Miracle-dz/UniFAR-FTUs huggingface dataset:
BIOLOGICALLY INSPIRED VECTOR FIELDS TO GENERATE HAIR DIRECTIONS

This paper describes how biologically inspired vector fields can be used to partially automate the manual and time-consuming process of specifying hair directions. This approach replicates the consequence of stretching of skin from natural hair development process, in contrast to replicating the appearance of hair. The direction of each hair on the surface of an arbitrary 3D model is determined by interpolating the solution vector field that satisfies a set of user-defined constraints describing the stretching of skin. Results found that the generated hair directional pattern closely resembles that found naturally. Further investigation revealed that the presence of naturally occurring hair types and the varying distribution of hair directions induced by the calculated vector field enhanced the realism of hair coats generated using this approach. Aside from hair or fur, this approach can also be applied to hair-like masses such as grass, feathers, or scales.
Insights into Chibby's structural elements and their interplay in Wnt signaling protein-protein interactions

ii Co-Authorship Statement. iv Dedication . vi Acknowledgments. vii Table of Contents. viii List of Tables . xii List of Figures . xiii List of Abbreviations . xvi Chapter 1. 1 1 Introduction . 1 1.1 Introduction to Wnt Signaling . 1 1.2 Wnt/β-catenin signaling in human disease and therapeutic development . 5 1.3 Regulation of β-catenin in Wnt signaling. 7 1.4 The Wnt signaling antagonist Chibby. 8 1.5 Structural features and characterization of Cby. 13 1.6 Structure of β-catenin and modes of interaction with Wnt signaling components16 1.7 Structure, function and binding modes of 14-3-3 proteins . 19 1.8 The Cby antagonist TC-1. 23 1.9 Scope of thesis . 25 1.10 References. 28 Chapter 2. 36 2 Structural Analysis of the 14-3-3ζ/Chibby Interaction Involved in Wnt/β-catenin Signaling . 36 2.1 Introduction. 36 2.2 Materials and Methods. 40 ix 2.2.1 Expression and Purification of 14-3-3ζ . 40 2.2.2 Peptide Synthesis . 41 2.2.3 Crystallization and Structure Determination . 41 2.2.4 NMR Experiments . 42 2.2.5 Isothermal Titration Calorimetry (ITC) Experiments. 42 2.2.6 Accession Numbers . 43 2.3 Results. 44 2.3.1 Phosphorylation of serine 20 on Cby is critical for its binding to 14-3-3ζ . 44 2.3.2 Flanking residues of the consensus 14-3-3 binding motif play important roles in the Cby/14-3-3ζ association. 45 2.3. 3 Molecular basis of the interaction between 14-3-3ζ and the non-canonical mode II binding-motif of Cby. 49 2.3. 4 An S22P mutation to Cby enhances its interaction to 14-3-3ζ . 52 2.3. 5 Probe for secondary interactions between 14-3-3ζ and Cby using NMR spectroscopy. 56 2.3. 6 Mapping the Cby peptides binding regions on 14-3-3ζΔC12 . 62 2.3. 7 Cby binds to all human 14-3-3 isoforms. 68 2.3. 8 14-3-3 phosphomimetic mutations fail to abrogate the 14-3-3/Cby 18-mer interaction . 68 2.4 Discussion . 72 2.5 Acknowledgements. 78 2.6 References. 79 Chapter 3. 84 3 Conformational characterization of the intrinsically disordered protein Chibby: Interplay between structural elements in target recognition . 84 3.1 Introduction. 84 3.2 Materials and Methods. 87
Population Polymorphism Study Among Tulsi (Ocimum sp.) Ecotypes In Assam, India Using Morphological And Biochemical Parameters

