Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of RAB25 and RAB11 GTPases in bladder tumorigenesis

Activation of FGFR3 by point mutation, translocation and overexpression is one of the most frequent events in bladder cancer. The dysfunction of RAB25, a GTPase involved in endocytic recycling of transmembrane receptor, has been shown in many cancers. Gene expression data in bladder cancer indicates that RAB25 expression is significant higher in tumors carrying altered FGFR3. The thesis project aimed to investigate the potential role of RAB25, proteins from the same family (RAB11A and RAB11B) and their effectors RAB11FIP2 and MYO5B in 1) the tumorigenesis of tumors carrying altered FGFR3 and 2) the trafficking and the signaling of FGFR3. Our results demonstrate that depletion of these proteins by siRNA significantly reduces cell viability in cells expressing constitutively activated forms of FGFR3. The effects of RAB25 and RAB11 silencing on FGFR3 trafficking and signaling and the expression of FGFR3 target genes suggest that the RAB11- and RAB25-mediated recycling can sustain the signaling by protecting altered FGFR3 from the degradation pathway, and can provide a platform for FGFR3 signaling We also compared the subcellular distribution of wild type and mutant (S249C) forms of FGFR3. These two forms localize to different compartments including early endosomes, late endosomes and recycling compartments. The S249C FGFR3 mutant preferentially localizes to the endocytic recycling compartment. Our findings shed light to the molecular mechanisms underlying the relationships between the trafficking and signaling of FGFR3 in the context of bladder cancer.
Development of a predictive model for ‘Lapins’ sweet cherry dry matter content using a visible/near-infrared spectrometer and its potential application to other cultivars

Abstract: This work was conducted to determine if a useful model could be developed for a portable visible/near-infrared spectrometer for non-destructively predicting dry matter content in ‘Lapins’ and other cultivars of sweet cherries. Absorptions at a range of 948–957 nm (default selected by the instrument model-building program) or 858–1008 nm (user selected) were used to create models associating absorption values with actual measured dry matter contents of cherries. The best model was created using the user selected waveband and this model was determined to be highly predictive of dry matter, with a resolution of 0.5% dry matter content. External validation of this model was carried out using three different sweet cherry cultivars (Staccato™, Sentennial™, and Sovereign™) and the model was found to be robust, i.e., quite accurate in predicting dry matter content in these other cultivars, with R 2 values of 0.96, 0.94, and 0.99, and root mean square error of prediction values of 0.51, 0.74, and 0.56, respectively. The results indicate that dry matter in sweet cherries can be predicted accurately and non-destructively using visible/near-infrared spectroscopy. In the case of the cherry cultivars tested in this paper, a model developed using ‘Lapins’ fruit was reliable in predicting dry matter in these other cultivars.
Parameters affecting plant defense pathway mediated recruitment of entomopathogenic nematodes

ABSTRACT Entomopathogenic nematodes are natural enemies and effective biological control agents of subterranean insect herbivores. Interactions between herbivores, plants, and entomopathogenic nematodes are mediated by plant defense pathways. These pathways can induce release of volatiles and recruit entomopathogenic nematodes. Stimulation of these plant defense pathways for induced defense against belowground herbivory may enhance biological control in the field. Knowledge of the factors affecting entomopathogenic nematode behaviour belowground is needed to effectively implement such strategies. To that end, we explore the effect of elicitor, elicitor dose, mechanical damage, and entomopathogenic nematode release distance on recruitment of entomopathogenic nematode infective juveniles to corn seedlings. Increasing doses of methyl jasmonate and methyl salicylate elicitors recruited more entomopathogenic nematodes as did mechanical damage. Recruitment of entomopathogenic nematodes was higher at greater release distances. These results suggest entomopathogenic nematodes are highly tuned to plant status and present a strategy for enhancing biological control using elicitor-stimulated recruitment of entomopathogenic nematodes.
Bacillus thuringiensis serovar. israelensis has no effect on Drosophila suzukii Matsumura

