Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-genome assembly of Culex tarsalis

The mosquito, Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted on Cx. tarsalis ecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. Salivary gland-specific gene expression has also revealed genes involved in blood feeding. However, genetic studies of this mosquito have been hindered by the lack of a reference genome. To facilitate genomic studies in Cx. tarsalis, we have assembled and annotated a reference genome (CtarK1) based on PacBio HiFi reads from a single male. Using the Cx. tarsalis transcriptome and protein sequences from Culex quinquefasciatus, approximately 17,456 protein-coding genes, including the para insecticide resistance gene, were annotated in the CtarK1 genome. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. The CtarK1 assembly is 790Mb with an N50 of 58kb. Using full mitochondrial genome alignments with other sequenced mosquito genomes we present a Bayesian phylogeny, which estimates that the divergence of Cx. tarsalis from Culex quinquefasciatus, the most closely related mosquito species with a genome, occurred 15.8-22.2 million years ago.
Causes of hospital admission of AIDS patients in southern Brazil, 2007 to 2012

ABSTRACT Introduction : The acquired immunodeﬁ ciency syndrome (AIDS) epidemic is a worldwide phenomenon that has been modiﬁ ed with the implementation of effective antiretroviral therapy. The objective of this study was to determine the leading causes of hospitalization among human immunodeﬁ ciency virus (HIV)-positive individuals. Methods : A cross-sectional study with patients admitted to a general hospital in southern Brazil, between January 2007 and May 2012. Results : Medical records of 550 hospital admissions (230 patients) were reviewed, with an average of 2.4 hospitalizations per patient. Infectious diseases were the most prevalent causes of hospitalization. Overall, 44.8% patients died and their deaths were associated with longer hospital stays. Conclusions : Opportunistic infections remained the leading causes of hospitalization. Keywords: Acquired immunodeﬁ ciency syndrome. Hospitalization. AIDS-related opportunistic infections.In Brazil, since the beginning of the epidemic in 1980 through June 2011, there have been 608,230 cases of acquired immunodeficiency syndrome (AIDS) and 241,469 deaths, with an incidence rate of 17.9/100,000 population in 2010
Optimum Harvest of Low-chill Melting and Non-melting Flesh Peach Cultivars for Direct Ripening and Ripening following Low Temperature Storage

The physical and chemical characteristics of two melting flesh (MF) cultivars, TropicBeauty and Flordaprince, and two non-melting flesh (NMF) cultivars, UFSun and Gulfking, with advancing maturities, were determined at harvest, after ripening at 20 °C for 7 days (i.e., direct ripening) and after storage at 0 °C for 14 days then ripening at 20 °C for 7 days (i.e., ripening following low temperature storage). The NMF cultivars were able to retain flesh firmness better than the MF cultivars as fruit matured and ripened on the tree and after the two storage treatments. The NMF fruit of the least mature to the most advanced maturity groups (MGs) were ≈2 to 7 times firmer than the MF fruit in the same MGs after ripening in both storage conditions. For both MF and NMF fruit, a significant reduction of titratable acidity (TA) occurred with no significant changes in soluble solids content (SSC) and total soluble sugar (TSS) as maturity and ripening progressed on the tree and after ripening in both storage conditions. Minimum quality standards of “ready for consumption” peaches were used as general guidelines to determine the optimum harvest maturity of all four cultivars. The NMF fruit ripened directly had wider optimum harvest maturity ranges and could be harvested at more advanced stages than the MF fruit. The MF fruit that ripened following low temperature storage needed to be picked at earlier maturity stages than those that were directly ripened. The optimum harvest maturity of NMF UFSun for the low temperature storage treatment was more advanced than that of the other three cultivars due to abnormal softening found in the lower MGs after ripening. Linear correlation analyses showed that the skin ground color (GC) a* values of both MF cultivars and NMF ‘UFSun’ were highly correlated with the flesh color (FC) a* values, suggesting that GC a* values can be an informative harvest indicator for this NMF cultivar instead of the traditionally used FC. The GC a* values also had high linear correlation with TA for all four cultivars, suggesting that TA can be a potential maturity index for both MF and NMF peaches. Significant correlations of GC a* values and flesh firmness (GC-FF) were found in all four cultivars in one year but only in MF peaches in both years, showing that flesh firmness was the most consistent maturity indicator for the MF cultivars in this study.
Disturbance observer approach for fuel-efficient heavy-duty vehicle platooning

