scholarly journals phylopath: Easy phylogenetic path analysis in R

2017 ◽  
Author(s):  
Wouter van der Bijl
Keyword(s):  
Experimental Data ◽  
Path Analysis ◽  
Observational Data ◽  
Brain Size ◽  
Causal Models ◽  
List Type ◽  
Binary Variables ◽  
Link Type ◽  
The Relationship

AbstractConfirmatory path analysis allows researchers to evaluate and compare causal models using observational data. This tool has great value for comparative biologists since they are often unable to gather experimental data on macro-evolutionary hypotheses, but is cumbersome and error-prone to perform.I introducephylopath, anRpackage that implements phylogenetic path analysis (PPA) as described by Von Hardenberg & Gonzalez-Voyer (2013). In addition to the published method, I provide support for the inclusion of binary variables.I illustrate PPA andphylopathby recreating part of a study on the relationship between brain size and vulnerability to extinction.The package aims to make the analysis straight-forward, providing convenience functions and several plotting methods, which I hope will encourage the spread of the method.phylopathis released under the GPL-3 license, and is freely available on CRAN (https://cran.r-project.org/web/packages/phylopath/index.html) and GitHub (https://github.com/Ax3man/phylopath).

scholarly journals phylopath: Easy phylogenetic path analysis in R

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4718 ◽  
Author(s):  
Wouter van der Bijl
Keyword(s):  
Experimental Data ◽  
Path Analysis ◽  
Observational Data ◽  
Brain Size ◽  
R Package ◽  
Causal Models ◽  
Binary Variables ◽  
The Relationship

Confirmatory path analysis allows researchers to evaluate and compare causal models using observational data. This tool has great value for comparative biologists since they are often unable to gather experimental data on macro-evolutionary hypotheses, but is cumbersome and error-prone to perform. I introducephylopath, an R package that implements phylogenetic path analysis (PPA) as described by von Hardenberg & Gonzalez-Voyer (2013). In addition to the published method, I provide support for the inclusion of binary variables. I illustrate PPA andphylopathby recreating part of a study on the relationship between brain size and vulnerability to extinction. The package aims to make the analysis straight-forward, providing convenience functions, and several plotting methods, which I hope will encourage the spread of the method.

scholarly journals Understanding primate brain evolution

2007 ◽  
Vol 362 (1480) ◽  
pp. 649-658 ◽  
Author(s):  
R.I.M Dunbar ◽  
Susanne Shultz
Keyword(s):  
Life History ◽  
Path Analysis ◽  
Group Size ◽  
Brain Size ◽  
Brain Evolution ◽  
Primate Brain ◽  
The Social ◽  
Large Brain ◽  
Brain Data ◽  
The Relationship

We present a detailed reanalysis of the comparative brain data for primates, and develop a model using path analysis that seeks to present the coevolution of primate brain (neocortex) and sociality within a broader ecological and life-history framework. We show that body size, basal metabolic rate and life history act as constraints on brain evolution and through this influence the coevolution of neocortex size and group size. However, they do not determine either of these variables, which appear to be locked in a tight coevolutionary system. We show that, within primates, this relationship is specific to the neocortex. Nonetheless, there are important constraints on brain evolution; we use path analysis to show that, in order to evolve a large neocortex, a species must first evolve a large brain to support that neocortex and this in turn requires adjustments in diet (to provide the energy needed) and life history (to allow sufficient time both for brain growth and for ‘software’ programming). We review a wider literature demonstrating a tight coevolutionary relationship between brain size and sociality in a range of mammalian taxa, but emphasize that the social brain hypothesis is not about the relationship between brain/neocortex size and group size per se ; rather, it is about social complexity and we adduce evidence to support this. Finally, we consider the wider issue of how mammalian (and primate) brains evolve in order to localize the social effects.

Identifying Physico-Chemical Laws from the Robotically Collected Data

2019 ◽  
Author(s):  
Liwei Cao ◽  
Danilo Russo ◽  
Vassilios S. Vassiliadis ◽  
Alexei Lapkin
Keyword(s):  
Experimental Data ◽  
Numerical Models ◽  
Predictor Variable ◽  
Physical Models ◽  
Training Data ◽  
Mixed Integer ◽  
Physico Chemical ◽  
Data Points ◽  
Future Work ◽  
The Relationship