The spotted wing drosophila (SWD), Drosophila suzukii, is an invasive species to the USA, and Europe and biological control methods are urgently sought for. In this study, the potential of commercial microbial control products based on the Dipteran‐specific B. thuringiensis serovar. israelensis (B.t.i.) were evaluated in laboratory experiments. These products were tested on SWD larvae and adults but neither one showed more than 10% mortality. A repellent effect of the products to SWD adults was also ruled out. We conclude that B.t. i. products are not suitable for SWD control.
Neuronal processing under naturally correlated input conditions

Correlations in the activity of neurons are an ubiquitous phenomenon[4] in mammalian cortex, whose function is not yet understood. The effect of correlated activity on single neurons has only been studied using fairly general correlational patterns for the input statistics. In this study EFP-data from the visual cortex of cats [1] was used to generate more realistic correlational input patterns, whose most prominent feature is given by the correlated, yet phaseshifted activity of neurons belonging to populations of different preferred orientation. We studied their effect on single neuron processing and learning behavior using a detailed reconstruction of a L5 pyramidal cell from a cat's striate cortex.
The cause of fruit flavour differences associated with the fungicide prochloraz.

Commercial development of the fungicide prochloraz for the control of pre- and post-harvest diseases in fruit crops has been restricted by the occasional occurrence of 'musty' taints. The primary aims of this research were to identify the cause of taint and and its means of formation. Sensitive and selective residue methodology based upon determination by gas chromatography with mass selective detection was devised, validated and used to establish 2,4,6-trichloroanisole (2,4,6-TCA) as the direct cause of taint by analysis of field-treated samples and studies involving 14C-radiolabelled prochloraz. Evaluation of analytical results in conjunction with corresponding sensory data led to proposals of flavour threshold levels ranging between 0.04 and 1.0mug/kg for 2,4,6-TCA in different fruit types. Formation of the anisole in pre-harvest treatment situations was shown to proceed via the minor plant metabolite 2,4,6-trichlorophenol (2,4,6-TCP) as the direct precursor; under post-harvest conditions, however, metabolism of prochloraz was minimal, and 2,4,6-TCA taints arose primarily from 2,4,6-TCP as an impurity (measured at 0.9% w/w) in the commercial emulsifiable concentrate formulation. Detailed investigation of the relationship between 2,4,6-TCP and 2,4,6-TCA under controlled conditions demonstrated that certain fruit types possess a capacity for direct O-methylation of the phenol to the anisole, whereas others do not. These findings were generally consistent with occurrences of taints associated with prochloraz. Kinetic studies of the active O-methyltransferase system in apple homogenates indicated the same Vmax value for 2-chlorophenol, 2,4-dichlorophenol, 2,6-dichlorophenol and 2,4,6-TCP. Reactivity in this series was found to be closely related to the ability of the molecules to to form effective nucleophiles for reaction with s-adenosylmethionine as the assumed methyl donor, and a linear relationship was established between chlorophenol pKa and log(apparent Km). The O-methylation of 2,4,6-TCP, whilst inhibited competitively by other o-chlorophenolic substrates, remained unaffected by the addition of representative plant o-diphenolics previously reported as substrates for O-methylation in plants.
Fire regimes and environmental gradients shape vertebrate and plant distributions in temperate eucalypt forests

