Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical and molecular characterization of hepatitis B virus infection in human immunodeficiency virus-positive Southern African adults, facilitated by newly developed bioinformatic tools

Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) share transmission routes and are endemic in sub-Saharan Africa. Mpumalanga is the second-smallest of the nine South Africa provinces, but has the second-highest HIV prevalence of 15.4%. No in-depth study on HBV/HIV co-infection in this province has been undertaken. Routinely, the prevalence of HBV infection is determined serologically by detecting HBsAg. However, HBV infection can occur in the absence of HBsAg, generally termed occult HBV infection (OBI). HIV infection has been shown to be a risk factor for the development of OBI. The “Taormina” definition of OBI, which requires stringent polymerase chain reaction (PCR) amplification of at least two different regions of the HBV genome to determine HBV-positivity, was used to determine the prevalence and characteristics of HBV infection in antiretroviral treatment (ART)-naïve HIV-positive adults in a new rural adult cohort. The study group consisted of 298 adults (114 men and 184 women) with median age, CD4 count and BMI of 34 years, 147 cells mm−3 and 22 kg m−2, respectively. The presence of HBV serological markers was determined by enzyme linked immunoassay (ELISA) tests. HBV DNApositivity was determined by PCR of at least two of three different regions of the HBV genome and real-time PCR was used to determine the viral loads. Liver fibrosis was determined using the aspartate aminotransferase-to-platelet ratio index. Bioinformatic tools and a database to store clinical and molecular data were developed to facilitate processing and analysis of clinical and molecular data. An online web interface provided access to data from the database and the R programming language was used to analyze clinical data extracted from the database. Of the 298 participants, 231 (77.5%) showed at least one HBV marker, with 53.7% HBV DNA-negative (resolved) and 23.8% HBV DNA-positive (current infection) [8.7% HBsAg-positive;15.1% HBsAg-negative].
Reassessing the Role of Shared Mobility Services in a Transport Transition: Can They Contribute the Rise of an Alternative Socio-Technical Regime of Mobility?

Recent years have seen a proliferation of platform-based “shared mobility services” (SMS) such as car-, bike-, and e-scooter-sharing in many cities in Germany and around the world. At the same time, these services have become the subject of intense debates: Are they replacing private car travel, thus contributing to sustainable mobility in cities? Or are they drawing users away from public transit and cycling while obstructing public space? From the perspective of sustainable mobility politics, it seems far from clear which role these new services could play in transitioning to a less car-centric mobility system. While a number of potential effects and ensuing governance issues of shared mobility services (e.g., regarding questions of equitable access, data governance, the role of public versus private actors) have already been studied, this article explores the role of shared mobility services (SMS) in triggering system dynamics and feedback loops in the context of sustainability transitions. The article connects questions regarding the sustainability effects of “shared mobility services” with the role of “push” measures to reduce private car traffic in cities. Using a theoretical framework from socio-technical transitions research and from the sociology of technology, it describes the recent growth of shared mobility services in Berlin as an example of the upscaling dynamics of socio-technical niche innovations. Drawing on a series of workshops with mobility service providers and representatives of public authorities, it analyses the potential for conflict as well as for coalition-building between service providers and public authorities. Based on the theoretical concept of the role of feedback loops and windows of opportunity for transitions, it shows how the market growth of shared mobility services has added momentum to an already ongoing political debate over the legitimate use of public space in Berlin. Against this backdrop, the article discusses how growing numbers of car-, bike-, and e-scooter-sharing vehicles could open up windows of opportunity for re-distributing space away from private cars. The article concludes that supporting and regulating SMS will be key to steering their growth in the direction of sustainability.
Poverty and patriarchy as contributors to child sexual abuse.

ii SIGNED STATEMENT OF ORIGINALITY.iii DEDICATION.iv ACKNOWLEDGEMENTS.v LIST OF FIGURES.vi LIST OF ACRONYMS.vii TABLE OF CONTENTS.viii CHAPTER 1: . 1 1.
TWO CONIFERS (TAXODIACEAE) OF THE BOHEMIAN CENOMANIAN (CZECH REPUBLIC, CENTRAL EUROPE)

