Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing the accuracy of genus-level data to predict species diversity in Cenozoic marine diatoms

Correlations between past biotic diversity and climate can inform humanity’s response to predictions of future global climate change, e.g., extinction risk with global warming. Paleodiversity studies, however, frequently use genera as a proxy for species diversity, a practice that has often been questioned. Tests using actual data of the impact of using species-level versus genus-level taxonomy in paleodiversity-paleoenvironmental studies are also lacking. We conduct such a test, based on a recent study that showed a strong correlation of Cenozoic marine planktonic diatom species diversity to geochemical climate proxies. Using an updated version of the data set, we still find a strong correlation of Cenozoic diatom species diversity to environment. Using identical data but instead genera results in the loss of all significant correlations of diversity to environmental change. This occurs due to the earlier rise and later stability in genus versus species diversity data, a pattern known to be common between taxonomic ranks in the fossil record, and in general models of diversification. We conclude that studies of paleodiversity, particularly those addressing biotic responses to future environmental change, need to demonstrate the adequacy of genera as a proxy for species diversity, or use species-level data.
Spongivory by nudibranchs on the coast of Rio de Janeiro state, southeastern Brazil (Mollusca, Gastropoda)

Nudibranch gastropods are carnivores and most dorid nudibranchs are spongivores, preying on a single or a few species of sponges. The feeding biology has important biological, ecological and evolutionary implications, and many characteristics of nudibranchs likely arose from co-evolution with diet organisms. Data on spongivory by dorid nudibranchs are available for many species from the IndoPacific, eastern Pacific and the Mediterranean Sea, but such information is scarce for the southwestern Atlantic. In this study we provide qualitative data on spongivory by dorid nudibranchs along the coast of Rio de Janeiro State, southeastern Brazil, including the identification of the species involved. A total of 94 spongivory events were observed between 12 nudibranch and 13 sponge species, greatly expanding our knowledge of predator-prey interactions. Among the sponges preyed upon, one species belongs to the class Homoscleromorpha (Plakina sp.) and 12 species to the class Demospongiae. Our observations show that spongivorous nudibranchs have a more diverse diet than previously thought. Additional observations on a higher number of species from different biogeographic regions are needed for a better understanding of the feeding preferences of the diverse and ecologically important spongivorous dorid nudibranchs.
Genotype by environment interaction in sesame (Sesamum indicum L.) cultivars in Uganda

Sesame (Sesamum indicum L.) is an important and ancient oilseed crop cultivated in hot, dry climates for its oil and protein rich seeds. On the African continent, Uganda ranks seventh in sesame production. The improvement of new genotypes with the desired yield stability and performance in different environments is an important issue in breeding programs. In order to identify high yielding and stable sesame genotypes across environments, field experiments were conducted with 16 genotypes for four seasons (2011-2013) at three locations, viz. Serere, Kaberamaido and Ngetta. The objective of the study was to use additive main effects and multiplicative interaction (AMMI) and genotype by genotype environment interaction (GGE) biplot statistical analysis to identify the stability and yield potential of sixteen sesame genotypes. The results of AMMI analysis of variance for seed yield (kg/ha) showed that all the sources of variations that included treatments, genotypes, environments, blocks, interactions, IPCA1 and IPCA 2 were highly significant (P<0.001). The combined analysis of variance indicated that season, season x location, genotype and location x genotype had highly significant (P<0.001) variation. The GGE biplot suggested the existence of only one sesame mega-environment with genotype G9 (Local 158-1) best adapted in that mega-environment followed by G1 (Ajimo A1-6//7029)-1-1. The mega-environment had environments K2011B, K2012A, K2012B, N2012B and K2013B. The vertex genotypes which indicated that they were the most responsive in their respective environments were G2 (Ajimo A1-6//7029)-1-9, G3 (Local 158//6022)-1-2-1, G8 (EM15-3-2), G9 (Local 158-1), G12 (Renner 1-3-1-16) and G14 (Renner 1-3-1-17-1). Genotypes G2 and G12 performed poorly in poor environments. Genotypes were categorized into stable and high yielding, stable but poor yielding, unstable but good yielding and unstable and poor yielding. Environment K2013B was the most discriminating environment. According to the ideal-genotype biplot, genotype G9 (Local 158-1) was the best performing genotype and Kaberamaido was the nearest to ideal environment. It was officially released as Sesim 3 variety for commercial production because of its yield, stability, tolerance to pests and high oil content. Key words: Adaptation, additive main effects and multiplicative interaction (AMMI), genotype environment interaction (GGE) biplot, principal component analysis, stability.
A Salivary Calcium Binding Protein in Patients with Oral Squamous Cell Carcinoma in Relation to Smoking

