Quantitative Biology

Univariate and multivariate methods for association of the genom-ic variations with the end-or-endo phenotype have been widely used for genome wide association studies. In addition to encoding the SNPs, we advocate usage of clustering as a novel method to encode the structural variations, SVs, in genomes, such as the deletions and insertions polymorphism (DIPs), Copy Number Variations (CNVs), translocation, inversion, etc., that can be used as an independent fea-ture variable value for downstream computation by artificial intelli-gence methods to predict the endo-or-end phenotype. We introduce a clustering based encoding scheme for structural variations and om-ics based analysis. We conducted a complete all genomic variants association with the phenotype using deep learning and other ma-chine learning techniques, though other methods such as genetic al-gorithm can also be applied. Applying this encoding of SVs and one-hot encoding of SNPs on GTEx V7 pilot DNA variation dataset, we were able to get high accuracy using various methods of DMWAS, and particularly found logistic regression to work the best for death due to heart-attack (MHHRTATT) phenotype. The genom-ic variants acting as feature sets were then arranged in descending order of power of impact on the disease or trait phenotype, which we call optimization and that also uses top univariate association into account. Variant Id P1_M_061510_3_402_P at chromosome 3 & position 192063195 was found to be most highly associated to MHHRTATT. We present here the top ten optimized genomic va-riant feature set for the MHHRTATT phenotypic cause of death.

Motivation: Cryo-Electron Tomography (cryo-ET) visualizes structure and spatial organization of macromolecules and their interactions with other subcellular components inside single cells in the close-to-native state at sub-molecular resolution. Such information is critical for the accurate understanding of cellular processes. However, subtomogram classification remains one of the major challenges for the systematic recognition and recovery of the macromolecule structures in cryo-ET because of imaging limits and data quantity. Recently, deep learning has significantly improved the throughput and accuracy of large-scale subtomogram classification. However often it is difficult to get enough high-quality annotated subtomogram data for supervised training due to the enormous expense of labeling. To tackle this problem, it is beneficial to utilize another already annotated dataset to assist the training process. However, due to the discrepancy of image intensity distribution between source domain and target domain, the model trained on subtomograms in source domainmay perform poorly in predicting subtomogram classes in the target domain. Results: In this paper, we adapt a few shot domain adaptation method for deep learning based cross-domain subtomogram classification. The essential idea of our method consists of two parts: 1) take full advantage of the distribution of plentiful unlabeled target domain data, and 2) exploit the correlation between the whole source domain dataset and few labeled target domain data. Experiments conducted on simulated and real datasets show that our method achieves significant improvement on cross domain subtomogram classification compared with baseline methods.

Data analysis pipelines are known to be impacted by computational conditions, presumably due to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipelines are unclear. We present Spot, a tool to identify which processes in a pipeline create numerical differences when executed in different computational conditions. Spot leverages system-call interception through ReproZip to reconstruct and compare provenance graphs without pipeline instrumentation. By applying Spot to the structural pre-processing pipelines of the Human Connectome Project, we found that linear and non-linear registration are the cause of most numerical instabilities in these pipelines, which confirms previous findings.

The glutamatergic modulator ketamine has been shown to rapidly reduce depressive symptoms in patients with treatment-resistant major depressive disorder (TRD). Although its mechanisms of action are not fully understood, changes in cortical excitation/inhibition (E/I) following ketamine administration are well documented in animal models and could represent a potential biomarker of treatment response. Here, we analyse neuromagnetic virtual electrode timeseries collected from the primary somatosensory cortex in 18 unmedicated patients with TRD and in an equal number of age-matched healthy controls during a somatosensory 'airpuff' stimulation task. These two groups were scanned as part of a clinical trial of ketamine efficacy under three conditions: a) baseline; b) 6-9 hours following subanesthetic ketamine infusion; and c) 6-9 hours following placebo-saline infusion. We obtained estimates of E/I interaction strengths by using Dynamic Causal Modelling (DCM) on the timeseries, thereby allowing us to pinpoint, under each scanning condition, where each subject's dynamics lie within the Poincaré diagram - as defined in dynamical systems theory. We demonstrate that the Poincaré diagram offers classification capability for TRD patients, in that the further the patients' coordinates were shifted (by virtue of ketamine) toward the stable (top-left) quadrant of the Poincaré diagram, the more their depressive symptoms improved. The same relationship was not observed by virtue of a placebo effect - thereby verifying the drug-specific nature of the results. We show that the shift in neural dynamics required for symptom improvement necessitates an increase in both excitatory and inhibitory coupling. We present accompanying MATLAB code made available in a public repository, thereby allowing for future studies to assess individually-tailored treatments of TRD.

