Miracle-dz/UniFAR-FTUs huggingface dataset:
Species of Antarctoscyphus Peña Cantero, García Carrascosa and Vervoort, 1997 (Cnidaria: Hydrozoa: Symplectoscyphidae) collected by US Antarctic expeditions: biogeographic implications

ABSTRACT Antarctoscyphus is one of the most characteristic genera of Antarctic benthic hydroids, with nine of the 10 known species considered to be endemic to the Antarctic; only Antarctoscyphus elongatus is also present in the sub-Antarctic region of Kerguelen. Accordingly, the genus was considered to have an Antarctic–Kerguelen distribution. Here we present the results of the study of the species of Antarctoscyphus collected from different Antarctic areas and from the Magellan region, during several expeditions under the United States Antarctic Research Program between 1958 and 1986. A scanning electron microscopy survey of all known species of the genus was carried out. Eight of the 10 known species of Antarctoscyphus were found in the collection, with A. spiralis and A. elongatus being the most frequently found species, whereas A. biformis, A. fragilis and A. gruzovi were found only once. The type material of A. biformis was reviewed and re-described. This study represents the second records for A. biformis and A. fragilis. The new records allow updating of the biogeographic knowledge on the distribution of several species: A. mawsoni, so far considered endemic to East Antarctica, and A. asymmetricus, considered endemic to West Antarctica, are here considered to have a Circum-Antarctic distribution. Additionally, A. fragilis, previously considered endemic to the Weddell Sea, is now considered to have a West Antarctic–Patagonian distribution, as it was recorded off the Pacific Magellan region. The records gathered here allow us to change the distribution pattern of the genus from Antarctic–Kerguelen to Pan-Antarctic. The study has allowed us to increase the known bathymetric range for some species, some reaching much deeper waters than previously known. Hence, A. fragilis, A. grandis and A. mawsoni, hitherto considered shelf species, are reported from bathyal bottoms of the continental slope. A general discussion on the bathymetric and geographic distribution of all known species is included. www.zoobank.org/urn:lsid:zoobank.org:pub:1C7ED3F2-3FF1-4C5C-85BB-FAAF557AC2ED
Metabolic costs of hybridization in Newts

Abstract. Heterospecific hybrids often suffer from a lowered fitness relative to parental species. Contextdependent intrinsic costs of hybridization are partially due to a malfunction in cell biochemical machinery that affects metabolic rates at the organismal level. This study examines whether heterospecific hybridization influences the metabolic costs of maintenance in F1 hybrids between closely related newts, Triturus carnifex and T. dobrogicus. When controlled for body size, oxygen consumption in hybrid newts was 59–76 % higher than in the parental species. This suggests that high standard metabolic rates in hybrids may contribute to the costs of hybridization in newts.
The effect of thyme (Thymus caucasicus) ethanol extract on Varroa mite (Varroa destructor), an ectoparasite mite of Apis mellifera meda (Hym: Apidae)

Chemical control of the Varroa mite ( Varroa destructor ), which is one of the most important pests of honey bees, is practiced on a worldwide scale. However, because of abundant use of different acaricides, the mites have become resistant to many of them. We chose to apply non-synthetic chemicals for control of Varroa mites by using thyme ( Thymus caucasicus ) ethanol extract on honey bees. In September-October 2013, we collected wild thyme growing in Kurdistan mountains, ground it, and its ethanol extract was made by using 95% ethylic alcohol. We used a randomized complete design with ten treatments of different concentrations of ethanol extract of thyme as a statistical model and one control with pure 95% ethanol with four replications. The interior temperature of the brood chamber was measured to be 30 ± 1°C, and the ambient temperature surrounding them was 33 ± 2°C. We sprayed the extracted thyme solution on honey bees and counted the number of dead mites by picking them out from the bottom board of each hive at every 12 h, 24 h, and 48 h intervals after spraying. The results showed that the use of the thyme extract influenced significantly the percentage of mortality of dead mites in the extract-sprayed treatment and the control treatment. The percentage of mortality of the honey bees in control hives and the honey bees treated by thyme ethanol extract did not have a significant difference. Results of our experiment using ethanol extract of thyme showed that its use in hives was safe without a high risk of mortality for honey bees.
Serum Nesfatin-1 Levels in Experimentally-Induced Polycystic Ovary in Lean and Obese Albino Rats = مستويات النسفاتين-1 في مصل دم الجرذان البيضاء النحيلة والسمينة المحدث بها تجريبيا تكيس المبيض

