Miracle-dz/UniFAR-FTUs huggingface dataset:
Residence time, expansion toward the equator in the invaded range and native range size matter to climatic niche shifts in non‐native species

Aim Identifying climatic niche shifts and their drivers is important for the accurate prediction of the risk of biological invasions. The niches of non-native plants and birds have recently been assessed in large-scale multispecies studies, but such large-scale tests are lacking for non-native reptiles and amphibians (herpetofauna). Furthermore, little is known about the factors that contribute to niche shifts when they occur. Based on the occurrence of 71 reptile and amphibian species, we compared native and non-native realized niches in 101 invaded ranges at a global scale and identified the factors that affect niche shifts. Location Global except the Antarctic. Methods We assessed climatic niche dynamics in a gridded environmental space that allowed niche overlap and expansion into climatic conditions not colonized by the species in their native range to be quantified. We analysed the factors that affect niche shifts using a model-averaging approach, based on generalized linear mixed-effects models. Results Approximately 57% of the invaded ranges (amphibians, 51%; reptiles, 61%) showed niche shifts (≥ 10% expansion in the realized climatic niche). Island endemics, species introduced to Oceania and invaded ranges outside the native biogeographical realm all showed a higher proportion of niche shifts. Niche shifts were more likely for species that had smaller native range sizes, were introduced earlier into a new range or invaded areas located at lower latitudes than the native range. Main conclusions The proportion of niche shifts for non-native herpetofauna was higher than those for Holarctic non-native plants and European non-native birds. The ‘climate-matching hypothesis’ should be used with caution for species undergoing niche shifts, because it could underestimate the risk of their establishment.
Genetic analyses reveal declining trends and low effective population size in an overfished South African sciaenid species, the dusky kob (Argyrosomus japonicus)

Overfishing has led to the collapse of many marine fish stocks along the South African coast, particularly species characterised by predictable distribution patterns and vulnerable life-history traits. Dusky kob (Argyrosomus japonicus) is an estuarine-dependent sciaenid fish that has been severely depleted by overfishing and is currently managed by suboptimal management measures aggravated by poor enforcement and compliance to regulations. The present study utilised microsatellite markers to evaluate levels of genetic diversity and population structuring of dusky kob along the South African coast, including five estuarine areas. Results showed signatures of bottlenecking, low and declining trends of effective population size and weak differentiation among samples collected along 2000km of coastline, indicating that dusky kob continues to be subject to the detrimental influence of fishing pressure. Additionally, because dusky kob is a key species in the emerging South African aquaculture sector, parentage analyses were used to successfully identify the origin of first-generation (F1) individuals from a commercial hatchery, hence allowing traceability of farmed products and discrimination between wild and farmed fish. Findings from the present study provided essential information to aid future management of wild populations, as well as to establish sustainable fish farming.
The prevalence of Sarcocystis infection in meat-production by using digestion method in Ahvaz, Iran

: Introduction and objective: Sarcocystis is an obligatory intercellular protozoan parasite which can induce infection and clinical signs in carnivorous and herbivorous host. Humans acquire infection by ingestion of cyst or eating raw and undercooked infected meat or meat-production. The main goal of this study is to detect prevalence of the parasites in meat-production such as hamburger, sausage and hot dogs and determine its important role in human health. Materials and methods: Seventy five samples of hamburger, sausage and hot dogs (each 25 samples) were collected from retail stores in Ahvaz southwest of Iran. The samples were examined by digestion method using pepsin and HCl for detecting Sarcocystis parasite by light microscope. Results: Sarcocystis species were seen in 56% for hamburger, 20% for hot dogs and 8% for sausage. Conclusion: The results of this study indicated that the rate of the Sarcocystis sp. infection in meat-production is considerable and would be important for human. Many Sarcocystis sp. can infect meat many species from canine and feline definitive host. A molecular test such as PCR is needed to identify the parasite species. Digestion method is a sensitive, rapid and simple test for diagnosing Sarcocystis infection in meat. To prevent human infection, consumption of raw or under-cooked meat and meat-produced hyper endemic area should be avoided. Significance and impact of the study: Regarding to meat-born disease transmitted to human, to detect protozoa parasites in meat and their products can be important to prevent transmission of parasites which have cyst stage and promote hygienic level in human community.
A phylogenetic reassessment of Hyalenna Forbes and Dircenna Doubleday, with a revision of Hyalenna (Lepidoptera: Nymphalidae: Ithomiinae)

