Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization and machine learning in MRI: applications in rapid MR image reconstruction and encoding models of cortical representations

OPTIMIZATION AND MACHINE LEARNING IN MRI: APPLICATIONS IN RAPID MR IMAGE RECONSTRUCTION AND ENCODING MODELS OF CORTICAL REPRESENTATIONS Mohammad Shahdloo Ph.D. in Electrical and Electronics Engineering Advisor: Tolga Çukur February 2020 Magnetic Resonance Imaging (MRI) is a non-invasive medical imaging modality that is widely used by clinicians and researchers to picture body anatomy and neuronal function. However, long scan time remains a major problem. Recently, multiple techniques have emerged that reduce the acquired MRI signal samples, hence dramatically accelerating the acquisition. These techniques involve sophisticated signal reconstruction procedures that in essence require solving regularized optimization problems, and clinical adoption of accelerated MRI critically relies on self-tuning solutions for these problems. Further to this, recent experimental approaches in cognitive neuroscience favor employing naturalistic audio-visual stimuli that closely resemble humans’ daily-life experience. Yet, these modern paradigms inevitably lead to huge functional MRI (fMRI) datasets that require advanced statistical and computational techniques to uncover the large amount of embedded information. Here, we propose a novel efficient datadriven self-tuning reconstruction method for accelerated MRI. We demonstrate superior performance of the proposed method across various simulated and in vivo datasets and under various scan configurations. Furthermore, we develop statistical analysis tools to investigate the neural representation of hundreds of action categories in natural movies in the brain via fMRI, and study their attentional modulations. Finally, we develop a model-based framework to estimate temporal extent of semantic information integration in the brain, and investigate its attentional modulations using fMRI data recorded during natural story listening. In short, the methodological and analytical approaches introduced in this thesis greatly benefit clinical utility of accelerated MRI, and enhance our understanding of brain function in daily life.
How do patients enter the healthcare system after the first onset of multiple sclerosis symptoms? The influence of setting and physician specialty on speed of diagnosis

Background: Diagnosing multiple sclerosis (MS) early is crucial to avoid future disability. However, potentially preventable delays in the diagnostic cascade from contact with a physician to definite diagnosis still occur and their causes are still unclear. Objective: To identify the possible causes of delays in the diagnostic process. Methods: We analyzed the data of the Swiss MS Registry. With logistic regression, we modeled the time from the first contact to the first consultation (contact-to-evaluation time, ⩽1 month/>1 month) and the evaluation-to-diagnosis time (⩽6 months/>6 months). Potential factors were health system characteristics, sociodemographic variables, first symptoms, and MS type. Results: We included 522 participants. Mostly, general practitioners (67%) were contacted first, without delaying the diagnosis. In contrast, first symptoms and MS type were the major contributors to delays: gait problems were associated with longer contact-to-evaluation times, depression as a concomitant symptom with longer evaluation-to-diagnosis times, and having primary progressive MS prolonged both phases. In addition, living in mountainous areas was associated with longer contact-to-evaluation times, whereas diagnosis after 2000 was associated with faster diagnoses. Conclusion: For a quicker diagnosis, awareness of MS as a differential diagnosis of gait disorders and the co-occurrence of depression at onset should be raised, and these symptoms should be attentively followed.
On the use of continuous wavelet transforms to analyse accelerometer data collected by the NAT device to characterise Parkinson's disease

