Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

Phylogenetics has witnessed dramatic increases in the sizes of data matrices assembled to resolve branches of the tree of life, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these four programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets from diverse animal, plant, and fungal lineages with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation–based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the relative performance of the programs. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses.
Influence of extraction process on antioxidant activity and rutin content in Physalis peruviana calyces extract

Physalis peruviana is an exotic fruit highly valued for its bioactive compounds. This work evaluates the effect of some variables of the extraction process of P. peruviana calyces (considered waste material) on total phenolic content, rutin content, and in vitro antioxidant activity of the extracts obtained. First, the influence of certain factors of the extraction process on the above mentioned response variables were analyzed. The response variables were then evaluated using in vitro assays such as NO (nitric oxide) and DPPH (1,1-diphenyl-2- picrylhydrazyl) uptake for antioxidant activity; the Folin-Ciocalteu method for total phenolic content; and the external standard method by HPLC-DAD for quantification of rutin. The results showed that the optimal conditions needed to obtain the best results for the response variables evaluated are the use of ethanol 70% as extraction solvent, and a percolation time of 72 hours, these being the factors that positively influenced the results.
A Reconfigurable Scan Architecture With Weighted Scan-Enable Signals for Deterministic BIST

We present a new scan-based built-in self-test (BIST) technique, which is based on weighted scan-enable signals and a reconfigurable scan-forest architecture. A testability measure is proposed to guide test pattern generation and produce patterns with few care bits. This approach can effectively reduce the amount of test data that needs to be stored on-chip. The proposed BIST method relies on the pseudorandom and deterministic phases. The scan-forest architecture is configured as a single scan tree for deterministic test vector application in the second phase. It is found that a linear feedback shift register, with size equal to the maximum number of the care bits in the deterministic patterns for the random-resistant faults, is sufficient to encode deterministic vectors for the benchmark circuits. Experimental results for benchmark circuits demonstrate the effectiveness of the proposed method for single stuck-at faults. In addition, experimental results show that the patterns applied to the circuit under test provide more n-detection than those applied by a traditional scan-chain architecture with a single test session.
Efficient matching for the Iterative Closest Point algorithm by using low cost distance metrics

Since its introduction, the Iterative Closest Point algorithm (ICP) has become one of the most popular methods for the geometric alignment of three-dimensional models. Given two point clouds, named model and source, the algorithm iteratively refines a transformation which is applied to the source cloud in order to minimize the difference or distance between both point clouds. Many applications of multiple fields currently use this algorithm to reconstruct 2D or 3D surfaces from different data measurements due to its simplicity and effectiveness. However, one of the main problems of the algorithm is the high computational cost of certain complex phases when dealing with high density point clouds. This fact renders impossible some of the applications of the algorithm. The goal of this work is the improvement of the ICP algorithm so that a broader range of computational resources demanding problems can be addressed. For that, a convergence analysis and validation of point-to-point distance metrics with a lower computational cost than the Euclidean one which is used as a de facto standard in the existing implementations in the literature of the algorithm. Keywords—Convergence of numerical methods, Error analysis, Computational geometry, Computational efficiency, ICP algorithm.
The Role of Vitamin C in Enhancement of Fracture Healing in Fracture with Periosteal Stripping at Sprague-Dawley White Rats Femur

Introduction. Fracture Healing still become a problem. There are many things to do to enhance and avoid thecomplication of fracture healing. Vitamin C is one of the ways to enhance the fracture healing. The purpose of thisstudy is to know the role of vitamin C in enhancement the fracture healing in fracture with periosteal stripping atSprague-Dawley white rats femur. The objective of the study is to know the role of vitamin C in enhancement offracture healing in fracture with periosteal stripping at Sprague-Dawley white rats femur by using RUST score andhistomorphometry. Materials and methods. This is an experimental study. This study used 32 rats which were performed fracturizationat the femur, periosteal stripping, internal fixation with K-wire and were given vitamin C supplementation orally indifferent dose, 5 mg, 10 mg, 20 mg and control. The evaluation at the second and fourth week radiologically usingRUST score and histologically using histomorphometry. Results. The RUST score evaluation at the second week showed that the result between groups were not statisticallysignificant but at the fourth week the RUST score showed statistically significant result especially for the groupreceiving 20 mg vitamin C.The histomorphometry evaluation at the second and fourth week showed the enhancementof fracture healing by decreasing the amount of cartilage and increasing amount of woven bone along the study butwere statisically not significant.Conclusions. There is enhancement of fracture healing with supplementation of vitamin C as shown by with RUSTscore evaluation at the fourth week. Histomorphometry evaluation showed enhancement of fracture healing withsupplementation of vitamin C. The larger dose of vitamin C give better histological grade but still not statisticallysignificant. Keywords: Enhancement of fracture healing, vitamin C, RUST score, histomorphometry
A New Model of Solar Flares

