Miracle-dz/UniFAR-FTUs huggingface dataset:
Landscape Context Affects Use of Restored Grasslands by Mammals in a Dynamic Agroecosystem

Abstract Habitat loss from agricultural expansion is one of the leading causes of endangerment for terrestrial vertebrates. Restoration programs such as the Conservation Reserve Program (CRP) and State Acres for Wildlife Enhancement (SAFE) were initiated in part to ameliorate grassland loss. Previous assessments of grassland restoration efforts have not focused on medium and large mammals because of sampling difficulties. More generally, few assessments of restoration outcomes consider effects of landscape context. We integrated camera trapping with occupancy modeling to assess mammal responses on 30 restored grassland sites in a dynamic agroecosystem in Illinois from 2014 to 2015. We tested hypotheses about the effects of local habitat conditions and landscape context on use of restored grasslands by four focal species: raccoons (Procyon lotor), eastern cottontails (Sylvilagus floridanus), coyotes (Canis latrans), and white-tailed deer (Odocoileus virginianus). Most species showed seasonal differences in grassland use that reflected the dynamic nature of the surrounding agricultural matrix (i.e., loss of hiding cover and supplemental food from crop harvesting). Landscape context also was important; species occurrences were related to grassland size and isolation, distances to human structures, and distances to nearest forest. The red fox (Vulpes vulpes) was not detected on any site, despite >5000 camera nights of sampling, indicating further research is needed to understand how competitive interactions with coyotes might limit the distribution of this smaller canid. Grasslands created by the CRP and SAFE programs provide habitat for medium and large mammals. Understanding how use of these habitats depends on landscape context can enable managers to strategically place new grasslands to either promote colonization by games species or to deter use by raccoons, an important predator of grassland bird nests.
Fate of β-Lactoglobulin, α-Lactalbumin, and Casein Proteins in Ultrafiltered Concentrated Milk after Ultra-high Temperature Processing

A simple apparatus has been developed for a new "microcube" encapsulation of fluid milk samples in their prefixation preparation for electron microscopy. The new 39 technique is based on making cubic wells in an agar gel layer, filling them with fluid milk samples, and sealing them with another agar gel layer. The individual wells are then separated by cutting from the initial block, providing . 5 mm walls around the samples. The embedded material (milk, buttermilk, yogurt, etc.) is fixed, dehydrated, and embedded in a resin for transmission electron microscopy. The procedure is simpler, more versatile, reliable, and reproducible than other encapsulation methods used to prepare similar food samples. Agar gel tubes used in the other methods have several disadvantages such as the need for manual dexterity of the experimenter to make them, and difficulty in sealing the filled capsules properly. Results obtained by the microcube procedure were compared with results obtained by two methods using agar gel tubes and also by mixing a warm agar sol with fluid food samples. This latter method is simpler than agar encapsulation, but shows agar strands in the micrographs of the milk samples. This is particularly undesirable when investigating, for example, intermicellar strands of gelled UHT-sterilized milk concentrates. Microcube encapsulation produces superior quality images of the fluid food structure. 1 Coauthored by M. C. Alleyne, D. J. McMahon, N. N. Youssef and S. Hekmet. Reprinted by permission of SMI Publications.
Shroom3 Localization and Apical Constriction during the Development of the Crystalline Lens in Mouse Embryos

ii Dedication . iv Acknowledgments. v Vita . vi List of Tables . ix List of Figures . x Chapter 1: Introduction . 1 Lens Anatomy . 1 Lens Development. 3 Apical Constriction and Shroom3 . 9 Chapter 2: Materials and Methods . 15 Animal Maintenance and Use . 15 Genotyping Protocol . 15 Polymerase Chain Reaction . 16 Mouse Embryo Embedding and Cryosectioning . 17 Immunofluorescence . 17 viii Modified Staining Procedure . 19 X-gal Staining Protocol . 20 Shape/Area Quantificiation . 21 Chapter 3: Results . 23 Shroom3 Localization with X-gal Staining . 23 Shroom3 Localization with Antibody Staining . 24 Apical Constriction . 28 Actin and Non-Muscle Myosin Localization . 32 Chapter 4: Conclusion and Discussion . 34 Localization of Shroom3 . 35 Cell Shape . 37 Actin-Myosin Complexes and Localization . 38 Potential Further Research . 40 Conclusion . 41 References . 42 Appendix A: Summary Schematic of Ocular Morphogenesis Pathways . 47
FLORISTIC COMPOSITION AND PLANT COMMUNITY TYPES IN MAZE NATIONAL PARK, SOUTHWEST ETHIOPIA

