Miracle-dz/UniFAR-FTUs huggingface dataset:
Bridging the gap between policy and practice: a qualitative analysis of providers’ field experiences tinkering with directly observed therapy in patients with drug-resistant tuberculosis in Addis Ababa, Ethiopia

Objectives Drug-resistant tuberculosis (DR-TB) is one of the major public health threats in low-income countries such as Ethiopia. It is intertwined with larger socioeconomic and political factors that complicate its management and control. Whether directly observed therapy (DOT) is serving its purpose—better patient adherence and treatment outcome—still remains a debatable issue. To contribute to this discussion, this study explored health workers’ field experiences tinkering with DOT in patients with DR-TB in Addis Ababa, Ethiopia. Design A qualitative study using in-depth interviews and focus group discussion. Setting Ten public healthcare facilities: eight health centres at Addis Ababa Health Bureau level and two TB-specialised hospitals at the Federal Health Bureau level in Ethiopia. Participants 18 healthcare providers working with DR-TB patients. Results Three findings emerged from the analysis. First, the purpose of DOT is to ensure that patients go to healthcare facilities and swallow pills under the observation of a healthcare provider. Thus, its rigid application could lead to the emergence of more DR-TB. Second, DOT should be tinkered with and its practice improved by incorporating more counselling and health education, with more flexibility towards, and attentiveness of, patient context. Third, there exists a family-like patient-provider relationship, and providers do understand their patients and empathise with them to provide better healthcare services. Conclusion If rigidly implemented, DOT could lead to more DR-TB—a problem DOT was invented to resolve. Front-line healthcare providers are sensitive to the tragic experiences of DR-TB patients and empathise with them. Thus, they do not strictly implement DOT and are willing to take any blame resulting from tinkering with it. It is high time to shape the practice of DOT for DR-TB patients, with meaningful contributions from front-line healthcare providers.
2‐Deoxyglucose terminates pilocarpine‐induced status epilepticus in neonatal rats

Neonatal status epilepticus (SE) is a life‐threatening medical emergency. Unfortunately, up to 50% of neonates with SE are resistant to current antiseizure drugs, highlighting the need for better treatments. This study aims to explore a novel metabolic approach as a potential alternative treatment to control neonatal SE, using the glycolytic inhibitor 2‐deoxyglucose (2‐DG).
Conservation Genetics of Freshwater Turtles

Turtles have long life spans, overlapping generations and promiscuous mating systems. Thus, they are an ideal system with which to investigate the application of conservation genetics methods and assumptions to long-lived organisms. Turtles are also one of the most threatened groups of vertebrates and conservation genetics studies are essential to effective recovery of turtle species. This thesis has two main objectives: 1) to evaluate some common population genetics assumptions with respect to turtles and other long-lived organisms, and 2) to collect important information on the population genetics of threatened turtles in Ontario, which can be used to inform species recovery. In Chapters Two and Three, I describe the development of novel microsatellite markers for the snapping turtle and spiny softshell. In Chapter Four I demonstrate significant genetic structure in populations of the endangered spotted turtle in Ontario, and find that “bottleneck tests” may fail to detect recent population declines in small turtle populations. I also show that spotted turtles do not show the typical correlation between population size and genetic diversity. In Chapter Five I use microsatellite markers developed in Chapter Two and document population structure in the widespread snapping turtle for the first time. I compare these results with results from Chapter Four to test the traditionally accepted hypothesis that genetic diversity is reduced in small, isolated populations compared to large, connected populations. As in Chapter Four, my results suggest that the usual patterns of genetic structure and loss of diversity may not apply to turtles. In Chapter Six I conduct a conservation genetics study of the endangered Blanding’s turtle. Finally, in Chapter Seven I combine results from spotted, snapping and Blanding’s turtles to test whether vagility predicts population structure, genetic diversity and significant barriers to gene flow in three species sampled across a single landscape. Analyses reveal minimal congruence in barriers to gene flow and the three species show unexpected and contrasting patterns of diversity across the landscape. Discordant patterns among species highlight areas for further research and shed light on possible cryptic behaviour, and I discuss potential further directions for research in the Summary. %%%%PhD
Impact of organic acids on chloride depletion of inland transported sea spray aerosols

Abstract. Heterogeneous reactions on sea spray aerosols (SSA) are the main pathway to drive the circulation of chlorine, nitrogen, and sulfur in the atmosphere. The release of Cl will significantly affect the physicochemical properties of SSA. However, the impact of organic acids and mixing state on chloride depletion of SSA is still unclear. Hence, the size and chemical composition of individual SSA particles during the East Asian summer monsoon were investigated by a single particle aerosol mass spectrometer (SPAMS). According to the chemical composition, SSA particles were classified into SSA-Aged, SSA-Bio and SSA-Ca. In comparison to the aged Na-rich SSA particles (SSA-Aged), some additional organic species related to biological origin were observed in SSA-Bio, and each of two types accounts for approximately 50 % of total SSA particles. SSA-Ca may associated with organic shell of Na-rich SSA particles, which only accounts for ~ 3 %. Strongly positive correlations between Na and organic acids (including formate, acetate, propionate, pyruvate, oxalate, malonate, succinate, and glutarate) were observed for the SSA-Aged (r2 = 0.52, p
What are the ingredients for food systems change towards sustainability?—Insights from the literature