The genus Ocimum, (family Lamiaceae ) , displays great variability. Prevalence of cross pollination, polyploidy and interspecific hybridization has complicated its taxonomy, making its systematic study difficult. This study investigated the morphological and biochemical variability among 18 ecotypes collected from different parts of the Assam state, India. Considerable diversity was found using all the approaches. The quantitative morphological parameters showed wide variability, not always co-relating with their geographical distances. The Euclidean distance ranged between 6.06 (between the closest accessions) and 59.00 (between the most distant accessions). Phylogenetic analysis divided the accessions into two major clusters sharing approx. 76% identity, and a minor cluster (with three accessions) sharing only approx. 65% identity with the other two. A great deal of diversity was found in the qualitative characters too; that divided the ecotypes into two to five groups. The biochemical characters also revealed wide polymorphism; the distance varied from 1.690 to 58.574. Similar to the morphological characters, the biochemical parameters too did not always correlate with geographical distances. The phylogenetic mapping divided the accessions into two major clusters, sharing approx. 80% similarity. Further work will be needed to correlate the distance based on the morphological and the biochemical characters.
Causes and Consequences of Hybrid Incompatibilities in Arabidopsis thaliana

two seemingly different phenotypes are linked genetically. One of the genes that I identified to be involved in this hybrid incompatibility is a microtubule-associated protein. This family of proteins has never before been associated with the phenotypes that I describe. Therefore, further study of this incompatibility is expected to detail new pathways regulating shoot architecture and anthocyanin accumulation.
Primulina yingdeensis, a new species from Guangdong, China, and P. rosulata, a new combination (Gesneriaceae), based on morphological and molecular evidence

Abstract: Based on morphological and molecular data, a new species of Gesneriaceae, Primulina yingdeensis, from Guangdong, China, is described and illustrated. It is morphologically most similar to P. hochiensis and P. hochiensis var. rosulata, but the three taxa differ from each other in discrete characters. They share yellow honey guides, but in the new species these are strongly ridged and with glands. At the same time, also based on morphological and molecular data, P. hochiensis var. rosulata is raised to the rank of species, as P. rosulata. Citation: Ning Z. -L. , Pan B. , Wen F. , Kang M. & Zhuang X. -Y. 2016: Primulina yingdeensis, a new species from Guangdong, China, and P. rosulata, a new combination (Gesneriaceae), based on morphological and molecular evidence. — Willdenowia 46: 399–409. doi: http://dx.doi. org/10.3372/wi.46. 46308 Version of record first published online on 15 November 2016 ahead of inclusion in December 2016 issue.
Lipid and lipoprotein profile changes in dairy cows in response to latepregnancy and the early postpartum period

Abstract. In dairy cows the peripartum period involves endocrine and metabolic changes to compensate for the increased energy requirement aggravated by reduced feed intake. Cows adjust to the resulting negative energy balance with the mobilization of lipids from adipose tissue that, if excessive, could lead to many transition disorders compromising the offspring's growth and well-being. The aim of this study was to evaluate the dynamic changes in serum lipid and lipoprotein profiles in five dairy cows during the peripartum period. For each cow body condition score (BCS) and body weight (BW) measurements as well as blood sampling was carried out 60, 30 and 15 days before calving (−60, −30 and −15 BC), at calving day (C) and on days 15, 30 and 60 after calving (+15, +30 and +60 AC). Blood samples were tested for serum total lipids, phospholipids, triglycerides, very low-density lipoproteins (VLDLs), total cholesterol (Total-Chol), high-density lipoproteins (HDLs) and low-density lipoproteins (LDLs). One-way repeated measures analysis of variance (ANOVA) was applied to determine the effect of the peripartum period on the studied parameters in cows. A statistically significant effect of the peripartum period (P
Genetic Polymorphism in Bangladeshi Aromatic Rice through RAPD Analysis

Genetic polymorphism and relationships among 25 aromatic rice varieties of Bangladesh were established using random amplified polymorphic DNA (RAPD) primers. Out of sixty 10-mer RAPD primers screened initially, three were chosen and used in a comparative analysis of different varieties of indigenous Bangladeshi aromatic rice. Of the 24 total RAPD fragments amplified, 4 (16.67%) were found to be shared by individuals of all eight varieties. The remaining 20 fragments were found to be polymorphic (83.33%). Pair-wise estimates of similarity ranged from 0.111 to 0.844. Highest genetic diversity was determined between PL-8 and PL-12 genotypes (0.844). The amount of genetic diversity within aromatic rice germplasm was quite high as determined by the genetic similarity coefficients between genotypes. Genetic similarities obtained from RAPD data were also used to create a cluster diagram. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the varieties and the 25 aromatic rice genotypes were grouped into 4 clusters where cluster I includes the maximum number of varieties (11). Cluster VI includes minimum number of varieties (3). This Study offered a rapid and reliable method for the estimation of variability between different varieties which could be utilized by the breeders for further improvement of the local aromatic rice varieties.
Nucleoporin-mediated regulation of the Kcnq1ot1 imprinted domain

