Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic Divergence Time, Algorithms for Improved Accuracy and Performance

The inference of species divergence time is a key step in the study of phylogenetics. Methods have been available for the last ten years to perform the inference, but, there are two significant problems with these methods. First, the performance of the methods does not yet scale well to studies with hundreds of taxa and thousands of DNA base pairs. A study of 349 taxa was estimated to require over 9 months of processing time. Second, the accuracy of the inference process is subject to bias and variance in the specification of model parameters that is not completely understood. These parameters include both the topology of the phylogenetic tree and, more importantly for our purposes, the set of fossils used to calibrate the tree. In this work, we present new algorithms and methods to improve the performance of the divergence time process. We demonstrate a new algorithm for the computation of phylogenetic likelihood and experimentally illustrate a 90% improvement in likelihood computation time on the aforementioned dataset of 349 taxa with over 60,000 DNA base pairs. Additionally we show a new algorithm for the computation of the Bayesian prior on node ages that is experimentally shown to reduce the time for this computation on the 349 taxa dataset by 99%. Using our high performance methods, we present a novel new method for assessing the level of support for the ages inferred. This method utilizes a statistical jackknifing technique on the set of fossil calibrations producing a support value similar to the bootstrap used in phylogenetic inference. Finally, we present efficient methods for divergence time inference on sets of trees based on our development of subtree sharing models. We show a 60% improvement in processing times on a dataset of 567 taxa with over 10,000 DNA base pairs.
Gliosarcoma Protein - Protein Interaction Network Analysis and Gene Ontology

Background: Gliosarcoma (GS) is a rare primary neoplasm of the central nervous system. It is a subtype of glioblastoma and has a biphasic pattern consisting of glial and malignant mesenchymal elements. Its onset is between the fourth and sixth decade of life. Objectives: Since protein - protein interaction (PPI) network analysis can provide useful information about molecular aspects of diseases, the aim of this study is GS protein analysis via PPI network and gene ontology assessment. Methods: The related genes to GS were gathered from STRING DB and organized in the interacted network by Cytoscape software version 3.6. 0. The network was analyzed based on topological parameters and the central nodes were introduced. The significant clusters were identified by ClusterONE and the cluster included more key genes enriched via gene ontology by ClueGO. Results: Nine crucial genes including TP53, EGFR, PTEN, EGR1, VEGFA, HSP90AA1, IL2, KNG1, and HSP90AB1 were introduced as related key genes to GS. Two significant clusters contain most of central genes. Twenty - one elements of cluster - 1, which included 7 key genes, were enriched via gen ontology and 115 related terms were determined and discussed. Conclusions: The nine introduced central genes may play main roles in pathology of GS. However, experimental investigation is proposed to validate the findings.
The Role of the Experiment in the Study of the Language Material

The article deals with the role of the experiment in the study of the language material. As it is known the learning of voices is very difficult, and it requires great attention. In this case it is necessary to use the opportunities of experimental phonetics. It should be stressed that the role of experiment in the investigation of the language facts through experiment has long been proved. The author uses expedient to investigate the acoustic peculiarities of the language voices. The intonation is used to be closely related to the various emotions of a person in the speech acts. In recent years, the application of principles, conceptual schemes, ideas and concepts derived from psycho- and sociolinguistics and linguistic pragmatics in the field of intonation has become widespread. Intonation must be studied at the communicative level. Semantic categories expressed in intonation units usually refer to the communicative components of speech. In the grammatical structure of the sentence, they can correspond to the composition of any length. Accordingly, the "sphere of activity" of intonation units can have different components from word to sentence at the hierarchical level.
On the structure of streamwise wall-shear stress fluctuations in turbulent channel flows

In this study, we use a two-dimensional clustering methodology to identify the high-and low-speed structures of the streamwise wall-shear fluctuations in turbulent channel flows at different Reynolds numbers. The statistical properties of the high- and low-speed structures, such as geometrical characteristics, fluctuating intensities and conditional velocity fluctuations, are shown to be remarkably asymmetrical. The low-speed structures are closely related with the celebrated attached eddies. Our work may aid to the future development of the attached-eddy model.
Anomalous Upper-Ocean Circulation of the Western Equatorial Pacific following El Niño Events