Parkinson’s disease (PD) is treated using drugs with powerful side-effects, and has similar symptoms to a range of other diseases. It is therefore important to diagnose PD accurately, and then to monitor its progression, to avoid mis-prescribing and under- and over-prescription of these drugs. Although diagnosis by experts in PD is fairly accurate, there is certainly room for improvement, and most initial diagnoses are carried out by non-expert medical staff with a much lower degree of accuracy. It is therefore desirable that automatic methods of diagnosis and monitoring be developed, and this Thesis examines the use of wavelets like those used in the Continuous Wavelet Transform (CWT), using wavelets extracted from the data itself, to try and detect features in the data pertaining to PD patients and controls. We believe that we have successfully automatically detected distinct features, with the proviso that this has been done with very little data, opening up the possibility of tracking the development of the disease as different characteristics alter in importance, or of distinguishing subtypes of PD (analyses of the genome have determined that such subtypes exist). However, the CWTs generated by wavelets corresponding to individual features, do not suffice as a basis for diagnosis, as the features may only be intermittently present. In combination, either with other wavelets of the same type, or other methods entirely, diagnosis remains a possibility. We used Neural Acquisition Tracker (NAT) devices to obtain tri-axial accelerometer data as input to these methods, and will analyse the effect of finite bandwidth on their performance. We believe the following list sums up the main novelty of our techniques: Libraries of motion shapes: at least within the field of the analysis of the motion of PD subjects; Representing motion shapes: by equivalence classes of piecewise polynomial wavelet triplets, which are invariant under rotations and reflections; Distance functions: working out the form of a distance based on the L_2 distance between individual functions, but which works on the equivalence classes mentioned above; hierarchical k-medoids: an approximation to k-medoids, using the clustering of cluster centres, which runs faster than k-medoids.
Establishing a Nurse Practitioner Residency Program in a Rural Federally Qualified Health Center: A Feasibility Analysis and Pilot Study

Rural communities are disproportionately underserved and have been identified as a priority population to improve health outcomes and access to care (Agency for Healthcare Research and Quality [AHRQ], 2015). National organizations have recognized a deficit in primary care providers, recommended nurse practitioners (NPs) as a solution, and supported NP residency programs as a means to prepare and recruit qualified practitioners into communities (Institute of Medicine [IOM], 2010; The Patient Protection and Affordable Care Act [PPACA], 2010). However, there are only three primary care NP residency programs in rural California (National Nurse Practitioner Residency and Fellowship Training Consortium [NNPRFTC], 2015). A pilot NP residency program and feasibility analysis was designed to evaluate current program structures and funding sources while promoting the development and implementation of NP residency programs within rural Federally Qualified Health Centers (FQHCs). Evaluation metrics included competency self-assessments, content-based evaluations of a web-based didactic module, and qualitative program evaluations. The results of this pilot study showed an increase in self-reported clinical competence as well as knowledge acquisition with the didactic module. An opportunity exists to model new NP residency programs off the pilot activities and structures identified in this project within rural FQHCs.
Effects of prescribed surface fires on ground- and shrub-nesting Neotropical migratory birds in a mature Indiana oak forest, USA.

A large body of scholarly work has documented that fire was an important influence on the structure and species composition of many forest types in the eastern United States in the past (see reviews by Abrams 1992, Lorimer 1993, Pyne 1982). However, state and federal fire suppression policies, initiated early in the twentieth century, have caused vegetation in many parts of this region to change substantially from that which prevailed before suppression (Abrams 1992, Lorimer 1993, Pyne 1982). Within forests that were historically dominated by oak (Quercus L. spp.) and pine (Pinus L. spp.), abundance of species that are fire-tolerant, but shade-intolerant, has decreased, while abundance of firesensitive species that are more shade-tolerant has increased.
Clinicohistopathological study of cutaneous vasculitis

Background: Vasculitides comprise a group of disorders characterized by inflammation directed at blood vessels, identified by histologic examination. Biopsy is the gold standard for the diagnosis of cutaneous vasculitis. Aims:1) to study in detail, the classic histopathological features of cutaneous vasculitis and correlate them with the clinical features for the emergence of a composite diagnosis of cutaneous vasculitis.2) to evaluate the role of Direct Immunofluorescence in the diagnosis of cutaneous vasculitis. Materials and Method: this cross sectional descriptive study was conducted in the Department of Pathology, Government Medical College, Thiruvananthapuram, during a period of 2 years in 90 cases having a clinical diagnosis of cutaneous vasculitis. Histopathological findings of the skin biopsy specimens were noted. Direct Immunofluorescence was done in a selected number of cases. Data was analyzed using SPSS software. For all statistical evaluations, a 2-tailed probability of value, <0.05 was considered significant. Results: This study shows good correlation between clinical and histopathological diagnosis (93.3% of cases) and is statistically significant. DIF acts as an adjuvant investigation in cases suspected to be immunologically mediated.
PCR Assays Based on invA Gene Amplification are not Reliable for Salmonella Detection

