Miracle-dz/UniFAR-FTUs huggingface dataset:
Remote sensing of larch phenological cycle and analysis of relationships with climate in the Alpine region

This research aims at developing a remote sensing technique for monitoring the interannual variability of the European larch phenological cycle in the Alpine region of Aosta Valley (Northern Italy) and to evaluate its relationships with climatic factors. Phenological field observations were conducted in eight test sites from 2005 to 2007 to determine the dates of completion of different phenological phases. MODerate Resolution Imaging Spectrometer (MODIS) 250 m 16‐days normalized difference vegetation index (NDVI) time series were fitted with double logistic curves and the dates corresponding to different features of the curves were determined. Comparison with field data showed that the features of the fitted NDVI curve that allowed the best estimate of the start and end of the growing season were the zeroes of its third derivative (MAE of 6 and 4 days, respectively). The start and end of season were also estimated with the spring warming (SW) and growing season index (GSI) phenological models. MODIS start and end of season dates generally agreed with those obtained by the SW and GSI climate‐driven phenological models. However, phenological models provided erroneous results when applied in years with anomalous meteorological conditions. The relationships between interannual variability of the larch phenological cycle and climate were investigated by comparing the mean start and end of season yearly anomalies with air temperature anomalies. A strong linear relationship (R2=0.91) was found between mean spring temperatures and mean start of season dates, with an increase of 1 °C in mean spring temperature leading to a 7‐day anticipation of mean larch bud‐burst date. Leaf coloring dates were found to be best related with mean September temperature (R2=0.77), but with higher spring temperatures appearing to lead to earlier leaf coloring.
The functional response does not predict the local distribution of European Rabbits (Oryctolagus cuniculus) on grass swards: experimental evidence

Summary 1. The relationship between available biomass and short-term rate of intake (functional response) of herbivores is expected to provide a link between their food supply, and their distribution. 2. The functional response of captive wild rabbits (Oryctolagus cuniculus L.) on artificially produced broad-leaved (Lolium perenne L.) and narrow-leaved (Festuca ovina L.) grass swards was quantified. 3. The general prediction that habitat selection varied with biomass, and reflected the potential rate of intake defined by the functional response, was also tested. The main alternative predictions, that both intake rate and habitat selection increased asymptotically with biomass, or were biased towards intermediate habitat standing crop biomasses, were distinguished. 4. There was no relationship between biomass and short-term rate of intake on the narrow-leaved Festuca swards, but on the broad-leaved Lolium sward the short-term rate of intake increased asymptotically with biomass. 5. In a field experiment on Lolium swards, a population of free-living wild rabbits selected the shortest swards with the lowest biomasses, and which provided the lowest potential rates of intake. 6. Results demonstrate that free-living wild rabbits do not select habitats that provide the maximum potential rate of intake, nor did they select foraging habitat with intermediate standing crops. It is suggested that their selection of foraging areas in these grasslands which typify rabbit foraging habitat, is dominated by antipredator considerations rather than purely by rate of intake.
Polypeptide electrophoretic pattern of Matricaria chamomilla and Anthemis nobilis under salt and Fe- deficiency stress

In order to study the effects of salinity and Fe-deficiency on electrophoresis pattern of polypeptides in two chamomile genera (Matricaria chamomilla and Anthemis nobilis), a factorial experiment was conducted based on completely randomized block design with three replications, in 2010. The experimental factors were two chamomile genera M. chamomilla and A. nobilis, four levels of salinity (0, 50, 100 and 150 mM NaCl) and two levels of iron (0 and 100 mM). The patterns of proteins extracted from stress-treated leaves of M. chamomilla were not different from the control plants; except for new of 14 and 18 kDa polypeptides which appeared in stress-treated individuals. M. chamomilla produced fewer protein bands compared to A. nobilis and its electrophoretic profile had lower variation. A. nobilis lost its many bands under salinity stresses and iron deficiency. A. nobilis roots synthesized osmotin, (26 kDa MW) and their leaves under salinity stresses and iron deficiency synthesized protein bands of 42, 40, 37 and 15 kDa molecular weight. It was therefore suggested that the alteration in the pattern of protein synthesis in A. nobilis and M. chamomilla under stress condition is related with specific adaptive response to stresses.
Identification and evaluation of suitable reference genes for gene expression studies in the whitefly Bemisia tabaci (Asia I) by reverse transcription quantitative realtime PCR

