Miracle-dz/UniFAR-FTUs huggingface dataset:
IS6110 FAFLP PCR, a tool for genomic mapping enabling investigation of evolutionary relationships of Mycobacterium tuberculosis in resource poor settings

Tuberculosis (TB) is an important communicable disease affecting the human population world-wide. Despite the efforts of the scientific community, national governments and WHO in controlling the disease, TB still remains a major killer in resource poor settings. New rapid assays and techniques that are simple and cost-effective are urgently needed to identify, treat and understand pathogenesis including the geographical distribution of the disease. The aim of the thesis is to develop a novel genomic mapping tool using Insertion Element, IS6110 that could aid in epidemiological studies of Mycobacterium tuberculosis complex (MTBC) in low and middle income countries. IS6110, a bacterial transposon, plays an essential role in changing the physical and biochemical traits of MTBC. Due to their transposition in TB genomes, they are used as epidemiological markers for differentiation of TB organisms and the mapping of these elements could also shed light on the putative altered function of adjacent genes. In the era of Whole Genome Sequencing (WGS) where repeat elements are difficult to sequence with short read technologies, a rapid and simple method of insertion site mapping using IS6110 FAFLP PCR was developed. This work is aimed at developing a rapid, cost-effective and robust genomic tool box exploiting the IS6110 FAFLP PCR assay that can both identify and characterise the TB genotypes / genetic lineages in any geographical location. For the first time using the assay above, TB samples from Nepal were categorised into different genetic lineages. Fifty-five percent of the samples analysed belong to Principal Genetic Group 1 (PGG1), Beijing and Central Asian strains. Also, new primers were designed targeting the Beijing and the T- groups using the FAFLP derived data that gave rise to the development of rapid lineage specific PCR assays. In addition, it was noticed that 3.9% of the Nepalese strains tested in this research work were likely multi-drug resistant (MDR-TB) using PCR targeting the Rifampicin-resistance-determining region (RRDR) of the rpoB region. It is demonstrated here that IS6110 FAFLP methodology could easily characterise the TB samples into different genetic lineages provided they have more than four IS6110 copies. In addition, lineage specific PCR does not need any expensive instruments or reagents except for PCR blocks and gel visualisers, and could be very effective in the rapid identification of different TB genotypes within hours. These data also add to knowledge about the circulating strains of TB in Nepal, currently a poorly characterised region of the world in this regard, and could help in contact tracing studies by epidemiologists. The IS6110 FAFLP technique thus can be employed in any geographical location to map TB genetic lineages where there is little or no information available on the prevailing TB strains.
Coding accuracy of administrative drug claims in the Ontario Drug Benefit database.

BACKGROUND Every year in Ontario, the records of over 42 million prescriptions dispensed to persons eligible for Ontario Drug Benefit (ODB) benefits are transmitted to a central database. The ODB database is the second largest database of medications in Canada, containing records on almost half of all medications dispensed in Ontario. There is no information about the reliability of the coding on the ODB drug claims database and, therefore, the objective of this study was to estimate the reliability of coding of the Drug Identification Number, and the date, quantity and duration of the dispensation on claims sent to the ODB. METHODS To meet this objective, approximately 100 randomly selected prescriptions dispensed from each of 50 pharmacies in southern Ontario between July 1, 1998 and December 31, 1999 were audited. For each claim, the written information on the prescription was compared with the electronic information submitted to the ODB database. Logistic regression was used to test the association between coding errors and the location, owner affiliation, and productivity of each pharmacy (defined as the annual volume of dispensations divided by the annual number of hours worked by all pharmacists and pharmacy assistants). RESULTS Of the 183 pharmacies owners invited to participate, consent to abstract information was obtained in 50, yielding a participation rate of 27%. Of the 5155 dispensed prescriptions, 37 errors were found, yielding an overall error rate of 0.7% (95% CI 0.5% to 0.9%). None of the characteristics of pharmacies that were examined (location, owner affiliation, productivity) was associated with coding errors. CONCLUSIONS Pharmacists almost always dispense the medication that is prescribed and this information is reliably transmitted to the ODB drug claims database. This means that any conclusions drawn by researchers using these data are not likely to be compromised by low coding reliability.
Leading the world: Public sector reform and e-government in Korea

