Miracle-dz/UniFAR-FTUs huggingface dataset:
Cystic Fibrosis Patients Evaluation in the Last Decades in a Referral Center, Tehran-Iran

Background Cystic fibrosis (CF) is the most prevalent lethal chronic genetic and multivariate disease, widespread in Iranian population. The aim of this study was to evaluate the condition of patients with CF from various dimensions in the last decades in Iran. Materials and Methods In this cross-sectional study the data were collected from disease registrydatabase of CF patients in Pediatric Respiratory Disease Research Center in Masih Daneshvari, Tehran, Iran. The patients were divided into female and male.The data were collected based on province, birthplace province, marital status, and degree of education, parental consanguinity ratio, age, and age of onset of symptoms, age of onset of diagnosis and body mass index (BMI). Results Majority of patients (n=169, 59.3%) were male, born in Tehran province (n=81, 28.4%), and live in Tehran province (n=102, 35.8%). Majority of parents (61.1%, n=174) had consanguineous relation and the rest (n=94, 33%) did not have any consanguineous relation. Results show that mean of age, age of diagnosis, mean for expression of first symptoms and mean of time interval between the onset of symptoms and the diagnosis of the disease were 14.52, 2.51, 6.57, and 4.07 years, respectively. Results showed that high percentage of patients (n=191, 67%) had lower BMI ( 25). Correlation coefficient also showed positive relation between start age of symptoms and diagnosis age of disease. Conclusion In Iran, CF is a multisystem disease and age for its expression is different. Since mean for time interval between the onset of symptoms and the diagnosis of the disease
GAIT PARTITIONING WITH SMART SOCKS SYSTEM

Gait is a very complex movement, involving the central nervous system and a significant part of the skeletomuscular system. Any disease that is affecting one or more of the involved parts will reflect in the gait. Therefore, gait analysis has been studied extensively in the context of early disease diagnostics, post-operation rehabilitation monitoring, and sports injury prevention. Gait cycle phase partitioning is one of the most common gait characteristic analysis methods, which utilizes the cyclical nature of human gait. Pressure sensitive mats and insoles are considered the gold standard, but some inherent limitations of these methods urge researchers to seek for alternatives. One of the proposed alternatives is Smart Sock systems, which contain textile pressure sensors. The main limitation of Smart Sock systems is the limited number of sensors, thus complicating gait phase partitioning by these systems. The present paper describes gait phase partitioning using plantar pressure signal obtained by a Smart Sock system. Six-phase partitioning was achieved, including such gait phases as initial contact, loading response, mid stance, terminal stance, pre-swing and swing phase. Mean gait cycle time values obtained from the experimental data were in accordance with the ones found in the literature.
Effect of Brine Water on Discharge of Cations in Membrane Capacitive Deionization and Its Implications on Nitrogen Recovery from Wastewater

We examined the desorption behavior of cations in membrane capacitive deionization (MCDI) from the cathode into high-concentration brine through a cation-exchange membrane (CEM) brine, during mineral recovery. Several major issues were explored to demonstrate the suitability of the mineral recovery process: discharge behavior using different solution chemistries, desorption efficiencies of various regeneration methods for the enrichment of ions, and desorption selectivity among selected cations. The desorption efficiency was hampered when the adsorbed cations migrated toward the brine solution against a higher ionic-strength gradient and was further lowered by the enhanced membrane resistance under the low concentration of the adsorbed ions on the cathode. Furthermore, the electrochemically adsorbed ions were limitedly discharged by the cost-effective regeneration method (short-circuiting). The cations were preferentially released in the order of K+ > Na+ > Mg2+, as mainly determined by their physiochemic.
Ear Nose and Throat (ENT) Manifestations in Granulomatosis with Polyangiitis in Patients from Saudi Arabia

