Miracle-dz/UniFAR-FTUs huggingface dataset:
The fractional coalescent

A new approach to the coalescent is introduced. The fractional coalescent (f-coalescent) extends the Kingman's n-coalescent allowing more variability in the patterns of the waiting times. These changes in the waiting times could be caused by population size changes or selection processes. The f-coalescent is derived by applying fractional calculus, in particular the fractional Poisson process which itself is based on the expansion to the fractional waiting times of the conventional Poisson process. The f-coalescent introduces an additional parameter α affecting the steepness of the waiting time function. With an α = 1, Kingman's n-coalescent and the f-coalescent are equivalent. The f-coalescent has been implemented in the population genetic model inference software MIGRATE. With an α = 1, as expected, both, the n-coalescent and f-coalescent implementation deliver the same results. When either data is simulated under models that allow for α < 1 or for real datasets, then Bayes factor comparisons show an improved model fit of the f-coalescent over the n-coalescent.
Engineered Marrow Macrophages for Cancer Therapy: Engorgement, Accumulation, Differentiation, and Acquired Immunity

The ability of a macrophage to engulf and break down invading cells and other targets provides a first line of immune defense in nearly all tissues. This defining ability to ‘phagos’ or devour can subsequently activate the entire immune system against foreign and diseased cells, and progress is now being made on a decades-old idea of directing macrophages to phagocytose specific targets such as cancer cells. Physical properties of cancer cells influence phagocytosis and relate via cytoskeleton forces to differentiation pathways in solid tumors. Here, SIRPα on macrophages from mouse and human marrow was inhibited to block recognition of CD47, a ‘marker of self. ’ These macrophages were then systemically injected into mice with fluorescent human tumors. Within days, the tumors regressed, and fluorescence analyses showed that the more the SIRPαinhibited macrophages engulfed, the more they accumulated within tumors. In vitro phagocytosis experiments on transwells revealed that macrophage migration through micropores was inhibited by eating. However, during the 1-2 weeks of tumor residency, donor macrophages quickly differentiated toward nonphagocytic, high-SIRPα tumor associated macrophage. Analyses of macrophages on soft or stiff collagenous gels demonstrated a stiffness-driven upregulation of SIRPα. Tissue stiffness also seems to have a role in the development of cancer. Meta-analyses suggest that genomic variation across tumors scales with the stiffness of the tumor tissue of origin. These genomic changes give rise to neoantigens that are important for the development of monocyte/macrophage immunotherapies. Indeed, marrow-derived macrophages can phagocytose melanoma cells and present neoantigens leading to the activation of T-cells. Unlike past injections of anti-CD47 which cause anemia, no measurable impact on blood profiles, weight, or development of GvHD was observed from systemic injections of SIRPα-inhibited donor macrophages. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Pharmacology First Advisor Dennis E. Discher Subject Categories Pharmacology This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/2164 ENGINEERED MARROW MACROPHAGES FOR CANCER THERAPY: ENGORGEMENT, ACCUMULATION, DIFFERENTIATION, AND ACQUIRED IMMUNITY
The Effect of Huanglongbing on Young Citrus Tree Water Use

S . Understanding the role of Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus on citrus ( Citrus sp.) water use is critical for determining if changes in water management of commercial citrus orchards affected by this disease is necessary. Reference evapotranspiration (ET o ) is the most used methodology for irrigation scheduling, particularly in light of reports that indicate the lack of water for irrigation will become a major problem in many places around the world including Florida. The objectives of this study were to determine citrus tree water relationship [water use, sap ﬂow, and stem water potential ( Y )] as affected by ET o and HLB. The study was initiated on Jan. 2014 on two sweet orange ( Citrus sinensis ) cultivars included Hamlin and Valencia grown in a ﬁne sandy soil texture (sandy, siliceous, and hyberthermic Arenic Alaquods) in a greenhouse. Twelve weighing lysimeters of each cultivar (six HLB-affected and six nonaffected trees) were used to determine selected water relation parameters. Results indicated a signiﬁcant reduction in water use, Y , and sap ﬂow for affected trees when compared with nonaffected trees. Citrus water use of healthy trees during the 2-year study was 31% and 27% greater than HLB-affected trees for ‘Hamlin’ and ‘Valencia’, respectively. Lower water use of HLB-affected trees resulted in 10% and 15% greater available soil water content than healthy ‘Hamlin’ and ‘Valencia’ trees, respectively. Therefore, reducing the water supply for HLB-affected trees than healthy trees may be a desirable practice that would lead to signiﬁcant water savings.
Distribution Changes, Genetic Population Structure, and a Novel Environmental DNA (eDNA) Detection Method for Darters (Subgenus Nothonotus) in the Upper Ohio River Watershed

