Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction of Electron Back-scattered Diffraction datasets using an evolutionary algorithm

In materials science and particularly electron microscopy, Electron Back-scatter Diffraction (EBSD) is a common and powerful mapping technique for collecting local crystallographic data at the sub-micron scale. The quality of the reconstruction of the maps is critical to study the spatial distribution of phases and crystallographic orientation relationships between phases, a key interest in materials science. However, EBSD data is known to suffer from distortions that arise from several instrument and detector artifacts. In this paper, we present an unsupervised method that corrects those distortions, and enables or enhances phase differentiation in EBSD data. The method uses a segmented electron image of the phases of interest (laths, precipitates, voids, inclusions) gathered using detectors that generate less distorted data, of the same area than the EBSD map, and then searches for the best transformation to correct the distortions of the initial EBSD data. To do so, the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) is implemented to distort the EBSD until it matches the reference electron image. Fast and versatile, this method does not require any human annotation and can be applied to large datasets and wide areas, where the distortions are important. Besides, this method requires very little assumption concerning the shape of the distortion function. Some application examples in multiphase materials with feature sizes down to 1 $\mu$m are presented, including a Titanium alloy and a Nickel-base superalloy.
Structure-Preserving Community In A Multilayer Network: Definition, Detection, And Analysis

Multilayer networks or MLNs (also called multiplexes or network of networks) are being used extensively for modeling and analysis of data sets with multiple entity and feature types as well as their relationships. As the concept of communities and hubs are used for these analysis, a structure-preserving definition for them on MLNs (that retains the original MLN structure and node/edge labels and types) and its efficient detection are critical. There is no structure-preserving definition of a community for a MLN as most of the current analyses aggregate a MLN to a single graph. Although there is consensus on community definition for single graphs (and detection packages) and to a lesser extent for homogeneous MLNs, it is lacking for heterogeneous MLNs. In this paper, we not only provide a structure-preserving definition for the first time, but also its efficient computation using a decoupling approach, and discuss its characteristics & significance for analysis. The proposed decoupling approach for efficiency combines communities from individual layers to form a serial k-community for connected k layers in a MLN. We propose several weight metrics for composing layer-wise communities using the bipartite graph match approach based on the analysis semantics. Our proposed approach has a number of advantages. It: i) leverages extant single graph community detection algorithms, ii) is based on the widely-used maximal flow bipartite graph matching for composing k layers, iii) introduces several weight metrics that are customized for the community concept, and iv) experimentally validates the definition, mapping, and efficiency from a flexible analysis perspective on widely-used IMDb data set. Keywords: Heterogeneous Multilayer Networks; Bipartite Graphs; Community Definition and Detection; Decoupling-Based Composition
Clinical Investigation : Genitourinary Cancer Value of PET / CT and MR Lymphography in Treatment of Prostate Cancer Patients With Lymph Node Metastases

Value of PET/CT and MR Lymphography in Treatment of Prostate Cancer Patients With Lymph Node Metastases Ansje S. Fortuin, M.D.,* Willem M.L. L.G. Deserno, M.D., M.Sc., Ph.D.,* Hanneke J.M. Meijer,M.D.,yGerrit J. Jager,M.D., Ph.D.,x Satoru Takahashi,M.D., Ph.D.,* Oscar A. Debats, M.D., M.Sc.,* Sven N. Reske, M.D., Ph.D.,{ Christian Schick, M.D.,{ Bernd J. Krause, M.D., Ph.D.,k Inge van Oort, M.D., Ph.D.,z Alfred J. Witjes, M.D., Ph.D.,z Yvonne L. Hoogeveen, Ph.D.,* Emile N.J. Th. van Lin, M.D., Ph.D.,y and Jelle O. Barentsz, M.D., Ph.D.* Departments of *Radiology, yRadiation Oncology, and zUrology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; xDepartment of Radiology, Jeroen Bosch Hospital’s, Hertogenbosch, The Netherlands; {Department of Nuclear Medicine, University of Ulm, Ulm, Germany; and jjDepartment of Nuclear Medicine, Technische Universität München, München, Germany
Training on the Edge: The why and the how