ABSTRACT Heavy-duty vehicle platooning has received much attention as a method to reduce fuel consumption by keeping inter-vehicle distance short. When a platoon follows a fuel-optimal velocity profile calculated using preview road slope information, significant improvement in the fuel economy occurs. To calculate the optimal velocity in the existing method, however, platoon should acquire expensive road slope data in advance. As an alternative, we propose a road slope estimation method, which enables platoon to calculate the optimal velocity profile without the usage of actual road slope data. Other major challenges in platoon operation include overcoming the effect of the vehicle model uncertainties and external disturbances for ensuring the control performance. The most significant part of the disturbances arises from slopes along a route. Existing method for reducing the effect of the slope employs a feed-forward type compensation in the control loop by combining the vehicle position acquired from GPS and the slope database. However, this method exhibits limitations: the mass of the vehicles in the platoon is uncertain which lowers the accuracy of the feed-forward compensation, and the platoon requires the pre-acquired slope database. To overcome these limitations, we propose an alternative method employing disturbance observer. Simulations of various scenarios are conducted to show the efficacy of the proposed method using the actual road slope data of a Swedish highway.
Islamic input in medical program: a realization of a holistic medical education

An important learning outcome of a medical curriculum is to produce safe doctors over a period of training. The learning process should equip undergraduates to become competent practitioners who are able to provide holistic care to patients, physically, emotionally, psychologically and spiritually. They should have the expertise to attend to patient’s medical and health needs that are delivered in the most ethical manner through mastery of good communication skill and portrayal of compassion during the provision of care. This constitutes the basic attributes of medical professionalism that one should develop during medical training and enhanced throughout one’s career life. For Muslim medical professionals, they need to conform to the Islamic core values that constantly promote the ideals of professionalism, which include positive attitudes such as dedication, respect, compassion, empathy, honesty, altruism, responsibility, integrity, self-improvement, magnanimity and accountability. In achieving this, a holistic medical curriculum should be adopted that ensures applications of behavioural and ethical standards, based on the Islamic worldview, over a period of training. The training process would enable them to execute their duties as safe doctors, at the end of training, with greater accountability and within the realms of acceptable legal rulings for the benefit of the society and also be in conformity with the demands of the Maqasid al Shariah. This paper discusses the ideals of holistic medical education and the experience of IIUM in implementing its curriculum (Islamic Input in Medical Program, IIMP), which primarily aimed at developing four main attributes of medical professionalism of expertise, ethic, communication and other skills such as leadership, competency in medical fiqh and ethical reasoning skills in approaching medical ethical dilemmas. The challenges, the success and way forward for improvement are also discussed.
Sex Ratio of Empoasca pteridis Dhlb. (Hemiptera: Cicadellidae) and Its Seasonal and Annual Variation in Alfalfa Field

Fieldwork was performed at the experimental field of the Institut of Forage Crops, Pleven, Bulgaria during the period 2006-2009. To measure the abundance and sex ratio of Empoasca pteridis moving in alfalfa stand, net sweeping was carried out weekly during the growing season. Samples were taken along the diagonals of a crop from the plant growth to the harvest of each regrowth in the flowering stage. It was found that the population growth of leafhoppers in alfalfa reached a peak just before harvest, and the peaks increased from the first to the third harvest. The sex ratios of E. pteridis successively decreased from the first to the fourth growth cycle. In addition, the first, second and third growth cycles were initially strongly female-biased, and the sex ratio decreased over time successively and occupied the lowest value immediately before cutting. In the fourth growth cycle, the sex proportion was equalized. Significant impact on female density had the temperature factor and the predominance of females was a consequence of the higher temperature and negligible amount of rainfall. It was found also that the sex ratio of E. pteridis in the third growth cycle was characterized by a high homeostaticity and stress resistance and is the most stable in relation to the changing environment.
Feature extraction on faces : from landmark localization to depth estimation

This thesis focuses on learning algorithms that extract important features from faces. The features of main interest are landmarks; the two dimensional (2D) or three dimensional (3D) locations of important facial features such as eye centers, nose tip, and mouth corners. Landmarks are used to solve complex tasks that cannot be solved directly or require guidance for enhanced performance, such as pose or gesture recognition, tracking, or face verification. The application of the models presented in this thesis is on facial images; however, the algorithms proposed are more general and can be applied to the landmarks of other forms of objects, such as hands, full body or man-made objects. This thesis is written by article and explores different techniques to solve various aspects of landmark localization. In the first article, we disentangle identity and expression of a given face to learn a prior distribution over the joint set of landmarks. This prior is then merged with a discriminative classifier that learns an independent probability distribution per landmark. The merged model is capable of explaining differences in expressions for the same identity representation. In the second article, we propose an architecture that aims at uncovering image features to do tasks that require high pixel-level accuracy, such as landmark localization or image segmentation. The proposed architecture gradually extracts coarser features in its encoding steps to get more global information over the image and then it expands the coarse features back to the image resolution by recombining the features of the encoding path. The model, termed Recombinator Networks, obtained state-of-the-art on several datasets, while also speeding up training. In the third article, we aim at improving landmark localization when only a few images with labelled landmarks are available. In particular, we leverage a weaker form of data labels that are easier to acquire or more abundantly available such as emotion or head pose. To do so, we propose an architecture to backpropagate gradients of the weaker labels through landmarks, effectively training the landmark localization network. We also propose an unsupervised loss component
The Newly-Recognised Refugees Most at Risk of Homelessness in England

