both a transmembrane domain and a large periplasmic domain. Protein unfolding in sodium dodecyl sulfate (SDS) and urea was monitored using the intrinsic fluorescence and circular dichroism spectroscopy. The SDS denaturation curve displayed a sigmoidal profile, which could be fitted with a two-state unfolding model. To investigate the unfolding of separate domains, a triple mutant was created, in which all three Trp residues in the transmembrane domain were replaced with Phe. The SDS unfolding profile of the mutant was comparable to that of the wild type AcrB, suggesting that the observed signal change was largely originated from the unfolding of the soluble domain. Strengthening of trimer association through the introduction of an inter-subunit disulfide bond had little effect on the unfolding profile, suggesting that trimer dissociation was not the rate-limiting step in unfolding monitored by fluorescence emission. Under our experimental condition, AcrB unfolding was not reversible. Furthermore, we experimented with the refolding of a monomeric mutant, AcrBΔloop , from the SDS unfolded state. The CD spectrum of the refolded AcrBΔloop superimposed well onto the spectra of the original folded protein, while the fluorescence spectrum was not fully recovered. In summary, our results suggested that the unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild-type AcrB.

Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution

The four-domain structure of chitinase 60 from Moritella marina (MmChi60) is outstanding in its complexity. Many glycoside hydrolases, such as chitinases and cellulases, have multi-domain structures, but only a few have been solved. The flexibility of the hinge regions between the domains apparently makes these proteins difficult to crystallize. The analysis of an active-site mutant of MmChi60 in an unliganded form and in complex with the substrates NAG4 and NAG5 revealed significant differences in the substrate-binding site compared with the previously determined complexes of most studied chitinases. A SAXS experiment demonstrated that in addition to the elongated state found in the crystal, the protein can adapt other conformations in solution ranging from fully extended to compact.