Granulomatosis with polyangiitis (GPA) frequently affects ear, nose and throat (ENT) at disease onset. Our aim was to report on our experience with the ENT manifestations in GPA patients, therapy and outcome. A retrospective study of GPA patients was performed who followed up in Rheumatology clinics at King Khalid University hospital, Riyadh during the period 1990-2016. Demographics, different ENT manifestations, laboratory and diagnostic features, therapy and outcome of GPA patients were retrieved from their medical charts. ENT involvement was observed in 15 (65.2%) of the 23 GPA cases identified. Otologic symptoms were noted in 3 (13.0%), nose and sinus symptoms in 13 (56.5%) and throat symptoms in 3 (13.0%) GPA patients. Epistaxis (39.1%) was the most prevalent nose and sinus symptom followed by sinusitis (30.4%), otitis media and hearing loss were the frequent otologic symptoms, oral ulcers and hoarseness of voice constituted frequent throat symptoms in GPA patients. Of the 15 ENT-GPA patients, 9 were males and 6 were females (male: female; 1.5: 1). Their mean age at disease onset was 33.8 ± 18.3 (range 11-57) years and mean duration of disease was 10.1 ± 5.9 (range 1-20) years. ANCA was positive in 93.3% ENT-GPA patients, 73.3% had c-ANCA and 20.0% had p-ANCA. Infections were noted in 33.3% ENT-GPA patients that included pneumonia, septicemia, esophageal candidiasis, bacterial meningitis and herpes zoster. All patients received oral prednisolone, 60.0% received intravenous cyclophosphamide, 20.0% refractory cases received rituximab doses, and the disease outcome was good. Comparison of ENT- GPA with non- ENT GPA cohort showed that 26.7% ENT-GPA patients had renal involvement compared to 87.5% non ENT-GPA patients (p = 0.009). Our study showed that the frequency of ENT symptoms in our GPA patients was less compared to other studies, and the disease outcome was good. Renal involvement was significantly less frequent in ENT-GPA cohort compared to non ENT-GPA cohort.
The Impact of First Complete Remission by PET-CT and Time to Next Treatment on Survival of Follicular Lymphoma Patients

We retrospectively analyzed the impact of initial positron emission tomography and computed tomography (PET-CT) complete remission (CR) and time to next treatment (TTNT) on patient outcome in follicular lymphoma. Between 2002 and 2014, 150 patients could be evaluated for treatment response and long-term outcome. The CR after first line treatment with either rituximab-cyclophosphamide, oncovin, and prednisolone (R-COP) or rituximab-cyclophosphamide, doxorubicin, oncovin, and prednisolone (R-CHOP) was 89% and partial response (PR) was 7%. The 5- and 10-year survival rates were 86.0% and 62.6%, respectively. In five years, 11% of patients had died of lymphoma and 3% from other causes. Forty-seven patients (31%) underwent a second line of treatment comprising 19 (40%) with a TTNT shorter than 24 months and 28 (60%) longer than 24 months. There was no difference in overall survival (OS) between R-COP (86%) and R-CHOP (77%) at 5 years, but there were more next treatment events in the R-COP compared with the R-CHOP group on longer follow-up (60% versus 35% at 8 years). For PET-CT response, there was a significant OS difference between initial CR and PR patients (88% versus 70%, p < 0.01), and a longer TTNT was seen in initial CR patients. Patients with a TTNT longer than 24 months had better OS compared with patients with a shorter TTNT (93% versus 54% at 5 years, p < 0.01). In conclusion, patients with initial PET-CT CR and TTNT longer than 24 months had better OS compared with those achieving only PR and shorter TTNT. PET-CT CR should be considered the treatment goal during initial treatment, and more aggressive treatment should be considered for patients with a TTNT of less than 24 months.
Study on performance efficient trees for multicast communication

