Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of competition intensity on recruitment of palatable and unpalatable grasses

In this study, we made an attempt to reveal how competition intensity from established plants impacts on palatable and unpalatable grass seedlings recruitment, in a natural mesic grassland of central Argentina. Our objective was to assess the seedling recruitment of a palatable species (Chascolytrum subaristatum) and an unpalatable species (Nassella trichotoma) in microsites differing in competition intensity from established plants. Identity (C. subaristatum and N. trichotoma) and defoliation severity were used as surrogate for competition intensity. In March 2017, we permanently marked established individuals of N. trichotoma and C. subaristatum and placed two circular plots adjacent to each individual. In one plot we added seeds of N. trichotoma and in the other seeds of C. subaristatum. After seeding, established plants were randomly assigned to one of three level of defoliation: without defoliation, low defoliation severity and high defoliation severity. From April to November 2017 (i.e. over a complete annual growing cycle), we measured seedling density, recruitment and growth. Our results supported the hypothesis that seedlings of palatable grasses are more competitive than seedlings of unpalatable grasses. Seedling of the palatable grass C. subaristatum recruited successfully regardless the intensity of competition from established plants, whereas seedlings of the unpalatable grass N. trichotoma recruited better under low competitive pressure from established plants. Our results suggest that the availability of microsites with low competitive pressure from the established vegetation, created by selective grazing of palatable grasses, promotes the recruitment of unpalatable grass seedlings. This mechanism may contribute to the species replacement process commonly observed in heavy grazed grasslands.
Unexpected massive enmeshments of the Sharpchin barracudina Paralepis coregonoides Risso, 1820 in mesopelagic sediment traps in the Levantine Basin, SE Mediterranean Sea

This study reports exceptional penetrations of the Sharpchin Barracudina Paralepis coregonoides into pelagic, open-sea sediment traps in the Levant Basin of the SE Mediterranean Sea . This first substantiated record of the species at the Levant Basin has been observed in two sediment traps at 180 and 280 m depth, 50 km offshore the coast of Israel. Over one year of deployment (November 2016 till November 2017), 483 adult individuals have been repeatedly entrapped inside the automatic sediment traps that were covered with a 25 mm baffler mesh for the first half year and then replaced with a smaller 1 cm mesh for the second half. This undesirable catch of such an elusive and understudied species provided a unique opportunity to revise its distribution, abundance and genetic divergence. The continuous entrapment throughout the year of sexually mature individuals has confirmed that this species is common to the SE Mediterranean. In order to avoid unwanted entrapments that disrupt biogeochemical sediment studies, the installation of small mesh size nets on the conventional sediment trap openings must be considered in the pelagic zone of the SE Mediterranean, and probably elsewhere.
Voltage-sensitive dye imaging reveals inhibitory modulation of ongoing cortical activity

Voltage-sensitive dye imaging (VSDI) is a powerful technique for interrogating membrane potential dynamics in assemblies of cortical neurons, but with effective resolution limits that confound interpretation. In particular, it is unclear how VSDI signals relate to population firing rates. To address this limitation, we developed an in silico model of VSDI in a biologically faithful digital reconstruction of rodent neocortical microcircuitry. Using this model, we extend previous experimental observations regarding the cellular origins of VSDI, finding that the signal is driven primarily by neurons in layers 2/3 and 5. We proceed by exploring experimentally inaccessible circuit properties to show that during periods of spontaneous activity, membrane potential fluctuations are anticorrelated with population firing rates. Furthermore, we manipulate network connections to show that this effect depends on recurrent connectivity and is modulated by external input. We conclude that VSDI primarily reflects inhibitory responses to ongoing excitatory dynamics.
Factors affecting space use by wild boars (Sus scrofa) in high-elevation tropical forests

The wild boar (Sus scrofa Linnaeus, 1758) is considered one of the 100 worst invasive species in the world and is present in the high-elevation forests in Brazil. Our objective was to understand how landscape and atmospheric conditions affect space use by wild boars. We hypothesized that wild boars would be more frequent at lower elevations, warmer and wetter forested areas, and away from human disturbances. After three years of data collection (2013–2016) using 16 camera traps, 881 independent records were obtained with a mean of 4.44 ± 9.25 pigs per record. Wild boar frequency of occurrence was higher at lower elevations, in more humid and warmer areas, and farther away human disturbance factors, corroborating our initial hypothesis. Understanding space-use patterns of wild boars is necessary for the design of management strategies that target areas of more intense usage, as well as for defining more effective population-control techniques.
Genetic evidence of a northward range expansion in the eastern Bering Sea stock of Pacific cod