Abstract. A morphological study of adults and immature stages and a cladistic analysis were conducted to clarify the relationships amongst members of the sister nymphalid butterfly genera Dircenna Doubleday and Hyalenna Forbes. Two species formerly included in Dircenna, Ithomia paradoxa Staudinger and Dircenna hugia Schaus, clustered with Ithomia perasippa, the type species of Hyalenna. Therefore, the first two species are transferred from Dircenna to Hyalenna (comb.n.). Hyalenna and Dircenna as now conceived are both monophyletic and well supported by morphological apomorphies and branch support measures. The taxonomy and classification of Hyalenna are reviewed and seven species and twenty‐four taxa are recognized, including one new species, Hyalenna buckleyisp.n. , and eleven new subspecies: Hyalenna paradoxa incachacassp.n. , H. perasippa valenciassp.n. , H. perasippa ortygiosassp.n. , H. perasippa solitariassp.n. , H. buckleyi pomacochassp.n. , H. alidella exsulansssp.n. , H. alidella cinereolassp.n. , H. alidella vescassp.n. , H. sulmona balsamicassp.n. , H. sulmona hyalinassp.n. and H. sulmona tersassp.n. A key for the identification of all taxa, and illustrations of male and female genitalia for all species and adult specimens of all taxa (where known), are presented. The natural history of each species is summarized and the immature stages of H. paradoxa and H. sulmona are described for the first time.
In vitro evaluation of commercial fibrolytic enzymes for improving the nutritive value of low-quality forages

The aim of this work was to assess the effects of four doses of three commercial fibrolytic enzymes on ruminal fermentation of rice straw, maize stover and Pennisetum purpureum clon Cuba CT115 hay in batch cultures of ruminal micro-organisms from sheep. One enzyme was produced by Penicillium funiculosum (PEN) and two were from Trichoderma longibrachiatum (TL1 and TL2). Each liquid enzyme was diluted 200 (D1), 100 (D2), 50 (D3) and 10 (D4) - fold and applied to each substrate in quadruplicate over time and incubated for 120 h in rumen fluid. The D4 dose of each enzyme increased (P<0.05) the fractional rate of gas production and organic matter effective degradability for all substrates, and TL2 had similar effects when applied at D3. In 9 h incubations, PEN at D4, TL1 at all tested doses, and TL2 at D2, D3 and D4 increased (P<0.05) volatile fatty acid production and dry matter degradability for all substrates. The commercial enzymes tested were effective at increasing in vitro ruminal fermentation of low-quality forages, although effective doses varied with the enzyme.
THE EFFECT OF WORD CHAIN GAME ON STUDENTS VOCABULARY MASTERY OF THE TENTH YEAR STUDENTS OF SMK SWASTA ABDI NEGARA BINJAI IN ACADEMIC YEAR 2018/2019

The objective of this research was to get empirical evidence about the effect of word chain game on Student’s Vocabulary Mastery and to identify the students’ achievement in learning vocabulary through word chain game. This research used quantitative method. The sample of this research was the first grade of SMK Swasta Abdi Negara Binjai at academic year 2018/2019. With the total number 25 students from each class. The research conducted experiment in two different classes with word chain game was employed in an experimental class and other technique was employed in a controlled class. The data were collected through the achievement of pre-test and post-test from two classes. The result showed that teaching vocabularies by using word chain game was more effective than using conventional method. word chain game has served a positive influence. So, it can be concluded that word chain game has positive effect to the first grade students of SMK Swasta Abdi Negara Binjai in teaching vocabulary.
Kinetic mechanism and inhibitory study of protein arginine methyltransferase 1