Background: Salmonella surveillance relies on invA polymerase chain reaction (PCR) assays for the rapid detection of Salmonella; however, false-positive results have been reported using this method. Objectives: To evaluate the performance and specificity of the published and validated PCR protocols targeting invA gene for the detection of Salmonella. Methods: The performance and specificity of 11 different PCR primer sets were evaluated using Salmonella type strains and Citrobacter spp. , Escherichia coli and Serratia spp. isolates recovered during a Salmonella surveillance program. Results: It was revealed that the published PCR protocols using validated primers targeting invA and 16S rRNA genes generated false-positive signals. Importantly, a protocol targeting the ttrA/C genes was able to discriminate Salmonella and non-Salmonella isolates. Conclusions: Detection of Salmonella spp. by means of invA PCR amplification is not reliable. In fact, false-positive results are commonly obtained from Citrobacter, E. coli and Serratia isolates. It is recommended to use other loci, such as ttrA/C genes, for the accurate and reliable detection of Salmonella.
Prevalence of hepatitis B and C viruses infections among hemodialysis patients in Addis Ababa, Ethiopia

Background: HBV and HCV infections are the most important causes of morbidity and mortality in haemodialysis patients. Hepatitis viruses cause potentially life-threatening inflammation of the liver, characterized by acute and chronic forms of liver disease. The prevalence of hepatitis B virus (HBV) antigen and Anti- hepatitis C virus (HCV) antibody among haemodialysis (HD) patients in Addis Ababa was investigated using ELISA test method. The aim of this study was to assess the prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV). Methodology: Cross-sectional study was done in a total of 253 (188 male and 65 female) chronic hemodialysis patients from two governmental and three private hemodialysis centers. Demographic information of hemodialysis was collected. The status of HBsAg and anti-HCV was assessed by using ELISA method by separating serum from collected blood sample and screened for the presence of HBsAg and anti-HCV antibody in a period of April-May 2016. Results: In this study a total of 253 patients were recruited of whom 74.3% were men and the remaining 25.7% were females. HBsAg was positive in 1.2% (n=3/253) of the patients, anti- HCV antibodies were detected in 2.8% (n=7/253), 4% of patients had markers of at least one viral infection markers and 0.4% (n=1) were positive for both HBV and HCV infection. Conclusion: In our study done, the prevalence of HBV and HCV infections in hemodialysis centers in Addis Ababa, Ethiopia was lower. Even if, history of blood transfusion and the number of blood units transfused might be a risk factor for HBV and HCV gaining, further studies are needed to assess the role of demographic and clinical risk factors in the Hemodialysis patients.
Self-Care Practices of Preparatory School Students with Type 1 Diabetes Mellitus in ELBehira Governorate

Background: Type 1 diabetes (T1D) is more prevailing disease in adolescence. Intervening in self-care is crucial for disease management and to reduce the risk of diabetes-specific complications. The aim of the study was to assess self-care practices of preparatory school students with type 1 Diabetes Mellitus in EL Behira Governorate. Egypt. Subjects: A total number of 300 students constituted the subjects of the study. Research design: A descriptive research design was used. Setting: Data was gained from governmental preparatory schools in El-Behira governorate. Sampling students were chosen by multistage sampling technique. Tools: one tool was used for data collection, a structured interview schedule composed of three parts to collect data about socio-demographic characteristics, students’ knowledge about TID, and assessment of students’ self-care practices. Results: 53.3% of the studied diabetic preparatory school students have fair total self-care practices score while 29.7% of them have poor self-care practices. A significant difference was revealed between the studied diabetic students’ total score of knowledge and self-care practices. 76.7% of the studied diabetic preparatory school students have poor total knowledge score. A significant difference was revealed between the studied diabetic students’ total score of knowledge and self-care practices In addition, diabetic students' age, previous hospitalization due to hypo/hyperglycemic coma, duration of disease discovery and socioeconomic status were significantly varied among them in relation to their total knowledge and self-care practices scores. Moreover, diabetic students' gender, father's education, mothers' education, mother's working condition were significantly varied among them in relation to their total self-care practices score. Conclusion and recommendations: The results of the present study concluded that the highest percentage of the studied diabetic preparatory school students have either fair or poor self-care practices and poor total knowledge score, so it is recommended to develop hotlines, mass media campaigns for dissemination of accurate information about juvenile diabetes and establishing an accurate surveillance and documentation system of diabetic students for easy accessibility and provision of accurate information.
Mass trapping of the spruce bark beetle IPS typographus