Edge computing is a natural progression from cloud computing, where, instead of collecting all data and processing it centrally, as in a cloud computing environment, we distribute the computing power and try to do as much processing as possible, close to the source of the data. This model is being adopted quickly for various reasons, including privacy, and reduced power and bandwidth requirements on the edge nodes. While inference is commonly being done on edge nodes today, training on the edge is much less common. The reasons range from computational limitations, to its not being advantageous in reducing communications between the edge nodes. In this paper, we explore some scenarios where it is advantageous to do training on the edge, and the use of checkpointing strategies to save memory.
Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species

Bacterial populations can display high levels of genetic structuring but the forces that influence this are incompletely understood. Here, by combining modelling approaches with multilocus sequence data for the zoonotic pathogen Campylobacter, we investigated how ecological factors such as niche (host) separation relate to population structure. We analysed seven housekeeping genes from published C. jejuni and C. coli isolate collections from a range of food and wild animal sources as well as abiotic environments. By reconstructing genetic structure and the patterns of ancestry, we quantified C. jejuni host association, inferred ancestral populations, investigated genetic admixture in different hosts and determined the host origin of recombinant C. jejuni alleles found in hybrid C. coli lineages. Phylogenetically distinct C. jejuni lineages were associated with phylogenetically distinct wild birds. However, in the farm environment, phylogenetically distant host animals shared several C. jejuni lineages that could not be segregated according to host origin using these analyses. Furthermore, of the introgressed C. jejuni alleles found in C. coli lineages, 73% were attributed to genotypes associated with food animals. Our results are consistent with an evolutionary scenario where distinct Campylobacter lineages are associated with different host species but the ecological factors that maintain this are different in domestic animals such that phylogenetically distant animals can harbour closely related strains.
Proapoptotic Noxa is required for particulate matter‐induced cell death and lung inflammation

Elevated ambient levels of particulate matter air pollution are associated with excess daily mortality, largely attributable to increased rates of cardiovascular events. We have previously reported that particulate matter induces p53‐dependent apoptosis in primary human alveolar epithelial cells. Activation of the intrinsic apoptotic pathway by p53 often requires the transcription of the proapoptotic Bcl‐2 proteins Noxa, Puma, or both. In this study, we exposed alveolar epithelial cells in culture and mice to fine particulate matter <2.5 μm in diameter (PM25) collected from the ambient air in Washington, D. C. Exposure to PM25 induced apoptosis in primary alveolar epithelial cells from wild‐type but not Noxa_/_ mice. Twenty‐four hours after the intratracheal instillation of PM25, wildtype mice showed increased apoptosis in the lung and increased levels of mRNA encoding Noxa but not Puma. These changes were associated with increased permeability of the alveolar‐capillary membrane and inflammation. All of these findings were absent or attenuated in Noxa_/_ animals. We conclude that PM2 5‐induced cell death requires Noxa both in vitro and in vivo and that Noxa‐dependent cell death might contribute to PM‐induced alveolar epithelial dysfunction and the resulting inflammatory response. —Urich, D. ,Soberanes, S. , Burgess, Z. , Chiarella, S. E. , Ghio, A. J., Ridge, K. M. , Kamp, D. W. , Chandel, N. S. , Mutlu, G. M. , Budinger, G. R. S. Proapoptotic Noxa is required for particulate matter‐induced cell death and lung inflammation. FASEB J. 23, 2055–2064 (2009)
Transcriptional pausing and stalling causes multiple clustered mutations by human activation‐induced deaminase

