Miracle-dz/UniFAR-FTUs huggingface dataset:
WNT5A EXPRESSION IN HUMAN AND MURINE ATHEROSCLEROTIC LESIONS

CHRISTMAN, MARK A. , M.S., June 2007. Chemical Engineering WNT5A EXPRESSION IN HUMAN AND MURINE ATHEROSCLEROTIC LESIONS (50 pp.) Director of Thesis: Douglas J. Goetz Atherosclerosis is a chronic inflammatory disease that involves the formation of plaque within the intima. The secreted glycoprotein Wnt5a is a non-cannonical member of the Wnt family. Wnt5a expression has been shown in granulomatous lesions of M. turberculosis infected patients and in macrophages upon stimulation with lipopolysaccaride in vitro. Wnt5a has been linked to Toll-like receptor – 4 (TLR-4) signaling and TLR-4 has already been identified in atherosclerotic regions suggesting a cross-talk between Wnt5a and TLR-4. These observations lead to the hypothesis that Wnt5a is involved in atherosclerosis. To test this hypothesis, immunohistochemical analysis was performed on murine samples from the aortic sinus to the aortic arch and human carotid arteries from patients undergoing endarterectomy. Human and murine atherosclerotic lesions were immunostained for Wnt5a and its receptor Frizzled 5 (Fzd5) along with TLR-4. All samples were positive for Wnt5a and Fzd5 in the macrophage dense regions and had coincident TLR-4 expression. Wnt5a expression was also found to be in the smooth muscle cell region (media) from the human samples. These findings demonstrate Wnt5a and Fzd5 expression in human and murine atherosclerotic lesions. Approved: _____________________________________________________________ Douglas J. Goetz Professor of Chemical and Biomolecular Engineering I dedicate this to my parents, Mark and Kelly Christman. Thank you for everything.
Improved LC-MS chromatographic alignment increases the accuracy of label-free quantitative proteomics: Comparison of spectral counting versus ion intensity-based proteomic quantification strategies

The ability to provide an unbiased qualitative and quantitative description of the global changes to proteins in a cell or an organism would permit the systems-wide study of complex biological systems. Label-free quantitative shotgun proteomic strategies (including LC-MS ion intensity quantification and spectral counting) are attractive because of their relatively low cost, ease of implementation, and the lack of multiplexing restrictions when comparing multiple samples. Owing to improvements in the resolution and sensitivity of mass spectrometers, and the availability of analytical software packages, protein quantification by LC-MS ion intensity has increased in popularity. Here, we have addressed the importance of chromatographic alignment on protein quantification, and then assessed how spectral counting compares to ion intensity-based proteomic quantification. Using a spiked-in protein strategy, we analysed two situations that commonly arise in the application of proteomics to cell biology: (i) samples with a small number of proteins of differential abundance in a larger non-changing background, and (ii) samples with a larger number of proteins of differential abundance. To perform these assessments on biologically relevant samples, we used isolated integrin adhesion complexes (IACs). Technical replicate analysis of isolated IACs resulted in a range of alignment scores using the Progenesis QI software package and demonstrated that higher LC-MS chromatographic alignment scores increased the precision of protein quantification. Furthermore, implementation of a simple sample batch-running strategy enabled good chromatographic alignment for hundreds of samples over multiple batches. Finally, we applied the sample batch-running strategy and compared quantification by LC-MS ion intensity to spectral counting and found that quantification by LC-MS ion intensity was more accurate and precise. In summary, these results demonstrate that chromatographic alignment is important for precise and accurate protein quantification based on LC-MS ion intensity and accordingly we present a simple sample re-ordering strategy to facilitate improved alignment. These findings are not only relevant to label-free quantification using Progenesis QI but may be useful to the wide range of MS-based quantification strategies that rely on chromatographic alignment.
Variant requirements for DNA repair proteins in cancer cell lines that use alternative lengthening of telomere mechanisms of elongation

ii Dedication . iii Acknowledgments. iv Vita . v Publications . v List of Tables . ix List of Figures . x Chapter 1: Functions of DNA Repair Proteins in Alternative Lengthening of Telomere Mechanisms . 1 I. Telomere maintenance . 2 I.1 Telomere structure and function . 2 I.2 Telomerase . 4 I.3 Alternative lengthening of telomeres . 4 II. DNA repair proteins in ALT . 9 II.1 DNA damage sensors . 10 II.2 Chromatin modifiers . 12
Comparison Study of Dimensionally Stable Anodes for Degradation of Chlorpyrifos in Water