<p>A mixed-integer nonlinear programming (MINLP) formulation for symbolic regression was proposed to identify physical models from noisy experimental data. The formulation was tested using numerical models and was found to be more efficient than the previous literature example with respect to the number of predictor variables and training data points. The globally optimal search was extended to identify physical models and to cope with noise in the experimental data predictor variable. The methodology was coupled with the collection of experimental data in an automated fashion, and was proven to be successful in identifying the correct physical models describing the relationship between the shear stress and shear rate for both Newtonian and non-Newtonian fluids, and simple kinetic laws of reactions. Future work will focus on addressing the limitations of the formulation presented in this work, by extending it to be able to address larger complex physical models.</p><p><br></p>

Simulation on Extrusion Comminution Model of Roller Press

2010 ◽  
Vol 156-157 ◽  
pp. 1702-1707
Author(s):  
Xiang Wen Cheng ◽  
Jinchao Liu ◽  
Qi Zhi Ding ◽  
Li Ming Song ◽  
Zhan Lin Wang
Keyword(s):  
Experimental Data ◽  
Particle Size ◽  
Field Experiments ◽  
Size Ratio ◽  
Optimum Operating ◽  
Extrusion Force ◽  
Particle Size Ratio ◽  
Small Constant ◽  
Working Parameters ◽  
The Relationship

How to predict the relationship among particle size and among product size, to establish the relationship between the granularity and working parameters in the process of grinding and to determine the optimum operating parameters. With proposing BS squeeze crush model by L. Bass and the idea of roll surface division as the material uneven extrusion force are adopted. Based on field experiments the experimental data is analyzed, the select function and the breakage functions are fitted with MATLAB software, and obtaining their model. The comminution model is determined by the roller division. We obtain the model parameter through the experimental data. Through model analysis shows: the relationship between particle breakage and energy absorption, namely the smaller size of the same power, the lower broken; the breakage diminishes with the decrease of particle size ratio and it will be tending to a small constant when the smaller particle size ratio. The breakage functions rapidly decrease within ratio of between 0.2-0.7. This shows: the energy consumption will rapidly increase when the particle size of less than 0.2 in broken; the selection diminish with the decrease of particle size. Pressure (8-9MPa) should be the most appropriate value.

scholarly journals Homeopathy for Covid-19 in Primary Care: A structured summary of a study protocol for a randomized controlled trial

Trials ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ubiratan Cardinalli Adler ◽  
Maristela Schiabel Adler ◽  
Livia Mitchiguian Hotta ◽  
Ana Elisa Madureira Padula ◽  
Amarilys de Toledo Cesar ◽  
...  
Keyword(s):  
Primary Care ◽  
Alternative Hypothesis ◽  
University Hospital ◽  
List Type ◽  
Study Medication ◽  
Link Type ◽  
Care Protocol ◽  
Full Protocol ◽  
Isolation Period

Abstract Objectives To investigate the effectiveness and safety of homeopathic medicine Natrum muriaticum (LM2) for mild cases of COVID-19 in Primary Health Care. Trial design A randomized, two-armed (1:1), parallel, placebo-controlled, double-blind, clinical trial is being performed to test the following hypotheses: H0: homeopathic medicines = placebo (null hypothesis) vs. H1: homeopathic medicines ≠ placebo (alternative hypothesis) for mild cases of COVID-19 in Primary Care. Participants Setting: Primary Care of São Carlos – São Paulo – Brazil. One hundred participants aged 18 years or older, with Influenza-like symptoms and a positive RT-PCR for SARS-CoV-2. Willingness to give informed consent and to comply with the study procedures is also required. Exclusion criterium: severe acute respiratory syndrome. Intervention and comparator Homeopathy: 1 globule of Natrum muriaticum LM2 diluted in 20 mL of alcohol 30% and dispensed in a 30 ml bottle. Placebo: 20 mL of alcohol 30% dispensed in a 30 ml bottle. Posology: one drop taken orally every 4 hours (6 doses/day) while there is fever, cough, tiredness, or pain (headache, sore throat, muscle aches, chest pain, etc.) followed by one drop every 6 hours (4 doses/day) until the fourteenth day of use. The bottle of study medication should be submitted to 10 vigorous shakes (succussions) before each dose. Posology may be changed by telemedicine, with no break in blinding. Study medication should be maintained during home isolation. According to the Primary Care protocol, the home isolation period lasts until the 10th day after the appearance of the first symptom, or up to 72 hours without symptoms. Main outcomes The primary endpoint will be time to recovery, defined as the number of days elapsed before all COVID-19 Influenza-like symptoms are recorded as mild or absent during home isolation period. Secondary measures are recovery time for each COVID-19 symptom; score of the scale created for the study (COVID-Simile Scale); medicines used during follow-up; number of days of follow-up; number of visits to emergency services; number of hospitalizations; other symptoms and Adverse Events during home isolation period. Randomisation The study Statistician generated a block randomization list, using a 1:1 ratio of the two groups (denoted as A and B) and a web-based tool (http://www.random.org/lists). Blinding (masking) The clinical investigators, the statistician, the Primary Care teams, the study collaborators, and the participants will remain blinded from the identity of the two treatment groups until the end of the study. Numbers to be randomised (sample size) One hundred participants are planned to be randomized (1:1) to placebo (50) or homeopathy (50). Trial Status Protocol version/date May 21, 2020. Recruitment is ongoing. First participant was recruited/included on June 29,2020. Due to recruitment adaptations to Primary Care changes, the authors anticipate the trial will finish recruiting on April 10, 2021. Trial registration COVID-Simile Study was registered at the University Hospital Medical Information Network (UMIN - https://www.umin.ac.jp/ctr/index.htm) on June 1st, 2020, and the trial start date was June 15, 2020. Unique ID: UMIN000040602. Full protocol The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.

