Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal analyses of medication adherence data in hiv-infected illicit drug users

It has been long established that adherence to highly active antiretroviral therapy (HAART) is extremely important for therapeutic outcomes for the treatment of HIV-infection. With the advent of HAART, decreases in morbidity and mortality have been observed in HIVinfected individuals. However, these decreases have not generally been extended to injection drug users (IDUs) whom have additional barrier to access HAART, including adherence. Strategies such as directly observed therapy (DOT) have been successful in treating IDUs, especially when they are used in conjunction with methadone maintenance programs. Within these programs HAART and methadone are co-administered, which makes it possible to estimate HAART adherence through a surrogate, methadone adherence. With this in mind we sought to assess if ongoing illicit drug use within such a program would affect methadone adherence. Decreased methadone adherence was noted during periods of opiate use. Furthermore, we sought to assess the relationships between HAART adherence and each of virologic suppression and the emergence of drug resistance mutations. In the former, robust rates of virologic suppression were observed at every adherence level during maintenance therapy with the exception of the 80-90% adherence level where higher rates of virologic failure were observed. This may be explained by a phenomena observed when assessing the latter where higher rates of the accumulation of new drug resistance mutations were observed at the 80-90% level. Although this intermediate level of adherence has been previously described, the estimated range of adherence values reported in this thesis is much narrower than those reported in the literature.
Earthquake Rupture Scaling Relations for Mainland China

Magnitude‐rupture scaling relations describe how the length, width, and area of fault rupture vary with earthquake magnitude. These parameters are required in seismic hazard models to fit the models’ earthquakes onto faults and to define the site‐rupture distances needed in ground‐motion prediction equations. We collected the magnitude and rupture parameters of 91 earthquakes in Mainland China and nearby regions to study magnitude‐rupture scaling relations. We find no systematic deviations for the subsurface rupture length (RLD) obtained from different methods versus earthquake magnitude. We performed regressions of RLD versus magnitude and versus rupture width using general orthogonal regression. Then, we derived the relations between rupture area and magnitude. Our relations are not statistically different from the results derived by others using global datasets, if the parameters of the five pre‐1900 great earthquakes in eastern China are not used. However, if the five earthquakes are used, the magnitude‐rupture length scaling relation for large strike‐slip earthquakes in eastern China gives shorter rupture lengths than earthquakes in western China and other plate boundary regions in the world.
The complete chloroplast genome sequence of Habenaria ciliolaris (Orchidaceae)

Abstract Habenaria ciliolaris is a kind of orchid with ornamental value. In this study, we reported the complete chloroplast genome of H. ciliolaris. The complete chloroplast genome is 154,544 bp in length, consists of a pair of inverted repeat (IR, 25,455 bp) regions, a large single-copy region (LSC, 84,032 bp) and a small single-copy region (SSC, 19,602 bp). It contains 179 genes, including 133 protein-coding genes, 38 tRNAs, and 8 rRNAs. A maximum-likelihood phylogenetic analysis demonstrated a close relationship between H. ciliolaris and Habenaria radiata. This work will be valuable for genetic and phylogenetic studies on H. ciliolaris.
Learning to Detect an Odd Markov Arm

A multi-armed bandit with finitely many arms is studied when each arm is a homogeneous Markov process on an underlying finite state space. The transition law of one of the arms, referred to as the odd arm, is different from the common transition law of all other arms. A learner, who has no knowledge of the above transition laws, has to devise a sequential test to identify the index of the odd arm as quickly as possible, subject to an upper bound on the probability of error. For this problem, we derive an asymptotic lower bound on the expected stopping time of any sequential test of the learner, where the asymptotics is as the probability of error vanishes. Furthermore, we propose a sequential test, and show that the asymptotic behaviour of its expected stopping time comes arbitrarily close to that of the lower bound. Prior works deal with independent and identically distributed arms, whereas our work deals with Markov arms. Our analysis of the rested Markov setting is a key first step in understanding the difficult case of restless Markov setting, which is still open.
Comparing the Care of Pregnant Women in Ghana and the United States

