Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying the relative importance of competition, predation, and environmental variation for species coexistence

Coexistence theory and food web theory are two cornerstones of the longstanding effort to understand how species coexist. Although competition and predation are known to act simultaneously in communities, theory and empirical study of the two processes continue to be developed independently. Here, we integrate modern coexistence theory and food web theory to simultaneously quantify the relative importance of predation, competition, and environmental fluctuations for species coexistence. We first examine coexistence in a classic multi-trophic model, adding complexity to the food web using a novel machine learning approach. We then apply our framework to a parameterized rocky intertidal food web model, partitioning empirical coexistence dynamics. We find that both environmental fluctuation and variation in predation contribute substantially to species coexistence. Unexpectedly, covariation in these two forces tends to destabilize coexistence, leading to new insights about the role of bottom-up versus top-down forces in both theory and the rocky intertidal ecosystem.
Generation intervals in Canadian dairy cattle herds

Abstract: Genetic evaluation records for the Canadian Holstein, Ayrshire, Jersey, and Brown Swiss bulls and cows born from 1950 and 1960, respectively, were used to study the generation intervals (L) along the four-path selection model. The objectives of the study were to determine the L in the four dairy cattle breeds and the effects of some environmental factors and variations among herds or artificial insemination (AI) studs on the L achieved. Total L of the four selection paths was reduced by 55% from 29.2 yr in 1980 to 13.2 yr in 2016 in the Holstein breed. Substantial reductions in total L were also observed in the Ayrshire, Jersey, and Brown Swiss populations between 1980 and 2016. Unlike progeny year of birth, housing system, agricultural region in Québec (region) — as well as their interaction — were not important on realised L of sires and dams used on Canadian dairy farms. There were significant variations among herds and AI studs on the age of sires and dams used for breeding. The considerable variations in realised L among herds and AI studs offer opportunities to increase the annual rate of genetic progress in the four Canadian dairy cattle populations.
Nectins rather than E-cadherin anchor the actin belts at cell-cell junctions of epithelia

Cell-cell junctions support the mechanical integrity of epithelia by enabling adhesion and tension transmission between neighboring cells. The prevailing mechanistic dogma is that E-cadherin supports and transmits mechanical tension between cells through actin belts in a region named the zonula adherens. Using super-resolution microscopy on human intestinal biopsies and Caco-2 cells, we show that the zonula adherens consists of E-cadherin and nectin belts that are separated by about 150 nm along the apico-basal direction, the nectin belt being in the immediate vicinity of the actin belt. The segregation of nectins and E-cadherin increases as the tissue matures. Our data redefine the structure of the zonula adherens and show that nectins, rather than E-cadherin, are the major connectors of actin belts in epithelia.
Regional variation in iris colour of the White-browed Scrubwren Sericornis frontalis complex in digital photographs

A large sample ( n = 590) of location-tagged digital photographs was examined to assess regional or subspecific variation in iris colour of the White-browed Scrubwren Sericornis frontalis complex, which may be a diagnostic character misrepresented in the literature. The irides of the western/Spotted Scrubwren group ( maculatus , balstoni , mellori , ashbyi ) were found to be consistently more blue-green in colour compared with the remainder of the complex; this difference approached criteria for diagnosability and matched reported taxon boundaries. Lack of variation within the western group suggests a genetic rather than an ecophenotypic basis. Since juveniles of both groups have similar irides, this difference probably represents the acquisition of yellow-orange pigmentation with maturity in eastern but not western birds.
Analysis of transcription factor and histone modification dynamics in the nucleus of single living cells using a novel antibody-based imaging approach

Dans les cellules des eucaryotes, la transcription des genes est controlee par une plethore de complexes proteiniques. Cependant, la plupart de nos connaissances fondamentales sur la regulation de la transcription viennent des experiences biochimiques ou des experiences d’immunofluorescences utilisant des cellules fixees. Par consequent, beaucoup d’efforts ont ete consacre recemment pour obtenir des informations sur les mouvements dynamiques ou sur l’assemblage des facteurs de transcription directement dans des cellules vivantes. Nous avons developpe une strategie de marquage, appele « versatile antibody-based imaging approach » (VANIMA), dans laquelle des anticorps marques avec un fluorochrome sont introduit dans des cellules vivantes pour visualiser specifiquement des proteines endogenes ou des modifications post-traductionnelle. Nous avons pu montrer que VANIMA peut etre utilise pour etudier des processus dynamique des mecanismes fondamental de la biologie y compris les facteurs de la machinerie de transcription ainsi que les modifications des histones dans des cellules vivantes de cancer humaine en utilisant la microscopie conventionnelle ou a super-resolution. Dans l’avenir VANIMA va servir comme un outil valable pour reveler les dynamiques des processus endogenes en biologie y compris la transcription directement dans des cellules vivantes individuelles.
Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction

ABSTRACT Brycon orbignyanus is an endemic species from La Plata basin whose stocks have been presenting significant reductions throughout the Paraná River. Brycon orbignyanus is categorized as an endangered species. This study evaluated aspects of the bio-ecology of this species that may be related to this threat, highlighting its distribution, abundance, and diet as well as the corresponding relationships between its recruitment and flood regimes. Data were obtained from different parts of the upper Paraná River (stretches free and regulated by dams) from 1986 to 2010 with more detailed data collected from the free remnant of this basin. The results indicate that no records for species exist at more than half of the sampling points located in dam-regulated sections of the Paraná River, whereas specimens were collected from 75% sites in the free plain remnant. We observed a remarkable effect of the hydrological regime on recruitment as well as distinct food demands during ontogenetic development, with adults almost exclusively consuming fruits and seeds, revealing that these individuals are supported by riparian vegetation. Thus, it is concluded that changes in the natural flood regime as well as riparian vegetation removal threaten B. orbignyanus populations in the Paraná River basin.
The complete chloroplast genome of Yunnanopilia longistaminea (Opiliaceae), an endemic species in southwest China

Abstract The complete chloroplast genome sequence of Yunnanopilia longistaminea, an endemic species in southwest China, is presented in this study. The total genome size of Y. longistaminea was 148,503 bp in length, with a typical quadripartite structure including a pair of inverted repeat (IRs, 28,075 bp) regions separated by a large single copy (LSC, 84,547bp) region and a small single copy (SSC, 7805 bp) region. The all GC content was 37.3%. The genome contains 117 genes, including 72 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, 13 genes contain a single intron, and 3 genes have two introns. Further, a maximum-likelihood (ML) phylogenetic tree results that Y. longistaminea was closely related to the genera of Champereia manillana.
POPULATION DYNAMIC AND SPAWNING POTENTIAL RATIO OF SHORT MACKEREL (Rastrelliger brachysoma Bleeker, 1851) IN THE NORTHERN COAST OF JAVA

Short mackerel fish (Rastrelliger brachysoma) is one of small pelagic fish mostly exploited by mini purse seine fishing gear. Exploitation of short mackerel by mini purse seine has an increasing trend every year and suspected to have negative impacts. One of the negative impact is the decrease of fish abundance, so it is necessary to carry out population dynamics and Spawning Potential Ratio (SPR) studies through length-based approach to provide exploitation indicator as biology reference point. The result of length-weight relationship analysis shows that the growth pattern (b = 2.3483) is negative allometry. The estimated length at first capture and its first sexual maturity analysis shows that the value of length at first capture (Lc = 15.4 cm FL) is greater than the length at first sexual maturity (Lm = 15.21 cm FL). The estimated maximum length (L∞) is 21.05 cm FL with growth rates (K) is 1.01 year-1 and t0 at -0.177 years. The estimated total mortality (Z) was 5.48 year-1, natural mortality (M) was 2.02 year-1 and fishing mortality (F) was 3.46 year-1. The predicted exploitation rate (E) is 0.63 which higher than the optimum value (E = 0.5). The estimated length-based SPR (LB-SPR) of 30% (SPR > 20% or above limit) means that short mackerel fishing activity has full exploitation.
Distribution of
 Parthenium hysterophorus
 and one of its biological control agents (Coleoptera: 
 Zygogramma bicolorata
 ) in Nepal

Parthenium hysterophorus is a noxious invasive weed of both agricultural and natural ecosystems, spreading aggressively in Nepal. Management of this weed in Nepal has been limited, mainly because of the lack of geo-referenced data concerning the weed's distribution. We conducted a nationwide survey of P. hysterophorus and its coleopteran biological control agent Zygogramma bicolorata from 2013 to 2016 to determine their spatial distribution. Both were widespread, with the distribution of Z. bicolorata lagging behind the invasion front of P. hysterophorus. The weed was present in 21.2% of the 4838 locations examined, including several isolated satellite populations. The weed was found in the Tarai, Siwalik, Middle Mountains and High Mountains regions, reaching up to 2000 m asl. It has invaded natural and modified ecosystems including all six protected areas in the Tarai and Siwalik regions. Road access appears to be the major pathway for its long-distance dispersal. Zygogramma bicolorata had spread from the east to the west and was present in 15.4% of the weed occurrence locations, inflicting a low amount of damage. A CLIMEX modelling projection revealed the presence of additional geographic areas in Nepal which are climatically suitable for both P. hysterophorus and Z. bicolorata. Eradication of satellite populations of the weed by physical and chemical measures, and the release of Z. bicolorata into new, but climatically suitable, locations should be prioritised for P. hysterophorus management in Nepal. In conclusion, P. hysterophorus has rapidly become widespread in Nepal and the currently available biological control agent has not been able to prevent further spread of the weed.
The multipartite mitochondrial genome of Cynanchum auriculatum (Gentianales: Apocynaceae)

