Notes

Progression of a singular nomogram-based on the internet application to calculate axillary standing after neoadjuvant radiation treatment in cN+ breast cancer: A multicentre study on One,950 patients.
Slow wave and spindle coupling supports memory consolidation, and loss of coupling is linked with cognitive decline and neurodegeneration. Coupling is proposed to be a possible biomarker of neurological disease, yet little is known about the different subtypes of coupling that normally occur throughout human development and aging. Here we identify distinct subtypes of spindles within slow wave upstates and describe their relationships with sleep stage across the human lifespan.

Coupling within a cross-sectional cohort of 582 subjects was quantified from stages N2 and N3 sleep across ages 6-88 years old. Results were analyzed across the study population via mixed model regression. Within a subset of subjects, we further utilized coupling to identify discrete subtypes of slow waves by their coupled spindles.

Two different subtypes of spindles were identified during the upstates of (distinct) slow waves an "early-fast" spindle, more common in stage N2 sleep, and a "late-fast" spindle, more common in stage N3. We further found stages N2 and N3 sleep contain a mixture of discrete subtypes of slow waves, each identified by their unique coupled-spindle timing and frequency. The relative contribution of coupling subtypes shifts across the human lifespan, and a deeper sleep phenotype prevails with increasing age.

Distinct subtypes of slow waves and coupled spindles form the composite of slow wave sleep. Our findings support a model of sleep-dependent synaptic regulation via discrete slow wave/spindle coupling subtypes and advance a conceptual framework for the development of coupling-based biomarkers in age-associated neurological disease.
Distinct subtypes of slow waves and coupled spindles form the composite of slow wave sleep. Our findings support a model of sleep-dependent synaptic regulation via discrete slow wave/spindle coupling subtypes and advance a conceptual framework for the development of coupling-based biomarkers in age-associated neurological disease.
Next generation sequencing (NGS) enabled the fast accumulation of genomic data at public repositories. This technology also made it possible to better understand the regulation of gene expression by transcription factors and various chromatin-associated proteins through the integration of chromatin immunoprecipitation (ChIP-Seq). The Cistrome Project (Liu et al., 2011) has become one of the indispensable research portals for biologists to access and analyze data generated with thousands of ChIP-Seq experiments. Integrative motif analysis on shared binding regions among a set of experiments is not yet achievable despite a set of search and analysis tools provided by Cistrome via its web interface and the Galaxy framework (Afgan et al., 2016).

We implemented a python command-line tool for searching binding sequences of a transcription factor common to multiple ChIP-Seq experiments. We use the peaks in the Cistrome database as identified by MACS 2.0 (Zhang et al., 2008) for each experiment and identify shared peak regions in a genomic locus of interest. We then scan these regions for binding sequences using a binding motif of a transcription factor obtained from the JASPAR database (Fornes et al., 2020). MotifGenie is developed in collaboration with molecular biologists and its findings are corroborated by laboratory experiments.

MotifGenie is freely available at https//github.com/ceragoguztuzun/MotifGenie.
MotifGenie is freely available at https//github.com/ceragoguztuzun/MotifGenie.ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http//proteovision.chemistry.gatech.edu/.Free smartphone applications that aim to promote physical activity or reduce sedentary behavior at workplaces were questioned for its content such as technical features, behavior change techniques (BCT) and security concerns. To evaluate systematically whether smartphone apps are mapped adequately with BCTs and security concerns. Free apps in Google Play store were searched and coded for BCTs systematically in July 2020. Two reviewers independently coded apps that aimed to promote physical activity (n = 18) and reduce sedentary behavior (n = 16) using a taxonomy of 26 BCTs. BCTs, features and security concerns among apps promoting physical activity and reducing sedentary behavior were analyzed. While the features (social support, gamification, or rewards) help increase physical activity and decrease sedentary behavior, the apps do not typically include the above features. Further, the apps were based on an average of 13 (4-21) BCTs. The BCTs coded most frequently were "self-monitoring" (100%), "general encouragement" (97%), and "goal setting" (n = 94%). No significant relation between user rating and BCTs was found in the apps. Majority of the free apps that aimed to increase physical activity or reduce sedentary behavior at workplaces were not adequately based on BCTs and lacked essential features facilitating long term behavior compliance at workplaces. Hence, there is a need to develop newer applications mapped adequately with BCTs, involving the collaborative work of behavioral scientists, app developers and policymakers. check details Clinical Trial Registry of India CTRI/2020/03/024138.Serpentine tail structures are widely observed in the animal kingdom and are thought to help animals to handle various motion tasks. Developing serpentine robotic tails and using them on legged robots has been an attractive idea for robotics. This paper presents the theoretical analysis for such a robotic system that consists of a reduced complexity quadruped and a serpentine robotic tail. Dynamic model and motion controller are formulated first. Simulations are then conducted to analyze the tail's performance on the airborne righting and maneuvering tasks of the quadruped. Using the established simulation environment, systematic analyses on critical design parameters, namely the tail mounting point, tail length, torso center of mass (COM) location, tail-torso mass ratio, and the power consumption distribution, are performed. The results show that the tail length and the mass ratio influence the maneuvering angle the most while the COM location affects the landing stability the most. link2 Based on these design guidelines, for the current robot design, the optimal tail parameters are determined as a length of 2 times as long as the torso length and a weight of 0.09 times as heavy as the torso weight.
Single cell RNA-Seq (scRNA-Seq) has broadened our understanding of cellular heterogeneity and provided valuable insights into cellular functions. Recent experimental strategies extend scRNA-Seq readouts to include additional features, including cell surface proteins and genomic perturbations. These "feature barcoding" strategies rely on converting molecular and cellular features to unique sequence barcodes, which are then detected with the transcriptome.

