Miracle-dz/UniFAR-FTUs huggingface dataset:
Museum specimens provide phylogenomic data to resolve relationships of sack‐bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae)

Mimallonidae, the sack‐bearer moths, are a family of predominantly Neotropical moths containing nearly 300 described species. Mimallonidae feed on over 40 host plant families and are found in a variety of environments, but phylogenetic relationships of species within the family have never been investigated. We sequenced 515 loci using anchored hybrid enrichment target capture on ethanol‐preserved and dried museum specimens, with dates of collection ranging from 1985 to 2017. We sampled 47 species, representing 32 of the 36 described mimallonid genera. By incorporating 19 dry museum specimens, and recovering an average of over 400 loci for each, we illustrate the utility of natural history collections in anchored hybrid enrichment‐based phylogenomics. Maximum likelihood and multi‐species coalescent analyses provide robust support for the recognition of six higher‐level groups within Mimallonidae, which we designate as subfamilies: Zaphantinae St Laurent & Kawahara subfam.n. , Aurorianinae St Laurent & Kawahara subfam.n. , Mimalloninae Burmeister, Lacosominae Dyar, Druenticinae St Laurent & Kawahara subfam.n. and Cicinninae Schaus stat.n. Our phylogenetic results also robustly support eight new tribes: Lacosominae: Trogopterini St Laurent & Kawahara tribe n. , Lacosomini Dyar stat.n. , Alheitini St Laurent & Kawahara tribe n. ; Druenticinae: Luramini St Laurent & Kawahara tribe n. , Druenticini St Laurent & Kawahara tribe n. ; Cicinninae: Bedosiini St Laurent & Kawahara tribe n. , Psychocampini St Laurent & Kawahara tribe n. , Cicinnini Schaus stat.n. Three new genera are also described based on our phylogenetic results: Herbinalla St Laurent & Kawahara, gen.n. , Ulaluma St Laurent & Kawahara, gen.n. , Bedosiallo St Laurent & Kawahara, gen.n. Naniteta Franclemont, syn.n. is a synonym of Lacosoma Grote. Six genera are paraphyletic, and in total 19 new combinations are proposed: Macessoga laxa comb.n. , Lacosoma elassa comb.n. , Thaelia anysia comb.n. , Thaelia subrubiginosa comb.n. , Herbinalla caudina comb.n. , Druentica brosica comb.n. , Ulaluma valva comb.n. , Cicinnus eminens comb.n. , Roelmana pluridiscata comb.n. , Roelmana laguerrei comb.n. , Psychocampa joanna comb.n. , Psychocampa unalca comb.n. , Psychocampa hamata comb.n. , Psychocampa marona comb.n. , Bedosiallo eugenia comb.n. , Bedosiallo forbesi comb.n. , Bedosiallo moengus comb.n. , Bedosiallo styx comb.n. and Bedosiallo sylvia comb.n. This study is the first to implement the LEP1 probe set on a comprehensive taxonomic dataset that includes many museum specimens, and our results demonstrate that museum specimens can be used in anchored hybrid enrichment studies. Importantly, these data produce a robust phylogeny that will serve as a foundation for future studies on mimallonid evolution, such as host plant relationships and biogeography.
Asteraceae in the northern Espinhaço Range, Brazil: richness, endemism and conservation

Floristic inventories focussing on the Espinhaço Range have revealed an extensive diversity for Asteraceae and emphasize the high degree of endemism of its species. is study aims to explore the species-rich Asteraceae through a oristic survey, and by identifying endemic records for the municipality of Morro do Chapéu, Bahia. Samples were collected during six eld trips in di erent phytophysiognomies and approximately 1,400 exsiccatae from the main herbaria collections were examined. Asteraceae in Morro do Chapéu is represented by 18 tribes, 72 genera and 119 species. Eupatorieae and Vernonieae are the most species rich tribes and currently comprise 30 and 28 species, respectively, representing 50 % of the local Asteraceae ora. Baccharis represents the richest genus with seven species, followed by Lepidaploa and Mikania with six species each. Species belonging to Eupatorieae, namely Acritopappus santosii, Acritopappus sp. nov., Lapidia apicifolia, Stylotrichium edmundoi, Scherya bahiensis, Trichogonia tombadorensis and, additionally, a new species of Vernonieae, Stilpnopappus sp. nov., are endemic to the municipality. We provide a checklist and identi cation key for the species, and report the occurrence of endemism and their importance for the biological conservation.
Dental shape variation of Neogene Pachyrukhinae (Mammalia, Notoungulata, Hegetotheriidae): systematics and evolutionary implications for the late Miocene Paedotherium species

