Miracle-dz/UniFAR-FTUs huggingface dataset:
Playing to the Positives: Using Synergies to Enhance Kelp Forest Restoration

Kelp forests are highly productive foundation species along much of the world’s coastline. As a result, kelp are crucial to the ecological, social, and economic well-being of coastal communities. Yet, due to a combination of acute and chronic stressors, kelp forests are under threat and have declined in many locations worldwide. Active restoration of kelp ecosystems is an emerging field that aims to reverse these declines by mitigating negative stressors and then, if needed, introducing biotic material into the environment. To date, few restoration efforts have incorporated positive species interactions. This gap presents a potential shortcoming for the field as evidence from other marine ecosystems illustrates that the inclusion of positive species interactions can enhance restoration success. Additionally, as the climate continues to warm, this approach will be particularly pertinent as positive interactions can also expand the range of physical conditions under which species can persist. Here, we highlight how practitioners can use positive density dependence within and amongst kelp species to increase the chances of restoration success. At higher trophic levels, we emphasize how co-restoring predators can prime ecosystems for restoration. We also investigate how emerging technologies in genetic and microbial selection and manipulation can increase the tolerance of target species to warming and other stressors. Finally, we provide examples of how we can use existing anthropogenic activities to facilitate restoration while performing alternative purposes. As kelp forests continue to decline and the field of kelp restoration continues to develop, it is also important that we monitor these potential advancements and ensure they do not have unintended ecosystem effects, particularly with untested techniques such as genetic and microbial manipulations. Nevertheless, incorporating positive species interactions into future restoration practice stands to promote a more holistic form of restoration that also increases the likelihood of success in a shifting seascape.
Super-dosing effects of phytase in poultry and other monogastrics

Phytases have been used commercially since the early 1990s and have been the focus of considerable and sustained research for many decades. Despite this heroic effort there are still areas of persistent uncertainty such as the obscurity surrounding total compared with digestible calcium, appropriate modification to dietary sodium (and other electrolyte) concentrations, the usefulness of the amino acid and energy digestibility improvements and ultimately the effect of phytase on nutrient requirement. One further area which has attracted some attention recently is the effect of unconventionally high doses of phytase (i.e. >2,500 FTU/kg from Aspergillus niger or Escherichia coli) in an attempt to ostensibly ‘de-phytinise’ the diet. The effects of such ‘super’ doses of phytase can be considerable, and often beyond that which may be reasonably expected based on improvement in P digestibility per se. This review article addresses these effects and suggests mechanisms by which they may be explained.
BIOLOGIE ET PHYLOGEOGRAPHIE DE MONOCHAMUS GALLOPROVINCIALIS (COLEOPTERA, CERAMBYCIDAE) VECTEUR DU NEMATODE DU PIN EN EUROPE

Au Portugal ou il a ete recemment introduit accidentellement, le nematode phytopathogene invasif Bursaphelenhus xylophilus est vehicule et transmis par son vecteur indigene Monochamus galloprovincialis aux arbres hotes (Pinus pinaster). Pour estimer les risques d'invasion et de propagation en France et au reste de l'Europe, une etude approfondie de la biologie et de l'ecologie du vecteur M. galloprovincialis,, a ete menee dans ce pays, en parallele avec une etude de la variabilite genetique et morphologique de ses populations et de celles de son espece sœur M. sutor. Il a ete montre que M. galloprovincialis, present dans toutes les forets francaises, possede quatre stades larvaires qui ont ete decrits. La fecondite, la duree des stades larvaires et la longevite ont ete mesurees. L'existence d'une diapause au quatrieme stade larvaire a ete observee, dont l'effet est une synchronisation des emergences d'adultes ; une diapause prolongee semble exister chez une faible fraction de la population. Le developpement larvaire peut etre affecte par divers facteurs, dont les dimensions du rondin d'elevage. M. galloprovincialis a montre une preference pour Pinus sylvestris, mais il peut aussi bien se developper sur d'autres especes de Pinus notamment P. pinaster, essence majoritairement attaquee dans les regions du Sud Ouest. Il s'est avere que ce sont surtout les conditions climatiques et non l'essence hote, qui jouent un role important dans la distribution de cet insecte, ce qui a ete confirme par l'etude moleculaire. La proximite genetique et morphologique des especes M. galloprovincialis et M. sutor a ete mise en evidence par douze sites polymorphes du gene de la cytochrome oxydase I et quatre caracteres morphologiques dont trois correspondant a des caracteres de genitalias mâles. L'ensemble des resultats a permis de conclure qu'un grand nombre de facteurs favorables a la propagation du nematode sont reunis en France.
Hierarchical Order of Distinct Autoantibody Spreading and Progression to Type 1 Diabetes in the TEDDY Study