Genomic imprinting is an epigenetic phenomenon that restricts gene expression to one parental allele while the other copy is silent. How this duality is regulated is not fully understood. Using the Kcnq1ot1 imprinted domain as a model, previous work in the laboratory identified nucleoporin 107 as a candidate regulator of imprinted domain regulation. Within the Kcnq1ot1 domain resides the imprinting control region, the paternally expressed Kcnq1ot1 (Kcnq1 opposite transcript 1) noncoding RNA, nine maternal-expressed protein-coding genes, as well as genes that escape imprint regulation. On the maternal allele, the Kcnq1ot1 imprinting control region is methylated, silencing the embedded Kcnq1ot1 promoter and its transcription, and thereby permitting expression of neighbouring genes. On the paternal allele, the Kcnq1ot1 imprinting control region is unmethylated, allowing Kcnq1ot1 noncoding RNA transcription, which results in neighbouring protein-coding gene silencing. In the present study, I showed that depletion of nucleoporin 107, nucleoporin 62 and nucleoporin 153 in mouse extraembryonic endoderm stem cells reduced Kcnq1ot1 noncoding RNA expression and volume, decreased Kcnq1ot1 imprinted domain positioning at the nuclear rim and reactivated normally silent paternal alleles of a core group of protein-coding genes in the domain. Paternal alleles of additional protein-coding genes were also reactivated but in a nucleoporin-specific manner. While DNA methylation at the Kcnq1ot1 imprinting control region was not changed, nucleoporin 107, nucleoporin 62 and nucleoporin 153 depletion led to alterations in active and repressive histone modifications and a reduction in cohesin complex protein interactions at the Kcnq1ot1 imprinting control region. Therefore, I identified a novel mechanism of imprinted domain regulation, namely nucleoporin-mediated imprinted domain regulation at the Kcnq1ot1 domain in extraembryonic endoderm stem cells. Next, I demonstrated that this novel nucleoporin-mediated mechanism also regulated the Kcnq1ot1 imprinted domain in embryonic stem and trophoblast stem cells, albeit for a different subset of genes. While CTCF and the cohesin complex interacted at the same sites within the paternal Kcnq1ot1 imprinting control region in a NUP107, NUP62 and NUP153 dependent manner in embryonic stem cells, trophoblast stem cells lacked CTCF and cohesin binding at the Kcnq1ot1 imprinting control region. My results establish an important role for nucleoporins NUP107, NUP62 and NUP153 in mediating imprinted domain regulation in all three cell lineages.
Spatial and temporal aspects of leaf growth inhibition

Elevated concentrations of NaCl in plant growth media cause a reduction in leaf growth. In grass es, where the leaf growth zone is a small part of the entire leaf, it is important to locate the expanding region and spatially quantify the extent of growth reduction under stress. This will allow comparisons and correlations with possible physiologically important factors. We studied the spatial distribution of growth within the intercalary growth zone of sorghum (Sorghum bicolor (L.) Moench, cv. NK 265) leaves. Salinity (100 mM NaCl) shortened the length of the growth zone from 30 mm in the controls to about 24 mm, and reduced the maximal relative ele mental growth rate (REG rate). The extent of growth inhibition varied with spatial location along the elonga tion region. The growth in the basal 3-9 mm of salinized plants was not affected. Young leaves, while still enclosed in the protected whorl of older sheaths and elongating rapidly, were affected more severely by the stress than emerged leaves. The distribution of growth along the leaf growth zone was not steady throughout the elongation period. The length of the elongation region of young non emerged leaves increased with leaf age and reached a maximum of about 30 mm at leaf emergence. Toward the end of the elongation period, the growth zone shortened for both the control and salinized leaves, and was con fined to more basal regions. The maximal REG rate in
Genome-Wide Detection of Putative Oncofetal Genes in Human Hepatocellular Carcinoma by Splicing Pattern Comparison

