Miracle-dz/UniFAR-FTUs huggingface dataset:
An automated procedure for estimating the leaf area index (LAI) of woodland ecosystems using digital imagery, MATLAB programming and its application to an examination of the relationship between remotely sensed and field measurements of LAI.

Leaf area index (LAI) is one of the most important variables required for modelling growth and water use of forests. Functional-structural plant models use these models to represent physiological processes in 3-D tree representations. Accuracy of these models depends on accurate estimation of LAI at tree and stand scales for validation purposes. A recent method to estimate LAI from digital images (LAID) uses digital image capture and gap fraction analysis (Macfarlane et al. 2007b) of upward-looking digital photographs to capture canopy LAID (cover photography). After implementing this technique in Australian evergreen Eucalyptus woodland, we have improved the method of image analysis and replaced the time consuming manual technique with an automated procedure using a script written in MATLAB 7.4 (LAIM). Furthermore, we used this method to compare MODIS LAI values with LAID values for a range of woodlands in Australia to obtain LAI at the forest scale. Results showed that the MATLAB script developed was able to successfully automate gap analysis to obtain LAIM. Good relationships were achieved when comparing averaged LAID and LAIM (LAIM = 1.009 - 0.0066 LAID; R2 = 0.90) and at the forest scale, MODIS LAI compared well with LAID (MODIS LAI = 0.9591 LAID - 0.2371; R2 = 0.89). This comparison improved when correcting LAID with the clumping index to obtain effective LAI (MODIS LAI = 1.0296 LAIe + 0.3468; R2 = 0.91). Furthermore, the script developed incorporates a function to connect directly a digital camera, or high resolution webcam, from a laptop to obtain cover photographs and LAI analysis in real time. The later is a novel feature which is not available on commercial LAI analysis softwares for cover photography. This script is available for interested researchers.
Differential effects of cortisol on apoptosis and proliferation of carp B-lymphocytes from head kidney, spleen and blood

Abstract This study compared B lymphocytes isolated from different tissues with regard to their proliferation, apoptosis and the effects of cortisol on these processes. B-lymphocytes, isolated from the head kidney and spleen, were characterised by higher proliferation and lower intracellular calcium (Ca 2+ i ) response to Ig-crosslinking compared with peripheral blood B-lymphocytes. Cortisol induced high levels of apoptosis (160% of control levels) in peripheral blood B-lymphocytes, in combination with a stimulatory (LPS) signal. Head kidney and to a lesser extent spleen B-lymphocytes, although less sensitive than their equivalent in peripheral blood, underwent cortisol-induced apoptosis irrespective of extra stimulation up to 150% of control levels. Also proliferation with and without LPS stimulation was suppressed by cortisol. In view of the relatively modest concentration of cortisol (compared to plasma values measured during stress conditions) that is effective in inducing a significant increase in apoptosis in all three populations of B-cells, it is suggested that cortisol may be important for immunoregulation in both stressed and non-stressed conditions. This implies possible severe impact of stress on lymphocyte development and activity. Different sensitivity of B-cells to the corticosteroid, with respect to developmental stage and activity, may prevent excessive and long lasting depletion of B-lymphocytes.
DNA content polymorphism and tissue culture regeneration in Caribbean pine

The three varieties of Caribbean pine have significantly different amounts of nuclear DNA: Pinus caribaea var. caribaea, 11.5; P. caribaea var. hondurensis, 21; and, P. caribaea var. bahamensis, 25 pg. Dormant embryos of the three varieties had more nuclear DNA than germinating seedlings, and this extra DNA was spread through several classes from 2C to 7C; however, upon germination the seedling DNA rapidly reorganizes into the 2C–4C distribution typical of diploid plants. DNA content polymorphism of the dormant embryos among the three varieties was directly correlated with the diploid amount of DNA and with needle and cotyledon diversity. Buds regenerated from dormant embryo explants in tissue culture were genetically stable; however, the roots of regenerated plants had DNA contents ranging up to nine times the haploid amount. The instability is ascribed to the auxin content of the rooting medium, but buds regenerated or growing on this medium were stable. This bud stability and the production of buds on .
Developing tetraploid perennial ryegrass (Lolium perenne L.) populations