OBJECTIVE The first-appearing β-cell autoantibody has been shown to influence risk of type 1 diabetes (T1D). Here, we assessed the risk of autoantibody spreading to the second-appearing autoantibody and further progression to clinical disease in The Environmental Determinants of Diabetes in the Young (TEDDY) study. RESEARCH DESIGN AND METHODS Eligible children with increased HLA-DR-DQ genetic risk for T1D were followed quarterly from age 3 months up to 15 years for development of a single first-appearing autoantibody (GAD antibody [GADA], insulin autoantibody [IAA], or insulinoma antigen-2 autoantibody [IA-2A]) and subsequent development of a single second-appearing autoantibody and progression to T1D. Autoantibody positivity was defined as positivity for a specific autoantibody at two consecutive visits confirmed in two laboratories. Zinc transporter 8 autoantibody (ZnT8A) was measured in children who developed another autoantibody. RESULTS There were 608 children who developed a single first-appearing autoantibody (IAA, n = 282, or GADA, n = 326) with a median follow-up of 12.5 years from birth. The risk of a second-appearing autoantibody was independent of GADA versus IAA as a first-appearing autoantibody (adjusted hazard ratio [HR] 1.12; 95% CI 0.88–1.42; P = 0.36). Second-appearing GADA, IAA, IA-2A, or ZnT8A conferred an increased risk of T1D compared with children who remained positive for a single autoantibody, e.g., IAA or GADA second (adjusted HR 6.44; 95% CI 3.78–10.98), IA-2A second (adjusted HR 16.33; 95% CI 9.10–29.29; P < 0.0001), or ZnT8A second (adjusted HR 5.35; 95% CI 2.61–10.95; P < 0.0001). In children who developed a distinct second autoantibody, IA-2A (adjusted HR 3.08; 95% CI 2.04–4.65; P < 0.0001) conferred a greater risk of progression to T1D as compared with GADA or IAA. Additionally, both a younger initial age at seroconversion and shorter time to the development of the second-appearing autoantibody increased the risk for T1D. CONCLUSIONS The hierarchical order of distinct autoantibody spreading was independent of the first-appearing autoantibody type and was age-dependent and augmented the risk of progression to T1D.
A review of changes in the fish assemblages of Levantine inland and marine ecosystems following the introduction of non‐native fishes

Summary The arrival of non-native fishes in the Levant Basin began in the late 19th century. Whereas the presence of most of the 40 non-native freshwater fishes stem from intentional introductions, either for aquaculture or pest control, the 62 species of non-native marine fishes arrived by natural dispersal via the Suez Canal. Of the non-native freshwater species, five have established successful breeding populations (mosquitofish Gambusia affinis, common carp Cyprinus carpio, crucian carp Carassius carassius, swordtail Xiphophorus hellerii and rainbow trout Oncorhynchus mykiss), and seven are regularly stocked in natural habitats (thinlip mullet Liza ramada, flathead mullet Mugil cephalus, European eel Anguilla anguilla, grass carp Ctenopharyngodon idella, Asian silver carp Hypophthalmichthys molitrix, bighead carp Aristichthys nobilis, black carp Mylopharyngodon piceus). Some non-native species appear to have out-competed native species. Gambusia affinis may have caused the extirpation of two native cyprinid fishes from the Qishon River basin (Levant silver carp Hemigrammocapoeta nana and common garra Garra rufa) and the southern Dead Sea (endemic Sodom’s garra G. ghoerensis). The opening of the Suez Canal in 1869 allowed entry into the eastern Mediterranean of Indo-Pacific and Erythrean biota, with the latter now dominating the community structure (50–90% of fish biomass) and function (altered native food web) of the Levantine littoral and infra-littoral zones. The process has accelerated in recent years concurrent with a warming trend of the seawater. Record numbers of newly discovered non-native species is leading to the creation of a human-assisted Erythrean biotic province in the eastern Mediterranean.
A model‐derived short‐term estimation method of effective size for small populations with overlapping generations

If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rate increases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasing their risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and therefore of considerable conservation relevance. However, estimators of Ne that account for demographic parameters in species with overlapping generations require sampling of populations across generations, which is often not feasible in long‐lived species. We created an individual‐based model that allows calculation of Ne based on demographic parameters that can be obtained in a time period much shorter than a generation. It can be adapted to every life‐history parameter combination. The model is freely available as an r‐package NEff. The model was first used in a simulation experiment observing changes in Ne in response to different degrees of generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosity loss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of different recruitment rates only affected Ne for populations with low generational overlap. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata. Simulation results were compared to genetic analyses and matched estimates of the real population very well. Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring nor genetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne within short time periods and comparably low costs facilitating the use of Ne in applied conservation and management.
Putative drug targets in thypus causing Rickettsia prowazekii str. Madrid E: An in silico approach