Poleward species range shifts have been predicted to result from climate change, and many observations have confirmed such movement. Poleward shifts may represent a homogeneous shift in distribution, seasonal northward movement of specific populations, or colonization processes at the poleward edge of the distribution. The ecosystem of the Bering Sea has been changing along with the climate, moving from an arctic to a subarctic system. Several fish species have been observed farther north than previously reported and in increasing abundances. We examined one of these fish species, Pacific cod, in the northern Bering Sea (NBS) to assess whether they migrated from another stock in the eastern Bering Sea (EBS), Gulf of Alaska, or Aleutian Islands, or whether they represent a separate population. Genetic analyses using 3,599 single nucleotide polymorphism markers indicated that nonspawning cod collected in August 2017 in the NBS were similar to spawning stocks of cod in the EBS. This result suggests escalating northward movement of the large EBS stock during summer months. Whether the cod observed in the NBS migrate south during winter to spawn or remain in the NBS as a sink population is unknown.
The challenge of heterogeneous evidence in conservation

Conservation efforts to tackle the current biodiversity crisis need to be as efficient and effective as possible. To inform decision-makers of the most effective conservation actions, it is important to identify biases and gaps in the conservation literature to prioritize future evidence generation. We assessed the state of this global literature base using the Conservation Evidence database, a comprehensive collection of quantitative tests of conservation actions (interventions) from the published literature. For amphibians and birds, we investigated the nature of Conservation Evidence spatially and taxonomically, as well as by biome, effectiveness metrics, and study design. Studies were heavily concentrated in Western Europe and North America for birds and particularly amphibians. Studies that used the most robust study designs - Before-After Control-Impact and Randomized Controlled Trials - were also the most geographically restricted. Furthermore, there was no relationship between the number of studies in each 1×1 degree grid cell and the number of species, threatened species or data-deficient species. Taxonomic biases and gaps were apparent for amphibians and birds - some orders were absent from the evidence base and others were poorly represented relative to the proportion of threatened species they contained. Temperate forest and grassland biomes were highly represented, which reinforced observed geographic biases. Various metrics were used to evaluate the effectiveness of a given conservation action, potentially making studies less directly comparable and evidence synthesis more difficult. We also found that the least robust study designs were the most commonly used; studies using robust designs were scarce. Future research should prioritize testing conservation actions on threatened species outside of Western Europe and North America. Standardizing metrics and improving the robustness of study designs used to test conservation actions would also improve the quality of the evidence base for synthesis and decision-making.
The complete mitochondrial genome sequence and phylogenetic analysis of yellow weasel (Mustela sibirica)

Abstract In this study, we determined the complete mitochondrial genome sequence of the Mustela sibirica. The complete mitogenome of M. sibirica is 16,529 bp in length and consist of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a D-loop region. The overall base composition of the mitochondrial DNA is 32.88%A, 13.84%G, 27.32%T, and 25.96%C. The phylogenetic tree of the family Mustelidae constructed by using mitogenome sequences from 10 mustelid species of the family Mustelidae. These results provide necessary information for molecular phylogeny and evolutionary analysis of the M. sibirica.
Autism spectrum disorders : an epidemiological and clinical study

Background: Autism spectrum disorders (ASDs), defined as pervasive developmental disorders (PDDs) in DSM-IV and ICD-10, become manifest in childhood, ranging from a severe form, autism, to milder forms, Asperger syndrome (AS) and pervasive developmental disorder not otherwise specified (PDD-NOS)/atypical autism. AS is also specified in criteria by Gillberg and by Szatmari et al. Different diagnostic criteria sets, overlaps, inaccuracies and exclusion criteria of many comorbid psychiatric disorders in PDDs have caused confusion. In DSM-5, PDDs were replaced by one diagnosis called ASD. Aims and methods: This is an epidemiological study of 8-year-old children and a clinical study of 9to 16-year-old high-functioning outpatients with AS/autism (HFA). The epidemiological target population (n = 4,422) was rated via the Autism Spectrum Screening Questionnaire (ASSQ) by parents and/or teachers and a screened sample was examined in order to estimate the prevalence of ASDs, to discover deficits in the diagnostic criteria of ASDs, to evaluate DSM-5 draft criteria for ASD, and to assess cut-off scores for the Finnish ASSQ. Comorbid psychiatric disorders were identified and overall level of functioning rated in 50 subjects with AS/HFA. Results: The prevalence of AS according to DSM-IV was 2.5, to ICD-10 2.9, to Gillberg 2.7, and to Szatmari et al. 1.6 per 1,000. The prevalence of autism was 4.1 and that of ASDs 8.4 per 1,000 (DSM-IV). DSM-5 draft criteria were less sensitive in detecting AS/HFA. For 7to 12-yearold children (IQ ≥ 50), the optimal cut-off scores were 30 in clinical settings and 28 in total population screening using summed parent-rated and teacher-rated ASSQ scores. Comorbid psychiatric disorders were common (prevalence 74%) and often multiple; behavioral disorders in 44%, anxiety disorders in 42%, and tic disorders in 26%. Oppositional defiant disorder, depressive disorder and anxiety disorders as comorbidities indicated significantly lower levels of functioning. Conclusions: Our results indicate the need to standardize the diagnostic criteria. The ICD-11 criteria should be uniform and harmonize with DSM-5. Determining cut-off scores for ASD screening instruments in different languages and cultures is of utmost importance. Clinicians are reminded to investigate psychiatric comorbidity in ASDs in order to target treatment and rehabilitation precisely.
North Atlantic right whale shift to the Gulf of St. Lawrence in 2015, revealed by long-term passive acoustics