Paedotherium was the last representative of the pachyrukhines (Notoungulata, Hegetotheriidae), a small rabbit- or caviomorph rodent-like clade, with hypsodont and simplified dentition. In contrast to the Pliocene Paedotherium species, the Miocene species are less known and mainly represented by teeth. Different systematic studies of Paedotherium based on the same set of subtle trait variations of the cheek teeth have arrived at different proposals. With the aim of testing the validity and analysing the morphological variation of Paedotherium species, and assessing the definition and diagnostic value of teeth traits, we performed a dual approach: a traditional qualitative study and exploratory geometric morphometric analyses of the upper and lower cheek teeth (both, partial and complete series). In addition, the configurations of cheek tooth shape were used as landmark characters, in combination with traditional characters, to perform a phylogenetic analysis. We propose the validity of the late Miocene P. borrelloi Zetti, and the assignment of north-western Argentinian representatives of Paedotherium to P. aff. minor. Paedotherium borrelloi is morphologically more similar and phylogenetically more closely related to the Pliocene P. bonaerense than to other Paedotherium species. Our results suggest that during the late Miocene the coexistence of two Paedotherium lineages was already established, whose main morphological differences persisted or even intensified in Pliocene representatives, supporting a more complex evolutionary scenario than previously believed.
Optimization of Feminization of Oreochromis niloticus L. by Oral Administration of Diethylstilbestrol (DES): The Effects of Stocking Density, Treatment Duration and Environment

The effects of the treatment environment (tank and hapa), duration of treatment, and stocking density of fry on the success of feminization protocols were investigated. In the first of two studies, the fry were hormone-treated in concrete tanks (clear water) and hapa-inpond environments for three durations: 10, 15 and 20 days. All groups were administered diethylstilbestrol at 1000 mg•kg-1 of feed and stocked at 1000 fry m-2 . In the second study, fry were treated in hapas at three stocking densities: 1000, 2500 and 5000 m-2 . A shorter treatment duration of 10 days was sufficient for effective feminization (>90% phenotypically female populations) of fry held in tanks, whereas 15-20 days was required for effective treatment in hapas. Stocking density greater than 1000 fry m-2 did not significantly increase the induction of feminization but significantly reduced the growth and survival rate of the fish. The optimum feminization protocol is feeding DES at 1000 mg•kg-1 to fry held at 1000 m-2 for a treatment duration of 10 days in tanks and 15-20 days in hapas.
Biochemical, histological and molecular effect of clomiphene citrate on thyroid gland in albino rats

The present study investigates the effect of infertility drugs, clomiphene citrate (CC) and humegon, on the function of vital body organs. This study accomplished using 60 albino rats separated to 30 males and 30 females, which are divided into three groups 20 animal (10 male, 10 female) for each group. The first group (CC) fed daily with (0.3mg) of clomiphene citrate by intragastric gavage for 30 days. The second group (CC+H) fed daily with 50mg of clomiphene citrate for 30 days, and then injected with (0.23 IU) of humegon for 10 days. The animals were killed after the scheduled time and the required tests have been conducted in the laboratories of college of science and Al-Ramady teaching Hospital. Biochemical, histological and molecular changes were induced in these animals when treated with CC or CC with humegon. The biochemical tests included thyroid hormone (T3, T4) and thyroid stimulating hormone (TSH). Treated animals showed a significant decrease in TSH hormone in both groups (CC, CC+H). CC group showed significant increase in T3, while (CC + H) group showed significant decrease in T3. T4 value drop significantly in treated animals (CC; CC + H) in contrast with control group. The light microscopic examination of thyroid gland showed increase in follicular number and size surrounded with flat epithelial cells and filled with a large amount of colloid material. The molecular study included the examination of gene expression of TG and TPO genes. The results showed decrease the expression of TG gene, while the expression of TPO gene increased in male (CC) group and decreased in male (CC+H) group, and decreased in female in both CC and CC+H groups.
Bacterial resistance and susceptibility to antimicrobial peptides and peptidomimetics