THE extensive observational results and theoretical investigations of solar flares have recently been compiled in refs. 1 and 2. Most models of solar flares have assumed that the only reasonable mechanism for energy storage is that of magnetic field. Parker3 has recently criticized these theories and shown, in particular, that they do not explain the rapidity (102 sec) of the flash phase.
Dysadherin specific drug conjugates for the treatment of thyroid cancers with aggressive phenotypes

Background EDC1 is a novel type of antibody-drug conjugate which binds and inhibits the Na,K-ATPase on the surface of cancer cells expressing dysadherin. The purpose of this study was to determine the expression of dysadherin in different types of thyroid carcinoma, and evaluate the therapeutic potential of EDC1 for thyroid carcinomas. Methods Thyroid tissues from 158 patients were examined for dysadherin expression and correlation with clinicopathological features. Thyroid cancer cell lines were examined for the expression of dysadherin and effective dose range of EDC1. RESULTS One in 53 benign thyroid tissues and 62% of thyroid cancers expressed dysadherin. All anaplastic and a majority of papillary thyroid cancers overexpressed dysadherin, while 25% of follicular thyroid cancers was found to be positive for dysadherin. Dysadherin expression significantly correlated with extrathyroidal extension and lymph node metastases in papillary thyroid cancer. Five of six human thyroid cancer cell lines analyzed expressed high levels of dysadherin. Of those cells lines sensitive to EDC1, half maximal effective concentrations (EC50) were observed to be between 0.125 nM and 1 nM. Conclusions EDC1 showed selective inhibition of growth in thyroid cancer cells with moderate to high expression of dysadherin, thus could be a specific and effective treatment.
Microsurgical Keyhole Approach for Middle Fossa

To the Editor: We read with great interest the recently published article by Levy et al. (2). Regardless of the original description of this innovative keyhole approach to arachnoid cyst fenestration as a safe and effective method for treating middle fossa cysts, we had the impression that during the decision-making process, the authors focused their attention on the arachnoid cysts, placing important associated pathological findings in second place, specifically in the case of children with hydrocephalus. Arachnoid cysts presumably result from an aberration in the embryological development of the subarachnoid space (4). This hypothesis seems to be the reason for the actual disorder in the cerebrospinal fluid (CSF) circulation and why subarachnoid cysts are frequently associated with hydrocephalus. Whether the cyst is the cause of the ventriculomegaly is a clinical and therapeutic dilemma. In some patients, the location of the cyst interferes with the normal CSF circulation (i.e., those compressing the sylvian aqueduct or those obstructing the outlet foramina in the fourth ventricle); however, in some cases, there is no evident relationship between the cysts and the ventricular enlargement. In those situations, some authors support the idea that the hydrocephalus is communicating and the actual problem is in the subarachnoid space, similar to their subarachnoid cyst counterparts (5). This could be the reason for the low incidence of hydrocephalus (15–18%) in children with middle fossa arachnoid cysts (1, 3). In this article, Levy et al. (2) use the microsurgical keyhole approach as the initial procedure for treatment of middle fossa arachnoid cysts, including those in three moderately hydrocephalic patients. It is about those patients that we have some concerns. Were their complaints secondary to hydrocephalus or to the cysts? Why does the ventricular size remain stable after the surgical procedure? In this situation, it is advisable to determine whether these stable patients were functioning at their full potential or whether their neurological function could be improved after surgical diversion. In these patients, it is also necessary to define whether they had arrested or compensated hydrocephalus. Because this procedure provides communication between the cyst and the basal cisterns, we agree with the authors that the proposed technique is useful for arachnoid cysts without hydrocephalus. In patients harboring middle fossa arachnoid cysts and hydrocephalus, the diversion of the cyst could not be effective; thus, the ventricular enlargement should be approached independently, as suggested by Raffel and McComb (3).
Impact of collagen-alginate composition from microbead morphological properties to microencapsulated canine adipose tissue-derived mesenchymal stem cell activities