Abstract Cynanchum auriculatum is a Chinese herbal medicine species in the family Apocynaceae. The mitochondrial genome of C. auriculatum has heteroplasmy and consists of two chromosomes (chromosomes I and II), the lengths of which are 614,836 and 426,495 nucleotides. The multipartite mitochondrial genome encodes 57 genes, including 37 protein-coding genes, 17 transfer RNA genes, and three ribosomal RNA genes. Including 44 overlapping genes, we identified 57 genes on chromosome I and 44 genes on chromosome II. A phylogenetic tree revealed that C. auriculatum is most closely related to Asclepias syriaca.
Measuring anesthetic resistance in Drosophila by VAAPR

Volatile anesthetics are compounds which are commonly used to induce a reversable loss of consciousness (LOC) in animals. The molecular mechanism of how anesthetics induce LOC is largely unknown. However, observations have been made which show that there are genetically-encoded traits which influence the effective concentration of anesthetics in the inducement of LOC. Despite this long-term observation, little progress has been made in identifying genes involved in anesthetic sensitivity. One reason for this is that many techniques to test anesthetic sensitivity are technically challenging and are inhibitory for high-throughput studies. Here we introduce a technique for testing volatiles and aerosols with positional recording (VAAPR), a method which allows for high-throughput testing of the effect of anesthetics and other aerosolized drugs using Drosophila. Using VAAPR we show that the enzyme phospholipase D (PLD) significantly shifts the concentration of diethyl ether, chloroform, and isoflurane needed to induce LOC in Drosophila. We also show that PLD is required for a paradoxical hyperactivity phenotype. We expect that this technique will allow for additional genes to be found which control anesthetic sensitivity as well as other behavioral phenotypes.
Dental hygienists' role in education of oropharyngeal cancers caused by human papillomaviruses: a thesis

This qualitative design study collected Likert style survey data to describe feelings, perceptions, and attitudes of dental hygienists about their knowledge about oral HPV and its associated risks for OPC. The research quantitatively analyzed the dental hygienists responses from the survey to determine if relationships exist based upon dental hygienists’ demographics and knowledge, comfort, and likelihood to discuss oral HPV and HPV vaccine options with patients. The survey found that 81%of surveyed dental hygienists perform an intraoral exam on every patient they care for (n=341, 80.61%). The respondents also indicated that 49.88% (n=212) of dental hygiene patients complete a risk for oral cancer assessment. As a whole, dental hygienists are aware the incidence of oral HPV in oropharyngeal cancers is rising (n=400, 96.15%). They believe it is important for dental hygienists to provide oral HPV education to their patients and report feeling comfortable (n=257, 61.2%) and knowledgeable (n=296, 69.98%) to be doing so. However, the survey found 53.44% (n=225) of dental hygienists do not discuss the risk of oral cancers developing with HPV present and 61.81 (n=246) do not discuss the mode of transmission of oral HPV. They feel they would be more comfortable and likely to discuss oral HPV education with patients if they had more knowledge on the subject. DENTAL HYGIENISTS AND HUMAN PAPILLOMAVIRUSES
Instructional supervision and the role of high school department chairs

The study examined the perspectives of three high school department chairs and their work at providing instructional supervision to the teachers with whom they work. The study sought to understand the perspectives about supervision of the high school department chairs in three subject areas—math, science, and social studies—all considered high-stakes areas. Purposeful sampling was used to select three high school department chairs from one high school in northeast Georgia. Data were collected in semi-structured face-to-face interviews and analyzed using the constant comparative method. Data from each case were analyzed separately and then across cases in which three common propositions emerged: 1) High school department chairs experienced role conflict and ambiguity relative to providing instructional supervision, 2) The meaning of instructional supervision for the department chairs was intuitive and reflected differentiated approaches, and 3) Constraints, namely time and lack of emphasis, created obstacles for the department chairs. Findings of this study indicate that high school department chairs are unaware of their job description, are not given support to practice instructional supervision, and experience both role conflict and ambiguity in the course of completing the work of the department chair position. One implication of this study is that department chairs “negotiate” their roles relative to instructional supervision and have an “intuitive” sense of instructional supervisory practices.
Response of orthopterans to macroclimate changes: A 15-year case study in Central European humid grasslands

