Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of dietary zinc level on performance, zinc status, tissue composition and enzyme activities of juvenile Siberian sturgeon, Acipenser baerii (Brandt 1869)

Zinc (Zn) is one of the most essential trace elements required for growth and other metabolic functions including development, reproduction and immunity in most animals like fish (Liang, Yang, Liu, Tian, & Liang, 2012; Lin, Lin, Yang, Li, & Luo, 2013; Wang & Wang, 2015). It acts as an integral cofactor necessary for more than 200 enzymes such as carbonic anhydrase, alkaline phosphatase, DNA polymerases and alcohol dehydrogenase which are involved in protein metabolism, energy production, gene regulation and healthy maintenance of cell membranes (Eide, 2006; Fountoulaki et al., 2010; HoungYung, YuChun, LiChi, & MengHsien, 2014; Maret & Krezel, 2007). Zn also serves in synthesis of metallothionein, a cysteinerich protein served as a free radical scavenger, suggesting a biochemical role of Zn in the antioxidant defence system (Bales et al., 1994; Kaushik, 2001; Prasad et al., 1993). Fish can uptake Zn from water and diet via branchial and gastrointestinal routes (Sappal & Kamunde, 2009). However, ambient waterborne Zn concentration in most aquatic environments is not adequate to supply the metabolic requirements of ongrowing fish and a dietborne Zn concentration is mostly requested. Signs of Zn deficiency include growth dwarfism, eye cataract, skin erosion, mortality increase and immunity impairment through the effect of free radical action (Hidalgo, Exposito, Palma, & Higuera, 2002; Lin et al., 2013; Salgueiro et al., 2000). The protein and carbohydrate digestibility could also be altered by Zn insufficiency due to the decreased activity of alkaline Received: 16 May 2017 | Accepted: 5 January 2018 DOI: 10.1111/anu.12670
Tolerance of Kenaf to Selected Postemergence Herbicides

In field trials conducted in 1989 and 1990, fifteen postemergence herbicides were tested for phytotoxicity to kenaf. Clethodim (110 g ai ha–1), fluazifop (220 g ai ha–1), quizalofop (70 g ai ha–1), and sethoxydim (210 g ai ha–1) were not phytotoxic to kenaf in the cotyledonary stage. MSMA (2.2 kg ha–1) was not phytotoxic to kenaf at the cotyledonary or 35-cm stage. All other herbicides applied postemergence to kenaf caused significant injury.
Can net diversification rates account for spatial patterns of species richness?

The diversification rate hypothesis (DRH) proposes that spatial patterns of species richness result from spatial variation in net diversification rates. We developed an approach using a time-calibrated phylogeny and distributional data to estimate the maximum explanatory power of the DRH, over a given time period, to current species richness in an area. We used this approach to study species richness patterns of a large family of suboscine birds across South America. The maximum explanatory power of the DRH increased with the duration of the time period considered and grain size; it ranged from 13 – 37 fold local increases in species richness for T = 33 Ma to less than 2-fold increases for T ≤ 10 Ma. For large grain sizes (≤ 8° × 8°) diversification rate over the last 10 Ma could account for all the spatial variance in species richness, but for smaller grain sizes commonly used in biogeographical studies (1° × 1°), it could only explain < 16% of this variance. Thus, diversification since the Late Miocene, often thought to be a major determinant of Neotropical diversity, had a limited imprint on spatial richness patterns at small grain sizes. Further application of our approach will help determine the role of the DRH in explaining current spatial patterns of species richness. Note to readers This manuscript has been seen by a few researchers, some of whom suggested that before publishing our work in a peer-reviewed journal we should conduct simulations to demonstrate that our methods properly estimate the contribution of variance in diversification rates to spatial variation in species richness. Although we believe that our approach derives logically from theory and statistics and is therefore valid, we understand that it is rather unique and see why some readers would think that an independent validation is necessary. Unable to complete such validation in the near future, however, we decided to make this manuscript available as a preprint to share our ideas and hopefully stimulate discussion on what we believe is a most interesting topic. We also hope to receive feedback that may enable us to improve our work for publication in a journal at a later date.
A study of floral shape variation in Delphinieae (Ranunculaceae) using geometric morphometrics on herbarium specimens

Abstract The variation in the shape of flowers, the reproductive structures of angiosperms, is generally investigated in a qualitative way, or using multivariate statistical analyses of distance data (i.e. traditional morphometrics). In this study, we evaluate the application of geometric morphometric methods to flowers of herbarium specimens, a material that is still being massively overlooked as far as these methods are concerned. Flowers of Delphinieae (Ranunculaceae) are synorganized: the spurred and nectariferous dorsal petals are nested within the spur or hood of the dorsal sepal. The study of synorganized structures is challenging, and geometric morphometric-oriented investigation may provide working hypotheses for an evo-devo exploration of such hyperorgan formation. We analyze here the floral shape of Delphinieae using geometric morphometric methods and demonstrate the effectiveness of these methods on dry and compressed flowers. We also show the diagnostic value of the dorsal half of the perianth of the Delphinieae flower, and suggest some trends to help design future studies on the evolutionary development of spur formation and the co-evolution of Delphinieae flowers with their pollinators.
Evaluation of Shear Strength Parameters of Sandy Soils upon Microbial Treatment