Protein arginine methyltransferase 1 (PRMT1) is a key posttranslational modification enzyme that catalyzes the methylation of specific arginine residues in histone and nonhistone protein substrates, regulating diverse cellular processes such as transcriptional initiation, RNA splicing, DNA repair, and signal transduction. Recently the essential roles of PRMT1 in cancer and cardiovascular complications have intrigued much attention. Developing effective PRMT inhibitors therefore is of significant therapeutic value. The research on PRMT inhibitor development however is greatly hindered by poor understanding of the biochemical basis of protein arginine methylation and lack of effective assays for PRMT1 inhibitor screening. Herein, we report our effort in the kinetic mechanism study as well as the fluorescent probe and inhibitor development for PRMT1. New fluorescent reporters were designed and applied to perform single-step analysis of substrate binding and methylation of PRMT1. Using these reporters, we performed transient-state fluorescence measurements to dissect the rate constants along the PRMT1 catalytic coordinate. The data give evidence that the chemistry of
PHYLOGENETIC AND TAXONOMIC POSITION OF LEPOCINCLIS FUSCA COMB. NOV. (=EUGLENA FUSCA) (EUGLENACEAE): MORPHOLOGICAL AND MOLECULAR JUSTIFICATION 1

We studied the morphological diversity and analyzed the small subunit rDNA sequences of two taxa formerly known as Euglena spirogyra Ehr. and Euglena fusca (Klebs) Lemmermann. Our studies confirmed that the two should have the rank of a species, namely Lepocinclis spirogyroides (Ehr.) Marin et Melkonian and Lepocinclis fusca (Klebs) Kosmala et Zakryś comb. nov. (Euglenophyceae). We are defining new diagnostic features for these species, namely the size and the shape of the cells and the shape of the papillae, as well as designating epitypes for them.
Annual assessment of Echinococcus multilocularis surveillance reports submitted in 2019 in the context of Commission Delegated Regulation (EU) 2018/772

Abstract This report is part of the ‘Echinococcus multilocularis surveillance’ scientific reports which are presented annually by EFSA to the European Commission and are intended to assess the sampling strategy, data collection and detection methods used by Finland, Ireland, the United Kingdom (UK) and Norway in their respective surveillance programmes. The surveillance programmes of these four countries were evaluated by checking the information submitted by each of them and verifying that the technical requirements were fulfilled as laid down in Commission Delegated Regulation (EU) 2018/772 of 21 November 2017 supplementing Regulation (EU) No 576/2013 of the European Parliament and of the Council with regard to preventive health measures for the control of Echinococcus multilocularis infection in dogs, and repealing Delegated Regulation (EU) No 1152/2011. The information was divided into four different categories for assessment: the type and sensitivity of the detection method, the selection of the target population, the sampling strategy and the methodology. For each category, the main aspects that need to be considered in order to accomplish the technical requirements of the legislation were checked against compliance of several criteria. All the countries participating in this surveillance (Finland, the UK, Ireland and Norway) succeeded in the fulfilment of the technical legal requirements foreseen in Commission Delegated Regulation (EU) 2018/772 concerning these four different categories. Within the UK, Northern Ireland fulfils those requirements only when assuming a diagnostic test sensitivity value of 0.99, provided by the national reference laboratory, which is higher than the sensitivity value suggested by EFSA (conservative value of 0.78). None of the four countries recorded positive samples in the 12‐month reporting period. It should be noted that Malta did not have to report surveillance data in order to maintain its eligibility to continue applying preventive health measures for the control of E. multilocularis infection in dogs entering its territory, but to meet the conditions laid down in Article 4(1) of Commission Delegated Regulation (EU) 2018/772 including the submission of evidence to the European Commission of the absence of the red fox from the territory.
Use of Agaricus blazei and Lentinula edodes extracts for post-harvest control of gray mold in ‘Itália’ grape

