Miracle-dz/UniFAR-FTUs huggingface dataset:
Physiology in ecological niche modeling: using zebra mussel's upper thermal tolerance to refine model predictions through Bayesian analysis

Climate change and human‐mediated dispersal are increasingly influencing species’ geographic distributions. Ecological niche models (ENMs) are widely used in forecasting species’ distributions, but are weak in extrapolation to novel environments because they rely on available distributional data and do not incorporate mechanistic information, such as species’ physiological response to abiotic conditions. To improve accuracy of ENMs, we incorporated physiological knowledge through Bayesian analysis. In a case study of the zebra mussel Dreissena polymorpha, we used native and global occurrences to obtain native and global models representing narrower and broader understanding of zebra mussel’ response to temperature. We also obtained thermal limit and survival information for zebra mussel from peer‐reviewed literature and used the two types of information separately and jointly to calibrate native models. We showed that, compared to global models, native models predicted lower relative probability of presence along zebra mussel's upper thermal limit, suggesting the shortcoming of native models in predicting zebra mussel's response to warm temperature. We also found that native models showed improved prediction of relative probability of presence when thermal limit was used alone, and best approximated global models when both thermal limit and survival data were used. Our result suggests that integration of physiological knowledge enhances extrapolation of ENM in novel environments. Our modeling framework can be generalized for other species or other physiological limits and may incorporate evolutionary information (e.g. evolved thermal tolerance), thus has the potential to improve predictions of species’ invasive potential and distributional response to climate change.
Testing of the applicability of European diatom indices in the tropical rift valley lake, Lake Hawassa, in Ethiopia

Quantitative ecological monitoring of African lakes is needed to understand growing human pressures on ecosystems. Diatom-based indices are routinely used for this purpose elsewhere in the world, but have not yet been produced for the flora of African freshwater lakes. Here we tested the applicability of the European diatom indices on the biomonitoring system of Lake Hawassa, Ethiopia. Physico-chemical and benthic diatom sampling was done at nine sites with different degrees of human disturbance along the lakeshore area from February to November 2015 and 2016. A percentage disturbance score (PDS) was calculated at each site and categorised from no evident disturbance (0–25%) to high disturbance (75–100%). Based on this criterion and selected physico-chemical parameters, the sampling sites categorized into minimal, moderate and high disturbance. Seventeen diatom indices were calculated using Omnidia software version 5.3. Out of a total of 17 indices that were calculated using the Omnidia software, six were selected as potential metrics. The diatom indices had a high discrimination efficiency and were significantly correlated with most the environmental parameters (r > 0.6; p < 0.05). Among these, the trophic diatom index (TDI) and generic diatom index (IDG) showed the best potential to discriminate the three clustered sites, based on their ecological classification. Accordingly, although robust locally based indices are needed, the TDI and IDG diatom indices could be used in monitoring of water quality in tropical African rift lakes.
DNA Barcoding and Analysis of Nine Butterfly Species And Three Moth Species From Entopia Penang Butterfly Farm

This study aims to utilize cytochrome c oxidase subunit I (COI) DNA sequences in the classification of 22 butterfly and 8 moth species that were morphologically identified by Entopia Penang Butterfly Farm. COI of the mitochondrial gene has been chosen for evolutionary study of butterflies and moths because COI mitochondrial gene is maternally inherited with little or no recombination. This research revealed that 20 out of 22 butterflies were correctly classified while two butterflies and three moths were misidentified after the sequences were analyzed using Basic Local Alignment Search Tool (BLAST). Morphologically identified Cepora nadina (Sample ID: NCN1) was identified as Cepora iudith while Prioneris thestylis (NPT2) was identified as Prioneris philonome. Three moths; Dysphania malayanus (RDMA1), Nyctemera coleta (RNC1) and Nyctemera coleta (RNC2) were discovered as Bracca matutinata, Nyctemera regularis and Nyctemera baulus respectively. The outcome of this study further classified four butterfly species into subspecies, including Cepora nadina with subspecies andersoni, Prioneris philonome with subspecies themana, Pareronia valeria with subspecies lutescens and Elymnias nesaea classified into subspecies Elymnias nesaea lioneli. Analysis of nine butterfly species and three moth species demonstrates the value in attaching subspecies names to DNA barcode records and further helps to correct misidentified species. Overall, the relationship between butterfly and moth proves that butterfly and moth are distantly related.
Failure to engage the TPJ-pSTS during naturalistic scene processing in schizophrenia

