dataesr/scientific-paragraphs-categorization huggingface dataset:
Results Genome assembly and population sequencing. Based on synteny with the razorbill (Alca torda), a total of 13,328 puffin scaffolds were placed into 26 pseudo-chromosomes, leaving 17. 06 Mbp (1. 4%) unplaced and yielding an assembly of 1. 294 Gbp (Supplementary Data 1, Table  S1 ). This assembly contains 4,522 of the 4,915 genes (92. 0%) of complete protein-coding sequences from the avian set of the OrthoDB v9 database (Supplementary Data 1). We also assembled the puffin mitogenome (length of 17,084 bp) with a similar arrangement of genomic elements as other members within the Alcidae  39, 40  (Fig. S1 , Table  S2 ). For the 72 resequenced specimens, we analyzed a total of 5. 77 billion paired reads, obtaining an average fold-coverage of 7X (range 3. 0-10) for the nuclear genome and 591X (5.
3-1800) for the mitochondrial genome per specimen (Fig. 1a , Supplementary Data 2). One individual (IOM001) was removed from both datasets (nuclear and mitochondrial) due to a substantially lower number of mapped reads (endogeny) relative to all other samples (Supplementary Data 2) resulting in a large proportion of missing sites (Fig. S2 ). Additional filtering produced a final genotype likelihood dataset of 1,093,765 polymorphic nuclear sites and 192 mitochondrial single-nucleotide polymorphisms (SNPs, Supplementary Data 3) in 71 birds (36 males and 35 females). Genomic population structure. Genomic variation across 71 puffin mitogenomes defines 66 polymorphic haplotypes that indicate a recent global population expansion and show no significant population structure (Fig. 1b , Figs. S3, S4, Tables  S3, S4 ).
In contrast, we inferred four main population clusters using principal component analysis (PCA) of the nuclear wholegenome dataset (Fig. 1c ). Puffins from Spitsbergen are most distinct, while puffins from Bjørnøya are located between Spitsbergen and a larger, central cluster consisting of populations from Norway, Iceland, and the Faroe Islands (Fig. 1c , Fig. S5a ). Puffins from Canada form their own distinct cluster, as do those from the Isle of May, southeast Scotland (Fig. 1c , Fig. S5b ). Hierarchical PCA analyses of the cluster comprising the mainland Norwegian, Icelandic and Faroese colonies reveal further fine-scale structure separating Norwegian (Hornøya and Røst) and Faroese/Icelandic colonies (Fig. S5c ). Model-based clustering (ngsAdmix) agrees with the results from the PCA (Fig.
1d ). The optimal model fit for the entire dataset is either K = 2 or K = 4 (Fig. S6a ), as determined by the method of Evanno et al. 41. At K = 2, ngsAdmix separates Spitsbergen from the other colonies, with Bjørnøya being admixed (following separation along PCA 1), whereas at K = 4, ngsAdmix reflects the structure of three additional distinct clusters representing Spitsbergen, Canada, the Isle of May, and a central group with more shared ancestry (Fig. 1d ). The shared ancestry of the central group remains present in hierarchical admixture analyses excluding Spitsbergen and Bjørnøya individuals (Figs. S6b, S7 ). We find no fixed alleles and pairwise F ST values between colonies and genomic clusters are low (<0. 01) (Table  S4 ), apart from any comparisons involving the Spitsbergen population, which show substantially higher F ST values (0.
High Arctic puffins from Spitsbergen are genetically the most divergent group within our dataset harboring the highest genomewide differentiation. They are also characterized by significantly lower levels of genetic diversity, greater inbreeding coefficients, and longer and more abundant RoHs compared to other colonies. These observations may either result from a historical bottleneck followed by isolation (e. g. , founder effect), local adaptation to their extreme environment, or generally lower effective population sizes. Population abundance estimates of <10,000 breeding pairs on Spitsbergen compared to 500,000 in the West Atlantic, two million on Iceland and more than two million in the boreal East Atlantic potentially indicate a lower effective population size  28. The High Arctic puffins exclusively inhabit harsh, cold-current environments year-round, as they likely stay in an area bounded by the East Greenland ice edge, a latitudinal border at 70°N, and the front between the Barents and Greenland Sea during winter (Fig.
