Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of Potential Isolates of Rhizosphere Bacteria to Contro Budok Disease in Patchouli Plant

Synchytrium pogostemonis, the causal agent of budok disease, is one of the major limiting factors in patchouli production in Indonesia. Patchouli farmers usually control budok disease with chemical fungicides. Chemical control pollutes environment and disrupts agricultural ecosystem. Therefore, an environmentally friendly pest control should be conducted to control the disease. The objective of the study was to isolate and evaluate some rhizobacteria from the rhizosphere of patchouli and black pepper plants against Fusarium oxysporum f.sp. vanillae, F. solani, Sclerotium rolfsii. Potential rhizobacterial isolates were tested to control budok disease on a pot scale. The results showed that 26 rhizobacterial isolates from 100 tested were antagonistic to F. oxysporum, F. solani and S. rolfsii. Four rhizobacteria isolates (RL13-A, RL31-A, RL35-A, RL32-A) showed strong inhibition (>40 %) against the 3 pathogens. In polibag experiment, RL35-A, PS9, RL13-A, RL32-B, RL31-A isolates were able to suppress budok disease significantly by 84.01; 76.00; 65.99; 43.99; and 21.98 % respectively. These results indicated that RL35-A isolates have strong antagonistic effect compared to other isolates. Based on 16S rDNA analysis, RL35-A isolates possessed close relationship (99 %) with all species of Enterobacter sp. The antibiotic compound extracted from RL35-A culture broth using GC-MS analysis was identified as phenol, 2,6-dimethoxy-(canola). These results suggested that Enterobacter sp. was potential to be developed as biological agent for controlling budok disease in patchouli plants.
Population history explains the performance of an annual herb – Within and beyond its European species range

The centre–periphery hypothesis (CPH) predicts a decrease in population performance from the centre of the species range towards the edge, hindering further species expansion. To overcome ecological limitation, local adaptation of peripheral populations is assumed necessary to extend niche space and thus to potentially facilitate species’ range expansion. However, adaptive changes do not necessarily correspond to current ecological marginality. Instead, population history may provide a fuller context for understanding patterns of local adaptation within the species range. Here, we test whether local adaptation to current conditions or population history explains current species distribution in an annual heterocarpic species, Atriplex tatarica, in Europe. The ecological marginality and population history were estimated using species distribution modelling (SDM) and 13 microsatellite markers. To test for local adaptation, we evaluated the population performance of both currently central and currently peripheral populations by examining germination and growth traits under three temperature regimes which correspond to climates within, and also beyond, the species’ current range. In addition, we compared Bayesian estimates of population differentiation in neutral genetic markers and quantitative traits to test whether phenotypic differentiation evolved by local adaptation and/or by genetic drift. We found population performances were not higher under temperature regimes corresponding to their own habitats, suggesting that patterns of local adaptation in A. tatarica do not correspond to current centre–periphery gradient. In contrast, population genetic structure indicated a strong influence of population history on variation in the germination phenotype. Species distribution modelling suggested a more cold–tolerant genetic lineage was located at the species' range periphery during the last glacial period. Meanwhile, a less cold‐tolerant lineage occurred in more suitable areas of the Balkan Peninsula and southeastern Europe. Thus, the strong adaptive divergence of evolutionary lineages may reflect a past spatial arrangement of populations, suggesting evolutionary processes were ongoing before the species expansion in the Holocene. Synthesis. There is continuing debate concerning the speed of trait evolution during range expansion with climate change. Our results indicate that even though organisms expand rapidly, the accompanying evolutionary changes in phenotype may be much slower.
Some Principles of Organization in the Dorsal Lateral Geniculate Nucleus; pp. 268–282

A comparative survey shows that lamination is a basic feature of the mammalian dorsal lateral geniculate nucleus. Relay laminae receive input from the retina, project to the cerebral cortex and represent a complete hemiretina. They are distinguished from incomplete layers or leaflets and from groups of cells for which retinal connections or cortical projections are in question. The separate representations of the visual field in the relay laminae are precisely aligned so that each point in the visual field corresponds to a line passing from margin to margin through the nucleus and at right angles to the layers. Geniculate landmarks that provide clues regarding the organization of the layers are considered, and several experimental methods by which the laminar pattern can be displayed are evaluated.
Estimating and interpreting nonlinear receptive fields of sensory responses with deep neural network models

