Miracle-dz/UniFAR-FTUs huggingface dataset:
Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences

Abstract The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species’ original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
Measuring the Global Occurrence and Probabilistic Consequences of Wheat Stem Rust

Authorship is alphabetical. International Science and Technology Practice and Policy (InSTePP) Center in the Department of Applied Economics at the University of Minnesota; Commonwealth Scientific and Industrial Research Organization (CSIRO): E.H. Graham Center at Charles Sturt University at Wagga Wagga: Stakman-Bourlaug Cereal Rust Center at the University of Minnesota: Department of Agricultural Economics, Extension and Rural Development, University of Pretoria; and 6 Department of Economics, University of Adelaide
Novel methods for assessment of vulnerability to financial exploitation (FE)

ABSTRACT Financial exploitation (FE) is a complex problem influenced by many factors. This article introduces two novel methods for assessment of FE vulnerability: (1) performance-based measures of financial skills using web-based simulations of common financial tasks; (2) scam vulnerability measures based on credibility ratings of common scam scenarios. Older adults who were male, younger, Hispanic, more educated, with higher incomes performed better on the simulated financial tasks. Better performance was also related to higher cognitive function and numeracy, and more experience with technology. On the scenario-based measures, older adults who were male, younger, African American, less educated, and lower income showed higher FE vulnerability. Higher scam vulnerability was also related to poorer performance on the simulated financial tasks, lower cognitive function, less experience with technology, more financial conflict/anxiety, more impulsivity, and more stranger-initiated FE. Findings indicate that these novel measures show promise as valid indicators of vulnerability to FE.
Human fire maintains a balance of nature.

A perception of conflict between conservation of biodiversity and burning for socioeconomic protection persists in Australia. Numerous studies of ‘impacts of burning’ have concluded that burning depletes nutrients, simplifies vegetation structure by reducing woody vegetation and fallen timber, and threatens biodiversity. However ecological history shows that burning can maintain a dynamic balance in eucalypt ecosystems whereas nutrients, woody vegetation and fallen timber accumulate in the absence of fire, impairing their health, resilience, diversity and safety. Some recent studies of fire and nutrient cycling have elucidated the underlying processes and provided insights into the intervals between fires that can maintain health, resilience and diversity. Human fire is part of the ‘balance of nature’ in eucalypt ecosystems.
Effects of short-term enclose on the community characteristics of three types of degraded alpine grasslands in the north Tibet

An experiment was conducted to determine the response of alpine grassland communities to enclose in the northern Tibetan by monitoring the community change of three types of degraded alpine grasslands.The results of this study showed that the short-term enclose greatly increased vegetation height,cover and above-ground biomass,and the number of plant species in the three types of degraded alpine grasslands.The response of cover and height of alpine steppe and alpine meadow to the short-term enclose was slower than the response of the number of plant species of alpine steppe and alpine meadow to the short-term enclose.The short-term enclose quickly increased the above-ground biomass of the three alpine grasslands,but did not affect the plant species diversity of alpine grassland communities.This study suggested that the combination of the short-term enclose and fertilizer was the effective way to restore the degraded alpine steppes and alpine meadows and the combination of the long-term enclose and fertilizer and reseeding benefited the restoration of degraded alpine desert grassland.
Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities

Abstract We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant variants belonging to Desulfobulbaceae, Desulfuromonadales, Arcobacter sp. , Vibrio spp. , and Sulfuriferula sp. Although dominant diazotrophs fell within known nifH clusters I and III, only a few of these variants were frequently recovered in a 5-year weekly nifH times series in the coastal NW Atlantic presented herein, notably S. stutzeri and variants belonging to Desulfobacterales and Desulfuromonadales. In addition, the majority of dominant Arctic nifH variants shared low similarity (< 92% nucleotide identities) to sequences in a global noncyanobacterial diazotroph catalog recently compiled by others. We further detected UCYN-A throughout the CAG at low-levels using quantitative-PCR assays. Temperature, depth, salinity, oxygen, and nitrate were most strongly correlated to the Arctic diazotroph diversity observed, and we found a stark division between diazotroph communities of the Labrador Sea versus Baffin Bay and the CAA, hence establishing that a previously unknown biogeographic community division can occur for diazotrophs in the CAG.
Erwiniaceae bacteria play defensive and nutritional roles in two widespread ambrosia beetles

