Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-Resource Unsupervised NMT: Diagnosing the Problem and Providing a Linguistically Motivated Solution

Unsupervised Machine Translation has been advancing our ability to translate without parallel data, but state-of-the-art methods assume an abundance of monolingual data. This paper investigates the scenario where monolingual data is limited as well, finding that current unsupervised methods suffer in performance under this stricter setting. We find that the performance loss originates from the poor quality of the pretrained monolingual embeddings, and we offer a potential solution: dependency-based word embeddings. These embeddings result in a complementary word representation which offers a boost in performance of around 1.5 BLEU points compared to standard word2vec when monolingual data is limited to 1 million sentences per language. We also find that the inclusion of sub-word information is crucial to improving the quality of the embeddings.
Domain Informed Neural Machine Translation: Developing Translation Services for Healthcare Enterprise

Neural Machine Translation (NMT) is a deep learning based approach that has achieved outstanding results lately in the translation community. The performance of NMT systems, however, is dependent on the availability of large amounts of in-domain parallel corpora. The business enterprises in domains such as legal and healthcare require specialized vocabulary but translation systems trained for a general purpose do not cater to these needs. The data in these domains is either hard to acquire or is very small in comparison to public data sets. This is a detailed report of using an open-source library to implement a machine translation system and successfully customizing it for the needs of a particular client in the healthcare domain. This report details the chronological development of every component of this system, namely, extraction of data from in-domain healthcare documents, a pre-processing pipeline for the data, data alignment and augmentation, training and a fully automated and robust deployment pipeline. This work proposes an efficient way for the continuous deployment of newly trained deep learning models. The deployed translation models are optimized for both inference time and cost.
Extraction of betacyanin from red beet root (Beta vulgaris L.) and to evaluate its antioxidant potential.

Red Beet root is a rich source of betacyanin. These are nitrogen containing compounds widely used as non toxic food colorants. The deep red color of beets is due to the presence of betalain pigments. There are two categories of betalains: the purple betacyanins and yellow betaxanthines pigments (Salisbury et al.,1991), functionally replace anthocyanins in 13 taxons grouped in Caryophyllales order. The major advantages of betalains as dietary antioxidants are their bioavailability, which is greater than most flavanoids, and their superior stability in comparison to anthocyanin. Although they are used as food colourants, remain understudied in terms of their antioxidant potential. So the present study was attempted to extract and to evaluate the content of betalain and its antioxidant potential by enzymatic and non enzymatic method from red beet root. This study has revealed that some of the antioxidant enzymes that are found to provide a protection against the reactive oxygen species are superoxide dismutase, catalase, peroxidase, glucose-6-phosphate dehydrogenase and ascorbate oxidase were found to be higher. The non-enzymatic method was done by quantification of vitamin C, and DPPH method. From HPTLC analysis, it was confirmed the presence of two flavanoid compounds. So the above study reveals that, the high antioxidant potential may be due to presence of these two flavanoid compounds. Because of its high antioxidant potential, the production of beet root pigments has to be performed using cell suspensions and transformed roots in bioreactors.
A Trajectory-Unified Method for Constructing the Feasible Region of OPF Problems

Abstract The feasible region plays an important role in optimal power flow (OPF) problems. However, constructing the feasible region of general optimal power flow problems is a challenging task. In this paper, a trajectory-unified (TJU) method is developed to compute the feasible region of general large-scale OPF problems. This is the first attempt, to our knowledge, to develop a numerical method to compute feasible regions of OPF problems. In addition, the projection of the computed feasible region into a desired low-dimensional sub-space is presented. By employing the proposed TJU method, we compute the feasible region of a 9-bus and the IEEE 118-bus OPF problem. It is shown that the feasible region of a power system grows in size from light-loading conditions to medium-loading conditions while it shrinks in size from medium-loading conditions to heavy-loading conditions. This discovery of a geometric property of the feasible solution asserts the observations that OPF problems are generally easy to solve during medium-loading conditions but are generally difficult to solve during heavy-loading conditions.
Patients’ experiences and satisfaction with home treatment for acute mental illness: a mixed-methods retrospective study