The ability to search for and detect social cues, such as facial expressions of emotion, is critical to the understanding of complex dynamic social situations. This ability involves the coordinated actions of multiple cognitive domains, including face-emotion processing, mentalization, and visual attention. Individuals with schizophrenia are generally impaired in social cognition, and have been shown to have deficits in all of these domains. However, the whether the neural substrates of these impairments are shared or separate remains unclear. One candidate region for a shared substrate is the right temporoparietal junction/posterior superior temporal sulcus (TPJ-pSTS), which contains areas belonging to all of the cortical networks underlying these domains. Here we use functional MRI to examine differences in cortical activity evoked by a naturalistic movie, and link these results to impaired visual scanning and social cognition. 27 schizophrenia participants and 21 healthy controls watched a 15-minute clip of the movie “The Good, the Bad, and the Ugly” while high resolution multiband BOLD-fMRI activity was recorded. Inter-subject correlation was used to measure the evoked activity. BOLD-fMRI activity was also correlated with motion content in the movie, with the average activity in other cortical areas, and with frequency of saccades made during the movie. Visual scanning performance was measured in a separate behavioral experiment, and social cognition measured by The Awareness of Social Inference Test (TASIT). Contrasting the groups revealed that the TPJ-pSTS has the largest engagement deficit in both cortical hemispheres in schizophrenia patients versus healthy controls. Follow-up analyses find that brain activity in this region is less correlated with the motion content of the movie, that this region is abnormally synchronized to the other cortical areas involved in the cognitive domains underlying visual scanning of social scenes, and that activity this region is less correlated with the saccades made during the movie. Lastly, schizophrenia participant visual scanning performance of this clip was impaired compared to healthy controls, and correlated across the two groups with social cognition. These results indicate that the TPJ-pSTS plays less of an integral role in the coordination of face-emotion processing, mentalization, and visual attention in schizophrenia participants versus healthy controls. This functional deficit then impacts the visual scanning of a complex dynamic visual scenes, which in turn affects the comprehension of that scene. These findings indicating that the TPJ-pSTS is potentially the shared substrate for all of these deficits will lead to new treatments targeting this region to improve social cognition in individuals with schizophrenia.
Assessment of anesthesia on physiological stability and BOLD signal reliability during visual or acoustic stimulation in the cat

Background Neuroimaging methods including fMRI provide powerful tools to observe whole-brain functional networks. This is particularly powerful in animal models, allowing these networks to be probed using complementary methods. However, most animals must be anesthetized for neuroimaging, giving rise to complications resulting from anesthetic effects on the animal’s physiological and neurological functions. For example, an established protocol for feline neuroimaging involves co-administration of ketamine and isoflurane – the latter of which is known to suppress cortical function. New Method Here, we compare this established protocol to alfaxalone, a single-agent anesthetic for functional neuroimaging. We first compare the two in a controlled environment to assess relative safety and to measure physiological stability over an extended time window. We then compare patterns of auditory and visually-evoked activity measured at 7T to assess mean signal strength and between-subjects signal variability. Results in Comparison with Existing Methods We show that alfaxalone results in more stable heart and respiratory rates over the 120 minutes testing period, with evidence of smaller between measurements variability in respiratory rates within this time window, when compared to ketamine plus isoflurane. Moreover, we demonstrate that both agents evoke similar mean BOLD signals across animals, but that alfaxalone elicits more consistent BOLD activity in response to sound stimuli across all ROIs observed. Conclusions Alfaxalone is observed to be more physiologically stable, evoking a more consistent BOLD signal across animals than the co-administration of ketamine and isoflurane. Thus, an alfaxalone-based protocol may represent a better approach for neuroimaging in animal models requiring anesthesia.
Does vegetation change over 28 years affect habitat use and reproductive success?

ABSTRACT Individuals should prefer and use habitats that confer high fitness, but habitat use is not always adaptive. Vegetation in natural landscapes changes gradually and the ability of species to adaptively adjust their habitat use to long-term changes is largely unstudied. We studied nest patch and territory use over 28 yr in Orange-crowned Warblers (Oreothlypis celata) in a system that has undergone natural long-term changes in vegetation. Abundance of maple (Acer grandidentatum), its preferred nesting habitat, gradually declined from 1987 to 2015. We examined whether habitat use and its fitness consequences changed as the availability of preferred habitat decreased. We used resource selection function models to determine changes over time in the probability of using a nest patch given available patches, and the probability of using a territory given available territories. We estimated nest survival to evaluate changes over time in the fitness consequences of nest patch use. We also compared habitat use (nest patch and territory) and fitness (nest survival) between areas with naturally reduced abundance of maple and experimentally increased abundance of maple (fenced areas). Nest patch use depended on maple abundance and did not change drastically across 28 yr, even though the availability of preferred maple patches decreased over time. In contrast, nest survival tended to decrease over time. We did not see differences in nest patch use and nest survival between unfenced and fenced areas, unlike territory use, which increased with the abundance of maple in fenced areas and decreased in unfenced areas. Our study depicts one example of relatively unchanged habitat use in the face of decreased availability of preferred vegetation across years, with a resulting decrease in reproductive success. Investigating changes in habitat use and fitness consequences for animals exposed to long-term habitat change is necessary to understand adaptive behavioral responses.
Using environmental niche modelling to investigate the importance of ambient temperature in human-crocodilian attack occurrence for two species of crocodilian

