Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods

Many biological studies require the capture of individuals for sampling, for example for measurement of morphological or physiological traits, or for marking individuals for later observations. Capture methods employed often vary both within and between studies, and these differing methods could be more or less effective in capture of different individuals based on their morphology or behavior. If individuals that are prone to capture by the selected method differ with respect to traits of interest, such sampling bias could generate misleading or simply inaccurate results. The selection of capture methods could introduce two different forms of sampling bias, with the individuals that are sampled differing from the population at large or with individuals sampled via one method differing from individuals that could be sampled using a different method. We investigated this latter form of sampling bias by comparing individual birds sampled using two common capture techniques. We caught free-ranging black-capped chickadees (Poecile atricapillus) using walk-in traps baited with seed and mist nets paired with playback of an audio stimulus (conspecific mobbing calls). We measured 18 traits that we expect might vary among birds that are trappable by these differing methods—one that targets birds that are food motivated and potentially less neophobic and another that targets birds that respond readily to a perceived predation risk. We found no differences in the sex, morphology, initial and stress-induced corticosterone concentrations, behavioral response to a novel object, or behavioral response to a predator between individuals captured by these two methods. Individual variation in the behavioral response to a novel object was greater among birds caught by mist nets, suggesting this method might provide a sample that better reflects population-level individual variation. We do not know if the birds caught by these two methods provide a representative sample of the population at large, but can conclude that selection of either of these two common capture methods can similarly sample mean trait values of a population of interest. To accurately assess individual variation, particularly in behavior, mist nets might be preferable.
Life history and habitat do not mediate temporal changes in body size due to climate warming in rodents

Temporal changes in body size have been documented in a number of vertebrate species, with different contested drivers being suggested to explain these changes. Among these are climate warming, resource availability, competition, predation risk, human population density, island effects and others. Both life history traits (intrinsic factors such as lifespan and reproductive rate) and habitat (extrinsic factors such as vegetation type, latitude and elevation) are expected to mediate the existence of a significant temporal response of body size to climate warming but neither have been widely investigated. Using examples of rodents, we predicted that both life history traits and habitat might explain the probability of temporal response using two tests of this hypothesis. Firstly, taking advantage of new data from museum collections spanning the last 106 years, we investigated geographical and temporal variation in cranial size (a proxy for body size) in six African rodent species of two murid subfamilies (Murinae and Gerbillinae) of varying life history, degree of commensality, range size, and habitat. Two species, the commensal Mastomys natalensis, and the non-commensal Otomys unisulcatus showed significant temporal changes in body size, with the former increasing and the latter decreasing, in relation with climate warming. Commensalism could explain the increase in size with time due to steadily increasing food availability through increased agricultural production. Apart from this, we found no general life history or habitat predictors of a temporal response in African rodents. Secondly, in order to further test this hypothesis, we incorporated our data into a meta-analysis based on published literature on temporal responses in rodents, resulting in a combined dataset for 50 species from seven families worldwide; among these, 29 species showed no significant change, eight showed a significant increase in size, and 13 showed a decline in size. Using a binomial logistic regression model for these metadata, we found that none of our chosen life history or habitat predictors could significantly explain the probability of a temporal response to climate warming, reinforcing our conclusion based on the more detailed data from the six African species.
Irisin Regulates the Functions of Hepatic Stellate Cells