Abstract Background Home treatment (HT) has been proposed as a patient-centred alternative to acute mental inpatient care although evidence of patient-reported outcomes has remained limited. Aims The aim of this study was to examine patient experiences and satisfaction with HT. Methods This retrospective mixed-methods study included telephone interviews of 159 patients receiving HT between 2016 and 2019. Associations between patients’ characteristics and global satisfaction (ZUF-8 scale) were assessed. Differences between HT patients and inpatients were tested on a propensity score -matched inpatient sample. Qualitative analyses were conducted using thematic analysis. Results Global satisfaction with HT was slightly higher than in the inpatient sample (p = 0.019). There was no relationship between satisfaction and patients’ characteristics, such as gender, age, main psychiatric diagnosis, and treatment duration, but satisfaction was higher for patients who perceived HT as their only treatment option. Participants particularly appreciated the person-centred care and practical support whereas staff continuity and medical treatment were main sources of dissatisfaction. Conclusion The results indicate that HT seems to be a more patient-centred alternative to inpatient treatment and might close a gap in the psychiatric care of patients who preferred not to use inpatient services but needed higher treatment intensity than outpatient treatment.
Psychometric properties of the Turkish version of Participation and Environment Measure for Children and Youth.

BACKGROUND Participation in daily activities provides many opportunities for children with and without disabilities to improve cognitive, physical, and communication abilities, to develop social relationships, and to promote adaptive behaviors. To examine the psychometric properties of the Participation Environment Measure for Children and Youth (PEM-CY) in Turkish children and youth with and without a disability. METHODS A total of 410 parents of children with (n = 232) and without (n = 178) disabilities, aged 5-17 years, were included in this study. Cronbach's alpha (α) and intraclass correlation coefficients (ICCs) were evaluated for internal consistency and test-retest reliability, respectively. Discriminant validity was determined by comparing the differences in participation and environment scores for disability groups and age intervals with the two-way analysis of variance (ANOVA) followed by post-hoc analyses when results were statistically significant. RESULTS Internal consistency (0.67-0.80) and test-retest reliability (0.67-0.93, p<0.0001) ranged from moderate to very strong for different summary scores. Discriminant validity of the Turkish version of PEM-CY was supported by significant differences between children with and without disabilities on participation and environment scales (p < 0.05). We identified some significant age differences, but they did not follow consistently. CONCLUSIONS The Turkish version of the PEM-CY is a valid and reliable tool to determine the participation and environmental factors in the home, at school, and in community settings in Turkish children and youth aged 5-17 years, with and without disabilities.
Loss of the cbd-1 gene causes intracellular trafficking defects in C. elegans

ii ACKNOWLEDGEMENTS iv LIST OF FIGURES vi LIST OF TABLES vii Chapter 1: Introduction 1 1. Modern Advances in Reproductive Biology 1 2. Fertilization in Mammals and Non-Mammals 6 3. C. elegans as a model organism to study fertilization in vivo 8 3.1 Ovulation, fertilization, and egg activation 10 3.2 Intracellular Trafficking and Endocytosis in Oocytes 13 4. Functional genomic analyses in C. elegans 14 Chapter 2: Materials and Methods 22 1. C. elegans strains 22 2. RNAi methods 22 3. DAPI staining 22 4. Live imaging and analysis 22 Chapter 3: Phenotypic analysis of cbd-1 depletion via RNAi 24 1. Background 24 2. RNAi depletion of cbd-1 24 Chapter 4: Discussion 40 1. cbd-1 controls intracellular trafficking events important to 40 oocyte development and egg activation 2. Perspectives and future directions 41
Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline‐rich tyrosine kinase 2‐beta: Insights from molecular dynamics simulations