Background: Polycystic ovary syndrome (PCOS) is a very common problem in reproductive age; Obesity and insulin resistance (IR) play critical roles in its etiology. Limited studies have investigated the link between nesfatin-1 levels and PCOS. However, these studies are controversial. Objectives: This study aimed to evaluate possible changes of serum nesfatin-1 Levels in letrozole-induced PCOS in lean and obese rats, and its association with some hormonal and metabolic parameters. Material and methods: Forty two young virgin healthy female albino rats were used. Rats were divided into three equal groups: Group I (control), group II (lean PCOS) rats fed ordinary rodent diet for 9 weeks, and then received a daily single dose of letrozole orally (0.5 mg/kg/BW) for 21 days. Group III (obese PCOS) rats fed high fat diet for 9 weeks, and then received a daily single dose of letrozole (0.5 mg/kg/BW) orally for 21 consecutive days. At the end of experiment, serum levels of Nesfatin-1, free testosterone, LH, FSH, estradiol, progesterone, glucose and insulin were detected. BMI and HOMA-IR were calculated. Ovarian histopathology was done. Results: In obese polycystic ovary group, serum nesfatin-1 level was significantly lower and accompanied by significant hyperinsulinemia, hyperglycemia, insulin resistance, and high BMI when compared to both of lean polycystic and control groups. Moreover, serum nesfatin-1 level significantly negative correlated with serum insulin levels, serum glucose levels, HOMA-IR, and BMI, but correlated positively with LH levels. In lean polycystic group, serum nesfatin-1 level did not significantly change, when compared to control group, In addition, there was an absence of any significant change in serum insulin levels, serum glucose levels, HOMA-IR, or BMI. Conclusion: Serum nesfatin-1 level seemed to be related to several metabolic syndrome parameters rather than to polycystic ovary syndrome. Our findings raised a possibility that nesfatin-1 level played some role in PCOS. Therefore, larger scale and more detailed molecular studies in vivo and vitro on ovarian function are needed.
Local adaptation and sexual selection drive intra-island diversification in a songbird lineage: differential divergence in autosomes and sex chromosomes

Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to test the relative importance of two major evolutionary mechanisms, adaptation to local ecological conditions by natural selection, or mechanisms of reproductive isolation such as assortative mating mediated by sexually selected mating signals or post-zygotic incompatibilities. Whereas local adaptation is expected to affect many loci throughout the genome, traits acting as mating signals are expected to be located on sex chromosomes and have a simple genetic basis. We used genome-wide markers to test these predictions in Reunion Island’s gray-white eye (Zosterops borbonicus), which has recently diversified into five distinct plumage forms. Two of them correspond to a polymorphic highland population that is separated by a steep ecological gradient from three distinct lowland forms that show narrow contact zones in plumage color traits, yet no association with environmental variables. An analysis of population structure using genome-wide SNP loci revealed two major clades corresponding to highland and lowland forms, respectively, with the latter separated further into three independent lineages corresponding to plumage forms. Coalescent tests of alternative demographic scenarios provided support for divergence of highland and lowland lineages with an intensification of gene flow in the last 60,000 years. Landscapes of genomic variation revealed that signatures of selection associated with elevation are found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. A gene ontology analysis identified TYRP1, a Z-linked color gene, as a likely candidate locus underlying color variation among lowland forms. Our results are consistent with the role of natural selection in driving the divergence of locally adapted highland populations, and the role of sexual selection in differentiating lowland forms through reproductive isolation mechanisms, showing that both modes of lineage divergence can take place at very small geographic scales in birds.
Prebiotic attributes of inulin enriched biscuits: sensory and nutritional aspects