Background Hepatic stellate cells (HSCs) are known to play a fundamental role in the progression of liver fibrosis. Once HSCs are activated, they are involved in proliferation, migration, and contractility which are characteristics of liver fibrogenesis. Recent studies have shown that irisin, a myokine secreted during physical exercise, has a protective effect in various metabolic diseases, especially in renal fibrosis. However, whether irisin is involved in HSC activation and other processes associated with liver fibrosis has not yet been investigated. In this study, we reveal the role of irisin in HSC activation as well as in proliferation, migration, and contractile properties of HSCs in vitro. Methods LX-2 cells, immortalized human HSCs, were treated with transforming growth factor beta 1 (TGF-β1), a core regulator of HSC fibrosis, with or without irisin, and markers of the aforementioned processes were analyzed. Further, an inflammatory response was stimulated with TGF-β1 and lipopolysaccharide (LPS) in combination with irisin and the expression of cytokines was measured. Results Recombinant irisin significantly suppressed the expression of TGF-β1-stimulated fibrosis markers including alpha-smooth muscle actin and collagen type 1 alpha 1 and prevented the TGF-β1-induced proliferation, migration, and contractility of LX-2 cells. Additionally, irisin ameliorated the production of interleukin-6 (IL-6) and IL-1β induced by TGF-β1 and LPS treatments. Conclusion These findings suggested that irisin potently improved the progression of hepatic fibrosis by regulating HSC activation, proliferation, migration, contractility, and HSC-mediated production of inflammatory cytokine.
Forest before the trees in the aquatic world: global and local processing in teleost fishes

Background The study of illusory phenomena is important to understanding the similarities and differences between mammals and birds’ perceptual systems. In recent years, the analysis has been enlarged to include cold-blooded vertebrates, such as fish. However, evidence collected in the literature have drawn a contradictory picture, with some fish species exhibiting a human-like perception of visual illusions and others showing either a reversed perception or no susceptibility to visual illusions. The possibility exists that these mixed results relate to interspecific variability in perceptual grouping mechanisms. Therefore, we studied whether fish of five species exhibit a spontaneous tendency to prioritize a global analysis of the visual scene—also known as global-to-local precedence—instead of focusing on local details. Methods Using Navon-like stimuli (i.e., larger recognisable shapes composed of copies of smaller different shapes), we trained redtail splitfin, zebrafish, angelfish, Siamese fighting fish and three spot gourami to discriminate between two figures characterized by congruency between global and local information (a circle made by small circles and a cross made by small crosses). In the test phase, we put global and local cues (e.g., a circle made by small crosses) into contrast to see whether fish spontaneously rely on global or local information. Results Like humans, fish seem to have an overall global-to-local precedence, with no significant differences among the species. However, looking at the species-specific level, only four out of five species showed a significant global-to-local precedence, and at different degrees. Because these species are distantly related and occupy a broad spectrum of ecological adaptations, we suggest that the tendency to prioritize a global analysis of visual inputs may be more similar in fish than expected by the mixed results of visual illusion studies.
A comparison of common metrics used to quantify the effectiveness of conservation interventions

Background Evidence-based conservation is urgently needed to identify, apply and promote effective interventions for mitigation of threats and recovery of the natural environment. Estimation of intervention effectiveness is subject to robust study design and statistical analysis, and much progress is documented in these fields. In contrast, little is understood about the accuracy and biases (underestimation and overestimation) of different effectiveness metrics and how they are affected by sample size. Methods In this study, a dataset (n = 500 cases) consisting of random, positive, integer numbers was simulated to produce frequency input data for the 2 × 2 contingency table. For each case, three metrics of the relative risk, odds ratio and the magnitude of change were calculated, their disparity was estimated and the characteristics of treatment (with intervention) and control (without intervention) samples significantly affecting this disparity were studied by means of linear regression. Further, four case studies from different conservation interventions are provided to support the results. Results The study has shown that the relative risk and the magnitude of change produce identical estimates of intervention effectiveness only when treatment and control samples are equal, or when the number of target outcomes (e.g., number of livestock killed by predators) in treatment sample reaches zero. In other situations, the magnitude of change gives overestimates or underestimates, depending on relationships between treatment and control sample sizes. The table summarizing the conditions of equalities and biases between these two metrics is provided. These conditions are valid for both reduction-aimed interventions reducing negative target outcomes (e.g., livestock protection to reduce livestock losses to predators) and for addition-aimed interventions increasing positive target outcomes (e.g., establishment of protected areas to increase species presence). No significant effects on the odds ratio were found. Conclusion Researchers should set equal treatment and control sample sizes so that to produce identical estimates of intervention effectiveness by the relative risk and the magnitude of change. Otherwise, these estimates are biased if produced by the magnitude of change and the relative risk should be used instead. As setting equal treatment and control samples can be impractical, I encourage researchers and practitioners to use the relative risk in estimation of intervention effectiveness. This will not take additional efforts as both metrics are calculated from the same contingency table. Treatment and control sample sizes, along with their sub-samples affected and not by an intervention, should be explicitly reported by researchers to allow independent evaluation of intervention effectiveness. This approach can help obtain more accurate information on intervention effectiveness for making better decisions in conservation actions.
COMBINING ABILITY STUDIES FOR BIOCHEMICAL TRAITS IN BRASSICA RAPA (L.) SSP. DICHOTOMA (ROXB.) HANELT