Sensory processing by neural circuits includes numerous nonlinear transformations that are critical to perception. Our understanding of these nonlinear mechanisms, however, is hindered by the lack of a comprehensive and interpretable computational framework that can model and explain nonlinear signal transformations. Here, we propose a data-driven framework based on deep neural network regression models that can directly learn any nonlinear stimulus-response mapping. A key component of this approach is an analysis method that reformulates the exact function of the trained neural network as a collection of stimulus-dependent linear functions. This locally linear receptive field interpretation of the network function enables straightforward comparison with conventional receptive field models and uncovers nonlinear encoding properties. We demonstrate the efficacy of this framework by predicting the neural responses recorded invasively from the auditory cortex of neurosurgical patients as they listened to speech. Our method significantly improves the prediction accuracy of auditory cortical responses particularly in nonprimary areas. Moreover, interpreting the functions learned by neural networks uncovered three distinct types of nonlinear transformations of speech that varied considerably in primary and nonprimary auditory regions. By combining two desired properties of a computational sensory-response model; the ability to capture arbitrary stimulus-response mappings and maintaining model interpretability, this data-driven method can lead to better neurophysiological models of the sensory processing.
Male age affects female mating preference but not fitness in the monandrous moth Dendrolimus punctatus Walker (Lepidoptera: Lasiocampidae)

It is widely accepted that male age can influence female mating preference and subsequent fitness consequences in many polyandrous species, yet this is seldom investigated in monandrous species. In the present study, we use the monandrous pine moth Dendrolimus punctatus to examine the effects of male age on female mating preference and future reproductive potential. In multiple male trials, when permitted free mating from an aggregation consisting of virgin males aged 0 (young), 2 (middle‐aged) and 4 (old) days, virgin females preferentially mate with young and middle‐aged males, although mating latency and mating duration are independent of male age. In single male trials, when virgin females are randomly assigned single virgin males of known age, a negative correlation is found between mating success and male age in this species. However, we find that male age also has no effect on mating latency and mating duration. Further fitness analysis reveals that females do not receive benefits in terms of oviposition period, total egg production, average daily egg production, percentage of egg hatching, longevity, expected reproduction and relative expected reproduction from mating with young and middle‐aged males compared with mating with old males. The results of the present study are the first demonstrate that females mated preferentially with younger males but gain no apparent fitness benefits in a monandrous moth species.
Sugar profile and enzymatic analysis of stingless bee honey collected from local market in Malaysia

Commercial honey is widely available in the market, raising questions whether the honeys are good in quality or otherwise, Thus, this research was designed to compare the quality of harvested stingless bee honey and commercial honey available in the Malaysian market by measuring their sugar profile and enzyme activity. The analysis showed that the honey contained moisture between 16.6% - 32.1%, various sugar starting with fructose (15.03 – 48.44 g/100 g), glucose (12.16 – 40.09 g/100 g), sucrose (<0.01 – 7.29 g/100 g), Fructose + Glucose (F+G) (15.03- 80.25 g/100 g), Fructose/Glucose (F/G) (0.78 – 1.63), and G/W (0.47 – 1.89). Also, diastase activity and Invertase activity of the honey varied from 1.82 to 6.11 DN and 0.27 IN to 4.94 IN, respectively. Eight honey samples including harvested honey, H. Itama and G.Thoracica showing comparable results with past studies and within the limits of Malaysian Standard. However, all honey samples demonstrate lower enzyme activity suggesting that honey from stingless bee has low enzyme activity compare to Apis mellifera honey.
Emulsifier as a Feed Additive in Poultry and Pigs-A review

The recent increase in feed price has prompted scientific investigation to find effective strategy to reduce feed cost without compromising the performance and health of animals. It is well documented that young animals have physiological limitation to absorb fat because of low level of natural lipase production and a low rate of bile salt production due to which fat digestibility is incomplete consequently leading to greater requirement for energy sources and therefore a hike in feed price. A particular strategy that has drawn the attention of nutritionists is the use of exogenous emulsifier. Emulsifier is a substance that stabilizes the mixture of two products such as oil and water that do not mix together and prevents the coalescence of the globules of the dispersed phase. Emulsifier can be natural or synthetic and can be used to improve fat digestibility and enhance energy efficiency thereby reducing feed cost. Various studies indicate that the selection of natural and synthetic sources of emulsifier should be based on hydrophiliclipophilic balance. The aim of this review is to summarize the current knowledge on the use of emulsifier as a feed additive in poultry and pigs.
The role of integrin αv and CD44 in GBM migration in human brain