scholarly journals Influential Path of Social Risk Factors toward Suicidal Behavior—Evidence from Chinese Sina Weibo Users 2013–2018

2021 ◽  
Vol 18 (5) ◽  
pp. 2604
Author(s):  
Yujin Han ◽  
He Li ◽  
Yunyu Xiao ◽  
Ang Li ◽  
Tingshao Zhu
Keyword(s):  
Risk Factors ◽  
Path Analysis ◽  
Suicide Prevention ◽  
Suicidal Behavior ◽  
Empirical Support ◽  
National Bureau ◽  
Social Risk ◽  
Analysis Model ◽  
The Relationship ◽  
Path Analysis Model

(1) Purpose: The purpose of this study was to determine suicidal risk factors, the relationship and the underlying mechanism between social variables and suicidal behavior. We hope to provide empirical support for the future suicide prevention of social media users at the social level. (2) Methods: The path analysis model with psychache as the mediate variable was constructed to analyze the relationship between suicidal behavior and selected social macro variables. The data for our research was taken from the Chinese Suicide Dictionary, Moral Foundation Dictionary, Cultural Value Dictionary and National Bureau of Statistics. (3) Results: The path analysis model was an adequate representation of the data. With the mediator psychache, higher authority vice, individualism, and disposable income of residents significantly predicted less suicidal behavior. Purity vice, collectivism, and proportion of the primary industry had positive significant effect on suicidal behavior via the mediator psychache. The coefficients of harm vice, fairness vice, ingroup vice, public transport and car for every 10,000 people, urban population density, gross domestic product (GDP), urban registered unemployment rate, and crude divorce rate were not significant. Furthermore, we applied the model to three major economic development belts in China. The model’s result meant different economic zones had no influence on the model designed in our study. (4) Conclusions: Our evidence informs population-based suicide prevention policymakers that incorporating some social factors like authority vice, individualism, etc. can help prevent suicidal ideation in China.

scholarly journals COVID-19 uncertainty and sleep: the roles of perceived stress and intolerance of uncertainty during the early stage of the COVID-19 outbreak

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dan Wu ◽  
Tingzhong Yang ◽  
Daniel L. Hall ◽  
Guihua Jiao ◽  
Lixin Huang ◽  
...  
Keyword(s):  
Path Analysis ◽  
Perceived Stress ◽  
Mediation Analysis ◽  
Early Stage ◽  
Intolerance Of Uncertainty ◽  
Policy Implications ◽  
Self Report ◽  
Poor Sleep ◽  
The Relationship

Abstract Background The COVID-19 pandemic brings unprecedented uncertainty and stress. This study aimed to characterize general sleep status among Chinese residents during the early stage of the outbreak and to explore the network relationship among COVID-19 uncertainty, intolerance of uncertainty, perceived stress, and sleep status. Methods A cross-sectional correlational survey was conducted online. A total of 2534 Chinese residents were surveyed from 30 provinces, municipalities, autonomous regions of China and regions abroad during the period from February 7 to 14, 2020, the third week of lockdown. Final valid data from 2215 participants were analyzed. Self-report measures assessed uncertainty about COVID-19, intolerance of uncertainty, perceived stress, and general sleep status. Serial mediation analysis using the bootstrapping method and path analysis were applied to test the mediation role of intolerance of uncertainty and perceived stress in the relationship between uncertainty about COVID-19 and sleep status. Results The total score of sleep status was 4.82 (SD = 2.72). Age, place of residence, ethnicity, marital status, infection, and quarantine status were all significantly associated with general sleep status. Approximately half of participants (47.1%) reported going to bed after 12:00 am, 23.0% took 30 min or longer to fall asleep, and 30.3% slept a total of 7 h or less. Higher uncertainty about COVID-19 was significantly positively correlated with higher intolerance of uncertainty (r = 0.506, p < 0.001). The mediation analysis found a mediating role of perceived stress in the relationship between COVID-19 uncertainty and general sleep status (β = 0.015, 95%C.I. = 0.009–0.021). However, IU was not a significant mediator of the relationship between COVID-19 uncertainty and sleep (β = 0.009, 95%C.I. = − 0.002–0.020). Moreover, results from the path analysis further showed uncertainty about COVID-19 had a weak direct effect on poor sleep (β = 0.043, p < 0.05); however, there was a robust indirect effect on poor sleep through intolerance of uncertainty and perceived stress. Conclusions These findings suggest that intolerance of uncertainty and perceived stress are critical factors in the relationship between COVID-19 uncertainty and sleep outcomes. Results are discussed in the context of the COVID-19 pandemic, and practical policy implications are also provided.