Stable peptidomimetics mimicking natural antimicrobial peptides (AMPs) have emerged as a promising class of potential novel antibiotics. In the present study, we aimed at determining whether the antibacterial activity of two a-peptide/b-peptoid peptidomimetics against a range of bacterial pathogens was affected by conditions mimicking in vivo settings. Their activity was enhanced to an unexpected degree in the presence of human blood plasma for thirteen pathogenic Gram-positive and Gram-negative bacteria. MIC values typically decreased 2to 16-fold in the presence of a human plasma concentration that alone did not damage the cell membrane. Hence, MIC and MBC data collected in these settings appear to represent a more appropriate basis for in vivo experiments preceding clinical trials. In fact, concentrations of peptidomimetics and peptide antibiotics (e.g. polymyxin B) required for in vivo treatments might be lower than traditionally deduced from MICs determined in laboratory media. Thus, antibiotics previously considered too toxic could be developed into usable last-resort drugs, due to ensuing lowered risk of side effects. In contrast, the activity of the compounds was significantly decreased in heat-inactivated plasma. We hypothesize that synergistic interactions with complement proteins and/or clotting factors most likely are involved. © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
Effects of growth-promoters on the productivity of Arundo donax L. (NileFiber™) as a purpose-grown biofuel feedstock in Nova Scotia1

Abstract: Arundo donax L. is a perennial grass species of Mediterranean origin. Its high biomass yield potential in its native climate has contributed to A. donax being an important biofuel feedstock crop. This study investigates the potential of A. donax as a purpose-grown biomass feedstock for advanced biofuel production in Nova Scotia. The effects of nine different growth-promoters (bacterial and fungal species, a seaweed extract, and a lipo-chitooligosaccharide) and two inoculation methods on A. donax biomass productivity were investigated through three experimental trials: one greenhouse and one field trial inoculated by a post-planting application of the supplements around the plant stem (soil drenching) and one greenhouse trial with inoculation by root soaking just prior to planting (2016). The survival of A. donax over the winter was also evaluated over two winter seasons (2014–2015 and 2015–2016). Penicillium bilaiae Chalab. illustrated the most consistent positive effects on biomass productivity across experimental trials and the plants’ higher phosphorus concentrations suggest that P. bilaiae was helping the plant access soil phosphorus. The root soaking inoculation method resulted in more positive effects in measured growth parameters compared with the soil drench method. Despite a very mild winter in one of the 2 yr tested, A. donax did not successfully overwinter in the field in either year. The presence of growth-promoters did not enhance biomass productivity substantially in the field. Moreover, due to its low overwintering survivability, this study suggests that A. donax is not well suited as a biomass feedstock crop in Nova Scotia.
Prevalence and leukotoxic profile of biofilm forming Staphylococcal strains isolated from a tertiary care hospital in Mysore

Background: Staphylococci causes chronic skin infections, device associated infections, ear infections, bone infections and post-operative infections. It secretes toxins such as Pantone-Valentine Leukocidin which prolongs the infection in hospitalized patients. Aim: To investigate the prevalence of Staphylococcal biofilm associated strains and to understand the correlation between biofilm production, multi-drug resistance and leukotoxicity. Methods: 280 Staphylococcal clinical isolates obtained from biofilm associated infections are collected from a tertiary care hospital in Mysore. They were screened for the production of biofilm, multi-drug resistance and leukotoxicity. They were also screened for icaAB and PVL luk F/S genes by PCR. Correlation between leuktoxicity and biofilm production was established by finding the leukotoxic potential of biofilm positive strains. Findings: Among 280 Staphylococcal clinical isolates, 34.6% showed biofilm production. Out of these isolates, 25% showed the presence of icaAB genes and 29% showed the presence of PVL luk F/S genes. Presence of icaAB gene was found to be higher in isolates obtained from implant associated infections. But the prevalence of PVL luk F/S genes was higher in chronic skin infections. 78% of the isolates displayed multi-drug resistance and methicillin resistant strains were comparitively high in device associated infections (77%). Strong biofilm producing PVL positive isolates from chronic skin infections showed increased leucotoxicity compared to PVL negative, weak and moderate biofilm producers. Conclusion: Statistical analysis revealed that PVL in association with biofilms can promote higher leukotoxicity compared to non biofilm producers. This study foresee the essential role of biofilm production, multi-drug resistance and toxins for the increased Staphylococcal pathogenesis.
The complete chloroplast genome of Angelica nitida