During pregnancy, factors such as maternal nutrition, location of delivery, the number of antenatal care visits, maternal age, and more can all impact the health of both the mother and the developing fetus. All of these factors are subject to change based on where the mother lives and the resources that her country has to offer her. The objective of this paper was to compare and contrast the nutritional and non-nutritional care of pregnant women in Ghana and the United States and its impact on maternal/child mortality in the two countries. The information collected for this project was taken from online databases, websites, and books as well as a reflection from the author’s experience in the Ghana Health Service. The results of this project conclude that the United States is more equipped to care for its pregnant women, though Ghana has also made significant improvements in its maternal care in the past few years. Background: Nutritional Factors that Affect Birth Outcomes: Role of Maternal Nutrition in Fetal Development Eating a varied diet is important to sustain the mother’s health during pregnancy and any person’s health for that matter, but is even more vital for the developing fetus, who depends on certain micronutrients in the different stages of gestation. Understanding which nutrients are required during pregnancy for the proper development of the fetus is crucial for minimizing the risk of birth defects or other unwanted pregnancy outcomes; deficiencies in specific micronutrients can have detrimental impacts on the infant’s health after birth. Iron deficiency is one of the most common deficiencies worldwide, as more than two billion people around the world are suspected to have an iron deficiency [1,2]. Women are often even more susceptible to iron deficiencies than men, and research has found that 40% of fertile, nonpregnant women have
High-content screening for rare respiratory diseases: readthrough therapy in primary ciliary dyskinesia

Development of therapeutic approaches for rare respiratory diseases is hampered by the lack of systems that allow medium-to-high-throughput screening of fully differentiated respiratory epithelium from affected patients. This is a particular problem for primary ciliary dyskinesia (PCD), a rare genetic disease caused by mutations in genes that adversely affect ciliary movement and consequently mucociliary transport. Primary cell culture of basal epithelial cells from nasal brush biopsies, followed by ciliated differentiation at air-liquid interface (ALI) has proven to be a useful tool in PCD diagnostics but the technique’s broader utility, including in pre-clinical PCD research, has been limited by the number of basal cells that it is possible to expand from such biopsies. Here, we describe a high-content, imaging-based screening method, enabled by extensive expansion of PCD patient basal cells and their culture into differentiated human respiratory epithelium in miniaturised 96-well transwell format ALI cultures. Analyses of ciliary beat pattern, beat frequency and ultrastructure indicate that a range of different PCD defects are retained in these cultures. We perform a proof-of-principle personalized investigation in reduced generation of motile cilia (RGMC), a rare and very severe form of PCD, in this case caused by a homozygous nonsense mutation (c.441C>A; p.Cys147*) in the MCIDAS gene. The screening system allowed multiple drugs inducing translational readthrough to be evaluated alone or in combination with inhibitors of nonsense-mediated decay. Restoration of basal body formation in the patient’s nasal epithelial cells was seen in vitro, suggesting a novel avenue for drug evaluation and development in PCD. Summary We describe primary cell culture of nasal epithelial cells from patients with primary ciliary dyskinesia including differentiatiation of these to a ciliary phenotype and high-content screening in miniaturised air-liquid interface cultures.
The positive experience of encountering wolves in the wild

Large carnivores often impact human livelihoods and well‐being. Previous research has mostly focused on the negative impacts of large carnivores on human well‐being but has rarely considered the positive aspects of living with large carnivores. In particular, we know very little on people's direct experiences with large carnivores like personal encounters and on people's awareness and tolerance toward their exposure to large carnivores. Here, we focus on the wolf (Canis lupus), and report on a phone survey in Germany. We examined whether encounters with wolves were positive or negative experiences and quantified people's awareness and tolerance related to their exposure to wolves. We found that the majority of people reported positive experiences when encountering wolves, regardless of whether wolves were encountered in the wild within Germany, in the wild abroad, or in captivity. The frequency of encounters did not affect the probability to report positive, neutral, or negative experiences. Moreover, people in Germany expressed a high tolerance of living in close vicinity to wolves. These findings are novel and important because they highlight the positive aspects of living in proximity with large carnivores in human‐dominated landscapes.
Commenting on chiropractic: A YouTube analysis

Abstract Numerous studies have examined health-related YouTube videos, but very few studies have also investigated the health-related discussions taking place in YouTube comment sections. Taking up the topic of chiropractic, a popular form of “alternative medicine”, this study first sought to determine if debates or controversies surrounding chiropractic were present in the comments on popular YouTube chiropractic videos. If debates were present, the goal was then to use iterative coding methods to map out how debates were unfolding by describing the general characteristics of the discussions as well as the arguments used by opposing groups. Lastly, the objective was to determine levels of hostility in the debates. Our results demonstrate that there are debates taking place over the efficacy and legitimacy of chiropractic. Furthermore, while our study maps out a wide variety of arguments and debate characteristics, key findings show that those arguing “for chiropractic” rely primarily on personal anecdotes and simultaneously raise issues with “pills” and the pharmaceutical industry. Those opposing chiropractic primarily argue that chiropractic is not sufficiently supported by evidence or “science” and often provide links to additional literature. Overall, hostility levels are quite low in the debates. With an abundance of perspectives being shared in a wide variety of manners, this study suggests that YouTube constitutes a space where individuals can discuss and debate health-related topics like chiropractic. In addition, it sheds light on the rationale underpinning diverse chiropractic-related perspectives and arguments.
Tomorrow Never Dies: biodegradation and subsequent viability of invasive macrophytes following exposure to aquatic disinfectants