Two most frequent Taxodiaceous conifers Quasisequoia crispa (Velenovský) comb. n. and Cunninghamites lignitum (Sternberg) comb. n. of the Bohemian Cenomanian are revised and described on the basis of their leaf cuticles and ovuliferous cones. The definition of the genus Cunninghamites Presl in Sternberg is emended. The description of Quasisequoia crispa is enlarged basing on numerous foliage shoots and several cones and cone scales. Its sterile foliage consists of compressions of Pagiophyllum-like amphistomatic leaves arranged in helix. Impressions, compressions and three-dimensionally preserved specimens of ovuliferous cones consist of about 30 helically arranged cone scales. Each cone scale bears seeds probably in two rows. Cunninghamites lignitum is nomenclaturally revised. Its definition is emended basing on numerous foliage shoots and several ovuliferous cones. Sterile leaves are acicular, flattened, amphistomatic and helically arranged. Its ovuliferous cones are preserved three dimensionally as compressions, or impressions. They consist of helically arranged peltate cone scales, each bearing four seeds.
Taxonomical study on benthic dinoflagellates collected in coral reefs.

Taxonomical study on eleven species of benthic dinoflagellates was conducted. They were collected from algal samples harvested on coral reefs of French Polynesia, New Caledonia and the Ryukyu Islands, Japan. They were classified into 4 species of Prorocentrum, 2 species of Amphidinium, 3 species of Ostreopsis, coolia monotis and Gambierdiscus toxicus, including 4 new species, Prorocentrum emarginatum sp. nov., Prorocentrum concavum sp. nov., Ostreopsis lenticularis sp. nov. and Ostreopsis ovata sp. nov.
Chromium Concentration in Soil, Feeds and Plasma of Animals in Chittoor District of Andhra Pradesh

Heavy metal such as chromium is potential bioaccumulative toxins of dairy production system. The heavy metal content of dairy feeds however, remains poorly documented, particularly in India. In this survey chromium content of 142 soil, 142 water, 608 dairy ration components and 790 plasma samples of crossbred cattle sampled from 66 mandals of Chittoor district of Andhra Pradesh was detected. The chromium concentration in soil was below the permissible limit, the dry forages like paddy straw and groundnut straw contained Cr to a considerable extent (<1.6 mg/Kg), while all the green forages except Sweet Sudan Grass did not contain chromium in detectable concentration. Highest chromium concentration was found in particularly mineral mixtures and to a lesser extent in concentrates like rice bran, wheat bran home made concentrate mixtures and compounded cattle feeds. Plasma chromium concentration of anoestrous cows was more (P<0.01) followed by pregnant cows, heifers, anoestrous heifers and lactating cows. The study indicated that there are no toxic levels of chromium in soil and dairy feeds.
“EFFECT OF ANTERIOR NASAL PACKING ON MIDDLE EAR FUNCTION
AND HEARING: A PROSPECTIVE STUDY”

IntroductionThe Eustachian tube provides an anatomic communication between the middle ear and nasopharynx, and maintains pressure equality across the tympanic membrane. ObjectiveTo see the effect of anterior nasal packing on Otological symptoms, middle ear pressure and hearing Materials and methodThis prospective study was carried out during period of September 2018 till August 2019. 100 ears were taken in the study. Middle ear pressure and hearing threshold were evaluated by Tympanometry and Audiometry respectively. ResultsPostoperatively two days after anterior nasal packing, there was increase in no. of patient ears with ear fullness, ear ache, tinnitus, hearing threshold and abnormal negative middle ear pressure. After removal of nasal packing up to twelve weeks, improvement in middle ear pressure and hearing threshold was seen. ConclusionAnterior nasal packing causes decrease in middle ear pressure and increase in hearing threshold. Key wordsEustachian tube, Middle ear pressure, Hearing threshold
Estimate of Gillnet Selectivity Parameters and True RelativeAbundance of Oreochromis niloticus and Sarotherodon galileus,Using Four Indirect Methods, with Gillnets Principally of ThreeDifferent Meshes in Thevolta Lake, Ghana

