Miracle-dz/UniFAR-FTUs huggingface dataset:
PADRÃO ESPACIAL DE ESPÉCIES FLORESTAIS: ESTUDO DE CASO COM Ocotea odorifera (Vell.) Rohwer

Distinction between generating mechanisms of the spatial patterns of forest species – case study with Ocotea odorifera . The objective of this research was the understanding of the processes and generating mechanisms of the spatial distribution of Ocotea odorifera , discriminating influences of the environment from those arising due to interactions between individuals. For this, coordinates from species trees were taken in a region of 25 hectares of Mixed Rain Forest (FOM) sampled in the National Forest (FLONA) of Irati. These data, described as a spatial point process, were evaluated by two Spatial Statistics techniques. Initially, a Kernel intensity estimator verified the global patterns of trees dispersion in the sampled region, and posteriorly, the non-homogeneous Ripley’s K function was used to study the local patterns. It was verified that the species clusters were localized in the highest areas of the sampled region, possibly in better drained soils. Furthermore, attraction was found amongst the specie's individuals, originating clusters in the largest scales analyzed, as shown by the non-homogeneous Ripley’s K function.
Ecological factors influencing lifetime productivity of pink salmon (Oncorhynchus gorbuscha) in an Alaskan stream

Ecological factors underlying freshwater productivity and marine survival of pink salmon (Oncorhynchus gorbuscha) were evaluated by analyzing a 30 year time series of local environmental data and censuses of migrating adult and juvenile fish collected at Auke Creek, Alaska. Freshwater productivity was influenced primarily by spawning habitat limitation and less so by stream temperature and flow. Furthermore, a trend of declining freshwater productivity was detected over the time series, which may be related to observed declines in spawning substrate quality and in the duration of the adult migration. Marine survival was highly variable among brood years and was influenced by physical conditions in the nearshore marine environment; warm sea-surface temperatures during nearshore residency were associated with higher marine survival rates, whereas high stream flows late in the fry emigration period were associated with reduced marine survival. Simulations of adult recruitment, based on ecological factors in .
Developing and communicating strategies for controlling virus diseases in vegetable cucurbit crops

Virus diseases cause serious yield and quality losses in field grown cucurbit crops worldwide. In Australia, the main viruses of cucurbits are Papaya ringspot virus (PRSV), Squash mosaic virus (SqMV), Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV). Plants infected early have severely distorted fruit. High infection incidences, of ZYMV and PRSV in crops cause losses of marketable fruit of up to 100% and infected crops are often abandoned. Two new alternative hosts of ZYMV were identified, the native cucurbit Cucumis maderaspatanus and wild legume Rhyncosia minima. No new alternative hosts of PRSV, SqMV or WMV were found in Western Australia or Queensland. Seed transmission of ZYMV (0.7%) was found in seedlings grown from ZYMV-infected fruit of zucchini but not of pumpkin. None was detected with PRSV or SqMV in zucchini or pumpkin seedlings, respectively. ZYMV spread to pumpkins by aphids was greater downwind than upwind of a virus source. Delaying sowing by 2 weeks decreased ZYMV spread. Millet non-host barriers between pumpkin plantings slowed ZYMV infection. Host resistance gene (zym) in cucumber cultivars was effective against ZYMV. Pumpkin cultivars with resistance gene (Zym) became infected under high virus pressure but leaf symptoms were milder and infected plants higher yielding with more market-acceptable fruit than those without Zym. Most zucchini cultivars with Zym developed severe leaf and fruit symptoms. ZYMV, PRSV, WMV and SqMV spread readily from infected to healthy cucurbit plants by direct leaf contact. ZYMV survives and remains infective on diverse surfaces for up to 6 hours but can be inactivated by some disinfectants. Phylogenetic analysis indicates at least three separate introductions of ZYMV into Australia, with new introductions rarely occurring. ZYMV isolates clustered into three groups according to collection location i) Kununurra, ii) Northern Territory and iii) Carnarvon, Qld and Vic. A multiplex Real-Time PCR was developed which distinguished between the three groups of Australian isolates. Integrated disease management (IDM) strategies for virus diseases of vegetable cucurbit crops grown in the field were improved incorporating the new information gathered. These strategies are aimed at causing using minimal extra expense, labour demands and disruption to normal practices.
Identification of Novel Substrates of the Ubiquitin E3 Ligase RNF126 and Characterization of its Role in Lipid Droplet Homeostasis