Crocodilians are responsible for more attacks on people than any other large predator, which has important implications for human safety and crocodilian conservation. Understanding the drivers of crocodilian attacks on people could help minimise future attacks and inform conflict management. Crocodilian attacks follow a seasonal pattern for many species; however, there has been limited analyses of the relationship between fine-scale contemporaneous environmental conditions and atack occurrence. Here, we use methods from environmental niche modelling to explore the relationships between abiotic predictors and human attack occurrence at a daily temporal resolution for two species: the Nile crocodile (Crocodylus niloticus) in South Africa and Swaziland (renamed Eswatini), and the American alligator (Alligator mississippiensis) in Florida. Our results indicate that ambient daily temperature in the most important abiotic temporal predictor of attack occurrence for both species, with attack likelihood increasing sharply at temperatures above 18°C and peaking at 28°C. It is likely that this relationship is explained partially by human propensity to spend time in and around water in warmer weather, but also by the effect of temperature on crocodilian hunting behaviour and physiology, especially the ability to digest food. We discuss the potential of our findings to contribute to the management of crocodilians, with benefits for human safety and conservation, as well as the application of environmental niche modelling to analysing human conflict with other species, including ectotherms and endotherms.
Behavior of Vine Varieties Resistant to Fungal Diseases in the Somontano Region

The vine is highly susceptible to numerous fungal diseases, the incidence and severity of which are increasing because of climate change. To fight them, large amounts of phytosanitary products are generally used, although they entail important economic and environmental costs. The new fungus resistant vine varieties (PIWI) constitute one of the most active lines of research on plant material in viticulture and are regarded as a viable solution to respond to the requirements of European Directive 2009/128/EC. In the present work, the evolution and impact of the three main fungal diseases (powdery mildew, downy mildew and botrytis bunch rot) were monitored in plots in the Somontano region (Huesca, Spain), comparing three PIWI varieties (Sauvignon Kretos, Souvignier gris and Muscaris) with a susceptible control variety (Sauvignon blanc) in real field growing conditions over three successive years (2016–2018). The main ampelographic characters of each variety were studied and a weekly follow-up was carried out to track the development of each disease, relating it to climatic variables. Regardless of the climatic conditions (one of the growing seasons was rainy and the other two corresponded to dry years, with differences in the distribution of rainfall), the three PIWI varieties hardly presented any symptoms, demonstrating a high resistance to downy mildew and powdery mildew and even to botrytis. Principal component analysis results pointed to a differential behavior versus the control and treated Sauvignon blanc plants in terms of disease resistance. Based on production results, despite the youth of the plantation, the excellent potential of Sauvignon Kretos variety was observed. However, from the analysis of the quality of wine obtained in microvinifications from these fungus resistant varieties in the second and third year, the one obtained from Muscaris seemed to have the best organoleptic properties. Apart from environmental considerations, given that these fungus resistant varieties can significantly contribute to the sustainability of wineries, they may also respond to the demand of consumers who want zero-pesticide products or of the supporters of ecological products adjusted to European regulations.
Attention-dependent preparatory processing of naturalistic narratives is correlated with speech comprehension

While human speech comprehension is thought to be an active process that involves top-down predictions, it remains unclear how predictive information is used to prepare for the processing of upcoming speech information. We aimed to identify the neural signatures of preparatory processing of upcoming speech. Participants selectively attended to one of two competing naturalistic, narrative speech streams, and a temporal response function method was applied to derive event-related-like neural responses from electroencephalographic data. Regression analysis revealed that neural signatures with latencies as early as −450 ms prior to speech onset were significantly correlated with speech comprehension performance. The preparatory process involved a distributed network. These preparatory signatures were attention dependent; activity prior to the attended speech was negatively correlated with comprehension performance, whereas the opposite was found for unattended speech. Our findings suggest that attention plays an important role in the preparation to process upcoming speech.
Protein Crowding mediates Passive Membrane Remodeling in ESCRT-induced Formation of Intraluminal Vesicles