Abstract This study presents a reliable method for performing reverse transcription quantitative real-time PCR (RT-qPCR) to measure gene expression in the whitefly Bemisia tabaci (Asia I) (Gennadius) (Hemiptera: Aleyrodidae), utilising suitable reference genes for data normalisation. We identified orthologs of commonly used reference genes (actin (ACT), cyclophilin 1 (CYP1), elongation factor 1&agr; (EF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13A), and &agr;-tubulin (TUB1A)), measured the levels of their transcripts by RT-qPCR during development and in response to thermal stress, and evaluated their suitability as endogenous controls using geNorm, BestKeeper, and NormFinder programs. Overall, TUB1A, RPL13A, and CYP1 were the most stable reference genes during B. tabaci development, and TUB1A, GAPDH, and RPL13A were the most stable reference genes in the context of thermal stress. An analysis of the effects of reference gene choice on the transcript profile of a developmentally-regulated gene encoding vitellogenin demonstrated the importance of selecting the correct endogenous controls for RT-qPCR studies. We propose the use of TUB1A, RPL13A, and CYP1 as endogenous controls for transcript profiling studies of B. tabaci development, whereas the combination of TUB1A, GAPDH, and RPL13A should be employed for studies into thermal stress. The data presented here will assist future transcript profiling studies in whiteflies.
Habitat Suitability Assessment of the Rare Perennial Plant Armeria Arenaria (Pers.) Schult. (Plumbaginaceae) along the French Mediterranean Coastline

Abstract Baumel, A. , S. Youssef, G. Ongamo & F. Médail (2013). Habitat suitability assessment of the rare perennial plant Armeria arenaria (Pers.) (Plumba ginaceae) Schult. along the French Mediterranean coastline. Candollea 68: 221–228. In English, English and French abstracts. A major challenge in conservation biology is to identify the factors driving abundance and demographic regeneration of rare species populations. We assess habitat suitability within a protected area for Armeria arenaria (Pers.) Schult. (Plumbaginaceae), a small perennial polycarpic plant and keystone species of a threatened plant community on the rocky crystalline coastline of South-East France. The factors associated with the occurrence and abundance of adult plants and juveniles of this species were investigated by an “Outlier Mean Index analysis” (OMI). A second census was conducted three years later to test the reliability of inferences about habitat suitability. The results underline the importance of fine scale habitat heterogeneity to understand the variation of abundance. Moreover only a portion of the habitat of Armeria arenaria is suitable for regeneration, underlying the necessity to consider both abundance and regeneration to set conservation and management priorities.
Digital Native/Digital Immigrant Divide: EFL Teachers’ Mobile Device Experiences and Practice

The purpose of this study was to examine how Thai EFL high-school teachers view and use mobile devices (such as smart phones) in educational settings, and if the age-based digital native/digital immigrant divide would highlight any differences in responses. The participants were 55 Thai EFL teachers in 8 schools of different sizes in Southern Thailand, who were split into digital-native and digital-immigrant subgroups during data analysis. Participants completed a 35-item Likert-type scale covering a range of topics related to mobile devices in the EFL setting including their ability, experience, school/personal policy, instructional utilization, and whether they supported mobile devices as a learning aid. The results showed that while digital native teachers consistently responded more positively towards the benefits/uses of mobile devices in EFL teaching/learning than the older digital immigrant teachers often at a significant level, all teachers -regardless of age- agreed on the benefits and promotion of mobile devices as EFL learning aids. Results of this study expand the knowledge base of EFL teachers’ mobile device experiences and practice while raising awareness of significant differences between digital natives and digital immigrants, and recommendations are made for policymakers, schools, and teachers.
Halomethane production by vanadium‐dependent bromoperoxidase in marine Synechococcus

