UNSUPERVISED LEARNING IN PHYLOGENOMIC ANALYSIS OVER THE SPACE OF PHYLOGENETIC TREES

A phylogenetic tree is a tree to represent an evolutionary history between species or other entities. Phylogenomics is a new field intersecting phylogenetics and genomics and it is well-known that we need statistical learning methods to handle and analyze a large amount of data which can be generated relatively cheaply with new technologies. Based on the existing Markov models, we introduce a new method, CURatio, to identify outliers in a given gene data set. This method, intrinsically an unsupervised method, can find outliers from thousands or even more genes. This ability to analyze large amounts of genes (even with missing information) makes it unique in many parametric methods. At the same time, the exploration of statistical analysis in high-dimensional space of phylogenetic trees has never stopped, many tree metrics are proposed to statistical methodology. Tropical metric is one of them. We implement a MCMC sampling method to estimate the principal components in a tree space with the tropical metric for achieving dimension reduction and visualizing the result in a 2-D tropical triangle

Tropical Geometry of Phylogenetic Tree Space: A Statistical Perspective

Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. As data objects, they are characterized by the challenges associated with "big data," as well as the complication that their discrete geometric structure results in a non-Euclidean phylogenetic tree space, which poses computational and statistical limitations. We propose and study a novel framework to study sets of phylogenetic trees based on tropical geometry. In particular, we focus on characterizing our framework for statistical analyses of evolutionary biological processes represented by phylogenetic trees. Our setting exhibits analytic, geometric, and topological properties that are desirable for theoretical studies in probability and statistics, as well as increased computational efficiency over the current state-of-the-art. We demonstrate our approach on seasonal influenza data.Comment: 28 pages, 5 figures, 1 tabl

Evaluation of the reporting quality of clinical practice guidelines on gliomas using the RIGHT checklist

Background: The reporting quality of clinical practice guidelines (CPGs) for gliomas has not yet been thoroughly assessed. The International Reporting Items for Practice Guidelines in Healthcare (RIGHT) statement developed in 2016 provides a reporting framework to improve the quality of CPGs. We aimed to estimate the reporting quality of glioma guidelines using the RIGHT checklist and investigate how the reporting quality differs by selected characteristics. Methods: We systematically searched electronic databases, guideline databases, and medical society websites to retrieve CPGs on glioma published between 2018 and 2020. We calculated the compliance of the CPGs to individual items, domains and the RIGHT checklist overall. We performed stratified analyses by publication year, country of development, reporting of funding, and impact factor (IF) of the journal. Results: Our search revealed 20 eligible guidelines. Mean overall adherence to the RIGHT statement was 54.6%. Eight CPGs reported more than 60% of the items, and five reported less than 50%. All guidelines adhered to the items 1a, 3, 7a, 13a, while no guidelines reported the items 17 or 18b (see http://www.rightstatement.org/right-statement/checklist for a description of the items). Two of the seven domains, "Basic information" and "Background", had mean reporting rates above 60%. The "Review and quality assurance" domain had the lowest mean reporting rate, 12.5%. The reporting quality of guidelines published in 2020, guidelines developed in the United States, and guidelines that reported funding tended to be above average. Conclusions: The reporting quality of CPGs on gliomas is low and needs improvement. Particular attention should be paid on reporting the external review and quality assurance process. The use of the RIGHT criteria should be encouraged to guide the development, reporting and evaluation of CPGs

A Novel Non-Volatile Inverter-based CiM: Continuous Sign Weight Transition and Low Power on-Chip Training

In this work, we report a novel design, one-transistor-one-inverter (1T1I), to satisfy high speed and low power on-chip training requirements. By leveraging doped HfO2 with ferroelectricity, a non-volatile inverter is successfully demonstrated, enabling desired continuous weight transition between negative and positive via the programmable threshold voltage (VTH) of ferroelectric field-effect transistors (FeFETs). Compared with commonly used designs with the similar function, 1T1I uniquely achieves pure on-chip-based weight transition at an optimized working current without relying on assistance from off-chip calculation units for signed-weight comparison, facilitating high-speed training at low power consumption. Further improvements in linearity and training speed can be obtained via a two-transistor-one-inverter (2T1I) design. Overall, focusing on energy and time efficiencies, this work provides a valuable design strategy for future FeFET-based computing-in-memory (CiM)

Identification and expression pattern analysis of the OsSnRK2 gene family in rice