The study was conducted from July to December, 2018, in the Volta Lake, with gillnets principally of mesh sizes, 7.62 cm, 8.89 cm and 10.16 cm, and an additional mesh size of 6.35 cm, using four indirect methods to investigate gillnet selectivity parameters for Oreochromis niloticus and Sarotherodon galileus and to estimate the true relative abundance of the fish populations from the gillnet catches. A total of 1,969 fish samples of both species was measured for standard length, and selectivity parameters determined by comparison of catches of length classes of successive pairs of gillnets. The study determined selection factors of 1.96 and 1.92 for Oreochromis niloticus and Saratherodon galileus respectively and being nearly equal was attributed to both species having similar body shape. The distribution of the selection curves was skewed, due to various factors, but the resultant asymmetry was corrected by the Beverton/ Holt method which minimized the standard deviations of the curves to one-tenth of the normal Holt method for selectivity determination. The gillnet selectivity parameters assessed provided the bench mark for guidance for re-formulation ofthe fisheries regulations on mesh size restrictions for sustainable management of the two tilapiine fish species. Gillnet catches of the two species were significantly different from the true relative abundance of the fish populations due to the selectivity of gillnets. To reflect true abundance and be qualified for more advanced fisheries resources management work, the gillnet data should be adjusted using the probability of capture generated through the selectivity studies.
The Role of Vertical Supply Links in Boosting Growth

The external environment is critical in the quest for growth. Strong global demand can provide the lift that amplifies the fruits of structural reforms, while global headwinds can mean a delay. As Chapter 9 highlighted, however, the reforms that will provide growth in the longer term can also be important to facilitating the medium-term external rebalancing required in many European countries. The nature of international trade has changed dramatically in the past few decades. Production processes have increasingly involved production chains stretching across many countries, with each nation specializing in one or more stages of production. As a result, intra-industry trade now dominates world merchandise trade, and because products cross borders multiple times, world trade has grown faster than both global GDP and global value added in manufacturing ( Figure 10.1 ). In this globalized environment, reforming the domestic economy, while necessary, may not be sufficient if done in isolation. Countries need to find their place in these cross-border production chains to benefit the most from global trade and output growth. The analysis of vertical supply links poses a data challenge. Official trade statistics are measured in gross terms that include both intermediate inputs and final products, thus double counting the value of those goods that cross international borders more than once. As cross-border production links become more important, official trade statistics are becoming less meaningful as a gauge of the value contributed by a country in a particular sector, also reducing their usefulness as a tool for measuring export competitiveness and informing policy advice. Figure 10.2 illustrates this point: suppose a German car maker ships $50,000 worth of car components to Hungary. A factory in Hungary then assembles the car and sells it to a dealership in France for $55,000.The gross or official trade statistics would record $50,000 worth of exports from Germany to Hungary as well as $55,000 worth of export from Hungary to France. But in value-added terms, Hungary’s exports to France would be only $5,000. 1
Relationship between Platelet Indices and Coronary Heart Disease in Malaysian Population

Coronary Heart Disease (CHD) is a major cause of mortality worldwide and in Malaysia. Early screening and diagnosis reduce the mortality rate of this disease by 15%-30%. CHD is caused by atherosclerosis and platelets have been found to play a major role in the development of atherosclerotic lesions. Although other biomarkers exist for CHD, platelet indices can be detected earlier and are routinely available. Hence this project was undertaken to study the relationship between platelet indices and CHD, as well as to find the diagnostic significance of platelet indices by comparing with other inflammatory biomarkers of CHD. This is a case control study carried out from July 2019 to September 2019, at the National Heart Institute, Kuala Lumpur, Malaysia. The study population consisted of 100 normal control subjects and 100 case study subjects. Once eligibility was confirmed, patient data was filled in the case study forms, while the observational laboratory data consisting of platelet indices, were collected from the Sysmex XN-1000 analyser. Statistical analysis was then carried out using the SPSS 16.0 Software, whereby an independent sample ttest was done and a p-value of less than 0.05 was considered statistically significant. Results showed that the levels of PDW, MPV and P-LCR were increased significantly (p-value less than 0.05) in CHD patients, while the levels of PC and PCT between the two groups showed no statistically significant difference. Nevertheless, it was found that these elevations could also be due to other risk factors, such as gender, smoking, Diabetes Mellitus, and hypertension. Hence, further research should be carried out to study the potential mechanisms behind the increase of platelet indices levels as a result of CHD alone, as it has the potential to be a beneficial risk predicting factor for CHD.
The Breeding Biology of Leach's Petrel, Oceanodroma leucorhoa