iii Acknowledgements v List of Figures xi List of Tables xiv Acronyms xv Chapter 1: Introduction 1 1.1 Background 1 1.1.1 Internet Multicast 1 1.1.2 Optical Internet Multicast 7 1.1.3 Types of Multicast Membership 10 1.1.4 Delay Constrained Multicast 12 1.1.5 Performance Metrics used in Multicast 13 1.1. 6 Performance Efficient Trees in Multicast 14 1.2 Motivations 15 1.3 Objectives 18 1.4 Contributions of the Thesis 20 1.5 Organization of the Thesis 24 Chapter 2: Literatures Review 26 2.1 Overview of Internet Multicast 26 2.2 Minimum Cost Tree Construction in Multicast 28 2.2.1 Minimum Cost Tree Multicast 28 2.2.2 Minimum Spanning Tree Algorithms 29 2.2.3 Shortest Path Algorithm 30 2.2.4 Minimum Cost Tree Algorithms using Single Tree Construction 31 2.2. 5 Minimum Cost Tree Algorithms using Shared-Tree Construction 37 2.3 Minimum Cost Tree Construction in Dynamic Membership Multicast 39 2.3.1 Dynamic Membership Multicast 39 2.3.2 Performance Metrics used for Dynamic Membership Multicast 39 2.3. 3 Algorithms for Minimum Cost Tree Construction in Dynamic Membership Multicast 41 2.3. 3.1 Non-Rearrangeable Algorithms 42 2.3. 3.2 Rearrangeable Algorithms 45 2.4 Multicast Capable (MC) and Wavelength Conversion Capable (WCC) Nodes Placement in Optical Multicast 54 2.4. 1 Performance Metrics used for MC and WCC Nodes Placement Problems 54 2.4. 2 Placement of Multicast Capable (MC) Nodes 55 2.4. 3 Placement of Wavelength Conversion Capable (WCC) Nodes 57 ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library
Supporting PCR-related activity with Implicit Culture

Polymerase Chain Reaction (PCR) is a very common kind of experiment conducted in laboratories over the world. However, the procedure is highly sensitive to the choice of parameters and varies depending on the local practices of each laboratory. In this paper, we present an analysis of the PCR-related activities in a biological laboratory and identify the information needs of the biologists performing PCR. Then, we produce a set of requirements to a system for PCR support and describe an architecture of such system using Implicit Culture concepts. Finally, we introduce a working prototype of the system, its design, implementation and evaluation results. This work is the result of close collaboration with biologists, individual interviews and on-site observations in laboratory.
Iranian Nurses' Attitudes Toward Nurse-Physician Collaboration and its Relationship with Job Satisfaction

Introduction: Although nurses and physicians are known to share the common goal of improving the quality of health care, there has traditionally been a relational gap between them. The aim of the present study was to investigate the attitude of Iranian nurses about physician-nurse collaboration and its relationship with their job satisfaction. Methods: In this cross-sectional study, a total of 232 nurses were recruited from three educational hospitals of Zanjan University of medical sciences. Three questionnaires were used in this study; (a) Demographic data questionnaire, (2) Jefferson Scale of Attitudes toward Physician–Nurse Collaboration (JSAPNC), and (3) Minnesota Satisfaction Questionnaire. Results: In this study, the mean age of the participants was 33.22(SD= 6.13) years, 83.8% of nurses were female, 90.8% had a baccalaureate degree in nursing, and 82.5 % had rotational work shifts. The mean score of physician-nurse collaboration was found to be 48.07 (SD= 8.95) (ranged from 15 to 60), and the mean score of job satisfaction scale was 57.78 (SD = 14.67) (ranged from 20 to 100). There was a significant positive correlation between the attitudes toward physician–nurse collaboration and job satisfaction among the nurses (r=0.59, P≤0.001). Conclusion: The results indicated that the collaboration between nurses and physicians increases the job satisfaction of nurses working in clinical settings. Therefore, nurses and physicians should develop a new culture of collaboration with each other with the mutual goal of high quality patient care. Moreover, health care administrators should implement the strategies that strengthen the development of physician–nurse collaboration.
Implementation of a Multiple Switch Time Approach toStyle-Based Motion Segmentation

This thesis presents progress on segmenting human movement based on a notion of movement quality. This research is an extension of a style-based motion classification where, here, this classification is used to segment long motion phrases into smaller, discrete motion snippets. In particular, this thesis presents a given trajectory that is segmented into three shorter trajectories that each has their own length and quality. The objective of the thesis is to refine this segmentation, extend it to an arbitrary number of segmentation points, apply it to motion capture data and explore other extensions. A key novel contribution of this thesis is the analytical derivation of first order necessary conditions for optimality. The research may be used to build a library of motion primitives and aid the study of motion recognition in automation.
Combining Ability Analysis and Heterotic Effects for Cotton Fiber Quality Traits