Epidemic louse borne typhus and Brill-Zinsser disease caused by Rickettsia prowazekki is a public health problem spanning world around. The epidemic disease spread by arthropod mainly louse. The treatment includes use of various antibiotics; some of them occasionally may show resistance. An advanced stage of thyphus is difficult to treat due to lack of precise diagnosis or under diagnosis. The main objective of the current studies, in view with above problems is mining the putative drug targets in thypus causing Rickettsia prowazekii by insilico methods. In this study the insilico genomic approach is used to find out the alternative or additional membrane putative drug targets (vaccine targets). The deferential comparative genomics approach mines out the membrane bound non-homologous proteins that are essential for survival of the bacteria and are part of unique metabolic pathway. Availability of the proteome of Rickettsia prowazekki has made possible the analysis for finding the drug targets. A total of 5 membrane associated drug targets were identified following the algorithm from among 837 proteins in the proteome of Rickettsia prowazekii str. Madrid E. Homology modeling of the membrane associates proteins was performed. The 3- D structure of such proteins can be further extended for other in silico studies like virtual screening of natural drugs, tracing of epitopes and putative biodiagnostic tools. The specific membrane drug targets can also act as biodiagnostic markers.
Bounded Modality

What does ‘might’ mean? One hypothesis is that ‘It might be raining’ is essentially an avowal of ignorance like ‘For all I know, it’s raining’. But it turns out these two constructions embed in different ways—in particular as parts of larger constructions like Wittgenstein (1953)’s ‘It might be raining and it’s not’ and Moorean sentences like ‘It’s raining and for all I know, it’s not’ (Moore, 1942). A variety of approaches have been developed to account for those differences. All approaches agree that both Moore sentences and Wittgenstein sentences are classically consistent. In this paper I argue against this consensus. I adduce a variety of data which I argue can best be accounted for if we treat Wittgenstein sentences as being classically inconsistent. This creates a puzzle, since there is decisive reason to think that pMight pq is consistent with pNot pq. How can it also be that pMight p and not pq and pNot p and might pq are inconsistent? To make sense of this situation, I propose a new theory of epistemic modals which aims to account for their subtle embedding behavior and shed new light on the dynamics of information in natural language.
Forest age and isolation affect the rate of recovery of plant species diversity and community composition in secondary rain forests in tropical Australia

Questions: Which factors affect the diversity and species composition of tropical secondary rain forests in a region with little information regarding their contribution to global biodiversity? Can older secondary forests approach the diversity and composition of mature forests following 100 yr of pasture use? Location: Tropical secondary rain forest, northeast Australia. Methods: We identified trees, shrubs and vines ≥2.5 cm DBH in a chronosequence comprising 33 sites, aged 3–60 yr since the formation of closed canopy (9–69 yr since pasture abandonment) and compared them with eight sites in nearby mature forest remnants. Results: Species richness and community composition were strongly influenced by secondary forest age but did not attain values of mature forest. Sites in close proximity to mature forests had higher plant richness, whereas low soil fertility appeared to depress species recruitment. Thus, multiple factors operated in secondary forest community assembly. Unusual tree community patterns that suggest accelerated or slowed successional trajectories were observed at several sites. Conclusions: Secondary forests in our study region contained important plant diversity for conservation, particularly in older sites, however, even the oldest secondary forests (60 yr) did not converge with the species composition and diversity of mature forests. The protection of mature forest tracts and remnants must be a priority if we are to maintain high levels of plant diversity in tropical landscapes, conserve rare species and facilitate the recruitment of plant species in recovering forests.
Turf and Ornamental Plant Tolerances to Endothall in Irrigation Water II. Turf Species

a.i. on st. augustinegrass for the amine and dipotassium formulations of en- dothall respectively, and 958 mg·L -1 a.i. for the dipotassium formulation on bermudagrass. There was no effect on bermudagrass dry weights when exposed to the amine formulation of endothall in Expt. 2 at concentrations up to 1600 mg·L -1 a.i. There is a low risk of inhibiting growth of turf spe- cies at endothall concentrations used for aquatic weed control considering the maximum use concentrations, typical uses of the products, and de- composition rates.
Movements by Adult Coho Salmon in the Lower Elwha River, Washington