THE Procellariiformes are the most pelagic of all seabirds. A delayed reproductive maturity, a reduced clutch size, a prolonged incubation and nestling period, and low mortality rates are consequences of their pelagic ecology. Lack (1954, 1966), Ashmole (1963), Serventy (1967), and others have discussed the evolution of this breeding strategy. These authors conclude that nesting on predator-free islands limits seabirds to small clutches by the need to search for widely dispersed or fluctuating food organisms. The age of first breeding is delayed because young, inexperienced birds cannot provide for the additional demands of reproduction and nestling care. The prolongation of the incubation and nestling periods is thought to be an adaptation to an irregular feeding schedule. The reduced reproduction rate, coupled with a density-dependent mechanism, necessitates the Iongevities characteristic of the group. This paper adds to the life history of Leach's Petrel as described by Gross (1935), Ainslie and Atkinson (1937), Gross (1947), and Huntington (1962, 1963) and relates the renesting attempts of failed breeders to Lack's theory of the reproductive rates of birds. The observations reported in this paper were made during a study of the movements of Leach's Petrel, Oceanodro•na leucorhoa, at the Bowdoin Scientific Station on Kent Island, Grand Manan, New Brunswick, Canada. Kent Island supports the southernmos.t large colony of Leach's Petrel in the Atlantic; an estimated 15,000 pairs breed on the island (Wilbur, MS). I spent 20 weeks on the island, from 3 June to 14 August 1965 and from 6 June to 17 August 1966.
Studies of polyadenylation regulation of U1A mRNA by an RNP complex containing U1A and U1 snRNP

OF THE DISSERTATION.ii ACKNOWLEDGMENTS.iv TABLE OF CONTENTS.v LIST OF ILLUSTRATIONS.viii CHAPTER I: INTRODUCTION.1 A. 3’-end Processing of Mammalian Pre-mRNAs.3 RNA Cis-Acting Sequence Elements.3 Polyadenylation Signal (PAS). 3 Downstream Sequence Elements (DSE). 4 Cleavage Site (pA). 4 Auxiliary Elements.5 Cleavage and Polyadenylation Protein Factors.5 Cleavage/Polyadenylation Specificity Factor (CPSF). 6 Cleavage Stimulatory Factor (CstF). 7 Mammalian Cleavage Factor I (CF Im). 8 Mammalian Cleavage Factor II (CF IIm). 9
An Analysis of Calorie Consumption and Elasticity in Vietnam

This paper analyzes calorie consumption in Vietnam using the household survey data. The data suggest that food insecurity is still a major problem in Vietnam, with nearly 40 percent of the population being unable to meet their calorie requirement. Employing nonparametric and parametric estimation techniques, the paper examines the relationship between household calorie consumption and per capita household expenditure in Vietnam. The analysis indicates a positive and significant relationship between per capita expenditure and per capita calorie consumption. The mean calorie elasticity is estimated to be between 0.21 and 0.31 by the parametric method and 0.20 by non-parametric method. In addition, simulated income and food price changes indicate that undernutrition is very responsive to changes in income and food prices.
ERAD 2014-THE EIGHTH EUROPEAN CONFERENCE ON RADAR IN METEOROLOGY AND HYDROLOGY

To better understand an unpredictable atmosphere, meteorologists create scientific conceptual models to aid in identifying favorable severe-weather environments and assist in overall threat recognition, especially in terms of supercells and tornadogenesis (e.g., Johns 1993; Doswell et al. 1996; Andra et al 2002). Scientifically based conceptual models of the environment (e.g., Johns and Doswell 1992), supercells (e.g., Doswell and Burgess 1993), and tornadogenesis (e.g., Wicker and Wilhelmson 1995) allow a forecaster to develop expectations about a given severe weather event. As storms develop, forecasters use conceptual models to anticipate future storm characteristics and develop predictions for potential hazards posed by the storms (Andra et al. 2002). These predictions act as building blocks for accurate decisions about a warning’s location, timing, and type (Hahn et al. 2003). In addition, conceptual models can affect how a forecaster interprets radar data. Heinselman et al. (2012) note that forecasters lowered their thresholds for issuing tornado warnings in a tropical environment, while Lindley and Morgan (2004) discuss a reluctance by forecasters to issue tornado warnings due to their environmental conceptual models despite the presence of radar signatures supportive of tornado warnings. Matching current storm attributes to existing conceptual models therefore appears to be a key to successful anticipation of hazardous events and by extension, accurate warnings (Andra et al. 2002).
An Empirical Study of Tokenization Strategies for Various Korean NLP Tasks

