Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent introduction of Gracilaria parvispora (Gracilariales, Rhodophyta) in Baja California, Mexico

Abstract Gracilaria parvispora is reported for the first time as an invasive species in northwestern Mexico based on morphological, anatomical and molecular data. The species is widely distributed in the region, where it colonizes sandy and rocky habitats from intertidal areas down to a depth of 1.5 m. The morphological and anatomical data from the Mexican specimens matched the circumscription of the species in Hawaiian waters. Two molecular markers (rbcL and cox1) showed that the Mexican populations were closer to the Hawaiian populations than the Korean populations, which may relate to a similarity in seawater temperatures between Hawaii and Baja California. Gracilaria parvispora formed extensive mats together with Gracilaria vermiculophylla. It was found in stomach samples from a green turtle (Chelonia mydas) in the coastal lagoons of Baja California Sur. The ecological impacts of the two alien Gracialria species on other native species and communities have yet to be determined. This is the first demonstration of a second invasive Gracilaria species, following the introduction of G. vermiculophylla into the northwestern Mexico region.
RAPD analysis as a tool for discriminating marble trout from hybrids (marble trout · brown trout) in the zones of hybridization

Summary Marble trout (Salmo marmoratus) is an endangered salmonid, characteristic of the Po river system and the Adriatic river system of western Balkan. In order to establish an efficient source of purebreds designed for marble trout repopulation, it is very important to develop a tool for reliable selection of pure individuals out from the hybrid zone. Marble trout, brown trout (S. trutta) and their hybrids were included in the investigation. Of 200 random amplified polymorphic DNA (RAPD) primers tested, 14 were species specific showing a clear inter-specific polymorphism. In most cases, the hybrids exhibited a combination of the fragments found in parental lineages but no novel fragments. Some fragments, previously detected in both species, were absent in some hybrids indicating parental heterozygosity at those loci, whereas some of the species-specific fragments were found in all the hybrids analysed suggesting homozygous state of such loci in either of the parental lineages. The RAPDs can be, provided the transmission of banding patterns has been previously tested on two generation material, very successful tool for the detection of genetic variation in closely related individuals, in this particular case, between marble trout and the hybrids, enabling an efficient sorting of purebreds out from the zone where hybridization takes place.
A biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data

Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model or Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of co-regulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known and one OR nucleotides were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.
Genetic studies on Trebbiano and morphologically related varieties by SSR and AFLP markers

Several grapevine varieties are named Trebbiano and have similar phenotypical characteristics ( e.g. whitish berries, late ripening, vigorous growth). Other vines share many of the morphological characteristics of Trebbiano but have different names. In order to clarify the relationships between some of these varieties, a study was carried out with 7 Trebbiano varieties and 17 cultivars that are morphologically similar to Trebbiano. AFLP and SSR analyses were performed to define genetic similarity among the Trebbiano cultivars as well as between the Trebbiano cultivars and related varieties. Results show a large degree of variability between most of the cultivars and suggest that they do not share a common ancestor. Genetic analysis revealed that cv. Verdicchio is identical with Trebbiano di Soave which is very similar to Trebbiano di Lugana.
Size‐induced phenotypic reaction norms in a parasitoid wasp: an examination of life‐history and behavioural traits

The amount of resources available during development often affects body size, causing phenotypic variation in life-history traits and reproductive behaviours. However, past studies have seldom examined the reaction norms of both life-history and behavioural traits versus body size. We measured the phenotypic plasticity of several life-history (age-specific egg load, egg size, longevity) and behavioural (oviposition rate, host marking rate, walking speed) traits of the egg parasitoid Telenomus podisi Ashmead (Hymenoptera: Scelionidae) in response to body size variation. We predicted that life-history traits would show more evidence of size compensation than behavioural traits, resulting in fewer positively-sloped size versus trait reaction norms among the former. As predicted by life-history models, smaller wasps appear to shift resource allocation towards early-life reproduction, having a similar egg load to large individuals 9 days after emergence. Surprisingly, longevity was unaffected by body size. However, egg size, the number of offspring produced during oviposition bouts, and the rate of subsequent egg synthesis were greater for larger individuals. In addition, as predicted, the reaction norms of behavioural traits versus body size were all positively sloped. Thus, despite possible adaptive compensatory plasticity of life-history traits by small individuals, behavioural constraints directly related to body size would contribute to maintaining a positive size–fitness relationship.
Fluctuating asymmetry in bank vole populations (Rodentia, Arvicolinae) reflects stress caused by landscape fragmentation in the Mont-Saint-Michel Bay