The focal adhesion kinase (FAK) and the proline‐rich tyrosine kinase 2‐beta (PYK2) are implicated in cancer progression and metastasis and represent promising biomarkers and targets for cancer therapy. FAK and PYK2 are recruited to focal adhesions (FAs) via interactions between their FA targeting (FAT) domains and conserved segments (LD motifs) on the proteins Paxillin, Leupaxin, and Hic‐5. A promising new approach for the inhibition of FAK and PYK2 targets interactions of the FAK domains with proteins that promote localization at FAs. Advances toward this goal include the development of surface plasmon resonance, heteronuclear single quantum coherence nuclear magnetic resonance (HSQC‐NMR) and fluorescence polarization assays for the identification of fragments or compounds interfering with the FAK‐Paxillin interaction. We have recently validated this strategy, showing that Paxillin mimicking polypeptides with 2 to 3 LD motifs displace FAK from FAs and block kinase‐dependent and independent functions of FAK, including downstream integrin signaling and FA localization of the protein p130Cas. In the present work we study by all‐atom molecular dynamics simulations the recognition of peptides with the Paxillin and Leupaxin LD motifs by the FAK‐FAT and PYK2‐FAT domains. Our simulations and free‐energy analysis interpret experimental data on binding of Paxillin and Leupaxin LD motifs at FAK‐FAT and PYK2‐FAT binding sites, and assess the roles of consensus LD regions and flanking residues. Our results can assist in the design of effective inhibitory peptides of the FAK‐FAT: Paxillin and PYK2‐FAT:Leupaxin complexes and the construction of pharmacophore models for the discovery of potential small‐molecule inhibitors of the FAK‐FAT and PYK2‐FAT focal adhesion based functions.
Cell Wall Nonlinear Elasticity and Growth Dynamics: How Do Bacterial Cells Regulate Pressure and Growth?

In my thesis, I study intact and bulging Escherichia coli cells using atomic force microscopy to separate the contributions of the cell wall and turgor pressure to the overall cell stiffness. I find strong evidence of power–law stress–stiffening in the E. coli cell wall, with an exponent of 1.22 ± 0.12, such that the wall is significantly stiffer in intact cells (E = 23 ± 8 MPa and 49 ± 20 MPa in the axial and circumferential directions) than in unpressurized sacculi. These measurements also indicate that the turgor pressure in living cells E. coli is 29± 3 kPa. The nonlinearity in cell elasticity serves as a plausible mechanism to balance the mechanical protection and tension measurement sensitivity of the cell envelope. I also study the growth dynamics of the Bacillus subtilis cell wall to help understand the mechanism of the spatiotemporal order of inserting new cell wall material. High density fluorescent markers are used to label the entire cell surface to capture the morphological changes of the cell surface at sub-cellular to diffraction-limited spatial resolution and sub-minute temporal resolution. This approach reveals that rod-shaped chaining B. subtilis cells grow and twist in a highly heterogeneous fashion both spatially and temporally. Regions of high growth and twisting activity have a typical length scale of 5 μm, and last for 10-40 minutes. Motivated by the quantification of the cell wall growth dynamics, two microscopy and image analysis techniques are developed and applied to broader applications beyond resolving bacterial growth. To resolve densely distributed quantum dots, we present a fast and efficient image analysis algorithm, namely Spatial Covariance Reconstruction (SCORE) microscopy that takes into account the blinking statistics of the fluorescence emitters. We achieve sub-diffraction lateral resolution of 100 nm from 5 to 7 seconds of imaging, which is at least an order of magnitude faster than singleparticle localization based methods such as STORM and PALM. SCORE is insensitive to background and can be applied to different types of fluorescence sources, including iii but not limited to organic dye and quantum dot that are tested experimentally in this thesis. The second development is an extension from tracking single quantum dot to the more general cases of moving objects at high density based on active contour model. I add a repulsive interaction between open contours to the original model and treat the trajectories as extrusions in the temporal dimension. This technique is applicable to a broad range of problems and two specific tracking problems are chosen as illustrations: (i) the quantification of walking and chasing behaviors of Drosophila and (ii) the study of trajectories of gliding bacteria Myxococcus xanthus on flat surface. I demonstrate the capability of this high-through and highly automated analysis method for studying social and group behaviors in interacting organisms.
HIV stigma in UK press reporting of a case of intentional HIV transmission