scholarly journals Inter-professional agreement and collaboration between extended scope physiotherapists and orthopaedic surgeons in an orthopaedic outpatient shoulder clinic – a mixed methods study

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Merete Nørgaard Madsen ◽  
Maria Lange Kirkegaard ◽  
Thomas Martin Klebe ◽  
Charlotte Lorenzen Linnebjerg ◽  
Søren Martin Riis Villumsen ◽  
...  
Keyword(s):  
Treatment Plan ◽  
Random Order ◽  
Primary Diagnosis ◽  
Diagnosis And Treatment ◽  
List Type ◽  
Professional Collaboration ◽  
Relational Coordination ◽  
Orthopaedic Surgeons ◽  
Link Type ◽  
Shoulder Disorders

Abstract Background Extended scope physiotherapists (ESP) are increasingly supplementing orthopaedic surgeons (OS) in diagnosing patients with musculoskeletal disorders. Studies have reported satisfactory diagnostic and treatment agreement between ESPs and OSs, but methodological study quality is generally low, and only few studies have evaluated inter-professional collaboration. Our aims were: 1) to evaluate agreement on diagnosis and treatment plan between ESPs and OSs examining patients with shoulder disorders, 2) to explore and evaluate their inter-professional collaboration. Methods In an orthopaedic outpatient shoulder clinic, 69 patients were examined independently twice on the same day by an ESP and an OS in random order. Primary and secondary diagnoses (nine categories) and treatment plan (five categories, combinations allowed) were registered by each professional and compared. Percentage of agreement and kappa-values were calculated. Two semi-structured focus-group interviews were performed with ESPs and OSs, respectively. Interviews were based on the theoretical concept of Relational Coordination, encompassing seven dimensions of communication and relationship among professionals. A thematic analysis was conducted. Results Agreement on primary diagnosis was 62% (95% CI: [50; 73]). ESPs and OSs agreed on the combination of diagnoses in 79% (95% CI: [70; 89]) of the cases. Partial diagnostic agreement (one professional’s primary diagnosis was also registered as either primary or secondary diagnosis by the other) was 96% (95% CI: [91; 100]). Across treatment categories, agreement varied between 68% (95% CI: [57; 79]) and 100%. In 43% (95% CI: [31; 54]) of the cases, ESP and OS had full concordance between treatment categories chosen, while they agreed on at least one recommendation in 96% (95% CI: [91; 100]). Positive statements of all dimensions of relational coordination were found. Three themes especially important in the inter-professional collaboration emerged: Close communication, equal and respectful relationship and professional skills. Conclusions In the majority of cases, the ESP and OS registered the same or partly the same diagnosis and treatment plan. Indications of a high relational coordination implying a good inter-professional collaboration were found. Our results support that ESPs and OSs can share the task of examining selected patients with shoulder disorders in an orthopaedic clinic. Trial registration ClinicalTrials.gov Identifier: NCT03343951. Registered 10 November 2017

347 Clinical outcomes of ovarian cancer patients treated with ALKS 4230, a novel engineered cytokine, in combination with pembrolizumab: ARTISTRY-1 trial

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A372-A373
Author(s):  
Ira Winer ◽  
Lucy Gilbert ◽  
Ulka Vaishampayan ◽  
Seth Rosen ◽  
Christopher Hoimes ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
T Cells ◽  
Tumor Microenvironment ◽  
Tumor Marker ◽  
Solid Tumors ◽  
Cd8 T Cells ◽  
Comprehensive Cancer Center ◽  
List Type ◽  
Link Type ◽  
Heavily Pretreated