Background: Calcium binding protein regulates many important cellular functions such as cell proliferation, cell motility and differentiation. Over-expression of calcium BP was detected in different human cancers, including oral squamous cell carcinoma (OSCC). Therefore the aim of the present study was to evaluate the role of calcium binding protein in OSCC, quantified in stimulated saliva, and its association with smoking. Materials and methods: The present study included 20 patients with oral squamous cell carcinoma who used to be smokers, and 40 control subjects. Calcium binding protein was assessed by ELISA technique, in stimulated saliva collected from all groups. Results: Salivary calcium binding protein was significantly higher in smoker patients with oral squamous cell carcinoma than smoker and nonsmoker control healthy looking subjects. Conclusions: Salivary calcium binding protein play a significant role, as a non-invasive approach, in the early diagnosis and follow up of oral squamous cell carcinoma patients.
Effect of pre-harvest application of salicylic acid on postharvest behaviour of ‘Amrapali’ mango fruits during storage

Mango is a highly perishable and deteriorates at a very fast rate during storage. In contrast to the common practice of postharvest application of growth regulators, we have studied the effect of pre-harvest application of the ethylene biosynthesis inhibitor, viz. salicylic acid (SA) at three different concentrations (75, 150 and 200 ppm) on ‘Amrapali’ mango fruits. The results indicate that pre-harvest application of salicylic acid, one week before the commercial harvest could effectively modulate the postharvest behaviour of the mango fruits during storage at ambient conditions (30 ± 5°C and 50 ± 5% RH). Although the mango was responsive to all the treatments, SA (200 ppm) was found to be effective in delaying the ripening cum senescence processes through suppression of respiration rate (105.43 ml CO2 kg−1h−1) and ethylene production rates (0.20 μl C2H4 kg−1 h−1) and retention of high firmness (21.76 N), colour (26.31 ΔE), TSS (27.72°B) and titratable acidity (0.53%) compared to untreated fruits.
Assessment of disease problems in different clonal plantations of Eucalyptus spp. in South India

Availability of healthy stock of seedlings for planting, and their disease-free condition subsequently in the field are the important aspects of the management. Eucalyptus is an economically important plantation species extensively cultivated in different parts of the country. Wide range of fungal and bacterial pathogens attack seedlings, saplings and trees of Eucalyptus causing major losses in nurseries and plantations. An attempt was made to identify different disease problems on clonal plantations of Eucalyptus in Andhra Pradesh, Kerala and Tamil Nadu (South India). In the present investigation, seven different fungal pathogens viz., Alternaria, Cercospora, Coniella, Cylindrocladium, Corticium, Lasiodiplodia and Pestalotiopsis were recorded causing leaf and stem diseases in three different clonal plantations in South India. There was a variation in the incidence and distribution of these diseases during two year period of observations. Leaf spot disease caused by Alternaria alternata was recorded in all the 3 study locations. Cylindrocladium leaf blight disease was observed on 2 locations. Twenty different clones of Eucalyptus were screened against pink disease pathogen Corticium salmonicolor by using toxin rooted shoot cutting bioassay method under in vitro. This study is a preliminary selection of comparatively resistant or tolerant clones of Eucalyptus.
GENETIC DIVERSITY AND CHARACTER ASSOCIATION STUDIES FOR SOME ECONOMIC TRAITS IN RICE (ORYZA SATIVA L.)