In the present study, two dimensionally stable anodes, Ti/IrO 2 and Ti/IrO 2 -SnO 2 , have been developed in order to degrade chlorpyrifos in chloride-free environment. The chemical oxygen demand (COD) results revealed that Ti/IrO 2 -SnO 2 electrode had degraded 78.2% of COD after 6 h of electrolysis. COD removal followed pseudo second-order kinetics. Radical scavenger studies confirmed that the hydroxyl radical can be the major factor responsible for degrading chlorpyrifos. The anodic charge decreased from 153.76 to 145.15 mC while accelerated lifetime showed 7 h increment, indicating the higher stability of Ti/IrO 2 - SnO 2 anode. The qualitative identification of oxides of both electrodes was studied by X-ray diffraction. Roughness parameters and topography were determined using AFM images.
Size and Age Structure of Anadromous and Landlocked Populations of Rainbow Smelt

AbstractRainbow Smelt Osmerus mordax are widely distributed in both anadromous and landlocked populations throughout northeastern North America; abundance, size at age, and maximum size vary widely among populations and life histories. In the present study, size at age, von Bertalanffy growth parameters, population age distributions, and precision and bias in age assessment based on scales and sectioned otoliths were compared between ecotypes and among populations of Rainbow Smelt. To compare the ecotypes, we collected spawning adults from four anadromous and three landlocked populations in Maine during spring 2014. A significant bias was identified in only one of four scale comparisons but in four of seven otolith comparisons; however, a comparable level of precision was indicated. Anadromous populations had larger and more variable size at age and von Bertalanffy growth parameters than landlocked fish. Populations were composed of ages 1–4; six populations were dominated by age-2 or age-3 individuals, a.
Characterization of Higher-order Chromatin Structure in Bone Differentiation and Breast Cancer: A Dissertation

Higher-order genome organization is important for the regulation of gene expression by bringing different cis-regulatory elements and promoters in proximity. The establishment and maintenance of long-range chromatin interactions occur in response to cellular and environmental cues with the binding of transcription factors and chromatin modifiers. Understanding the organization of the nucleus in differentiation and cancer has been a long standing challenge and is still not well-understood. In this thesis, I explore the dynamic changes in the higher-order chromatin structure in bone differentiation and breast cancer. First, we show dynamic chromatin contact between a distal regulatory element and the promoter of Runx2 gene, which encodes the Runtrelated transcription factor 2 (RUNX2) that is essential for bone development. Next, via using a genome-wide approach, we show that breast cancer cells have altered long-range chromatin contacts among small, gene-rich chromosomes and at telomeres when compared with mammary epithelial cells. Furthermore, we assess the changes in nuclear structure and gene expression of breast cancer cells following Runt-related transcription factor 1 (RUNX1) deficiency, an event frequently observed in breast cancer. Finally, I present the role of the central ATPase subunit of the SWI/SNF complex, SMARCA4 (BRG1), in mediating nuclear structure and gene expression. Taken together, the research presented in this thesis reveals novel insight and paradigm for the dynamic changes in disease and differentiation, as well as uncovers previously unidentified roles for two chromatin regulatory proteins, RUNX1 and SMARCA4.
Human-specific methylated regions are enriched in schizophrenia