Fire is a global driver of ecosystem structure, function, and change. Problems common to fire scientists and managers worldwide include a limited knowledge of how multiple taxonomic groups within a given ecosystem respond to recurrent fires, and how interactions between fire regimes and environmental gradients influence biodiversity. We tested six hypotheses relating to fire regimes and environmental gradients in forest ecosystems using data on birds (493 sites), mammals (175 sites), and vascular plants (615 sites) systematically collected in dry eucalypt forests in southeastern Australia. We addressed each of these hypotheses by fitting species distribution models which differed in the environmental variables used, the spatial extent of the data, or the type of response data. We found (1) as predicted, fire interacted with environmental gradients and shaped species distributions, but there was substantial variation between species; (2) multiple characteristics of fire regimes influenced the distribution of forest species; (3) common to vertebrates and plants was a strong influence of temperature and rainfall gradients, but contrary to predictions, inter-fire interval was the most influential component of the fire regime on both taxonomic groups; (4) mixed support for the hypothesis that fire would be a stronger influence on species occurrence at a smaller spatial extent; only for vertebrates did scale have an effect in the direction expected; (5) as predicted, vertebrates closely associated with direct measures of habitat structure were those most strongly influenced by fire regimes; and (6) the modeled fire responses for birds were sensitive to the use of either presence–absence or abundance data. These results underscore the important insights that can be gained by modeling how fire regimes, not just fire events, influence biota in forests. Our work highlights the need for management of fire regimes to be complemented by an understanding of the underlying environmental gradients and key elements of habitat structure that influence resource availability for plants and animals. We have demonstrated that there are general patterns in biotic responses to fire regimes and environmental gradients, but landscape management must continue to carefully consider species, scale, and the quality of biodiversity data to achieve biodiversity conservation in fire-prone forests.
Multidrug-resistant Staphylococci Found on Book Surfaces in East London Libraries

There is an increase in the presence of drug-resistant staphylococci outside of the nosocomial and healthcare setting. Although the presence of staphylococci has been studied in several public spaces, nothing is known on the presence of staphylococci in public libraries. Book surfaces from public libraries in the East London area, United Kingdom were swabbed and cultured and identity of the isolates determined by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS). Seven different staphylococcal species were identified by MALDI-TOF-MS analysis. This short study provides evidence of the presence of multidrug-resistant staphylococci in public libraries in the East London area.
Isolation and Characterization of N Fixing Bacteria from Elephant Foot Yam (Amorphophallus paeoniifolius (Dennst.)Nicolson) Growing Regions of South India

Isolation and screening of 130 bacteria from the rhizosphere region of elephant foot yam ( Amorphophallus ) growing area of South India for their ability to fix atmospheric nitrogen ( Kjeldhal technique) resulted in the identification of 62 isolates having varying levels of nitrogen fixing ability in Jensen's nitrogen free medium. The most potent nitrogen fixing isolates were tested for their efficiency to release plant growth promoting substances like indole acetic acid (IAA), ammonia (NH 3 ), hydrogen cyanide (HCN) and catalase enzyme. Morphological and molecular characterization of the two potent bacterial strains led to the identification of them as Bacillus cereus strain ANctcri-1 (HQ286640) and Pseudomonas aeuroginosa ANctcri-11 (JX974833). A study on the effect of various physiological conditions on growth of this potent bacteria revealed their facultative alkaliphilic halo tolerant nature.
Haploinsufficiency of Parkinsonism Gene SYNJ1 Contributes to Dopamine neuron Vulnerability in Aged Mice

Parkinson’s disease (PD) is an age-dependent neurodegenerative disorder characterized by the loss of substantia nigra dopaminergic (DAergic) neurons in ventral midbrain (MB). Identification of interactions between aging and the known risk variants is crucial to understanding the etiology of PD. Recessive mutations in SYNJ1 have recently been linked to familial early-onset atypical Parkinsonism. We now show an age-dependent decline of SYNJ1 expression in the striatum as well as in striatal DAergic terminals of aged mice. Heterozygous deletion of SYNJ1 in mice causes selective elevation of PIP2 in the MB, and manipulation of PIP2 levels also impairs synaptic vesicle recycling preferentially in MB neurons. SYNJ1+/− mice display progressive PD-like behavioral alterations and DAergic terminal degeneration. Furthermore, we found down-regulation of human SYNJ1 transcripts in a subset of sporadic PD brains, corroborating the role of an age-dependent decrease in SYNJ1 in predisposing DAergic neuron vulnerability and PD pathogenesis.
Predictive Eel Population Model Based on Fish Habitat Dependency and Fishing Pressure on Pisodonophis boro (Hamilton) in the Godavari Delta, India