Here, we introduce FBA, a flexible and streamlined package to perform quality control, quantification, demultiplexing, multiplet detection, clustering, and visualization of feature barcoding assays.

FBA is available on PyPi at https//pypi.org/project/fba and on GitHub at https//github.com/jlduan/fba.

Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.Tails are a defining characteristic of chordates and show enormous diversity in function and shape. Although chordate tails share a common evolutionary and genetic-developmental origin, tails are extremely versatile in morphology and function. For example, tails can be short or long, thin or thick, feathered or spiked, and they can be used for propulsion, communication, or balancing, and they mediate in predator-prey outcomes. Depending on the species of animal the tail is attached to, it can have extraordinarily multi-functional purposes. Despite its morphological diversity and broad functional roles, tails have not received similar scientific attention as, for example, the paired appendages such as legs or fins. This forward-looking review article is a first step towards interdisciplinary scientific synthesis in tail research. We discuss the importance of tail research in relation to five topics 1) Evolution and Development, 2) Regeneration, 3) Functional Morphology, 4) Sensorimotor Control, and 5) Computational and Physical Models. Within each of these areas, we highlight areas of research and combinations of long-standing and new experimental approaches to move the field of tail research forward. To best advance a holistic understanding of tail evolution and function, it is imperative to embrace an interdisciplinary approach, re-integrating traditionally siloed fields around discussions on tail-related research.
Human and animal studies suggest that hypothalamic-pituitary-adrenal axis (HPA-A) function may be programmed in utero; however, these findings are inconsistent. Given the powerful metabolic actions of cortisol, it is important to clarify the influence of early life on adult HPA-A function.

To determine the relationship between fetal growth and HPA-A stress response to a psychosocial stressor in young adults.

Multigenerational, prospective cohort study (The Raine Study) conducted between 1989 and 1991.

King Edward Memorial Hospital, Perth, Western Australia, Australia.

917 participants aged 18 from Gen 2 of the Raine Study.

Measures of Hypothalamic-Pituitary-Adrenal-Axis function before and after exposure to the Trier Social Stress Test.

In fully adjusted models, an inverse linear relationship was observed between birth weight and and plasma measures of 1) baseline cortisol (β = -0.90%, 95% CI -1.73 to -0.07; p = 0.03); 2) peak cortisol (β = -0.78%, 95% CI -1.51 to -0.06; p=0.03); 3) AUCg (β = -0.89%, 95% CI -1.60 to -0.18; p=0.01); and 4) adrenal sensitivity (β = -1.02, 95% CI -1.85 to -0.18; p=0.02). Similar results were demonstrated for per cent optimal birth weight. link3 No consistent quadratic relationships were identified. No associations were found between measures of fetal adiposity and HPA-A function at age 18, or fetal growth and HPA-A response pattern. Removal of anticipatory responders from the models substantially attenuated the observed relationships.

We observed an inverse linear relationship between fetal growth and HPA-A function at age 18. This differs from the inverse parabolic relationship (inverted U curve) reported in adults of advanced age. Altered adrenal sensitivity may underlie this relationship.
We observed an inverse linear relationship between fetal growth and HPA-A function at age 18. This differs from the inverse parabolic relationship (inverted U curve) reported in adults of advanced age. Altered adrenal sensitivity may underlie this relationship.
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