BackgroundALKS 4230 is a novel engineered cytokine that selectively targets the intermediate-affinity interleukin-2 receptor complex to activate CD8+ T cells and natural killer cells.1 The ARTISTRY-1 trial (NCT02799095) has shown encouraging efficacy and acceptable tolerability of ALKS 4230 among patients with advanced solid tumors.2 We report a detailed analysis of ovarian cancer (OC) patients who received combination therapy in ARTISTRY-1.MethodsARTISTRY-1 is an ongoing multicohort phase 1/2 trial exploring intravenous ALKS 4230 as monotherapy and combined with pembrolizumab. OC patients were enrolled into a cohort with mixed anti PD 1/L1 unapproved tumor types who had progressed on prior chemotherapy. OC patients received ALKS 4230 (3 µg/kg) on days 1–5 and pembrolizumab (200 mg) on day 1 of a 21 day cycle. Outcomes presented include antitumor activity (RECIST v1.1) and safety as of 7/24/2020. To evaluate changes in tumor microenvironment (TME), baseline and on-treatment biopsies were collected.ResultsFourteen heavily pretreated patients with OC were enrolled. Patients received a median of 5 (range, 2 11) prior regimens and all were previously treated with platinum based therapy. Among 13 evaluable patients with ≥1 assessment, 9 experienced disease control and 4 experienced disease progression; median treatment duration was approximately 7 weeks. Three patients experienced an objective response, including 1 complete response, 1 partial response (PR), and 1 unconfirmed PR; all were platinum resistant and negative for BRCA mutations. Five patients experienced tumor burden reductions (table 1). Treatment-related adverse events at the doses tested have generally been transient and manageable, with the majority being grade 1 and 2 in severity. Overall, based on preliminary data, the combination with ALKS 4230 did not demonstrate any additive toxicity to that already established with pembrolizumab alone. Additional safety and efficacy data are being collected in ongoing cohorts. In the monotherapy dose escalation portion of the study, ALKS 4230 alone increased markers of lymphocyte infiltration in 1 paired melanoma biopsy (1 of 1; on treatment at cycle 2); CD8+ T cell density and PD-L1 tumor proportion score increased 5.2- and 11 fold, respectively, supporting evidence that ALKS 4230 has immunostimulatory impact on the TME and providing rationale for combining ALKS 4230 with pembrolizumab (figure 1).Abstract 347 Table 1Summary of response observations among patients with ovarian cancerAbstract 347 Figure 1Increased markers of lymphocyte tumor infiltrationAn increase in CD3+CD8+ T cells (A, red = CD3; blue = CD8; purple = CD3+CD8+; teal = tumor marker), GranzymeB (B, red = CD8; green = granzymeB; yellow = granzymeB+CD8+; teal = tumor marker), and PD-L1 (C, red = PD-L1; blue = tumor marker) in the tumor microenvironment of a single patient was observed after the patient received monotherapy ALKS 4230ConclusionsThe combination of ALKS 4230, an investigational agent, and pembrolizumab demonstrates an acceptable safety profile and provides some evidence of tumor shrinkage and disease stabilization in some patients with heavily pretreated OC. This regimen could represent a new therapeutic option for these patients.AcknowledgementsThe authors would like to thank all of the patients who are participating in this trial and their families. The trial is sponsored by Alkermes, Inc. Medical writing and editorial support was provided by Parexel and funded by Alkermes, Inc.Trial RegistrationClinicalTrials. gov NCT02799095Ethics ApprovalThis trial was approved by Ethics and Institutional Review Boards (IRBs) at all trial sites; IRB reference numbers 16–229 (Dana-Farber Cancer Institute), MOD00003422/PH285316 (Roswell Park Comprehensive Cancer Center), 20160175 (Western IRB), i15-01394_MOD23 (New York University School of Medicine), TRIAL20190090 (Cleveland Clinic), and 0000097 (ADVARRA).ReferencesLopes JE, Fisher JL, Flick HL, Wang C, Sun L, Ernstoff MS, et al. ALKS 4230: a novel engineered IL-2 fusion protein with an improved cellular selectivity profile for cancer immunotherapy. J Immunother Cancer 2020;8:e000673. doi: 10.1136/jitc-2020-000673.Vaishampayan UN, Muzaffar J, Velcheti V, Winer I, Hoimes CJ, Rosen SD, et al. ALKS 4230 monotherapy and in combination with pembrolizumab (pembro) in patients (pts) with refractory solid tumors (ARTISTRY-1). Oral presentation at: European Society for Medical Oncology Annual Meeting; September 2020; virtual.

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