Methods Ethical statement. Feather and blood samples of puffins included in this study were collected and handled under the following permits. were legally hunted during the hunting period of 1 July-15 August. 5. Faroe-Feathers came from predated birds collected in the field after the predator was finished with them. Draft reference genome assembly. A de novo Atlantic puffin draft genome was generated from the blood of a female Atlantic puffin. Read data were sequenced on three Illumina HiSeqX lanes using the 10x Genomics Chromium technology and assembled with the Supernova assembler (v2. 1. 1)  62 after subsampling to 0. 8 billion and 1 billion reads to maximize performance and remain within the computational capacity of the assembler. We refined the two assemblies through several steps, including merging of 'haplotigs', removal of contaminant sequences, misassembly correction, re-scaffolding using mapping coverage and linkage information, and gap filling (Supplementary Data 1a).
The most complete and continuous 800 M and 1000 M assemblies together with the 3rd best assembly overall were selected for a second round of refinement (Supplementary Data 1b) resulting in a total of 72 draft assemblies. Of these, we kept the four most complete and continuous assemblies for additional gap filling and polishing, after which the most complete draft genome was selected for downstream analyses (Supplementary Data 1c). The puffin mitogenome was confidently identified by blasting (blastn) all scaffolds shorter than 25 kb against a custom-built database of 135 published mitogenomes of the order 'Charadriiformes' and annotated with the MITOS web server  63  (Fig. S1 ). The remaining nuclear scaffolds were ordered and concatenated into "pseudo-chromosomes" by mapping them to the razorbill genome (Alca torda-NCBI: bAlcTor1 primary, GCA_008658365.
1) and applying 200 N's as padding between each scaffold. We combined unmapped scaffolds into an "unplaced" pseudo-chromosome. We assessed the order and placement of scaffolds by investigating synteny in coverage and length between the puffin and razorbill chromosomes (Table  S1 ). Details on the draft reference genome assembly and refinement can be found in the Supplementary File. DNA extraction and sequencing. Samples from a total of 72 puffins collected across 12 breeding colonies (Fig. 1a ) were made available for the present study by SEAPOP (http://www. seapop. no/en), SEATRACK (http://www. seapop. no/en/ seatrack) and ARCTOX (http://www. arctox. cnrs. fr/en/home-Canadian colonies). These samples had been collected between 2012 and 2018 and consisted of blood preserved in EtOH or lysis buffer, or feathers (Supplementary Data 2).
We extracted DNA using the DNeasy Blood & Tissue kit (Qiagen) following the manufacturer's protocol for animal blood or the nail/hair/feathers protocol applying several modifications for improved lysis and DNA yield. Individuals that had no sexing data associated with them were sexed using PCR amplification of specific allosome loci and visualization via gel electrophoresis. Genomic libraries were built by the Norwegian Sequencing Centre and sequenced on an Illumina HiSeq4000. We processed sequencing reads in PALEOMIX v1. 2. 14  64  and split the resulting bam files into nuclear and mitochondrial bam files. Additional details on the DNA extraction, sexing, sequencing and mapping are listed in the Supplementary File. Mitogenome analyses. Genotypes across the mitochondrial genome were jointly called with GATK v4.
1. 4  65 by using the HaplotypeCaller, CombineGVCFs, and GenotypeGVCFs tool. We filtered genotypes according to GATKs Best Practices  66  and set genotypes with a read depth <3 or a quality <15 as missing. Indels and nonbiallelic SNPs were removed and only SNPs present in all individuals were kept for subsequent analyses. The SNP dataset was annotated (Supplementary Data 3) with snpEff  67  utilizing the annotation of the newly assembled mitogenome of the Atlantic puffin and converted into a mitogenome sequence alignment. To serve as an outgroup, we appended four other species of the family Alcidae, i. e. , the Razorbill (Alca torda, NCBI: CM018102. 1), the Crested Auklet (Aethia cristatella, NCBI: NC_045517. 1), the Ancient Murrelet (Synthliboramphus antiquus, NCBI: NC_007978. 1) and the Japanese Murrelet (Synthliboramphus wumizusume, NCBI: NC_029328.