Two types of trap devices, baited trap-logs and plastic pheromone traps, were used in Sweden for mass trapping of Ips typographus in 2007. We studied the catch efficiency of these two types of traps and factors that might influence the measured efficiency at two research stations in southern Sweden: Asa station is situated north of the city Växjö in central Småland, and Tönnersjöheden close to Halmstad at the west coast.
The influence of angiotensin I-converting enzyme (ACE) I/D gene polymorphism on cardiovascular and muscular adaptations following 8 weeks of isometric handgrip training (IHG) in untrained normotensive males

We examined the association between the angiotensin I-converting enzyme (ACE) I/D gene polymorphism and isometric handgrip (IHG) training on cardiovascular and muscular responses among normotensive males. Thirty (II = 10, ID = 10, and DD = 10) normotensive untrained males underwent IHG training at 30% of their maximal voluntary contraction 3 days per week for 8 weeks. Cardiovascular and muscular variables were measured before IHG, after a session of IHG and after 8 weeks of IHG. No significant interaction effect was found between ACE I/D genotype and IHG training session on all dependent variables (all p > 0.05). There was a significant main effect of IHG training session on systolic blood pressure (SBP) (p = 0.002), mean arterial pressure (MAP) (p = 0.015) and handgrip strength (HGS) (p = 0.001) scores, while no difference in diastolic blood pressure (DBP), pulse pressure, or heart rate scores was found. A greater improvement in cardiovascular parameters following 8 weeks of IHG training was observed in participants with the D allele than the I allele (SBP reduction: ID+DD genotype group (-5.53 ± 6.2 mmHg) vs. II genotype group (-1.52 ± 5.3 mmHg)); MAP reduction: ID + DD genotype group (-2.80 ± 4.5 mmHg) vs. II genotype group (-1.45 ± 3.5 mmHg). Eight weeks of IHG training improved cardiovascular and muscular performances of normotensive men. Reduction in SBP and MAP scores in D allele carriers compared to I allele carriers indicates that the ACE I/D polymorphism may have an influence on IHG training adaptation in a normotensive population.
The First-Person Singular Imperative in Chukchi

In this paper, I consider the semantics and distribution of the first-person singular from in the Chukchi language. The main aim of the present study is to describe different contexts in which this form can be used and provide a formal analysis to its syntactic and semantic properties. I show that the distribution of this form is non-trivial and challenging for the current theories of the Imperative. In addition to standard uses in root (non-embedded) contexts, this form can appear dependent clauses with a desiderative predicate and in rationale clauses. Although the availability of embedded of Imperative forms have been reported for a number of languages (for an overview see [Kaufmann 2014]), I am not aware of any studies that would state the possibility of using such forms in rationale clauses. Taking as a starting point the theory developed in [Stegovec 2018], I propose and examine a hypothesis that the productivity of the form in root contexts is due to the fact the imperative modal operator can have event antecedents
Effect of organic acids and salts in the feed on fattening performance of broilers