Background Despite the reduced fertility of patients, schizophrenia has a prevalence of ~1% in the general population. One explanation for this persistence is that schizophrenia is a by-product of human evolution. This hypothesis is supported by evidence suggesting that recently-evolved genomic regions in humans are involved in the genetic risk for schizophrenia. We tested if genetic variants located within human-specific differentially methylated regions (DMRs) are enriched for association with schizophrenia. Methods We used analytical tools that evaluate the polygenic enrichment of a set of genomic variants against all genomic variants. SNPs identified in genome-wide association studies (GWAS) of schizophrenia and 11 other phenotypes were classified according to their location in previously defined human-specific DMRs. These DMR SNPs were then tested for enrichment of association with the GWAS trait. Results Schizophrenia was the only trait in which GWAS SNPs within human-specific DMRs showed clear enrichment of association that passed the genome-wide significance threshold. The enrichment was not observed for Neanderthal or Denisovan DMRs. The enrichment seen in human DMRs is comparable to that for genomic regions tagged by Neanderthal Selective Sweep markers, and stronger than that for Human Accelerated Regions. Conclusions Regions where DNA methylation modifications have changed during recent human evolution harbor more schizophrenia-associated genetic variants than expected. Our study further supports the hypothesis that genetic variants conferring risk of schizophrenia co-occur in genomic regions that have changed as the human species evolved. Our results also suggest that interaction with the environment might have contributed to that association.
Global Malmquist indices of productivity change in Egyptian wheat production

This study aims to measure the total factor productivity of the main governorates of wheat production in Egypt during the time period 1990-2012 and decompose it into technical change, efficiency change and scale change. We used Global Malmquist TFP index as a non-parametric approach. The results indicated that the contribution of technical change component is more important than the efficiency change component. In fact technical change rose, 25.7%, while efficiency change presented a little decline, 3.7%. The decomposition of efficiency change indicated that the main problem of wheat production in Egypt was scale efficiency that worsened by 5.5%.
Changes in forest community structures of tropical montane rain forest on the slope of Mt. Trus Madi in Sabah, Malaysia

ADAM,J. H. 2001. Changes in forest community structures of tropical montane rain forest on the slope of Mt. Trus Madi in Sabah, Malaysia. Changes of the forest community structures in relation to increasing altitude were studied along the slope of Mt. Trus Madi in Sabah, Malaysia. The total number of species, Shannon-Wiener diversity index, Menhinick richness index, rarefaction index, mean diameter, mean basal area, mean biomass and mean tree height were higher at 600 m (plot 1) and declined in descending order at 1400 m (plot 2), 1800 m (plot 3) and 2400 m (plot 4). Density, Simpson diversity index and evenness index were lower at 600 m and increased in ascending order at 1400,1800 and 2400 m. The dominant and co-dominant species with the highest and second highest importance values were different between plots. Shorea dasyphyttaznA S. agami were dominant at (500 m, and were replaced respectively at 1400,1800 and 2400 m by Phyllocladus hypophyllus and Eugenia ampullaria, E. hirta and Knema latericia, and E. kinabaluensis and Leptospermum recurvum. Family Myrtaceae was dominant at all elevations except at 600 m, which was dominated by Dipterocarpaceae. Families Polygalacea, Podocarpaceae, Clusiaceae and Theaceae were dominant at 600,1400,1800 and 2400 m respectively. The biomass of trees was distributed unevenly between species and family at all altitudes. The most dominant species and family by biomass at 600 m were Pamshorea sp. and Dipterocarpaceae; at 1400 m they were S. dasyphylla and Dipterocarpaceae; at 1800 m Garcinia dryobalanoides, and Clusiaceae; and at 2400 m E. kinabaluensis and Myrtaceae. Regression, ANOVA and coefficient of determination indicate significant negative relationships between the number of species, Shannon-Wiener diversity index, Menhinick richness index, rarefaction index, mean diameter, mean basal area, mean biomass and mean tree height with increasing altitude. However, there was a very significant increase in density, Simpson diversity index and species evenness with increasing altitude.
Oil Palm Plantations Affect Movement Behavior of a Key Member of Mixed-Species Flocks of Forest Birds in Amazonia, Brazil