ncofetal genes are those genes that express themselves similarly in fetal and tumorous adult tissues but differently or below detectable levels in normal adult tissues. These genes are thought to play important roles in cell proliferation, differentiation and carcinogenesis. They have recently been used as biomarkers of cancer. For example, the alpha-fetoprotein (AFP) is one of the most commonly used diagnostic markers for hepatocellular carcinoma (HCC). In this paper, we present a computational method that compares the distributions of co-expression splicing patterns to detect potential biomarker genes in HCC, according to the cDNA/EST data. Using this method, we successfully identified 84 putative oncofetal genes (POFG) in HCC. We also found that the fetal and tumorous isoforms of POFG tended to be longer than their normal counterparts. Our preliminary screening of domain compositions of those long fetal/tumorous isoforms re-discovered a pleckstrin homology (PH) domain on AKT2, which is known to be cancer-related.
Physical activity and breast cancer survival: an epigenetic link through reduced methylation of a tumor suppressor gene

The study was conducted to determine the effect of physical activity on DNA methylation and to predict the consequence of this effect concerning gene expression and breast cancer survival. Blood samples, collected from 12 breast cancer patients who participated in a randomized clinical trial of exercise, were examined for exercise-related changes in DNA methylation using a methylation micro- array. Tumor samples of 348 breast cancer patients were analyzed with qRT-PCR and qMSP to determine gene expression and methylation identified in the microarray analysis. Cox regression models were developed to predict survival outcomes in association with gene expression and methylation. After 6 months of moderate-intensity aerobic exercise, changes in DNA methylation (P \ 5 9 10 -5 )i n peripheral blood leukocytes were detected in 43 genes from a panel of 14 495. Based on the list, we analyzed gene expression in association with overall survival in breast tumors and found three genes whose methylation was reduced after exercise were favorably in association with overall survival, i.e., higher expression associated with better survival. Of the three genes, L3MBTL1 was a putative tumor suppressor gene with known function to repress chromatin for transcription, which is activated mainly in germline stem cells. Further analyses of tumor features among patients indicated that high expression of L3MBTL1 was associated with low grade and hormone receptor- positive tumors, as well as low risk of disease recurrence and breast cancer death. In conclusion, the study suggests that increasing physical activity after a breast cancer diagnosis may affect epigenetic regulation of tumor suppressor genes, which have favorable impacts on survival outcomes of breast cancer patients.
Circulation of Dengue Virus Type 3 Genotype III in Africa Since 2008

Dengue virus type 3 (DENV-3) genotype III circulated across East Africa between 1984 and 1993, but no additional case was detected until the return of a European traveler from Cameroon in 2006. Since then, DENV-3 genotype III has been reported in many countries like Tanzania, Senegal and Cote d’Ivoire. Fifteen strains of DENV-3 were isolated from Africa by the laboratory of French National Reference Center for arboviruses between 2008 and 2012. The objective of the present study was to establish the phylogeny of new strains of DENV-3 genotype III isolated in Africa to better understand their origin(s) and diversity. Analyses showed that the Cote d’Ivoire 2008 strain was phylogenetically linked with the strains responsible for all the epidemics that occurred since then in West Africa including Cape Verde. This strain was also phylogenetically linked with the strain isolated in China in 2009. The Tanzanian 2010 strains cluster included the strains isolated in the Union of Comoros, Madagascar and China. Strains isolated from sporadic cases in La Reunion in 2012 clustered with the Thailand strain. These results evidenced the diversity of DENV-3 genotype III isolated in Africa between 2008 and 2012. The impact of air travel, tourism and trades should play a major role in the DENV spreading over continental Africa and African archipelagoes.
Effects of Distillation Time on the Pinus ponderosa Essential Oil Yield, Composition, and Antioxidant Activity

