Miracle-dz/UniFAR-FTUs huggingface dataset:
Redundans: an assembly pipeline for highly heterozygous genomes

Many genomes display high levels of heterozygosity (i.e. presence of different alleles at the same loci in homologous chromosomes), being those of hybrid organisms an extreme such case. The assembly of highly heterozygous genomes from short sequencing reads is a challenging task because it is difficult to accurately recover the different haplotypes. When confronted with highly heterozygous genomes, the standard assembly process tends to collapse homozygous regions and reports heterozygous regions in alternative contigs. The boundaries between homozygous and heterozygous regions result in multiple assembly paths that are hard to resolve, which leads to highly fragmented assemblies with a total size larger than expected. This, in turn, causes numerous problems in downstream analyses such as fragmented gene models, wrong gene copy number, or broken synteny. To circumvent these caveats we have developed a pipeline that specifically deals with the assembly of heterozygous genomes by introducing a step to recognise and selectively remove alternative heterozygous contigs. We tested our pipeline on simulated and naturally-occurring heterozygous genomes and compared its accuracy to other existing tools. Our method is freely available at https://github.com/Gabaldonlab/redundans.
Towards a probabilistic regional reanalysis system for Europe: evaluation of precipitation from experiments

A new development in the field of reanalyses is the incorporation of uncertainty estimation capabilities. We have developed a probabilistic regional reanalysis system for the CORDEX-EUR11 domain that is based on the numerical weather prediction model COSMO at a 12-km grid spacing. The lateral boundary conditions of all ensemble members are provided by the global reanalysis ERA-Interim. In the basic implementation of the system, uncertainties due to observation errors are estimated. Atmospheric assimilation of conventional observations perturbed by means of random samples of observation error yields estimates of the reanalysis uncertainty conditioned to observation errors. The data assimilation employed is a new scheme based on observation nudging that we denote ensemble nudging. The lower boundary of the atmosphere is regularly updated by external snow depth, sea surface temperature and soil moisture analyses. One of the most important purposes of reanalyses is the estimation of so-called essential climate variables. For regional reanalyses, precipitation has been identified as one of the essential climate variables that are potentially better represented than in other climate data sets. For that reason, we assess the representation of precipitation in our system in a pilot study. Based on two experiments, each of which extends over one month, we conduct a preliminary comparison to the global reanalysis ERA-Interim, a dynamical downscaling of the latter and the high-resolution regional reanalysis COSMO-REA6. In a next step, we assess our reanalysis system's probabilistic capabilities versus the ECMWF-EPS in terms of six-hourly precipitation sums. The added value of our probabilistic regional reanalysis system motivates the current production of a 5-year-long test reanalysis COSMO-EN-REA12 in the framework of the FP7-funded project Uncertainties in Ensembles of Regional Re-Analyses (UERRA).
Angioimmunoblastic lymphadenopathy long‐term follow‐up study

The clinical course of 41 previously reported patients with angioimmunoblastic lymphadenopathy with dysproteinemia (AILD) on whom follow‐up information has been obtained for five or more years is described. Of the 41 patients, 27 achieved a complete remission (CR). The durations of the CR ranged from two to 214 months, with a median of 48 months. Nine of these 27 complete responders are still alive and well without evidence of disease, whereas the remaining 18 patients have died of pneumonia, septicemia, immunoblastic lymphoma, or unrelated causes. These 27 patients had a significantly longer median survival (51 mos) than did the 14 patients who had partial or no response (9 mos) (P = 0.0006). Only two of these 14 patients who did not initially achieve a CR are alive (survivals, 66 months and 70 months). There was a trend suggesting that patients who received combination chemotherapy which included prednisone had a slightly longer survival than did the remaining patients (P = 0.087). Lymphocytopenia was evident in a higher proportion of dead patients than in those who remained alive (P = 0.089). Cancer 52:318‐321, 1983.
MUX-PLMs: Pre-training Language Models with Data Multiplexing