The UK has set itself the ambitious target of zero new HIV transmissions by 2030. HIV stigma is a significant barrier to achieving this target. Media reporting plays an important role in shaping social representations of HIV and of stigma. Between 2016 and 2018, the media in the UK reported on the Daryll Rowe case – the first criminal prosecution for intentional transmission of HIV in the UK. This article examines the way that UK newspapers reported this case, which may have exacerbated HIV stigma. Using Nexis, 178 UK newspaper articles were extracted and subjected to qualitative thematic analysis through a social constructionist lens. Informed by social representations theory, the analysis yielded three discursive themes: (1) Representing the perpetrator through HIV-focussed metaphors; (2) Constructing volitional ambiguity; and (3) Anchoring the lived experience of HIV to misery and death. UK newspapers constructed an ‘evil vs victimhood’ dichotomy in relation to Rowe and the men infected with HIV, respectively. This article argues that news coverage of the Rowe story constructs HIV in ways that are inconsistent with public health messaging. Reporting failed to note innovations in HIV treatment and prevention but instead disseminated stigmatising social representations of HIV. This is important because stigma impedes effective HIV prevention, engagement with HIV care and ultimately our ability to achieve the zero-infections target.
A long view of cumulative technological culture

Abstract We agree that the emergence of cumulative technological culture was tied to nonsocial cognitive skills, namely, technical-reasoning skills, which allowed humans to constantly acquire and improve information. Our concern is with a reading of the history of cumulative technological culture that is based largely on modern experiments in simulated settings and less on phenomena crucial to the long-term dynamics of cultural evolution.
Global variations in the prevalence, treatment, and impact of atrial fibrillation in a multi-national cohort of 153,152 middle-aged individuals.

AIMS To compare the prevalence of electrocardiogram (ECG)-documented atrial fibrillation (or flutter) (AF) across eight regions of the world, and to examine anti-thrombotic use and clinical outcomes. METHODS AND RESULTS Baseline ECGs were collected in 153,152 middle-aged participants (ages 35 to 70 years) to document AF in two community-based studies, spanning 20 countries. Medication use and clinical outcome data (mean follow up of 7.4 years) were available in one cohort. Cross sectional analyses were performed to document the prevalence of AF and medication use, and associations between AF and clinical events were examined prospectively. Mean age of participants was 52.1 years, and 57.7% were female. Age and sex-standardized prevalence of AF varied 12-fold between regions; with the highest in North America, Europe, China and Southeast Asia (270-360 cases per 100,000 persons); and lowest in the Middle East, Africa, and South Asia (30-60 cases per 100,000 persons)(p < 0.001). Compared with low-income countries (LICs), AF prevalence was 7-fold higher in middle-income countries (MICs) and 11-fold higher in high-income countries (HICs)(p < 0.001). Differences in AF prevalence remained significant after adjusting for traditional AF risk factors. In LICs/MICs, 24% of participants with AF and a CHADS2 score ≥1 received anti-thrombotic therapy, compared with 85% in HICs. AF was associated with an increased risk of stroke (hazard ratio [HR: 2.29; 95% confidence interval [CI] 1.49-3.52) and death (HR: 2.97; 95% CI 2.25-3.93); with similar rates in different country income levels. CONCLUSIONS Large variations in AF prevalence occur in different regions and country income settings, but this is only partially explained by traditional AF risk factors. Anti-thrombotic therapy is infrequently used in poorer countries despite the high risk of stroke associated with AF. TRANSLATIONAL PERSPECTIVE We examined atrial fibrillation (AF) prevalence in 153,152 middle-aged participants spanning 20 countries. Age and sex-standardized prevalence of AF varied by as much as 12-fold between regions; highest in North America, Europe, China and Southeast Asia (270-360 cases per 100,000 persons); and lowest in the Middle East, Africa, and South Asia (30-60 cases per 100,000 persons)(p < 0.001); and by as much as 11-fold between groups of countries at different income levels (p < 0.001). Global variations were poorly explained by traditional AF risk factors. Future studies are needed to understand the predominant determinants driving the variation in AF burden across different regions of the world.
Epigenetic loss of the transfer RNA-modifying enzyme TYW2 induces ribosome frameshifts in colon cancer