This paper contributes to documenting a change in the distribution of North Atlantic right whales Eubalaena glacialis (NARWs) that occurred in the 2010s, when the whales largely abandoned their traditional summering grounds in the Gulf of Maine/Bay of Fundy/Scotian shelf. Data from a year-round passive acoustic monitoring (PAM) network in the Gulf of St. Lawrence were exploited to build the time series of NARW incursions into this inland sea of the Northwest Atlantic, from June 2010 to November 2018. NARWs visited the southern Gulf of St. Lawrence every year from June to January, until ice freeze-up. The earliest detections were made at the end of April and the latest in mid-January. Call occurrence peaked between August and the end of October. NARW contact calls were not detected at the most upstream station at Les Escoumins, in the Lower St. Lawrence estuary, or at the northeastern connection of Belle Isle Strait with the Atlantic, which was monitored from November 2010 to November 2011. The mean daily occurrence of NARWs in the feeding grounds off Gaspé quadrupled after 2015 compared to 2011−2014. Long-term continuous PAM data provided invaluable information to document this marine mammal distribution shift.
Imprecise neural computations as source of human adaptive behavior in volatile environments

Everyday life features uncertain and ever-changing situations. In such environments, optimal adaptive behavior requires higher-order inferential capabilities to grasp the volatility of external contingencies. These capabilities however involve complex and rapidly intractable computations, so that we poorly understand how humans develop efficient adaptive behaviors in such environments. Here we demonstrate this counterintuitive result: simple, low-level inferential processes involving imprecise computations conforming to the psychophysical Weber Law actually lead to near-optimal adaptive behavior, regardless of the environment volatility. Using volatile experimental settings, we further show that such imprecise, low-level inferential processes accounted for observed human adaptive performances, unlike optimal adaptive models involving higher-order inferential capabilities, their biologically more plausible, algorithmic approximations and non-inferential adaptive models like reinforcement learning. Thus, minimal inferential capabilities may have evolved along with imprecise neural computations as contributing to near-optimal adaptive behavior in real-life environments, while leading humans to make suboptimal choices in canonical decision-making tasks.
A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

The mammalian visual system, from retina to neocortex, has been extensively studied at both anatomical and functional levels. Anatomy indicates the cortico-thalamic system is hierarchical, but characterization of cellular-level functional interactions across multiple levels of this hierarchy is lacking, partially due to the challenge of simultaneously recording activity across numerous regions. Here, we describe a large, open dataset (part of the Allen Brain Observatory) that surveys spiking from units in six cortical and two thalamic regions responding to a battery of visual stimuli. Using spike cross-correlation analysis, we find that inter-area functional connectivity mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas. Classical functional measures of hierarchy, including visual response latency, receptive field size, phase-locking to a drifting grating stimulus, and autocorrelation timescale are all correlated with the anatomical hierarchy. Moreover, recordings during a visual task support the behavioral relevance of hierarchical processing. Overall, this dataset and the hierarchy we describe provide a foundation for understanding coding and dynamics in the mouse cortico-thalamic visual system.
Emotional Eating and Poor General Lifestyle Prevalent among Obese Young Adults