An integral component of public management reform in Korea has been e-government, a field in which Korea has been a pioneer and in which it is the world leader. This article examines the Korean model of public management reform in the context of the developmental state and democratisation to describe and explain the emergence and expansion of e-government practices. The growth of e-government is tracked and the crucial role of the Ministry of Public Administration and Security delineated. Also covered are Government for Citizens initiatives, the provision of particular services, the mushrooming use of smart phones and emerging patterns of citizen participation, especially as related to local-level governance. The article demonstrates how much can be achieved in e-government and provides a model from which other countries can choose appropriate practices.
Fantastic beasts and why to conserve them: animals, magic and biodiversity conservation

Abstract There is a broad set of human beliefs, attitudes and behaviours around the issue of magical animals, referring to both mythical animals not recognized by science and extant animals that are recognized by science but have magical properties. This is a broad issue ranging from spiritual beliefs around mythical animals living in Malagasy forests, to cultural heritage associated with the Loch Ness Monster in Scotland. Beliefs and behaviours around magical animals can have positive and negative impacts on biodiversity conservation goals. Yet, so far, the discipline of conservation biology has not adequately considered magical animals, neglecting to account for the broader knowledge from outside the natural sciences on this issue, and taking a narrow, utilitarian approach to how magical animals should be managed, without necessarily considering the broader impacts on conservation goals or ethics. Here we explore how magical animals can influence conservation goals, how conservation biology and practice has thought about magical animals, and some of the limitations of current approaches, particularly the failure to consider magical animals as part of wider systems of belief and culture. We argue that magical animals and their implications for conservation merit wider consideration.
ENVIRONMENTAL JUSTICE AND WHERE IT SHOULD BE ADDRESSED IN THE 21ST CENTURY CONCERNING THE TRANSPORTATION INDUSTRY: HISTORICAL PERSPECTIVE AND SUMMARY

There is an underlying tug of war going on in the world of transportation: human rights versus environmental rights. This paper outlines the differences between human rights and environmental rights through a review of Title VI of the Civil Rights Act of 1964, Title VIII of the Civil Rights Act of 1968 (Fair Housing Act), the National Environmental Policy Act of 1969 (NEPA), and various executive orders that are related to environmental protection and human rights. An analysis of a number of legal cases concerning environmental justice (i.e., human rights) is also provided. This analysis offers various planning tools that the reader can use to minimize environmental justice concerns as they relate to transportation projects. Also shown are ways in which transportation planners and engineers can use these planning tools while working with strategies to solve major transportation issues or problems. Finally, environmental justice is examined as it relates to needed research to fill existing gaps with available tools.
Nontuberculous Mycobacteria from Household Plumbing of Patients with Nontuberculous Mycobacteria Disease

To determine whether plumbing could be a source of nontuberculous mycobacteria (NTM) infection, during 2007–2009 I isolated NTM from samples from household water systems of NTM patients. Samples from 22/37 (59%) households and 109/394 (28%) total samples yielded NTM. Seventeen (46%) of the 37 households yielded >1 Mycobacterium spp. isolate of the same species as that found in the patient; in 7 of those households, the patient isolate and 1 plumbing isolate exhibited the same repetitive sequence-based PCR DNA fingerprint. Households with water heater temperatures <125°C (<50°C) were significantly more likely to harbor NTM compared with households with hot water temperatures >130°F (>55°C) (p = 0.0107). Although households with water from public or private water systems serving multiple households were more likely to have NTM (19/27, 70%) compared with households with a well providing water to only 1 household (5/12, 42%), that difference was not significant (p = 0.1532).
Printing Radio!: An audience research experiment looking for new ways of global textual services