Abstract In a breeding programme aimed at developing tetraploids from Australian adapted germplasm, a root‐tip squash technique was initially used for ploidy determination. The highest recovery of tetraploids (39.7%) was obtained by treatment of 1‐week‐old seedlings with 0.1% colchicine concentration. Significant cultivar × colchicine concentration interaction was observed in seedling survival, highlighting the difference in response of the cultivars to colchicine treatment. Subsequently, flow cytometric estimation of the nuclear DNA content in young leaf tissues was used to screen the C1 and C2 generations. The speed and the efficiency of this method make it possible to examine a large number of plants. In the C1 population the percentage of tetraploids, diploids, and aneuploids was 25, 72.7, and 2.3% respectively, while in the C2 generation the percentage of tetraploids, diploids, and aneuploids was 43, 2, and 55% respectively.
Ceramide Regulates Atypical PKCζ/λ-mediated Cell Polarity in Primitive Ectoderm Cells

In mammals, the primitive ectoderm is an epithelium of polarized cells that differentiates into all embryonic tissues. Our study shows that in primitive ectoderm cells, the sphingolipid ceramide was elevated and co-distributed with the small GTPase Cdc42 and cortical F-actin at the apicolateral cell membrane. Pharmacological or RNA interference-mediated inhibition of ceramide biosynthesis enhanced apoptosis and impaired primitive ectoderm formation in embryoid bodies differentiated from mouse embryonic stem cells. Primitive ectoderm formation was restored by incubation with ceramide or a ceramide analog. Ceramide depletion prevented plasma membrane translocation of PKCζ/λ, its interaction with Cdc42, and phosphorylation of GSK-3β, a substrate of PKCζ/λ. Recombinant PKCζ formed a complex with the polarity protein Par6 and Cdc42 when bound to ceramide containing lipid vesicles. Our data suggest a novel mechanism by which a ceramide-induced, apicolateral polarity complex with PKCζ/λ regulates primitive ectoderm cell polarity and morphogenesis.
Extratos, decoctos e óleos essenciais de plantas medicinais e aromáticas na inibição de Glomerella cingulata e Colletotrichum gloeosporioides de frutos de goiaba

The main disease of the guava (Psidium guajava L.), after harvesting, is anthracnose, caused by Glomerella cingulata and Colletotrichum gloeosporioides. This pathogen and chemical residues of fungicides in fruits are considered the mains problems for exportation. In this work was evaluated the fungitoxic effect of extracts, decoctions and essential oils of medicinal and aromatic plants in the mycelium growth of the pathogens, in vitro, to be recommended as an alternative to chemical control in postharvest. To prepare the aquous extracts a 10% and the decoctions (sub-products of hydrodistillation) were added in PDA medium, autoclaved and distributed into Petri dishes. The essential oils were added in three equidistant points by Petri dishes contening PDA medium. Discs of the isolates of the pathogen were placed on the center of the Petri dishes. The fungitoxic effect was evaluated by measuring the diameter of the colonies when the pathogens or any other treatment reached the border of the Petri dishes. The aquous extract and the essential oil from the clove inhibit in 100% of G. cingulata and C. gloeosporioides growth, and the last one was totally inhibited by the essential oil of the lemon grass. The decoctions of rosemary, ginger, calendula, orange (Citrus sinensis) showed inhibition potencial to control both isolates of the pathogen. In the control of C. gloeosporioides also had good results the decoctions of mayweed, chamomile and tagetes. The total or partial mycelium growth inhibition of the Glomerella cingulata e Colletotrichum gloeosporioides showed the existence of compounds biologically actives with fungitoxic effect, in the extracts, decoctions and essential oils of medicinal and aromatic plants. This indicated a potential application of this products as an alternative to control anthracnose in guavas fruits.
Effects of water hyacinth (Eichhornia crassipes) leaf protein concentrate as soybean protein replacement in white shrimp Litopenaeus vannamei (Boone) postlarvae diet

The potential of water hyacinth leaf protein concentrate (WHLPC) as an alternative protein source to soybean meal in formulated diets for the white shrimp Litopenaeus vannamei (Boone) postlarvae, was assessed. Isonitrogenous and isolipidic diets were formulated containing 40% protein and 8% lipid. WHLPC replaced 0%, 25%, 50% and 75% of soybean meal protein in the formulated diets. Twenty postlarval Litopenaeus vannamei weighing 5.0 ± 0.00032 mg were randomly assigned to twelve 30-L aquarium tanks and were fed experimental diets for 70 days. Results show that the overall biological performance of shrimp in terms of specific growth rate (SGR), protein efficiency ratio (PER), feed efficiency (FE) and survival in treatment receiving the 25% WHLPC replacement is comparable to that of the control diet. Replacement levels beyond 25% exhibited significant depression in terms of growth performance of the shrimp. Collectively, these findings indicate that WHLPC can replace 25% of soybean meal protein in the formulated diets of L. vannamei.
Tropical Forest Management and Conservation of Biodiversity: an Overview