Abstract Angelica nitida is an endemic species in China. The complete chloroplast genome sequence of A. nitida was generated by de novo assembly using whole genome next generation sequencing. The complete chloroplast genome was 146,512bp in length and constructed out of four parts – a large single copy (LSC) region of 93,298bp, a small single copy (SSC) region of 18,068bp and two inverted repeat (IRa and IRb) regions of 17,573bp each. The genome annotation predicted a total of 113 genes, including 80 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that A. nitida is most closely related to Angelica dahurica.
Estimation of extractable protein in botanical fractions of legume and grass species

With a globally strong interest in bio-based products such as fuels and chemicals, a feasible source of protein for the industry with positive economic impacts could be from leaves. However, more knowledge is needed on how to improve the content of extractable protein. Grasses and legumes have a high content of protein with a favourable amino acid composition. The extractable true protein was estimated at two harvest dates in leaf and stem of the legume species white clover (Trifolium repens L.), red clover (Trifolium pratense L.) and lucerne (Medicago sativa L.) and the grass species perennial ryegrass (Lolium perenne L.) and tall fescue (Festuca arundinacea L.) using the Cornell Net Carbohydrate and Protein System. Extractable true protein was more concentrated in the leaf than in the stem of all the species. Easily extractable true protein in the leaf constituted 63%–68% and 54% of crude protein in legumes and grasses respectively. If the cell wall-bound true protein in the leaf can be extracted, concentration of extractable true protein may increase by 7%–14% and 21%–26% of crude protein in legume and grass respectively. Legume leaf could be superior to grass leaf for protein production in a biorefinery due to higher extractable true protein both on a mass basis and per hectare. In white clover leaf, a significant decline in concentration of extractable true protein with maturity was simultaneous with a substantial increase in extractable true protein per hectare.
Dried brewers grains in growing rabbits: nutritional value and effects on performance

Two assays were carried out to determine i) the nutritional value of dried brewers’ grains and ii) the effects of inclusion of this ingredient in growing rabbit diets on animal performance and economic performance of the breeding unit. In the digestibility assay, a total of 28 male rabbits were distributed in 2 groups differing in the diet offered to animals: a reference diet (35.51% neutral detergent fibre and 16.50% crude protein [CP]) and a test diet (60% of reference diet and 40% of dried brewers grains). The dried brewers’ grain contained 37.9% of CP and 3371 kcal digestible energy/kg dry matter. In the performance study, 80 weaned rabbits (40 males and 40 females) were allotted at 40 d of age to 5 groups differing in the inclusion levels of dried brewers’ grains (0, 7, 14, 21 and 28%) from 40 d to 90 d of age. Inclusion of dried brewers’ grains did not affect the live weight at 90 d, the feed intake between 40 d and 90 d or the dressing percentage of rabbits (on average 223 g, 96 g/d and 51.3%, respectively). There was no effect of diet on the meat quality parameters (69.5% water holding capacity, 25.6% cooking loss, 3.4 kg/cm 2 Warner-Bratzler shear force and pH 5.70) and inclusion levels above 14% reduced the feed cost (–18%; P
The use of loop AMP in detection of Shiga-toxin (stx) gene among escherichia coli from aquaculture and other environments