4 Acknowledgements . 5
The Informational Role of Upstairs and Downstairs Trading

The author assumes that customers do not continuously participate in all markets and that intermediaries are repositories of information about the ("unexpressed") demands of currently nonparticipating customers. A model of downstairs (i.e., centralized) versus upstairs (i.e., fragmented) markets is developed based on the assumption that upstairs (and not downstairs) dealers may possess information about unexpressed demand. The equilibrium liquidity of both markets is characterized by the trade-off between the benefits of information about unexpressed demand and the cost to the customer of trading in a fragmented market. Copyright 1992 by University of Chicago Press.
Non-Tariff Barriers in Selected CIS Countries

The purpose of this paper is to measure and analyse how intensively CIS countries apply nontariff barriers (NTBs) to restrict foreign trade in regard to certain products and total trade. Five CIS countries were selected for this analysis, in particular Ukraine, Russian Federation, Moldova, Belarus, and the Kyrgyz Republic. We first consider measurement methods usually applied to NTBs, review other studies measuring NTBs in CIS countries, and then describe our own findings on the matter. This analysis was made in the framework of the EU Eastern Neighbourhood: Economic Potential and Future Development (ENEPO) project seeking to examine different aspects of the European Union’s relations with its neighbours to the East.
Supplemental Nutrition Assistance Program (SNAP) Participation Leads to Modest Changes in Diet Quality

Recent research has shown that the Supplemental Nutrition Assistance Program (SNAP) effectively reduces food insecurity. Questions remain, however, about the extent to which SNAP affects the quality of adult participants’ diets. These questions have surfaced in the context of the increasing public costs of diet-related illnesses, such as diabetes, high blood cholesterol, and heart disease, and have led to discussions about restricting the use of SNAP benefits to purchase some food items. This report examines Healthy Eating Index (HEI) scores for adults in low-income households that do and do not participate in SNAP. To disentangle the choice of whether to participate in SNAP from diet choices, this model uses a unique data set that matches State-level SNAP policy variables to individual-level data from four waves of the National Health and Nutrition Examination Survey (NHANES). Two important kinds of results emerge: the effect of SNAP on the diet quality of those who choose to enroll, and a total comparison of SNAP participants and nonparticipants after SNAP’s effects are taken into account. On the first, this report shows that SNAP participation results in a large increase in the likelihood of consuming whole fruit and a slightly lower consumption of dark green/orange vegetables. On the second, the report finds that SNAP participants have slightly lower HEI scores (both total and components) than nonparticipants, meaning that they have slightly lower diet quality. They do, however, consume less saturated fat and sodium than nonparticipants.
A Mis-signalling Problem? The Troubled Performance Relationship between Credit Unions and Local Government in the UK

This article argues that the development of British credit unions is being held back by the unclear objectives and performance measures set by different external stakeholders. Credit unions are particularly vulnerable to contradictory accountability requirements, because they can serve a number of different socio-economic purposes. They may therefore face multiple lines of managerial and political accountability in a situation where they remain highly dependent on external stakeholders for funding. Survey evidence shows that the measures widely used to gauge credit union performance are not consistent with the policy objectives of the key stakeholders setting them. Taken together, they also fail to provide a balanced scorecard to support effective internal management decision making and external scrutiny. It is contended that key stakeholders need to compensate for the currently skewed performance scorecard with indicators that are sensitive to credit unions' specific objectives and to the stage they have reached in the credit union life cycle of development. Proposals for a wider and more appropriate suite of performance indicators are therefore outlined.
Unusual optical coherence tomography and fundus autofluorescence findings of eclipse retinopathy

A 63-year-old female patient complained of dimness in the central field of vision in the left eye after viewing an annular partial eclipse without adequate eye protection on 22 July 2009. Fundoscopy showed a wrinkled macular surface. Fundus autofluorescence study revealed well-demarcated hyperautofluorescence at the fovea. Optical coherence tomography demonstrated tiny intraretinal cysts. Fluorescein angiography and indocyanine green angiography were unremarkable. Epimacular membrane developed in the following month with deteriorated vision. Vitrectomy, epiretinal membrane and internal limiting membrane peeling were performed. Vision was restored to 20/20 after the operation. Direct sun-gazing may damage the retinal structures resulting in macular inflammation and increased focal metabolism, which explains the hyperautofluorescence. It may also induce epimacular membrane. Fundus autofluorescence might represent a useful technique to detect subtle solar-induced injuries of the retina. The visual prognosis is favorable but prevention remains the mainstay of treatment. Public health education is mandatory in reducing visual morbidity.
Heterozygous lipoprotein lipase deficiency: frequency in the general population, effect on plasma lipid levels, and risk of ischemic heart disease.

