Analysis of Y-chromosome and mtDNA variability in the Madeira Archipelago population

The Atlantic archipelago of Madeira is made up of two islands (Madeira and Porto Santo) with 250,000 inhabitants. These islands were discovered and settled by the Portuguese in the 15th century and played an important role in the complex Atlantic trade network in the following centuries. The genetic composition of the Madeira Islands’ population was investigated by analyzing Y-chromosomal bi-allelic and STR markers in three different regions of the main island plus Porto Santo. We compared the results with mtDNA data and used the Y-chromosome STRs to determine the variability within each haplogroup. A sample of 142 unrelated males divided into four groups (Funchal City, West Madeira, North and East Madeira and Porto Santo) were analyzed. Significant genetic differences between these regions and the population of Funchal were found. The population of Funchal had lower gene diversity than expected.info:eu-repo/semantics/publishedVersio

Aligning Neural Machine Translation Models: Human Feedback in Training and Inference

Reinforcement learning from human feedback (RLHF) is a recent technique to improve the quality of the text generated by a language model, making it closer to what humans would generate. A core ingredient in RLHF's success in aligning and improving large language models (LLMs) is its reward model, trained using human feedback on model outputs. In machine translation (MT), where metrics trained from human annotations can readily be used as reward models, recent methods using minimum Bayes risk decoding and reranking have succeeded in improving the final quality of translation. In this study, we comprehensively explore and compare techniques for integrating quality metrics as reward models into the MT pipeline. This includes using the reward model for data filtering, during the training phase through RL, and at inference time by employing reranking techniques, and we assess the effects of combining these in a unified approach. Our experimental results, conducted across multiple translation tasks, underscore the crucial role of effective data filtering, based on estimated quality, in harnessing the full potential of RL in enhancing MT quality. Furthermore, our findings demonstrate the effectiveness of combining RL training with reranking techniques, showcasing substantial improvements in translation quality.Comment: 14 pages, work-in-progres

Distribution of polymorphisms IL4 -590 C/T and IL4 RP2 in the human populations of Madeira, Azores, Portugal, Cape

Abstract: The IL4 gene is located on chromosome 5q23.3-31.2. Polymorphisms within this cytokine gene, like the derivative allele T of IL4-590, have been reported as being associated to elevated IgE serum levels and asthma. In the present work, the allelic and genotypic frequency of the IL4-590 and IL4 RP2 polymorphisms was carried out in 599 individuals from Madeira, Azores, Portugal mainland, Cape Verde and Guinea-Bissau and in a sample of 101 asthmatics from Madeira population. In all populations the polymorphisms were in LD and presented a significant dissimilar allelic and genotypic distribution (p<0.05) except between mainland Portugal and Madeira when compared to Azores. Significant differences regarding both loci were found between Madeira population and the group of asthmatics. Genotype 183183TT frequency is higher for African populations while 253253CC prevails in Caucasian populations. The existence of a Hardy-Weinberg Disequilibrium in Guinea-Bissau population not observed in neutral markers leads to the hypothesis of natural selection occurring in these loci probably associated to a rapid population growth an hypothesis strengthened by neutral STRs D5S818 and CSF1PO gene diversity.info:eu-repo/semantics/publishedVersio

Y-chromosome lineages from Portugal, Madeira and Açores record rlements of sephardim and berber ancestry

A total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Ac¸ores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78–83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese subpopulations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.info:eu-repo/semantics/publishedVersio

Bridging the Gap: A Survey on Integrating (Human) Feedback for Natural Language Generation

Many recent advances in natural language generation have been fueled by training large language models on internet-scale data. However, this paradigm can lead to models that generate toxic, inaccurate, and unhelpful content, and automatic evaluation metrics often fail to identify these behaviors. As models become more capable, human feedback is an invaluable signal for evaluating and improving models. This survey aims to provide an overview of the recent research that has leveraged human feedback to improve natural language generation. First, we introduce an encompassing formalization of feedback, and identify and organize existing research into a taxonomy following this formalization. Next, we discuss how feedback can be described by its format and objective, and cover the two approaches proposed to use feedback (either for training or decoding): directly using the feedback or training feedback models. We also discuss existing datasets for human-feedback data collection, and concerns surrounding feedback collection. Finally, we provide an overview of the nascent field of AI feedback, which exploits large language models to make judgments based on a set of principles and minimize the need for human intervention.Comment: Work in Progres

Mitochondrial DNA studies of Lisbon immigrants from Portuguese speaking African countries

Since the end of the 1970s, Portugal has had an important role in migratory movements, becoming a destination for immigrants of a wide range of nationalities, mainly from African countries. According to PORDATA, until the end of 2014 there were 40,000 immigrants from Cape Verde, 20,000 from Angola, 18,000 from Guinea-Bissau, and 3,000 from Mozambique living in Portugal, and of those, >80 per cent live in the Lisbon region. This may be one of the main contributors to genetic variation of Lisbon residents in the present and the future. Mitochondrial DNA (mtDNA) has features that make it desirable for forensics, namely, high copy number, lack of recombination, and matrilineal inheritance. These features are also important in evolutionary and population studies. We aim to characterize mtDNA diversity in immigrants from Portuguese Speaking African Countries (PALOP) living in Lisbon and their potential contribution to genetic variation of Lisbon population. Blood samples were collected from 439 PALOP immigrants living in Lisbon, of which 173 immigrants from Angola, 103 immigrants from Cape Verde, eighty-three immigrants from Mozambique and eighty immigrants from Guinea-Bissau, from January 2000 to December 2016. The control region of the mtDNA was amplified using two pairs of primers—L15971/H016 and L16555/H639, and sequenced by BigDye Terminator v.3.1 Cycle Sequence (AB). Sequenced products were detected in a sequencer Genetic Analyzer 3130 (AB). Finally the results were analysed by Sequencing Analysis v.5.2 software and also compared with Revised Cambridge Reference Sequence (rCRS) using SeqScape v.3 (AB) software. The haplogroups were determined based on Phylotree, build 17. Genetic distances and other genetic parameters were calculated with Arlequin software ver.3.5 and analysed and represented with PhyML 3.0. For each sample, the complete sequence of the control region was obtained. The comparison of the sequences obtained with the rCRS, among the 439 analysed individuals, allowed the identification of 319 different haplotypes, corresponding to 164 different haplogroups distributed by ten macrohaplogroups. Macrohaplogroup L was the most common with 386 haplotypes followed by U with fifteen haplotypes, H with twelve haplotypes, M and T with six haplotypes, K with five, R with four, X and J with two and HV with one. PALOP’s immigrants presented a high number of unique haplotypes, most of them belonging to macrohaplogroup L, originating from sub-Saharan regions of Africa.This macrohaplogroup is uncommon in European and Portuguese populations. Consistent with this, phylogenetic analysis showed the establishment of two distinct groups, one composed of the Portuguese population and another of the African populations. In comparing the different immigrant populations living in Lisbon, the genetically closest community to the Portuguese population is Mozambique and the furthest is Cape Verde, followed by Guinea-Bissau and Angola. Our results show that the PALOP immigrants living in Lisbon are genetically heterogeneous. The increase in genetic diversity in Lisbon due to immigrants from PALOP countries may have a major impact on haplotypic and allelic frequencies, on which all forensic and medico-legal investigations are based