Many detrimental effects on the environment, economy, and society are associated with the structure and practices of food systems around the world. While there is increasing agreement on the need for substantive change in food systems towards sustainability, divergent perspectives exist on what the appropriate points of intervention and strategies to achieve such change are. Change in diets and nutrition, the importance of social food movements, and sustainable farming practices are all disparately featured in the literature; yet, there is little effort to compare and integrate these perspectives. This review offers a comprehensive overview of perspectives on food systems change towards sustainability. We discern where there is convergence and assess how the literature reflects emergent theory on sustainability transformation. We analyzed more than 200 peer-reviewed articles employing an approach that combines quantitative and qualitative analysis. First, we performed a semantic hierarchical cluster analysis of the full texts to identify thematic clusters representing different perspectives on sustainability transformations and transitions of food systems. Second, we conducted a qualitative text analysis for representative articles of each cluster to examine how deep changes in the food system are conceptualized. We identified five distinct approaches to food systems change that are currently discussed, i.e. Alternative food movements, Sustainable diets, Sustainable agriculture, Healthy and diverse societies, and Food as commons. Each approach provides a nuanced perspective on identified sustainability problems, envisioned sustainable food systems, and proposed actions to change food systems towards sustainability. The findings offer guidance for researchers and practitioners working on food systems change towards sustainability.
When ‘green’ challenges ‘prime’: empirical evidence from government bond markets

ABSTRACT We examined co-movement between green bonds and triple-A government bonds during December 2008–November 2019. We determined that two markets followed the heavy tail dependence using Student’s t-copulas. Using transfer entropy, further evidence was obtained for the causal relationship between the two markets, which was described by three categories such as ‘no effect,’ ‘mono-direction,' and ‘bi-direction'; this relationship indicated the sender and the receiver of return shocks on these markets. Our results highlight the presence of contagion risk between green bonds and prime government bonds, which has practical implications for risk management.
Socioeconomic risk of droughts under a 2.0°C warmer climate: Assessment of population and GDP exposures to droughts in China

Socioeconomic development and natural ecosystems of China are strongly affected by droughts. The socioeconomic risk of droughts in China should be quantified under climate change. This study assessed drought impacts on population and gross domestic product (GDP) under the 2.0°C‐warmer climate scenario, by implementing multiple general circulation model (GCM) simulations under the representative concentration pathway (RCP). Using the standardized precipitation evapotranspiration index (SPEI), we calculated drought frequencies in the base period (1986–2005) and 2.0°C‐warmer climate (2040–2059 in RCP4.5). Then, population and GDP exposures were evaluated by combining the drought frequency with population and GDP simulations under a shared socioeconomic pathway (SSP). Droughts were likely to occur more frequently under the 2°C‐warmer climate, especially for inland areas of northern China (i.e., Xinjiang, Xizang, Qinghai, Ningxia, Shaanxi, Gansu provinces), consisting mainly of mild and moderate droughts. Population exposure to drought was projected at 4.94 ± 0.36 × 109 person‐months, around 2% increase over the base period value. GDP exposure would increase significantly to 2.08 ± 0.15 × 1014 PPP $‐months, approximately 14‐fold over the base period. Probability analysis showed nearly 50% of the grid cells of China's entire territory undergoing more than an 11‐fold increase in GDP exposure. Our findings indicated the climate and GDP effects were primary contributors, respectively, to the changed population and GDP exposures to drought. Population and GDP exposures were distributed unequally across the country, having a large impact in the east where both population and economic activity are highly agglomerated. Our results reveal an urgent need to design and implement effective adaptation measures to overcome droughts, especially in eastern China.
Effect of the Abnormal Expression of BMP-4 in the Blood of Diabetic Patients on the Osteogenic Differentiation Potential of Alveolar BMSCs and the Rescue Effect of Metformin: A Bioinformatics-Based Study

