Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular evidence for the pattern and timing of cladogenesis in dasyurid marsupials

Abstract Recent molecular studies have provided estimates of phylogeny for nearly all living and recently extinct species in the Order Dasyuromorphia, the dominant clade of insectivorous-carnivorous marsupials in Australasia. We review these studies along with morphology-based ones, and present an analysis of all cytochrome b , 12S rRNA, and protamine P1 gene sequences available. In light of these results, we provide a revised suprageneric classification and assess the implications of molecular and paleontological data for dasyurid cladogenesis. Molecular results divide extant dasyurids (Dasyuridae) into four major clades apart from the numbat (Myrmecobiidae) and thylacines (Thylacinidae). We recognize these clades as tribes Dasyurini ( Dasyurus, Phascolosorex , and allied genera) and Phascogalini ( Antechinus, Murexia, Phascogale ) in the Subfamily Dasyurinae, and tribes Sminthopsini ( Sminthopsis, Ningaui, Antechinomys ) and Planigalini ( Planigale ) in the Subfamily Sminthopsinae. Each tribe shows a basal radiation of lineages corresponding to genera or species groups. Our results concur with the most recent previous synthesis of dasyurid phylogeny in many respects, but subsumption of New Guinean «phascolosoricines» and «muricines» within Dasyurini and Phascogalini, respectively, constitute significant differences. In particular, the sister-pairing of «phascolosoricines» with a Dasyurus–Sarcophilus clade implied by molecular data is difficult to reconcile with anatomy. Divergence rates of mitochondrial sequences are calibrated approximately by comparing thylacine-to-dasyurid distances with the age of the oldest thylacinid ( Badjcinus , latest Oligocene). Estimated cladogenic dates suggest that extant subfamilies shared a common ancestor around 24 Mya and that major radiations began late in the mid-Miocene, consistent with the results of previous paleontological studies. The late-middle and late Miocene corresponds to an episode of faunal turnover in Australian marsupials (including the decline of thylacinid and bandicoot genera, as well as the rise of dasyurids) and to a time when uplift of the New Guinean highlands accelerated the transition from rainforest to drier habitats. Our findings are consistent with the hypothesis that continent-wide climate changes modulated macroevolution across these independent marsupial clades.
Using association features to enhance the performance of Naive Bayes text classifier

The co-occurrence of words can make contributions to automatic text classification. However, this information cannot be represented in the feature set when only using primitive features, and can only be partially represented when using n-grams as features. In this paper, we define a novel feature, association feature, to describe this information. In order to make the association features which we selected to be good discriminators, we proposed an approach to create association feature set, including redundancy pruning algorithm and feature selection algorithm. The experiment result shows that the performance of Naive Bayes text classifier could be improved by using association features, which also means that the selected set of association features can make more contributions to text classification than primitive features, and n-grams.
Knowledge management framework based on brain models and human physiology

ix Keywords . ix Resumo . xi Palavras chave . xi Index . xiii List of Figures . xviii List of Tables . xxi Acronyms . xxiii SECTION I – Introduction to the Research Work . 1 1. Introduction . 3 1.1. Observation . 4 1.2. Motivation . 9 1.3. Vision . 10 1.4. Research Areas – An Overview . 10 Knowledge Management . 12 1.4. 1. Neurophysiology, Brain Models and Physiology . 12 1.4. 2. Neuropsychology, Sensations, Perceptions and Emotions . 13 1.4. 3. 1.5. Dissertation Outline . 14 2. Work Plan . 17 2.1. Research Question . 19 Problem introduction . 19 2.1.1. Research Questions and Scientific Challenges . 20 2.1.2. 2.2. Hypothesis and Approach . 22 2.3. Doctoral Research Approach . 23 SECTION II -­‐ Literature Review . 27
Studying the Evolution of Build Systems

As a software project ages, its source code is improved by refining existing features, adding new ones, and fixing bugs. Software developers can attest that such changes often require accompanying changes to the infrastructure that converts source code into executable software packages, i.e., the build system. Intuition suggests that these build system changes slow down development progress by diverting developer focus away from making improvements to the source code. While source code evolution and maintenance is studied extensively, there is little work that focuses on the build system. In this thesis, we empirically study the static and dynamic evolution of build system complexity in proprietary and open source projects. To help counter potential bias of the study, 13 projects with different sizes, domains, build technologies, and release strategies were selected for examination, including Eclipse, Linux, Mozilla, and JBoss. We find that: (1) similar to Lehman’s first law of software evolution, Java build system specifications tend to grow unless explicit effort is invested into restructuring them, (2) the build system accounts for up to 31% of the code files in a project, and (3) up to 27% of source code related development tasks require build maintenance. Project managers should include build maintenance effort of this magnitude in their project planning and budgeting estimations. i
Neurocognitive insights on conceptual knowledge and its breakdown