Glioblastoma (GBM) is the most common primary adult malignant brain tumor. Recurrence is driven invading tumor cells that escape surgical resection and demonstrate resistance to standard-of-care chemotherapy and radiotherapy. A large body of research has been conducted on tumor cell motility. However, typical in vitro models make use of polystyrene culture dishes, which exhibit significantly different physical parameters than brain tissue. Here we report on the use of human organotypic brain slices as an ex vivo approach for the dynamic study of GBM cell motility. Temporal lobectomy tissue from epilepsy patients was obtained and cut into 350µm thick slices. After the tissue slices had a week’s incubation for recovery, fluorescently labeled tumor cells were seeded. We then tracked individual tumor cells using time-lapse fluorescent confocal microscopy. Quantification of motility characteristics, including mean squared displacement, total path length, and consistency, allowed for comparison of different conditions, including knockdown of cell surface proteins integrin αv (ITGAV) and CD44. Human organotypics demonstrated minimal variability across specimen in terms of motility parameters, including total path length, averaged instantaneous velocity, and consistency. Knockdown of the traditional motility protein ITGAV showed little effect on overall motility while knockdown of CD44 resulted in a significant reduction in both averaged instantaneous velocity and total path length. When the same parameters were examined using Matrigel, ITGAV and CD44 both showed decreased motility, highlighting the impact of the physical environment on cell behavior. Finally, cell motility in mouse organotypic slices was decreased when compared to human organotypic slices. Here we demonstrate the use of human organotypic brain slices in the study of GBM cell invasion. This model system offers a physiologically-relevant environment in which to examine the dynamic process of cell motility.
Ancestry of the AUTS2 family–A novel group of polycomb-complex proteins involved in human neurological disease

Autism susceptibility candidate 2 (AUTS2) is a neurodevelopmental regulator associated with an autosomal dominant intellectual disability syndrome, AUTS2 syndrome, and is implicated as an important gene in human-specific evolution. AUTS2 exists as part of a tripartite gene family, the AUTS2 family, which includes two relatively undefined proteins, Fibrosin (FBRS) and Fibrosin-like protein 1 (FBRSL1). Evolutionary ancestors of AUTS2 have not been formally identified outside of the Animalia clade. A Drosophila melanogaster protein, Tay bridge, with a role in neurodevelopment, has been shown to display limited similarity to the C-terminal of AUTS2, suggesting that evolutionary ancestors of the AUTS2 family may exist within other Protostome lineages. Here we present an evolutionary analysis of the AUTS2 family, which highlights ancestral homologs of AUTS2 in multiple Protostome species, implicates AUTS2 as the closest human relative to the progenitor of the AUTS2 family, and demonstrates that Tay bridge is a divergent ortholog of the ancestral AUTS2 progenitor gene. We also define regions of high relative sequence identity, with potential functional significance, shared by the extended AUTS2 protein family. Using structural predictions coupled with sequence conservation and human variant data from 15,708 individuals, a putative domain structure for AUTS2 was produced that can be used to aid interpretation of the consequences of nucleotide variation on protein structure and function in human disease. To assess the role of AUTS2 in human-specific evolution, we recalculated allele frequencies at previously identified human derived sites using large population genome data, and show a high prevalence of ancestral alleles, suggesting that AUTS2 may not be a rapidly evolving gene, as previously thought.
Detection of Escherichia coli, Salmonella spp. and Staphylococcus aureus in Ready-to-Eat Food in Al-Ahsa Province, Saudi Arabia

The study aimed to identify and characterize foodborne- Staphylococcus aureus, Escherichia coli and Salmonella spp. in Al-Ahsa Province, Kingdom of Saudi Arabia (KSA), as potential reservoir of human infection and transmitters of antimicrobial resistance. A total of 90 sandwich samples (consist of minced meat and vegetables) were aseptically collected from fast-food cafeterias. Conventional bacteriological techniques were used to isolate Staph aureus, E. coli and Salmonella spp. For E. coli isolates, molecular analysis was made. Staph aureus was confirmed from 11.11% of specimens of which 30% were MRSA. MRSA were resistant to erythromycin, nitrofurantoin and Trimethoprim/ Sulfamethoxazole. Non-MRSA were resistant to ciprofloxacin and all Staph aureus isolates were sensitive to vancomycin which may be a choice for treatment. At a rate of 5.56%, E. coli was confirmed by conventional techniques and VITEK 2 system; E. coli strain O157: H7 was not identified from the isolates. Molecular analysis indicated that 4 strains belonged to Shiga toxigenic E. coli (STEC) family and one strain was Shigella flexneri. Antimicrobial susceptibility analysis of isolates showed two strains (40%) were extended-spectrum β-lactamases (ESBL) positive that were demonstrated to be susceptible to imipenem but resistant to ciprofloxacin. On the other hand, three strains (60%) were identified as ESBL negative which were susceptible to all tested antibiotics. Salmonella spp. were not isolated from any food specimen in the present study. From ready-to-eat food in Al-Ahsa Province, KSA, Staph aureus MRSA and Non-MRSA were susceptible to vancomycin. Using molecular methods, E. coli and Shig. flexneri were confirmed from food with ESBL positive susceptible to imipenem but resistant to ciprofloxacin.
Using software Vortex as a tool towards conservation actions for sharks

