Design of compensation algorithms for zero padding and its application to a patch based deep neural network.

In this article, compensation algorithms for zero padding are suggested to enhance the performance of deep convolutional neural networks. By considering the characteristics of convolving filters, the proposed methods efficiently compensate convolutional output errors due to zero padded inputs in a convolutional neural network. Primarily the algorithms are developed for patch based SRResNet for Single Image Super Resolution and the performance comparison is carried out using the SRResNet model but due to generalized nature of the padding algorithms its efficacy is tested in U-Net for Lung CT Image Segmentation.

Bayesian two-stage modeling of longitudinal and time-to-event data with an integrated fractional Brownian motion covariance structure.

It is difficult to characterize complex variations of biological processes, often longitudinally measured using biomarkers that yield noisy data. While joint modeling with a longitudinal submodel for the biomarker measurements and a survival submodel for assessing the hazard of events can alleviate measurement error issues, the continuous longitudinal submodel often uses random intercepts and slopes to estimate both between- and within-patient heterogeneity in biomarker trajectories. To overcome longitudinal submodel challenges, we replace random slopes with scaled integrated fractional Brownian motion (IFBM).

Multilevel joint model of longitudinal continuous and binary outcomes for hierarchically structured data.

Joint modeling has been a useful strategy for incorporating latent associations between different types of outcomes simultaneously, often focusing on a longitudinal continuous outcome characterized by an LME submodel and a terminal event subject to a Cox proportional hazard or parametric survival submodel. Applications to hierarchical longitudinal studies have been less frequent, particularly with respect to a binary process, which is commonly specified by a GLMM. Furthermore, many of the joint model developments have not allowed for investigations of nested effects, such as those arising from multicenter studies.

Predicting Individualized Lung Disease Progression in Treatment-Naive Patients With Lymphangioleiomyomatosis.

Background: Lung function decline varies significantly in patients with lymphangioleiomyomatosis (LAM), impeding individualized clinical decision-making.

Research Question: Can we aid individualized decision-making in LAM by developing a dynamic prediction model that can estimate the probability of clinically relevant FEV decline in patients with LAM before treatment initiation?

Study Design And Methods: Patients observed in the US National Heart, Lung, and Blood Institute (NHLBI) Lymphangioleiomyomatosis Registry were included. Using routinely available variables such as age at diagnosis, menopausal status, and baseline lung function (FEV and diffusing capacity of the lungs for carbon monoxide [Dlco]), we used novel stochastic modeling and evaluated predictive probabilities for clinically relevant drops in FEV.

Temporal dynamics in meta longitudinal RNA-Seq data.

Identification of differentially expressed genes has been a high priority task of downstream analyses to further advances in biomedical research. Investigators have been faced with an array of issues in dealing with more complicated experiments and metadata, including batch effects, normalization, temporal dynamics (temporally differential expression), and isoform diversity (isoform-level quantification and differential splicing events). To date, there are currently no standard approaches to precisely and efficiently analyze these moderate or large-scale experimental designs, especially with combined metadata.

Capillary-Force-Pattern Formation of Indium-Zinc-Oxide Thin-Film Transistor.

Studies of the pattern-formation technique used with solution-processed oxide thin-film transistors (TFTs) continue to explore its uses as an efficient manufacturing method. However, research remains to be completed to achieve high performance and to apply the refined technique to various current industrial technologies. We studied the patterning technique of solution-processed indiumzinc-oxide (IZO) by using the capillary-force phenomenon, the method of controlling the pattern of the IZO semiconductor layer, and approaches to reducing problems such as the cracking that occurs during patterning.

Palatable Food Affects HPA Axis Responsivity and Forebrain Neurocircuitry in an Estrous Cycle-specific Manner in Female Rats.

Eating palatable foods can provide stress relief, but the mechanisms by which this occurs are unclear. We previously characterized a limited sucrose intake (LSI) paradigm in which twice-daily access to a small amount of 30% sucrose (vs. water as a control) reduces hypothalamic-pituitary-adrenocortical (HPA) axis responses to stress and alters neuronal activation in stress-regulatory brain regions in male rats.

The role of PDF neurons in setting the preferred temperature before dawn in .

Animals have sophisticated homeostatic controls. While mammalian body temperature fluctuates throughout the day, small ectotherms, such as achieve a body temperature rhythm (BTR) through their preference of environmental temperature. Here, we demonstrate that pigment dispersing factor (PDF) neurons play an important role in setting preferred temperature before dawn.