Conceptual knowledge reflects our multi-modal ‘semantic database’. As such, it brings meaning to all verbal and non-verbal stimuli, is the foundation for verbal and non-verbal expression and provides the basis for computing appropriate semantic generalizations. Multiple disciplines (e.g. philosophy, cognitive science, cognitive neuroscience and behavioural neurology) have striven to answer the questions of how concepts are formed, how they are represented in the brain and how they break down differentially in various neurological patient groups. A long-standing and prominent hypothesis is that concepts are distilled from our multi-modal verbal and non-verbal experience such that sensation in one modality (e.g. the smell of an apple) not only activates the intramodality long-term knowledge, but also reactivates the relevant intermodality information about that item (i.e. all the things you know about and can do with an apple). This multi-modal view of conceptualization fits with contemporary functional neuroimaging studies that observe systematic variation of activation across different modality-specific association regions dependent on the conceptual category or type of information. A second vein of interdisciplinary work argues, however, that even a smorgasbord of multi-modal features is insufficient to build coherent, generalizable concepts. Instead, an additional process or intermediate representation is required. Recent multidisciplinary work, which combines neuropsychology, neuroscience and computational models, offers evidence that conceptualization follows from a combination of modality-specific sources of information plus a transmodal ‘hub’ representational system that is supported primarily by regions within the anterior temporal lobe, bilaterally.
Privacy, surveillance, and the proportionality principle: The need for a method of assessing privacy implications of technologies used for surveillance

Developments in technology have created the possibility for law enforcement authorities to use for surveillance purposes devices that are in the hands or private premises of individuals (e.g. smart phones, GPS devices, smart meters, etc.). The extent to which these devices interfere with an individual's private sphere might differ. In the European Union, surveillance measures are considered lawful if they have been issued in conformity with the legal rules and the proportionality principle. Taking a fundamental rights approach, this paper focuses on the information needed for adopting proportionate decisions when authorizing the use for surveillance of devices that are not built for surveillance purposes. Since existing methods of privacy assessment of technologies do not offer the required information, this paper suggests the need for a new method of assessing privacy implications of technologies and devices which combines an assessment of privacy aspects with the different dimensions of surveillance.
Gastrotrich fauna of elodeids and bottom sediments in a euthrophic

Species diversity of gastrotrich communities on elodeids and in bottom sediments of a eutrophic lake were compared in this paper. Twenty three species of Gastrotricha (20 in bottom sediments and 15 on elodeids) belonging to one family Chaetonotidae Zelnika were found in studied habitats. Species diversity of both habitats was reflected in diversity indices equal to 2.67 and 2.54 for bottom sediment and elodeid fauna, respectively. Eudominants in the bottom sediments were three species: Chaetonotus oculifer Kisielewski, Ch. similis Zelnika and Heterolepidoderma gracile Remane. The group of eudominants among elodeid fauna consisted of four species: Ch. macrochaetus Zelnika, H. macrops Kisielewski, H. ocellatum Mecnikow and Lepidodermella squamata Dujardin. In both studied habitats the percentage share of gastrotrich eudominants exceeded 40%. The similarity of gastrotrich fauna on elodeids to that in bottom sediments was low and equalled 38%. The analysis of percentage shares of eudominant species in the fauna of bottom sediments and in epiphytic fauna in the studied eutrophic lake and earlier studies on fauna from both habitats in lakes of different trophic status allow to supplement autecological characteristics of H. ocellatum Mecnikow and to classify it in the group of species closely related to vegetation.
Left ventricular ejection fraction and mitral regurgitation assessment: A comparison study between echocardiography and angiography

Introduction: Measurement of the left ventricular ejection fraction (LVEF) is a common tool for evaluating the left ventricle (LV) systolic function. The aim of this study was to evaluate and compare the LVEF and mitral regurgitation (MR) severity as estimated by angiography and echocardiography in patients with coronary artery disease (CAD) and LV systolic dysfunction. Methods: In this observational study, 39 men and 11 women at a mean age of 60 years were recruited. The patients underwent catheterization and echocardiography, and the data on the LVEF and MR by both methods were registered. Results: The mean LVEF by echocardiography and angiography was significantly correlated (correlation coefficient = 0.698; P < 0.0001). Although there was agreement between these methods in the estimation of the mean EF (mean difference in the LVEF = 1.23 ± 7.63% and 95% limit of agreement = −12.5–19) and the κ coefficient was 45.7% (P = 0.001), the estimated mean EF was 32.6 ± 10.25% by echocardiography and 29.8 ± 8.2% by angiography (P = 0.007). Furthermore, there was a statistically significant difference in the estimated MR severity between the two methods (P = 0.0001), with echocardiography reporting higher degrees of severity than angiography. Conclusions: In our patients with CAD and LV systolic dysfunction, after the exclusion of age, sex, number of diseased coronary arteries, and myocardial infarction history from the analysis, although the mean LVEF by echocardiography and angiography was significantly correlated, echocardiography estimated higher LVEF values than angiography, especially in the patients with triple-vessel disease. Moreover, echocardiography showed higher degrees of MR severity than angiography.
Patient satisfaction with services at public and faithbased primary health centres in Lagos State: A comparative study