ABSTRACT A new method for soil stabilization known as microbial-induced calcite precipitation (MICP) has been the focus of research in this area during the last decade. In this method, the reaction of microorganisms in the presence of urea and calcium chloride is used to produce calcite. Despite the large numbers of bacteria in soil, Sporobacillus pasteurii (previously known as Bacillus pasteurii) has the most capability to create cementation between soil particles in the MICP method due to its high urease activity. In this paper, the effect of MICP treatment on the shear strength characteristics of a sandy soil was studied. The change in the shear strength of sandy soil upon MICP treatment was measured using a strain-controlled direct shear test before and after treatment of the soil samples. The results showed an increase of 44–86% in the shear strength of the sandy soil after 15 days of MICP treatment compared to the untreated soil. The enhanced shear strength was the result of an increase in both the cohesion intercept and angle of internal friction. The increase in the cohesion intercept was more significant than the increase in the angle of internal friction.
Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion

Below‐ground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR‐based nematode identification techniques are well available, but high‐throughput sequencing (HTS) might be more suitable for non‐targeted nematode community analyses. We compared effectiveness of qPCR‐ and HTS‐based approaches with morphological nematode identification while examining how climate warming‐induced plant range expansion may influence below‐ground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is a range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach. HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant‐feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances. Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost‐effective, in‐depth methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.
Beech versus spruce deadwood as forest microhabitat: does it make any difference to bryophytes?

Abstract The presence data of 153 bryophyte species, recorded on beech (BDW) and spruce (SDW) deadwood in the managed forests within a montane watershed, were analysed by controlling for different plot size, substrate pH and elevation. Only three pleurocarpous species, which were probably remnant epiphytes from live wood, showed relative specificity for BDW, but none to SDW. The few species displaying preference for BDW or SDW were generally true epixylic, mosses and hepatics, respectively. The chances of occurrence of epiphytic (early successional) and epixylic (mid-late successional) taxa on either deadwood species increased and respectively, decreased with the substrate pH. There was no consistent relationship between bryophyte preference to BDW/SDW and elevation. Neither total nor threatened species richness was related to deadwood species identity. However, at 100 cm2 resolution and within certain extension range, the cumulative number of bryophyte species was significantly higher on BDW than on SDW, despite no significant difference in species pool size. Threatened species richness increased monotonically towards lower elevations, suggesting that valley bottoms might act as refugia with high air humidity. The number of threatened species and in particular, the presence of Lophozia ascendens, were good predictors of total bryophyte richness regardless of deadwood species identity.
Prognostic role of L1CAM, androgen receptor, and epithelial growth factor receptor expressions in triple-negative breast cancer

Background Triple-negative breast cancer (TNBC) is a heterogeneous disease that has high diversity with regard to biology and treatment and an aggressive clinical behavior because of poor differentiation and lack of targeted therapeutics. Based on this heterogeneity and the lack of well-defined molecular targets, the treatment of TNBC patients is highly challenging. Therefore, it is essential to identify additional reliable molecular prognostic markers to allow a better treatment. Aim The aim of this study was to evaluate the potential prognostic role of L1CAM, androgen receptor (AR), and epithelial growth factor receptor (EGFR) expressions in TNCB and to investigate the association between these markers and the different clinical and pathological data. Materials and methods The associations between the expression of L1CAM, AR, and EGFR and the clinicopathological variables were evaluated in 55 patients with TNBC using immunohistochemical staining methods. Results A total of 19 (34.5%) cases were positive for L1CAM, 18 (32%) were positive for AR, whereas 31 (56%) exhibited positivity for EGFR. L1CAM staining was significantly associated with high tumor grade (P=0.001) and lymph-node metastasis (P=0.001). Positive AR staining was inversely associated with lymphovascular invasion (P=0.004) and EGFR expressions (P=0.003). EGFR expression was significantly associated with the presence of necrosis (P=0.001) and tumor grade (P=0.001). Conclusion Data obtained from this study advocate that L1CAM, AR, and EGFR could be used as useful prognostic markers and potential therapeutic targets for patients with TNBC.
Antibacterial, antioxidant, and cytotoxic activities of the corticolous lichens Canoparmelia aptata, Pannaria sp., and Parmotrema gardneri collected from Mt. Banahaw, Quezon, Philippines