Ubiquitin E3 ligases confer specificity by recognizing target substrates and mediating the final step of the ubiquitination process. Despite this critical role, our understanding of their physiological partners and biological functions remains limited. Here we use a proximity-based protein screen called BioID to explore novel interacting proteins and substrates of the ubiquitin E3 ligase RNF126. We demonstrate that RNF126 can associate with p97 as well as its co-factors UBXD1 and UBXD8 and show that UBXD1 and UBXD8 are bonafide substrates of RNF126. To determine a functional role, we explored the role of RNF126 in UBXD8 mediated functions. We found that stable knockdown of RNF126 in HeLa cells results in smaller LDs following oleate stimulation and that this is due to defective expansion. Together, this work demonstrates the successful use of BioID to identify substrates of ubiquitin E3 ligases and furthers our understanding of the role of ubiquitin in LD biology.
Transport of Tail-anchored Proteins to the Inner Nuclear Membrane

In contrast to the well-studied process of nucleocytoplasmic transport of soluble macromolecules, little is known about the targeting of integral membrane proteins to the inner nuclear membrane (INM), therefore the targeting of INM-proteins was studied in this work. Two major models haven been proposed for INM-protein transport, the diffusion-retention model, which assumes passive diffusion of proteins from the ER membrane, across the nuclear pore complex (NPC) to the INM and the transport factor-mediated model, where membrane proteins are believed to translocate across the NPC into the nucleus upon binding to nuclear import receptors. In this work, the targeting of proteins to the INM was studied for several tail-anchored (TA)-proteins, which contain only a single C-terminal transmembrane domain (TMD). As a model protein, the well-established INM-protein emerin was used. With the help of membrane insertion assays, we showed that emerin, expressed in bacteria or a cell-free lysate, can be post-translationally integrated into ER membranes by the TRC40-pathway. The involvement of the TRC40-system was shown by use of inhibitory fragments of the ER-membrane receptors WRB and CAML in the membrane insertion reaction. An interaction between emerin and TRC40 could further be confirmed by proximity ligation assays. Additionally, TRC40 knockdown experiments demonstrated a reduction of emerin localized at the nuclear envelope. An important objective of this work was to verify correct targeting of emerin and other integral membrane proteins to the INM. To accomplish this, we performed differential permeabilization experiments, and established a rapamycin-based dimerization assay. These experiments allowed us to confirm the localization of emerin at the INM in a microscopy based approach. In addition to wild type emerin, we also analyzed mutants. Mutations in the emerin gene in the TMD or in the C-terminal part lead to the neuromuscular disease Emery-Dreifuss muscular dystrophy. As the TMD of emerin is crucial for anchoring of emerin in a membrane, several C-terminal emerin mutations were selected and studied for their post-translational membrane insertion and localization at the INM. Several of these mutants showed severely disturbed TRC40-binding, membrane integration and INM-targeting. The efficiency of targeting to the INM might therefore rely on properties within the TMD or at least the C-terminal region of emerin. The disease could therefore be a consequence of an impaired transport process or a reduced retention at the INM. Apart from emerin, other putative tail-anchored INM-proteins like LAP2β, LEMD1, PTP1B, VAPB and LRRC59 were confirmed to localize to the INM using the rapamycin assay. Furthermore, some of them were shown to use a post-translational membrane insertion mechanism at the ER.
Sex-specific foraging: The distributional ecology of a polychaete-eating shorebird