In intensively farmed, reclaimed areas (polders) of Mont-St-Michel Bay, France, bank voles (Clethrionomys glareolus) live in fragmented hedgerows, where populations are small and dispersal rates and genetic diversity are low. These small populations are likely to have been exposed to potential environmental and/or genetic stress. The sensitivity of development to stress can be measured by fluctuating asymmetry (FA). FA was calculated for three samples from a disturbed area and one sample from an adjacent, more connected and undisturbed landscape. Size FA was estimated from 16 measurements of the skull and teeth whilst shape asymmetry was estimated from the skull alone. Bank voles in fragmented hedgerows of the disturbed area had a higher degree of FA than bank voles from the more extensive and more connected hedges of the undisturbed area. These results were confirmed by the study of shape asymmetry, body mass and centroid size of the skull. There were no differences in FA between the three disturbed area samples. We conclude that FA does not reveal differences in the development of bank voles living in isolation under different local conditions in the various parts of the disturbed area. However, FA may allow differentiation between populations from greatly contrasting landscapes. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 37–44.
Reimagining teaching as a social work educator : a critical reflection

The purpose of the paper is to explore how the Bachelor of Social Work (bi-culturalism in practice) programme of Te Wãnanga o Aotearoa has influenced the author to rethink her teaching style, attitude towards using spirituality in social work, and epistemological stance in research. A critical reflexive method was used to deconstruct the author’s previous assumptions and to reconstruct them. Three previous and reimagined assumptions were explored. First, before the reconstruction, the author’s assumption was “teachers are always experts”. The reconstructed assumption is, “teachers are not always experts but humble knowers and learners”. Second, the author believed that, as spirituality was personal and subjective it would not be taught in social work; and the author also considered only verifiable theories as valid knowledge. Now the author reimagines that social workers need spiritual theories and principles as well. Finally, as to research, the reimagination has made the author shift her epistemological stance from a positivistic paradigm to an Indigenous Mãori paradigm of whakapapa (genealogy) that has inspired her to rediscover the whakapapa of her ancestors’ knowledge. The reflective accounts of reconstruction were explored by using the author’s teaching practice at Te Wãnanga o Aotearoa, her contextual background and her own spiritual identity.
Periphyton as an early indicator of perturbation in recreational lakes

We looked for empirical relationships between periphyton biomass and recreational development in the Laurentian lakes of Quebec (Canada). We compared the response of periphyton (as chlorophyll a) on rocks and sediments with that of phytoplankton. Epilithon and epipelon biomass increased significantly with lake recreational development (as percentage of cleared land within a 50 m riparian strip) but was not related with open-water phosphorus concentration. In contrast, phytoplankton was related to open-water phosphorus but did not increase along the gradient of lake development. Periphyton stoichiometric composition also changed with increasing lake development. High C:P and C:N ratios were found in pristine lakes, whereas lower periphyton molar ratios, which approached the optimal stoichiometric composition for benthic microalgae, were observed in the most developed lakes. Our findings suggest that periphyton, positioned near the land–water interface, has access to land-derived nutrients before they are d.
Eradication of black rot (Guignardia bidwellii) from grapevines by drastic pruning

A drastic pruning strategy was developed to eradicate the fungal disease black rot (Guignardia bidwellii), which is exotic in Australia, from grapevines, while minimizing the economic cost of returning an affected vineyard to its previous quality and production levels. The protocol involved cutting off vines at the top of the trunk, removing debris from the ground beneath and between vines, mulching the vineyard floor, removing low watershoots during vine regrowth and applying a targeted fungicide programme. The protocol was initially evaluated and consequently modified in Australia using an endemic grapevine disease, black spot or anthracnose (Elsinoe ampelina), as an analogous model system. Then, it was validated in a black-rot-infested vineyard in New York, USA. Following two seasons of disease-conducive weather conditions, no black rot was detected on treated vines, whereas leaf and fruit infections developed on the untreated control vines. These results confirmed the efficacy of the protocol for eradicating black rot from vineyards while allowing vines to return quickly to previous yield and quality levels without replanting. The protocol may have applicability to disease eradication protocols for other perennial crops as well. Evidence is also presented on the efficacy and potential pitfalls of burning infected grapevine material to eradicate E. ampelina.
Morphological Analysis of Narrow-petaled Cultivars of Rhododendron macrosepalum Maxim.