This paper is a much abridged version of World Bank Environment Department Paper 75, “Biodiversity Conservation in the Context of Tropical Forest Management,” by the same authors. It is the first paper in the bank's Impact Studies Series, which addresses the broader questions of the positive and negative effects of human activities on biodiversity. A more complete set of data supporting the arguments herein are in the appendices and text of the World Bank paper, which can be accessed from http://www.worldbank. org/biodiversity.
NF-κB Protects HIV-1-Infected Myeloid Cells from Apoptosis

Abstract HIV-1 infection of primary monocytic cells and myeloid cell lines results in sustained NF-κB activation. Recently, NF-κB induction has been shown to play a role in protecting cells from programmed cell death. In the present study, we sought to investigate whether constitutive NF-κB activity in chronically HIV-1-infected promonocytic U937 (U9-IIIB) and myeloblastic PLB-985 (PLB-IIIB) cells affects apoptotic signaling. TNFα and cycloheximide caused infected cells to undergo apoptosis more rapidly than parental U937 and PLB-985 cells. Inhibition of TNFα-induced NF-κB activation using the antioxidant N -acetylcysteine (NAC) resulted in increased apoptosis in both U937 and U9-IIIB cells, while preactivation of NF-κB with the non-apoptotic inducer IL-1β caused a relative decrease in apoptosis. Inhibition of constitutive NF-κB activity in U9-IIIB and PLB-IIIB cells also induced apoptosis, suggesting that NF-κB protects cells from a persistent apoptotic signal. TNFα plus NAC treatment resulted in a marked decrease in Bcl-2 protein levels in HIV-1-infected cells, coupled with an increase in Bax protein compared to uninfected cells, suggesting that the difference in susceptibility to TNFα-induced apoptosis may relate to the differences in relative levels of Bcl-2 and Bax. The protective role of NF-κB in blocking TNFα- and HIV-1-induced apoptosis was supported by studies in Jurkat T cells engineered to express IκBα repressor mutants (TD-IκB) under the control of a tetracycline-responsive promoter. Cells underwent apoptosis in response to TNFα only when NF-κB activation was inhibited by TD-IκB expression. As was observed for the U9-IIIB cells, TNFα treatment also induced a marked decrease in Bcl-2 protein levels in TD-IκB expressing cells. These experiments demonstrate that apoptotic signaling is perturbed in HIV-1-infected U9-IIIB cells and indicate that NF-κB activation may play an additional protective role against HIV-1-induced apoptosis in myeloid cells.
Relationships Between RNA–DNA Ratio, Prey Density, and Growth Rate in Atlantic Cod (Gadus morhua) Larvae

The protein, DNA, and RNA content of larvae maintained at 1.0 plankter/mL increased at the rates of 9.3, 9.9, and 9.8% per day, respectively, for the 5 wk after hatching. Protein reserves of larvae held at 0 or 0.2 plankters/mL were depleted by 45 and 35%, respectively, prior to death 12–13 d after hatching. Starved larvae had similar protein concentrations (percent of dry weight), lower RNA concentrations, and higher DNA concentrations than fed larvae. Larvae held at higher plankton densities had higher RNA–DNA ratios and faster growth rates than larvae held at lower plankton densities. The RNA–DNA ratio was significantly correlated (P < 0.01) with the protein growth rate. The RNA–DNA ratio appears to be a useful index of nutritional status in larval Atlantic cod (Gadus morhua) and may be useful for determining if cod larvae were in a period of rapid or slow growth at the time of capture. Key words: RNA–DNA ratio, starvation, protein, nucleic acids, growth, larval fish, Atlantic cod
Phylogeny of Braya and Neotorularia (Brassicaceae) based on nuclear ribosomal internal transcribed spacer and chloroplast trnL intron sequences