Mooring measurements at ~140°E in the western equatorial Pacific Ocean documented greatly intensified eastward subsurface currents, which largely represent the nascent Equatorial Undercurrent, to ~67 cm s−1 in boreal summer of 2016. The eastward currents occupied the entire upper 500 m while the westward surface currents nearly disappeared. Historical in situ data observed similar variations after most El Niño events. Further analysis combining satellite and reanalysis data reveals that the eastward currents observed at ~140°E are a component of an anomalous counterclockwise circulation straddling the equator, with westward current anomalies retroflecting near the western boundary and feeding southeastward current anomalies along the New Guinea coast. A 1.5-layer reduced-gravity ocean model is able to crudely reproduce these variations, and a hierarchy of sensitivity experiments is performed to understand the underlying dynamics. The anomalous circulation is largely the delayed ocean response to equatorial wind anomalies over the central-to-eastern Pacific basin emerging in the mature stage of El Niño. Downwelling Rossby waves are generated by the reflection of equatorial Kelvin waves and easterly winds in the eastern Pacific. Upon reaching the western Pacific, the southern lobes of Rossby waves encounter the slanted New Guinea island and deflect to the equator, establishing a local sea surface height maximum and leading to the detour of westward currents flowing from the Pacific interior. Additional experiments with edited western boundary geometry confirm the importance of topography in regulating the structure of this cross-equatorial anomalous circulation.
Political Science Is a Data Science*

This discussion is about changes in the world, changes that affect us as academics, changes that affect us as empirical researchers (qualitative and quantitative), and changes that affect our students and our universities/ colleges I am an empirical social scientist, a political methodologist, and a statistician, so I will only discuss topics along these lines where I am qualified to make comments As of this re-rewriting, the country and the world are in various levels of lockdown and recovery because of Covid-19 During this difficult process it is clear that data and privacy issues are changing rapidly There is evidence that some governments are using the pandemic to extend their reach into data spheres that were more difficult to monitor and control before I hope that this is a temporary trend and that people around the world can keep some control over their data as challenging world events unfold © 2021 by the Southern Political Science Association All rights reserved
Design of low-profile frequency reconfigurable antenna for multiband applications

ABSTRACT An inverted G-shaped frequency reconfigurable antenna is presented. By inserting two PIN diodes in horizontal and vertical strips, we achieve multiple reconfigurable operating frequency bands in the range of 3 GHz to 10 GHz. The proposed antenna has been fabricated on low-cost FR4 substrate with 1.6 mm thickness. The overall antenna dimensions are 40 × 48 mm2 having a partial ground. It covers different wireless applications such as WLAN, WiMAX, Long-Distance Radio Telecommunications, and X-band Satellite Communication. The presented antenna is optimised using simulation while the results are validated by measuring the prototype in all cases. Results are provided in each case and discussed in detail as well. The proposed antenna will be one of the promising candidates for wireless application.
The risk of moose Alces alces collision: A predictive logistic model for moose-train accidents

We used logistic models to estimate the risk of moose-train collisions for the Rørosbanen railway in Norway. During 1990–1997, a total of 13,506 train departures were registered along Rørosbanen during the months when the risk of collision was highest (December to March). The statistical model selected to predict the risk of moose-train collisions included train route, time of day, lunar phase and average train speed, as well as two climatic covariables, i.e. snow depth and temperature. Trains running at night, in the morning or in the evening experienced a higher risk of collision with moose Alces alces than day trains. The probability of collision was also higher during nights of full moons than during nights of half or no moons. As observed previously with trains in Norway moose-kills increased with increasing snow depth and decreasing temperatures. To test the predictability of the model, we used a logistic model based on train departures during 1990–1996 to predict the number of moose-train accidents during winter 1996/97. Although the model had a satisfactorily high predictability, the best models would probably be those based on a combination of both temporal and spatial aspects. We discuss how logistic models may be applied to introduce remedial actions on high-risk routes or during high-risk periods.
Rheological investigations of water-soluble polysaccharides extracted from Moroccan seaweed Cystoseira myriophylloides algae

The rheological properties and spectrum infrared of polysaccharides extracted from Cystoseira myriophylloides algae were investigated in the concentrations range from 3 to 9% (w/v) and at different temperatures. Results of rheological characteristics in a steady shear rate showed pseudoplastic properties and the dynamic rheological properties showed a fluid-like viscoelastic behavior. The flow and viscoelastic characteristics of polysaccharides were described using the power-law (the Ostwald model). The values of flow behavior index of the sample were close to unity (0.91) for 3% and it decreased up to 0.71 for 9% revealing the shear-thinning (pseudoplastic) nature of these polysaccharides. Moreover, the consistency coefficient increased non-linearly with concentration and it was described by a power law. The flow behavior as a function of temperature was satisfactorily described using the Arrhenius law and the activation energy values were extracted. It decreased from 15.68 and 17.21 kJ/mol when the concentration increased from 5 to 9% (w/v). Additionally, in dynamic rheological measurements, tan δ > 1 and G″ > G′ reveling a shear-thinning behavior. Finally, the analysis of the FTIR spectra of these polysaccharides showed the presence of uronic acid groups. This behavior would suggest that polysaccharides extracted from Cystoseira myriophylloides could be an interesting additive as thickeners.
Microscopic, serological and molecular detection of Babesia bigemina in buffaloes (Bubalus bubalis) in Wasit province, Iraq