Abstract The purpose of this study was to identify the effect of collagen-alginate composition on the size and shape of microbeads and the proliferation and osteogenic properties of microencapsulated canine adipose-derived mesenchymal stem cells (ASCs) in vitro. Canine ASCs were microencapsulated in mixtures of various collagen-alginate compositions using a vibrational technologic encapsulator. The size and shape of the resultant microbeads were measured using a light field microscope and the viability of the microencapsulated canine ASCs was evaluated using a live/dead viability/cytotoxicity kit. Proliferation and osteogenic potentials of microencapsulated canine ASCs were evaluated using an alamarBlue proliferation assay and an alkaline phosphatase assay, respectively. As the collagen ratio increased, the size and size variation of microbeads increased and the shape of microbeads became more irregular. Nonetheless, homogeneous microbeads were created with no significant difference in size and shape, in the range of 0.75% alginate mixed with 0.099% collagen solution in 1.2% alginate solution. There were no significant differences in viability of the ASCs in the various collagen-alginate compositions. Both proliferation and osteogenic properties, in vitro, increased with increasing collagen ratio. Microencapsulation of canine ASCs with appropriate collagen-alginate composition increases cell proliferation and osteogenic properties, in vitro, without significant effects on the shape and size of microbeads and cell viability. Microencapsulation with adequate collagen-alginate composition may produce injectable microbeads that could enhance the therapeutic efficacy of stem cells.
Beyond rigidity - dynamic process lifecycle support : A Survey on dynamic changes in process-aware information systems (Special Issue Paper)

The economic success of an enterprise increasingly depends on its ability to react to changes in its environment in a quick and flexible way. To cope with emerging business trends, responsiveness to change is a significant competitive advantage. Similar to the lifecycle in conventional information systems development, studies on lifecycle support for business processes are often sweeping the issues of runtime change management under the banner of maintenance. However, the pervasiveness of dynamic changes in business processes warrants targeted attention. This paper presents a detailed review of challenges and techniques that exist for the lifecycle management of dynamic processes. For each of the lifecycle phases we discuss the needs and deliberate on various developments from both academia and industry.
On Availability for Blockchain-Based Systems

Blockchain has recently gained momentum. Startups, enterprises, banks, and government agencies around the world are exploring the use of blockchain for broad applications including public registries, supply chains, health records, and voting. Dependability properties, like availability, are critical for many of these applications, but the guarantees offered by the blockchain technology remain unclear, especially from an application perspective. In this paper, we identify the availability limitations of two mainstream blockchains, Ethereum and Bitcoin. We demonstrate that while read availability of blockchains is typically high, write availability - for transaction management - is actually low. For Ethereum, we collected 6 million transactions over a period of 97 days. First, we measured the time for transactions to commit as required by the applications. Second, we observed that some transactions never commit, due to the inherent blockchain design. Third and perhaps even more dramatically, we identify the consequences of the lack of built-in options for explicit abort or retry that can maintain the application in an uncertain state, where transactions remain pending (neither aborted nor committed) for an unknown duration. Finally we propose techniques to mitigate the availability limitations of existing blockchains, and experimentally test the efficacy of these techniques.
PCL and PCL-based materials in biomedical applications

Abstract Biodegradable polymers have met with an increasing demand in medical usage over the last decades. One of such polymers is poly(ε-caprolactone) (PCL), which is a polyester that has been widely used in tissue engineering field for its availability, relatively inexpensive price and suitability for modification. Its chemical and biological properties, physicochemical state, degradability and mechanical strength can be adjusted, and therefore, it can be used under harsh mechanical, physical and chemical conditions without significant loss of its properties. Degradation time of PCL is quite long, thus it is used mainly in the replacement of hard tissues in the body where healing also takes an extended period of time. It is also used at load-bearing tissues of the body by enhancing its stiffness. However, due to its tailorability, use of PCL is not restricted to one type of tissue and it can be extended to engineering of soft tissues by decreasing its molecular weight and degradation time. This review outlines the basic properties of PCL, its composites, blends and copolymers. We report on various techniques for the production of different forms, and provide examples of medical applications such as tissue engineering and drug delivery systems covering the studies performed in the last decades.
Increased Amygdala Response to Shame in Remitted Major Depressive Disorder