Abstract The contribution of this paper is to analyse statistical data to assess whether homelessness among people who have recently been granted refugee status in England is concentrated amongst particular groups of these refugees. The methodology was quantitative analysis using logistic regression of the Home Office’s Survey of New Refugees (SNR), which they carried out in 2005-7. We tested the relative role played by pre-migration demographic factors, post-migration life experience factors, and government immigration policy in accounting for patterns found, and drew on literature to interpret the meaning of our statistical results. Our analysis clearly suggests that refugee and asylum policy contribute to homelessness among newly-recognised refugees. This interpretation is supported by the qualitative evidence from services providing assistance to refugees, and evidence put to the All Party Parliamentary Group on Refugees (2017). Action to address the housing problems of refugees moving on from accommodation provided for asylum seekers should be considered a high policy priority, albeit that associations between homelessness, household size, and age also present intervention opportunities.
Application of Delphi Method and Fuzzy Analytic Hierarchy Process in Modeling Environmental Performance Assessment in Urban Medical Centers

Medical centers (that is, hospitals and clinics) in metropolitan areas produce substantial amounts of hazardous waste in both solid and liquid (wastewater) forms. Unless medical centers manage their waste with appropriate care, the significant hazards posed to urban residents and areas far outweigh the benefits of their services. Therefore, comprehensive environmental management programs need to be developed in order to minimize the associated impacts and improve environmental performance. In addition to identifying the environmental consequences, developing a comprehensive performance assessment program requires a deep understanding of the factors involved and their corresponding shares. Thus, the aim of this paper is to model environmental performance assessment in urban medical centers. Firstly, relevant criteria, sub-criteria and indicators were identified using the Delphi method. Next, Fuzzy Analytical Hierarchy Process (AHP) was applied to rank the factors and a balanced scoring was established to model the environmental performance assessment in medical centers. The adequate consistency index confirms Fuzzy AHP accuracy and consequently, the scores. The model was applied in Sarem Specialized Hospital in Tehran, Iran. The results indicate that the hospital has good environmental performance. The results show that the waste disinfection indicator, was rated the highest and most important index with a score of 84.The other indicators were ranked in terms of treated sewage and source separation of waste and application of mechanisms to control water consumption respectively with scores of 38, 26.5 and 25.
Rekam Medis Elektronik Menggunakan Sistem Penyimpanan Foto Intraoral Gigi untuk Aplikasi Teledentistry berbasis Internet of Things

Rekam Medis Elektronik (RME) dalam dunia kedokteran digunakan untuk memudahkan pencatatan kondisi pasien. Sistem informasi yang berisi catatan medis pasien ini memudahkan peninjauan kembali histori pemeliharaan kesehatan dan pengobatan pasien oleh dokter maupun tenaga medis lainnya. Aplikasi teledentistry berbasis Internet of Things (IoT) dapat digunakan untuk melakukan telediagnosis dan teleconsultation dalam hal pencatatan dan penyimpanan data secara jarak jauh sehingga meminimalisir kesalahan yang biasa dilakukan dalam pencatatan secara manual. Kamera intraoral gigi digunakan sebagai alat perekam foto gigi yang dapat digunakan antara lain untuk memudahkan diagnosis, konsultasi dan dokumentasi pasien. Dengan demikian sebuah aplikasi teledentistry berbasis IoT dapat dikembangkan dengan mengintegrasikan sebuah kamera intraoral gigi dengan aplikasi rekam medis elektronik. Penelitian ini bertujuan untuk mengembangkan sebuah sistem yang memungkinkan seorang dokter atau perawat untuk mengambil foto intraoral gigi yang secara otomatis dapat langsung tersimpan di dalam aplikasi rekam medis elektronik terpusat. Alat perekam foto yang digunakan dalam penelitian ini menggunakan kamera intraoral gigi yang tersedia di pasaran dan memiliki antarmuka untuk dihubungkan ke komputer. Foto yang baru diambil akan langsung dikirimkan ke server di mana aplikasi rekam medis elektronik terpasang. Dengan demikian dokter gigi dapat mengakses data pasien yang baru saja ditangani beserta foto-foto pelengkapnya dari mana pun.
Speciation without Species: A Final Word

Here I present the several models currently popular for understanding speciation in prokaryotes, in particular bacteria. I will argue that “speciation”, as a process or collection of independent but interacting processes sometimes serving to form genotypic and/or phenotypic clusters, can be studied effectively without any definition of “species” or any requirement that all prokaryotic lineages match such a definition. This has always been so, but formal acknowledgement would have a freeing effect.
The concept of education in higher education in England, 1960 - 1997, with special reference to adult continuing education.

