Determinants of aid allocations on UNDP 16 projects in countries with armed conflict or political instability

The United Nations (UN) is a multilateral organization that addresses issues that transcend national boundaries. The UN Membership approved in 2015 “The 2030 Agenda for Sustainable Development”, which is built on 17 Sustainable Development Goals (SDGs) that serve as the guidelines to all countries - developed and developing - in a global partnership towards achieving a better world (UN, 2022). The UN Development Program (UNDP) is one of the 15 UN agencies that focus on international development to achieve the SDGs. The thesis studies factors determining UNDP SDG 16 (Peace, Justice and Strong Institutions) aid allocations for projects in countries with armed conflict or political instability (UNDP, 2019b). The topic’s relevance lies in the UNDP`s mission statement: “to eradicate poverty and reduce inequality. We help countries to develop policies, leadership skills, partnering abilities, institutional capabilities, and to build resilience to achieve the Sustainable Development Goals.” Thus, the multilateral organization’s transparency and criteria affecting the decision-making process behind the allocation of project funds is an important topic to research. The objective is to determine the factors that affect aid allocations under SDG 16 related to projects in countries with armed conflict or political instability during 2016-20. The research targets aid allocations for projects for peaceful resolution in countries with armed conflict or political instability as a dependent variable relying on the indicators of the recipient country`s requirements based on GDP per capita, number of victims during the years of conflict, and democracy indexes, etc. A panel data set of 150 observations covering 2016-2020 on 30 recipient countries and ten donor countries was collected to build an econometric model (fixed-effects and random-effects models), together with partial qualitative analysis on the data-generating stage to define the factors affecting the UNDP project aid allocations to recipient countries under SDG 16. The key findings of the thesis suggest, as expected, that there is insufficient understanding of the decision-making process in the UNDP allocation system. According to findings, the poorer countries with the larger territory and smaller populations tend to be chosen to receive aid for SDG 16 projects from the UNDP. The results suggest that conflict-specific variables, such as civilian casualties and the size of the country affected by conflict or political instability are considered during the aid allocation decision-making process, which was to be expected based on the specifics of the projects analyzed. Moreover, there is evidence, through both qualitative and quantitative methods to suggest that US interest levels in the country in conflict (e.g., Afghanistan) have a major influence on aid allocation within UNDP SDG 16 projects. Nevertheless, there is no evidence in the data that suggest there is an influence of the amount of monetary contribution by the top 10 donor countries on the aid allocation process for SDG 16 projects.M-ECO

Repeated patterns of gamma-ray flares reveal structured jets of blazars as likely neutrino sources

Fermi-LAT observations provide continuous and regularly-sampled measurements of gamma-ray photon flux for hundreds of blazars. Many of these light curves, spanning almost 15 years, have been thoroughly examined for periodicity in multiple studies. However, the possibility that blazars may exhibit irregularly repeating flaring patterns in their gamma-ray light curves has not been systematically explored. In this study, we aim to find repeating episodes of flaring activity in the 100 brightest blazars using Fermi-LAT light curves with various integration times. We use a Bayesian Blocks representation to convert the time series into strings of symbols and search for repeating sub-strings using a fuzzy search algorithm. As a result, we identify 27 repeated episodes in the gamma-ray light curves of 10 blazars. We find that the patterns are most likely produced in structured jets composed of a fast spine and a slower sheath. When individual emission features propagate in the spine, they scatter seed photons produced in the non-uniform sheath through the inverse Compton mechanism, resulting in a set of gamma-ray flares with a similar profile every such passage. Additionally, we explore the theoretically-predicted possibility that the spine-sheath structure facilitates the production of high-energy neutrinos in blazar jets. Using the catalogue of track-like events detected by the IceCube neutrino telescope, we find evidence supporting this hypothesis at a $3.5\sigma$ significance level.Comment: Submitte

Polyploid Arabidopsis species originated around recent glaciation maxima

Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary history of plants, however they do not seem to be uniformly distributed along the time axis. For example, many of the detected ancient whole-genome duplications (WGDs) seem to cluster around the K/Pg boundary (similar to 66 Mya), which corresponds to a drastic climate change event and a mass extinction. Here, we discuss more recent polyploidy events using Arabidopsis as the most developed plant model at the level of the entire genus. We review the history of the origin of allotetraploid species A. suecica and A. kamchatica, and tetraploid lineages of A. lyrata, A. arenosa and A. thaliana, and discuss potential adaptive advantages. Also, we highlight an association between recent glacial maxima and estimated times of origins of polyploidy in Arabidopsis. Such association might further support a link between polyploidy and environmental challenge, which has been observed now for different time scales and for both ancient and recent polyploids

SNP Detection in Pinus pinaster Transcriptome and Association with Resistance to Pinewood Nematode

Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studiesinfo:eu-repo/semantics/publishedVersio

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals

Functional prediction of proteins from the human gut archaeome

AbstractThe human gastrointestinal tract contains diverse microbial communities, including archaea. Among them,Methanobrevibacter smithiirepresents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as IBD and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation ofM. smithiiproteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut andM. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer betweenClostridiaspecies andM. smithii, which includessporulation stage V proteins AEand AD. Our study broadens the understanding of archaeal biology, particularlyM. smithii,and highlights the importance of considering both sequence and structure for the prediction of protein function

Gradual evolution of allopolyploidy in Arabidopsis suecica.

Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution

SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode

Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies.SUPPLEMENTARY MATERIALS : Supplementary Figure S1. Type of SNPs identified in P. pinaster RNA-seq analysis; Supplementary Figure S2. Boxplots of the height and diameter at the base of the stem of inoculated plants (half-sib family 440) and t-test results for the comparison of these parameters’ means between susceptible and resistant plants; Supplementary Figure S3. Association analysis of the SNPs in the six sequenced gene fragments under different genetic models with resistance to PWN; Supplementary Figure S4. Genotypes distribution for SNPs associated with phenotype; Supplementary Table S1. Summary of PCR conditions and sequencing results of the 26 SNPs selected for validation; Supplementary Table S2. Summary of mapping statistic per sample and per sequencing lane; Supplementary Table S3. SNPs detected in P. pinaster RNA-seq data; Supplementary Table S4. Details and functional annotation of the SNPs with an Fst ≥ 0.80; Supplementary Table S5. Allele frequencies and Hardy–Weinberg Equilibrium significance values calculated by SNPassoc; Supplementary Table S6. Non-significant results of the haplotype association analysis obtained with SNPassoc. All analyses were performed using a logistics regression model.DATA AVAILABILITY STATEMENT : The sequencing data presented in this study are openly available in European Nucleotide Archive (ENA) at EMBL EBI under accession number PRJEB51636.This work was supported by Fundação para a Ciência e a Tecnologia, I.P. (FCT/MCTES), through Grants GREEN-it (UID/Multi/04551/2013), BioISI (UIDB/04046/2020 and UIDP/04046/2020) and the doctoral fellowship SFRH/BD/111687/2015 (to I.M.). Support was also provided by FCT/MCTES through national funds (PIDDAC) and co-financed by Fundo Europeu de Desenvolvimento Regional (FEDER) of the EU, through Programa Operacional Regional de Lisboa do Portugal 2020 or other programs that may succeed—PTDC/BAA-MOL/28379/2017, LISBOA-01-0145-FEDER-028379.https://www.mdpi.com/journal/forestsBiochemistryGeneticsMicrobiology and Plant Patholog

The kinetics of L10 superstructure formation in the Cu–56Au alloy (at. %): resistometric study

Due to the improved strength properties compared to the equiatomic Cu–50 at. % Au alloy, non-stoichiometric Cu–56 at. % Au alloy can be used both in dentistry and as a corrosion-resistant conductor of weak electrical signals in tool engineering. The work studies the kinetics of the disorder→order phase transformation in the Cu–56Au alloy, during which the disordered fcc lattice (A1-phase) is rearranged into an atomically ordered one with the L10 superstructure. The initial disordered state of the alloy was obtained in two ways: applying plastic deformation by 90 % or quenching at a temperature of above 600 °C (i. e., from the region of the A1-phase existence). To form the L10 superstructure, annealing was carried out at temperatures of 200, 225, and 250 °C. The annealing duration ranged from 1 h to 2 months. Resistometry was chosen as the main technique to study the kinetics of the disorder→order transformation. The temperature dependences of the electrical resistivity of the alloy in various structural states are obtained. The authors constructed the graphs of the electrical resistance dependence on the annealing time logarithm, based on which, the rate of the new phase formation was estimated. To evaluate the structural state of the alloy at various transformation stages, the authors used X-ray diffraction analysis (XRD). The crystal structure rearrangement during the transformation is shown by the example of splitting the initial cubic A1-phase peak (200) into two tetragonal ordered L10 phase peaks – (200) and (002). Based on the resistometry and X-ray diffraction analysis data, the authors carried out a quantitative assessment of the rate of the disorder→order phase transformation in the alloy under the study. It is established that the values of the converted volume fraction (resistometry) and the long-range order degree (X-ray diffraction analysis) are close. The study shows that in the temperature range of 200–250 °C, the rate of atomic ordering according to the L10 type in the nonstoichiometric alloy Cu–56 at. % Au is maximum at 250 °C. It is identified that the disorder→order transformation in the initially quenched specimens of the investigated alloy proceeds approximately an order of magnitude faster than in preliminarily deformed specimens

The gut microbiome molecular complex in human health and disease

The human gut microbiome produces a functional complex of biomolecules, including nucleic acids, (poly) peptides, structural molecules, and metabolites. This impacts human physiology in multiple ways, especially by triggering inflammatory pathways in disease. At present, much remains to be learned about the identity of key effectors and their causal roles