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast trnL intron were used to examine the evolutionary relationships and generic delimitations of Braya, Neotorularia, Dichasianthus, and Sisymbriopsis. Several species, especially the North American - Asian Braya (= Neotorularia) humilis (C.A. Mey.) B.L. Rob. , were previously assigned to more than one genus. Sequence data were obtained from all Braya species, except Braya pilosa Hook. , seven species of Neotorularia, one of Dichasianthus, and two of Sisymbriopsis. Maximum parsimony analyses showed a poly phyletic origin for Neotorularia, with the genus split into three or four major clades. For both the ITS and trnL sequence data, three species (Neotorularia brachycarpa (Vassilcz.) Hedge & J. Leonard, Neotorularia gamosepala (Hedge) O'Kane & Al-Shehbaz, and Neotorularia humilis (C.A. Mey.) Hedge & J. Leonard) fell within the Braya clade; Neotorularia korolkowii (Regel & Schmalh.) Hedge & J. Leonard formed a se.
Observations on spore ultrastructure in six species of Grimmia (Bryopsida)

The spores of six species, namely Grimmia decipiens, G. elatior, G. funalis, G. orbicularis, G. pulvinata and G. trichophylla were studied by means of TEM, SEM and LM. TEM is here used for the first time on spores of this genus. Ultrastructural spore features allowed a clear characterisation of all six species. In addition, we observed the ultrastructure of the spore wall to be different from the typical Bryopsida type, with a multilaminar structure of the exine, not previously reported in mosses. The possible evolutionary, ecological and taxonomical significance of the spore features are discussed.
Clubroot in Australia: the history and impact of Plasmodiophora brassicae in Brassica crops and research efforts directed towards its control

Abstract Plasmodiophora brassicae, the obligate biotrophic plant pathogen causing clubroot of Brassica crops, has been present in Australia since the 1890s. The disease spread rapidly in vegetable Brassica crops, causing widespread losses during the 1980s and 1990s due to the increasing intensity of Brassica production and the extensive use of transplants. In response to the escalating problems caused by this disease in vegetable Brassica crops, a survey and pilot studies were initiated in 1993. This grew to become a coordinated national programme delivering clubroot research, development and extension to the Brassica industry until 2010. The key outcome of the programme was reduced crop losses through more effective and sustainable management of clubroot. This was achieved by the development and implementation of integrated, disease management strategies involving the use of good farm and nursery hygiene, early disease detection, application of lime (as calcium oxide) to maintain soil alkalinity, use of calcium and boron fertilizers, and strategic application of fungicides. Successful use of these integrated strategies reduced industry reliance on soil fumigants for disease control. This review details the history and impact of clubroot in Australia and research efforts directed towards its control.
SURVIVAL AND REPRODUCTION OF WILD TURKEY HENS IN CENTRAL ONTARIO

Abstract Recent success of Eastern Wild Turkey (Meleagris gallopavo silvestris) reintroductions across southern Ontario has prompted wildlife managers to investigate the potential of extending the northern limit of this subspecies' range. We monitored the survival and reproduction of introduced Wild Turkeys on the Precambrian Shield in central Ontario during 1999–2001. Mean annual survival of 39 radio-tagged hens was 0.288 ± 0.057 SE. Summer and winter survival rates differed between the first and second years of the study. Spring and fall survival rates did not differ significantly between years. Reproductive parameters that characterized the population included a nesting rate of 0.588, mean clutch size of 10.0 eggs/nest, nest success of 0.500, hatching rate of 0.81, hen natality rate of 1.18 females hatched/female, poult survival of 0.54, and fall recruitment of 0.63 juvenile females/breeding hen. Success of the pilot Wild Turkey introduction in central Ontario was compromised by high predation, low numbers of introduced birds, and a prolonged period of deep snow during 2000–2001.
Temperature regulation in the Dusky Munia, Lonchura fuscans (Cassin) (Estrildidae)

Dusky munias are small (9.5 g) tropical seed-eating members of the family Estrildidae. Adaptations of munias to hot-humid conditions were examined by measuring body temperatures (Tb), rates of oxygen consumption [V(O2)] and evaporative water loss (Mwe) at night at ambient temperatures (Ta) between 17 and 44oC. Within the zone of thermal neutrality (30-39oC) night-time Tb averaged 38.9oC (range 37.6-41.loC). Above 30oC, Tb increased with increasing To, reaching a maximum of 44.1oC at a Ta of 43.8oC. For the most part, dusky munias were unable to maintain Tb lower than Ta at high temperatures. The mean standard metabolic rate of munias was 1.87 ml O2 g-1 h-1. This is only 51% of the value predicted for passerine birds of comparable size. Below thermal neutrality, V(O2) (in ml g-l h-1) varied with Ta (oC) in accordance with the equation V(O2) = 8.37-0.218Ta. The slope of the line relating V(O2) to Ta below thermal neutrality is 19% lower than predicted, indicating that munias are better insulated than other birds of comparable size. Dusky munias have relatively high rates of Mwe at Ta's below 34oC (mean 7.68 mg water g-1 h-1), but exhibit little capacity to increase the rate of evaporation at high Ta's. Review of metabolic data for birds reveals that the standard metabolic rate of tropical species averages 67% of the level predicted from body mass. Thus, adaptation to hot-humid climates appears to have involved a reduction in the level of metabolism.
A probability distribution model for age–age correlations and its application in early selection