Combining ability was studied in 6 x 6 complete diallel cross in Brassica rapa (L.) ssp. dichotoma (Roxb.) Hanelt. Significant differences were observed for all the traits except protein and glucosinolate content. GCA mean squares were non-significant for all the traits. SCA and RCA components of variation were significant for all the traits with the respective exception of oleic acid and oil content. Prevalence of non-additive genetic control was detected for all the traits except oleic acid content for which maternal effects were more important. ACC-403, ACC-909 were good general combiners for oil content and linolenic acid; ACC-902, ACC-1500 for oleic acid and ACC-265 the worse general combiner for erucic acid. Based on desirable SCA effects and mean performance the cross combinations ACC-265 x ACC-909, ACC-403 x ACC1500 (oil content); ACC-909 x ACC-902, ACC-909 x ACC-1500 (oleic acid content); ACC-403 x ACC-1500 (linolenic acid content) and ACC-265 x ACC-403; ACC-909 x ACC-1500; ACC-265 x ACC-902 (erucic acid content) were superior and can be further exploited.
Germination studies on some annual species from an arid region of Western Australia

Annual floras of the arid regions of Western Australia have been described by Gardner (1942) and Wilcox (1963), who noted that the typical flora which occurs after winter rains is predominantly of dicotyledons, whereas monocotyledons, especially grasses, make up a large proportion of the summer-germinating annuals. Analogous differences between summer and winter floras occur in arid regions of North America, and Went (1948, 1949) attributed the differences to germination requirements. As there is no equivalent study of the germination requirements of annuals in the arid zones of Australia, the following analysis was carried out to evaluate the relation between germination requirements and the composition of the summer and winter floras. The area studied in detail is a station property, Mileura, in the Murchison Region of Western Australia (latitude 26022' S; longitude 117? 20' E) (Fig. 1). The area forms part of a broad watershed drained by the Murchison River into the Indian Ocean. There is little relief in the land surface, and the soils are mainly leached red-earths overlying a siliceous hard-pan. The land types of the Murchison Region have been described by Mabbutt et al. (1963). On their land system classification, the majority of the study area is of the sandy red-earths of the Belele and Ero Land Systems, while the remainder is composed of the rocky Sherwood Land System and the saline river flats of the Beringarra Land System. The area falls within a zone receiving an average of less than 200 mm of rainfall annually. Arnold (1963) gives a general account of the weather of the whole Murchison Region. She points out that the rainfall results both from winter and summer falls, with tropical cyclones and local thunderstorms accounting for the precipitation in the summer months from November to March, and extra-tropical depressions bringing rain in the cooler months from May to August (Fig. 2). Rainfall is extremely variable, great differences between the falls occurring each year. Arnold notes that droughts are common if the condition of introduced stock is taken as a criterion. Moreover, Davies (1968) points out that sufficient rain falls to recharge the drainage channels in at least 80% of the summers and 90% of the winters. There is a wide difference between the mean monthly maximum and minimum temperatures in the two seasons. This, allied with the two periods of rainfall, gives sharply delineated growing seasons (Fig. 2). Temperatures in the top 0-5 cm of soil can rise to very high levels in the summer months, with mean maxima of over 65? C for four months of the year. The major annual vegetation over most of the station is 'annual short grass-mixed forb' and 'short grass-chenopod' pastures described by Wilcox & Speck (1963), with the
A model describing the interactive roles of predation, competition and tidal elevation in structuring mussel populations