Data multiplexing is a recently proposed method for improving a model’s inference efﬁciency by processing multiple instances simultaneously using an ordered representation mixture. Prior work on data multiplexing only used task-speciﬁc Transformers without any pre-training, which limited their accuracy and generality. In this paper, we develop pre-trained multiplexed language models (MUX-PLMs) that can be widely ﬁnetuned on any downstream task. Our approach includes a three-stage training procedure and novel multiplexing and demultiplexing mod-ules for improving throughput and downstream task accuracy. We demonstrate our method on BERT and ELECTRA pre-training objectives, with our MUX-BERT and MUX-ELECTRA models achieving 2x/5x inference speedup with a 2-4 % drop in absolute performance on GLUE and 1-2 % drop on token-level tasks. 1
Increasing Treatment Rates for Hepatitis C in Primary Care

Background: Despite antiviral agents that can cure the disease, many individuals with Hepatitis C Virus (HCV) remain untreated. Primary care clinicians can play an important role in HCV treatment but often feel they do not have the requisite skills. Methods: We implemented a population-based improvement intervention over 10 months to support treatment of HCV in a primary care setting. The intervention included a decision-support tool, education for clinicians, enhanced interprofessional team supports, mentorship, and proactive patient outreach. We used process and outcome measures to understand the impact on the proportion of patients who initiated treatment and achieved Sustained Virologic Response (SVR). We used physician focus groups and pharmacist interviews to understand the context and mechanisms influencing the impact of the intervention. Results: Between December 2018 and June 2020, the percentage of HCV RNA positive patients who started treatment rose from 66.0% (354/536) to 75.5% (401/531) with 92.5% (371/401) of those starting treatment achieving SVR. Qualitative findings highlighted that the intervention helped raise awareness and confidence among physicians for treating HCV in primary care. A collaborative team environment, education, mentorship, and a decision-support tool integrated into the electronic record were all enablers of success although patient psychosocial complexity remained a barrier to engagement in treatment. Conclusion: A multifaceted primary care improvement initiative increased clinician confidence and was associated with an increase in the proportion of HCV RNA positive patients who initiated curative treatment.
Defining a role for fibroblasts in the persistence of chronic inflammatory joint disease

The most surprising feature of the inflammatory response in rheumatoid arthritis is not that it occurs but that it does not resolve. The persistence of the chronic inflammatory response in conjunction with ongoing joint destruction is an all too familiar finding in many patients with rheumatoid arthritis. Despite the use of effective anti-inflammatory agents and disease modifying drugs, a significant proportion of patients with rheumatoid arthritis continue to have resistant disease. Complete clinical remission is unusual for more than six months and a formal cure of the disease remains elusive. In this report we focus on how attempts to address the question of why rheumatoid arthritis persists have led to a different interpretation of the pathogenesis of rheumatoid disease; one in which alterations in stromal cells such as fibroblasts play an important role in the switch from resolving to persistent disease.
Towards a magmatic ‘barcode’ for the south-easternmost terrane of the Kaapvaal Craton, South Africa

v 1. CHAPTER: 01 – INTRODUCTION 1 1.1. Statement Of The Problem 1 1.2. LIPs and reconstructions using barcoding and palaeomagnetism 6 1.3. Locality 13 1.4. Methodology 15 2. CHAPER: 02 – GEOLOGICAL SETTING 17 2.1. Regional Geology 17 2.1.1. The amalgamation of the Kaapvaal Craton 17 2.1.2. Mesoto Neoarchaean supracrustal successions and intrusions 20 2.1.3. Palaeoproterozoic supracrustal successions and intrusions 25 2.1.4. The Mesoproterozoic to the Mesozoic 28 2.2. Local Geology 29 2.2.1. The Archaean Basement 32 2.2.2. The Pongola Supergroup 32 2.2. 3. The Hlagothi Complex 34 2.2. 4. Dyke and sill swarms and provinces 35 3. CHAPTER: 03 – GEOLOGY 41 3.
The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES)

