Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of measures of crowding, group size, and diversity

In ecology, diversity is often measured as the mean rarity of species in a community. In behavioral sciences and parasitology, mean crowding is the size of the group to which a typical individual belongs. In this paper, focusing mostly on the mathematical aspect, we demonstrate that diversity and crowding are closely related notions. We show that mean crowding can be transformed into diversity and vice versa. Based on this general equivalence rule, notions, relationships, and methods developed in one field can be adapted to the other one. In relation to crowding, we introduce the notion “effective number of groups” that corresponds to the “effective number of species” used in diversity studies. We define new aggregation indices that mirror evenness indices known from diversity theory. We also construct aggregation profiles and orderings of populations based on aggregation indices. By uniting the mathematical interpretation of the ecological notion of diversity and the ethological notion of typical group size (or crowding, in parasitology), our insight opens a new avenue of both theoretical and methodological research. This is exemplified here using real-life abundance data of avian parasites.
Postemergence Control and Glyphosate Tolerance of Doveweed (Murdannia nudiflora)

Doveweed is a problematic weed of lawns and sod production, as well as golf course roughs, fairways, and tees. End-user reports of selective POST control options are inconsistent and control is often short-lived. In addition, inconsistent control with non-selective herbicides such as glyphosate is common. The goals of this research were: (1) evaluate selective POST doveweed control options in ‘Tifway’ hybrid bermudagrass turf; (2) compare efficacy of single vs. sequential applications of selective POST herbicides; (3) quantify doveweed tolerance to glyphosate; and (4) quantify recovery of foliar applied glyphosate following treatment with a C14-glyphosate solution. A single application of sulfentrazone + metsulfuron; thiencarbazone + iodosulfuron + dicamba or 2,4-D + MCPP + dicamba + carfentrazone; or thiencarbazone + foramsulfuron + halosulfuron provided >60% control 2 weeks after initial treatment (WAIT). A second application of these treatments 3 WAIT improved control 6 WAIT. Two applications of 2,4-D + MCPP + dicamba + carfentrazone or thiencarbazone + foramsulfuron + halosulfuron provided ~80% control 6 WAIT. Doveweed was tolerant to glyphosate application up to 5.68 kg ae ha-1. Absorption of 14C-glyphosate was compared between doveweed with cuticle intact, doveweed with a disturbed cuticle, and smooth crabgrass. 14C-glyphosate recovery from the leaf surface of doveweed plants with an intact cuticle was 93.6%. In comparison, 14C-glyphosate recovery from the leaf surface of doveweed plants with a disrupted cuticle and the leaf surface of crabgrass plants was 79.1 and 70.5%, respectively. Nomenclature: Bromoxynil; carfentrazone; dicamba; foramsulfuron; glyphosate; halosulfuron; iodosulfuron; mecoprop; metsulfuron; MSMA; quinclorac; sulfentrazone; thiencarbazone; 2,4-D; doveweed, Murdannia nudiflora (L.) Brenan; smooth crabgrass, Digitaria ischaemum (Schreb.) Schreb. ex Muhl. ; ‘Tifway’ bermudagrass, Cynodon dactylon (L.) Pers. × Cynodon transvaalensis Burtt-Davy.
Biochemical And Histological Biomarkers Of Zn Pollution In Nile Tilapia, (Oreochromis niloticus).

Zinc (Zn) is an essential trace element for most organisms including fish, but above certain limit Zn will be toxic. In the present study the toxic effects of zinc (Zn) on the liver structure of Nile tilapia, Oreochromis niloticus were investigated. Additionally, we estimated different Zn concentration influence on the degree and nature of histological changes in the liver of exposed fish. Histological changes in the liver included hepatocyte degeneration, nuclear pycnosis, cellular swelling, and congestion of blood vessels were estimated. Also the activities of superoxide dismutase (SOD), glutathione (GSH) concentration and Malondialdehyde (MDA) formation were also determined. Glutathione reductase (GR), glutathione peroxidase (GPx) and Glutathione S-transferase (GST) activities were decreased in comparison with the control. Also hepatopancreatic injury was further confirmed by the inductions of two biochemical markers, glutamate-oxalacetate transaminase (GOT) and glutamate-pyruvate transaminase (GPT). Changes in SOD, CAT, GST, GPx, and GR activities indicated that Zn caused oxidative damage in O. niloticus. However, the significant changes in MDA content suggested that these enzymes played important roles in scavenging the oxidative free radicals induced by Zn in O. niloticus. The formation of oxygen free radicals might be a factor in the toxicity of
Molecular cloning and expression analysis of the highly conserved eukaryotic translation initiation factor 5A (eIF‐5A) from Antheraea pernyi