Ethiopia has established protected areas throughout the country and designated many areas of land in order to conserve the natural resources and biodiversity. Hence, identification of the diversity in these protected areas is essential for conservation and management purposes. The study was conducted with the objective to investigate and document the floristic composition and plant community types of Maze national park. A preferential sampling technique was used as a sampling design and a total of 65 plots with a size of 20 m x 20 m (400 m 2 ) were laid out for the woody species; a sub-plot of 5 m x 5 m was used at the center of each quadrat to assess the herbaceous species. A total of 144 species of vascular plants belonging to 109 genera and representing 37 families with, 40%, 37%, 17%, and 6% herbs, trees, shrubs and climbers respectively were recorded and identified. The most diverse family was Fabaceae followed by Poaceae, Euphorbiaceae, and Asteraceae. Combretum adenogonium, Rhus natalensis, Panicum maximum, are the most frequently occurring tree layer, shrub layer and herb layer plant species respectively. The output of TWINSPAN (Two-Way Indicator Species Analysis) has shown a cluster of 6 plant community types. The Analysis of Variance (ANOVA) has shown that there was statistically significant difference among plant communities in species richness, altitude, diversity and evenness at 95% confidence interval with a P value <0.05. Anthropogenic activities in Maze National Park were identified to exert high pressure on the vegetation and wildlife in the area resulting in the loss of biodiversity underpinned by troubled natural habitat. The most feasible recommendation to reverse the undesirable condition in the national park is to actively participate the local people in the conservation activities of the national park via ecotourism which is one form of sustainable tourism.
Metabolomics – an analytical strategy for identification of toxic mechanism of action

Blood plasma is a well-known body fluid often analyzed in studies on the effects of toxic compounds as physiological or chemical induced changes in the mammalian body are reflected in the plasma metabolome. Sample preparation prior to LC–MS based analysis of the plasma metabolome is a challenge as plasma contains compounds with very different properties. Besides, proteins, which usually are precipitated with organic solvent, phospholipids, are known to cause ion suppression in electrospray mass spectrometry. We have compared two different sample preparation techniques prior to LC-qTOF analysis of plasma samples: the first is protein precipitation; the second is protein precipitation followed by solid phase extraction with sub-fractionation into three sub-samples: a phospholipid, a lipid and a polar sub-fraction. Molecular feature extraction of the data files from LC-qTOF analysis of the samples revealed 1792 molecular features from the protein precipitation procedure. The protein precipitation followed by solid phase extraction procedure with three sub-samples gave a total of 4234 molecular features. This suggests that sub-sampling into polar, lipid and phospholipid fractions enables extraction of more metabolomic information as compared to protein precipitation alone. Chromatography showed good separation of the metabolites with little retention time drift (<1 s) and a mass accuracy below 3 ppm was observed. The performance of the method was investigated using plasma samples from rats administered the environmental pollutant perfluorononanoic acid. © 2014 Elsevier B.V. All rights reserved.
Calcium Propionate and Feather Meal as Glucogenic Precursors in Lactating Saanen Goats

An experiment was conducted to evaluate the effect of propionate and feather meal on milk production and milk chemical composition in goats in mid-lactation. Eighteen Saanen goats with an average body weight of 54.8±7.1 kg were were randomly assigned to three treatments having 6 animals each. Goats in the CON group received the control diet plus 40 mL of sugarcane molasses but no glycogenic precursors. Goats in the CAPS group received the control diet plus 15 g of salts of calcium propionate dissolved in 40 mL of sugarcane molasses per goat daily while goats in the FEME group received the control diet plus 106 g of feather meal dissolved in 40 mL of sugarcane molasses. Milk production was higher (P<0.01) in goats supplemented with salts of calcium propionate or feather meal compared to those in the control group. Supplemented goats showed higher blood glucose concentration than those in the CON. The results suggested that use of glucose precursors increased the production of milk in goats.
Sequence Analysis of the Internal Transcribed Spacer (ITS) Region of the Nuclear Ribosomal DNA (nrDNA) and Chloroplast trnL-F Region (cpDNA) of Some Lactuca L. (Asteraceae) Species in Turkey