The habitat dependency of the rice-paddy eels, Pisodonophis boro is described in this paper with emphasis on natural production. The eels use mangrove mudflats as homing ground for feeding and breeding; perform anadromous migration during breeding season; total mangrove dependency of the eels has been confirmed from field observations on eel fishery and mangrove degradation during the period 1981-2012. Total loss of mangrove habitat resulted in migration or mortality of the species and recruitment of the fish populations preceded rejuvenation and ramification of mangrove flora and associated fauna. Pisodonophis boro needs perennial freshwater inflow for successful reproduction; thus, the annual breeding cycle is triggered and regulated by the freshwater release from the river dam, and the artisanal fishery is correlated to these events. Sexes are separate and females with bilobed ovaries grow larger. The fish is being caught by trap nets and hooks as these have a sediment burrowing behavior and carnivorous food habits. A novel method of estimating eel population by applying Mini Tab. 16 software and the unique SARIMA, 1.1. 1 model is highlighted. Critical factors influencing/triggering migration of eels from the Godavari estuary to the freshwater canals and paddy fields were seasonality, temperature and salinity. Smoked eels are delicacies of the entire central delta with a total population of 12,00,438; the proximate composition of the fish was analysed and health problems if any in smoked fish consumers was assessed by documenting health symptoms.
Complete mitochondrial genome sequence of Glaucosoma buergeri (Pempheriformes: Glaucosomatidae) with implications based on the phylogenetic position

Abstract The complete mitochondrial genome sequence of pearl perch (Glaucosoma buergeri) was determined using a PCR-based method. The genome was 16,529 bp in length and included 37 genes (13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes) and two non-coding regions (control region and origin of the light strand replication). A maximum likelihood analysis was conducted to confirm the phylogenetic position of this species using almost all the data available on Pempheriformes in the database. The complete mitochondrial genome sequence data obtained from our study would be useful for analyzing the evolutionary relationships of the Pempheriformes and population genetics of the Glaucosomatidae.
Insecticidal and synergistic activity of two monoterpenes against diamondback moth (Lepidoptera: Plutellidae)

Abstract We examined the insecticidal activity of linalool and thymol, against diamondback moth, Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae), and whether they would synergise the activity of spinosad against this pest. Both linalool and thymol were toxic to diamondback moth larvae by topical and oral exposure, but orders of magnitude less so than spinosad. We found that low concentrations of linalool weakly synergised spinosad, increasing its toxicity more than twofold. An interaction between spinosad, and acetone meant it was not possible to identify any potential synergisms between thymol and spinosad. Our results demonstrate limited potential for thymol and linalool to act as biopesticides or synergists for managing diamondback moth.
Statistical and Analytical Study of Guided Abstractive Text Summarization

The process of creating condensed version of given text document by collecting only the important information in it is called abstractive summarization. This involves structuring the information into sentences which are simple and easy to understand. This article presents the analytical study of the process that generates abstractive summary using unified model with attribute based information extraction (IE) rules and class based templates. Classification of the document into several categories is achieved by term frequency/ inverse document frequency (TF/IDF) rules. To generate the information intensive summaries, we use templates for sentence generation. The IE rules are designed to address the complexities involved in Indian regional languages. This paper statistically analyzes the adaptation of the methodology over multiple Indian languages and many document categories. Comparisons between abstractive and extractive summaries are also presented.
Further polyphyly of pinnotheroid crabs: the molecular phylogenetic position of the polychaete-associated Aphanodactylidae