Bootstrap-generated distributions of age–age correlations of stem volume in a red pine (Pinusresinosa Ait.) spacing trial supported the contention of the β distribution as a realistic model for age–age correlations in small populations where normal approximations are inappropriate. The model describes age–age correlations as a repeatability of tree performance. The orthonormal decomposition of the total variance into among- and within-tree variance components was derived from Fourier-transformed time series of the trait values. Applications for early selections include (i) finding the optimum selection age for various numbers of selections made and (ii) predictions of age–age correlations.
Climate warming and the agonistic behaviour of invasive crayfishes in Europe

SUMMARY 1. Climate warming often leads to shifts in the strength and sign of agonistic interactions amongspecies, which in turn may change their distribution ranges. Notwithstanding the ubiquity of thisphenomenon, there is scant literature about how interspeciﬁc agonistic behaviour changes withaltered thermal regime, especially for invasive species such as three widespread North Americancrayﬁshes in Europe (Orconectes limosus, Procambarus clarkii and Pacifastacus leniusculus). 2. We conducted a laboratory study to analyse some descriptors of agonistic behaviour in ﬁghtingdyads of similarly sized males of the three species’ combinations, both at 20 °C (the current maxi-mum water temperature in the study area, central France) and 27 °C (the maximum expected in thenext 80 years under the more pessimistic IPCC greenhouse gas emission scenario). 3. The results showed signiﬁcantly different responses to warming by the three crayﬁshes. At 27 °C,O. limosus spent more time motionless and P. leniusculus was more often the subordinate, indepen-dent of the opponent. On the contrary, the agonistic strategy of P. clarkii did not change with temper-ature: when engaged in ﬁghting, this species outcompeted both O. limosus and P. leniusculus.4. Caution should be taken when extrapolating laboratory studies to the ﬁeld, but these results,combined with outputs of previous modelling exercises, suggest that European catchments willbecome dominated by P. clarkii with climate warming. Ultimately, this might lead to impoverishedbiodiversity, simpliﬁed food webs and altered ecosystem services.Keywords: agonistic behaviour, alien species, interspeciﬁc competition, North American crayﬁshes,temperature
Morphometric changes, gonad histology, and fecundity estimates in migrating New Zealand freshwater eels (Anguilla spp.)

Abstract During transition from the non‐migrant feeding stage to the migrant stage in Anguilla australis and A. dieffenbachii the eyes increase in area by a factor of 2 in males and of 1.5–1.6 in females. A. dieffenbachii is more sexually advanced at the beginning of the spawning migration. In males the gonadosomatic ratio (GSR) was 0.5–2.7 and histological sections showed spermatocytes as the most common stage of spermatogenesis. For A. australis the GSR was 0.03–0.70, and histologically spermatogonia were predominant. In A. dieffenbachii females the mean GSR was 8.12, mean egg diameter was 0.33 mm, and histological sections showed that most eggs were at the stage of yolk deposition. In contrast, the mean GSR of A. australis females was 3.5, mean egg diameter was 0.22 mm, and few eggs were at the yolked stage. Egg counts showed that fecundity increased with total length. Fecundity estimates for 23 A. dieffenbachii (total length 711–1452 mm) varied from 1.05 million to 20.83 million and for 26 A. australi.
Meria laricis, an anamorph of Rhabdocline

Meria laricis, a needle cast pathogen of Larix spp. in North America and Europe, has no known ascigerous state, possibly having permanently lost the ability to reproduce sexually and thus rep- resenting an obligately asexual mitosporic holo- morph. Comparisons of nucleotide sequences from the internal transcribed spacer region of M. laricis, Rhabdocline spp. , and several genera of inoperculate discomycetes show that isolates of M. laricis form a monophyletic clade within the ascomycete genus Rhabdocline. Cladistic analysis of infraspecific taxa of Rhabdocline and ordinal placement of the genus are discussed. Results of cladistic analysis suggest that possession of an amyloid ascus pore is an unreliable character for differentiation of species and subspe- cies.