In addition, an Ewens-Watterson test 73 , Chakraborty's test of population amalgamation  74  , and Fu's F s test  75  were conducted for each of those groups. To further identify population differentiation, the proportion of sequence variation (Φ ST ) was estimated for all pairs of populations and genomic clusters. Hierarchical AMOVA tests subsequently determined the significance of a priori subdivisions into colonies and genomic clusters. Calculation of Φ ST and AMOVA tests were also conducted in Arlequin. Additional details on the mitochondrial analyses are given in the Supplementary File. Nuclear genome clustering and phylogenetic analyses. The majority of population genomic analyses were based on nuclear genotype likelihoods as implemented in ANGSD v. 0. 931  76. After assessing the quality of the mapped sequencing data in an ANGSD pre-run, we removed an individual from the Isle of May from the dataset.
Genotype likelihoods for nuclear SNPs covered in all individuals were calculated and filtered in ANGSD. Accounting for linkage disequilibrium, we further pruned the dataset by only selecting the most central site within blocks of linked sites (R 2 > 0. 2) as in Orlando and Librado  77. Subsequently, all variants located on the Z-pseudo-chromosome and "unplaced scaffolds" were excluded from the analyses yielding a final genotype likelihood panel consisting of 1,093,765 sites. We investigated genomic population structure with a PCA of the genotype likelihood panel using PCAngsd v0. 982  78. Individual ancestry proportions were estimated using a maximum likelihood (ML) approach implemented in ngsAdmix v32  79  , with the number of ancestral populations (K) set from 1 to 10 and conducting 50 replicate runs for each K.
42  by computing the fraction of the entire genome falling into RoHs, with the entire genome being the total length of windows scanned. Additional details on these analyses can be found in the Supplementary File. Patterns of gene flow and admixture. Assessing potential patterns of IBD within the breeding range of the puffin, the program EEMS  43  was used to model the association between genetic and geographic data by visualizing the existing population structure and highlighting regions of higher-than-average and lowerthan-average historic gene flow. We calculated a pairwise genetic distance matrix in ANGSD by sampling the consensus base (-doIBS 2 -makeMatrix 1) at the sites included in the genotype likelihood set (see Nuclear cluster and phylogenetic analyses) for each sample. The matrix was fed into 10 independent runs of EEMS, each consisting of one MCMC chain of six million iterations with a two million iteration burn-in, 9999 thinning iterations, and 1000 underlying demes.
Supplementing the results of the EEMS analysis, we conducted a traditional IBD analysis by determining geographical and genetic distances between the 12 colonies and assessing the significance of the correlation between the two distance matrices with a Mantel test  83  and a multiple regression on distance matrix (MRM)  84  analysis. F ST was used as a proxy for genetic distance and computed for each population pair in ANGSD by applying two-dimensional (2D), folded SFS. We converted pairwise F ST values to Slatkin's linearized F ST  85. Least Cost Path distances (paths over water only) between colony coordinates (latitude/longitude) were calculated using the R package marmap  86  and used as geographic distances. We performed the Mantel test (999 permutations) and MRM analysis with the R package ecodist  87.
Those served as input for a reduced dbRDA to calculate the marginal effect of each variable and for a partial dbRDA with variance partitioning to estimate the separate effects of IBD and IBE. Similar to the MRM analyses and Mantel tests, these analyses were repeated on subsets of colonies by progressively removing the colony from the geographic, environmental, and genetic distance matrices, whose removal led to the highest increase in variance explained in the resulting global dbRDA model. Methods and R code for the dbRDA were found at https://github. com/laurabenestan/db-RDA-and-db-MEM  90. Additional assessments of gene flow and admixture were conducted by calculating f3-statistics and multi-population D-statistics (aka ABBA BABA test)  91. We calculated f3-statistics in Treemix for each unique combination of ((A,B),C)) of the 12 puffin populations.
D-statistics were calculated in ANGSD (-doAbbababa2) for each combination of ((A,B),C),Outgroup) using the 12 puffin colonies. The outgroup was generated in ANGSD using the 10xGenomics sequencing data of the razorbill mapped to the puffin reference genome (see Nuclear cluster and phylogenetic analyses). Evaluating genome-wide patterns of genetic differentiation, pairwise F ST values between the Norway/Iceland/Faroe cluster and the Spitsbergen, Isle of May, Canada colonies (three comparisons) were calculated in sliding windows of 50 kb with 12. 5 kb steps across the 25 pseudo-chromsomes by applying 2D, folded SFS. The window size of 50 kb was chosen for sliding window analyses because LD decays to ca. 10% (R < 0. 025) within this distance (Fig. S19 ). Additional details on the IBD, admixture, and sliding-window analyses are given in the Supplementary File.
