Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the invasiveness of Acacia stricta and Acacia implexa : is eradication an option?

This study is the first detailed assessment of an invasion anywhere in the world by Acacia implexa (Benth.) (screw-pod wattle). It evaluates the threat of this species to native ecosystems in South Africa. The current survey found approximately 30 000 A. implexa individuals spread over about 600 ha in three geographically distinct populations all in the Western Cape, South Africa. Population structures indicate rapidly increasing populations at all sites, predominantly by vegetative suckering. Populations appear capable of rapidly densifying if given the opportunity, creating monocultures and even out-competing other invasive acacias. Although seed viability is high, there is relatively low recruitment from seed, likely as a result of high seed predation. While this appears to have limited population spread rates, seeds have begun to spread via roads and watercourses, in particular along the Eerste River near Stellenbosch and so there is a possibility of a dramatic increase in the extent of all three populations. Formal risk assessment and bioclimatic niche modelling indicate that this species has the potential to spread over large parts of South Africa, particularly in the Western Cape and along the eastern coast. We consider eradication a feasible management goal, but given the strong ability of A. implexa to resprout, proper control and follow-up would be essential to prevent re-establishment of dense stands and further spread. We support the proposed listing of the species as category 1a under the National Environmental Management: Biodiversity Act.
Molecular adaptation of the chloroplast matK gene in Nymphaea tetragona, a critically rare and endangered plant of India

Sustainable utilization of plant genetic resources for food and agriculture has been increasingly discussed at both national and international forums. Besides exploitation, conservation of plant genetic resources has become an integral part of these discussions. Conservation aims at maintaining the diversity of living organisms, their habitat and the interrelationship between organisms and their environment. For achieving such goals, appropriate conservation strategies have to be adopted. Determining the genetic makeup of a particular plant species is of critical importance when planning a suitable conservation strategy. In this study, we sequenced the chloroplast trnK intron, matK and rbcL gene aimed at understanding the rarity of Nymphaea tetragona, a critically rare and endangered plant of India found at only one location. We extended our investigation to other Nymphaea species such as N. nouchali, N. pubescens and N. rubra that are commonly available throughout India. Interestingly, matK gene of N. tetragona revealed high number of non-synonymous substitutions. Molecular evolutionary analysis indicated that three of these sites may be under mild selective pressures. Such adaptive changes at the DNA and protein sequence level of matK gene may have been associated with the colonization of N. tetragona, suggesting that it could have migrated from China.
A Functional Assay for Putative Mouse and Human Definitive Endoderm using Chick Whole-Embryo Cultures

Introduction: Embryonic stem cells (ESCs) represent a prospective cell source for treating degenerative diseases such as diabetes. Several studies have addressed the generation of definitive endoderm (DE) from this cell source by attempting to recapitulate the signaling events occurring during embryogenesis. However, the subsequent differentiation of DE has failed to generate functional insulin-producing beta cells. To assure that we have the correct starting material, we need to fully characterize ESC-derived DE, by assessing whether the cells are functionally equivalent to the in vivo counterpart. Thus, the purpose of this study is to describe a method whereby the in vivo functionality of DE derived from ESCs can be assessed. Methods: By directed differentiation, putative DE was derived from human and mouse ESCs. This putative DE was subsequently transplanted into the endoderm of chick embryos to determine any occurrence of integration. Putative DE was analyzed by gene and protein expression prior to transplantation and 48 h post transplantation. Results: Putative DE, derived from mouse and human ESCs, was successfully integrated within the chick endoderm. Endoderm-specific genes were expressed in the putative DE prior to integration and endoderm-specific proteins were assessed 48 h post transplantation. Conclusions: We describe the detailed methodological procedure for transplanting putative DE derived from ESCs, and the subsequent analysis of the migration and development of the grafted cells. Our result show that putative DE integrates with the chick endoderm and participate in the development of the chicken gut, indicating the generation of functional DE from ESCs. This functional assay can be used to assess the generation of functional DE derived from both human and mouse ESCs and provides a valuable tool for cell characterization. This is an important initial step in the differentiation process towards fully functional beta cells.
Apical dominance and growth in vitro of Alstroemeria