Transcription of the rearranged immunoglobulin gene and expression of the enzyme activation‐induced deaminase (AID) are essential for somatic hypermutations of this gene during antibody maturation. While AID acts as a single‐strand DNA‐cytosine deaminase creating U · G mispairs that lead to mutations, the role played by transcription in this process is less clear. We have used in vitro transcription of the kan gene by the T7 RNA polymerase (RNAP) in the presence of AID and a genetic reversion assay for kanamycin‐resistance to investigate the causes of multiple clustered mutations (MCMs) during somatic hypermutations. We find that, depending on transcription conditions, AID can cause single‐base substitutions or MCMs. When wild‐type RNAP is used for transcription at physiologically relevant concentrations of ribonucleoside triphosphates (NTPs), few MCMs are found. In contrast, slowing the rate of elongation by reducing the NTP concentration or using a mutant RNAP increases several‐fold the percent of revertants containing MCMs. Arresting the elongation complexes by a quick removal of NTPs leads to formation of RNA‐DNA hybrids (R‐loops). Treatment of these structures with AID results in a high percentage of KanR revertants with MCMs. Furthermore, selecting for transcription elongation complexes stalled near the codon that suffers mutations during acquisition of kanamycin‐resistance results in an overwhelming majority of revertants with MCMs. These results show that if RNAP II pauses or stalls during transcription of immunoglobulin gene, AID is likely to promote MCMs. As changes in physiological conditions such as occurrence of certain DNA primary or secondary structures or DNA adducts are known to cause transcriptional pausing and stalling in mammalian cells, this process may cause MCMs during somatic hypermutation. —Canugovi, C. , Samaranayake, M. , Bhagwat, A. S. Transcriptional pausing and stalling causes multiple clustered mutations by human activation‐induced deaminase. FASEB J. 23, 34‐44 (2009)
Microgeographic socio‐genetic structure of an African cooperative breeding passerine revealed: integrating behavioural and genetic data

Dispersal can be motivated by multiple factors including sociality. Dispersal behaviour affects population genetic structure that in turn reinforces social organization. We combined observational information with individual‐based genetic data in the Karoo scrub‐robin, a facultative cooperatively breeding bird, to understand how social bonds within familial groups affect mating patterns, cause sex asymmetry in dispersal behaviour and ultimately influence the evolution of dispersal. Our results revealed that males and females do not have symmetrical roles in structuring the population. Males are extremely philopatric and tend to delay dispersal until they gain a breeding position within a radius of two territories around the natal site. By contrast, females dispersed over larger distances, as soon as they reach independence. This resulted in male neighbourhoods characterized by high genetic relatedness. The long‐distance dispersal strategy of females ensured that Karoo scrub‐robins do not pair with relatives thereby compensating for male philopatry caused by cooperation. The observed female‐biased strategy seems to be the most prominent mechanism to reduce the risk of inbreeding that characterizes social breeding system. This study demonstrates that tying together ecological data, such as breeding status, determining social relationships with genetic data, such as kinship, provides valuable insights into the proximate causes of dispersal, which are central to any evolutionary interpretation.
Climate effects on life cycle variation and population genetic architecture of the black bean aphid, Aphis fabae

Aphid species may exhibit different reproductive modes ranging from cyclical to obligate parthenogenesis. The distribution of life cycle variation in aphids is generally determined by ecological forces, mainly climate, because only sexually produced diapausing eggs can survive harsh winters or periods of absence of suitable host plants. Aphids are thus interesting models to investigate intrinsic and environmental factors shaping the competition among sexual and asexual lineages. We conducted a Europe‐wide sampling of black bean aphids, Aphis fabae, and combined population genetic analyses based on microsatellite data with an experimental determination of life cycle strategies. Aphids were collected from broad beans (Vicia faba) as well as some Chenopodiaceae, but we detected no genetic differentiation between aphids from different host plants. Consistent with model predictions, life cycle variation was related to climate, with aphids from areas with cold winters investing more in sexual reproduction than aphids from areas with mild winters. Accordingly, only populations from mild areas exhibited a clear genetic signature of clonal reproduction. These differences arise despite substantial gene flow over large distances, which was evident from a very low geographic population structure and a lack of isolation‐by‐distance among 18 sites across distances of more than 1000 km. There was virtually no genetic differentiation between aphids with different reproductive modes, suggesting that new asexual lineages are formed continuously. Indeed, a surprising number of A. fabae genotypes even from colder climates produced some parthenogenetic offspring under simulated winter conditions. From this we predict that a shift to predominantly asexual reproduction could take place rapidly under climate warming.
Abnormal proteins can form aggresome in yeast: aggresome‐targeting signals and components of the machinery