In the current study, sequence analysis of some Turkish Lactuca L. species using nrITS DNA and trn L-F cpDNA sequences were performed to elucidate phylogenetic relationships among the taxa under study. Hieracium umbellatum was used as an outgroup. Different plant materials of Lactuca were collected from different parts of Turkey during excursions of summer 2013. Plant materials were either kept in silica gel or kept fresh for immediate DNA isolation. Both phenol chloroform-isoamyl alcohol method and commercial kits were used to extract genomic DNA for PCR reactions. ITS4 and ITS5A primers were utilized for ITS region, while trn Le and trn Lf primers were used to amplify the trn L-F region. Obtained DNA sequences were edited both manually and by using BioEdit 7.0. 4.1. Sequencing data were aligned via ClustalW program and analyzed using PAUP 4.01b10 software. nrITS sequences varied from 639 nucleotides to 735 nucleotides. Average nucleotide composition for nrITS was 22.1% (T), 27.9% (C), 23.2% (A) and 26.8% (G). It was also found that divergence values differed between 0.0000 and 0.10290. The trn L-F sequences varied from 296 nucleotides to 385 nucleotides. Average nucleotide composition of trn L-F sequences was 34.1% (T), 18.4% (C), 31.6% (A) and 16.0% (G). It was also found that divergence values differed between 0.0000 and 0.09674. Neighbour Joining (NJ) trees were constructed in order to identify the relationships among Lactuca species. Phylogenetic trees based on ITS region were found to be more useful than phylogenetic trees based on trn L-F region. After analysis of the results obtained, the data suggest that Lactuca contains 2 clades, with clade 1 having 2 subclades. These results support the prior phylogenetic studies on Lactuca and hence provide an up to date review of Turkish Lactuca species.
Side-necked Versus Hidden-necked: A Comparison of Shell Morphology Between Pleurodiran and Cryptodiran Turtles

Abstract: This study explores the potential morphological differences between pleurodiran and cryptodiran turtle shells. Pleurodires (Suborder Pleurodira), as suggested by their name, retract their heads into the shell by bending the neck to the side; this is different from cryptodires (Suborder Cryptodira), which withdraw their necks along a sagittal plane. Pleurodires also have evolved a unique pelvic morphology typified by two columnar pelvic elements sutured to both the carapace and plastron; in contrast, the pelvic girdle in cryptodires is loosely connected to the shell. These differences might put very different selective pressures on shell shape in these animals: The different head retraction strategies in the two groups could lead pleurodires to evolve wider and flatter anterior apertures while the differences in pelvic structure might permit the evolution of flatter carapaces (particularly in the posterior carapace) and narrower bridges as compared to cryptodires. We used 3D landmark data to characterize shell shape and used phylomorphospace plots to examine patterns of diversification within pleurodires. We also used analyses of variance to examine morphological differences between the shell shapes of cryptodire and pleurodire turtles. We found significant phylogenetic signal in pleurodire shell shape. Clustering of pleurodires in shape space primarily followed phylogeny, with all major clades occupying distinct regions of shell shape space. Pleurodires overlapped most strongly in shell shape with aquatic cryptodires, both swimmers (including sea turtles) and bottom-walkers (such as chelydrids). Future studies could seek additional support for the hypotheses, through mechanical tests of shell performance, that the mechanism of neck retraction or the presence of columnar pelvic girdles can influence the functional performance of turtle shells.
Modern Approach in Animal Breeding by Use of Advanced Molecular Genetic Techniques