The goal of present study was to detect an incidence of Babesia bigemina in apparently healthy buffaloes using of three different diagnostic assays. An overall of 179 buffaloes (Bubalus bubalis) in some rural regions in Wasit province /Iraq, were submitted for collection of blood samples during the period of December 2016 to February 2017. Initially, a thin blood smear slides were prepared and stained with Giemsa stain for microscopy, afterwards, the blood samples have been centrifuged for obtaining of serums and blood clots that examined by an indirect-ELISA and PCR, respectively. The overall results of testing all samples were revealed on 3 (1.68%), 46 (25.7%) and 21 (11.73%) positive animals by microscopy, indirect-ELISA and PCR, respectively. The significant differences (P  0.05) were showed between the results of three diagnostic tests, and within the cross-classification values of microscopy to indirect-ELISA, microscopy to PCR, and indirect-ELISA to PCR.
Post-covid syndrome

The aim is to study the frequency and symptoms of post-COVID syndrome in patients with pneumonia caused by SARS-CoV-2, who were treated in an outpatient setting. Materials and methods. Personal monitoring results of the health state of 62 patients who suffered pneumonia caused by the SARS-CoV-2 and were treated in the outpatient setting between May 2020 and September 2021 were analyzed. The patients were divided into 3 clinical groups depending on age, concomitant diseases, and extent of the process in the lungs. The examination results were processed on a personal computer using the statistical package Statistica program, version 10. Results. The prevalence of post-COVID syndrome with the symptoms that characterize it is significantly higher in patients who have not been vaccinated with the COVID-19 vaccine, who have suffered pneumonia caused by SARS-CoV-2 of a moderate-to-severe course with the process extent in the lungs from 25 % to 50 %, with its repeated cases, regardless of age and the presence of concomitant pathologies. Prolonged COVID-19 (early post-COVID syndrome) and post-COVID syndrome are main complications of COVID-19 with the most common symptoms such as general fatigue, depression, impaired memory concentration, sleep disorder, myalgia/arthralgia. Conclusions. Even a mild course of pneumonia caused by SARS-CoV-2 is accompanied by post-COVID syndrome, which requires long-term supervision and practice of rehabilitation techniques for such patients. Treatment of pneumonia caused by the SARS-CoV-2 with the moderate-to-severe course in outpatient conditions leads to an increase in the frequency and severity of the post-COVID syndrome course. Vaccination with a vaccine against COVID-19 to prevent the development of a severe course of pneumonia caused by the SARS-CoV-2 remains an urgent issue. Identified dental manifestations (stomatitis, periodontitis, and periodontal disease) should be considered by dentists in the early period of post-COVID syndrome, and dental pathology examination should be continued during the treatment of pneumonia caused by SARS-CoV-2 in post-COVID syndrome.
Voltammetric determination of cholecalciferol at glassy carbon electrode performed in water ethanol mixture

To confirm or disprove previous hypotheses, cyclic voltammetry of 0.5 mM cholecalciferol (vitamin D 3 ) at glassy carbon electrode (GCE) and platinum disk electrode (PtE) in pure acetonitrile and water‑ethanol mixture at 50 mV·s ‑1 has been used to investigate the oxidation mechanism. The oxidation occurs in two one-electrone steps. According to calculation of the highest electron density in cholecalciferol molecule which is evidently delocalized over carbon atoms of the three conjugated double bonds (C19, C10, C5-C8) points to part of the molecule involved in oxidation processes. An oxidation peak (at +0.925 V vs. Ag/AgCl) was used to develop direct voltammetric method based on differential pulse voltammetry for the vitamin D 3 determination at GCE performed in 40% ethanol containing 0.1 M LiClO 4 . Under optimization of analytical procedure, it was found that a composition of the supporting electrolyte used significantly affects a current response of oxidation peak obtained. Satisfactory sensitivity was achieved in the 1:1 water‑ethanol mixture containing 0.05 M lithium perchlorate as as supporting electrolyte. The linear range for vitamin D 3 determination was 2.4 × 10 -6 - 3.5 × 10 -4 M with the detection limit of 8.0 × 10 -7 M. This work demonstrates a fact that the GCE is suitable electroanalytical device for analysis of various food supplements and medicaments.
Uniform convergence of penalized splines

Penalized splines are popular for nonparametric regression. We establish the minimax rate optimality of penalized splines for uniform convergence, thus improving the existing rate in the literature. The result is applicable to several types of penalized splines that are commonly used and holds under mild conditions on the design points.
A Pedagogic Experience in Designing a Healthcare Analytics Course: Lessons Learned.