BACKGROUND Patients with mutations on both alleles of the lipoprotein lipase gene resulting in complete lipoprotein lipase deficiency exhibit the chylomicronemia syndrome with severe hypertriglyceridemia and increased risk of pancreatitis and possibly of ischemic heart disease. This study examined frequency, lipid levels, and risk of ischemic heart disease for heterozygous carriers of lipoprotein lipase mutations known to cause the chylomicronemia syndrome in the homozygous state. METHODS AND RESULTS Two mutations were screened for in 9259 individuals in a general population sample and in 948 patients with verified ischemic heart disease. The percent frequencies of heterozygous individuals with the Gly188-->Glu and Ile194-->Thr substitutions in the general population were 0.06% (95% CI, 0.04% to 0.23%) and 0% (95% CI, 0.00% to 0.12%), respectively. The Gly188-->Glu substitution was associated with an increase in plasma triglycerides of 0.8+/-0.3 mmol/L (mean+/-SEM) and a decrease in plasma HDL cholesterol, apo A-I, and glucose levels of 0.45+/-0.07 mmol/L, 17+/-6 mg/dL, and 1.1+/-0.2 mmol/L, respectively. On multiple logistic regression analysis allowing for age, sex, plasma cholesterol, plasma lipoprotein (a), hypertension, diabetes mellitus, smoking, and body mass index, both plasma triglycerides and HDL cholesterol levels were independent predictors of ischemic heart disease. Finally, the Gly188-->Glu substitution was more common among patients with verified ischemic heart disease (percent frequency of heterozygous individuals, 0.32%) than among individuals from the general population (odds ratio, 4.9; 95% CI, 1.2 to 19.6). The effects of the Gly188-->Glu substitution were more pronounced than those of the common Asn291-->Ser substitution. CONCLUSIONS Heterozygous lipoprotein lipase deficiency due to the Gly188-->Glu substitution appears to increase plasma triglycerides and reduce HDL levels and may thereby predispose carriers to ischemic heart disease.
Aquisição de Conhecimento de Senso Comum e Inferencialista (Acquisition of Common Sense and Inferentialist Knowledge [in Portuguese]

This paper presents a semi-automated method for the acquisition of common sense and inferentialist concepts in Portuguese. Its innovative feature is a module of reasoning over the existing knowledge that aims to offer original content to the user helping in the expression of semantic relationships and validation of new concepts. This reasoning process is based on heuristics and syntactic analysis of noun phrases. A qualitative evaluation with users who interacted with the system built on the proposed method showed that the interactions made in the process of AC are more productive since the user is reminded about semantic relations and common sense about the new concept. Resumo. Este artigo apresenta um método semi-automático para aquisição de conceitos (AC) de senso comum e inferencialista na língua portuguesa. O método tem como diferencial um módulo de raciocínio sobre conhecimento preexistente que visa oferecer ao usuário conteúdo inicial que o ajude a externar e a validar relações semânticas de novos conceitos. Esse processo de raciocínio se baseia em heurísticas e na análise sintática de sintagmas nominais. Uma avaliação qualitativa com usuários que interagiram com o sistema, construído com base no método proposto, indicou que as interações realizadas no processo de AC são mais produtivas visto que o usuário é lembrado e instigado sobre relações semânticas de senso comum acerca do
Relationships between fibrosis amounts assessed by morphometry and liver stiffness measurements in chronic hepatitis or steatohepatitis