Typically, tokenization is the very first step in most text processing works. As a token serves as an atomic unit that embeds the contextual information of text, how to define a token plays a decisive role in the performance of a model. Even though Byte Pair Encoding (BPE) has been considered the de facto standard tokenization method due to its simplicity and universality, it still remains unclear whether BPE works best across all languages and tasks. In this paper, we test several tokenization strategies in order to answer our primary research question, that is, “What is the best tokenization strategy for Korean NLP tasks? ” Experimental results demonstrate that a hybrid approach of morphological segmentation followed by BPE works best in Korean to/from English machine translation and natural language understanding tasks such as KorNLI, KorSTS, NSMC, and PAWS-X. As an exception, for KorQuAD, the Korean extension of SQuAD, BPE segmentation turns out to be the most effective. Our code and pre-trained models are publicly available at https://github.com/kakaobrain/kortok.
Guiding Attention for Self-Supervised Learning with Transformers

In this paper, we propose a simple and effective technique to allow for efficient self-supervised learning with bi-directional Transformers. Our approach is motivated by recent studies demonstrating that self-attention patterns in trained models contain a majority of non-linguistic regularities. We propose a computationally efficient auxiliary loss function to guide attention heads to conform to such patterns. Our method is agnostic to the actual pre-training objective and results in faster convergence of models as well as better performance on downstream tasks compared to the baselines, achieving state of the art results in low-resource settings. Surprisingly, we also find that linguistic properties of attention heads are not necessarily correlated with language modeling performance.
RESIDUAL YOLK IN CAPTIVE AND WILD-CAUGHT HATCHLINGS OF THE RED-EARED SLIDER TURTLE (TRACHEMYS SCRIPTA ELEGANS)

Laboratory studies of turtles that lay flexibleshelled eggs have disclosed a predictable pattern of variation in hatchling characteristics dependent on the hydric environment of incubation. In general, hatchlings of such turtles are larger in linear measures and in wet mass when the hydric environment of incubation is relatively wet than are hatchlings from drier hydric regimes. However, the larger hatchlings from wetter incubation conditions retain less residual
Adversarial Boot Camp: label free certified robustness in one epoch

Machine learning models are vulnerable to adversarial attacks. One approach to addressing this vulnerability is certification, which focuses on models that are guaranteed to be robust for a given perturbation size. A drawback of recent certified models is that they are stochastic: they require multiple computationally expensive model evaluations with random noise added to a given input. In our work, we present a deterministic certification approach which results in a certifiably robust model. This approach is based on an equivalence between training with a particular regularized loss, and the expected values of Gaussian averages. We achieve certified models on ImageNet-1k by retraining a model with this loss for one epoch without the use of label information.
Understanding the Mechanics of SPIGOT: Surrogate Gradients for Latent Structure Learning

Latent structure models are a powerful tool for modeling language data: they can mitigate the error propagation and annotation bottleneck in pipeline systems, while simultaneously uncovering linguistic insights about the data. One challenge with end-to-end training of these models is the argmax operation, which has null gradient. In this paper, we focus on surrogate gradients, a popular strategy to deal with this problem. We explore latent structure learning through the angle of pulling back the downstream learning objective. In this paradigm, we discover a principled motivation for both the straight-through estimator (STE) as well as the recently-proposed SPIGOT - a variant of STE for structured models. Our perspective leads to new algorithms in the same family. We empirically compare the known and the novel pulled-back estimators against the popular alternatives, yielding new insight for practitioners and revealing intriguing failure cases.