In mammalian cells, abnormal proteins that escape proteasome‐dependent degradation form small aggregates that can be transported into a centrosome‐associated structure, called an aggresome. Here we demonstrate that in yeast a single aggregate formed by the huntingtin exon 1 with an expanded polyglutamine domain (103QP) represents a bona fide aggresome that colocalizes with the spindle pole body (the yeast centrosome) in a microtubule‐dependent fashion. Since a polypeptide lacking the proline‐rich region (P‐region) of huntingtin (103Q) cannot form aggresomes, this domain serves as an aggresome‐targeting signal. Coexpression of 103Q with 25QP, a soluble polypeptide that also carries the P‐region, led to the recruitment of 103Q to the aggresome via formation of hetero‐oligomers, indicating the aggresome targeting in trans. To identify additional factors involved in aggresome formation and targeting, we purified 103QP aggresomes and 103Q aggregates and identified the associated proteins using mass spectrometry. Among the aggresome‐associated proteins we identified, Cdc48 (VCP/p97) and its cofactors, Ufd1 and Nlp4, were shown genetically to be essential for aggresome formation. The 14‐3‐3 protein, Bmh1, was also found to be critical for aggresome targeting. Its interaction with the huntingtin fragment and its role in aggresome formation required the huntingtin N‐terminal N17 domain, adjacent to the polyQ domain. Accordingly, the huntingtin N17 domain, along with the P‐region, plays a role in aggresome targeting. We also present direct genetic evidence for the protective role of aggresomes by demonstrating genetically that aggresome targeting of polyglutamine polypep‐tides relieves their toxicity. —Wang, Y. , Meriin, A. B. , Zaarur, N. , Romanova, N. V. , Chernoff, Y. O. , Costello, C. E. , Sherman, M. Y. Abnormal proteins can form aggresome in yeast: aggresome‐targeting signals and components of the machinery. FASEB J. 23, 451‐463 (2009)
Antioxidant enzyme activity in Pinus mugo Turra, P. sylvestris L. and in their putative hybrids

Specific activity dynamics and isozyme composition of antioxidant enzymes ascorbate peroxidase (APX), catalase (CAT) and superoxide dismutase (SOD) were followed during the vegetation period in the young needles of Pinus mugo Turra, P. sylvestris L. and their putative hybrids. Tested enzymes differed in their dynamics showing the highest APX and CAT activities in the spring and autumn and the highest SOD activity in summer. The outlined course of enzyme activity was characteristic for all the three taxa compared. The level of specific enzyme activities was relatively constant in investigated taxa reaching statistical significance in some months of the scored period only. The same was true of the antioxidant enzyme activities of P. mugo individuals growing at different altitudes. Of the enzymes assayed, catalase was the most active. Hybrid individuals exhibited prevailingly intermediate level of their enzyme activity compared to the parental species. The dynamics of SOD correlated with intensity of UV irradiation during vegetation period. Partial correlation was observed between specific enzyme activities and isozyme composition.
Fragmentation can increase spatial genetic structure without decreasing pollen‐mediated gene flow in a wind‐pollinated tree