Orthoptera is a good indicator taxon of macroclimate changes. In our case study, we analyzed data of orthopterans, vegetation, and macroclimate collected yearly from 2002 through 2017 in Central European humid grasslands. During the study period, the annual mean temperature increased, while the relative abundance of moderately hygrophilic orthopteran species decreased significantly. On the other hand, the species richness and diversity of the assemblages increased due, mostly, to an increase of graminicole/thermophilic species. According to our results, the conservation of the hygrophilic orthopteran assemblages of Central European humid grasslands under global warming can only be ensured by adequate land management, which can at least mitigate the effects of climate change resulting in the warming and drying of humid habitats.
Metrics of disturbance in a redwood forest ecosystem: responses of stream amphibians to repeated sediment infusions

Disturbances are part of the natural dynamics of Earth’s ecosystems, with these events more common now in the Anthropocene. Yet metrics for calibrating these impacts and measuring an ecosystem’s capacity to recover are lacking. Highway construction in 1989 to bypass Prairie Creek Redwoods State Park in California resulted in storm-driven infusion of exposed sediments into five streams; five nearby streams that were not intersected by the bypass construction were not affected by this event and served as controls for a natural experiment. A second large storm event in 1995 contributed sediment loads into all ten streams resulting in a disturbance gradient that allowed us to examine the effects of repeated sediment disturbances. We evaluated the impacts of these stresses on three resident stream amphibian species in 1990 and again in 1996. In 1990, the impacted streams had sixfold higher pool sediment loads and significantly lower larval tailed frog (Ascaphus truei) densities and lower densities of coastal giant salamanders (Dicamptodon tenebrosus) and southern torrent salamanders (Rhyacotriton variegatus) compared with the un-impacted streams. During the six years between these storm events, pool bowl sediment loads increased 14-fold in the previously un-impacted streams and threefold in the previously impacted streams. Larval tailed frogs and torrent salamanders further declined in both sets of streams in 1996 although nonsignificantly. In contrast, giant salamander densities increased in both stream sets. Of the three species, giant salamanders appeared the most resistant to the depositional events, while the other two species appeared to decline relative to the intensity of the sediment disturbances but still persist. We believe these results demonstrate the usefulness of these three amphibians as metrics for measuring the effects of this common disturbance type on the ecological resilience of stream networks in this and other temperate northwest forest ecosystems.
Taxonomic notes on the New Zealand flora: lectotypes and a new combination in Blechnaceae

ABSTRACT Blechnaceae is a medium-sized family of ferns in New Zealand with one genus, 23 indigenous species, two naturalised species and two nothospecies. A new combination, Blechnum × digenum (Parris) Brownsey & Perrie, is made for the hybrid between Blechnum molle (Parris) Christenh. and B. parrisiae Christenh. 11 lectotypes are chosen for basionyms relevant to New Zealand – Lomaria dura T. Moore, L. filiformis A. Cunn. , L. membranacea Colenso ex Hook. , L. nigra Colenso, L. oligoneuron Colenso, L. parvifolia Colenso, L. paucijuga Colenso, L. pumila Raoul, L. rotundifolia Colenso, Parablechnum procerum var. acuminatum C. Presl, and Stegania procera var. stipulosa A. Rich. No type material has been found for Blechnum capense var. auriculatum Domin, B. capense var. contractum Domin, B. capense var. hookerianum Domin, Lomaria paleacea Potts, or Lomaria pygmaea Colenso, and the types for these names remain undesignated. Lectotypes are being chosen where possible for all names at specific and subspecific rank, for which no holotype was designated by the original author, in order to fix the application of the name concerned. Justification for the choice is provided in each case. This article is a contribution towards clarifying the taxonomic and nomenclatural status of New Zealand plants for the plant names database (Ngā Tipu Aotearoa) and the electronic Flora of New Zealand.
Decoding the neural dynamics of oculomotor decision making in humans

Freely choosing an action between alternatives activates a widely distributed decision circuit in the brain. Primate studies suggest that oculomotor decision processes are encoded by high-frequency components of local field potentials (LFPs) recorded in frontal and parietal areas. To what extent these LFP observations extend to oculomotor decision-making in humans is unknown. Here, we address this question using intracerebral EEG recordings from 778 sites across six surgical epilepsy patients. Free saccade choices were associated with sustained high gamma (60-140 Hz) activity during the delay period in prefrontal and parietal areas. Importantly, employing single-trial signal classification to contrast free, instructed and control trials, we were able to isolate decision-related activity from sensory and motor processes. Our findings provide the first direct electrophysiological evidence in humans for the role of high gamma activity in parietal and prefrontal areas in the intrinsically driven process of choosing among competing behavioral alternatives during free choice. Highlights First LFP recordings in humans performing an oculomotor decision-making task Free-choice saccade trials exhibit sustained frontoparietal high gamma activity Machine learning analytics unravel underlying spectral and temporal brain dynamics Single-trial saccade-locked gamma distinguish planning and execution processes