An investigation was carried out to assess the nature and magnitude of genetic diversity was in 57 genotypes of rice using Mahalanobis D 2 statistics. They were evaluated for thirteen yield and yield attributing characters and based on D2 analysis, 57 genotypes were grouped into 13 clusters. Clusters II and IV was the largest cluster containing 14 genotypes each followed by cluster III with 11 genotypes. The pattern of distribution of genotypes within different clusters was random and independent of geographical origin or region of adaptation. The characters like days to maturity (34.21%), days to flowering (27.44), grain length (19.55%) and grain width (12.16%) contributing maximum towards diversity. Hence these characters can be given consideration for selection of genotypes for future breeding programmes. The effective tillers (0.474), spikelet fertility (0.323), biological yield (0.723) and harvest index (0.744) in land races, plant height (0.542), panicle length (0.356), effective tillers (0.436), spikelet fertility (0.317), biological yield (0.766) and harvest index (0.744) in new plant types and panicle length (0.386), spikelets and grains per panicle (0.459, 0.498), biological yield (0.627) and harvest index (0.627)in japonicas were positively associated with grain yield indicating that these are the important characters and can be strategically used to improve the yield of rice.
Bacterial and phage interactions influencing Vibrio parahaemolyticus ecology

Vibrio parahaemolyticus, a human pathogenic bacterium, is a naturally occurring member of the microbiome of the Eastern oyster. As the nature of this symbiosis in unknown, the oyster presents the opportunity to investigate how microbial communities interact with a host as part of the ecology of an emergent pathogen of importance. To define how members of the oyster bacterial microbiome correlate with V. parahaemolyticus, I performed marker-based metagenetic sequencing analyses to identify and quantify the bacterial community in individual oysters after culturally-quantifying V. parahaemolyticus abundance. I concluded that despite shared environmental exposures, individual oysters from the same collection site varied both in microbiome community and V. parahaemolyticus abundance, and there may be an interaction with V. parahaemolyticus and Bacillus species. In addition, to elucidate the ecological origins of pathogenic New England ST36 populations, I performed whole genome sequencing and phylogenetic analyses. I concluded ST36 strains formed distinct subpopulations that correlated both with geographic region and unique phage content that can be used as a biomarker for more refined strain traceback. Furthermore, these subpopulations indicated there may have been multiple invasions of this non-native pathogen into the Atlantic coast.
Feed input and excreta collection time in metabolisable energy assays for ducks

Three experiments were conducted to determine the optimal feed input and excreta collection time by a bioassay of dietary true metabolisable energy ( TME) for ducks. In experiment 1 and experiment 2, the time for the unabsorbed feed passage through the alimentary canal was determined by measuring the DM and energy of excreta and feed residues in the alimentary canal at different periods. In experiment 3, the feed input of force-feeding was studied and a total of 70 mature Pekin drakes were allotted to 7 groups, each group containing 10 birds. After fasting for 36 h, one group served as a negative control to measure metabolic faecal energy plus endogenous urinary energy and the drakes of the other 6 groups were force-fed pelleted feed 30 g, 50 g, 70 g, 90 g, 110 g, and 150 g per bird, respectively. Energy excretion of the periods of 16-28 h after force-feeding was significantly higher than that of the periods after 32 h, and the total energy excretion of the periods after 32 h (P 0.05). Metabo- lisable energy decreased significantly with an increase in feed input when the feed input was higher than 70 g (P < 0.05). It was concluded that the optimal time of feed withdrawal before tube-feeding and during excreta collection would be 32-36 h. The optimal feed input was 50 g to 70 g per drake.
DÉVELOPPEMENT D'UN ESSAI PCR POUR L'IDENTIFICATION DES ESPÈCES DE CAMPYLOBACTER