Abstract. Pea crabs of the superfamily Pinnotheroidea De Haan, 1833 are known for their obligate commensal relationships with other marine invertebrates. The concomitant specialisations and adaptations of pinnotheroids have resulted in superficially similar body forms that include a high degree of structural reduction. This has confounded interpretation of their phylogenetic position in the Brachyura and interrelationships within Pinnotheroidea, though all were nevertheless believed to be united by a monophyletic origin of obligate commensalism. The family Aphanodactylidae Ahyong & Ng, 2009 was proposed for a group of genera associated with tube-dwelling polychaetes formerly classified in Pinnotheridae, and provisionally retained in the Pinnotheroidea. We investigated the phylogenetic position of Aphanodactylidae using molecular data from three markers (mitochondrial 12S and 16S rRNAs, and nuclear histone H3) covering five of the 12 described aphanodactylid species and a total of 15 thoracotreme families. We found Aphanodactylidae to be monophyletic, but widely distant from Pinnotheridae and instead most closely related to Macrophthalmidae (Ocypodoidea) and Varunidae (Grapsoidea). Therefore, the family Aphanodactylidae is corroborated, but its placement in Pinnotheroidea is rejected. Instead, the phylogenetic position of Aphanodactylidae, as clearly distant from other pinnotheroids, demonstrates that obligate commensalism has evolved independently multiple times within Thoracotremata.
Profiling copy number variation and disease associations from 50,726 DiscovEHR Study exomes

Copy number variants (CNVs) are a substantial source of genomic variation and contribute to a wide range of human disorders. Gene-disrupting exonic CNVs have important clinical implications as they can underlie variability in disease presentation and susceptibility. The relationship between exonic CNVs and clinical traits has not been broadly explored at the population level, primarily due to technical challenges. We surveyed common and rare CNVs in the exome sequences of 50,726 adult DiscovEHR study participants with linked electronic health records (EHRs). We evaluated the diagnostic yield and clinical expressivity of known pathogenic CNVs, and performed tests of association with EHR-derived serum lipids, thereby evaluating the relationship between CNVs and complex traits and phenotypes in an unbiased, real-world clinical context. We identified CNVs from megabase to exon-level resolution, demonstrating reliable, high-throughput detection of clinically relevant exonic CNVs. In doing so, we created a catalog of high-confidence common and rare CNVs and refined population frequency estimates of known and novel gene-disrupting CNVs. Our survey among an unselected clinical population provides further evidence that neuropathy-associated duplications and deletions in 17p12 have similar population prevalence but are clinically under-diagnosed. Similarly, adults who harbor 22q11.2 deletions frequently had EHR documentation of neurodevelopmental/neuropsychiatric disorders and congenital anomalies, but not a formal genetic diagnosis (i.e., deletion). In an exome-wide association study of lipid levels, we identified a novel five-exon duplication within LDLR segregating in a large kindred with features of familial hypercholesterolemia. Exonic CNVs provide new opportunities to understand and diagnose human disease.
Impacts de la prédation sur un grand herbivore aux niveaux de l'individu et de la population

La predation peut avoir des effets tres importants a la fois sur l’ecologie ainsi que sur l’evolution des communautes biologiques. Elle peut notamment etre une force selective favorisant des predateurs plus efficaces et des proies moins vulnerables. De plus, des etudes montrent que les predateurs agissent sur les proies, non seulement directement en les tuant, mais qu’ils peuvent egalement influencer le comportement des proies et induire des reponses physiologiques ou morphologiques. Pourtant, aujourd’hui, encore peu de choses sont connues sur comment les predateurs peuvent influencer les populations de proies, notamment chez les grands herbivores. Les etudes les plus detaillees sur les grands herbivores sont en effet situees dans l’hemisphere Nord, souvent dans des endroits ou ces herbivores n’ont plus de predateurs. Lors de cette these j’ai etudie une population de grands herbivores et l’impact de la predation sur celle-ci : la population de zebres des plaines (Equus quagga) dans le parc national de Hwange au Zimbabwe et son interaction avec les lions. J’ai etudie la dynamique de populations des zebres dans la zone d’etude, mais j’ai egalement travaille sur le zebre au niveau individuel, en tentant de mieux comprendre quels etaient les comportements anti-predateurs utilises par les zebres, ainsi que leurs couts potentiels, tout en m’interessant aux differences entre individus. Cette population de zebres est fortement impactee par la predation, de maniere a la fois directe et indirecte, et les comportements anti-predateurs mis en place par les zebres sont couteux.