Considerable amount of cases of Shiga-toxin producing Escherichia coli (STEC) has been reported which result in the need to detect the presence of this harmful E. coli in food and environmental sources. Diseases caused by STEC are Hemolytic Uremic Syndrome (HUS) and Hemorrhagic Colitis (HC). A lot of samples being used in researches are mostly from retailed chain store or farms. The need to look into aquaculture and other environmental water is very crucial since there are very few researches done on aquaculture and other environmental water. In this study, samples were taken from Asajaya Empurau fish farm, Damai river stream, Permai beach and Permai rainforest resort. Enterobacteriaceae were successfully isolated using Eosin Methylene Blue agar and E. coli were successfully identified through a series of biochemical test. DNA was isolated using boiling method and Loop-AMP was conducted to detect toxigenic genes carried by E. coli. It was found that none of the isolates were carried stx 1 or stx 2 gene. However, multiplex-PCR detected three isolates which carried stx 1 and stx 2 gene. (GTG)s-PCR was carried out to detect the diversity among the isolates and was found that the genetic diversity among E. coli isolates were not high. Two major clusters with one of the cluster having 2 sub clusters were detected. Water quality for Damai downstream, Damai middle stream, Permai beach, Permai rainforest resort were classed at class lIB which is safe for water recreational activities with body contact.
Physiological roles of tryptophan in teleosts: current knowledge and perspectives for future studies

22 Tryptophan is an essential amino acid with a huge functional versatility, in addition to 23 its participation in protein synthesis. Because of the complexity of its metabolism, and 24 the functional relevance of several of its metabolites, it directly or indirectly participates 25 in a wide array of physiological pathways. This amino acid is a precursor for the 26 synthesis of the neurotransmitter/neuromodulator serotonin (5HT), the hormone melatonin 27 and kynurenine and related compounds such as kynurenic acid, quinolinic acid or niacin. 28 Because of this, it has a key role in the regulation of processes ranging from the 29 neuroendocrine to the immune system in vertebrates. In aquaculture, extensive research 30 has been performed to optimize the levels of tryptophan in the commercial diets for 31 many fish species. Providing adequate levels of this amino acid is critically important for 32 fish growth but also for fish welfare, since tryptophan has been shown to modulate fish 33 behaviour, stress responses, and antioxidant and immune systems. Currently available data 34 suggest a wide variation in tryptophan requirements of different species ranging 0.3-1.2 35 % of dietary protein level, but recent evidence also show that fish tryptophan 36 requirements can greatly vary depending on the rearing conditions of the fish. We also 37 review here the participation of tryptophan and related metabolites in different 38 physiological functions that are crucial for fish welfare. The review covers the 39 involvement of tryptophan in 5HT- and melatonin-mediated functions, along with its 40 participation in the regulation of the immune system and its role as an antioxidant and 41 antitoxic agent in fish. 42
Estimation of daily reference evapotranspiration by neuro computing techniques using limited data in a semi-arid environment

ABSTRACT In this paper, the daily reference evapotranspiration (ET0) for Bulawayo Goetz was estimated from climatic data using neuro computing techniques. The region lacks reliable weather data and experiences inconsistencies in the measuring process due to inadequate and obsolete measuring equipment. This paper aims to propose neuro computing techniques as an alternative methodology to estimating evapotranspiration. Firstly, ET0 was calculated using FAO-56 Penman-Monteith (PM) equation from available climatic data. Data was divided into training, testing and validation for neuro computing purposes. The study also investigated the effect of different normalisation techniques on neuro computing ET0 estimation accuracy. In another application, neuro-computing ET0 estimates were compared against those obtained using empirical methods and their calibrated versions. The Z-score normalisation technique for all data sets gave best results with a Multi-layer perceptron (5–5-1) model having RMSE, MAE and R2 values in the range 0.12–0.25 mm day−1, 0.08–0.15 mm day−1 and 0.94–0.99 respectively. There were no significant differences in ET0 estimation accuracy by neuro computing techniques due to normalisation technique. The Neuro computing techniques were superior to empirical methods in ET0 estimation for Bulawayo Goetz. The Neuro computing techniques are recommended for use in cases of limited climatic data at Bulawayo Goetz.
Wolves at the crossroad: Fission–fusion range biogeography in the Western Carpathians and Central Europe

Population fragmentation represents a leitmotif of conservation biology, but the impact of population reconnection is less well studied. The recent recolonization of large carnivores in Europe is a good model for studying this phenomenon. We aim to show novel data regarding distribution and population genetic structure of the grey wolf in Central Europe, a region considered a frequent crossroad and contact zone of different phylogeographic lineages, in a biogeographic context.