The black mussel Choromytilus meridionalis can survive when exposed in air up to 50 per cent of the time, but it is normally restricted to about 30 per cent exposure by extremes of temperature and desiccation. Growth rates vary greatly with location and tidal elevation, but as they grow, the mussels compete intensively for space, consequent mortality rates being proportional to growth rate. Because growth declines with tidal elevation and as terminal size is approached, losses attributable to competition tend to be greatest in lowshore and sublittoral regions and early in life. There are many predators of mussels, each differing in its feeding rate and technique. The quantities and size distributions of C. meridionalis taken by communities of natural predators at selected sites are estimated. Total predator consumption is compared with rates of loss as individual mussels increase in size and compete for space. Fast-growing populations with large terminal sizes can support dense predator communities with l.
On the relation between basal and field metabolic rates in birds and mammals

Basal metabolic rate (BMR) is widely assumed to be an index of energy expenditure of free-living animals. However, few attempts have been made to check if the assumption is valid. In this study field metabolic rates (FMR) of 58 species of birds and mammals have been compared with their BMRs. FMR tends to increase with increasing body mass slower than BMR, but the difference was significant only in marsupials. A correlation between mass-independent FMR and BMR (residuals from regressions) is very high in eutherians (mainly rodents), but it is weak in birds and approaches zero in marsupials. The assumption of a proportionality between BMR and energy expenditure of animals does not have a sound experi-
Using genetic variants to evaluate the causal effect of cholesterol lowering on head and neck cancer risk: A Mendelian randomization study

Introduction Head and neck squamous cell carcinoma (HNSCC), which includes cancers of the oral cavity and oropharynx, is a cause of substantial global morbidity and mortality. Strategies to reduce disease burden include discovery of novel therapies and repurposing of existing drugs. Statins are commonly prescribed for lowering circulating cholesterol by inhibiting HMG-CoA reductase (HMGCR). Results from some observational studies suggest that statin use may reduce HNSCC risk. We appraised the relationship of genetically-proxied cholesterol-lowering drug targets and other circulating lipid traits with oral (OC) and oropharyngeal (OPC) cancer risk. Methods and findings We conducted two-sample Mendelian randomization (MR). For the primary analysis, germline genetic variants in HMGCR, NPC1L1, CETP, PCSK9 and LDLR were used to proxy the effect of low-density lipoprotein cholesterol (LDL-C) lowering therapies. In secondary analyses, variants were used to proxy circulating levels of other lipid traits in a genome-wide association study (GWAS) meta-analysis of 188,578 individuals. Both primary and secondary analyses aimed to estimate the downstream causal effect of cholesterol lowering therapies on OC and OPC risk. The second sample for MR was taken from a GWAS of 6,034 OC and OPC cases and 6,585 controls (GAME-ON). Analyses were replicated in UK Biobank, using 839 OC and OPC cases and 372,016 controls and the results of the GAME-ON and UK Biobank analyses combined in a fixed-effects meta-analysis. We found limited evidence of a causal effect of genetically-proxied LDL-C lowering using HMGCR, NPC1L1, CETP or other circulating lipid traits on either OC or OPC risk. Genetically-proxied PCSK9 inhibition equivalent to a 1 mmol/L (38.7 mg/dL) reduction in LDL-C was associated with an increased risk of OC and OPC combined (OR 1.8 95%CI 1.2, 2.8, p= 9.31 x10-05), with good concordance between GAME-ON and UK Biobank (I2= 22% ). Effects for PCSK9 appeared stronger in relation to OPC (OR 2.6 95%CI 1.4, 4.9) than OC (OR 1.4 95%CI 0.8, 2.4). LDLR variants, resulting in genetically-proxied reduction in LDL-C equivalent to a 1 mmol/L (38.7 mg/dL), reduced the risk of OC and OPC combined (OR 0.7, 95%CI 0.5, 1.0, p= 0.006). A series of pleiotropy-robust and outlier detection methods showed that pleiotropy did not bias our findings. Conclusion We found limited evidence for a role of cholesterol-lowering in OC and OPC risk, suggesting previous observational results may have been confounded. There was some evidence that genetically-proxied inhibition of PCSK9 increased risk, while lipid-lowering variants in LDLR, reduced risk of combined OC and OPC. This result suggests that the mechanisms of action of PCSK9 on OC and OPC risk may be independent of its cholesterol lowering effects, but further replication of this finding is required.
Incidence and management of plant parasitic nematodes under continuous vegetable production in a rainforest agroecology in Nigeria