Oil palm (Elaeis guineensis) is a rapidly expanding crop in the Amazonian region of Brazil. Brazilian law requires all landowners, including oil palm plantations, to maintain forest reserves and forested riparian corridors as a way to limit biodiversity losses. Because of these laws and the forest-like structure of oil palm, these plantations may function as habitat for some native species in the region. We tested this assumption by experimentally translocating Cinereous Antshrikes (Thamnomanes caesius), a forest understory insectivorous bird and nuclear member of mixed-species flocks, from forest reserves to riparian corridors within a large oil palm plantation landscape and tracked their movements back to their home ranges. In total, we recorded the movements of 18 individuals, 8 of which were translocated. The other 10 individuals were tracked within their home ranges in the forest reserves. Six of the eight translocated birds successfully returned to their forest home range, but only one bird flew through the more direct route back through the oil palm matrix while the rest took longer routes through adjoining riparian corridors. Homing time for translocated birds averaged 9.57 (±2.23 SE) days. The home range of birds within the forest reserves averaged 2.39 (±0.69 SE) ha, and, with the exception of the single returning bird, Cinereous Antshrikes were never detected in oil palm. Our results suggest that oil palm plantations are a barrier to movements of our study species, and that riparian corridors connecting forest fragments may be effective routes for dispersal.
The influence of lipids in the epidermis and cocoons on cutaneous water loss in Australian hylid frogs, Cyclorana spp

ii Dedication . iii Acknowledgments. iv Vita . v List of Tables . viii List of Figures . ix Chapter 1: Introduction . 1 Chapter 2: Methods . 6 2.1 Study animals . 6 2.2 CWL measurements . 6 2.3 Respiratory water loss . 8 2.4 Cocoon samples . 9 2.5 Calculations . 10 2.6 Lipid extraction . 10 2.7 Thin-layer chromatography . 12
Population size determines the type of nucleotide variations in humans

It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. Here, we examined whether the types of genetic variations are dictated by the effective population size. Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).
In vitro efficacy of oil from the seeds of Carapa guianensis aulb. (meliaceae) against Damalinia caprae (Gurlt, 1843) (Mallophaga: Trichodectidae)

This research aimed to evaluate the in vitro efficacy of Carapa guianensis (andiroba) seed oil against Damalinia caprae. It was used 900 specimens of adult D. caprae distributed in nine groups. Each group had four replications of 25 specimens. The groups were subjected to seven concentrations of oil from the seed of C. guianensis (100%, 50%, 30%, 20%, 10%, 5% e 2,5%). There were two control groups: one was a negative control using distilled water and the other was a positive control using Monosulfiram. Evaluations were conducted at 1, 3, 6, 24, 48 and 72 hours following immersion. The evaluations were conducted until all the lice in the treated groups were dead. Treatments with seed oil from C. guianensis in the concentrations of 100%, 50%, 30% and positive control showed 100% mortality one hour after immersion. In the other treatments the death of D. Caprae occurred until up to six hours after the beginning of the experiment.
Environmental Factors Regulate the hlyE Gene Expression in Both S. typhi and E. coli in a Similar Way to Display Haemolytic Activity

Haemolysin (HlyE) is an essential virulence factor of Salmonella, Escherichia coli and other enteric bacteria. Although, a substantial degree of haemolytic activity is not seen under normal culture conditions in these organisms, however, the non-haemolytic E. coli K-12 showed significant haemolytic activity under stress conditions. To confirm this phenomenon in other enteric bacteria, in this study, the production of haemolysin in Salmonella enterica serovar Typhi under stress conditions, like oxygen and glucose starvations in vitro was investigated during March-December 2015. For this, S. typhi was cultured under oxygen or glucose starvation condition separately and this organism showed high haemolytic activity. The activity was found to be much higher when both the conditions were applied together. Also, the role of the transcription factor SlyA of S. typhi was investigated on induction of haemolytic activity. When E. coli K-12 was transformed with plasmid containing the gene of SlyA, the recombinant bacteria without any starvation condition, also showed similar haemolytic activity that was exhibited by S. typhi grown under oxygen and glucose starvation conditions. All these findings suggest that both environmental factors like oxygen or glucose starvation and overexpression of the transcription factor SlyA have important role in inducing hlyE gene expression in S. typhi.
Anti-Bacterial Effect of Propolis Extract in Oil Against Different Bacteria