Trend analysis showed that in the Dutch Wadden Sea bivalve-feeding birds decreased during the last 30 years, while the worm-feeding birds have increased in that same time. It seems that the decline of bivalve-feeding birds is linked the decrease in available resources, but little is known about the cause of increase in worm-feeding birds. The bar-tailed godwit has been chosen as a model species. This shorebird is a worm specialist and shows high intra- and intersexual differences in size and breeding plumage. The females have a larger body and longer bills than males. This sexual dimorphism has led to different diets: the females mainly forage on deep burying lugworms, whereas the males mainly forage on small shallow burying prey. The difference in occurrence between the sexes at different non-breeding sites was mainly determined by the availability of food (prey burying depth) and not by latitude or flight distance to their Arctic breeding grounds. With increasing conspecific densities, intake rates levelled off in females, but not in males. Both in the field and in the laboratory, lugworms responded to probes by retracting themselves in their burrow, out of reach of the longer-billed females. To predict as to where and how many birds can forage in a certain habitat, measurements were done in the field, as well as in the lab. Although field measurements may yield a consistency test of the distributional patterns in a specific ecological context, they cannot be mechanistically interpreted and are therefore not generally applicable. Using the parameters obtained from the experiment, it was found that in the winter, when lugworms are buried deepest, only the longer-billed females remain in the Waddenzee, while the shorter-billed birds moved to other estuaries, such as the Wash in England. Therefore, not only morphological differences between the sexes, but even within the sexes, play a major role in the distributional ecology of this polychaete feeding shorebird.
Prosody Classification: Confirmation to Prosody Conversion

— Prosody classification is one of the challenging tasks in prosody conversion. To determine whether we can convert the prosody or not, prosody classifications is main task. If we can classify the prosody, then it’s sure we can convert the prosody. In this paper, we focused on the classification of prosody. We demonstrated the approach of classifying the prosody using the multi-class support vector machine. In first part, we considered spectral as well as prosodic features for classification. In second part, we considered only prosodic features. In second part, the classification accuracy is more. In SVM, we used the combination of RBF (radial basis function) and polynomial kernel function which gave better accuracy than single RBF kernel function. The successful prosody classification leads to confirmation of prosody classification.
Isolation of Indigenous Hydrocarbon Transforming Bacteria from Oil Contaminated Soils in Libya: Selection for Use as Potential Inocula for Soil Bioremediation

The Libyan oil industry has left a significant legacy of contamination and methods are required to remediate oil-contaminated soils in the area. In this work hydrocarbon utilizing microorganisms were isolated and identified from contaminated soil samples obtained from an oil Refinery (Zawia, Libya). After initial screening of eleven isolates capable of growth on hexadecane, the five most promising hydrocarbon–utilizing bacteria were isolated and tested for biosurfactant production and emulsification activity. They were identified (using 16S rRNA sequence analysis) as Pseudomonas putida, Pseudomonas species, Betaproteobacterium, Actinomyces species, and Bacillus species. Among the five species tested, Pseudomonas putida showed superior performance in terms of growth on hydrocarbons (1.0×1010 CFU (ml)), E24 emulsifying activity (86%) and ability to transform hydrocarbons in pure culture. Interestingly, gas chromatographic analysis of crude oil treated with P. putida showed a decrease in heavy hydrocarbon fractions demonstrating a clear potential for this microbe to be used as a soil inoculant in bioremediation.
Habitat requirements and population estimate of the endangered Ecuadorian Tapaculo Scytalopus robbinsi