Context: The primary health care is the first point of contact between a patient and the health-care system. The quality of services provided at public health facilities has gradually declined, precipitating the emergence of alternative service providers. Patient satisfaction is an important indicator for assessing the quality of care in health service provision. Aim: The aim of this study is to compare the patient's satisfaction among attendees at a public and a faith-based primary health center (PHC). Settings and Design: Study design involves comparative cross-sectional in PHCs. Materials and Methods: A total of 700 respondents were recruited consecutively from a public and a faith-based PHC. Data were collected using an adapted General Practice Assessment Questionnaire. Four domains of quality of care were assessed. Statistical Analysis Used: SPSS software version 17 was employed in the data analysis, and the level of significance was set at P < 0.05. Results: Affordability was the most important reason for the choice of a health facility by 47.0% of the public PHC patients, and this was higher than in 41.0% of the patients attending the faith-based PHC. The mean quality of care score was higher among the faith-based (0.90 ± 0.12) than in public (0.85 ± 0.21) PHC attendees (P < 0.001). Patients' satisfaction was higher among the respondents attending the faith-based PHC (P < 0.001). The factors significantly associated with high patient satisfaction among the public PHC attendees included older age, higher educational levels, being married, and perceived good quality of services, while for the faith-based PHC, it included the younger age group, higher levels of education, being married, and closeness to the facility (P < 0.001). Conclusion: Accessibility was scored lowest in both PHCs, while effectiveness was highest in the faith-based PHC. Patients' satisfaction was higher among those who attended the faith-based PHC. It is recommended aspects of accessibility such as waiting time should be a focus of health managers.
THE DYNAMICS OF NATURAL SELECTION AND VICARIANCE IN THE DOMINICAN ANOLE: PATTERNS OF WITHIN‐ISLAND MOLECULAR AND MORPHOLOGICAL DIVERGENCE

Abstract. — The larger islands of the Lesser Antilles are ecologically and geologically complex and are inhabited by single, but morphologically variable, Anolis species. Although earlier work has indicated that a large part of the morphological variation in Anolis oculatus from Dominica can be attributed to selection, a history of recurrent volcanic activity over the last few million years suggests that vicariance may have also played a significant role. We report a study of variation in the cytochrome b gene of mitochondrial DNA across the island to address this issue. We uncovered a very high degree of polymorphism, with an overall gene diversity of 0.97 and a nucleotide diversity of 0.04. Sequences, on average, differ by 3.82% and the maximum pairwise divergence (corrected for multiple hits) is 9.29%. Most haplotypes are restricted to single localities (a pattern not changed by increasing the sample size). Phylogenetic analysis revealed the presence of two distinct lineages on the island with strong phylogeographic structure. One of these is geographically restricted to a relatively small part of the central Caribbean coast. Sublineages were also discernible within the other more widely distributed lineage, but resolution within and support for these sublineages was poor. The phylogeographic pattern is not congruent with generalized body shape and scalation, but is significantly correlated with color pattern. Even when correcting for this lineage effect with partial Matrix correspondence tests, the relationship between color pattern and vegetation is reaffirmed, suggesting that although both vicariance and selection have played a role in the morphological differentiation of this species, selection for current environmental conditions has been more important. We discuss the causes of the phylogeographic structure in light of the volcanic history of the island and highlight the exceptional instance of congruence between all morphological character systems and lineage boundaries, which occurs at the transition between the northern and southern Caribbean ecotypes.
Preconception care: Assessing the level of awareness, knowledge and practice amongst pregnant women in a tertiary facility