Abstract The Elwha and Glines Canyon dams caused a dramatic decline in the numbers of all species of native Pacific salmonids (Oncorhynchus spp.) in the Elwha River. During the fall of 2005 and 2006, we radiotagged 49 adult coho salmon (O. kisutch) and tracked their movements between the Elwha River mouth and Elwha Dam (7.3 rkms). Half of all tagged fish were never relocated, likely due to emigration from the river. The remainder tended to migrate quickly and directly to one or two areas saturated with large woody debris and gravel, known to be high quality spawning habitat, and remain there. However, 7 of the 13 tagged fish in 2005 made multiple upstream and downstream movements prior to spawning. No tagged fish in either year migrated farther upstream than a rock weir approximately 4.9 km from the river mouth and 2.4 km downstream from the Elwha Dam, possibly indicating a migration barrier for coho salmon. We did not detect qualitative differences in migration behavior between hatchery and unknown-origin fish, but we did find that males moved slightly larger distances after tagging than females (average, 3.6 km for males, 2.5 km for females, t-test, P = 0.41). A large flow event on 6 November 2006 caused 8 of 11 tagged fish residing in the river to emigrate; none of these fish returned. Results both confirm ideas of coho salmon biology and raise concerns regarding environmental impacts on coho salmon recolonization following dam removal.
Influence of subclinical endometritis on the reproductive performance of dairy cows.

The aim of this study was to evaluate the influence of subclinical endometritis (SE) on the reproductive performance of dairy cows. Ninety-four dairy cows of parity 1 to 8, distributed in 25 herds, were examined once between 30 and 45 days in milk using transrectal palpation, vaginoscopy and ultrasonography. A cytological sample of the endometrium was taken only from cows with an apparent healthy uterus (n=65). Serum glucose, total cholesterol, triglycerides, non-esterified fatty acids, β-hydroxybutyrate, total proteins, albumin, urea and hepatic enzymes were analyzed. Reproductive indexes were recorded during the next 11 months. Endometrial cytology was considered indicative of SE if percentage of polymorphonuclear neutrophils was superior to 5% of all cells present in the smear, except erythrocytes. Results indicated that 14.9% of the cows sampled for uterine cytology had SE, and that healthy cows become pregnant significantly before than those with SE (hazard ratio=2.35; 95% confidece interval: 1.05-5.3). From all the metabolic and productive variables analyzed, only triglycerides affected negatively to reproduction; serum albumin concentration, body condition score and milk production had positive effects on the reproductive performance. In conclusion, our results indicate that SE has a negative impact on reproductive performance and uterine cytology is necessary to diagnose it since almost 15% of the affected animals were not detected by other diagnosis methods.
Impact of dispersal status on estimates of local population growth rates in a Temminck's stint Calidris temminckii population

Due to different costs and benefits associated with dispersal and philopatry, life history traits of immigrants and philopatric individuals may differ. Despite of the apparent effects, dispersal status is only rarely considered in analyses of population dynamics. We analysed whether dispersal status explains variation in life history traits of an endangered Temminck's stint Calidris temminckii population breeding at the Baltic Sea. We also estimated the impact of immigration and dispersal status on the population growth rate (λ) with a population matrix model, in which immigrants and philopatric individuals are separated to their own stages. We found that philopatric individuals had a higher apparent survival than immigrants in both sexes. In reproductive parameters, variation due to dispersal status was not clear. Nests incubated by philopatric individuals survived better than those of immigrants, but this did not translate in hatchling production per breeding attempt. Models described a sink population in which the inclusion of both immigration rate to the population and the dispersal status of individuals into the model increased estimates of λ. When the better success of philopatric individuals was considered, the population growth appeared more stable (λ=0.972). If this was not taken into account, λ implied a strong decline (λ=0.911). The results support the hypothesis that immigrants exhibit lower components of lifetime reproductive success and therefore contribute less to population growth and the gene pool than local recruits. While we cannot distinguish whether this difference reflects higher mortality or permanent emigration, the latter explanation seems more plausible. Our results highlight the importance of considering immigration and dispersal status in population modelling. In the case of the endangered study population, the results implied that management options directed to improve local recruitment would be a profitable option.
Learning through social interaction: Kenyan women against female genital cutting in Kenya

Abstract Female Genital Cutting (FGC) is a human rights issue that involves the partial or total removal of the external female genitalia for non-medical reasons. Drawing on in-depth interview data collected in 2017 with 20 women from three FGC-practising ethnic groups in Kenya, I argue that informal learning through social interaction plays a critical role in the ability of Kenyan women to oppose and work against FGC in their communities. In addition to knowledge gained through formal education such as schooling and anti-FGC campaigns, women learned about FGC and ways to resist the practice through social interaction with family members, role models and peers from non-FGC practising communities. These interactions have framed challenging FGC as a worthy behaviour to pursue. They also helped women reframe ‘success. ’ While a hallmark of being a successful woman has traditionally been tied to FGC, through these interactions, women learned that they can achieve a respected status as a woman without undergoing FGC. Finally, they provided support for women to stay resilient in resisting FGC. Overall, informal learning is important for understanding how some Kenyan women resist FGC.