This study presents a contextual active learning perspective on how a healthcare data analytics course was designed and delivered to students enrolled in a graduate business analytics degree. Industry and academia emphasizes the need to integrate context-specific learning, however contextual analytics courses are not widely offered in business schools. This course ’s pedagogical approach seeks to address this need by embracing a contextual active approach. Such approach is based on the following key components: (1) Active learning – designing each module of the course to include activities and lessons to promote active participation of learners, (2) contextual development – modules are developed using healthcare as the focus and context for all activities, (3) online adaptation – the course is delivered online in an unsynchronized mode and therefore the development adapts to online delivery intended to maximize learning. This course integrates a collaborative project with a healthcare industry partner where students analyze anonymized dataset for the purpose of a more contextual and experiential healthcare experience.
Feature extraction and classification methods of facial expression: a survey

Facial Expression is a significant role in affective computing and one of the non-verbal communication for human computer interaction. Automatic recognition of human affects has become more challenging and interesting problem in recent years. Facial Expression is the significant features to recognize the human emotion in human daily life. Facial Expression Recognition System (FERS) can be developed for the application of human affect analysis, health care assessment, distance learning, driver fatigue detection and human computer interaction. Basically, there are three main components to recognize the human facial expression. They are face or face’s components detection, feature extraction of face image, classification of expression. The study proposed the methods of feature extraction and classification for FER.
Resisting the Pressures of Globalisation: The Repeated Failure of Elite Sport Reforms in Re-United Germany

During the German divide, the two Germanys developed quite different elite sport systems. After reunification, the expensive and compromised East German state sport system was dismantled and the West German neo-corporatist policy approach to elite sport prevailed. The neo-corporatist approach is characterised by a large number of veto players which constantly bargain over influence and scarce resources. Globalisation and the diffusion of East German policy approaches have increased the competitive intensity in international sport and made the neo-corporatist approach increasingly anachronistic. Declining competitiveness has inspired several initiatives of the federal government to reform elite sport policymaking. So far, German elite sport seems to represent a policy domain where neo-corporatism resists the pressures of globalisation.
Hiding hate speech: political moderation on Facebook

Facebook facilitates more extensive dialogue between citizens and politicians. However, communicating via Facebook has also put pressure on political actors to administrate and moderate online debates in order to deal with uncivil comments. Based on a platform analysis of Facebook’s comment moderation functions and interviews with eight political parties’ communication advisors, this study explored how political actors conduct comment moderation. The findings indicate that these actors acknowledge being responsible for moderating debates. Since turning off the comment section is impossible in Facebook, moderators can choose to delete or hide comments, and these arbiters tend to use the latter in order to avoid an escalation of conflicts. The hide function makes comments invisible to participants in the comment section, but the hidden texts remain visible to those who made the comment and their network. Thus, the users are unaware of being moderated. In this paper, we argue that hiding problematic speech without the users’ awareness has serious ramifications for public debates, and we examine the ethical challenges associated with the lack of transparency in comment sections and the way moderation is conducted in Facebook.
The evolution of termite immunity

The termites are a derived eusocial lineage of otherwise non-social cockroaches. Understanding the proximal and ultimate drivers of this major evolutionary transition represents an important goal in biology. One outstanding question concerns the evolution of termite immunity, which is thought to have undergone broad-sweeping adaptations in order to enhance group-level immune protection. To understand the evolutionary origins of termite immunity, we conducted qualitative and quantitative transcriptome analyses along a gradient of sociality. Firstly, we aimed to identify large-scale genetic shifts in immune traits linked to eusociality by comparing immune gene repertoires in solitary and subsocial cockroaches and across a range of eusocial termite lineages. Secondly, we compared the responses of a solitary cockroach, a subsocial wood-roach and different castes of a lower termite species to a non-specific immune challenge, in order to understand how sociality may have influenced the evolution of immune gene regulation. Firstly, we found that termites have a broadly representative repertoire of canonical immune genes as compared to gregarious cockroaches and subsocial wood-roaches. Secondly, with respect to immune challenge, the solitary cockroach and the subsocial wood-roach displayed a similarly comprehensive induced response, while the termite response was considerably dampened by comparison and strongly influenced by caste; with reproductives displaying a generally higher constitutive level of immune-gene expression compared to sterile castes. In summary we did not find termite eusociality to be associated with significant changes in immune gene diversity, but rather to be linked with significant modifications to the regulation of immunity following the origin of division of labour.