Summary Field studies were conducted in 2012 and 2013 in the tropical rainforest zone of Nigeria to investigate the effects of a composted, pelletised organo-mineral fertiliser applied as an organic amendment at 5 metric tonnes (MT) ha-1 or at 10 MT ha-1 in four replications, on soil population densities of five genera of plant-parasitic nematodes and on crop yields of Telfairia occidentalis (fluted pumpkin). The experimental field was naturally infested with Meloidogyne incognita, Tylenchus spp. , Helicotylenchus spp. , Hirschmaniella spp. , and Longidorus spp. The compost was applied as an amendment to soil planted with T. occidentalis 3 weeks after seedling emergence. At the end of both annual experiments, the addition of compost as a soil amendment resulted in 16.25 - 65.75% reductions in the populations of all five genera of plant-parasitic nematodes compared to an increase in each nematode population in the untreated control plots. There was also a higher crop yield of T. occidentalis in all eight treated plots compared to the control plots. Compost applied at 10 MT ha-1 reduced the soil populations of all nematode species significantly, with correspondingly higher yields of the crop compared to 5 MT compost ha-1 in both years of study. Correlation analysis showed that the population density of each nematode species had a negative effect on the cumulative leaf biomass (fresh weight) of the test crop. The results of this study suggest that nematodes constrained the production of T. occidentalis under continuous cropping and that a composted, pelletised organo-mineral fertiliser, applied as a soil amendment at 10 MT ha-1, suppressed soil populations of all five nematodes significantly and increased yields of T. occidentalis by 109 - 366% compared to the untreated control plots.
Leveraging spatial structure with CapsuleNet for identification of the land use classes

Urban land use classes of complex nature are marked by the presence of multiple land covers and/or objects in the specific spatial order. The spatial configuration of the constituent parts of the land use class is generally unique. To the extent that the specific spatial configuration is defining characteristic of a given land use class. These characteristics can be effectively leveraged to identify the land use class. In this research, we exploit the unique spatial structure of the constituent parts for the land use class for its detection. We use capsule network (CapsuleNet) for detecting some of the urban land use classes such as parking lot and golf courses. CapsuleNets use a group of neurons (called capsules) in a convolutional layer to detect a specific image primitive. Each subsequent layer detects higher order primitives, and its relationship with the lower level primitives. Thus, multiple such layers build a hierarchy of parts to learn the whole object, in this case the land use class. We conducted multiple experiments for detecting parking lots and golf courses in a collection of urban images. We used NWPU-RESISC45 dataset for conducting our experiments. Furthermore, we compared the results of CapsuleNet based architecture with standard architecture such as VGG16, which do not consider the spatial structure of the features. Our initial experiments suggest improvement in accuracy in classification of the land use classes such as parking lot and golf courses.