En la proteccion de uva ‘Italia’ en postcosecha contra la Botrytis cinerea se evaluo in vivo los efectos directos e indirectos de los extractos acuosos de la seta Agaricus blazei y Lentinula edodes por el tratamiento de los racimos antes o despues de la inoculacion con el patogeno. Para ello se realizaron dos pruebas: 1) los racimos de uva fueron inoculados y, despues de 4 h, rociados con diferentes concentraciones de los extractos de basidiocarpos (0.0, 2.5, 5.0, 10.0, 20.0 o 40 , 0%), 2) racimos fueron o no, rociados con extractos de A. blazei (5,0%) 24, 48, 72 o 96 h antes de la inoculacion del hongo. Para la inoculacion, en cada racimo fueran heridos 10 bayas, haciendose un hueco de ±2 mm de profundidad, procediendo a continuacion, rociar la suspension de conidios (10 5 conidios mL -1 ). Despues del tratamiento, los grupos se mantuvieron a 25±1 o C/80-90% de humedad relativa y fue evaluado diariamente la incidencia y severidad de podredumbre. Lo efecto in vitro de extractos de A. blazei y L. edodes en el control del patogeno fue evaluado para determinar si estos agentes ejercen un efecto directo sobre el crecimiento micelial y la germinacion de conidias de B. cinerea . Los resultados mostraron que los extractos de A. blazei y L edodes no pudieran controlar la pudricion causada por B. cinerea en uva ‘Italia’, cuando se aplica antes o despues de la inoculacion del hongo. In vitro, los extractos de los basidiocarpos estimulan la germinacion de las esporas de B. cinerea en las concentraciones ensayadas; en relacion a lo crecimiento del micelio, L. edodes se ha retrasado, mientras que A. blazei estimulado.
Isolation, identification and characterization of 2,2-dichloropropionic acid utilizing bacteria

2,2-dichloropropionic acid (2,2-DCP) is an artificial halogenated compound used as herbicide. A bacterium able to utilize 2,2-DCP as sole carbon source was isolated from soil in Melaka rubber estate. The bacterium was identified as Labrys sp. strain Wy1 using bacterium’s 16S rRNA partial sequence. The cells doubling time was 34.6 hours in liquid minimal media supplied with 20 mM 2,2-DCP as sole carbon source. Utilization of 2,2-DCP was confirmed by detection of chloride ion released at 0.27 mM. An endophytic bacterium isolated from Axonopus compressus which was identified as Burkholderia cepacia strain Wy5 was also able to utilize 2,2-DCP as sole carbon source. The bacterium has cells doubling time 2.7 hours and chloride ion released was also detected at 47.28 ± 0.25 mM in minimal media contained 20 mM 2,2-DCP. Cell free extract (CFE) of Burkholderia cepacia Wy5 was further characterized due to its higher activity towards 2,2-DCP compared to Labrys sp. Wy1. Dehalogenase found in CFE of Burkholderia cepacia Wy5 has optimal enzyme specific activity at pH8 (0.83 µmol [Cl-] min-1 mg-1) and 40oC (0.78 µmol [Cl-] min-1 mg-1). The dehalogenase was also able to react with other a-haloalkanoic acid including monochloroacetic acid, DL-2-chloropropionic acid and DL-2-bromopropionic acid, but not 3-chloropropionic acid. “Group I” and “Group II” dehalogenase primers were used to amplify dehalogenase gene from both strains Wy1 and Wy5 but only Burkholderia cepacia Wy5 showed positive result. The dehalogenase gene fragment amplified was designated “deh-wy5” and subsequent analysis showed it belongs to Group I dehalogenase. Customized primers based on D,L-dex gene were designed to amplify complete sequence of deh-wy5 due to high similarity between partial sequence of deh-wy5 and D,L-dex. Complete sequence of deh-wy5 was eventually amplified and found to be identical (100%) to D,L-dex.
Implication de l'équilibre hormonal dans les mécanismes de maturation phénolique du raisin : étude du rôle de l'acide abscissique sur la composition et la biosynthèse des tanins de la pellicule