Can you imagine living in a world without plants such as orchids, mahogany trees, and cacti? Or a world without populations of great whales, sea turtles, and parrots? The vast diversity of the world’s plant and animal life is disappearing at a faster rate than new species are being discovered and recorded. Scientists estimate that within the next 30 years, more than one-fifth of the millions of types of plants, animals, and other organisms living here on Earth will become extinct. Faced with these frightening facts, representatives from around the world have united in ratifying the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) to protect the world’s wild plant and animal species by regulating their use in commercial trade. CITES representatives are working to ensure that tomorrow’s generation will have a chance to see the rich and plentiful wild fauna and flora we see today.
EXPLORING THE MOMENTS AND MEMORY OF TOURIST EXPERIENCES IN PERU

i Acknowledgements iv Dedication v Declaration of Co-Authorship / Previous Publication vi Statement of Originality viii List of Tables xii List of Figures xiii Chapter 1: Introduction 1 Defining the Problem 1 Purpose and Objectives 3 Overview of Research Approach 4 Dissertation Outline 17 Chapter 2: The Dimensions of the Tourist Experience 23 Introduction 23 Multiple Definitions of the Tourist Experience 24 Development of the Tourist Experience Literature 25 Dimensions of Experience: Phases, Influences, and Outcomes 27 Tourist Experience Conceptual Model 30 The Influential Realm 32 Personal Realm 35 Conclusion 49 Chapter 3: The Experience Sampling Method: Examining its Use and Potential in Tourist Experience Research 51
Compatibility and Investment in the U . S . Electric Vehicle Market

Competing standards often proliferate in the early years of product markets, potentially leading to socially inefficient investment. This paper studies the effect of compatibility in the U.S. electric vehicle market, which has grown ten-fold in its first five years but has three incompatible standards for charging stations. I develop and estimate a structural model of consumer vehicle choice and car manufacturer investment that demonstrates the ambiguous impact of mandating compatibility standards on market outcomes and welfare. Compatibility may benefit consumers by providing access to all existing charging stations. However, firms may cut back on their investments because the benefits from one firm’s investments spill over to rivals. Firm response in investment may erode consumer gains from compatibility. I estimate my model using U.S. data from 2011 to 2015 on vehicle registrations and charging station investment and identify demand elasticities with variation in federal and state subsidy policies. Counterfactual simulations show that mandating compatibility in charging standards would decrease duplicative investment in charging stations by car manufacturers and increase the size of the electric vehicle market. ∗I am deeply grateful to my PhD advisors Ariel Pakes, Elie Tamer, Robin Lee, James Stock, and Christopher Knittel for their continual guidance and support. I thank Evan Herrnstadt, Gaston Illanes, Divya Kirti, Shanjun Li, Daniel Pollmann, Frank Schilbach, Robert Stavins, Che-Lin Su, Richard Sweeney, Thomas Wollmann, Matthew Zaragoza-Watkins, Yufei Zhao, Fanyin Zheng and participants in the Harvard Industrial Organization, Labor/PF, and Environmental workshop and lunches for helpful conversations, comments, and suggestions. Data purchased for this research is generously supported by the Lab for Economic Applications and Policy. I thank John Smart and Sera White at the Idaho National Laboratory for generously sharing knowledge of the U.S. federal programs that deployed electric vehicle charging infrastructure. †MIT Sloan School of Management, lijing@mit.edu
Occupational skin disorders in a subset of Nigerian hairdressers