Background: Propolis is one of the most potent natural antibiotics. Propolis as an active natural substance is attractive due to its antimicrobial properties. Propolis has been used in folk medicine for centuries. It is known that propolis possesses antimicrobial, antioxidative, anti-ulcer and anti-tumor activities. Therefore, propolis has attracted much attention in recent years as a useful or potential substance used in medicine. Objectives: The purpose of this study was to verify the activity of an oily liquid extract of propolis that called propolis extract in oil against some Gram-positive and Gram-negative bacteria. Methods: In this experimental study antimicrobial activity of oily liquid extract of propolis called propolis extract in oil with different concentration of ethanol, methanol and dimethyl sulfoxide as diluents against different bacteria species. The duration of study set up was from Nov 2014 to Sep 2015. Chi-Square and Kappa methods, using Open Epi and Graph Pad Prism Software (Graph Pad, San Diego, California, USA). Graphs were plotted by Microsoft Excel software. Results: In the agar diffusion tests, using wells containing propolis suspension with methanol / dimethyl sulfoxide / ethanol per wells, the some of bacteria were most sensitive to the effect of propolis preparations. No growth inhibition zone was shown in the agar diffusion test with paper disks impregnate with methanol/ dimethyl sulfoxide suspension. Conclusions: The evaluation of the examination results showed that the effectiveness of the extract against bacteria may be explained by the fact that the effect of oily propolis was statistically significant by the introduction of methanol and dimethyl sulfoxide.
Pollination Ecology of Sabatia Campenstris Nutt. (Gentianaceae)

Flower timing studies in June and July (1972) on populations of Sabatia campestris Nutt. show this plant to be allogamous (out crossing) under natural field conditions. However, when environmental factors reduce populations of solitary bees or when flower populations are particularly extensive and dense, the uncollected pollen causes retention of anthers into the period of style opening and stigma presentation. Then autogamy (self-pollination) occurs. Pollinators observed were solitary bees in the genera Calliopsis, Dialictus , and infrequently Augochlorella . Pollen viability is generally excellent. A chromosomal count of n=12 indicated the presence of aneuploid races in this plant species. The lengthening of petals from anthesis to wilting and calyx from bud to fruit production indicates flower size cannot be used as a taxonomic character to separate species.
Anticiper l'émergence d'anomalies génétiques grâce aux données génomiques

Avec le récent développement des approches reposant sur le génotypage et séquençage à haut débit, identifier la mutation responsable d’une anomalie à partir de quelques cas est beaucoup plus simple qu’auparavant. Toutefois, il n’est pas toujours possible d’observer des cas et de disposer du matériel biologique correspondant. Cet article présente deux approches reposant sur l’analyse de données à haut débit, permettant d’identifier des mutations récessives létales ou d’orienter plus efficacement leur recherche à partir des données de séquence du génome. La première approche utilise les données de génotypage à haut débit pour rechercher des régions du génome présentant un déficit en homozygotes. Cette méthode a déjà permis de caractériser plusieurs mutations dans chacune des races bovines analysées. Dans la seconde approche, on recherche dans les données de séquence disponibles des variants dont l’annotation suggère qu’ils ne sont pas tolérés à l’état homozygote. Le nombre de faux positifs est élevé, mais ces données permettent d’orienter la phase d’observation et de diagnostic plus efficacement et, dans les cas les plus favorables, d’anticiper l’émergence de l’anomalie. Des exemples sont fournis avec le gène RP1 responsable de dégénérescence rétinienne ou le gène EDAR responsable de l’absence de poils et de dents.
Optimasi asam tartrat dan natrium karbonat dalam pembuatan granul effervescent ekstrak sambiloto (andrographis paniculata ness) secara granulasi basah dengan metode desain faktorial

xviii BAB I. PENDAHULUAN . 1 A. Latar Belakang . 1 1. Perumusan masalah . 3 2. Keaslian Penelitian . 3 3. Manfaat penelitian . 4 B. Tujuan Penelitian . 4