Eukaryotic initiation factor 5A (eIF‐5A) is a highly conserved protein found in all eukaryotic organisms that plays a key role in the regulation of many cellular processes including translation elongation, cell proliferation, programmed cell death, mRNA turnover and decay, and abiotic stress responses. In this study, the eIF‐5A gene from the Chinese oak silkworm Antheraea pernyi (Lepidoptera: Saturniidae) was characterized. The full‐length ApeIF‐5A cDNA of 1056 bp includes a 5′‐untranslated region (UTR) of 138 bp, a 3′‐UTR of 435 bp, and an open reading frame of 483 bp encoding a polypeptide of 160 amino acids. The deduced ApeIF‐5A protein shares 99 %, 82 %, and 72 % sequence identity with orthologs in Bombyx mori, Drosophila melanogaster and Homo sapiens, indicating high conservation during animal evolution. Real‐time quantitative reverse transcription PCR revealed expression in all four developmental stages and in all nine tissues tested, consistent with an important role in development. After challenge with lipopolysaccharide, the expression levels of ApeIF‐5A were markedly upregulated. Phylogenetic analysis of amino acid sequences revealed A. pernyi eIF‐5A was closely related to B. mori eIF‐5A, consistent with traditional classification and other molecular data. The results indicate the potential value of eIF‐5A in phylogenetic analysis.
Review Structure and morphogenesis of bacteriophage T4

Bacteriophage T4 is one of the most complex viruses. More than 40 different proteins form the mature virion, which consists of a protein shell encapsidating a 172-kbp double-stranded genomic DNA, a 'tail,' and fibers, attached to the distal end of the tail. The fibers and the tail carry the host cell recognition sensors and are re- quired for attachment of the phage to the cell surface. The
Effect of breed on food preference tests for dogs

This study aimed to determine the differences among four dog breeds as to food selectivity, choice agreement, and the number scores that best evaluate the degree of food choice agreement. For that, 115 food preference tests were analyzed. In each of those tests, 20 dogs were used (eight Beagles, four Labradors, four Siberian Huskies, and four Basset Hounds), in two evaluation days. The medians of intake difference between two diets were calculated for days one, two, and for both days to determine if there were selectivity difference among breeds. A randomized block experimental design was applied, and medians were submitted to the test of Friedmann. Food choice agreement and the degree of agreement among breeds were evaluated by the kappa index, using two different scales. Basset Hounds were the most selective when two different foods were offered, whereas Labradors were the least selective. When performing food preference tests, Siberian Huskies and Basset Hounds are recommended; however, they must be used individually to prevent that the results of one breed could neutralize those of the other breed. The use of a scale of food preference with three scores is recommended in order to obtain results that are more reliable.
Leucocyte Profiles and Family Size in Fledgling Greylag Geese (Anser Anser)

In precocial species, large brood sizes are usually considered as beneficial and individuals in larger broods grow faster and are more dominant compared to individuals in small broods. However, little is known whether family size also beneficially affects the offspring's physiology. In the present study, we investigated whether leucocyte profiles in fledgling Greylag Geese (Anser anser) are affected by (1) family size, (2) individual characteristics, i.e. age, body condition or sex, or (3) characteristics of the parents, i.e. previous reproductive success. From spring 2013 to autumn 2015, we collected blood samples from 100 juvenile Greylag Geese from 20 different pairs. From these samples we determined the absolute leucocyte number, an individual's differential blood cells count and an individual's haematocrit (HCT). The number of fledglings in a family and therefore the number of siblings a focal individual had, was positively related to the percentage of basophils, negatively to the heterophils/lymphocytes ratio (H/L), and tended to be negatively related to the percentage of monocytes and eosinophils in a sample. H/L ratio was negatively related to age in days and tended to be negatively related to body condition, whereas the percentage of basophils tended to be positively related to it. Absolute leucocyte number did not differ between individuals depending on family size. However, composition of different leucocyte types (basophils, eosinophils, H/L ratio) was modulated mostly by the social environment (family size) and not by the characteristics of the individual or the parents. In conclusion, even though we did not find clear evidence of a positive health effect, i.e. a better immune system, in fledgling Greylag Geese of large versus small families, our results suggest that family size modulates different components of the immune system hinting at its stress-reducing effect.
Raman tweezers in microfluidic systems for analysis and sorting of living cells

We have devised an analytical and sorting system combining optical trapping with Raman spectroscopy in microfluidic environment, dedicated to identification and sorting of biological objects, such as living cells of various unicellular organisms. Our main goal was to create a robust and universal platform for non-destructive and non-contact sorting of micro-objects based on their Raman spectral properties. This approach allowed us to collect spectra containing information about the chemical composition of the objects, such as the presence and composition of pigments, lipids, proteins, or nucleic acids, avoiding artificial chemical probes such as fluorescent markers. The non-destructive nature of this optical analysis and manipulation allowed us to separate individual living cells of our interest in a sterile environment and provided the possibility to cultivate the selected cells for further experiments. We used a mixture of polystyrene micro-particles and algal cells to test and demonstrate the function of our analytical and sorting system. The devised system could find its use in many medical, biotechnological, and biological applications.
Antibacterial Properties of Essential Oil of Heracleum persicum (Golpar) and Foodborne Pathogens

