Miracle-dz/UniFAR-FTUs huggingface dataset:
An evolutionary genomics approach towards analysis of genes implicated in transmission of trypanosomes between tsetse fly and mammalian host

iii DECLARATION . v ACKNOWLEDGEMENTS . vi TABLE OF CONTENTS . vii LIST OF FIGURES . viii LIST OF TABLES . ix LIST OF ABBREVIATIONS . x CHAPTER ONE: LITERATURE REVIEW AND THESIS RATIONALE . 1 CHAPTER TWO: METHODS . 27 CHAPTER THREE: RESULTS AND ANALYSIS. 36 CHAPTER FOUR: DISCUSSION AND CONCLUSION. 56 REFERENCES . 65 APPENDICES . 77 APPENDIX I: Outline of PHRED and PHRAP . 77 APPENDIX II: List of Perl scripts. 79
Factor Performance 2010–2019: A Lost Decade?

The factors in the widely used Fama–French model experienced a negative average return during the 2010–2019 period. Perhaps surprisingly, such a lost decade is not unprecedented in history, as factor performance in the 2010s was, in fact, remarkably similar to factor performance in the 1990s. By contrast, many other factors did deliver a positive premium during the past decade. These factors include low risk, price momentum, earnings momentum, analyst revisions, seasonals, and short-term reversal. Thus, there appears to be a clear dichotomy in recent factor performance: while generally accepted factors struggled, various factors that are considered to be inferior or redundant remained effective. TOPICS: Factor-based models, style investing, volatility measures Key Findings • The factors in the widely used Fama–French model experienced a negative average return during the 2010–2019 period. This lost decade is remarkably similar to the 1990–1999 period. • Many other factors did deliver a positive premium during the past decade—for example, low risk, price momentum, earnings momentum, analyst revisions, seasonals, and short-term reversal. • In sum, there has been a clear dichotomy in recent factor performance: Although generally accepted factors struggled, other factors remained effective.
A Deep Learning approach to Hyperspectral Image Classification using an improved Hybrid 3D-2D Convolutional Neural Network

In recent years, the task of Hyperspectral Image (HSI) classification has appeared in various fields, including Remote Sensing. Meanwhile, the evolution of Deep Learning, and the prevalence of the Convolutional Neural Network (CNN) has revolutionized the way unstructured, especially visual, data are processed. 2D CNN have proved highly efficient in exploiting the spatial information of images, but in HSI classification, data contain both spectral and spatial features. To make use of these characteristics, many variations of a 3D CNN have been proposed, but a 3D Convolution comes at a high computational cost. A fusion of 3D and 2D convolutions decreases processing time by distributing spectral-spatial feature extraction across a lighter, less complex model. An enhanced Hybrid network architecture is proposed alongside a data preprocessing plan, with the aim of achieving a significant improvement in classification results. Four benchmark datasets (Indian Pines, Pavia University, Salinas and Data Fusion 2013 Contest) are used to compare the model to other hand-crafted or deep learning architectures. It is demonstrated that the proposed network outperforms state-of-the-art approaches in terms of classification accuracy, while avoiding some commonly used, computationally expensive design choices.
Application of a Genetic Algorithm to Optimize the Performance of a Visible Light Communications System: Key Concepts and Preliminary Results

Visible light communications is considered an important pillar technology of future 5G and beyond 5G networks. In this paper, we discuss the application of a genetic algorithm for optimizing the performance of a visible light communications link. We show how the parameters of the link pertinent to the transceiver design can be selected using a suitable mixed-integer genetic algorithm and the appropriate fitness function. We propose a suitable fitness function based on the achieved data rate and discuss how performance constraints related to the bit error rate can be incorporated in the optimization. For each candidate design, the fitness function can be calculated with an analytical model described in this work. Preliminary results indicate the proposed optimization scheme can indeed be used to design visible light communication systems achieving high spectral efficiency.
Symbolic Reasoning for Automatic Signal Placement

Explicit signaling between threads is a perennial cause of bugs in concurrent programs. While there are several runtime techniques to automatically notify threads upon the availability of some shared resource, such techniques are not widely-adopted due to their run-time overhead. This paper proposes a new solution based on static analysis for automatically generating a performant explicit-signal program from its corresponding implicit-signal implementation. The key idea is to generate verification conditions that allow us to minimize the number of required signals and unnecessary context switches, while guaranteeing semantic equivalence between the source and target programs. We have implemented our method in a tool called Expresso and evaluate it on challenging benchmarks from prior papers and open-source software. Expresso-generated code significantly outperforms past automatic signaling mechanisms (avg. 1.56x speedup) and closely matches the performance of hand-optimized explicit-signal code.
Mechanism design for efficient allocation of electric vehicles to charging stations