In evergreen azalea, unique old mutational cultivars, whose flower have split figure, have been collected and is called “sai-zaki” in Japanese. The morphology of leaves and flowers of the wild-type and sai-zaki cultivars ‘Hanaguruma’, ‘Gin-no-zai’, and ‘Seigaiha’ of R. macrosepalum was investigated. In contrast to the gamopetalous corolla of the wild type, all sai-zaki cultivars formed the choripetalous corolla type, which consisted of 5 independent petals. The width of the leaf, sepal, and petal of all sai-zaki cultivars, except for the sepal of ‘Gin-no-zai’, all tended to be narrower than the wild type; in particular, all lateral organs of ‘Seigaiha’ were extremely narrow compared with the wild type. In contrast to the normal pistil of the wild type, ‘Hanaguruma’ and ‘Gin-no-zai’, normal and malformed pistils we’re observed in ‘Seigaiha’. Epidermal cell size was not related to the narrowness of lateral organs in the wild-type and sai-zaki cultivars. These results indicate that the sai-zaki trait of materials, at least ‘Seigaiha’, would be a common mutation in the growth of lateral organs in the transverse plane. All sai-zaki cultivars showed fertility. The sai-zaki trait of old Japanese cultivars from the Edo era is expected to provide new breeding material that offers the opportunity to generate additional morphological novelties.
StatSAW: modelling lumber product assortment using zero-inflated Poisson regression

Realistic forestry value chain simulations require accurate representations of each component. For primary processing, this is complicated by the fact that a single raw material is converted into a wide range of lumber products. The aim of this study was to develop statistical models for predicting lumber product assortment from tree size information, while taking into account the high proportion of zeros in the data. Lumber recovery was simulated from a database of 1013 laser-scanned Picea mariana (Mill.) Britton, Sterns & Poggenb. and Abies balsamea (L.) Mill. stems using the sawing simulator Optitek. The number of boards per stem of specific products was modelled with zero-inflated Poisson regression using stem diameter and height as covariates. The number of boards per stem was strongly related to both diameter and height, but also changed according to input prices for lumber products. Zero-inflated models outperformed ordinary Poisson regression in all cases. The developed models will be integrated i.
The synergic and antagonistic activity of Cry1Ab and Cry2Aa proteins against lepidopteran pests

Cry1Ab and Cry2Aa were overexpressed in Escherichia coli BL21(DE3), and their proportions were determined for evaluating their synergic and antagonistic interactions on Ephestia kuehniella and Plodia interpunctella. Results indicated antagonistic interaction on both lepidopteran pests, and it was concluded that 1 : 1 combination of Cry1Ab:Cry2Aa should be avoided in control programmes for these larvae.
Six microsatellite loci in forest musk deer, Moschus berezovskii

Through an improved enrichment protocol, 20 microsatellite loci were isolated and characterized in an endangered animal, forest musk deer (Moschus berezovskii). In which, six loci showed high polymorphism with five to 13 alleles in 48 sampled individuals. The observed and expected heterozygosities were 0.362–0.955 and 0.784–0.906, respectively. The average polymorphism information content (PIC) was 0.8108 in these six microsatellites and they could be the valuable genetic markers for further investigation of forest musk deer species.
The lived experience of non-fluent English learners in learning English

Johar, D. A. 2017. The Lived Experience of Non-fluent English Learners in Learning English, Yogyakarta: English Studies Graduate Program, Sanata Dharma University. This research attempts to describe the lived experience of non-fluent English language learners in learning English. The researcher conducted this research in order to understand the process these English learners underwent in learning English under the circumstances of being non-fluent. English has become an essential skill to be possessed in Indonesia. Most Indonesian students study English at an average of nine years; from elementary to high school. This continuous English education means that the study of English encompasses almost their entire academic life. However, despite having had approximately twelve years of experience learning English, some English department students are non-fluent in English. This phenomenon has intrigued the researcher in finding out how this non-fluency affected the learning process of these learners within the classroom environment. This study was conducted as an attempt to help the readers understand the problems faced by non-fluent English learners throughout the language learning process. Regarding this issue, the researcher focuses on the aspects related to the participants’ experiences in learning English, mainly their motivation, their beliefs, their feelings, and their actions, therefore the hermeneutics phenomenology method was used in conducting this study.In-depth interviews were conducted with each research participant. The interviews were recorded, then transcribed. The participants of the study consisted of three last year undergraduate students studying in the English Department of a University in Yogyakarta. The result of the study showed three major themes: inferiority, anxiety, and amotivation. The result showed that the participants chose not to participate in class because they felt intimidated due to their lack of fluency in speaking English. It also showed that the class environment itself did not support them to develop their fluency. From the findings of this study,the researcher hopes to be able to raise the empathic understanding ofthe readers in general, and other students and teachers especially, towards non-fluent English learners. A suggestion from this study includes the improvement of the English teachers in their teaching and evaluation methods in order to give equal chances and support to those students who are less fluent in English.
An innovative biological named entity recognition system using support vector machine and web evidence