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a class of plant-specific serine/threonine (Ser/Thr) protein kinase that plays an important role in rice stress tolerance, growth and development. However, systematic bioinformatics and expression pattern analysis have not been reported. In the current study, ten OsSnRK2 genes were identified in the rice genome and located on 7 chromosomes, which can be classified into three subfamilies (I, II, and III). Many cis-regulatory elements were identified in the promoter region of OsSnRK2 genes, including hormone response elements, defense and stress responsive elements, indicating that the OsSnRK2 family may play a crucial role in response to hormonal and abiotic stress. Quantitative tissue analysis showed that OsSnRK2 genes expressed in all tissues of rice, but the expression abundance varied from different tissues and showed varietal variability. In addition, expression pattern of OsSnRK2 were analyzed under abiotic stress (salt, drought, salt and drought) and showed obvious difference in diverse abiotic stress. In general, these results provide useful information for understanding the OsSnRK2 gene family and analyzing its functions in rice in response to ABA, salt and drought stress, especially salt-drought combined stress

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths

Evolutionary hypotheses provide important underpinnings of biological and medical sciences, and comprehensive, genome-wide understanding of evolutionary relationships among organisms are needed to test and refine such hypotheses. Theory and empirical evidence clearly indicate that phylogenies (trees) of different genes (loci) should not display precisely matching topologies. The main reason for such phylogenetic incongruence is reticulated evolutionary history of most species due to meiotic sexual recombination in eukaryotes, or horizontal transfers of genetic material in prokaryotes. Nevertheless, many genes should display topologically related phylogenies, and should group into one or more (for genetic hybrids) clusters in poly-dimensional “tree space”. Unusual evolutionary histories or effects of selection may result in “outlier” genes with phylogenies that fall outside the main distribution(s) of trees in tree space. We present a new phylogenomic method, CURatio, which uses ratios of total branch lengths in gene trees to help identify phylogenetic outliers in a given set of ortholog groups from multiple genomes. An advantage of CURatio over other methods is that genes absent from and/or duplicated in some genomes can be included in the analysis. We conducted a simulation study under the coalescent model, and showed that, given sufficient species depth and topological difference, these ratios are significantly higher for the “outlier” gene phylogenies. Also, we applied CURatio to a set of annotated genomes of the fungal family, Clavicipitaceae, and identified alkaloid biosynthesis genes as outliers, probably due to a history of duplication and loss. The source code is available at https://github.com/QiwenKang/CURatio, and the empirical data set on Clavicipitaceae and simulated data set are available at Mendeley https://data.mendeley.com/datasets/mrxts7wjrr/1

Marrow Adipose Tissue: Its Origin, Function, and Regulation in Bone Remodeling and Regeneration

Marrow adipose tissue (MAT) is a unique fat depot in the bone marrow and exhibits close relationship with hematopoiesis and bone homeostasis. MAT is distinct from peripheral adipose tissue in respect of its heterogeneous origin, site-specific distribution, and complex and perplexing function. Though MAT is indicated to function in hematopoiesis, skeletal remodeling, and energy metabolism, its explicit characterization still requires further research. In this review, we highlight recent advancement made in MAT regarding the origin and distribution of MAT, the local interaction with bone homeostasis and hematopoietic niche, the systemic endocrine regulation of metabolism, and MAT-based strategies to enhance bone formation

Skeleton model based behavior recognition for pedestrians and cyclists from vehicle sce ne camera

With the significant advances in computer vision research, skeleton model based human pose recognition has become more accurate and time-efficient, although most of the applications are limited in laboratory environment or on surveillance videos. This paper proposes a pose tracking and behavior recognition method from in-vehicle scene camera. It will not only detect pedestrians on the road, but also generate their skeleton models describing head, limb, and trunk movements. Based on these more detailed movements of body parts, the proposed method is designed to track poses of pedestrians and cyclists with the potentials to enable automated pedestrian gesture reading and non-verbal interactions between autonomous vehicles and pedestrians. The proposed algorithm has been tested on different databases including TASI 110-car naturalistic driving database and Joint Attention for Autonomous Driving (JAAD) database. Results show that key frames describing different pedestrian and cyclist negotiation gestures are detected from the raw video streams using the proposed method. These results will improve our understanding of pedestrian and cyclist's intentions and can be further used for autonomous vehicle control algorithm development

Tropical Geometry of Phylogenetic Tree Space A Statistical Perspective

Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. As data objects, they are characterized by the challenges associated with “big data,” as well as the complication that their discrete geometric structure results in a non-Euclidean phylogenetic tree space, which poses com- putational and statistical limitations. We propose and study a novel framework based on tropical geometry and discuss its implications in the statistical analysis of evolutionary biological processes represented by phylogenetic trees. Our setting exhibits analytic, geometric, and topological properties that are desirable for theoretical studies in probability and statistics, as well as increased computational efficiency over the current state-of-the-art. We demonstrate our approach on seasonal influenza data