In Alstroemeria, micropropagation is achieved by axillary bud outgrowth. However, the multiplication rate is rather low (1.2–2.0 per cycle of 4 weeks) due to strong apical dominance. Even though several factors (i.e. culture media, growth regulators, and environmental conditions) have been studied, no significant improvements have been achieved. Basic research on apical dominance mechanism in Alstroemeria is therefore required. This may enhance the understanding how apical dominance controls axillary bud outgrowth in this plant and others. A second drawback in micropropagation of Alstroemeria is the slow growth of rhizomes. In this respect mineral nutrition and the effect of stress are significant. The former is implicated in storage organ growth to literature studies, in particular phosphate. The latter, the effect of stress, is based on observations of growers who noticed a strong increase of rhizome growth after moderate abiotic stress. This research deals with the backgrounds of growth of Alstroemeria in vitro. It deals with (1) the regulation of apical dominance, (2) the growth of rhizomes by applying abiotic stress and (3) the growth of rhizomes by adapting the formulation of inorganic nutrients. Alstroemeria is characterized by strong apical dominance. We observed that the outgrowth of axillary buds is inhibited byboth rhizome and aerial shoot tips. The hormonal regulation is like the regulation in model plants (Arabidopsis, pea, petunia) involving as promoting hormone cytokinin and as inhibiting ones auxin and the carotenoid-derived hormones namely strigolactones (SLs). The involvement of SLs is examined in more detail. Fluridone, an inhibitor of SL synthesis, promotes the outgrowth of lateral rhizomes. It is supposed that SLs act by inhibiting auxin transport. Our experiment to measure auxin transport seem to agree with this. We also found that the auxin transport inhibitors TIBA and NPA reverse the effect of fluridone. The moderate heat stress, and also cold stress and anaerobic stress strongly promote rhizome growth. The increase of growth is not reduced by stress-protective treatments. Therefore, we conclude provisionally that this phenomenon is itself a response of plantlets to protect them from future adverse conditions. Alstroemeria explants rapidly consume organics and inorganics from the nutrient medium but so far no relationship could be established with poor growth. There are marked differences with respect to mineral composition of the rhizome and the aerial shoot for Ca, P and Mg.
RESEARCH NOTES: SUMMER HABITAT USE AND HOME-RANGE ANALYSIS OF THE ENDANGERED INDIANA BAT

JENNIFER M. MENZEL,1 U.S. Forest Service, Northeastern Research Station, Parsons, WV 26287, USA W. MARK FORD, U.S. Forest Service, Northeastern Research Station, Parsons, WV 26287, USA MICHAEL A. MENZEL, Alston & Bird, LLP, Atlanta, GA 30309, USA TIMOTHY C. CARTER, Southern Illinois University, Carbondale, IL 62966, USA JAMES E. GARDNER, Missouri Department of Conservation, Jefferson City, MO 65102, USA JAMES D. GARNER, Illinois Department of Natural Resources, Springfield, IL 62702, USA JOYCE E. HOFMANN, University of Illinois Museum of Natural History, Champaign, IL 61820, USA
Oral necrobacillosis ('lumpy jaw') in a free-ranging population of eastern grey kangaroos (Macropus giganteus) in Victoria

A high prevalence (54%) of oral necrobacillosis, commonly referred to as ‘lumpy jaw’ based primarily on the presence of cranial osteological lesions, is reported from a free-living population of Macropus giganteus in Victoria. Lesions were found primarily in the maxillary bone and the mandible, in association with the rostral region of the dental arcade. Autopsy data provided additional evidence that the osteological lesions observed were due to oral necrobacillosis. Lesions were more common in older kangaroos. The study was carried out during a drought with limited pasture availability and heavy faecal contamination of pasture, conditions that may have contributed to the high prevalence of the disease.
Population Genetics and Speciation in Outcrossing Species in the Nematode Genus Caenorhabditis