Fragmentation reduces population sizes, increases isolation between habitats and can result in restricted dispersal of pollen and seeds. Given that diploid seed dispersal contributes more to shaping fine‐scale spatial genetic structure (SGS) than haploid pollen flow, we tested whether fine‐scale SGS can be sensitive to fragmentation even if extensive pollen dispersal is maintained. Castanopsis sclerophylla (Lindley & Paxton) Schottky (Fagaceae), a wind‐pollinated and gravity seed‐dispersed tree, was studied in an area of southeast China where its populations have been fragmented to varying extents by human activity. Using different age classes of trees in areas subject to varying extents of fragmentation, we found no significant difference in genetic diversity between prefragmentation vs. postfragmentation C. sclerophylla subpopulations. Genetic differentiation among postfragmentation subpopulations was also only slightly lower than among prefragmentation subpopulations. In the most fragmented habitat, selfing rates were significantly higher than zero in prefragmentation, but not postfragmentation, cohorts. These results suggest that fragmentation had not decreased gene flow among these populations and that pollen flow remains extensive. However, significantly greater fine‐scale SGS was found in postfragmentation subpopulations in the most fragmented habitat, but not in less fragmented habitats. This alteration in SGS reflected more restricted seed dispersal, induced by changes in the physical environments and the prevention of secondary seed dispersal by rodents. An increase in SGS can therefore result from more restricted seed dispersal, even in the face of extensive pollen flow, making it a sensitive indicator of the negative consequences of population fragmentation.
Strategic promiscuity helps avoid inbreeding at multiple levels in a cooperative breeder where both sexes are philopatric

In cooperative breeders, the tension between the opposing forces of kin selection and kin competition is at its most severe. Although philopatry facilitates kin selection, it also increases the risk of inbreeding. When dispersal is limited, extra‐pair paternity might be an important mechanism to avoid inbreeding, but evidence for this is equivocal. The red‐winged fairy‐wren is part of a genus of cooperative breeders with extreme levels of promiscuity and male philopatry, but is unique in that females are also strongly philopatric. Here, we test the hypothesis that promiscuity is an important inbreeding avoidance mechanism when both sexes are philopatric. Levels of extra‐pair paternity were substantial (70% of broods), but did not arise through females mating with their helpers, but via extra‐group mating. Offspring were more likely to be sired by extra‐pair males when the social pair was closely related, and these extra‐pair males were genetically less similar to the female than the social male and thus, inbreeding is avoided through extra‐pair mating. Females were consistent in their choice of the extra‐pair sire over time and preferred early moulting males. Despite neighbouring males often being close kin, they sired 37% of extra‐pair offspring. However, females that gained paternity from neighbours were typically less related to them than females that gained paternity further away. Our study is the first to suggest that mating with both closely related social partners and neighbours is avoided. Such sophistication in inbreeding avoidance strategies is remarkable, as the extreme levels of promiscuity imply that social context may provide little cue to relatedness.
Estimating selfing rates from reconstructed pedigrees using multilocus genotype data

Several methods have been developed to estimate the selfing rate of a population from a sample of individuals genotyped for several marker loci. These methods can be based on homozygosity excess (or inbreeding), identity disequilibrium, progeny array (PA) segregation or population assignment incorporating partial selfing. Progeny array–based method is generally the best because it is not subject to some assumptions made by other methods (such as lack of misgenotyping, absence of biparental inbreeding and presence of inbreeding equilibrium), and it can reveal other facets of a mixed‐mating system such as patterns of shared paternity. However, in practice, it is often difficult to obtain PAs, especially for animal species. In this study, we propose a method to reconstruct the pedigree of a sample of individuals taken from a monoecious diploid population practicing mixed mating, using multilocus genotypic data. Selfing and outcrossing events are then detected when an individual derives from identical parents and from two distinct parents, respectively. Selfing rate is estimated by the proportion of selfed offspring in the reconstructed pedigree of a sample of individuals. The method enjoys many advantages of the PA method, but without the need of a priori family structure, although such information, if available, can be utilized to improve the inference. Furthermore, the new method accommodates genotyping errors, estimates allele frequencies jointly and is robust to the presence of biparental inbreeding and inbreeding disequilibrium. Both simulated and empirical data were analysed by the new and previous methods to compare their statistical properties and accuracies.