Abstract Ambrosia beetles are fungal-growing insects excavating galleries deep inside the wood. Their success as invaders increased scientific interest towards them. However, most studies on their microbiota targeted their fungal associates whereas the role of bacterial associates is understudied. To explore the role of abundant microbial associates, we isolated bacteria from active galleries of two widespread ambrosia beetles, Xylosandrus crassiusculus and X. germanus. These isolates were classified within the Erwiniaceae family and through a phylogenetic analysis including isolates from other insects we showed that they clustered with isolates obtained from ambrosia and bark beetles, including Erwinia typographi. The whole genome analysis of the isolate from active galleries of X. crassiusculus suggested that this bacterium plays both a nutritional role, by providing essential amino acids and enzymes for the hydrolysis of plant biomass, and a defensive role, by producing antibiotics. This defensive role was also tested in vitro against fungi, including mutualists, common associates, and parasites. The bacteria inhibited the growth of some of the common associates and parasites but did not affect mutualists. Our study supported the hypothesis of a mutualist role of Erwiniaceae bacteria in ambrosia beetles and highlighed the importance of bacteria in maintaining the symbiosis of their host with nutritional fungi.
Proposal for targeted, neo-evolutionary-oriented, secondary prevention of early-onset endometriosis and adenomyosis. Part I: pathogenic aspects

Abstract The potential for repeated ovulation and menstruation is thought to have provided a Darwinian advantage during the Palaeolithic. Reproductive conditions remained relatively stable until the pre-industrial era, characterized by late menarche, very young age at first birth, multiple pregnancies, and prolonged periods of lactational amenorrhoea. For hundreds of thousands of years, menstruators experienced few ovulatory cycles, even though they were genetically adapted to ovulate and menstruate every month. In the post-industrial era, the age at menarche gradually declined, the age at first birth progressively increased, and breastfeeding became optional and often of short duration. This created a mismatch between genetic adaptation and socio-environmental evolution, so that what was initially a probable reproductive advantage subsequently contributed to increased susceptibility to diseases associated with lifetime oestrogen exposure, such as ovarian, endometrial and breast cancer and, hypothetically, also those associated with the number of ovulatory menstruations, such as endometriosis and adenomyosis. The incidence of endometriosis shows a steep and progressive increase around the age of 25 years, but given the consistently reported delay in diagnosis, the actual incidence curve should be shifted to the left, supporting the possibility that the disease has its roots in adolescence. This raises the question of whether, from an evolutionary point of view, anovulation and amenorrhoea should not still be considered the physiological state, especially in the postmenarchal period. However, an increase in the frequency of endometriosis in recent decades has not been demonstrated, although this deserves further epidemiological investigation. In addition, as endometriosis occurs in a minority of individuals exposed to retrograde menstruation, other important pathogenic factors should be scrutinised. Research should be resumed to explore in more detail the transtubal reflux of not only blood, but also endometrial cells, and whether they are systematically present in the peritoneal fluid after menstruation. If repetitive ovulatory menstruation during the early reproductive years is shown to increase the risk of endometriosis and adenomyosis development and progression in susceptible individuals, hormonal interventions could be used as secondary prevention in symptomatic adolescents.
Pollution Status and Effect of Crude Oil Spillage in Ughoton Stream Ecosystem in Niger Delta

The present study evaluates the pollution status and the physico-chemical characteristics of Ughoton stream water as it affects the quality of water and its impact on Ughoton stream ecosystem. Surface water samples were collected at various distances, 50,100, 250, and 500 m downstream from an oil well. The potentially toxic elements, Fe, Mn, Zn, Ca, Cr, Cd, Ni, and Pb were analyzed. Other parameters including cations, hydrocarbonoclastic, heterotrophic bacteria and Total hydrocarbon were analyzed. The study reveals most of the parameters; pH, DO, BOD, and COD are within limits set by World Health Organization (WHO) for surface water. The heavy metal concentrations in the stream water are also below the threshold levels associated with the toxicological effects and the regulatory limits. However, the high concentration of nutrients, hydrocarbonoclastic and heterotrophic bacteria confirmed high pollution status. The hydrocarbonoclastic and heterotrophic bacteria count ranged from 96 to 520 and 48 to 284 per 100 ml respectively. Pollution nature of Ughoton stream water is further confirmed by its oil films coated environment; the pollution load exceeded tolerance limit of stream that empties into major river. Therefore, The Ughoton stream water is considered as a threat to Ughoton natural ecosystem. Key words: Physico-chemical parameters, hydrocarbonoclastic and heterotrophic bacteria, freshwater stream.
Phenotypic and genomic analysis of a large-scale Corynebacterium diphtheriae outbreak among migrant populations in Europe