Campylobacter spp. are the leading cause of bacterial diarrhea worldwide with a high economic cost. The phenotypic methods used in medical microbiology laboratories are time-consuming, differentiate only Campylobacter jejuni from other Campylobacter spp. and do not distinguish between the two subspecies of Campylobacter jejuni. The development of molecular tests able to overcome these deficiencies is important from an epidemiological perspective. This research concentrates on the development of a PCR assay tuf-napA multiplex for the identification of Campylobacter jejuni at the level of its two subspecies as well as Campylobacter coli. This multiplex was then applied to Campylobacter spp. isolates at the CHUL of CHUQ for the study period from January 2007 to January 2010 to define the molecular epidemiology in the hospital. The ability of tuf gene to serve as target gene for discriminating Campylobacter spp. was established here for the first time.
Conidial aquatic fungi of nainital, Kumaun Himalaya, India

Fourteen species of conidial aquatic fungi, viz., Alatospora flagellata, A. pulchella, Anguillospora furtiva, Dimorphospora foliicola, Dwayaangam dichotoma, Flabellocladia gigantea, Lemonniera alabamensis, L. cornuta, L. pseudofloscula, L. terrestris, Magdalaenaea monogramma, Tetracladium maxilliforme, Tricladiopsis flagelliformis and Trinacrium incurvum collected from high altitude freshwater streams of NainiTal, Kumaun Himalaya, (India) are briefly described. These species were recovered from submerged leaf litter and water foam accumulated at stream barriers. All the species reported hereunder are new to the Indian aquatic fungi and show wide distribution.
Dual‐polarization radar products for biological applications

The upgrade of the national network of next-generation weather surveillance radars (NEXRAD) in the United States to dual polarizations has been completed, providing three additional routine data products: total differential phase (ψDP), differential reflectivity (ZDR), and copolar correlation coefficient (ρHV). The application and interpretation of these products in the context of aerial bird, bat, and insect movements is an actively developing research front, with potential implications for ecological and conservation studies. The following conceptually derives the definition of these products specifically for NEXRAD weather surveillance radars in the case of biological scatterers. Several cases are presented that illustrate characteristic values and variability of polarimetric quantities for birds and insects, and highlight site-specific differences within the NEXRAD network. Finally, a short prospectus of future directions and applications within the field of polarimetric radar aeroecology is outlined.
Effects of soil substrate heterogeneity and moisture on interspecific competition between Alternanthera philoxeroides and four native species

Aims Clonal plant species have the potential for high relative performance in heterogeneous environments, and this might increase the competitive ability and invasiveness of introduced clonal plant species. It was hypothesized that clonal species whose performance responds more to heterogeneity of a resource have higher competitive ability in habitats where this resource is more heterogeneous and that this relationship is stronger when other resources are less limiting. Methods To test these hypotheses, the perennial clonal herb Alternanthera philoxeroides, which is invasive in China, was grown alone or with each of four clonal perennial, co-occurring herbs native to China, i.e. Alternanthera sessilis, Cynodon dactylon, Hemarthria altissima and Wedelia chinensis. Plants were given homogeneous or heterogeneous soil substrate crossed with low and high levels of soil moisture. Important Findings Effects of heterogeneity on the accumulation of mass and ramets and on competitive effect and response of A. philoxeroides differed between native species and interacted with effects of soil moisture. A. philoxeroides reduced the final total mass or ramet number of the native species except A. sessilis, and the negative competitive effects on H. altissima and C. dactylon were more pronounced in heterogeneous than in homogeneous soil. Competitive response of A. philoxeroides was more negative to A. sessilis than to the other native species. Across native species, the competitive response of A. philoxeroides was more negative in heterogeneous than in homogeneous soils at low moisture level, but the reverse was true at high moisture level. Results do not consistently support either hypothesis, but do suggest that competitive ability can be partly explained by individual species traits such as size, and that some competitive effects and responses are emergent properties of interspecific interactions.
Anatomical Features of the Transverse Sections of the Leaves of Loranthaceae in Nigeria