1.Contextual feature extraction 35,384 sentences were collected from 724 full-text articles, each of which has at least one of 1153 preidentified gene/protein names. Contextual features with various word stems were hand-selected from the pool of meaningful words that occur most frequently in the 5-word windows centered at the gene/protein names. 2. Training set preparation 1000 AGI names (e.g. AG1G01080), 1000 gene aliases (e.g. COP1) and 1000 enzymes (e.g. dehydratase) in Arabidopsis were randomly selected from TAIR [1] database, all of which are considered as known positive cases and are assumed to share similar contextual patterns with genes/proteins in plant UBQ system. Random words from articles in a different knowledge domain other than plant genomics served as negative cases, whose contextual patterns should be distinct from the ones of genes/proteins. 3. Search for web evidence Instead of human annotated values, supportive web evidence [2] was automatically retrieved to characterize each feature. The whole web was searched through Yahoo! Search BOSS service [3]. Each term in the dataset was queried with and without a context, and the feature value is defined as:
Population genetics and demographic inferences in a recovering shorebird, the African Black Oystercatcher Haematopus moquini

The extensive literature on the African Black Oystercatcher is a testament to what is now a conservation success story. Here we provide the first genetic insight into the population dynamics of this recovering shorebird and an assessment of genetic variation within the species using microsatellite markers. Although behavioural studies suggest strong natal philopatry, we found a single genetic cluster across all of the locations sampled and a significant signal of isolation by distance suggesting some geographical structuring. The microsatellite markers used in this study are useful at a population level, and the limited genetic variation detected is likely to be due to a low historical population size.
Experimental pathogenicity of Erwinia aphidicola to pea aphid, Acyrthosiphon pisum

Pea aphids were reared aseptically in the laboratory and fed on strains of Erwinia aphidicola, Erwinia herbicola, Klebsiella pneumoniae, Escherichia coli and bacterium W, an aphid enterobacterium, by mixing with a synthetic diet to determine whether these bacteria have pathogenicity to the insect. It turned out that Er. aphidicola and Er. herbicola grew in aphid gut, while K. pneumo-niae, Es. coli and bacterium W were effectively eliminated. In the case of Er. aphidicola, ingestion of a single dose of 10 3 CFU/ml was enough to infect aphid gut and to prevent post-final ecdysis growth of the insect. As a result, the body weight of the infected aphids was significantly reduced (p<0.01). A concentration of 10 5 CFU/ml of Er. aphidicola caused aphid mortality. In contrast, Er. herbicola demanded 10 5 CFU/ml to colonize in aphid gut, and seemed to have no effect on insect health.
Cellular and molecular analysis of NDR and LATS kinases in dictyostelium

Ich versichere hiermit ehrenwörtlich, dass die vorgelegte Dissertation von mir selbständig und ohne unerlaubte Hilfe angefertigt ist. NdrA of Dictyostelium localizes to the centrosome and is required for efficient phagocytosis. Traffic, in press. cytokinesis in Dictyostelium discoideum. Dictyostelium discoideum by a SIN-related pathway. Eur. discoideum is regulated by a SIN-related pathway. of cytokinesis in Dictyostelium discoideum. of NDR kinases in Dictyostelium discoideum cytokinesis. Eur.
Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach

Fabre, P.‐H. , Galewski, T. , Tilak, M. ‐k. & Douzery, E.J.P. (2012) Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach. —Zoologica Scripta, 00, 000–000.
Classification of Subcellular Phenotype Images by Decision Templates for Classifier Ensemble

Subcellular localization is a key functional characteristic of proteins. An automatic, reliable and efficient prediction system for protein subcellular localization is needed for large‐scale genome analysis. The automated cell phenotype image classification problem is an interesting “bioimage informatics” application. It can be used for establishing knowledge of the spatial distribution of proteins within living cells and permits to screen systems for drug discovery or for early diagnosis of a disease. In this paper, three well‐known texture feature extraction methods including local binary patterns (LBP), Gabor filtering and Gray Level Coocurrence Matrix (GLCM) have been applied to cell phenotype images and the multiple layer perceptron (MLP) method has been used to classify cell phenotype image. After classification of the extracted features, decision‐templates ensemble algorithm (DT) is used to combine base classifiers built on the different feature sets. Different texture feature sets can provide suff.