Lichens are remarkable sources of bioactive secondary metabolites with potential chemotherapeutic properties. In this study, we evaluated the bioactivities of three corticolous lichens collected from Mount Banahaw in Quezon Province, Philippines. The lichens Parmotrema gardneri, Pannaria sp. , and Canoparmelia aptata were extracted with acetone and assayed for cytotoxicity, and antibacterial and antioxidant activities. Results showed that the lichen extracts of P. gardneri, Pannaria sp. and C. aptata were either active (13-19 mm, zone of inhibition, ZOI) or partially active (10-12 mm ZOI) against Pseudomonas aeruginosa and Staphylococcus aureus. For the cytotoxicity assay, P. gardneri had the lowest inhibition concentration (IC50) values of 12.29 and 20.24 μg/mL for the human gastric adenocarcinoma (AGS) and human lung carcinoma (A549), respectively. The same lichen extract rendered selectivity with IC50 of 66.35 μg/mL against the normal Madin Darby Canine Kidney (MDCK) cell lines. The extracts yielded low radical scavenging activity of less than 40% and generated low amounts of FeSO4 per milligram sample. Metabolic profiling detected the presence of protocetraric acid, usnic acid, zeorin, atranorin, chloroatranorin, and galbinic acid.
Changes In Muscle Biomarkers Following Swimming Exercise in Streptozotoxin-induced Rats.

Youngsik Kim · Storm Reid · Eunkee Park · Yehchan Ahn · Byunghwan Jeon. Changes In Muscle Biomarkers Following Swimming Exercise in Streptozotoxin-induced Rats. The Journal of Kinesiology, 2017, 19(3): 1-13 . [PURPOSE] The purpose of this study was to assess the effect of swimming exercise in diabetic atrophy by monitoring changes in biomarkers associated with musculoskeletal growth and abnormalities. [METHODS] Ninety-two male Sprague-Dawley rats were randomly divided into four groups: control plus exercise group (CO+Ex), control and no exercise group (CO+No Ex), diabetes plus exercise group (DM+Ex) and diabetes and no exercise group (DM+No Ex). Swimming exercise was implemented for 60 min/day, 5 day/week for a total of eight weeks. Muscle strength and atrophy biomarkers as well as muscle morphology were compared at the first, second, fourth and eighth week of experimentation. [RESULTS] ACE levels were significantly higher in the DM groups (p<.05), however swimming exercise did not significantly affect ACE levels. Irisin levels were significantly higher in the DM and DM+Ex groups compared to the CON, in week one (p<.05), and greater in the DM+Ex group at week two compared to CON+Ex (p<.05), but swimming did not significantly affect irisin levels over the eight-week period in DM rats. In terms of muscle damage, Myl3 expression was unchanged in the CON groups, but significantly higher in the DM+Ex group compared to the CON+Ex group (p<.05). AST was found to be in higher levels in the DM+No Ex group, compared to CON and CON+Ex (p<.05); and DM+Ex group, compared to the CON+Ex group at weeks one, four and eight (p<.05). Tibialis anterior muscle fibers were thicker in the DM+Ex group compared to DM+No Ex, but only at week four (p<.05). Otherwise, no other notable differences were recorded in muscle morphology. [CONCLUSIONS] These results suggest that swimming exercise alone may not be sufficient to induce muscle strength and/or protective effects against muscle atrophy associated with diabetes mellitus. However, this mode of exercise may be considered safe by not compounding the deteriorative effects of this disease.
Correlation between Performance, Carcass Traits and Blood Lipid Profile of Broilers Chicken Fed with Rations Supplemented with Plant Powders

Aims: Utilization of phytobiotics as growth promoter in broilers rearing is not efficiently applied by farmers. This study aimed to assess the relationship between performance, carcass traits and lipid profile of broilers (Cobb 500 strain) fed with different rations supplemented with or without plant powders using principal component analysis. Methodology: One hundred broilers aged twenty-one day were randomly allocated to 5 Original Research Article Ndomou et al.; JALSI, 17(2): 1-12, 2018; Article no.JALSI. 40681 2 experimental diets with 10 replicates consisting of the negative control diet without supplementation, the positive control diet containing 200 UI/kg of vitamin E and the other rations were obtained by adding Camellia sinensis leaves; Zingiber officinale root and Annona muricata flowers powders in the basal diet at 5 g/kg respectively. The performance traits were recorded weekly and on the 49 day, broilers were randomly slaughtered and their carcass collected for body measurements, while blood was collected for lipid profile determination. Results: The first two components explained about 69.58% of the total variation where the first component explaining 38.58% was associated with the treatment supplemented with the powders of Camellia sinensis and the second explaining 31% was associated with the negative control treatment. Conclusion: Thus the addition of camellia sinensis powders could be useful to enhance growth performance, carcass characteristics and blood lipids profile of broilers.
Urban wetland seed bank profiles in south-central New York State1,2