Significance Defects in transfer RNA (tRNA) modifications occur in human pathologies such as cancer; however, how these alterations contribute to the disease is poorly understood. One example is the tumor-specific hypomodification of position 37 of tRNAPhe, which was first described 45 y ago, although its cause and consequences have remained unknown. Here we report that the tRNAPhe hypomodification is due to promoter CpG island hypermethylation-associated transcriptional silencing of TYW2, a key enzyme in the synthesis of wybutosine derivatives. Furthermore, epigenetic loss of TYW2 in transformed cells provokes hypomodified tRNAPhe-mediated ribosome frameshifting, dysregulating mRNA abundance via nonsense-mediated decay. Importantly, TYW2 silencing in cancer cells confers enhanced migration and epithelial-to-mesenchymal features that are associated in early-stage colorectal cancer patients with poor clinical outcome. Transfer RNA (tRNA) activity is tightly regulated to provide a physiological protein translation, and tRNA chemical modifications control its function in a complex with ribosomes and messenger RNAs (mRNAs). In this regard, the correct hypermodification of position G37 of phenylalanine-tRNA, adjacent to the anticodon, is critical to prevent ribosome frameshifting events. Here we report that the tRNA-yW Synthesizing Protein 2 (TYW2) undergoes promoter hypermethylation-associated transcriptional silencing in human cancer, particularly in colorectal tumors. The epigenetic loss of TYW2 induces guanosine hypomodification in phenylalanine-tRNA, an increase in −1 ribosome frameshift events, and down-regulation of transcripts by mRNA decay, such as of the key cancer gene ROBO1. Importantly, TYW2 epigenetic inactivation is linked to poor overall survival in patients with early-stage colorectal cancer, a finding that could be related to the observed acquisition of enhanced migration properties and epithelial-to-mesenchymal features in the colon cancer cells that harbor TYW2 DNA methylation-associated loss. These findings provide an illustrative example of how epigenetic changes can modify the epitranscriptome and further support a role for tRNA modifications in cancer biology.
Distribution of the variant at AKIRIN2: c.*188G > A in Chinese cattle

Abstract Marbling score (MS), is an economically important trait in cattle. Previous results showed that a SNP (c.*188G > A) of akirin 2 (AKIRIN2) gene was associated with MS in Japanese Black cattle and Korean cattle. However, the distribution of the genotypic frequency of the single nucleotide polymorphism (SNP) has not been explored in Chinese cattle. In this study, we used polymerase chain reaction (PCR) and DNA sequencing to detect the variation in 1296 individuals from 39 Chinese cattle breeds, one semi-wild bovine species (Dulong) and three introduced breeds (Angus, Holstein and Brahman). Our study found the frequency of the A allele at this locus roughly diminished from north to south in Chinese cattle, and we detected statistically significant differences between Angus and Brahman (p < 0.05), Dulong and another two breeds (Angus and Holstein; p < 0.01) using Chi-Square Independence Test. Our results reflected the variation of AKIRIN2: c. *188G > A in Chinese cattle, which would help us better understand Chinese cattle genetic resources and provide reference for further research.