Combining ability and gene action can help breeders to select suitable parents and appropriate breeding strategy. In the present study combining ability analysis and heterotic effects for cotton fiber quality traits were studied in a set of diallel crosses involving six cotton genotypes. The aim of this study was to estimate general combining ability of parents, special combining ability of F1 diallel crosses, heterotic effects of F1 diallel crosses in in the breeding programme to develop high quality cotton varieties. Randomized complete block design was used to test 15 F1 diallel crosses, and 6 parents. Analysis revealed significant general combining ability effects for all the investigated traits and additive gene effects were important in the inheritance of the traits. Analysis also revealed significant SCA effects for only fiber fineness and spinning consistency index traits and additive and non-additive gene effects were important in the inheritance of the traits. General combining ability was found significant for all investigated traits, revealing the important role of additive gene effects. Specific combining ability was found significant for the Mic and SCI, revealing that non-additive gene effects, as dominant or epistatic are important, but not for Len, Str and SFI.
An Architecture Framework for Virtualization of IoT Network

The Internet of Things (IoT) market is constantly opening new business and market opportunities to connect the digital and physical worlds in many sectors such as smart-city, industry, agriculture, building, transportation, energy, etc. To support this major growth, we anticipate the adoption of mainstream Software Defined Networking SDN, Software Defined Radio (SDR) and Network Function Virtualization (NFV) technologies within the IoT systems to allow providing new ways of offering services in a more flexible, agile and cost-effective manner than today. This paper investigates the provision of NFV in the Internet of Things through the virtualization of full stack IoT functions, from radio processing functions to processing capabilities, that can be orchestrated dynamically and deployed on generic IoT devices. We provide a proof of concept to demonstrate the provisioning of end-to-end virtualized service function chain using the GNU Radio framework and dockers containers for isolation and VNF deployment and execution
Automated DEM/DSM Accuracy EstimatesTowards Land Change Detection

Recognition of buildings and other man-made objects from aerial images is an issue of considerable importance to many users of geo-information, including surveyors, geographers and planners. Integrating a priori information into procedures for the automatic recognition and reconstruction of cartographic objects from imagery has been examined by a number of researchers (Locherbach [1], Priestnall and Glover [2]). The general assumption that buildings are higher than their surrounding surface is used by various researchers such as Weidner and Forstner [3] to aid in detecting buildings from imagery. The results suggest that subtraction of a Digital Elevation Model (DEM) from a Digital Surface Model (DSM) is a feasible technique for detecting man-made objects from imagery. However, since DEM and DSM have inherent levels of accuracy, these accuracy levels will eventually be inherited by the residual surface (DSM-DEM). It is important to understand the inherent accuracy of both the DEM and DSM if the building height derived from these sources is to be used profitably in an object recognition strategy. This paper focuses on the extraction of building heights derived from the subtraction of the DEM from the DSM. Global Positioning Systems (GPS) and traditional surveying techniques have been employed to provide ground reference data for the validation of DEM and DSM which comprises an area of the University of Nottingham campus. The reliability of automated validation of DEM and DSM using synthetic ground reference data generated by a mathematical function along a selected profile is proposed. The results suggest that possible building structures are revealed above the residual surface and can also be detected below the residual surface by generating contour plots at various levels. The automatic validation of DEM and DSM proposed is a promising approached to the task of building extraction since it minimises time and cost by eliminating the need to gather ground reference data.
Effect of calcium, BAP and putrescine on somatic embryo induction in juvenile explants of Eucalyptus grandis × E. urophylla hybrids