Background: Antimicrobial resistance is a serious health threat to human society. Antibiotics and preservatives are also the most common modalities to increase the shelf life of foods. Objectives: Antibacterial activity of essential oil of Heracleum persicum (Golpar) fruit against some of the main foodborne bacteria was determined. Materials and Methods: Antibacterial activity of essential oil was evaluated against the bacteria (Staphylococcus aureus, Escherichia coli, Salmonella typhi, Vibrio cholera, and Yersinia enterocolitica) using disc diffusion method. Broth micro-dilution method was used to determine their minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The data was expressed as mean and standard deviation and analyzed using analysis of variance (ANOVA) in SPSS software (P < 0.05). Results: Comparing with S. typhi strains (inhibition zone = 18 ± 0.46 mm), essential oil was found to be more effective against V. cholera strains (inhibition zone = 34 ± 0.2 mm). The MIC value (%) of the essential oil against V. cholera and S. typhi were 8 and 32 respectively. Essential oil of H. persicum (Golpar) showed a good antimicrobial activity against foodborne pathogens. Conclusion: The results revealed that the essential oil of H. persicum can be used in food preservation systems to inhibit the growth of V. cholera strains and improve food quality and safety.
Pathways of organic matter in an estuarine mangrove trophic network assessed by carbon and nitrogen stable isotopes

Carbon and nitrogen stable isotopes were used to describe an estuarine mangrove food web in New Caledonia, SW Pacific. Isotopic values were measured for all components of the ecosystem, from various organic matter (OM) sources to predators. Primary producers showed δ13C values from −32.29‰ (Bruguiera gymnorhiza) to −24.67‰ (mouth particulate organic matter), whereas δ15N values ranged from 1.48‰ (Avicennia marina) to 10.17‰ (Eichomia crassipes). Two potential organic matter sources, i.e. the mangrove species and E. crassipes, appeared not to be directly used by consumers although were indirectly entering the food web through particulate and sedimentary organic matter pools (POM and SOM). Overall, invertebrates showed C-depleted and N-depleted values compared with fish, highlighting their lower trophic level. The highest trophic levels in this estuarine mangrove were represented by carangids (δ15N of 11.24‰ for Caranx sp. and 10.81‰ for Carangoides fulvoguttatus) and gerrids (δ15N of 10.42‰ for Gerres filamentosus). Two main pathways of organic matter were identified from sources of OM to end-members, i.e. from estuarine POM and SOM toward gerrids and from marine POM towards carangids. The food chain comprised three or four trophic levels, depending on the pathway of organic matter. The position of some consumer species within the reconstructed food web might imply that an important source of organic matter was probably missing, i.e. microphytobenthos. Despite an obvious connection, the role of river inputs as potential drivers of mangrove food web dynamics appeared important only during the wet season.
Efficacy of feeding frequency, feeding rates and formulated diets on growth and survival of rohu Labeo rohita brood stock under intensive rearing

An experiment was conducted to assess the efficacy of formulated diets and feeding strategies in brood stock management of Labeo rohita (Ham.). The experiment comprised of three factors i.e., two supplementary feeds (D1, routine diet vs. D2, diet supplemented with vitamin-mineral mixture @ 2%), two feeding rates (R1, 3% BW vs. R2 4% BW) and two feeding frequencies (F1, once-a-day vs. F2, twice-a-day feeding. There were 8 treatments regimes viz., T1 (D1, R1, F1), T2 (D1, R1, F2), T3 (D1, R2, F1), T4 (D1, R2, F2), T5 (D2, R1, F1), T6 (D2, R1, F2), T7 (D2, R2, F1), and T8 (D2, R2, F2). The yearlings of 12-16 months age were stocked at a density of 1,000 kg ha-1 (16 fish/ pond), fed for a period of 8 months and the effect of different treatments on survival and growth of fish was recorded. During the culture period, 100% survival of fish was recorded in all the treatments. At the end of culture period, total body length and body weight was higher in T8 (P
Effect of Seed Size, Pre Sowing Treatment and Potting Mixture on the Seedling Growth of Parkia roxburghii G. Don Seeds