The electrification of transport can significantly reduce CO2 emissions and their negative impact on the environment. In this paper, we study the problem of allocating Electric Vehicles (EVs) to charging stations and scheduling their charging. We develop an offline solution that treats EV users as self-interested agents that aim to maximise their profit and minimise the impact on their schedule. We formulate the problem of the optimal EV to charging station allocation as a Mixed Integer Programming (MIP) one and we propose two pricing mechanisms: A fixed-price one, and another that is based on the well known Vickrey-Clark-Groves (VCG) mechanism. We observe that the VCG mechanism services on average 1.5% more EVs than the fixed-price one. In addition, when the stations get congested, VCG leads to higher prices for the EVs and higher profit for the stations, but lower utility for the EVs. However, the VCG mechanism guarantees truthful reporting of the EVs’ preferences.
Correct regionalization of a tissue primordium is essential for coordinated morphogenesis

During organ development, tubular organs often form from flat epithelial primordia. In the placodes of the forming tubes of the salivary glands in the Drosophila embryo, we previously identified spatially defined cell behaviours of cell wedging, tilting and cell intercalation that are key to the initial stages of tube formation. Here we address what the requirements are that ensure the continuous formation of a narrow symmetrical tube from an initially asymmetrical primordium whilst overall tissue geometry is constantly changing. We are using live-imaging and quantitative methods to compare wild-type and mutants that either show disrupted cell behaviours or an initial symmetrical placode organisation, with both resulting in severe impairment of the invagination. We find that early transcriptional patterning of key morphogenetic transcription factors drives the selective activation of downstream morphogenetic modules, such as GPCR signalling that activates apical-medial actomyosin activity to drive cell wedging at the future asymmetrically-placed invagination point. Over time, transcription of key factors expands across the rest of the placode and cells switch their behaviour from predominantly intercalating to predominantly apically constricting as their position approaches the invagination pit. Misplacement or enlargement of the initial invagination pit leads to early problems in cell behaviours that eventually result in a defective organ shape. Our work illustrates that the dynamic patterning of the expression of transcription factors and downstream morphogenetic effectors ensures positionally fixed areas of cell behaviour with regards to the invagination point. This patterning in combination with the asymmetric geometrical set-up ensures functional organ formation.
Different evolutionary pathways of HIV-1 between fetus and mother perinatal transmission pairs indicate unique immune selection pressure in fetuses

Study of evolution and selection pressure on HIV-1 in fetuses will lead to a better understanding of the role of immune responses in shaping virus evolution and vertical transmission. Detailed genetic analyses of HIV-1 env gene from 12 in utero transmission pairs show that most infections (67%) occur within two months from childbirth. In addition, env sequences from long-term infected fetuses were highly divergent and formed separate phylogenetic lineages from their cognate maternal viruses. Host selection sites unique to infant viruses were identified in regions frequently targeted by broadly neutralizing antibodies and T cell immune responses. The identification of unique selection sites in the env gene of fetal viruses indicates that the immune system in fetuses is capable of exerting selection pressure on viral evolution. Studying selection and evolution of HIV-1 or other viruses in fetuses can be an alternative approach to investigate adaptive immunity in fetuses.
Malignant Priapism – What Do We Know About It?

Malignancy as an etiological factor involved in priapism pathogenesis is rare. Malignant priapism (MP) can arise as a result of penile tumor invasion, either from primary penile tumors or from metastatic penile tumors, or due to hematological malignancies. Non-urological penile metastases are associated with significant worse prognosis compared to urological penile metastases, the appearance of priapism in such cases affecting even more the prognosis and the survival of these patients. Patients diagnosed with hematological malignancies and priapism present significant higher survival rates compared to those who develop MP in the context of a non-hematological malignancy, this being related to the fact that hematological malignancies are more sensitive to chemo- and radiotherapy. Most malignant priapism cases are ischemic; therefore the management should be based on the initial steps of the IP therapeutic protocol. Considering the trigger factor that has led to the priapic event specific oncologic treatment can be added as well.
ORP1L regulates dynein clustering on endolysosmal membranes in response to cholesterol levels