La maturation de la pellicule du raisin est un phenomene complexe se caracterisant par des changements structuraux importants et l’accumulation de composes d’interet œnologique, dont les tanins. Malgre leurs proprietes biologiques et organoleptiques essentielles pour la qualite du fruit et des vins, peu de travaux concernent leur metabolisme et les modes de regulation de leur biosynthese. Neanmoins, le statut hormonal de la baie a ete plusieurs fois cite comme mode de regulation possible. Apres avoir montre que l'equilibre hormonal, la maturation technologique et phenolique ainsi que l'accumulation des composes phenoliques pouvaient etre modules par l'apport exogene d'acide abscissique (ABA) quelques jours apres la nouaison, nos resultats ont mis en evidence les modes d'action de ce regulateur dans la biosynthese des tanins. Il agit d'une part sur l'activite des enzymes impliquees dans cette voie et l’expression des genes qui les codent et, d'autre part, sur la composition, la structure et la localisation des tanins. Quel que soit le cepage (Cabernet-Sauvignon, Semillon) ou le modele d'etude (plein champ, culture cellulaire in vitro), tous nos travaux s'accordent pour confirmer le role preponderant de l'ABA comme declencheur de la veraison et modulateur du metabolisme des tanins. Les courbes d'evolution des teneurs en tanins ainsi que les profils d'activite enzymatique et d'expression des genes ont permis d'emettre l'hypothese d'une biosynthese precoce de ces composes avant la formation de la baie. Cela a ete confirme par l'etude des tanins dans les fleurs et les baies juste nouees, demontrant le determinisme precoce de ce metabolisme.
A genetically modified nucleopolyhedrovirus: effectiveness and in vivo expression in the black cutworm, Agrotis ipsilon (Huf.) (Lepidoptera: Noctuidae).

Baculoviruses are orally infectious to insects and are considered as viral insecticides and safe for the environment. To enhance their speed-of-kill, these viruses were genetically engineered to express insect enzymes. Efficiency of a recombinant virus, Autographa californica multiple nucleopolyhedrovirus expressing Manduca sexta juvenile hormone esterase (AcMsJHE), and its wild type (AcMNPV) for killing 1 instar larvae of Agrotis ipsilon (Huf.) was analyzed. Mortality rate of A. ipsilon larvae was higher with recombinant virus than wild type by 1.4 times on the level of LC50; at the same time it was 16.7% faster in killing than its wild type. Effect of virus infection on larval weight indicated that 3 instar larvae infected with 1000 PIBs/larva were dramatically reduced in weight with either recombinant or wild type viruses, although the percentage of reduction was higher with recombinant than wild type virus. Isoelectric focusing analysis showed that there were expression of juvenile hormone esterase in vivo, and it is believed that it is related to gene expression. These results indicated that the genetically engineered baculovirus, AcMsJHE, could provide effective control compared with its wild type for A. ipsilon and further support the potential use of genetically engineered baculoviruses in insect pest control.
Predicted Lean Body Mass and Fat Mass: Novel Insights Into Obesity, Chronic Disease, and Mortality Research

Body mass index (BMI) is widely used measure of overall adiposity in epidemiological studies. However, BMI has a critical limitation that it cannot distinguish different body compartments, and therefore fails to capture the true harmful effect of fat mass and the potentially beneficial effect of lean body mass on diverse health outcomes. Unfortunately, assessing body composition in a large epidemiological study is infeasible because it requires expensive and sophisticated technologies. Thus, the independent role of lean body mass and fat mass on health outcomes remains largely underexplored. In this dissertation exercise, I attempted to offer a practical solution to directly assess body composition and examine their associations with major health outcomes. Chapter 1 developed anthropometric prediction equations using simple anthropometric measures to assess lean body mass, fat mass, and percent fat from the National Health and Nutrition Examination Survey 1999-2006. The equations were validated in the independent dataset and using obesity-related biomarkers, suggesting their potential application in epidemiological studies. Using the developed anthropometric equations, Chapter 2 examined the association of predicted lean body mass and fat mass with all-cause and cause-specific mortality in the Health Professional Follow-up Study, and found a strong positive association between predicted fat mass and mortality and a U-shaped association between predicted lean body mass and mortality in men. In particular, I found evidence that low lean body mass may account for the increased risk of mortality in the lower BMI range, suggesting that the ‘obesity paradox’ controversy may be explained by understanding the role of body composition, especially lean body mass, on mortality. Chapter 3 further examined the association between predicted fat mass and type 2 diabetes risk in men, and compared with BMI and other obesity indicators. The predicted fat mass consistently demonstrated the stronger association among all