Tree bean, Parkia roxburghii G. Don, belongs to the family Leguminaceae and subfamily Mimosoidae, is a lesser known nutritious, leguminous tree which grows luxuriantly in North East India and South East Asia. It is also known as yongchak in Manipuri and Zongtan in Mizoram. It is distributed in India, Bangladesh, Burma (Myanmar), Thailand and the Malaysian region. The various plant parts like pods, seeds and flowers are consumed by the people of Mizoram, Manipur and Nagaland, raw or in various preparations such as salads and curries. It is a valued diet supplement and different edible parts of the plant are used medicinally. The pods are known to cure stomach disorders and regulate liver functions. The oil extract of the plant possesses insecticidal properties and the woods can be used as a source of paper pulp (Thangjam and Maibam, 2006). The tree bean being a fast-growing leguminous species with multiple uses is considered suitable for International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 8 (2017) pp. 629-638 Journal homepage: http://www.ijcmas. com
Gene regulation in the ventral midbrain of the developing chick embryo

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Polymorphism of microsatellite locus cams-336 in pepper varieties and closely related species

E.A. Snigir’ , O.N. Pyshnaya, E.Z. Kochieva , N.N. Ryzhova 1 Scientific center “Bioengineering”, RAS, Moscow 117312, Russia e-mail: ekochieva@yandex.ru 2 All-Russia Research and Development Institute of Vegetable Crops Selection and Seed Growing, RAAS, Moscow province, Odintsovo region, Lesnoy Gorodok 143080, Russia e-mail: pishnaya_o@mail.ru 3 M.V. Lomonosov Moscow State University, Moscow 119899, Russia
The complete mitochondrial DNA sequence of endemic honeybee Apis nuluensis (Insecta: Hymenoptera: Apidae) inhabiting Mount Kinabalu in Sabah Province, Borneo Island

Abstract The cavity-nesting honeybee Apis nuluensis inhabits only the highlands of Mount Kinabalu of Sabah, Borneo Island. The mitochondrial genome is a circular molecule of approximately 1.6 kb that includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.5%. The start codons ATC, ATG, and ATT were found in one, three, and nine genes, respectively, whereas the stop codon TAA was observed in all genes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies that predicted a sister taxon relationship between A. nuluensis and A. cerana.
Sexual dimorphism and sexual selection in cytheroidean ostracodes from the Late Cretaceous of the U.S. Coastal Plain

Abstract. Sexual dimorphism is common in many extant animals, but it is difficult to demonstrate in fossil species. Working with material from the Late Cretaceous of the U.S. Coastal Plain, we herein analyze sexual dimorphism in ostracodes from the superfamily Cytheroidea, a group whose extant members have males that are relatively more elongate than females. We digitized outlines of more than 6000 individual ostracode valves or carapaces, extracted size (area) and shape (length-to-height ratio) information, and used finite mixture models to assess hypotheses of sexual dimorphism. Male and female clusters can be discerned in nearly all populations with sufficient data, resulting in estimates of size and shape dimorphismfor 142 populations across 106 species; an additional nine samples are interpreted to consist only of females. Dimorphism patterns varied across taxa, especially for body size: males range from 30% larger to 20% smaller than females. Magnitudes of sexual dimorphism are generally stable within species across time and space; we can demonstrate substantial evolutionary changes in dimorphism in only one species, Haplocytheridea renfroensis. Several lines of evidence indicate that patterns of sexual dimorphism in these ostracodes reflect male investment in reproduction, suggesting that this study system has the potential to capture variation in sexual selection through the fossil record.
Influence of Degradable Polar Hydrophobic Ionic Polyurethanes and Cyclic Mechanical Strain on Vascular Smooth Muscle Cell Function and Phenotype

Vascular tissue engineering (VTE) with the use of polymeric scaffolds offers the potential to generate small-diameter (<6 mm) arteries. In this thesis, a degradable polar hydrophobic ionic (D-PHI) polyurethane porous scaffold was synthesized with the objective of demonstrating its potential application for VTE. D-PHI scaffold synthesis was optimized, maximizing isocyanate and methacrylate monomer conversion. Through the incorporation of a lysine-based crosslinker, scaffold mechanical properties and swelling were manipulated. Furthermore, D-PHI scaffolds demonstrated the ability to support the growth and adhesion of A10 vascular smooth muscle cells (VSMCs) during two weeks of culture. This study also investigated the effect of a double porogen approach on D-PHI scaffold properties, demonstrating an increase in the total scaffold porosity and pore interconnectivity. Specifically, it was found that the use of 10 wt% polyethylene glycol and 65 wt% sodium bicarbonate porogens resulted in a porous (79±3%) DPHI scaffold with the mechanical properties (elastic modulus=0.16±0.03 MPa, elongation-atyield=31±5%, and tensile strength=0.04±0.01 MPa) required to withstand the physiologicallyrelevant cyclic mechanical strain (CMS) that is experienced by VSMCs in vivo. Furthermore, the
Harnessing cell-to-cell variations to probe bacterial structure and biophysics

Harnessing cell-to-cell variations to probe bacterial structure and biophysics Julie A. Cass Chair of the Supervisory Committee: Professor Paul Wiggins Physics Department Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i)chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary timelapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.