The sub-cellular positioning of endolysosomes is crucial for regulating their function. Particularly, the positioning of endolysosomes between the cell periphery versus the peri-nuclear region impacts autophagy, mTOR (mechanistic target of rapamycin) signaling and other processes. The mechanisms that regulate the positioning of endolysosomes at these two locations are still being uncovered. Here, using super-resolution microscopy, we show that the retrograde motor dynein forms nano-clusters on endolysosomal membranes containing 1-2 dyneins, with an average of ~3 nanoclusters per endolysosome. These data suggest that a very small number of dynein motors (1-6) drive endolysosome motility. Surprisingly, dynein nano-clusters are slightly larger on peripheral endolysosomes having higher cholesterol levels compared to peri-nuclear ones. By perturbing endolysosomal membrane cholesterol levels, we show that dynein copy number within nano-clusters is influenced by the amount of endolysosomal cholesterol while the total number of nano-clusters per endolysosome is independent of cholesterol. Finally, we show that the dynein adapter protein ORP1L (Oxysterol Binding Protein Homologue) regulates the number of dynein motors within nano-clusters in response to cholesterol levels. We propose a new model by which endolysosomal transport and positioning is influenced by the cholesterol sensing adapter protein ORP1L, which influences dynein’s copy number within nano-clusters.
Are digital technology interventions effective to reduce loneliness in older adults? A systematic review and meta-analysis

Objective: To review the latest literature on the effectiveness of DTIs in reducing loneliness in (older) adults. Data Sources: Electronic searches in PubMed, Medline, CINAHL, EMBASE and Web of Science covering publication period from 1 January 2010 to 31 July 2019. Subjects: Adult men and women Design: Systematic review and meta-analysis Main Outcome Measure: Loneliness. Study Selection: Primary studies that used DTIs for tackling loneliness in adults (aged [≥]18 years) with follow-up measurements at least three months or more and publication in the English language. Data Extraction and Synthesis: Two researchers independently screened articles and extracted data on several variables: participants, interventions, comparators and outcomes. Data was extracted on the primary outcome i.e. loneliness measured at the baseline and follow-up measurements at three, four, six and twelve months after the intervention. Results: Six studies were selected from 4939 articles screened. Selected studies included 5 clinical trials (4 RCTs and 1 quasi experimental study) and one before and after study, which enrolled 646 participants (men =154 (24%), women =427 (66%), no gender information =65 (10%) with average age between 73 and 78 years (SD 6-11). Five clinical trials were included in the meta-analysis and standardised mean differences (SMD) were calculated for each trial and pooled across studies using a random effects model. The overall effect estimates were not statistically significant in follow-up measurements at three months (SMD= 0.02, 95% CI= -0.36, 0.40; P=0.92), four months (SMDs= -1.11, 95% CI= -2.60, 0.38; P=0.14) and six months (SMD= -0.11, 95% CI= -0.54, 0.32; P=0.61). The quality of evidence was very low to moderate in these trials. Conclusions: There is insufficient evidence to make conclusions that DTIs are effective in reducing loneliness in older adults. Future research may consider RCTs with larger sample sizes and longer duration of interventions and follow-up.
Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study

Background: By mid-July 2020, more than 108,000 COVID-19 cases had been diagnosed in Canada with more than half in the province of Quebec. To be prepared for a potential second wave of COVID-19 in the fall, it seems of utmost importance to analyze the epidemiological and socio-economic characteristics of the spring outbreak in the population. Method: We conducted an online survey of the participants of the CARTaGENE population-based cohort, composed of middle-aged and older adults. We collected information on socio-demographic, lifestyle, health condition, COVID-related symptoms and COVID-19 testing. We studied the association between these factors and two outcomes: the status of having been tested for SARS-CoV-2 and the status of having received a positive test when having been tested. These associations were evaluated with univariate and multivariate analyzes using a hybrid tree-based regression model. Results: Among the 8,129 respondents from the CARTaGENE cohort, 649 were tested for COVID-19 and 41 were positive. Medical workers and individuals having a contact with a COVID-19 patient had the highest probabilities of being tested (32% and 42.4%, respectively) and of being positive (17.2% and 13.0%, respectively) among those tested. 7.6% of the participants declared that they have experienced at least one of the four COVID-related symptoms chosen by the Public Health authorities (fever, cough, dyspnea, anosmia) but were not tested. Results from the tree-based model analyzes adjusted on exposure factors show that the combination of dyspnea, dry cough and fever was highly associated with being tested whereas anosmia, fever, and headache were the most discriminant factors for having a positive test among those tested. During the spring outbreak, more than one third of the participants have experienced a decrease in access to health services. There were sex and age differences in the socio-economic and emotional impacts of the pandemic. Conclusion: We have shown some discrepancies between the symptoms associated with being tested and being positive. In particular, the anosmia is a major discriminant symptom for positivity whereas ear-nose-throat symptoms seem not to be COVID-related. The results also emphasize the need of increasing the accessibility of testing for the general population.
Epidemiology of Venous Thromboembolism in SARS- CoV-2 Infected Patients: A Systematic Review and Meta-Analysis