The success rate of oral implants is lower in type 2 diabetes mellitus (T2DM) patients than in nondiabetic subjects; functional impairment of bone marrow-derived mesenchymal stem cells (BMSCs) is an important underlying cause. Many factors in the blood can act on BMSCs to regulate their biological functions and influence implant osseointegration, but which factors play important negative roles in T2DM patients is still unclear. This study is aimed at screening differentially expressed genes in the blood from T2DM and nondiabetic patients, identifying which genes impact the osteogenic differentiation potential of alveolar BMSCs in T2DM patients, exploring drug intervention regimens, and providing a basis for improving implant osseointegration. Thus, a whole-blood gene expression microarray dataset (GSE26168) of T2DM patients and nondiabetic controls was analyzed. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results, differentially expressed genes and signaling pathways related to BMSC osteogenic differentiation were screened, and major risk genes were extracted based on the mean decrease Gini coefficient calculated using the random forest method. Bone morphogenetic protein-4 (BMP-4), with significantly low expression in T2DM blood, was identified as the most significant factor affecting BMSC osteogenic differentiation potential. Subsequently, metformin, a first-line clinical drug for T2DM treatment, was found to improve the osteogenic differentiation potential of BMSCs from T2DM patients via the BMP-4/Smad/Runx2 signaling pathway. These results demonstrate that low BMP-4 expression in the blood of T2DM patients significantly hinders the osteogenic function of BMSCs and that metformin is effective in counteracting the negative impact of BMP-4 deficiency.
FrequentNet : A New Interpretable Deep Learning Baseline for Image Classification

This paper has proposed a new baseline deep learning model of more benefits for image classification. Different from the convolutional neural network(CNN) practice where filters are trained by back propagation to represent different patterns of an image, we are inspired by a method called "PCANet" in "PCANet: A Simple Deep Learning Baseline for Image Classification? " to choose filter vectors from basis vectors in frequency domain like Fourier coefficients or wavelets without back propagation. Researchers have demonstrated that those basis in frequency domain can usually provide physical insights, which adds to the interpretability of the model by analyzing the frequencies selected. Besides, the training process will also be more time efficient, mathematically clear and interpretable compared with the "black-box" training process of CNN.
Contractors in Iraq: Exploited Class or Exclusive Club?

Corporate privatization of security has generated a neoliberal iteration of an old profession: the private military contractor. This development has revolutionized security policies across the globe while reviving old patterns of inequality. Following neoliberal logic, outsourcing fosters two types of employment: the exploitative and the exclusive. The first refers to low-status individuals hired en masse to perform menial labor; the second refers to experts who perform functions central to the employer’s mission. We contribute to this discussion by focusing on the qualifications of a different subsample of this industry: American contractors who died while performing military and security functions in Iraq. We assert that such American employees directly engaged in mission-essential combat and security functions better fit the employment category of an exclusive, expert sector at the core of the private military industry.
A Phylogenetic Study of the Gibbons (Hylobates) Obtained Noninvasively from Hair

Variation in a 252nucleotide segment of the cytochrome b gene from 23 gibbons is described. DNA was extracted from hair, amplified, and directly sequenced. These sequences represent seven of the nine nominal species and three of the four hylobatid subgenera. Variation was observed at 55 sites, 42 of which are phylogenetically informative. Levels of transitional and transversional divergence between the taxa are similar to those reported for homologous mtDNA sequences in other mammals. Parsimony, maximum likelihood, and bootstrap analyses (1) support some traditional phylogenetic hypotheses (monophyly of the concolor gibbons), (2) suggest previously unrecognized affinities between the lar species group and Hylobates klossi and between I-I. lar and I-I. agdis unko, and (3) show that this segment does not contain information sufficient for completely resolving gibbon relationships at the subgeneric level. The study demonstrates the great potential of noninvasive DNA sampling for phylogenetic analyses of mammals. 0
Involvement of miR156 in the Regulation of Vegetative Phase Change in Plants

A BSTRACT . Plant growth and development are determined by complex exogenous and endogenous cues. A plant follows several temporally distinct developmental stages, including embryonic, vegetative, and reproductive. The vegetative stage, which is usually the longest stage, can be subdivided into juvenile and adult phases. The transition from the juvenile to the adult phase, also called the vegetative phase change, is characterized by anatomical, morphological, and physiological changes in the vegetative parts of the shoot. Recent studies in several systems have identiﬁed the genetic temporal mechanisms of this process, which is regulated by an endogenous age cue (i.e., microRNA156/157) and its targeted genes (i.e., Squamosa promoter binding protein-box transcription factors ). This review summarizes the recent advances in the study of the underlying regulatory mechanisms of vegetative phase change. This review also describes the modes of miRNA action and the functions of their targeted genes in this highly conserved developmental process. with argonaute (AGO) protein to play its function. These factors involved in miRNA biogenesis and function pathway have indirect inﬂuence of vegetative phase change by regulating the abundance or activity of miR156.
SIMULATION OF MANAGEMENT ENHANCEMENT SCENARIOS FOR THE JSC LATVIAN STATE FORESTS