Background. Increased numbers of cases of Corynebacterium diphtheriae infections were diagnosed in migrant-related facilities of Europe since summer 2022. Most cases involved cutaneous diphtheria, although some respiratory cases and fatalities were reported. A pan-European consortium was created to assess the clinical, epidemiological and microbiological features of this outbreak. Methods. All 363 toxigenic C. diphtheriae infection cases from ten European countries were included. Data from case interviews regarding countries of origin and transit routes of migrants were collected. Bacterial isolates underwent whole genome sequencing and antibiotic susceptibility testing. Phylogenetic relationships of outbreak isolates and their antimicrobial resistance genes were studied. Results. Four major genomic clusters were identified, revealing the multiclonal nature of the outbreak. Genes ermX, coding for erythromycin resistance, and genes pbp2m and blaOXA-2 for beta-lactam resistance, were detected in a subset of isolates. Isolates harboring ermX were resistant to erythromycin, and isolates carrying pbp2m were resistant to penicillin, but susceptible to amoxicillin, whereas those carrying blaOXA-2 remained susceptible to beta-lactams. Genomic variation within the four genomic clusters led to estimate their most recent common ancestors between 2017 and 2020. Conclusions. The multi-country distribution of each cluster demonstrated repeated cross-border spread. The increased number of C. diphtheriae cases among migrants is a cause for concern, particularly considering antimicrobial resistance phenotypes that threaten the efficacy of first-line treatments. This work provides important knowledge on modern C. diphtheriae infections, useful for addressing the reemergence of diphtheria in vulnerable populations and to guide clinical management and measures to control further dissemination.
Measuring the boundary gapless state and criticality via disorder operator

The disorder operator is often designed to reveal the conformal field theory (CFT) information in the quantum many-body system. By using large-scale quantum Monte Carlo simulation, we study the scaling behavior of disorder operator on the boundary in the two-dimensional Heisenberg model on the square-octagon lattice with gapless topological edge state. In the Affleck-Kennedy-Lieb-Tasaki (AKLT) phase, the disorder operator is shown to hold the perimeter scaling with a logarithmic term associated with the Luttinger Liquid parameter K. This effective Luttinger Liquid parameter K reflects the low energy physics and CFT for (1+1)d boundary. At bulk critical point, the effective K is suppressed but keep finite value, indicating the coupling between the gapless edge state and bulk fluctuation. The logarithmic term numerically capture this coupling picture, which reveals the (1+1)d SU(2)_1 CFT and (2+1)d O(3) CFT at boundary criticality. Our work paves a new way to study the exotic boundary state and boundary criticality.
The accretion history of the Milky Way – II. Internal kinematics of globular clusters and of dwarf galaxies

We study how structural properties of globular clusters and dwarf galaxies are linked to their orbits in the Milky Way halo. From the inner to the outer halo, orbital energy increases and stellar-systems gradually move out of internal equilibrium: in the inner halo, high-surface brightness globular clusters are at pseudo-equilibrium, while further away, low-surface brightness clusters and dwarfs appear more tidally disturbed. Dwarf galaxies are the latest to arrive into the halo as indicated by their large orbital energies and pericentres, and have no time for more than one orbit. Their (gas-rich) progenitors likely lost their gas during their recent arrival in the Galactic halo. If dwarfs are at equilibrium with their dark matter (DM) content, the DM density should anticorrelate with pericentre. However, the transformation of DM dominated dwarfs from gas-rich rotation-supported into gas-poor dispersion-supported systems is unlikely accomplished during a single orbit. We suggest instead that the above anticorrelation is brought by the combination of ram-pressure stripping and of Galactic tidal shocks. Recent gas removal leads to an expansion of their stellar content caused by the associated gravity loss, making them sufficiently fragile to be transformed near pericentre passage. Out of equilibrium dwarfs would explain the observed anticorrelation of kinematics-based DM density with pericentre without invoking DM density itself, questioning its previous estimates. Ram-pressure stripping and tidal shocks may contribute to the dwarf velocity dispersion excess. It predicts the presence of numerous stars in their outskirts and a few young stars in their cores.
Zircon U-Pb age and Hf isotope of Paleoproterozoic mafic intrusion on the western margin of the Yangtze Block and their implications