Early reports from China and Europe indicated that incidence of venous thromboembolism in COVID-19 patients may be high. In this meta-analysis of observational studies was designed to know worldwide prevalence of thromboembolic events in COVID-19 patients. Primary outcome of our review was to assess the proportion of patients with VTE. Secondary outcomes were to assess the proportion of patients with DVT and proportion of patients with PE. Random effect meta-analysis model with restricted maximum likelihood estimator was used for all analysis. Pooled proportion with 95% confidence interval (95% CI) and heterogeneity (I2) was reported for all outcomes. Data of 5426 patients from n=19 articles were included in this systematic review and meta-analysis. Incidence of VTE (95% CI), PE (95% CI) and DVT (95% CI) was 23 (10- 36) %, 12 (6- 17) % and 15 (8- 23) %. We have found a high but incidence of thromboembolic events in COVID-19 patients. Further well-designed studies are required in this area to identify true incidence and risk factors of it.
Natural Stable Isotopes for Determination of Gastrointestinal Transit Time in Fish

This study evaluated the application of stable isotopes of carbon as an alternative and more accurate method to determine gastrointestinal transit time (GTT) in fish by comparing it to the inert marker method. The stable isotope method detects alterations of the normal carbon flow in a biological system by analyzing naturally occurring isotopes of carbon, contrary to studies based on conventional techniques that apply external markers to the diet to determine GTT through visual observation of the color change in feces. Therefore, 320 pacu, Piaractus mesopotamicus juveniles were reared in 32 tanks under two different temperatures (25 and 29 C). The pacu juveniles received two different diets, one based on ingredients derived from C3 photosynthetic cycle plants and the other based on C4 plant ingredients, both containing titanium oxide (TiO2) as a marker. After 40 d, the isotopic signature of the diets was changed, and the marker was replaced by chromic oxide (Cr2O3). In the isotopic technique, the feces were analyzed to determine the exchange in the isotopic ratio of carbon δ13C. Both methods found that GTT was faster (nearly 6 h) in fish at 29 C when using the C4/C3 feeding strategy and slower in fish at 25 C using the C3/C4 strategy (15 h by inert marker and 18 h by the isotopic method). In conclusion, GTT determination in pacu juveniles using the stable isotope technique exhibits the same accuracy obtained with the inert marker method at temperatures suitable (nearly 29 C) for the metabolism of these animals.
Pan-cancer analysis of the metabolic reaction network

Metabolic reprogramming is considered a hallmark of malignant transformation. However, it is not clear whether the network of metabolic reactions expressed by cancers of different origin differ from each other nor from normal human tissues. In this study, we reconstructed functional and connected genome-scale metabolic models for 917 primary tumors based on the probability of expression for 3,765 reference metabolic genes in the sample. This network-centric approach revealed that tumor metabolic networks are largely similar in terms of accounted reactions, despite diversity in the expression of the associated genes. On average, each network contained 4,721 reactions, of which 74% were core reactions (present in >95% of all models). Whilst 99.3% of the core reactions were classified as housekeeping also in normal tissues, we identified reactions catalyzed by ARG2, RHAG, SLC6 and SLC16 family gene members, and PTGS1 and PTGS2 as core exclusively in cancer. The remaining 26% of the reactions were contextual reactions. Their inclusion was dependent in one case (GLS2) on the absence of TP53 mutations and in 94.6% of cases on differences in cancer types. This dependency largely resembled differences in expression patterns in the corresponding normal tissues, with some exceptions like the presence of the NANP-encoded reaction in tumors not from the female reproductive system or of the SLC5A9-encoded reaction in kidney-pancreatic-colorectal tumors. In conclusion, tumors expressed a metabolic network virtually overlapping the matched normal tissues, raising the possibility that metabolic reprogramming simply reflects cancer cell plasticity to adapt to varying conditions thanks to redundancy and complexity of the underlying metabolic networks. At the same time, the here uncovered exceptions represent a resource to identify selective liabilities of tumor metabolism.
Lymph node necrosis in systemic lupus erythematosus Note

The lymph node lesions of lupus lymphadenitis are characterized by necrosis sometimes accompanied by hematoxylin bodies, but only a few immunohistological analyses of this unique lesion have been reported. In this study we investigated the immunopathogenesis of these lesions. Lymph node specimens from four patients were analyzed immunohistochemically by applying recently developed monoclonal antibodies to immunocompetent cells. Necrosis occupied almost the entire lymph node in two cases (extensive type), whereas small foci of necrosis were found in the paracortex in the remaining two (localized type). No hematoxylin body formation was detected in any of the samples. Necrosis of the small muscular arteries, arterioles and venules was seen in the necrotic areas in all four cases. In one case of the localized type, necrotizing angitis was seen in a few arterioles and venules in the non‐necrotic area. By immunohistology, amorphous depositions of immunoglobulins and C3 were demonstrated in the walls of the arterioles and venules in two cases. Our findings indicate that vasculitis due to local deposition of immune complexes in the blood vessels may play an important role in the pathogenesis of necrosis in lupus lymphadenitis.