The study aims to develop an enriched functional biscuit with prebiotic inulin and to understand the impact of addition of different levels of inulin on sensory and nutritional properties of the biscuits. A standard biscuit and three variations namely P1, P2 and P3 were formulated and standardized through test and trial method to get consistent final products. Inulin was added replacing fat in the standard-0%, P1- 100% P2-62% and P3-37%. The biscuits were evaluated by 15 panel members for sensory attributes i.e. appearance, colour, flavour, taste, texture and overall acceptability. Nutrients analysis for energy, carbohydrate, protein, fat, fibre, free fatty acid and total antioxidant activity were done using standard procedures. Addition of inulin can give rise to products with different rheological behaviour and sensory characteristics. P2 (62% fat replaced) was acceptable with a high score for overall acceptability (7.45±0.39). Fat content was found to be highest in P3 (25.88gm). The inulin content in P1, P2 and P3 was 25.7gm, 34.5gm and 19.1 gm respectively. Antioxidant activity was also observed in all the biscuits and activity was highest in P2 (229.54μg). The partial replacement of fat by inulin in the production of biscuits was effective in reducing the fat content in the final product. A significant difference in taste (p=0.004) and texture (p=0.048) and was observed among the biscuit variations. The formulation P2, with 62 % fat replacement by inulin, presented similar results to the standard product, being the formulation with the greatest sensory acceptance and physical characteristics.
Detection of Phenotypic Network Signatures in Cultured Neuronal Networks

Neuronal networks grown in vitro provide a convenient method of assessing complex electrophysiological activity of interconnected neurons. This thesis uses dissociated neuronal cultures grown on Multielectrode Arrays (MEAs) to capture the electrical signals from neuronal networks comprised of thousands of neurons. The higher resolution and long-term extracellular recording capabilities that MEAs offer deems it to be a useful technology for assessing spatiotemporal patterns in neuronal networks. Though the MEA technology is advancing rapidly, so that substantial amounts of data are being generated with each recording episode, the data analysis and knowledge discovery pipeline is still at a stage where only a fraction of the information contained in these neuronal activity patterns are being used. This thesis investigates features that characterize different aspects of neuronal activity ranging from action potentials and network-wide bursting to local field potentials. It utilizes existing feature extraction methods as well as novel methods that have been optimized for dissociated cortical cultures. In particular, adaptive detection methods are introduced that can be used for both spontaneous activity of neuronal networks as well as for activity patterns that are invoked by the application of external compounds. By using the extracted network features, "network signatures" are created for typical responses evoked by different neuromodulatory compounds. "Network signatures", refer to typical changes in a set of measured parameters in a neuronal network, which are associated with a drug. Through the comparison of network signatures, this thesis derives insights into the mechanisms of action (MOA) of conolidine; an alkaloid with analgesic properties with unknown MOA. Led by its similarity to conolidine’s network signature, a MOA of cannabidiol, which is a cannabinoid derived from cannabis sativa,
Cross-regulation between CDK and MAPK control cellular fate

Commitment to a new cell cycle is controlled by a number of cellular signals. Mitogen-Activated Protein Kinase pathways, which transduce multiple extracellular cues, have been shown to be interconnected with the cell cycle. Using budding yeast as a model system, we have quantified in hundreds of live single cells the interplay between the MAPK regulating the mating response and the Cyclin-Dependent Kinase controlling cell cycle progression. Different patterns of MAPK activity dynamics could be identified by clustering cells based on their CDK activity, denoting the tight relationship between these two cellular signals. In mating mixtures, we have verified that the interplay between CDK and MAPK activities allows cells to select their fate, preventing them from being blocked in an undesirable cellular program.
Variation in Expression of Sub 1 Gene and Association with Submergence Stress Related Traits in Advance Rice ( Oryza sativa L.) Genotypes as a Tool of Climate Change Adaptation