Introduction Hairdressing is associated with a wide range of disorders. This is particularly true in the African hairdresser, who is saddled with the responsibility of ‘taming’ the rather difficult-to-manage African hair, and is thus exposed to a wide range of chemical, biological and physical materials in the hair grooming process. We therefore sought to determine the prevalence and pattern of occupational skin disorders among hairdressers in Ibadan, one of the oldest and largest cities in Nigeria. Methods This was a cross sectional study of hairdressers conducted in 2013 in Ibadan, Nigeria. Hairdressers and their apprentices were interviewed using a structured questionnaire, following which a thorough physical examination was performed to identify any skin disorder. Results A total of 226 hairstylists were recruited. The prevalence of occupational skin disorders in the study was 68.13%. The prevalence of specific skin disorders was 32.74% for nail disorders; 28.75% for traumatic skin disorders; and 2.64% for hand dermatitis. Conclusion There is a high prevalence of occupational skin disorders among hairdressers, and this may have personal and public health implications.
UniCon: Unidirectional Split Learning with Contrastive Loss for Visual Question Answering

Visual Question Answering (VQA) using multi-modal data facilitates real-life applications, such as home robots and medical diagnoses. However, one significant challenge is to design a robust learning method for various client tasks. One critical aspect is to ensure privacy, as client data sharing is limited due to confidentiality concerns. This work focuses on addressing the issue of confidentiality constraints in multi-client VQA tasks and limited labeled training data of clients. We propose the Uni directional Split Learning with Con trastive Loss (UniCon) method to overcome these limitations. The proposed method trains a global model on the entire data distribution of different clients, learning refined cross-modal representations through model sharing. Privacy is ensured
COVID-19: clinical and laboratory manifestations in novel coronavirus infection

COVID-19 is a highly contagious disease caused by the coronavirus of severe acute respiratory syndrome 2 (SARS-CoV-2). In 2020, due to the outbreak, it was considered by the World Health Organization (WHO) as a pandemic. The infection caused by the novel coronavirus has high mortality in a small portion of the infected population, especially in elderly, immunosuppressed, diabetic, cardiac, and hypertensive individuals. Many infected are asymptomatic (and may be carriers) or present mild or moderate flu-like symptoms. The most severe clinical picture of COVID-19 is characterized by an inflammatory cytokine storm, with hematological changes and coagulation dysfunction, which can lead to tissue damage and death. Nonspecific laboratory biomarkers may be either increased or decreased as the course of the disease progresses and are often useful in predicting complications of the disease, such as the use of D-dimer and platelet/lymphocyte ratio. Specific laboratory diagnosis is based on the detection of viral ribonucleic acid (RNA) by real-time polymerase chain reaction (RT-PCR) of nasal and oropharyngeal swab samples; it is more effective when performed in the first days after symptom onset. Serological tests are useful in detecting the immune response, since both class M (IgM) and class G (IgG) immunoglobulin antibodies can be detected seven days after the onset of clinical symptoms, and may extend for more than 25 days, although not exempting the individual from remaining infectious, depending on their viral load and clinical presentation. The rational use of specific laboratory markers must respect the disease chronology, and the correct interpretation may provide subsidies for a better management of affected patients, as well as identifying asymptomatic carriers or those with mild symptoms.
Unitary Differential Space-Time-Frequency Codes for MB-OFDM UWB Wireless Communications

In a multiple-input multiple-output (MIMO), multiband orthogonal frequency division multiplexing (MB-OFDM) ultra-wideband (UWB) system, coherent detection requires the transmission of a large number of symbols for channel estimation, thus reducing the bandwidth efficiency. For the first time, this paper proposes unitary differential space-time-frequency codes (DSTFCs) for MB-OFDM UWB communications, which increase the system bandwidth efficiency because no channel state information (CSI) is required. The proposed system would be useful when CSI is unavailable at the receiver, such as when the transmission of multiple channel estimation symbols is impractical or uneconomical. The coding and decoding algorithms for the proposed DSTFCs are then derived for both constant envelope modulation scheme, such as PSK (phase shift keying) and 4QAM (quadrature amplitude modulation), and multi-dimensional modulation scheme, such as DCM (dual carrier modulation). The paper also quantifies for the first time the diversity order of a DSTFC MB-OFDM system. Simulation results show that the application of DSTFCs can significantly improve the bit error performance of conventional differential MB-OFDM system (without MIMO), and even provide much better bit error performance than the conventional coherent MB-OFDM system (without MIMO) at high signal-to-noise ratios.
The index of families of boundary value problems for Dirac operators