Elasmobranchs, especially sharks, are part of the most threatened group of animals in the world. Among the factors that negatively affect these populations, the environmental degradation and disordered fishing can be highlighted. Although these threats are well known, the responses of most species to these factors are not fully understood, which makes it difficult to predict potential population responses according to conservation actions. The present study aims to develop a theoretical model based on a real population of white sharks (Carcharodon carcharias) that inhabit Gulf of Mexico, using their biological patterns to identify trends for the populations using Vortex (version 10.0.0.3) as a tool. The construction of the model was based on bibliographic data, considering parameters of life history, demographic rates and main known threats. Data were entered into Vortex software, and two population sizes were tested in the population viability analysis, indicating in both cases that the species tends to lose its genetic diversity over 500 years with a 12% and 51% of probability of extinction, respectively, considering exclusively its biological potential. This results can reflect on an mislead assumption of the real subpopulation’s size, which shows that the species is inserted into the vortex of extinction even with the existence of protective measures regarding white sharks on the location of the study, and it must incorporate neonates and juveniles individuals on the analysis to generate a consistent result. Despite this, the study suggests that the utilization of Vortex is capable of generating responses necessary for the conservation of sharks by analyzing stochastic events and life history in a simple way.
Stability analysis of prey predator model with Holling II functional response and threshold harvesting for the predator

This paper deals with a prey predator model with Holling response function of type II and continuous threshold harvesting in the predator population. The prey grows as a logistic model when there is no interaction with the predator. The predator is assumed decreasing due to natural death and interspecific interaction when there is no interaction with its prey. The existence of the interior equilibrium point is considered and the stability is analysed using linearization and eigenvalues methods. The phase portrait of the model is also used to determine the behaviour of populations. From the analyses of the model with harvesting we found that there exists a stable interior equilibrium point. The predator population will remain sustainable when the size of the populations are initially close enough to the equilibrium point. But when the threshold value is too high and the populations are initially quite far from the equilibrium point, then the predator population may stop being harvested at a certain time. Some numerical simulations are given to confirm the result of analysis.
Water availability and temperature induce changes in oxidative status during pregnancy in a viviparous lizard

1Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS-UMR 5321, Saint Girons, France; 2Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; 3Sorbonne Université, iEES Paris, CNRS-UMR 7618, Paris, France; 4ESPE de Paris, Sorbonne Université, Paris, France; 5Department of Biological Sciences, Ohio University, Athens, OH, USA and 6Centre de Recherche en Ecologie Expérimentale et Prédictive (CEREEPEcotron Ile De France), Ecole Normale Supérieure, CNRS-UMS 3194, PSL Research University, Saint-Pierre-lès-Nemours, France
Consistent female preference for rare and unfamiliar male color patterns in wild guppy populations

How genetic variation is maintained in ecologically important traits is a central question in evolutionary biology. Male Trinidadian guppies, Poecilia reticulata, exhibit high genetic diversity in color patterns within populations, and field and laboratory studies implicate negative frequency-dependent selection in maintaining this variation. However, behavioral and ecological processes that mediate this selection in natural populations are poorly understood. We evaluated female mate preference in 11 natural guppy populations, including paired populations from high- and low-predation habitats, to determine if this behavior is responsible for negative frequency-dependent selection and to evaluate its prevalence in nature. Females directed significantly more attention to males with rare and unfamiliar color patterns than to males with common patterns. Female attention also increased with the area of male orange coloration, but this preference was independent of the preference for rare and unfamiliar patterns. We also found an overall effect of predation regime; females from high-predation populations directed more attention toward males than those from low-predation populations. Again, however, the habitat-linked preference was statistically independent from the preference for rare and unfamiliar patterns. Because previous research indicates that female attention to males predicts male mating success, we conclude that the prevalence of female preference for males with rare and unfamiliar color patterns across many natural populations supports the hypothesis that female preference is an important process underlying the maintenance of high genetic variation in guppy color patterns.
Foliar application of endophytic Wickerhamomyces anomalus against grey mould in Eucalyptus dunnii

ABSTRACT Grey mould, caused by the fungus Botrytis cinerea, is one of the diseases that occur in seedlings of Eucalyptus dunnii. The control of this disease is carried out mainly with chemical fungicides, but such use should be restricted to cases of high severity. An interesting alternative is the biocontrol using endophytic microorganisms. We assessed the antagonistic potential of endophytic yeasts from coffee beans against B. cinerea in vitro and their potential for biocontrol of grey mould in detached leaves and three-month-old seedlings of E. dunnii. Ten strains significantly inhibited the growth of B. cinerea in vitro (59.9–86.9%), and Wickerhamomyces anomalus showed the highest inhibition of the pathogen. In the in vivo assays, W. anomalus remained viable for 10 days after spraying on leaves and reduced the severity of the grey mould in E. dunnii detached leaves and seedlings. The results were statistically similar to those obtained with chemical fungicide when sprayed weekly. This is the first report of the effectiveness of endophytic W. anomalus as a suppressor of the development of grey mould in E. dunnii.