To investigate the role of vanadium‐dependent bromoperoxidase (VBPO) for the production of halogenated methanes in marine prokaryotes, we measured VBPO activity and halomethane production in two strains of Synechococcus; one with VBPO (strain CC9311) and one without VBPO (strain WH8102). A mutant strain of CC9311, VMUT2, in which the gene for VBPO is disrupted, was also tested. A suite of halomethanes was measured in the headspace above cultures as well as in the culture medium with a purge‐and‐trap method. Monohalomethanes were the most consistently produced molecules among the three strains tested. Additionally, CC9311 produced 301 ± 109 molecules cell−1 d−1 of bromoform (CHBr3) when VBPO activity was detected, while production was not significantly different from zero when VBPO activity was not detected. VBPO activity and CHBr3 production were only detected when cultures of CC9311 were stirred, which may contribute to the often moderate to weak correlations between CHBr3 concentration and biological markers in the ocean. No production was seen by VMUT2 or WH8102. These data show that CHBr3 production rates are dramatically increased with or exclusive to the presence of VBPO, supporting its involvement in CHBr3 synthesis. This study thus provides genetic evidence that certain strains of marine Synechococcus, under particular conditions, can be a natural source of marine CHBr3, which contributes to ozone depletion in the stratosphere.
Genetic analysis of the mating system and opportunity for sexual selection in northern water snakes (Nerodia sipedon)

We used data collected over 3 years at two study sites to quantify the rates and consequences of multiple paternity and to determine the opportunity for selection on male and female northern water snakes (Nerodia sipedon). We sampled litters from 45 females that gave birth to 811 offspring. Using eight microsatellite DNA loci (probability of exclusion of nonparental males > 0.99), we assigned paternity to 93% of neonates from one study population and 69% of neonates from the other population. Observations of participation in mating aggregations predicted individual reproductive success poorly for two reasons. First, males regularly courted nonreproductive females. Second, more than half of all sexually mature males obtained no reproductive success each year, despite the fact that many of them participated in mating aggregations. The number of sires per litter ranged from one to five, with 58% of all litters sired by more than one male. Multiple paternity increased with female size, apparently both because bigger females mated with more males and because the larger litters of big females provide paternity opportunities to more males. Multiple paternity was also more prevalent in years with shorter mating seasons. We detected no advantage to multiple paternity in reducing either the number of unfertilized ovules or stillborn young. Despite the majority of males siring no young each year, some males fathered young with as many as three different females in one year. Male reproductive success increased by more than 10 offspring for each additional mate, whereas female success increased by fewer than 2 offspring for each additional mate. The opportunity for sexual selection was more than five times higher in males than females. Copyright 2002.
Genus Diversity of Actinomycetes in Cibinong Science Center, West Java, Indonesia

Actinomycetes are microorganisms that play important role to support human health and known as soil microorganisms. The aim of the research was to describe genus diversity of actinomycetes in Cibinong Science Center (CSC), West Java. Samples for isolation were soil and plant litters. The samples were air dried and ground. We employed isolation methods: dry heat (DH), sodium dodecyl sulphates-yeast extract (SDS-YE), rehydration and centrifugation (RC), and oil separation (OS). A total of 263 isolates of actinomycetes were isolated in CSC, in 2004-2006. Totally 58, 144, 50, and 11 isolates were isolated under each isolation methods, respectively. All isolates were identified using the 16S rRNA gene sequencing method. The results showed that the isolates were belonged to the family Kineosporiaceae , Micromonosporaceae , Nocardiaceae , Pseudonocardiaceae , Streptomycetaceae , Streptosporangiaceae , Mycobacteriaceae , Nocardioidaceae , Nocardiopsaceae , and Thermomonosporaceae . There were 23 genera under those families. Homology value of the isolates based on BLAST search using 16S rRNA gene sequence data as queries showed that 136, 91, 30, and 6 isolates were ≥99, 98, 97, and ≤96%, respectively, compared to the known sequence in data base. The later 6 isolates were interesting for further identification leading to new taxa. Recognized species of Streptomyces genera under the member of the Streptomycetaceae were dominant among other isolates.
DOES A LARGER CARRYING CAPACITY FOR AN EXOTIC SPECIES ALLOW ENVIRONMENT INVASION? — SOME CONSIDERATIONS ON THE COMPETITION OF RED AND GREY SQUIRRELS