Aquatic invasive alien species (IAS) negatively impact freshwater ecosystems worldwide. As suppression and eradication of established invader populations are often complex, costly and resource-intensive, the prevention of further invader spread is considered a key aspect of proactive management measures. Although broad-spectrum aquatic disinfectants have been suggested as a suitable decontamination mechanism to enhance invader spread-prevention strategies, inconsistencies concerning their effectiveness are reported within the literature. Here, we examine the use of two aquatic disinfectants, which were developed to kill damaging microbes, to induce substantial degradation of the apical fragmentary propagules of five invasive macrophytes: Crassula helmsii (Kirk) Cockayne; Egeria densa Planchon; Elodea canadensis Michx; Hydrocotyle ranunculoides Linnaeus; Lagarosiphon major (Ridley) Moss. Apical fragments were exposed to 0% (0 g L -1 ), 2% (20 g L -1 ) or 4% (40 g L -1 ) solutions of Virkon ® Aquatic and Virasure ® Aquatic, for submergence treatments of five, fifteen, thirty or sixty minutes. After 28 days, degradation of treated fragments was significantly greater than that of control groups, particularly for 4% solutions and longer exposure times. Despite this, sustained viability in relation to shoot and/or root regrowth was exhibited by almost all plant species. However, new shoot growth rates were significantly reduced following exposure to all treatments. At matched concentrations, there was no significant difference between the two disinfectants. Overall, it appears that the examined aquatic disinfectants will not curtail the spread of these invasive macrophytes. Yet, longer submergence times, multiple applications and synergistic effects of different biosecurity treatments may enhance preventative measures against further spread and this requires investigation.
Identificação da fauna endoparasitária do tambaqui Colossoma macropomum (Cuvier, 1818) cultivados no município de Cacaulândia - RO

As enfermidades causadas por parasitos em peixes sao responsaveis por grandes perdas na producao, gerando altas taxas de mortalidade ou diminuicao das taxas de crescimento levando a perda do valor comercial e, com isso, ocasionando prejuizo ao piscicultor. Sessenta peixes provenientes de duas pisciculturas localizadas no municipio de Cacaulândia – RO foram examinados, dentre os quais 59 estavam infectados por pelo menos um especime de acantocefalo Neoechinorhynchus buttnerae Golvan, 1956. Os peixes da Propriedade 01 apresentaram prevalencia de 96,67% e intensidade media de 235,67 e, os da Propriedade 02 a prevalencia foi de 100% e intensidade media de 48,27. Apesar da alta taxa de prevalencia nao foram observados casos de desnutricao ou mortes dos hospedeiros
From the horse’s mouth : oral assessment in Journalism education

Viva voces and practical oral assessments have been a recognised method of student assessment, in widely diverse academic fields for decades and perhaps even longer (Huxham et al., 2012). However, such assessment methods have not, hitherto, been utilised in London Metropolitan University’s Journalism education programme. This is, perhaps, somewhat surprising given that journalism is, by its very nature, a professional discipline that employs a variety of sensory modalities - extended through technological media - to achieve its effects and impact. This article will examine why this variety seems not to be reflected in the assessment regimes of associated journalism education programmes and will also raise the following questions: is this simply a preference that may need to be challenged, and, more provocatively, does it therefore suggest a lack of desire amongst Journalism educators to innovate? For the purpose of this paper, I will be examining the Journalism School in London Metropolitan University and, more specifically, the undergraduate programme of that school.
Independent segmental bone transport of the radius and ulna : a case report

Significant bone loss in the forearm involving both the radius and ulna is a difficult problem to manage. The functional outcome may be limited due to loss of pro- and supination. We present a case where significant bone loss of both the radius and the ulna in an adult patient was successfully reconstructed using segmental bone transport. The radius and ulna were transported independently from each other to try and maintain function. A reasonable functional result was achieved.
Flaunt the imperfections : Affective governance and London’s Alternative Investment Market

The literature of financial market design is predicated on the efficient market hypothesis (EMH), advocating transparency, liquidity, and universal information with a view to capturing efficient prices. This dominant understanding of the ‘perfect market’ is highly influential and has been played out in the technological transformation of ‘main board’ exchanges since the 1980s. Yet recent history provides a counterfactual: the 1995 formation of AIM, the London Stock Exchange’s junior market. AIM employs an alternative – but effective – mode of market organization based on market imperfections. Our historical sociology shows how AIM’s structure draws on affect – reputation, social relationships and practitioner knowledge to organise market governance; design choices were shaped by existing market relationships and practices as well as the institution’s strategic commitments and organisational path dependencies. While finance literature remains sceptical of AIM’s ‘privatised regulation’ we argue that the market’s design should be understood as fit for purpose: capable of producing informationally efficient prices. We characterize AIM as having a ‘Whitean’ design structure, compared with the ‘Fama’ design structure of senior markets. We conclude that the ‘Fama’ model is just one possible configuration of a financial market, and that a ‘Whitean’ producer market is also a viable design option.
Portfolio Optimization with Higher-order Stochastic Dominance Constraints