The anatomical characteristic of the transverse sections of leaves of the Nigerian parasitic family of Loranthaceae were investigated as a contribution to the taxonomy of the family especially in species identification and delimitation. The study revealed presence of palisade tissues for all the species except Tapinanthus bangwensis and T. globiferus. Second layer of palisade cells of Englerina gabonensis and Phragmanthera capitata with wavy outline. Prismatic crystals were present in most of the species and they were either associated with sclereids only or with sclerieds and xylem fibers. Acicular crystals were diagnostic to only Agelanthus bruneus. The presence of brachysclereids and astrosclereids are diagnostic features in the family. The anatomical features observed from the study could be utilized for taxonomic purposes especially as diagnostic features for easy identification of the species even when leaf material is in fragment. The information could also be used in monograph preparation for these medicinally useful species.
An Immunohistochemical Study of the PTEN/AKT Pathway Involvement in Canine and Feline Mammary Tumors

Simple Summary The PTEN/AKT pathway is involved in several human and animal tumors’ pathogenesis. This study investigates the PTEN/AKT pathway’s biological and prognostic values in canine and feline mammary tumors. PTEN, phospho-AKT (p-AKT) and Rictor expression was determined by immunohistochemistry in canine mammary adenomas and carcinomas and feline mammary carcinomas. In mammary tumors of both species p-Akt was inversely correlated with PTEN expression and positively with Rictor expression; p-Akt and Rictor expression correlated with poorer prognosis. This data could provide a rationale for further studies of this pathway in veterinary oncology due to prognostic and therapeutic implications. Abstract Phosphatase and tensin homolog deleted on chromosome10 (PTEN), phospho-v-Akt murine thymoma viral oncogene homolog (AKT), and the Rapamycin-Insensitive Companion of mTOR (Rictor) expression was investigated by immunohistochemistry in 10 canine mammary adenomas (CMAs), 40 canine mammary carcinomas (CMCs), and 30 feline mammary carcinomas (FMCs). All the CMAs, 25 of 40 CMCs (63%) and 7 of 30 FMCs (23%), were PTEN-positive. In dogs, no CMAs and 15 of 25 CMCs (37%) expressed phospho-AKT (p-AKT), while 24 of 30 FMCs (82%) were p-AKT-positive. One of 10 CMAs (10%), 24 of 40 CMCs (60%) and 20 of 30 FMCs (67%) were Rictor-positive. In the dog, PTEN expression correlated with less aggressive tumors, absence of lymphatic invasion, and longer survival. P-AKT expression correlated with more aggressive subtype, lymphatic invasion, and poorer survival and Rictor expression with lymphatic invasion. In cats, PTEN correlated with less aggressive carcinomas, absence of lymphatic invasion, and better survival. P-AKT and Rictor expression correlated with poorer survival. PTEN expression was inversely correlated with p-AKT and Rictor in both species, while p-AKT positively correlated with Rictor expression. A strong PTEN/AKT pathway involvement in behavior worsening of CMT and FMTs is demonstrated, providing a rationale for further studies of this pathway in veterinary oncology.
Original Contribution COLOUR TRAITS OF CHICKEN EGGS WITH DIFFERENT EGGSHELL PIGMENTATION

The study was carried out with 11 purebred groups of chickens at 48 weeks of age, laying eggs with white, tint, blue-green and brown shell pigmentation to investigate the colour characteristics of eggshells in the CIE L*a*b* colour system. On the basis of L*, a* and b* values, С* (Chroma), Hue o (the angle between b* and a* colour coordinates) and SCI (eggshell colour index) values were calculated. L* values decreased statistically significantly (Р<0.001) from 92.7 in white-shelled eggs to 40.2 in dark brown eggs. Brown eggs had a* values between 1.9 and 22.5, which increased from cream-coloured to dark brown shells. In bluegreen and tinted eggs, L* and b* values were similar. In blue-green eggs, the values of the a* colour coordinate were negative. There was a substantial variation in the colour of eggs not only within the groups, but also within the breed. The shell colour index (SCI) is suitable for reliable colour identification only in brown and non-pigmented eggs. SCI values lower than 70 could be recommended as reference values for brown pigmented shells whereas SCI values over 85 – for white-shelled eggs. Spectrophotometric analysis is appropriate for use in eggs with uniform pigmentation of the shell. The Hue о angle is not suitable for colour analysis of eggshells due to the extremely large variations and the possibility to obtain similar values but with different sign in eggs with similar colour.