This thesis reports a study of the concept of education in higher education and in adult continuing education within higher education in England in the period from 1960 to 1947. The period chosen has seen great changes in higher education: one aim of the study is to explore the associated changes, if any, in the understanding of the education provided in the changed system. The study begins with a consideration of the philosophy of education, the need to take account of the historical and social settings of concepts, the distinction between concepts and conceptions, and the issues of essentially contested concepts. A brief and selective review provides an historical background for the study. Three mam conceptions of education in mainstream higher education are identified. discussed and traced in the report of the Robbins Committee (1963) and other studies. Four main conceptions of education in adult continuing education are similarly identified. discussed and traced in the provision made by adult education departments. Consideration is given to conceptions of education developed within the radical tradition in education. A number of emerging ideas associated with developments of the 1990s, including the idea of lifelong learning, are identified and discussed with particular reference to the report of the Dearing Committee (1997). It is shown that higher education and adult continuing education alike have been dominated by one particular conception of education. The reasons for this dominance and its implications for the future of higher education are discussed in relation to the development of a mass system of higher education and the emergence outside higher education of a significantly different conception of education, here characterised as the 'commodity' view of education.
Search and Aggregation in Big Graphs

Recent years have witnessed a growing renewed interest in the use of graphs as a reliable means for representing and modeling data. Thereby, graphs enable to ensure efficiency in various fields of computer science, especially for massive data where graphs arise as a promising alternative to relational databases for big data modeling. In this regard, querying data graph proves to be a crucial task to explore the knowledge in these datasets. In this dissertation, we investigate two main problems. In the first part we address the problem of detecting patterns in larger graphs, called the top-k graph pattern matching problem. We introduce a new graph pattern matching model named Relaxed Graph Simulation (RGS), to identify significant matches and to avoid the empty-set answer problem. We formalize and study the top-k matching problem based on two classes of functions, relevance and diversity, for ranking the matches according to the RGS model. We also consider the diversified top-k matching problem, and we propose a diversification function to balance relevance and diversity. Moreover, we provide efficient algorithms based on optimization strategies to compute the top-k and the diversified top-k matches according to the proposed model. The proposed approach is optimal in terms of search time and flexible in terms of applicability. The analyze of the time complexity of the proposed algorithms and the extensive experiments on real-life datasets demonstrate both the effectiveness and the efficiency of these approaches. In the second part, we tackle the problem of graph querying using aggregated search paradigm. We consider this problem for particular types of graphs that are trees, and we deal with the query processing in XML documents. Firstly, we give the motivation behind the use of such a paradigm, and we explain the potential benefits compared to traditional querying approaches. Furthermore, we propose a new method for aggregated tree search, based on approximate tree matching algorithm on several tree fragments, that aims to build, the extent possible, a coherent and complete answer by combining several results. The proposed solutions are shown to be efficient in terms of relevance and quality on different real-life datasets
Predictors of Positive Outcomes in Pulmonary Rehabilitation

Aims: The study aims were to (1) determine the effect of participation in pulmonary rehabilitation on quality of life, severity of dyspnea, and exercise tolerance (2) evaluate predictors (number of pulmonary rehabilitation sessions attended, age, baseline quality of life, depression, and body mass index)of improvement in severity of dyspnea, exercise tolerance, and quality of life (3) to test if the amount of change in exercise tolerance and change in severity of dyspnea from the baseline to the end of pulmonary rehabilitation modifies the effect of the baselines variables on the change in quality of life from baseline to the end of rehabilitation. Study Design: A descriptive retrospective design was used. Methodology: We performed secondary analysis of records of 125 patients in the pulmonary rehabilitation registry in the University Hospitals of Cleveland / OH. The sample included all patients who completed six pulmonary rehabilitation sessions at least. Results: Pulmonary rehabilitation improved quality of life, alleviate severity of dyspnea and enhance exercise tolerance. Greater baseline body mass index was the only significant predictor Original Research Article Aloush et al.; BJMMR, 18(3): 1-7, 2016; Article no.BJMMR. 28901 2 for the improvement in exercise tolerance (unstandarized β coefficient= 1.5, P= 0.02). None of the baseline variables predicted the change in severity of dyspnea. Better baseline quality of life was the only significant predictor for the improvement in quality of life (unstandarized β coefficient= 0.3, P=0.03). Changes in severity of dyspnea and change in exercise tolerance did not modify the effect of the baseline variables on the change in quality of life from baseline to the end of rehabilitation. Conclusion: Positive rehabilitation outcomes are predicted by better baseline quality of life and higher body mass index. More research is needed to identify additional interventions to implement during rehabilitation to achieve positive outcomes in participants who have lower BMI and lower baseline quality of life.