The expansion of global economy and the rise of living standards are set to force the world’s consumption of raw material to nearly double by 2060, thus consumption of wood resources is forecasted to increase more than twofold. In Latvia, forests cover 52% of the total area. The total forest area in Latvia has continued to grow since the beginning of the 20 th century – in 1923 the forests covered only 27% of the country’s area; accordingly, the question is whether the value of forests continues to grow proportionally. One of the criteria for determining the value of forest is forest capital. A higher economic value of forest reflects the forest’s capability to produce more wood, and this allows generating higher revenues from forestry. It is the value of plantations of certain tree species as well as the quality of wood produced that increase the price of wood and consequently result in higher revenues. The largest supplier of wood in Latvia is the state-owned joint stock company Latvian State Forests (JSC LSF), which managed 1.6 million hectares of forestland in 2018. In 2018, 12.8 million cubic metres of roundwood were harvested in Latvia, of which 6 million cubic metres were harvested by the JSC LSF. Therefore, the research aims to design and assess potential scenarios of increasing the value of forest capital for the JSC LSF. The authors simulated potential scenarios for the JSC LSF in order to identify changes to be made in the current forest management pattern with the aim of increasing the value of forest capital. A higher value of forest capital would also mean greater public attention to the future use of existing resources. Calculations of the economic value of forests were carried out to identify necessary changes to be made in the management of state-owned forests in Latvia and to compare several management enhancement scenarios. The potential scenarios were assessed by five qualified experts, academics, representatives of business and public administration by employing the Analytic Hierarchy Process (AHP). The experts rated the possible scenarios for enhancing forest management relatively equally, giving slightly higher ratings to the potential scenario of quotation of the national forest management company on the stock exchange. The value of forest capital was calculated for each of the potential scenarios using the most commonly used net present value method (NPV). It was concluded that the potential scenario of lowering the diameter threshold for felling trees by two centimetres would lead to the greatest increase in the value of forest capital.
Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests and predictive modeling, reducing the data dimensionality problem. This work intends to establish a basis for the integration of gene expression measurements from several manufacturers, a problem that can be addressed at different levels. The reannotation process, will be addressed, representing a cornerstone of multiplatform integration. The proposed approach is based on a reannotation from probesets to transcripts, preserving valuable information for further analysis. This work will provide both the methods for this integration process, as well as computational tools to achieve these goals. World Health Organization ranks astrocytomas, brain tumors, in four grades, being the fourth grade the most aggressive. Glioblastoma, the fourth grade tumor, is one of the most severe human diseases that almost inevitability leads to death. Physicians address the classification in grades through direct inspection. In this context, there is a need for good automatic predictors of tumor grade, which are not affected by human misclassification errors and that can be made with less invasive diagnostic tools. Gene expression data from glial tumors will be used as case studies, considering data from Agilent, Affymetrix and Illumina platforms. This data will be used to perform the
Identification of potential acid sulfate soils at the Reda River mouth (northern Poland) using pH measurements

Potential acid sulfate soils (PASS) are coastal, inland or mine spoil soils with a high content of iron sulfides. Originally neutral or alkaline, and often with a low buffer capacity, these soils have the potential to produce sulfuric acid if drained or excavated (actual acid sulfate soils) (Pons, 1973; Dent and Pons, 1995). The problem associated with sulfide oxidation is the release of toxic substances (mainly heavy metals), which can be leached and transported in very acidic (pH <4) environments (Fältmarsch et al., 2008). Acid sulfate soils are commonly considered a serious global hazard, with a remarkably negative impact on ecosystems and human health (Dent and Pons, 1995; Andriesse and Van Mensvoort, 2006). Acid sulfate soil material is classified according to the presence of diagnostic properties such as hypersulfidic and sulfuric materials (Sullivan et al., 2010). Hypersulfidic material is described as sulfidic material (≥0.01% inorganic sulfidic S), which upon incubation (i.e. oxidation) at field capacity (generally at least 8 weeks) displays a pH drop of ≥0.5, compared to unoxidised conditions, to a value of <4. During field conditions, oxidation of hypersulfidic materials often leads to the development of a sulfuric horizon (pH <4). Both diagnostic materials are recognised in the World Reference Base for Soil Resources classification (IUSS Working Group WRB, 2015), with “sulfuric” being referred to as “thionic”. Sulfidic material that does not display a drop in pH to <4.0 is termed “hyposulfidic”. In Finland and Sweden, a lower diagnostic limit of pH <3.0 for recognition of hypersulfidic
Floral Meristems to Floral Organs: Genes Controlling Early Events in Arabidopsis Flower Development

Molecular and genetic studies show that the underlying mechanisms control­ ling flower development are largely conserved in distantly related dicotyledon­ ous plant species. These studies have identified early-acting genes that pro­ mote the formation of floral meristems and later-acting genes that determine the fate of floral organ primordia. The floral meristem identity genes lie at the top of a regulatory hierarchy that leads to the activation of the organ identity