Abstract Wetlands are important habitats in urban landscapes that reduce flooding and improve water quality, yet urban wetland seed banks are rarely studied. Our main objective was to profile urban wetland seed banks in south-central New York. We exposed sediment cores from four wetlands in Broome County, New York, to flooded and drawdown treatments for 16 mo, and recorded community composition and seedling density. We found high spatial variation in species richness and seedling density among the four sites. Species richness ranged from 28 to 56 species, with sample-based extrapolation (Sest), Jackknife1, and Chao1 analyses estimating similar expected species richness values (Sest projected 37.9–77.0 species, Jackknife1 analysis estimated 40.5–77.8 species, and Chao1 projected 32.2–79.1 species). Mean seedling density ranged from 3,367 seedlings/m2 to 19,132 seedlings/m2. These seed banks were dominated by obligate wetland species (75.8–93.3%). Invasive species comprised a high percentage of seedlings for three wetlands (40.8–80.9%), but not for the fourth site (4.2%). Lythrum salicaria, Typha sp. , and Ludwigia palustris were common species based on relative seedling density for three seed banks, while Leersia oryzoides, Schoenoplectus tabernaemontani, and Alisma triviale were common species in the fourth site. Similarity indices between the standing vegetation and their respective seed banks, based on presence/absence data, were low (13–34%). Species richness and seedling densities were within the ranges of natural wetland seed bank studies.
Tolerogenic transcriptome landscape in CD8+ T lymphocytes after exposure to erythrocyte-targeted antigens

Our group has recently shown induction of antigen-specific T cell tolerance through targeting of the antigen to erythrocytes in situ. The tolerogenic state is characterized by initial proliferation of antigen-specific T cells and subsequent acquisition of signatures associated with both deletional, anergic and regulatory T cell phenotypes. In this study we wished to further understand the molecular mechanisms behind induction of tolerance by erythrocyte-targeted antigens. RNA sequencing was performed to determine how gene expression response is regulated in tolerized ovalbumin-specific CD8+ T cells and which molecular pathways are activated after treatment with this technology. Treatment with erythrocyte-targeted antigens led to the upregulation of genes encoding several TCR co-inhibitory receptors such as CTLA4, PD1, LAG3, TIGIT and CD200R1, and lack of upregulation of cytotoxic and pro-inflammatory signaling molecule genes. Modulation in expression of the master transcription factors Egr2/NFatc1, Nur77 family and E2f1 was also observed, all known to be associated with the natural process of establishment of peripheral tolerance. Expression of these genes differed in response to treatment with soluble ovalbumin or SIINFEKL MHCI peptide, suggesting a specific mechanism of T cell modulation and tolerance induction in response to the erythrocyte-associated forms.
Effect of Different Propagating Media and Plant Growth Promoting Rhizobacteria on Rooting of Stem Cuttings and Survival Rate of Cuttings in Sarpagandha (Rauvolfia tetraphylla)

The experiment entitled “Effect of different propagating media and PGPRs on rooting of stem cuttings in Sarpagandha (Rauvolfia tetraphylla)" was conducted with 8 treatments in CRD design replicated for four times. , The cuttings raised in Red soil + sand + vermicompost + VAM + PSB + Pseudomonas fluroscens were significantly higher as they took minimum days for rooting and recorded maximum sprouting, number of roots(10.47), root volume(3.53cc) and survival rate (50 %) compared to all other treatments. So it is better to raise cuttings in Red soil + sand + vermicompost + VAM + PSB + Pseudomonas fluroscens.
Common octopus settled in human‐altered Mediterranean coastal waters: from individual home range to population dynamics

&NA; A spatially explicit capture‐recapture (SCR) model was applied to estimate simultaneously population parameters and individual activity (i.e. home range size) of O. vulgaris, based on experimental mark‐recapture data in a human‐altered Mediterranean coastal area. Seventy‐two octopuses were captured, tagged with subcutaneous PIT‐tags and released. Nineteen tagged individuals were recaptured (recapture rate: 26.4%) in the same area over the study period, which spanned over 6 months. Population sizes and densities decreased over the study period, from 337 octopuses (8 ind. ha−1) in September‐October to 105 octopuses (2.5 ind. ha−1) in February‐March. The highest recruitment probability was estimated to occur at the beginning of the study but it clearly decreased over time, while mortality probability during a fishing period slightly increased. Mean specific growth rate was 0.82 ± 0.11 day−1. Individual home range or activity area ranged from 2.8 ha to 7.3 ha (median home range radius: 121.8 m). Overall, these results suggest that human‐altered coastal habitats, which are characterized by abundant shelters, abundant food and absence of predators, can act as settlement and growth areas for juveniles and adults of O. vulgaris. Furthermore, the methodologies applied in this study are recommended as innovative tools to improve management actions of coastal resources.