As part of the lyosomal degradation pathway, the endosomal sorting complex required for transport (ESCRT) machinery sequester receptors at the endosome and simultaneously deform the membrane to generate intraluminal vesicles (ILVs). The role ESCRTs play in the membrane shape remodeling is not understood. We present a mathematical model, where ESCRT-induced alteration of the Gaussian bending rigidity and their crowding on the membrane facilitate ILV formation. The combination of mathematical modeling and experimental measurements shows that early ESCRT-driven budding does not require ATP consumption as only a small energy barrier needs to be overcome. Our model predicts that an ESCRT-free ILV forms, i.e., ESCRTs do not become part of the vesicle, but localize with a high density at the membrane neck, where the steep decline in the Gaussian curvature might trigger ESCRT-III/Vps4 assembly to enable neck constriction and scission.
Representations of the amacrine cell population underlying retinal motion anticipation

Retinal amacrine cells are a diverse population of inhibitory interneurons, posing a challenge to understand the specific roles of those interneurons in computations of the similarly diverse ganglion cell population. Here we study the predictive computation of motion anticipation, which is thought to compensate for processing delays when encoding moving objects. We recorded the membrane potential of the salamander amacrine cell population optically while recording electrically from ganglion cells with a multielectrode array. We find unexpectedly that ganglion cells with the greatest anticipation for moving stimuli exhibit a new type of predictive motion anticipation that is inconsistent with prior models of delayed inhibition. Based on the spatiotemporal correlations between thousands of amacrine and ganglion cell pairs, we modeled the contribution of the traveling wave of activity for different amacrine cell populations to the encoding of a moving bar. These models indicate that the population responses of slow biphasic amacrine cells create the greatest contribution to both types of ganglion cell motion anticipation, supporting a role for this specific amacrine cell class in the predictive encoding of moving stimuli. Significance Statement The prediction of moving stimuli is a widespread function occurring in both visual and auditory systems. The diversity of interneuron populations makes it a challenge to understand the mechanisms of these computations. To analyze how the retina anticipates motion, we optically measured inhibitory amacrine cell population activity simultaneously with electrical recording from ganglion cell populations. We then used computational modelling to assess which amacrine cell types have the right spatiotemporal responses to generate motion anticipation. In contrast to previous suggestions of a general role for inhibition, we find that slow biphasic amacrine cells specifically have the greatest contribution to motion anticipation, thus highlighting the need to directly measure and model the effects of interneuron populations in complex sensory computations.
Compost Tea Induced Callus Proliferation and Defense Response in Rice (Oryza sativa L.) Callus Cells

Rice (Oryza sativa L.) is the most important staple food crop which is central to the lives of billions of people around the world. Rice has shaped the culture, diets and economies of millions of people. Compost tea (CT) is a watery suspension made by steeping compost in water and fermented under aerated or non aerated conditions. CT is an enriched microbial liquid suspension and contains growth promoting biomolecules produced by microbes (Anil et al., 2017a; Weyens et al., 2009).
Characterization of the first complete chloroplast genome sequence of Celtis sinensis (Cannabaceae) and its phylogenetic implications

Abstract Celtis sinensis Pers. is a popular garden landscape tree in riparian areas and a valuable resistant tree in many extreme environments. Here, we determined the first complete chloroplast genome of C. sinensis using high-throughput sequencing technology. Our results showed the chloroplast genome of C.sinensis was 159,092 bp long and displayed a typical quadripartite structure consisting of a pair of inverted repeats with a length of 26,895 bp and separating by two single-copy regions (LSC, 86,085 bp and SSC, 19,217 bp). Besides, the chloroplast genome of C. sinensis totally contained 131 genes, including 87 protein coding genes, 36 transfer RNAs and eight ribosomal RNAs. Additionally, a maximum likelihood phylogenetic analysis based on the 19 chloroplast genomes demonstrated the monophyly of Cannabaceae and C. sinensis formed a sister clade to Celtis biondii.
The complete mitochondrial genome of a field cricket Turanogryllus eous (Insecta: Orthoptera)

Abstract The complete mitochondrial genome (mitogenome) of a field cricket Turanogryllus eous Bey-Bienko, 1956 was determined using next-generation sequencing. The mitogenome was 16,045 bp in length comprising 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. Relative to the ancestral insect gene order, T. eous possessed an inversion of trnN-trnS1-trnE. The control region contained 3.4 tandem copies of a 194-bp sequence. Phylogenetic analysis supported that T. eous was sister to the clade comprising Teleogryllus and Velarifictorus. This study provides essential genetic information for genetic diversity analysis of T. eous.