A framework is developed for portfolio optimization with higher-order Stochastic Dominance constraints. A finite system of restrictions on the lower partial moments can be used for evaluating the efficiency of a given benchmark and for constructing enhanced portfolios which dominate the benchmark for the relevant class of risk averters. The system can be linearlized for discrete distributions, allowing for implementation using Linear Programming. Imposing higher-order restrictions expands the set of improvement possibilities and mitigates the risk of suboptimality due to estimation error. A simulation study exemplifies these benefits, for a simple hypothetical investment problem. In an empirical application to equity industry rotation, accounting for kurtosis aversion and Decreasing Absolute Prudence improves out-of-sample performance beyond levels achieved using more permissive assumptions.
High-frequency study of two-dimensional materials

Two-dimensional (2D) materials show different properties from threedimensional materials owing to the quantum confinement they have in the vertical direction (perpendicular to their plane). Graphene, as the first established one-atom-thick 2D material, has received widespread attention owing to its versatile and rather extraordinary properties. Metasurfaces, as an artificial 2D material, have shown potential for new functional electromagnetic (EM) devices since they possess EM properties not found in natural materials. On top of that, the graphene-metasurface hybrid devices are receiving progressing attention. This thesis investigates the two 2D materials’ interactions with highfrequency signals, aiming to develop some exemplar applications, including a high-sensitive dielectric sensor, a THz-pulse detector, a broadband tunable THz polarizer, and tunable (MHz – GHz) acoustoelectric (AE) current source. The interaction of 2D materials with THz waves was first investigated. The resonant frequency of a THz split-ring resonator (SRR) was found to be altered by the introduction of etched trenches into the LC gap area, owing to a reduction in the effective permittivity, which allowed a significant enhancement in its sensitivity to overlaid dielectric material. Carriers in graphene can be accelerated by the electrical field of freespace THz pulse, which enabled a free-space THz detector, whose performances were also tested.
The Importance of Multi-Scale Temporal and Spatial Management for Cemetery Trees in Malmö, Sweden

Research Highlights: A large body of research highlighted the important contributions that urban forests make to cities and their inhabitants. However, our urban forests face threats from issues such as rapid urbanization, climate change, and the spread of pests and diseases. As such, proactive and effective management is necessary to ensure their long-term sustainability. Given the multiple spatial and temporal scales on which threats can arise, effective management needs to account for these scales and adjust accordingly. The degree to which this currently happens is unclear. Background and Objectives: The aim of this study was to determine the role of multi-scale management in urban forestry, using cemeteries in Malmö, Sweden as a case study. Cemeteries can provide extensive tree canopy but are not readily considered in urban forest management. We sought to determine (1) the threats to the current cemetery tree populations, (2) the extent of multi-scale cemetery tree management, (3) whether tree management plans promote multi-scale management, and (4) how cemetery tree management can be improved. Materials and Methods: Malmö cemetery tree inventories were analyzed with respect to size class and species diversity. Existing cemetery tree management plans were examined to determine the spatial and temporal scales of their recommendations. Interviews were conducted with cemetery managers to determine management priorities and actions. Results: We found that cemetery tree populations in Malmö suffer from a lack of age class and species diversity. Management tends to occur on short time scales and efforts focus mainly on addressing individual trees, although some consideration is given to large-scale species diversification. The management plans previously created for these cemetery trees make recommendations for age class and species diversification but are yet to be used extensively by cemetery managers. Conclusions: The long-term stability of Malmö’s cemetery tree populations is threatened by a lack of species and age diversity. Current management efforts emphasize addressing small-scale issues. Although there is a desire to improve species diversity, this can cause conflict with existing cultural values.
Ligand binding free energy and kinetics calculation in 2020

Ligand/protein binding (LPB) is a major topic in medicine, chemistry and biology. Since the advent of computers, many scientists have put efforts in developing theoretical models that could decode the alphabet of the LPB interaction. The success of this task passes by the resolution of the molecular mechanism of LPB. In the past century, major attention was dedicated to the thermodynamics of LPB, while more recent studies have revealed that ligand (un)binding kinetics is at least as important as ligand binding thermodynamics in determining the drug in vivo efficacy. In the present review, we introduce the most widely used computational methods to study LPB thermodynamics and kinetics. It is important to say that no method outperforms another, they all have pros and cons and the choice of the user should take carefully into account the system under investigation, the available structural and experimental data, and the goal of the research. A perspective on future directions of method development and research on LPB concludes the discussion.