A large number of mafic dykes occur in the Kang-Dian Axis of the western Yangtze Block,which had a great bearing on the early evolution of the Yangtze Block.In this paper,zircon U-Pb age,Hf isotope,and whole-rock geochemistry were studied for gabbros collected from Jiaopingdu area,which intruded into the Tongan Formation,with the purpose of constraining the age of the crystallization basement and the early evolution of the Yangtze Block.The zircons yielded a weighted mean 207 Pb/ 206 Pb age of 1694Ma±16Ma(MSWD=0.9),which is interpreted as the intrusion age.The results constrain the depositional age of the Tongan Formation to 1694Ma,implying that the Tongan Formation is of Paleoproterozoic.Geochemical data show that these gabbros have NMORB affinity.Initial Hf isotope ratios(176 Hf/ 177 Hf) i of the zircons range from 0.281881 to 0.281982,with corresponding e Hf(t) values of 6.2~9.8. These zircons give the depleted mantle model ages(t DM1) of 1738~1883Ma(1803Ma on average),slightly older than the time of the zircon growth.All these data suggest that the Paleoproterozoic gabbro was derived from a depleted mantle.In combination with the presence of abundant Archean to Paleoproterozoic detrital zircons in the Mesoproterozoic strata,the newly identified 1694Ma mafic intrusion in the western Yangtze block supports the existence of an Archean-Paleoproterozoic crystalline basement beneath the western Yangtze block.The results obtained by the authors also show that the tectonic event,which resulted in the intrusion of large quantities of late Paleoproterozoic mafic dykes in the western Yangtze block,was obviously younger than the continental collision and post-orogenic extension of Columbia supercontinent recorded in Yangtze block,and thus most probably linked to the breakup of Columbia supercontinent.
Multiplying matrices using n arithmetic operations

It is widely known that the lower bound for the algorithmic complexity of square matrix multiplication resorts to at least $n^2$ arithmetic operations. The justification builds upon the following reasoning: given that there are $2 n^2$ numbers in the input matrices, any algorithm necessarily must operate on each at least once. In this paper, we show that this is not necessarily the case for certain instances of the problem, for instance matrices with natural number entries. We present an algorithm performing a single multiplication and $(n - 1)$ sums, therefore using n arithmetic operations. The ingenuity of the approach relies on encoding the original $2n^2$ elements as two numbers of much greater magnitude. Thus, though processing each of the inputs at least once, it relies on a lower count of arithmetic operations. In the computational model used to analyze this problem, such encoding operation is not available, thus it is not clear this work affects the currently accepted complexity results for matrix multiplication, but the new algorithm complexity (when taking into account the encodings) is $3n^2 + 2n - 1$ operations. In addition, given the exponential increase in multiplication operands magnitude, its practical usage is constrained to certain instances of the problem. Nonetheless, this work presents a novel mathematically inspired algorithm while pointing towards an alternative research path, which opens the possibility of novel algorithms and a taxonomy of matrix multiplications and associated complexities.
SusHi 2.0 - Higgs production cross sections in BSM models

A new upcoming version of SusHi is introduced. It features unified input for the Standard Model (SM) and beyond the SM models (BSM) parameters for higher-order total cross sections for Higgs production in gluon fusion, heavy-quark annhilation, as well as Higgsstrahlung. Like previous versions of SusHi, it provides links to codes like 2HDMC and FeynHiggs, but can also process standard SLHA output of spectrum generators like SOFTSUSY and SPheno.
Quantum light microscopy

Much of our progress in understanding microscale biology has been powered by advances in microscopy. For instance, super-resolution microscopes allow the observation of biological structures at near-atomic-scale resolution, while multi-photon microscopes allow imaging deep into tissue. However, biological structures and dynamics still often remain out of reach of existing microscopes, with further advances in signal-to-noise, resolution and speed needed to access them. In many cases, the performance of microscopes is now limited by quantum effects -- such as noise due to the quantisation of light into photons or, for multi-photon microscopes, the low cross-section of multi-photon scattering. These limitations can be overcome by exploiting features of quantum mechanics such as entanglement. Quantum effects can also provide new ways to enhance the performance of microscopes, such as new super-resolution techniques and new techniques to image at difficult to reach wavelengths. This review provides an overview of these various ways in which quantum techniques can improve microscopy, including recent experimental progress. It seeks to provide a realistic picture of what is possible, and what the constraints and opportunities are.