Genetic progress for quantitative traits in livestock has been made by selection on phenotype or on Estimated Breeding Value derived from phenotype, have been very successful till date but, limitations like routinely recording of phenotypes which is a costly affair, sacrifice of animal for meat quality traits, recording in a particular sex for sex limited traits etc constraints the amount of genetic progress that can be made through conventional selection and breeding method. Molecular genetic techniques on the other hand are almost free from above mentioned limitations if applied with care. Molecular techniques like detection of DNA-level polymorphism by restriction fragment length polymorphism (RFLP), AFLP, SNP and a number of molecular markers are in frequent use to improve animal performance from one generation to next, both knock-out and/or over-expression of a gene have provided us a better understanding of a given gene and its relevance with respect to overall animal physiology, RNA interference (RNA I ) has been extensively leveraged to silent undesired disease specific genes in domestic animals and avian species, Mitochondrial DNA markers are particularly useful for studying evolutionary relationships among various taxa, DNA bar- coding based on mitochondrial genes has emerged as a powerful strategy for species identification. The origin and refinement of genetic markers clearly led to the development of innovative strategies against conventional breeding methods, which are slowly becoming obsolete.
Combined effects of dietary malic acid and Bacillus subtilis on growth, gut microbiota and blood parameters of Nile tilapia (Oreochromis niloticus)

The study investigated effect of dietary supplementation with malic acid, Bacillus subtilis and a mixture of the two (3 × 2 factorial trial) on Nile tilapia (Oreochromis niloticus) health. Treatment groups (T1–T6) were fed diets containing three levels of malic acid (0.0, 5.0 and 10.0 g/kg), each of which was supplemented with 0 and 1.1 × 105 cfu/g B. subtilis, respectively. Each treatment group was assigned randomly to triplicate groups of 35 fish (5.26 ± 0.06 g) in 18 tanks for 84 days. The results indicated that survival was higher in all dietary treatments as compared to the control fed fish. The highest values of FBW, WG and SGR (%), PER, PPV and ER were recorded in groups T4 and T6, which were fed diets supplemented with 5 g malic acid/kg and 1.1 × 105 cfu/g B. subtilis and 10 g malic acid/kg and 1.1 × 105 cfu/g B. subtilis, respectively. The best value of FCR was obtained in groups T4 and T6. The lowest total bacterial count in the gut and faeces was detected in fish from group T6. The values of haematocrit, haemoglobin, red blood cells, white blood cells, total protein, albumin and globulin were significantly higher (p < .05) in fish from groups T4 and T6 (diets supplemented with malic acid and B. subtilis). As compared to the control fed fish, te mixture of these substances are promising as immune enhancher in aquacultured fish.
Vitamin D Status and its Receptor Genes BsmI, FokI, ApaI, TaqI Polymorphism in Relation to Glucose Metabolism in Obese Iraqi Type 2 Diabetes Mellitus Patients

Background: Vitamin D receptor (VDR) gene polymorphisms are possibly involved in the development of type 2 diabetes mellitus (T2DM). However, the data to date have been inconclusive. Previous studies have suggested an influence of vitamin D receptor alleles on glucose metabolism and on susceptibility to type 2 diabetes mellitus in different ethnic populations through the action of vitamin D endocrine system which related with calcification and lipolysis, insulin secretion, and may be associated with many complicated disease including diabetes. To investigate the relationship between a single nucleotide polymorphism (SNP) of VDR gene and T2DM more studies had been done. However, different results have been found in different spots of the world. Therefore, more studies are needed to understand the variation in these results. This is the first study that shows the implication of the SNP of VDR gene in T2DM in Iraqi patients. Objective: To assess the correlation between serum 25(OH)D3 levels, and vitamin D receptor (VDR) polymorphisms (Fok1, BsmI, TaqI and ApaI), and glycemic control in obese T2DM Iraqi population, this study was performed. Materials and methods: 200 clinically diagnosed T2DM patients, distributed into three subgroups according to therapeutic pattern and 75 healthy controls from the Iraqi population were recruited in this study. The association between the VDR gene SNPs and the T2DM was determined using Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique, and genotype and allele frequencies were calculated between the T2DM and control groups. Results: No significant differences between mean age and the body mass index between both case and control groups were observed. According to current glycemic control consensus, results demonstrated only 20.5 percent of the T2DM patients met this target, which meant that 79.5 percent of the cases were suffering from poor glycemic control 25(OH)D3 levels were significantly lower in the T2DM patients than in the control group, being 17.49 ± 1.12 ng/ml and 31.26 ± 1.25 ng/ml, in the patient and control groups, respectively (p 20 < 30 ng/ml (chi-squared test, p<0.0001). The gene polymorphism analysis for T2DM showed that genotype and alleles frequencies for the VDR genes were in agreement with Hardy–Weinberg equilibrium in all cases. Conclusion: VDR gene polymorphism analysis revealed that neither genotypes nor alleles of VDR BsmI, ApaI showed a significant variation between T2DM patients and controls. In contrast‚ the FF genotype of VDR FokI and TT genotype of VDR TaqI showed a significant (P<0.0001) increase in T2DM patients in comparison to controls. FF and TT homozygotes had significantly higher baseline fasting glucose and HOMI-IR levels than f allele carriers. In addition, data found significantly elevated interlukin IL-6, TNF-α, IL -1β and decreased osteocalcin in association with the Taq1 polymorphism.
Influence of fire regime and other habitat factors on a eucalypt forest bird community in south-eastern Australia in the 1980s