Summary The Chocó-Tumbesian region of western Ecuador is one of the 25 global biodiversity hotspots harbouring high numbers of endemic species, which are heavily threatened by habitat loss and fragmentation. Moreover, ongoing climate change in the tropics drives species uphill as lower-lying areas are becoming constantly drier. Such upslope movement can pose major challenges for less mobile species, such as understorey birds which are confined to mature forests and unable to cross habitat gaps. Consequently, these species are threatened by a combination of upslope range shifts and forest fragmentation. In our study, we investigated population numbers and habitat requirements of the Ecuadorian Tapaculo Scytalopus robbinsi, which is endemic to the premontane cloud forests of south-western Ecuador. Comparing the microhabitat structure within territories with control sites revealed that Ecuadorian Tapaculos prefer old secondary forests. Moreover, connectivity between forest fragments was the strongest predictor of the presence of territories within them. We estimated the mean upslope shift of the distribution range as 100 m per decade and developed a model of habitat availability for the revised range. Extrapolating the number of territories from the study area to the distributional range of the Ecuadorian Tapaculo showed that the global population size is smaller than previously assumed. Our results suggest that the Ecuadorian Tapaculo is strongly affected by forest loss and degradation. Therefore, to prevent a continuing decline in population numbers or even extinction, conservation measures focusing on restoring connectivity between fragments and increasing habitat quality and quantity for the remaining populations need to be prioritised.
Genes from Arabidopsis involved in iron-sulfur cluster biogenesis

Iron sulfur [Fe-S] proteins are essential components of many major biological processes including electron transport, respiration, photosynthesis, hormone biosynthesis, and environmental sensing. The process of [Fe-S] cluster assembly in living cells is a controlled mechanism that is highly conserved across all kingdoms. Considerable progress has been made in deciphering this mechanism in bacteria, yeast, and mammals. The key players are the NifS/IscS/SufS proteins, which act as the sulfur donor, and the NifU/IscU/SufU proteins, which serve as a scaffold that binds Fe and upon which the cluster is assembled. Additional proteins are involved in the maturation and transport of the clusters. In eukaryotes there is redundancy in the proteins involved in this mechanism and the process is compartmentalized. Not much is known about the [Fe-S] cluster assembly mechanism in plants. In addition to the redundancy and compartmentalization seen in this machinery in eukaryotes, plants present a further challenge by offering chloroplasts as an additional site for [Fe-S] cluster assembly. The objective of this project has been to characterize Arabidopsis AtNFS1 and AtISU1-3, which show high homology to NifS/IscS and NifU/IscU, respectively, and are hypothesized to be key players in [Fe-S] cluster biogenesis in plants. Subcellular localization results of the AtNFS1 and AtISU1-3 proteins fused to GFP from this study are consistent with the presence of dual machinery in plants, with both mitochondria and chloroplasts as sites for [Fe-S] cluster
Pelagic food web response to whole lake N fertilization

Anthropogenic activities are increasing inorganic nitrogen (N) loadings to unproductive boreal lakes. In many of these lakes phytoplankton are N limited, consequently N fertilization may affect ecosystem productivity and consumer resource use. Here, we conducted whole lake inorganic N fertilization experiments with six small N limited unproductive boreal lakes (three control and three N enriched) in an area receiving low N deposition with one reference and two impact years. Our aim was to assess the effects of N fertilization on pelagic biomass production and consumer resource use. We found that phytoplankton primary production (PP) and biomass, and the PP: bacterioplankton production ratio increased after fertilization. As expected, the relative contribution of phytoplankton derived resources (autochthony) that supported the crustacean zooplankton community increased. Yet, the response in the consumer community was modest with autochthony only increasing in one of the three major zooplankton groups and with no effect on zooplankton biomass. In conclusion, our findings imply that newly available phytoplankton energy derived from N fertilization was not efficiently transferred up to zooplankton, indicating a mismatch between producer energy supply and consumer energy use with potential accumulation of phytoplankton biomass as the result.
Influence of guided inquiry on first-year students’ attitudes to laboratory activities and performance in physics