iv DEDICATION . vi ACKNOWLEDGEMENTS . vii LIST OF TABLES . x LIST OF FIGURES . xi Chapter One: Expanded Distributions of Three Etheostoma Darters (subgenus Nothonotus) within the Upper Ohio River Watershed . 1 1.1 Introduction . 3 1.2 Study Area . 5 1.3 Methods . 5 1.4 Results . 9 1.5 Discussion . 16 1.6 Summary/Conclusions . 23 Literature Cited . 24 Chapter Two: The genetic population structure of Etheostoma camurum (Bluebreast Darter) in the upper Ohio River watershed . 29 2.1 Introduction . 30 2.2 Methods. 35 2.3 Results . 43 2.4 Discussion . 59 2.5 Conclusions . 73 Literature Cited . 75 Chapter Three: Development of an aquatic environmental DNA (eDNA) method for detection of darters (subgenus Nothonotus) in the upper Ohio River watershed . 83 3.1 Introduction . 84 3.2 Methods. 90 3.3 Results . 100 3.4 Discussion . 114 3.5 Conclusions . 118 Literature Cited . 121
Harmful dinoflagellates and mitigation strategies in Korea

Harmful algal blooms (HABs) have been responsible for numerous fish kills and public health problem. Since 1995, massive C. polykrikoides-related fish kills and Alexandrium spp. -related shellfish poising from Korean waters. have been recorded To address this issue, geographic distribution of harmful algae, molecular methods for identifying harmful algae, HABs mitigation strategies, impact on some fisheries animals, life cycles, and toxicity have been studied to understand their bloom dynamics. The paper is a review on the studies of harmful dinoflagellates and mitigation.
Integrative Pathway Analysis Pipeline For Mirna And Mrna Data

INTEGRATIVE PATHWAY ANALYSIS PIPELINE FOR miRNA AND mRNA DATA by DIANA DIAZ Advisor: Dr. Sorin Draghici Major: Computer Science Degree: Master of Science The identification of pathways that are involved in a particular phenotype helps us understand the underlying biological processes. Traditional pathway analysis techniques aim to infer the impact on individual pathways using only mRNA levels. However, recent studies showed that gene expression alone is unable to capture the whole picture of biological phenomena. At the same time, MicroRNAs (miRNAs) are newly discovered gene regulators that have shown to play an important role in diagnosis, and prognosis for different types of diseases. Current pathway analysis techniques do not take miRNAs into consideration. In this project, we investigate the effect of integrating miRNA and mRNA expression in pathway analysis. In order to analyze biological pathways using miRNA expression data, we developed a novel method that augments KEGG pathways with microRNAs targeting genes. To validate our method, we analyzed nine GEO datasets. We also performed the analyses using just mRNA as well as using the integrative state-of-the-art method (microGraphite) to compare the results. In each case, we monitored the position of the pathway describing the given condition. We observed that our method outperforms the state-of-the-art approach. 100 AUTOBIOGRAPHICAL STATEMENT DIANA DIAZ EDUCATION • Master of Science (Computer Science), 2017 Wayne State University, Detroit, MI, USA • Master of Science (Computer Systems Engineering), 2009 The Andes University, Colombia • Bachelor of Engineering (Computer Systems Engineering), 2006 The Piloto University of Colombia, Colombia PUBLICATIONS 1. Diaz D, Donato M, Nguyen T, Draghici S. MicroRNA-Augmented Pathways (mirAP) and their applications to pathway analysis and disease subtyping. In proceedings of Pacific Symposium on Biocomputing (PSB) 2017. (2017). 2. Diaz D, Nguyen T, Draghici S. A Systems Biology Approach for Unsupervised Clustering of High-Dimensional Data. In proceedings of International Workshop on Machine Learning, Optimization and Big Data. (2016). 3. Nguyen T, Diaz D, Tagett R, Draghici S. Overcoming the matchedsample bottleneck: an orthogonal approach to integrate omic data. Scientific Reports, 6, 29251 (2016). 4. Diaz D, Draghici S. mirIntegrator: Integrating miRNAs into signaling pathways. Bioconductor (2015).
The Phylogeny of the Spleen

The spleen can exert different functions: hematopoiesis, immune response, blood filtration, and blood storage. Presence and importance of each function vary among different species and, within a single species, vary during ontogeny. During the course of evolution, loss of hematopoietic functions was accompanied by increased specialization of other functions. Increase in the complexity of immunological features can be seen in the passage from scattered lymphocytes to segregation of the white pulp, organization of T- and B-lymphocyte regions and, finally, appearance of germinal centers. The red pulp remained essentially the same in all nonmammalian vertebrates, with a microarchitecture that concentrates blood and allows its filtration. In our view, this high splenic hematocrit was eventually co-opted in teleosts and mammals to develop a new function: the storage of red blood cells. Finally, mammalian species evolved different features of the red pulp, increasing the specialization of the filtration function (pulp sinuses) and/or storing function (muscularization).
Assessing abundance and catch selectivity of Octopus cyanea by the artisanal fishery in Lakshadweep islands, India