The conjecture is explored, whether the main reason for an invader to replace antagonistic indigenous populations can be ascribed to the larger carrying capacity of the former. The final outcome of the analysis highlights that this may not always be the case, but anyway to fight an invasion repelling the alien species is a difficult task. Measures aimed at decreasing the grey squirrel reproductive rate might be a viable route, but to find their suitable implementation at affordable costs is far from easy.
Application of Object Recognition With Shape-Index Identification and 2D Scale Invariant Feature Transform for Key-Point Detection

Humans make object recognition look inconsequential. In this chapter, scale-invariant feature extraction and shape-index depiction are used on a range of images for identifying objects. The shape-index is attained and used as a local descriptor or key-point descriptor. First surface properties for shape index identification and second as 2D scale invariant feature transformed for key-point detection and feature extraction. The object recognition classification is compared results with shape-index identification and 2D scale-invariant feature transform for key-point detection with SIFT and SURF. The authors are using images from the ImageNet dataset, and with use of shift-index + SIFT descriptors, they are finding better accuracy at the classification stage.
Morphological and physiological response of Abaca (Musa textilis var. Laylay) to shade, irrigation and fertilizer application at different stages of plant growth.

Abaca is closely related to edible banana and grown primarily for its fibers. This study was carried out to investigate the effect of shade and irrigation-fertilization on abaca’s morphological and physiological performance. Light infiltration was reduced by 30%, 40%, and 50% of full sunlight using polypropylene shade nets. Irrigation was applied at a rate of 5 liters plant -1 application -1 day -1 . Placement application of N, P2O5, K2O using complete fertilizer was done at 14 grams plant -1 quarter -1 for the first six months and was increased to 40 grams plant -1 quarter -1 for the next six months after planting. Results showed that plant height, cumulative leaf area, pseudostem length and base girth of abaca significantly (p≤0.01) improved when the light was further reduced to 50%. Fertilizer application further enhanced (p≤0.05) the growth performance of abaca. Statistical analysis showed that shade and NPK fertilization positively affected dry matter production, crop growth rate, leaf area ratio and net assimilation rate from seedling to flagleaf stage. Net assimilation rate was strongly affected by shade at seedling stage and late vegetative stage (p<0.05) due to photoinhibition. Analysis of variance showed two-factor interaction effects between shade and irrigation-fertilization on leaf area ratio at early vegetative (p=0.016) and flagleaf (p=0.009) stages. The superior productivity of abaca in response to shade was due to avoidance of photoinhibition, photooxidative damage and midday depression that negatively affected the abaca grown under full sunlight at seedling and early vegetative stages which cannot be neutralized by irrigation and fertilizer application.
Simulated long‐term effects of harvest and biomass residue removal on soil carbon and nitrogen content and productivity for two Upper Great Lakes forest ecosystems

We used the ecosystem process model Biome‐BGC to simulate the effects of harvest and residue removal management scenarios on soil carbon (C), available soil nitrogen (N), net primary production (NPP), and net ecosystem production (NEP) in jack pine (Pinus banksiana Lamb.) and sugar maple (Acer saccharum Marsh) ecosystems in northern Wisconsin, USA. To assess harvest effects, we simulated short (50‐year) and long (100‐year) harvest intervals, high (clear‐cut) and low (selective) harvest intensities, and three levels of residue retention (15%, 25%, and 35%) over a 500‐year period. The model simulation of NPP, soil C accumulation, and NEP agreed reasonably well with biometric and eddy‐covariance measurements of these two ecosystems. The more intensive (50‐year rotation clear‐cuts with low residue retention) harvest scenarios tended to have the greatest NEP (420 and 678 t C ha−1 for the 500‐year interval for jack pine and sugar maple, respectively). All the harvest scenarios decreased mineral soil C and available mineral soil N content relative to the no‐harvest scenario for jack pine and sugar maple. The rate of change in mineral soil C decreased the greatest in the most intensive biomass removal scenarios (−0.012 and −0.072 t C ha−1 yr−1 relative to no‐harvest for jack pine and sugar maple, respectively) and the smallest decrease was observed in the least intensive biomass removal scenarios (−0.002 and −0.009 t C ha−1 yr−1 relative to no‐harvest for jack pine and sugar maple, respectively). The more intensive biomass removal harvest scenarios in sugar maple significantly decreased peak productivity (NPP) in the simulation period.
The Effectiveness of Gemfibrozil on Nicotine Dependence, Smoking Cessation, and its Symptom Among Smokers: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial

Background: Based on animal models, the antagonists of alpha-peroxisome proliferator-activated receptors (PPAR-α) such as fibrates decrease reinforcement, brain rewards, and nicotine-related effects. Objectives: The present study aimed at investigating the effect of Gemfibrozil on smoking cessation. Methods: This is a double-blind, randomized clinical trial that performed on 75 adult cigarette smokers from 200 smokers. Hence, 75 adult cigarette smokers were divided into two groups after matching. The experimental group (37 peoples) and the placebo group (38 peoples). The participants received 300 mg Gemfibrozil or placebo at the same amount twice a day for 7 weeks. This study was conducted in a university affiliated hospital, Kashan, Iran. To investigate nicotine dependency, signs of deprivation syndrome and smoking cessation, the Fagerstrom test, Minnesota Scale (MNWS), and exhalation carbon monoxide markers were used. Results: There was no significant difference in demographic characteristics between the two groups. At the seventh week, Fagerstrom mean score was 3.1 ± 3.1 and 5.1 ± 3.4 (P = 0.023) for the treatment and placebo groups respectively. According to the Minnesota criteria, the treatment group showed more increased weight gain and appetite, as well as more decreased desire to smoke (P 0.05). Conclusions: Gemfibrozil only reduced the symptoms of nicotine deprivation syndrome but did not show significant potential for smoking cessation.
Microhabitat analysis of the invasive exotic liana Lonicera japonica Thunb

Abstract We documented microhabitat occurrence and growth of Lonicera japonica to identify factors related to its invasion into a southern Illinois shale barren. The barren was surveyed for L. japonica in June 2003, and the microhabitats of established L. japonica plants were compared to random points that sampled the range of available microhabitats in the barren. Vine and leaf characters were used as measurements of plant growth. Lonicera japonica occurred preferentially in areas of high litter cover and species richness, comparatively small trees, low PAR, low soil moisture and temperature, steep slopes, and shallow soils. Plant growth varied among these microhabitats. Among plots where L. japonica occurred, growth was related to soil and light conditions, and aspects of surrounding cover. Overhead canopy cover was a common variable associated with nearly all measured growth traits. Plasticity of traits to improve invader success can only affect the likelihood of invasion once constraints to establishment and persistence have been surmounted. Therefore, understanding where L. japonica invasion occurs, and microhabitat interactions with plant growth are important for estimating invasion success.
Population structure of copper rockfish (Sebastes caurinus) reflects postglacial colonization and contemporary patterns of larval dispersal

The copper rockfish (Sebastes caurinus) is a benthic, nonmigratory, rocky reef species with pelagic larval and juvenile stages lasting several months. Adults are commonly distributed in temperate coastal waters of the Pacific Ocean from British Columbia to southern California, including the inland waterways of Puget Sound, Washington, a semi-enclosed fjord system of known postglacial origin. Here, we report the distribution of genetic variation at six microsatellite DNA loci from six locations throughout the species' range. Among four coastal samples, significant population subdivision was detected (FST = 0.007), and a significant correlation between genetic and geographic distance was observed. Divergence was large and significant between Puget Sound proper and coastal samples (FST = 0.087). A sample taken only 100 km north of Puget Sound (the Canadian Gulf Islands) was also highly divergent from Puget Sound and coastal samples and was genetically intermediate between the two. The Puget Sound sample also displayed significantly lower allelic diversity and a more substantial presence of private alleles. The patterns of genetic divergence and diversity are most consistent with a historical colonization followed by limited oceanographic exchange among geographically proximate locations.