This study evaluated the effect of distillation time (DT; 1.25, 2.5, 5, 10, 20, 40, 80, 160, 240, and 360 min) on essential oil yield, composition, and the antioxidant activity of ponderosa pine essential oil. Pine essential oil yield increased with length of the DT and reached maximum at 160 min DT. The major oil constituents were alpha-pinene and beta-pinene, ranging from 17% to 40% and from 21% to 29%, respectively, of the total oil. Overall, the concentration of alpha-pinene and beta-pinene was high at the initial DT (5-20 min) and decreased with increasing DT. The concentration of myrcene (range, 0.9% to 1.5%) was lowest at 5 min DT, then increased at 10 min DT, and did not change with longer DT. Overall, the concentrations of most other constituents (delta-3-carene, limonene, cis-ocimene, alpha-terpinyl acetate, germacrene-D, alpha-muurolene, gamma- cadinene, delta-cadinene, and germacrene-D-4-ol) were low at the initial DT and increased with increasing DT. Total yields (a function of oil yield and the concentration of individual constituents) of all constituents were generally the lowest at 5 min DT, increased with increasing DT, and reached maximum at 160 min DT. The antioxidant capacity of the pine oil in this study varied between 7.0 and 14.5 mmole Trolox/g and was unaffected by DT. This study demonstrated that DT can significantly modify the essential oil yield and composition of ponderosa pine needles. Furthermore, DT could be used to obtain pine oil with targeted chemical profiles. This report can also be used as a reference point for comparing literature reports, in which different DTs are used to extract essential oil of ponderosa pine.
Phylogenetic Diversity of Chytridiomycetes in a Temporary Forest Pond Surveyed Using Culture-Based Methods

Abstract Temporary forest ponds are depressions that annually cycle between non-inundated and inundated stages and are recognized as biodiversity hotspots for amphibians and other taxa. However, little is known about the microbial communities of temporary forest ponds and less is known about chytrids, an inconspicuous, early diverging lineage of fungi, present in such ponds. We sampled soil and water from a temporary forest pond in the Oakmulgee District of the Talladega National Forest. Chytrids were isolated from the samples using baits and standard isolating techniques. Isolated strains were identified using the monophyletic-species concept based on a molecular phylogeny inferred from an alignment of the nuclear large subunit rDNA. A total of 30 strains were isolated, which represented 7 species. Due to the limitations of a culture-based method in being able to culture all chytrids that are present, we have described only a portion of the chytrid community. This study, however, is foundational to future inventories that apply a multiphasic approach to further reveal chytrid diversity in this understudied and variable habitat.
A decision support model for individual tree stump harvesting options based on criteria for economic return and environmental protection

ABSTRACT Based on principles of multi-criteria analysis techniques, a model (MAPStump-E) for decision support on stump harvesting at stand level was developed. The model applies the concept that each stump can be attributed production values (economic) and environmental values (here soil protection and water quality). Individual tree stump information was incorporated directly from the production reports of harvesters and combined with high-resolution Geographical Information System data on topography and soil type to create a production submodel and a soil and water vulnerability submodel (SWM). To test the model, it was applied to a 45-ha study forest in south-central Sweden and the outcome of nine scenarios with varying bioenergy prices and environmental protection levels was examined. Combined analysis of the effects of production and environmental criteria on total dry mass of harvestable stumps at the study site showed that biomass prices had a stronger influence than environmental criteria. Conflict stumps were defined as stumps suitable for harvest based on production criteria, but unsuitable based on soil and water protection criteria. In a “medium” price scenario, the proportion of conflict stumps at the study site ranged from 6% to 18%, depending on protection level set.
Antibody-Direct Epifluorescent Filter Technique and Immunomagnetic Separation for 10-h Screening and 24-h Confirmation of Escherichia coli O157:H7 in Beef.

Rapid screening of beef for the presence of Escherichia coli O157:H7 was shown to be feasible using a 10-h enrichment in modified buffered peptone water and the antibody-direct epifluorescent filter technique (Ab-DEFT). The Ab-DEFT involved membrane filtration, fluorescent antibody staining and epifluorescence microscopy and was accomplished in less than 1 h. The procedure allowed detection of the pathogen artificially inoculated into beef patties at 0.1 CFU/g. The 10-h nonselective enrichment broth supported rapid growth, which provided sufficient numbers of cells for a positive determination by the Ab-DEFT after fewer than 10 microscope fields were scanned using a 40× objective lens. Immunomagnetic separation using anti- E. coli O157 Dynabeads® was used to confirm presumptively positive cultures within 24 h. The ease and rapidity of the Ab-DEFT may provide a substantial time and cost savings to the beef industry for screening beef for the presence of E. coli O157:H7.