Nous prouvons un theoreme de l'indice pour des familles arbitraires de problemes aux limites associes aux operateurs de Dirac. L'indice en K-theorie est decrit a l'aide d'une «interaction» le long de la frontiere. On peut utiliser ce resultat pour prouver une formule de decomposition qui generalise le theoreme de [9]
Unstable Brake Orbits in Symmetric Hamiltonian Systems

In this thesis we investigate the existence and stability of periodic solutions of Hamiltonian systems with a discrete symmetry. The global existence of periodic motions can be proven using the classical techniques of the calculus of variations; our particular interest is in how the stability type of the solutions thus obtained can be determined analytically using solely the variational problem and the symmetries of the system – we make no use of numerical or perturbation techniques. Instead, we use a method introduced in [41] in the context of a special case of the three-body problem. Using techniques from symplectic geometry, and specifically the Maslov index for curves of Lagrangian subspaces along the minimizing trajectories, we verify conditions which preclude the existence of eigenvalues of the monodromy matrix on the unit circle. We study the applicability of this method in two specific cases. Firstly, we consider another special case from celestial mechanics: the hip-hop solutions of the 2N -body problem. This is a family of Z2-symmetric, periodic orbits which arise as collision-free minimizers of the Lagrangian action on a space of symmetric loops [14, 53]. Following a symplectic reduction, it is shown that the hip-hop solutions are brake orbits which are generically hyperbolic on the reduced energy-momentum surface. Secondly we consider a class of natural Hamiltonian systems of two degrees of freedom with a homogeneous potential function. The associated action functional is unbounded above and below on the function space of symmetric curves, but saddle points can be
Three studies on fragmentation and coalescent processes

We study fragmentation processes which are linked to coalescent processes. First, we investigate the Bolthausen-Sznitman coalescent, which, after a time-reversal, becomes a time inhomogeneous fragmentation process. We describe its instantaneous dislocation measure in term of Poisson-Dirichlet laws and we deduce asymptotics of the size of the blocks at large and small times. We also study some additive coalescents after a time-reversal seen as fragmentation processes. We prove that the laws of these processes are absolutely continuous with respect to each other and we give the density. Finally, we characterize the law of interval fragmentations proving a one to one correspondence with fragmentations of ordered partitions.
GRAZING BEHAVIOUR OF THREE BREEDS OF CATTLE AT THE LIVESTOCK FARM UNAAB

A project was undertaken to investigate the grazing of three breeds of cattle -Muturu (4) Ntdama (6), and White Fulani (17) housed in UNAAB farm at the permanent site, Alabata, Abeokuta and grazed within the University. Parameters types of forage taken and their classification, Preference to forage, feeding pattern grazing times, Frequences of picking forage species, individual breed and behaviour. The weight was determined by estimation. The investigation reavealed that the animals were grazed in the range at about 4 km, from the farm centre in the direction of North, South, West and East. Forages preferentially grazed included : Dactyloctenium, aegptiam, Andropogon gayanus, AndrQpo90n tectrum,Panicum maximum, Brachiaria deflexa, Tephrosia sp,Stylosanthes bumilis and Pennisetum pedicellatum. Cattle usually moved out Qf their ranch around9 a. m. in the morning while grazing continues till around 6.30a. m. when they will then went back to their ranch. While grazing, they usually drink water one to four times. When grazing, the cattle moves about chewing the grass or plant only two or three times whilst at the same time moving its head from oneside to the other seeking the next patch of herbage to feed on. nthis manner, Cattle grazed mostly during the hours of daylight and cover on average abQut 4 km per day. It was therefore, revealed that, Cattle grazed in the same pattern. The estimated weights of theses experimental animals were range between 145 kg to 200 kg for, Muturu, while N'dama weight 200 kg to 250 kgt and finally , white Fulani breed weighed between 250 to 300 kg. All the animals were in good health states throughout the duration of the experiment.