Considering the constant improvement of Eucalyptus cloning and the search for new technologies to produce plantlets of this species, somatic embryogenesis has attracted interest from research groups and forestry companies that use advanced genetic breeding and cloning programs. The objective of the present study was to verify the effect of concentrations and sources of calcium, concentrations and effect time of cytokinin BAP and polyamine putrescine on the induction and development of somatic embryos in juvenile explants of Eucalyptus grandis x E. urophylla. Cotyledonary explants were inoculated into culture medium containing calcium chloride (MS medium) or calcium nitrate (JADS medium) as source of calcium. Different concentrations of calcium were also used, for MS medium containing: 4.40 gL-1 (control-Ca), 6.60 gL-1 (50% increase over control - Ca 50) and 8.80 gL-1 (increase of 100% over control – Ca 100) of calcium nitrate; and for JADS medium containing: 11.81 gL-1 (Ca), 17.72 gL-1 (Ca50) and 23.62 gL-1 (Ca100) of calcium chloride. Cotyledon explants were inoculated into the primary induction medium (PIM) containing 20.71 μM picloram as growth regulator. At 10, 20 and 30 days of primary induction, the explants were transferred to the secondary induction medium (SIM) containing 20.71 μM picloram and 11.10 μM BAP or 28.36 μM putrescine. The culture medium containing calcium nitrate provided higher callogenesis when compared to the medium containing calcium chloride. The increase in calcium concentration in the media did not provide higher percentage of induction of somatic pro-embryos. However, the addition of 28.36 μM putrescine to the culture medium provided a higher percentage of induction of somatic embryogenesis. The number of somatic pro-embryos formed per explant was higher when BAP and putrescine were added to the culture medium when compared to medium containing only picloram. To obtain a greater number of somatic pro-embryos of Eucalyptus grandis × E. urophylla, the JADS culture medium containing 28.36 μM putrecine should be used.
Tolerance of nonsynonymous variation is closely correlated between human and mouse orthologues

Genic constraint describes how tolerant a gene is of nonsynonymous variation before it is removed from the population by negative selection. Here, we provide the first estimates of intraspecific constraint for mouse genes genome-wide, and show constraint is positively correlated between human and mouse orthologues (r = 0.806). We assess the relationships between mouse gene constraint and knockout phenotypes, showing gene constraint is positively associated with pleiotropy (ie an increased number of phenotype associations (R2 = 0.65)), in addition to an enrichment in lethal, developmental, and craniofacial knockout phenotypes amongst the most constrained genes. Finally, we show mouse constraint can be used to predict human genes associated with Mendelian disease, and is positively correlated with an increase in the number of known pathogenic variants in the human orthologue (R2 = 0.23). Our metrics of mouse and human constraint are available to inform future research using mouse models.
Modeling and Design: a Hands-on Introduction to Biomedical Engineering

How can we impart the excitement of biomedical engineering to our freshmen from the moment they step on campus? We have found great success with “Modeling and Design” an innovative, required course which engages our students as biomedical engineers from their first day at Johns Hopkins. Small groups, guided by upperclassmen lab managers, teaching assistants, and faculty, work through five modules including modeling human efficiency, the arm, and the cardiovascular system, as well as a foam core design project. By the conclusion of the fifth module, an independent modeling project, 96% of the students appreciate the value of working in teams to tackle complex challenges. They have become adept at developing and testing their hypotheses, and presenting their results through written lab reports and oral presentations. By the end of the semester, 84% of freshmen “strongly agreed” or “agreed” that the course had met its goal of providing a solid introduction to modeling physiological systems, academic and career mentoring, exposure to research and design opportunities available at Johns Hopkins, and a concrete basis for a career choice in BME. More importantly, the course helps set up our students for long-term academic success, as indicated by a 94% freshmen/sophomore retention rate. Developing a mathematical model to describe a physiological system is a new concept for freshmen. For each project, the freshmen are provided with a one page background summary with just enough information to get started. Experimental testing of the mathematical model is an essential component of the learning process, and allows the students to collect data and perform a statistical analysis of their model. At first, the process of making assumptions, writing equations, developing an experimental protocol to test the model, and analyzing the results is daunting. By the final independent project, 88% of students felt exploring their own topic was an “excellent” or “good” learning experience and valued presenting their results at a final poster session. Not only do the freshmen benefit from the course, but the upperclassmen lab managers believe they have gained valuable leadership and professional skills, such as providing constructive feedback and public speaking.