Background: One of the components of health care for every woman of reproductive age is preconception care (PCC). The adoption of this care will assist the healthcare system to shift from the delivery of procedure-based acute care to the provision of counseling-based preventive care. Aims: The aim of this study is to determine the level of awareness, knowledge, and the practice of our women on PCC. Settings and Design: A descriptive cross-sectional study was carried out on 50 consenting pregnant women at the antenatal outpatient clinic. Subjects and Methods: All pregnant women who booked for antenatal care during the period of data collection were consecutively recruited through convenient sampling technique. Data were collected using pretested, semi-structured questionnaires to provide answers to the objectives of the study. Statistical Analysis Used: Data obtained were analyzed using SPSS software version 22 and expressed as frequency and percentages. The Chi-square was used to test for association with a value of P < 0.05 indicating statistical significance. Results: The mean age was 31.5 ± 3.8 years and majority (80%) had tertiary education. There is high level of awareness of PCC (76%); however, awareness of its practice in Nigeria is very low (34.2%). Only 34.2% had received PCC before index pregnancy. There is, therefore, a huge disconnection between their level of awareness and practice. Conclusions: There is the need to arm our women with detailed and accurate information on PCC, establish functional clinics with availability of evidence-based guidelines to improve uptake and pregnancy outcome.
Cooperative amino acid changes shift the response of the σ54‐dependent regulator XylR from natural m‐xylene towards xenobiotic 2,4‐dinitrotoluene

XylR is a σ54‐dependent transcriptional factor of Pseudomonas putida that activates the Pu promoter of the TOL plasmid upon binding its natural effector, m‐xylene. The search for mutants of the signal‐sensing module of XylR that respond to the xenobiotic compound 2,4‐dinitrotoluene recurrently yields protein variants with a broad effector range. These mutants had amino acid changes not only in the effector recognition moiety (A module), but also in the inter‐domain B linker of the protein. A random mutagenesis and selection/counterselection setup was adopted to optimize the 2,4‐DNT reaction of XylRv17, one of the best 2,4‐DNT responders and thus recreate how this regulator can adjust its specificity to novel effectors by individual changes on the evolving protein. Site‐specific mutagenesis was then used to decipher the contribution of individual mutations in XylRv17 and in one of the mutants evolved from it (XylR28) to the 2,4‐DNT response. This approach allowed us to capture a new XylR version with novel mutations that fixed the protein in an intermediate stage of the progress from an effector‐promiscuous, pluri‐potent protein type to a more specific form where the natural response to m‐xylene was decreased and the non‐native acquired response to 2,4‐DNT was increased.
Medical education in India: Past, present, and future

Medical education in global context has evolved over a period of time and so in India. With changing community needs, educational advancements and technological revolutions, we need to update the method of imparting knowledge and skills to the students. Major components of hidden curriculum like communication skills, attitude, empathy, altruism, professionalism, humanities etc need to be uncovered and delivered in a more systematic way. Ever increasing demand of doctors in the country has forced to establish new medical colleges across the country but the quality of Indian Medical Graduates produced out of them needs a lot to think and work upon. Reforms in curriculum Medical Council of India is planning to bring should be taken seriously and all efforts should be made to bring them to reality. In order to bring a competent Indian Medical Graduate in par with global standards should be the MANTRA of every medical education institution.
Dexamethasone Synergizes with Lenalidomide to Inhibit Multiple Myeloma Tumor Growth, But Reduces Lenalidomide-Induced Immunomodulation of T and NK Cell Function

To determine the effect of dexamethasone on the antimyeloma effects of lenalidomide, we tested in vitro proliferation, tumor suppressor gene expression, caspase activity, cell cycling, and apoptosis levels in a series of multiple myeloma (MM) and plasma cell leukemia cell lines treated with lenalidomide and dexamethasone, alone or in combination. The effect of dexamethasone on the immunomodulatory activities of lenalidomide such as T cell and natural killer (NK) cell activation was measured via interleukin [IL]-2 production, and interferon-γ and granzyme B production respectively. Lenalidomide inhibited proliferation in most cell lines tested, and this effect was enhanced by dexamethasone. This effect was observed in MM cells containing the high-risk cytogenetic abnormalities t(4;14), t(14;16), del17p, del13, and hypodiploidy. Mechanistically, lenalidomide plus dexamethasone synergistically induced expression of the tumor suppressor genes Egr1, Egr2, Egr3, p15, p21, and p27 in MM cell lines and MM patient cells. The combination activated caspases 3, 8, and 9 and induced cell cycle arrest and apoptosis. Lenalidomide alone increased T cell production of IL-2, and NK cell production of interferon-γ and granzyme B. Notably, dexamethasone antagonized these immunostimulatory effects of lenalidomide in a dose-dependent manner. These data further elucidate the mechanism of action of lenalidomide and dexamethasone in MM, and suggest that use of low-dose dexamethasone with lenalidomide may retain the antiproliferative effect of lenalidomide while permitting greater immunomodulatory effects of this combination regimen.