Aim: To evaluate the association between obesity and lifestyle factors, eating behaviors related to emotional eating, and body perception. Methods: A cross-sectional study was carried out with individuals of both sexes by taking anthropometric, biochemical and clinical measurements. Questionnaires were used to evaluate lifestyle, eating habits, emotional eating behavior and self-perception of body image. The participants were stratified according to body mass index (BMI). Results: A total of 318 subjects were evaluated (44% women), with an average age of 34 ± 8 years. Regarding the lifestyle questionnaire, the normal BMI group obtained a higher score [ 78.5 (71-82)] than did the overweight [76 (69-80)] and obesity groups [73 (65-79)], (p=0.005); this finding indicated that the normal BMI group had a healthier lifestyle. Conversely, the questionnaire on emotional behaviors related to emotional eating showed that the normal BMI group had lower scores [7 (3-13)] than the overweight [8 (3-15)] and obesity groups [12 (5 -21)], (p=0.008). Being a very emotional eater significantly increases the risk of obesity (OR= 3.83 (95% CI, 1.67-8.7) (p=0.002). Overall, 51.1% of the participants had a self-perception that was incorrect according to their BMI. Conclusion: Individuals frequently have a misperception of their body shape. People with obesity had lifestyle factors that were less favorable for their health as well as higher rates of emotional eating, both of which are risk factors for obesity.
Glycan Utilization Strategy of the Butyrate Producing Gut Symbiont Roseburia intestinalis

The N-terminal domain (residues 28–165) from the glycoside hydrolase family 10 from Roseburia intestinalis (RiCBMx), has been isotopically labeled and recombinantly expressed in Escherichia coli. Here we report 1H, 13C and 15N NMR chemical shift assignments for this carbohydrate binding module (CBM).
Physicochemical quality of hardy kiwifruit (Actinidia arguta L. cv. Cheongsan) during ripening is influenced by harvest maturity

Abstract Hardy kiwifruit is popular among consumers, but it has a short shelf-life. In this study, the influence of harvest maturity on the physicochemical properties of ‘Cheongsan’ hardy kiwifruit was investigated during storage at 22 °C. Harvested fruit were divided based on the soluble solids content (SSC) into ‘harvest 1’ and ‘harvest 2’ with 6% and 8% SSC, respectively. As the fruit continued growing on the vine, the fresh and dry weights at harvest were 1.3 and 1.7 times higher in ‘harvest 2’ than in ‘harvest 1’, respectively. There was no significant difference in titratable acidity between the two groups. Harvest maturity significantly affected the content of total phenolic compounds; ‘harvest 2’ fruit had 2.1 times higher concentration than that of ‘harvest 1’ fruit. The respiration rate rapidly increased after harvest, and the SSC also increased throughout the ripening, regardless of fruit maturity. ‘Harvest 2’ fruit exhibited significant reduction of weight loss and retained firmness during ripening compared with those of ‘harvest 1’ fruit. The ‘harvest 1’ fruit were not of adequate quality and spoiled before ripening. These data suggest that ‘Cheongsan’ hardy kiwifruit should be harvested when the SSC is greater than 8% to retain premium quality fruit.
The full-length mitochondrial genome of the Fernholm’s hagfish, Myxine fernholmi (Myxini; Myxiniformes; Myxinidae)

Abstract The full-length mitochondrial genome of the Fernholm’s hagfish, Myxine fernholmi (Myxini; Myxiniformes; Myxinidae) was analyzed by the primer walking method. Its mitogenome was 18,862 bp in total length and was composed of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The gene content and order were congruent with those of typical vertebrates. In the phylogenetic tree, M. fernholmi showed the closest relationship to M. glutinosa in the same genus and subfamily and well separated from the other hagfish in the subfamily Eptatretinae.
Phenotypic and Genotypic Characterization of Exopolysaccharide Producing Bacteria Isolated from Fermented Fruits, Vegetables and Dairy Products

© The Author(s) 2019. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License which permits unrestricted use, sharing, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Abdalrahim et al. J Pure Appl Microbiol, 13(3), 1349-1362 | September 2019 Article 5769 | https://doi.org/10.22207/JPAM.13. 3.06
New registers of colleters in species of Myrtaceae from Brazilian Cerrado

Abstract Colleters are secretory structures that produce a sticky substance, consisting of a mixture of mucilage, proteins, terpenes, pectic substances and even alkaloids, which lubricates and protects the shoot apical meristem. Several colleter types have been described and have taxonomic value in many botanical families. In Myrtaceae, the colleters description is recent and presents three new morphological types (conic, euryform and petaloid) that differ those already described for other eudicots. In this work, we report the colleters morphological types in six species of three genera belonging to the Myrteae tribe of Myrtoideae from the Brazilian Cerrado. The samples were fixed for light and scanning electron microscopy. Histochemical tests were carried out on the fresh and methacrylate-embedded material. The conic and euryform colleters from Myrtoideae species of the Cerrado did not differ either morphologically nor as to the secretion nature from those described for Myrtoideae species from others biomes, which may indicate their potential use for taxonomic purposes. Considering the hypothesis that the multiple fleshy-fruit lineages have evolved independently in Myrteae tribe, our results indicate the relevance of additional studies in order to recognize the pattern of distribution of colleters in Myrtaceae.