In Caenorhabditis nematodes, the androdioecious, self-fertilizing reproductive strategy has evolved relatively recently from gonochoristic, outcrossing ancestors. Transitions in mating system impact how genes are vertically transmitted between generations and horizontally between populations through gene flow. To date, species-wide studies have targeted selfing species, and we have limited understanding about how population genetic processes have shaped the genome structure and evolutionary history of outcrossing species of Caenorhabditis. To fill this gap, I investigate patterns of genetic variation and population genetic processes focusing on two outcrossing species in the genus, C. brenneri and C. remanei, using a survey of nucleotide polymorphisms in a multipopulation, multilocus context. I discover extensive genetic diversity in Caenorhabditis brenneri, termed hyperdiversity, giving this species the highest known levels of nucleotide polymorphism for any multicellular eukaryote. Genetic crosses between populations, extensive intra-locus recombination, and evidence of weak selection on codon usage all suggest that this is due to
Overstory Composition and Stand Structure Influence Herbaceous Plant Diversity in the Mixed Aspen Forest of Northern Minnesota

Abstract The relationship of herbaceous plant diversity to overstory composition and stand structure in the mixed aspen forest of northern Minnesota was investigated on 23 study sites that contained aspen in monoculture or in mixture with boreal conifers or northern hardwood species. On each site overstory species were placed into species groups: conifers, aspen and hardwoods other than aspen. Each site was then placed in one of three cover-type groups based on proportion of the overstory species groups: Aspen (>0.9 basal area in aspen), Aspen-Conifer (>0.15 basal area in conifer species) and Aspen-Hardwood (>0.15 basal area in hardwood species other than aspen). The relationships between diversity of herbaceous vegetation and the following factors were tested: (1) overstory composition, defined as the proportion of basal area by species group in the overstory and (2) stand structure. Stand structure was described by the vertical position and horizontal arrangement of balsam fir within the stand. In addition, relationships were tested with respect to other stand structural features such as shrub height and cover, average amount of plant material intercepted within the vertical profile and an index of plant occupancy within the vertical profile (modified Foliage Height Diversity Index-FDH). Understory herbaceous diversity (H′) and proportion of aspen basal area were significantly positively related whereas understory herbaceous diversity was significantly negatively related to proportion of hardwood basal area and not related to proportion of conifer basal area. Mixtures of overstory tree species provided a range of stand structures that can be represented by shrubs, subcanopy trees or the overstory trees. In the three cover-type groups different structural components were related to herbaceous diversity indicating that (1) overstory composition and stand structure interactively influence understory diversity patterns and (2) it is difficult to characterize stand structure for the range of stand conditions with a single measure. Increased diversity of structure (modified FHD) in the Aspen-Conifer group is negatively related with diversity (H′) of the herb layer. Composition of herbaceous species varied depending on presence or absence of conifers in the overstory. These patterns may be influenced by the interaction of a variety of resource levels and climate conditions, which, in turn, are controlled by factors such as tree architecture or shade tolerance of overstory trees.
Genetic Analysis of Host Plant Resistance to the Cassava Mosaic Disease

The genetic control of resistance to the cassava mosaic disease (CMD) in some African landraces, their relationship with the widely used resistant genetic stock, clone 58308, and molecular markers associated with resistance to CMD in the landraces were evaluated in this study. The F-i progenies of 54 cassava crosses and their parents (clone 58308, six improved clones and 15 African landraces) were evaluated in two genetic experiments in three environments in Nigeria. Genetic analysis revealed that additive gene effect was more important in the genetics of resistance to CMD among the landraces, while both additive and non-additive gene effecsts were important for
Nuclear and Cytoplasmic Changes in the Culex pipiens (Diptera: Culicidae) Alimentary Canal During Metamorphosis and Their Relationship to Programmed Cell Death