Statistics and reproducibility. The research sample included 72 adult Atlantic puffins (Fratercula arctica) across 12 colonies located in Svalbard, northern mainland Norway, Iceland, the Faroe Islands, Scotland, and Canada. The sample included six individuals per colony (12 colonies), including an equal sex ratio (3 males and 3 females per colony). All statistical tests were conducted using publicly available programs and packages as described in the methodological sections above. Reproducibility can be accomplished by following the sample collection and laboratory methods outlined above and by following the author's GitHub (https:// github. com/OKersten/PuffPopGen) using the specified parameters mentioned in in the code and methodological sections above.
Acknowledgements Financial support was provided by the  Nansen Foundation and the Faculty of Mathematical and Natural Sciences, University of Oslo (UiO). We are grateful to the  SEAPOP program  (www. seapop. no/en, Norwegian Research Council  grant number  192141 ), and the SEATRACK (http://www. seapop. no/en/seatrack)and ARCTOX (https://arctox. cnrs. fr/en/home) projects for collecting and sharing of samples. In particular, we thank  Dave Fifield  and  Greg Robertson  for the provision of puffin samples from  Gull Island , and  Árni Ásgeirsson  and  Róbert Arnar Stefánsson  for supplying samples from Breiðafjörður. The authors acknowledge support from the  National Genomics Infrastructure in Stockholm  funded by the  Science for Life Laboratory , the  Knut and Alice Wallenberg Foundation  and the  Swedish Research Council , and the  SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science  for assistance with massively parallel sequencing (reference genome) and access to the  UPPMAX computational infrastructure.
Data availability Raw read data analyzed in the current study have been deposited in the European Nucleotide Archive (ENA, www. ebi. ac. uk/ena) under study accession number PRJEB40631 (see Supplementary Data 2 for individual sample accession numbers). Nuclear and mitochondrial scaffolds (GCA_905066775. 1, CAJHIB010000001-CAJHIB010013329), as well as pseudo-chromosomes (GCA_905066775. 2, CAJHIB020000001-CAJHIB020000027), have been uploaded to ENA (Project PRJEB40926, Sample SAMEA7482542).
This article presents a study of the factors that influence the mechanism of soil-structure interaction with a pilot building having concrete walls and their impact on their performance. To illustrate the studies carried out, a numerical modeling of a four-floor concrete wall pilot building was performed, subjected to vertical actions, supported by a slab-on-ground foundation, using the Finite Element Method (FEM), together with specific 3D software for analysis and structural dimensioning in reinforced concrete. For the consideration of the geotechnical and structural system (foundation structure), the discrete spring model (Winkler model) coupled to the superstructure was used and the slab foundation thickness was varied by 16 cm, 25 cm and 40 cm. The local geotechnical formation was represented by a soft clay (SPT = 5) from the Belo Horizonte Metropolitan Region, Brazil.
Acknowledgments In this research, it was concluded that the SSI's consideration in the analyzed case study allowed a redistribution of the efforts along the structure as the slab-onground thickness (foundation structure) increased, being observed, thus, a relief of efforts in the more loaded central walls and additions to the walls of the periphery. Thus, regions with concentrations of tensions or settlements suffer relief, making it possible to have a better standardization of these variables and preventing that localized points of the foundation do not meet the design conditions, Ultimate Limit State (ULS) and Service or Use Limit State (SLS). Finally, this consideration in the designs brings with it the design of more realistic and often more economical designs, as seen in terms of the steel reinforcement bar ratio, where consumption has decreased by almost half.
The annual production data at the slaughterhouse are related to the quantity of ham pieces per mass allocation. The transport distance between groups of pork producers from the Brittany region and the slaughterhouse was estimated by weighting according to the regional distribution of production. Slaughter-cutting waste accounts for 15% of the live pig weight  [52]. The production plant also produces other meat products. The annual production data at the plant were related to the quantity of cooked ham per mass allocation. This study considered the absence of losses during the production of ham. This study also excluded the manufacture of additives (sodium ascorbate and aromatics) present in the processing of the product as well as their transport because they represent less than 0. 1% of the final composition of the product.