Aggregating transcriptomics data across hospitals can increase sensitivity and robustness of differential expression analyses, yielding deeper clinical insights. As data exchange is often restricted by privacy legislation, meta-analyses are frequently employed to pool local results. However, if class labels are inhomogeneously distributed between cohorts, their accuracy may drop. Flimma (this https URL) addresses this issue by implementing the state-of-the-art workflow limma voom in a privacy-preserving manner, i.e. patient data never leaves its source site. Flimma results are identical to those generated by limma voom on combined datasets even in imbalanced scenarios where meta-analysis approaches fail.

V-shaped and echelon formations help migratory birds to consume less energy for migration. As the case study, the formation flight of the Northern Bald Ibises is considered to investigate different effects on their flight efficiency. The effects of the wingtip spacing and wingspan are examined on the individual drag of each Ibis in the flock. Two scenarios are considered in this study, (1) increasing and (2) decreasing wingspans toward the tail. An algorithm is applied for replacement mechanism and load balancing of the Ibises during their flight. In this replacing mechanism, the Ibises with the highest value of remained energy are replaced with the Ibises with the lowest energy, iteratively. The results indicate that depending on the positions of the birds with various sizes in the flock, they consume a different level of energy. Moreover, it is found that also small birds have the chance to take the lead during the flock.

Brain tissue is a heterogeneous material, constituted by a soft matrix filled with cerebrospinal fluid. The interactions between, and the complexity of each of these components are responsible for the non-linear rate-dependent behaviour that characterizes what is one of the most complex tissue in nature. Here, we investigate the influence of the cutting rate on the fracture properties of brain, through wire cutting experiments. We also present a model for the rate-dependent behaviour of fracture propagation in soft materials, which comprises the effects of fluid interaction through a poro-hyperelastic formulation. The method is developed in the framework of finite strain continuum mechanics, implemented in a commercial finite element code, and applied to the case of an edge-crack remotely loaded by a controlled displacement. Experimental and numerical results both show a toughening effect with increasing rates, which is linked to the energy dissipated by the fluid-solid interactions in the process zone ahead of the crack.

The percentage of patients hospitalized due to hyponatremia is getting higher. Hyponatremia is the deficiency of sodium electrolyte in the human serum. This deficiency might indulge adverse effects and also associated with longer hospital stay or mortality, if it wasnt actively treated and managed. This work predicts the futuristic sodium levels of patients based on their history of health problems using multilayer perceptron and multivariate linear regression algorithm. This work analyses the patients age, information about other disease such as diabetes, pneumonia, liver-disease, malignancy, pulmonary, sepsis, SIADH, and sodium level of the patient during admission to the hospital. The results of the proposed MLP algorithm is compared with MLR algorithm based results. The MLP prediction results generates 23-72 of higher prediction results than MLR algorithm. Thus, proposed MLR algorithm has produced 57.1 of reduced mean squared error rate than the MLR results on predicting future sodium ranges of patients. Further, proposed MLR algorithm produces 27-50 of higher prediction precision rate.

Due to the fractal nature of retinal blood vessels, the retinal fractal dimension is a natural parameter for researchers to explore and has garnered interest as a potential diagnostic tool. This review aims to summarize the current scientific evidence regarding the relationship between fractal dimension and retinal pathology and thus assess the clinical value of retinal fractal dimension. Following the PRISMA guidelines, a literature search for research articles was conducted in several internet databases (Embase, PubMed, Web of Science, Scopus). This led to a result of 28 studies included in the final review, which were analyzed via meta-analysis to determine whether the fractal dimension changes significantly in retinal disease versus normal individuals

Canids display a vast diversity of social organizations, from solitary-living to pairs to packs. Domestic dogs have descended from pack-living gray wolf-like ancestors. Unlike their group living ancestors, free-ranging dogs are facultatively social, preferring to forage solitarily. They are scavengers by nature, mostly dependent on human garbage and generosity for their sustenance. Free-ranging dogs are highly territorial, often defending their territories using vocalizations. Vocal communication plays a critical role between inter and intraspecies and group interaction and maintaining their social dynamics. Barking is the most common among the different types of vocalizations of dogs. Dogs have a broad hearing range and can respond to sounds over long distances. Domestic dogs have been shown to have the ability to distinguish between barking in different contexts. Since free-ranging dogs regularly engage in various kinds of interactions with each other, it is interesting to know whether they are capable of distinguishing between vocalizations of their own and other groups. In this study, a playback experiment was used to test if dogs can distinguish between barking of their own group member from a non-group member. Though dogs respond to barking from other groups in territorial exchanges, they did not respond differently to the self and other group barking in the playback experiments. This suggests a role of context in the interactions between dogs and opens up possibilities for future studies on the comparison of the responses of dogs in playback experiments with their natural behavior through long-term observations.