Abstract The metamorphic programmed death of Culex pipiens (L.) alimentary canal cells was studied. Hoechst DNA, Acridine Orange, and TUNEL (terminal deoxynucleotidyl transferase mediated dUTP nick end labeling) staining of larval alimentary canal whole mounts showed that programmed death of polytene cells started during the 4th stadium. The cell death program was initiated in anterior stomach polytene cells and progressed to posterior stomach and gastric caeca polytene cells. Agarose gel electrophoresis confirmed that fragmentation of alimentary canal DNA into nucleosome size fragments occurred. Diploid nuclei of the anterior and posterior stomach increased in number during the time in which programmed death of polytene cells occurred. However, TUNEL staining showed that just before pupation there was also degradation of some diploid nuclear DNA in both the anterior and posterior stomach, which suggested that some of these cells also underwent programmed cell death. MTT (3-[4,5-Dimethylthiazol-2-yl]-2,5 diphenyltetrazolium bromide) staining of the alimentary canal indicated that mitochondrial activity persisted while polytene nuclei were degraded. In addition, histological examination of serial thick sections showed that prepupal midgut cells had vacuoles which suggested that cytoplasmic cell death occurred during metamorphosis.
Aceitação sensorial e caracterização de frozen yogurt de leite de cabra com adição de cultura probiótica e prebiótico

Goat's milk is recommended for people afflicted with cow milk intolerance and gastro-intestinal disorders. frozen yogurt was elaborated with 1% prebiotic (inulin), 0.25% starter culture (Streptococcus thermophilus and Lactobacillus bulgaricus) and 0.25% probiotic culture (Bifidobacterium animalis and Lactobacillus acidophilus) to verify probiotic potential (after 7 and 120 days of storage), physical-chemical quality and sensorial acceptance. During storage viable cells were reduced, mainly probiotic bacteria. Nevertheless, the product showed probiotic potential because of B. animalis and L. acidophilus sum, which reached the minimum desirable until the end of storage. Values of total dry matter (26.6±0.2%), protein (3.0±0.3%), fat (2.6±0.1%), pH (5.5±0.01) and acid lactic (0.2±0.01%) were similar to those descript by other researches for the same product. Sensorial evaluation was realized by 50 untrained panelists, with a 7- point hedonic scale and intention to purchase. The product received good scores for global appearance, color, aroma and taste. Texture and residual taste had lower acceptance rates. The intent to purchase showed that 61% of panelists asserted to buy the product against 39%, who would not buy it. Accordingly, this research showed the feasibility of elaborating the goat's milk frozen yogurt with addition of pre- and probiotics.
Screening of contaminated soils for biodegradable plastic producing bacteria and profiling of their resistance markers

Polyhydroxyalkanoates (PHA) are the biodegradable polyesters produced by bacteria to overcome the environmental stress. Contaminated environments have a large number of bacteria which can accumulate PHA as their energy reserves. Molasses, oil/ghee and sewerage contaminated soils were selected for the screening of biodegradable plastic- producing bacterial strains. The selected contaminated environments showed great diversity of bacterial flora, Pseudomonas (39.39%) being the most common. The 54 bacterial isolates were further screened by Sudan Black B staining after 48 h of incubation on polyhydroxyalkanoates (PHA) - detection media with glucose as a carbon source and Nile Blue A viable colony staining method. The PHA granules could not be detected in 6 bacterial isolates (AS1, AS2, AP2, AP1, LS13 and VM1). In soil samples contaminated with molasses (sugar industry waste), 95% and in samples contaminated with oil/ghee industry waste all bacterial isolates showed PHA accumulation ability. The accumulated PHA was extracted by direct addition of sodium dodesyl sulphate (SDS). The bacterial isolates SM5, SM11, PG5, UOS2, LS10, AP4 and LS3 accumulated more than 50% PHA of their wet cell mass. No correlation was observed between bacterial growth and the PHA production. The bacterial strains showed multiple resistant markers for selected antibiotics (penicillin and streptomycin) and heavy metals (copper and cadmium). A high level of resistance was observed for penicillin (100 - 4500 µg/ml) and copper (1.5 - 17 mM/ml) in PHA- producing strains. Key words: Biodegradable plastic, polyhydroxyalkanoates, molasses, oil/ghee, contaminated soil.
Spatial and temporal variability of phytoplankton at Jukrim-ri, Tongyeong-si, Korea