The infrastructure of the facilities, equipment, packaging used for temporary storage and products used for cleaning the facilities were not included. The influence of combined biopreservation and high-pressure processing was evaluated in terms of the life cycle of cooked ham from data on an industrial scale to assess the human health and environmental impacts of its potential application. In the conventional ham production scenario, an embedded amount of 0. 1 g per kilo of nitrites was included. No nitrites were assumed to be used in the innovative scenario. A high-pressure program of 600 MPa for 3 min at room temperature was used in this study (data from Villamonte 2014  [53] , and from a confidential report disclosed by Hiperbaric). A spray of 25 mg of commercial lactic starter slurry per kilo of ham was used for the biopreservation of the product.
The end of life of the packaging waste associated with the consumption of the product was included. The data on the energy consumption of the refrigeration were estimated according to the model of Nielsen et al. [52]  for a type A refrigerator. The waste was treated by incineration with energy recovery (52. 4%) or by storage (47. 6%). The steps included in the limits are shown in Figure  2. Allocation method: mass allocation. Inventory of inputs, emissions, and resources: The system was described and modeled with SimaPro 8. 5. 0. 0 software (PRé Sustainability, Amersfoort, The Netherlands)  [59]. The life cycle inventory included the flow of materials and energy within the system boundaries, adjusted to 1 kg of consumed cooked ham. The primary data (real) were measured and/or provided by officials of the French pork industry French National Pork Institute (IFIP) and a high-pressure processing equipment company (Hiperbaric in Spain).
Secondary data (from databases) were supplemented by the database and bibliography available for the reference technology path. The specifications and modalities of the reference and innovative processes were based on the data obtained from the partners, for example, the high-pressure treatment schedules and the inventory of resources needed to cultivate the preservation fermentation. The data for the raw material production step were collected from the Agribalyse French agricultural products database (version 1. 3)-the information obtained on pig slaughtering corresponded to an average French slaughterhouse. The data for cooked ham production were collected from conventional French meat producers. The technological level used in the slaughtering and manufacturing steps was modern or automated, and the site capacities were representative of French production.
The generic data originated from the EcoInvent 3. 3 database. The energy source was that of France and was acquired from this database. The quality of the related data was categorized into generic (pig breeding, distribution, and use) and specific (slaughter-cutting, production of cooked ham, and high-pressure treatment). This information was temporally representative of current production technologies and consumption habits, and based on available sources: livestock (Agribalyse V1. 1 February 2014, ILCD-Quality final note 4,5/5), slaughter-cutting and cooked ham production (from IFIP, 2014), distribution (from Villamonte, 2014  [53] ), and use (data from Villamonte, 2014  [53] ). To summarize, the flows that change between the different scenarios studied are, on the one hand, those linked to the unitary high-pressure treatment operation (i.
These nitrosating agents are derived from nitrites and favored by heat treatments. Human exposure represents only a fraction of the substance from the food transferred (nitrosamines via the ingestion pathway) to the entire human population. The potential risk to human health was calculated by the probable number of cases per kg of substance ingested by the population. The carcinogenic and noncarcinogenic effects were estimated by toxicity data for the substance from epidemiological studies. The severity of these effects (carcinogenic and noncarcinogenic) was expressed in terms of equivalent life lost per case of the disease (DALY. cas-1), a unit used by the World Health Organization  [60, 61]. DALY stands for disability-adjusted life years and is also frequently used precisely in LCA via damage-oriented and/or endpoint methods, which group the impacts according to the results in the cause-and-effect chain and clearly show the impact on a specific category of individuals.
These factors represented the variation in the probability of disease from the change in nitrosamine uptake over the course of the life of the targeted population. The unit for the potential for human toxicity of nitrosamines was case. kg -. The model expresses toxicity in comparative toxic units (CTUs). The effect factor is based on the extrapolation of ED50 (lethal dose for 50% of a given population). The carcinogenic effects were obtained from the Carcinogenic Potency Database. As the dose-response curve was linear, the EF (case. kg -  taken) was calculated according to Equation (3)  [67] : EF = 0. 5 ED 50 (3) To evaluate the significance of the indicator in relation to other indicators of the damage-oriented impact category of human health from the life cycle analysis of cooked ham, the severity factor for the carcinogenic effect of nitrosamines was considered 11.