Proneness to self-blaming moral emotions such as shame and guilt is increased in major depressive disorder (MDD), and may play an important role in vulnerability even after symptoms have subsided. Social psychologists have argued that shame-proneness is relevant for depression vulnerability and is distinct from guilt. Shame depends on the imagined critical perception of others, whereas guilt results from one’s own judgement. The neuroanatomy of shame in MDD is unknown. Using fMRI, we compared 21 participants with MDD remitted from symptoms with no current co-morbid axis-I disorders, and 18 control participants with no personal or family history of MDD. The MDD group exhibited higher activation of the right amygdala and posterior insula for shame relative to guilt (SPM8). This neural difference was observed despite equal levels of rated negative emotional valence and frequencies of induced shame and guilt experience across groups. These same results were found in the medication-free MDD subgroup (N = 15). Increased amygdala and posterior insula activations, known to be related to sensory perception of emotional stimuli, distinguish shame from guilt responses in remitted MDD. People with MDD thus exhibit changes in the neural response to shame after symptoms have subsided. This supports the hypothesis that shame and guilt play at least partly distinct roles in vulnerability to MDD. Shame-induction may be a more sensitive probe of residual amygdala hypersensitivity in MDD compared with facial emotion-evoked responses previously found to normalize on remission.
Original Contribution a Prospective Study of Plasma Ferritin Level and Incident Diabetes the Atherosclerosis Risk in Communities (aric) Study

The authors performed a case-cohort study nested within the Atherosclerosis Risk in Communities (ARIC) Study to determine the association between plasma ferritin level and risk of type 2 diabetes mellitus. Persons with incident cases of type 2 diabetes diagnosed over an average follow-up period of 7.9 years (n ¼ 599) were compared with a random sample of the cohort (n ¼ 690). After adjustment for age, gender, menopausal status, ethnicity, center, smoking, and alcohol intake, the hazard ratio for diabetes, comparing the fifth quintile of ferritin with the first quintile, was 1.74 (95% confidence interval: 1.14, 2.65; p-trend < 0.001). After further adjustment for body mass index and components of the metabolic syndrome, the hazard ratio was 0.81 (95% confidence interval: 0.49, 1.34; p-trend ¼ 0.87). From a causal perspective, there are two alternative interpretations of these findings. Elevated iron stores, reflected in elevated plasma ferritin levels, may induce baseline metabolic abnormalities that ultimately result in diabetes. Alternatively, elevated ferritin may be just one of several metabolic abnormalities related to the underlying process that ultimately results in diabetes, rather than a causal factor for diabetes. Longitudinal studies with repeated measurements of glucose and iron metabolism parameters are needed to establish the role of iron stores and plasma ferritin in diabetes development. Impaired glucose metabolism and diabetes mellitus are common clinical manifestations of iron overload in patients with hemochromatosis (1). More recently, moderately elevated iron stores below the levels commonly associated with hemochromatosis have also been implicated in the etiology of diabetes (2–4). Levels of plasma ferritin, a biomarker of iron stores, are elevated in persons with prevalent diabetes as compared with nondiabetic controls (2, 5). Markers of iron status are also correlated with the prevalence of the metabolic syndrome (6, 7) and with measures of insulin
Online gaming to find a new job: Examining job seekers' intention to use serious games as a self-assessment tool

Serious games can be used as self-assessment tools in recruiting processes. We develop a model explaining jobseekers’ intentions to use these applications, which help them to gain a realistic idea of the job at hand and allows them to submit their application only if the job truly fits their individual profile. Drawing on organizational justice theory and the technology acceptance literature, our model is empirically evaluated using data from 1,882 jobseekers. The results indicate that jobseekers’ intention to use self-assessments is driven in particular by its perceived ease of use, perceived usefulness, perceived enjoyment