Floods have now become most detrimental natural catastrophe worldwide due to radical climatic fluxes. Therefore, there is a dire necessity to develop a high yielding rice lines to deal with this scenario. For this purpose, a large scale experiment was conducted including one hundred and fifteen (115) rice genotypes having SUB1 gene imported from International Rice Research Institute (IRRI) Philippines, six local cultivars/approved varieties and three high yielding rice varieties i.e. Sabitri, IR6 and NSICRC222 being used as potential varieties in different countries of Asia as susceptible check and IR64-SUB1 as tolerant check. The genotypic screening was performed using two PCR-based DNA markers i.e. ART5 and SC3. Phenotypic screening was conducted in a natural pond to assess the interaction of SUB1 gene in natural stagnant flood water as well as the suitability of introgression of SUB1 gene into approved varieties and elite rice lines. The genotypes were assessed in terms of plant survival percentage, submergence tolerance index, physical condition, stem elongation, number of grains per panicle, thousand grain weight, grain yields and deviations in these traits after submergence stress. The PCR results suggested that both the primers ART5 and SC3 may be used as potential PCR-based markers for molecular screening of rice genotypes for SUB1 QTL. Furthermore, it confirmed the presence of SUB1 gene in all the lines imported from IRRI, while it was absent in all the local cultivars studied. All the genotypes with submergence tolerant gene (SUB1) showed significantly greater tolerance level in submergence stress of 14 days, as compared to other local cultivars/varieties, authenticating the effectiveness of SUB1QTL in conferring submergence tolerance. Significantly different performances of all the SUB1 genotypes in terms of all the studied traits indicate high Genotypic and Genotypic Environment Interaction (GEI) of SUB1QTL. Employment of SUB1 lines such as R105479:149-18, IR64-SUB1 and Rl05469:81-22-3 in breeding programs for developing flood tolerant rice varieties might further upsurge rice yields in flash flood areas. Correlation analysis revealed that plant survival percentage after submergence, reduced stem elongation during submergence and submergence tolerance index are very important traits for developing submergence tolerant lines.
Peptide-Binding Groove Contraction Linked to the Lack of T Cell Response: Using Complex Structure and Energy To Identify Neoantigens

Using personalized peptide vaccines (PPVs) to target tumor-specific nonself-antigens (neoantigens) is a promising approach to cancer treatment. However, the development of PPVs is hindered by the challenge of identifying tumor-specific neoantigens, in part because current in silico methods for identifying such neoantigens have limited effectiveness. In this article, we report the results of molecular dynamics simulations of 12 oligopeptides bound with an HLA, revealing a previously unrecognized association between the inability of an oligopeptide to elicit a T cell response and the contraction of the peptide-binding groove upon binding of the oligopeptide to the HLA. Our conformational analysis showed that this association was due to incompatibility at the interface between the contracted groove and its αβ–T cell Ag receptor. This structural demonstration that having the capability to bind HLA does not guarantee immunogenicity prompted us to develop an atom-based method (SEFF12MC) to predict immunogenicity through using the structure and energy of a peptide·HLA complex to assess the propensity of the complex for further complexation with its TCR. In predicting the immunogenicities of the 12 oligopeptides, SEFF12MC achieved a 100% success rate, compared with success rates of 25–50% for 11 publicly available residue-based methods including NetMHC-4.0. Although further validation and refinements of SEFF12MC are required, our results suggest a need to develop in silico methods that assess peptide characteristics beyond their capability to form stable binary complexes with HLAs to help remove hurdles in using the patient tumor DNA information to develop PPVs for personalized cancer immunotherapy.
Neural evidence for representationally specific prediction in language processing