This paper reports on the effect of Socratic questioning integrated with guidedinquiry (GI) on students’ attitudes to physics laboratory activities and academic performance. Ninety seven first-year Bachelor of Science physics students participated in this study at a well-established South African university. The students were assigned systematically to control (C) and experimental (E) groups. The C group did recipe-based practical activities, while the E group did GI practical activities. At the end of the semester, data were collected using the written practical and hands-on examinations, follow-up focus group interviews as well as the theory examinations. Results indicated that the E group outperformed the C group in certain questions, but also performed worse in most of the questions. Overall, there were differences between the C and E groups, however the differences were not statistically significant. We conclude that GI laboratory activities did not enhance first-year physics students’ academic performance. It was also found that, the E group students developed a positive attitude towards the GI practical activities, while the C group students appreciated the procedural approach followed in their recipe-based practical activities. The results of this study however, contribute to the understanding of current science laboratory practices, learning processes and the potential effects of inquiry-based instruction at university level.
Importance of pharmacognostic study of medicinal plants: An overview

The present review discusses the need and emphasizes the importance of pharmacognostic study of medicinal plants. This study is important and lays down parameters for standardization and authentication of medicinal plants with the help of which adulteration and substitution can be prevented. All the parameters to be evaluated in pharmacognostic study such as organoleptic characters, macroscopic study, microscopic study, powder study, physico chemical analysis (moisture content, loss on drying, ash values, extractive values), phytochemical analysis, fluorescence analysis are enlisted along with their importance. In the end 55 plants whose pharmacognostic studies have been done are listed along with their family and part evaluated for pharmacognostic study.
Components of Genetic Variation and Graphical Analysis (Wr-Vr) in Indian Mustard (Brassica juncea L. Czern & Coss.)

Indian mustard (Brassica juncea) is a naturally autogamous species, accounting the environmental condition and frequency of pollinating insect i.e. bees, 5-30% out crossing takes place Based on ploidy level, Indian mustard is an amphidiploid (2n=36), derived from interspecific cross between two diploid species i.e., Brassica rapa (2n=20) and Brassica nigra (2n=16) followed by natural chromosome doubling. The improved mustard seeds contain 39-44% oil. For International acceptance, erucic acid content should be <2%. Seed quality, Seed yield and other yield related parameters of Brassica oil seed crop has been tried to improve by several researchers (Monpara, 2007). Many authors applied different strategies for improving seed yield and quality attributed of Brassica (Singh et al., 2003; Gami et al, 2012). Gami and Chauhan (2013) and Patel et al., (2013) have also reported difference types of gene action and combining abilities in different sets of material studies. The various mating designs have been used for assessing the breeding International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 2 (2017) pp. 535-545 Journal homepage: http://www.ijcmas. com
Variable selection with a support vector machine for discriminating Cryptococcus fungal species based on ATR-FTIR spectroscopy

Variable selection with supervised classification is currently an important tool for discriminating biological samples. In this paper, 15 supervised classification algorithms based on a support vector machine (SVM) were applied to discriminate Cryptococcus neoformans and Cryptococcus gattii fungal species using ATR-FTIR spectroscopy. These two fungal species of the Cryptococcus genus are the etiological agents of Cryptococcosis, which is an opportunistic or primary fungal infection with global distribution. This disease is potentially fatal, especially for immunocompromised patients, like those suffering from AIDS. The multivariate classification algorithms tested were based on principal component analysis (PCA), successive projections algorithm (SPA) and genetic algorithm (GA) as data reduction and variable selection methods, being coupled to a SVM with different kernel functions (linear, quadratic, 3rd order polynomial, radial basis function, and multilayer perceptron). Some of these algorithms achieved very successful classification rates for discriminating fungal species, with accuracy, sensitivity, and specificity equal to 100% using both SPA-SVM-polynomial and GA-SVM-polynomial algorithms. These results show the potential of such techniques coupled to ATR-FTIR spectroscopy as a rapid and non-destructive tool for classifying these fungal species.