Summary The study was described in the seasonal and spatial patterns of phytoplankton on the water surface and basal layer below the surface depths for seven stations at Jukrim-ri in Korea. Although this area was not wide, but the phytoplankton community was very diverse with 54 taxa identified, representing four classes. Diatoms (Bacillariophyceae) exhibited the greatest diversity with 38 taxa identified, followed by dinoflagellates (Dinophyceae, 12 taxa); Cryptophyceae with three taxa, and Eugenophyceae represented by a single taxon. Water surfaces were shown with the relative higher individual density or abundance across areas than those of basal layer. For the community as a whole, the values of s-diversity for spatial variability were the lower than those of temporal variability. There was high taxonomic homogeneity of the phytoplankton community among four seasons. However, size distribution of abundance and biomass showed a statistically significant difference between south-north stations.
Camera Relocalization by Predicting Pairwise Relative Poses Using Convolutional Neural Network

We propose a new deep learning based approach for camera relocalization. Our approach localizes a given query image by using a convolutional neural network (CNN) for first retrieving similar database images and then predicting the relative pose between the query and the database images, whose poses are known. The camera location for the query image is obtained via triangulation from two relative translation estimates using a RANSAC based approach. Each relative pose estimate provides a hypothesis for the camera orientation and they are fused in a second RANSAC scheme. The neural network is trained for relative pose estimation in an end-to-end manner using training image pairs. In contrast to previous work, our approach does not require scene-specific training of the network, which improves scalability, and it can also be applied to scenes which are not available during the training of the network. As another main contribution, we release a challenging indoor localisation dataset covering 5 different scenes registered to a common coordinate frame. We evaluate our approach using both our own dataset and the standard 7 Scenes benchmark. The results show that the proposed approach generalizes well to previously unseen scenes and compares favourably to other recent CNN-based methods.
Reintroduction of Tigridiopalma magnifica, a rare and Critically Endangered herb endemic to China

Abstract Tigridiopalma magnifica, a perennial herb and the only species in the genus Tigridiopalma (Family Melastomataceae) is rare and endemic to China where it is categorized as Critically Endangered on the national Red List. Twelve locations with populations of T. magnifica have been identified (1 extinct, 11 extant). T. magnifica only grows in the surface soil on stone walls or rocks under the canopy of secondary forests and plantations and has no specific associated plant species. Canopy closure, soil water content and the distance to the closest stream are the main factors influencing the distribution of T. magnifica. We reintroduced T. magnifica plantlets produced by tissue culture into three locations: one within the species' original range, and 11.5 and 400 km from the species' original range. After 11 months survival rate was 40–58% but survival was higher and plantlet crowns were larger at the location within the species' original range than at the other two sites. The combination of advanced propagation techniques and ecological restoration could facilitate reintroduction and conservation of T. magnifica and other rare and threatened plants. This example of the successful reintroduction of a rare, threatened herb has implications for human-assisted migration and colonization of rare plant species under future climate change scenarios.
Column distance of convolutional codes over Zpr

Rosenthal et al. introduced and thoroughly studied the notion of Maximum Distance Profile (MDP) convolutional codes over (non-binary) finite fields refining the classical notion of optimum distance profile, see for instance [18, p.164]. These codes have the property that their column distances are maximal among all codes of the same rate and the same degree. In this paper we aim at studying this fundamental notion in the context of convolutional codes over a finite ring. We extensively use the notion of p-encoder to present upper-bounds on the column distances which allow to introduce the notion of MDP in the context of finite rings. A constructive method for (non necessarily free) MDP convolutional codes over Z p r is presented.