Objectives To examine the relationships between fibrosis amounts evaluated by morphometric analysis and liver stiffness measurement (LSM) as well as the influence of steatosis, of activity grade and of the type of chronic liver injury. Methods One hundred and fifty-two consecutive patients were selected from a prospective cohort of patients with concurrent liver biopsy and LSM on the basis of a more than 25 mm long liver biopsy. Morphometric quantification of collagen deposition was expressed as fibrosis area fraction (FAF). Steatosis, activity grade, and predominant type of liver injury (chronic hepatitis or steatohepatitis) were assessed. Results In the whole population (chronic viral hepatitis n = 96, alcoholic or nonalcoholic steatohepatitis n = 56), FAF was significantly correlated to LSM (ρ = 0.6, P<0.0001). Steatosis independently influenced LSM in patients without cirrhosis, but not activity grade. In the absence of cirrhosis, LSM and FAF were correlated in patients with chronic hepatitis (ρ = 0.49, P<0.0001) but not in those with steatohepatitis (ρ = 0.22, P = 0.16). In cirrhotic patients, LSM was correlated with fibrosis amount. (ρ = 0.43, P = 0.006). The area under the receiver operating characteristics curve of LSM was 0.75 for separating no or minor fibrosis from significant fibrosis and 0.9 for the diagnosis of cirrhosis. Conclusion LSM was significantly correlated with collagen deposition. However, the relationships between LSM and fibrosis amount seems to differ according to steatosis and to the pattern of liver fibrosis below the cirrhotic stage. Its performances are fair for segregating patients with no or minor fibrosis from those with significant fibrosis and high for the diagnosis of cirrhosis.
Poly(ADP‐ribose) polymerase‐1 activation in a primate model of multiple sclerosis

Multiple sclerosis (MS) is an immune‐mediated disabling neurological disorder involving inflammation, demyelination, axonal damage, and neurodegeneration. Poly(ADP‐ribose)polymerase‐1 (PARP‐1), a nuclear enzyme linked to DNA repair, has been shown to regulate the cellular inflammatory response through interactions with nuclear factor‐κB. Extensive PARP‐1 activation can, by separate mechanisms, also cause cell death. PARP‐1 activation in brain occurs in several settings associated with oxidative stress and DNA damage, and PARP‐1 inhibition has been shown to attenuate inflammation and improve neuronal survival in these settings. Here we studied the pattern of PARP‐1 activation in a nonhuman primate model of MS, marmoset (Callithrix jacchus) experimental allergic encephalomyelitis (EAE). Characteristic of this model is relapsing and remitting focal demyelination typical of human MS. Immunostaining for poly(ADP‐ribose), the enzymatic product of PARP‐1, showed PARP‐1 activation specifically in plaque areas of EAE brains. Robust immunostaining was found in astrocytes surrounding demyelinated EAE plaques and in scattered nearby microglia, oligodendrocytes, and neurons. The immunostaining also suggested PARP‐1 activation in occasional endothelial cells surrounded by microglia or infiltrating peripheral blood cells. Given the importance of PARP‐1 in both inflammation and cell death processes, these findings suggest that PARP‐1 activation may be a significant factor in the pathogenesis of MS. © 2005 Wiley‐Liss, Inc.
Economic Growth: Education vs. Research

Barro and Sala-i-Martin analyzed the empirical determinants of growth. They used a cross-sectional empirical framework that considered growth from two kinds of factors, initial levels of steady-state variables and control variables (e.g., investment ratio, infrastructure). Recent literature suggests that education is important in determining steadystate growth. Sequeira Following Baumol, we also consider the growth regression. We extend the previous research for Asian countries of Kim to developed countries. Following the implications of semi-endogenous growth theory, we regressed output growth on a constant, one-year lagged output (initial income) and the determinants of steady-state income [investment rate, population growth, the quadratic (or linear) function of R&D intensity and human capital measured by years of schooling or enrollment rate in secondary school]. The regression suggests higher significance in research efforts. This contradicts with that of Sequeira, which asserts the speed is determined by only education, preference and technology parameter. The coefficients for the determinants of steady-state income, especially for the quadratic function of R&D intensity, are significant and occur in the expected direction. Our results suggests that adopting appropriate growth policy related with R&D, an economy can grow more rapidly through transition dynamics or changing fundamentals.