Eine leistungsverbessernde Wirkung organischer Säuren in der Broilermast wurde bereits mehrfach nachgewiesen. Vor allem durch den Einsatz von Fumarsäure (Vogt et al. 1979, 1981; Kirchgessner etal. 1991; Skinner etal. 1991), Ameisensäure (Vogt et al. 1981) und Citronensäure (Vogt et al. 1981 ) konnten die Lebendmassezunahmen und die Futterverwertung verbessert werden. Dabei war bei Fumarund Ameisensäure auch für Broiler eine dosisabhängige Steigerung der Leistung zu erzielen (Vogt et al. 1979, 1981), die vergleichbar zu den Ergebnissen bei Absetzferkeln war. Allerdings lag das Zulageniveau der optimalen nutritiven Wirksamkeit beim Einsatz in der Fütterung von Absetz-· ferkeln für Fumarsäure (Kirchgessner und Roth 1976) und Ameisensäure (Ecke! et al. 1992) in etwa doppelt so hoch wie bei Broilern. Bei Absetzferkeln konnten neuerdings auch mit den Caund Na-Salzen der Ameisensäure wiederholt starke nutritive Effekte erzielt werden (Kirchgessner und Roth 1987 a, 1987b), die von einer anti mikrobiellen Wirkung des Säureanions im Verdauungstrakt auszugehen scheinen. Eine leistungsverbessernde Wirkung von Salzen der Ameisensäure in der Broilermast konnten Gwara et al. (1986) für Natriumformiat nachweisen. Aus diesem Grund wurde in der vorliegenden Untersuchung der Frage der optimalen leistungsverbessernden Wirksamkeit von Calciumformiat in der Broilermast nachgegangen. eben einer Dosis-Wirkungs-Studie war dabei auch der Einfluß des Säureanions, Kombinationswirkungen von Salz und Säure sowie eine vergleichende Betrachtung der Wirksamkeit organischer Säuren und Salze von besonderem Interesse .
COMPLICATIONS OF PANCREATITIS- CT EVALUATION

BACKGROUND Acute pancreatitis is a common condition with variable clinical course. Imaging studies play an important role in diagnosis and management of acute pancreatitis. Computed Tomography (CT) is undertaken to determine the role of CT in acute pancreatitis, to differentiate between oedematous and necrotising pancreatitis and to evaluate the complications and severity using Modified Computed Tomography Severity Index (MCTSI). MATERIALS AND METHODS This is a prospective observational study. Sixty patients with clinical suspicion of acute pancreatitis underwent contrast enhanced CT during two years period. MCTSI score for acute pancreatitis was calculated which includes assessment of pancreatic inflammation, necrosis and extrapancreatic complications. RESULTS Peripancreatic fat stranding was the common feature seen in 90% patients. Extrapancreatic complications were noted in 32 (53%) patients and pancreatic necrosis in 20 (33%) patients. CONCLUSION CECT of abdomen in acute pancreatitis helps in differentiating between oedematous and necrotising pancreatitis. The MCTSI helps in evaluating the percentage of pancreatic necrosis and to predict the possibility of developing local and systemic complications. Depending upon the MCTSI grading, the treatment plan can be implemented more effectively and accurately.
Particle Filters for Colour-Based Face Tracking Under Varying Illumination

Automatic human face tracking is the basis of robotic and active vision systems used for facial feature analysis, automatic surveillance, video conferencing, intelligent transportation, human-computer interaction and many other applications. Superior human face tracking will allow future safety surveillance systems which monitor drowsy drivers, or patients and elderly people at the risk of seizure or sudden falls and will perform with lower risk of failure in unexpected situations. This area has actively been researched in the current literature in an attempt to make automatic face trackers more stable in challenging real-world environments. To detect faces in video sequences, features like colour, texture, intensity, shape or motion is used. Among these feature colour has been the most popular, because of its insensitivity to orientation and size changes and fast processability. The challenge of colour-based face trackers, however, has been dealing with the instability of trackers in case of colour changes due to the drastic variation in environmental illumination. Probabilistic tracking and the employment of particle filters as powerful Bayesian stochastic estimators, on the other hand, is increasing in the visual tracking field thanks to their ability to handle multi-modal distributions in cluttered scenes. Traditional particle filters utilize transition prior as importance sampling function, but this can result in poor posterior sampling. The objective of this research is to investigate and propose stable face tracker capable of dealing with challenges like rapid and random motion of head, scale changes when people are moving closer or further from the camera, motion of multiple people with close skin tones in the vicinity of the model person, presence of clutter and occlusion of face. The main focus has been on investigating an efficient method to address the sensitivity of the colour-based trackers in case of gradual or drastic illumination variations.