Abstract. We investigated bird habitat relationships in extensive eucalypt forest in the Blue Mountains, New South Wales, in 1986–87, assessing the importance of fire regime variables compared with other habitat variables. Our study sites encompassed a wide range of postfire ages, fire frequencies and fire severity, but we found no major bird community differences corresponding to differences in fire regime. The more common forest bird species appeared well adapted to fire regime variation in the 1980s. Tree canopy height was a far greater influence, with more species and more birds in taller forests (interpreted as a result of higher soil fertility leading to higher productivity of bird foods and greater structural complexity in taller forests). Other trends were fewer birds where there was a rainforest understorey under the eucalypts (reflecting the general scarcity of rainforest birds in the Blue Mountains), and more birds where nectar-rich flowers were more abundant (reflecting the abundance of nectarivorous birds in the Blue Mountains, especially over winter). The climate has changed since the 1980s and fires threaten to become much more severe, extensive and frequent. How these changes will impact on forest birds, and what management responses are required, is a critical area for further study.
Application of Data Envelopment Analysis to Assess Performance Efficiency of Eight Faba Bean Varieties

Faba bean (Vicia faba L.) seeds are generally large which limits its adoption as cover crop and/or dual purpose cover crop/cash crop due to the high seed cost. The purpose of this study was to apply data envelopment analysis (DEA) by using seed size as input and fresh pod, fresh seed, and L-Dopa yield as output to evaluate efficiency of eight faba bean varieties. Eight faba bean varieties were evaluated in a 2-yr study. Four common methods of DEA were used for ranking faba bean varieties. Aquadulce and Delle Cascine out-yielded other varieties in both years. Averaged over 2 yr Aquadulce and Delle Cascine produced 16.15 and 16.27 Mg ha–¹fresh pod, respectively. However, Aquadulce had 21% lower seed size than Delle Cascine which significantly reduces the cost of production. L-Dopa yield ranged from 4 kg ha–¹ in Sweet Lorane to 46 kg ha–¹ in Aquadulce. Although no significant difference was found in fresh pod yield and fresh seed yield of Aquadulce and Delle Cascine, Aquadulce ranked first in both years while Delle Cascine ranked fourth in 2015 and third in 2016 due to its larger seed size and lower L-Dopa. Bell bean and Sweet Lorane had the smallest seed size yet their efficiency ranked last due to their low fresh pod yield, fresh seed yield, and L-Dopa yield. Results revealed that DEA could successfully use multiple traits in a single mathematical model without the need for the specification of tradeoffs among multiple measurements.
AHP METHOD IN THE FUNCTION OF LOGISTIC IN DEVELOPMENT OF SMART CITIES MODEL

A growing number of challenges that cities in the 21st century are faced, leads to the need for a new model of urban development. At the core of successful urban transformation stands the application of criteria for the necessary interventions and formation of cities in a "smarter" way, which will provide people adequate conditions for living while enhancing sustainable development in all areas. The papersubject is ranking the various criteria in the field of management, economics, livability, mobility, putting at the center people and their environment, in planning the "smart cities" development.Multi-criteria analysis is a good framework for stucturing steps in planning the smart cities. The aim is to provide decision-makers to rank the alternatives in order to find optimal solution using AHP and fuzzy AHP methods.