Previous studies suggest that people generate predictions during language comprehension at multiple linguistic levels. It has been hypothesized that, under some circumstances, this can result in the pre-activation of specific lexico-semantic representations. We asked whether such representationally specific semantic pre-activation can be detected in the brain ahead of encountering bottom-up input. We measured MEG activity as participants read highly constraining sentences in which the final word could be predicted. We found that both spatial and temporal patterns of the brain activity prior to the onset of this word were more similar when the same words were predicted than when different words were predicted. This pre-activation was transient and engaged a left inferior and medial temporal region. These results suggest that unique spatial patterns of neural activity associated with the pre-activation of distributed semantic representations can be detected prior to the appearance of new sensory input, and that the left inferior and medial temporal regions may play a role in temporally binding such representations, giving rise to specific lexico-semantic predictions.
Floristic Composition, Life-forms and Chorotypes of Al-Asabah region, Ash Shamayatayn District, Taiz Governorate, Yemen

The present study deals with the floristic composition of the flora, life forms and phytogeographical affinities in Al-Asabah region, Ash Shamayatayn district, Taiz governorate, Yemen, during the year 2013. In this research 34 families, 63 genera and 82 taxa were identified. Among them were 6 species of Pteridophyta, while the remaining 76 taxa belong to Angiospermae. The dicots are represented by 72 taxa, whereas the monocots are represented by 4 species. The largest of the families include: Acanthaceae, Asclepiadaceae, Asteraceae and Euphorbiaceae (7 species for each) and Fabaceae (6 species). The genera represented by the greatest number of species are Acacia and Heliotropium (4 species for both). It was also noted that the generic index is 1.30. The chief life forms include Chamaephytes (50%), Phanerophytes (20.73%) and Geophytes (12.20%). The Sudano-Zambezian element dominates and forms the major component of the floristic structure. Results also reveal that sixteen taxa (19.51%) are endemic, among them are five taxa (6.10%) which are endemic to Yemen alone, while the remaining (13.41%) are near endemic to the flora of Yemen.
Pervasive hybridizations in the history of wheat relatives

A comprehensive phylogenomic analysis reveals that the genomes of cultivated wheats result from multiple rounds of hybridization. Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought—Aegilops mutica, an overlooked wild species—instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.
Context dependent processing in the mouse olfactory bulb

Optimal behavioural strategies necessitate the ability to flexibly respond to sensory stimuli according to behavioural context. Contextual information can be defined as internally generated information that gives behavioural meaning to primary sensory stimuli, for example: hunger state, reward associations and other learned information. The olfactory bulb (OB) is the very first site of odour information processing, yet a large variety of contextual information has been described in its activity. To investigate the mechanistic basis of this, I used whole cell patch recordings from identified mitral and tufted cells in the olfactory bulb of the behaving mouse in vivo to measure how odour responses are shaped across rapid olfactory go/no-go learning episodes. While basic physiological properties do not differ between passively exposed and learning mice, I find that a variety of response changes occur specifically in the learning mouse within the very first sniff cycle. Mice acquire active sniffing behaviours during the odour stimulus across learning, a strategy associated with high motivation and fast reaction times. Responses can be tightly modulated on a trial by trial basis by the active sampling state of the mouse, though some inhibitory response changes occur independent of sniffing behaviour. Response changes due to active sampling appear to enhance both the discriminability and detectability of OB odour representation across the olfactory bulb, and exceed that predicted from feed-forward input alone, suggesting the involvement of top-down mechanisms. Response changes are highly correlated in tufted cells, but not mitral cells, indicating that mitral cell response changes may selectively increase discriminability of odourants. Altogether, active sampling overtly shapes odour responses on rapid timescales, likely enhancing odour representation to facilitate rapid olfactory behaviour. Finally, I explore how perception and coding for odour intensity remain robust despite variance in sniffing, and suggest that the olfactory bulb encodes sniffing parameters to allow sniff-independent perception of stimulus features. This dissertation thus begins to demonstrate the functional impact of active sampling on early sensory processing, and provides new perspectives on olfactory bulb function.