Differential Gene Expression (DEX) and Alternative Splicing Events (ASE) for Temporal Dynamic Processes Using HMMs and Hierarchical Bayesian Modeling Approaches.

In gene expression profile, data analysis pipeline is categorized into four levels, major downstream tasks, i.e., (1) identification of differential expression; (2) clustering co-expression patterns; (3) classification of subtypes of samples; and (4) detection of genetic regulatory networks, are performed posterior to preprocessing procedure such as normalization techniques.

Finding Clocks in Genes: A Bayesian Approach to Estimate Periodicity.

Identification of rhythmic gene expression from metabolic cycles to circadian rhythms is crucial for understanding the gene regulatory networks and functions of these biological processes. Recently, two algorithms, JTK_CYCLE and ARSER, have been developed to estimate periodicity of rhythmic gene expression. JTK_CYCLE performs well for long or less noisy time series, while ARSER performs well for detecting a single rhythmic category.

Random-effects meta-analysis for systematic reviews of phase I clinical trials: Rare events and missing data.

Phase I trials aim to establish appropriate clinical and statistical parameters to guide future clinical trials. With individual trials typically underpowered, systematic reviews and meta-analysis are desired to assess the totality of evidence. A high percentage of zero or missing outcomes often complicate such efforts.

Statistical modeling implicates neuroanatomical circuit mediating stress relief by 'comfort' food.

A history of eating highly palatable foods reduces physiological and emotional responses to stress. For instance, we have previously shown that limited sucrose intake (4 ml of 30 % sucrose twice daily for 14 days) reduces hypothalamic-pituitary-adrenocortical (HPA) axis responses to stress. However, the neural mechanisms underlying stress relief by such 'comfort' foods are unclear, and could reveal an endogenous brain pathway for stress mitigation.

The analytical landscape of static and temporal dynamics in transcriptome data.

Interpreting gene expression profiles often involves statistical analysis of large numbers of differentially expressed genes, isoforms, and alternative splicing events at either static or dynamic spectrums. Reduced sequencing costs have made feasible dense time-series analysis of gene expression using RNA-seq; however, statistical methods in the context of temporal RNA-seq data are poorly developed. Here we will review current methods for identifying temporal changes in gene expression using RNA-seq, which are limited to static pairwise comparisons of time points and which fail to account for temporal dependencies in gene expression patterns.

Time series expression analyses using RNA-seq: a statistical approach.

RNA-seq is becoming the de facto standard approach for transcriptome analysis with ever-reducing cost. It has considerable advantages over conventional technologies (microarrays) because it allows for direct identification and quantification of transcripts. Many time series RNA-seq datasets have been collected to study the dynamic regulations of transcripts.

Genetic diversity of microsatellite loci in hierarchically structured populations.

Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded.

Development of a noise metric for assessment of exposure risk to complex noises.

Many noise guidelines currently use A-weighted equivalent sound pressure level L(Aeq) as the noise metric and the equal energy hypothesis to assess the risk of occupational noises. Because of the time-averaging effect involved with the procedure, the current guidelines may significantly underestimate the risk associated with complex noises. This study develops and evaluates several new noise metrics for more accurate assessment of exposure risks to complex and impulsive noises.

Handle grip span for optimising finger-specific force capability as a function of hand size.

Five grip spans (45 to 65 mm) were tested to evaluate the effects of handle grip span and user's hand size on maximum grip strength, individual finger force and subjective ratings of comfort using a computerised digital dynamometer with independent finger force sensors. Forty-six males participated and were assigned into three hand size groups (small, medium, large) according to their hands' length. In general, results showed the 55- and 50-mm grip spans were rated as the most comfortable sizes and showed the largest grip strength (433.

A quantitative method for representing balance strategies of goal-directed human motions.

A movement index termed balance strategy vector (BSV) was developed as a research tool for studying human balance strategies during goal-directed motions. For a given motion (motion capture data), the BSV index quantitatively represents its balance strategy by computing how available body joint DoFs' angular motions affect the formation of the wholebody center-of-mass trajectory. The index facilitates easy and intuitive understanding of balance strategies of various human motions and can assist scientific investigations on human balance strategies.

Differentiation among populations with migration, mutation, and drift: implications for genetic inference.

Populations may become differentiated from one another as a result of genetic drift. The amounts and patterns of differentiation at neutral loci are determined by local population sizes, migration rates among populations, and mutation rates. We provide exact analytical expressions for the mean, variance, and covariance of a stochastic model for hierarchically structured populations subject to migration, mutation, and drift.