Subsistence fishery for cephalopods contributes significantly to the local economy of several Asian, African and island states. In addition to being unregulated and undocumented, recent studies indicate that low-scale fisheries can have detrimental effects on marine ecosystems. In the Lakshadweep islands, men, women and children have been involved in spear fishing for octopus for a long time, but there is a paucity of information on the biology and fishery of the octopus species in Indian waters. In this study, we estimated the population abundance, morphometry and sex ratio of Octopus cyanea . Moreover, we examined whether the current octopus spear fishing activity displayed size or sex selectivity, given that larger individuals are easier to spot and brooding females spend more time in crevices. O. cyanea surveys were conducted by snorkeling in the lagoons of Kavaratti and Agatti islands between November 2008 and April 2012. The estimated mean density of O. cyanea was 3 and 2.5 individuals per hectare in Agatti and Kavaratti, respectively. Individual mean weight was 923.36 g and 846.26 g in Agatti and Kavaratti and the male:female sex ratio 1.35:1 and 3.8:1, respectively. Comparison between visual counts and fisheries landings indicated that fishing effort was concentrated in areas of high juvenile abundance but without female-bias. Constructing a long-term database of fishery catches will help with stock assessment and understanding the factors that influence octopus populations. Implementation of a lower size limit of 500 g would act as a precautionary measure against catching very small octopuses.
Transient nocturnal site fidelity in juvenile green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) sea turtles on the shallow nearshore coral reefs of South Caicos, Turks and Caicos Islands

Opportunistic nocturnal catch-and-release turtle surveys were conducted on three nearshore, shallow coral reefs that fringe the main navigation channel to Cockburn Harbour, South Caicos, between 2005 and 2015. A total of 117 captures were made, representing 73 individual turtles (32 green, 41 hawksbill). Almost half of the green turtles were recaptured on at least one occasion, with a maximum time at liberty of 574 days (median = 94 days). Only 20% of hawksbill turtles were recaptured, with a maximum time at liberty of 587 days (median = 120 days). These data suggest that the study sites are utilised by a combination of transient visitors and short to medium-term resident turtles. However, no evidence of long-term nocturnal site fidelity was found. The size ranges observed in both species indicate that all turtles were immature, and the minimum sizes are consistent with previously reported settlement sizes from the region. Despite the lack of long-term fidelity, turtles were regularly encountered over the course of the study, indicating that these reefs are an important nocturnal refugium for local juvenile turtles in general.
Effects of reduced glutathione on Boer goat semen freezability

Objective: To evaluate the effects of reduced glutathione on the quality of cryopreserved Boer buck spermatozoa. Methods: The current study was carried out on five Boer bucks from which semen samples were collected by artificial vagina. After microscopical evaluation at 37 °C semen samples that fulfill the ideal requirements for extension were diluted in a tris–based extender including different concentrations of reduced glutathione (2, 5, 7 and 10 mM) and those without glutathione served as a control. Sperm motility, viability, acrosome integrity, DNA integrity, total antioxidant capacity and lipid peroxidation were assessed post-thawing. Results: The current results revealed that post-thawing motility, viability and acrosomal integrity were significantly improved [(66.67±5.50)%, 168.30±18.59 and (12.75±2.45)%, respectively] when 5 mM glutathione was added to semen extender; especially as compared with the control [(40.00 ±2.88)%, 95.00±8.90 and (25.75±3.46)%, respectively]. Similarly, at this concentration (5 mM) sperm DNA damage, tail length and tail moment of cryopreserved semen were significantly (P<0.05) reduced [(2.32±0.27)%, (1.64±0.49) μm and 3.55±0.63, respectively] compared with the control extender [(6.66±0.84)%, (4.09±0.47) μm and 26.47±0.51, respectively]. Moreover, addition of 5 mM glutathione to buck semen extender significantly (P<0.05) increased total antioxidant capacity [0.51±0.07) mμ/mL] and decreased lipid peroxidation of cryopreserved spermatozoa [(8.68±2.72) nmol/mL] compared with the control [(0.18±0.02) mμ/mL and (24.92±5.80) nmol/mL, respectively]. Conclusions: The addition of 5 mM glutathione to semen diluent improve freezability of Boer buck spermatozoa through DNA protection from deterioration and oxidative stress reduction. Moreover, 10 mM of glutathione exerts cytotoxic effects on Boer buck semen.
Evolutionary trends in Tetrastigma (Vitaceae): Morphological diversity and taxonomic implications

Tetrastigma (Miq.) Planch. (Vitaceae) is a genus with ca. 100 species showing great morphological diversity. Previous molecular phylogenetic studies suggested that traditional classification systems are not consistent with the molecular phylogeny, and Tetrastigma is undergoing further systematic investigation. We traced the evolutionary trends of 20 morphological characters within a robust phylogenetic framework. Our results revealed that many morphological characters show either multiple transitions or few state changes, however, some characters show distinct variation. The two subgenera in Tetrastigma (subgen. Tetrastigma and subgen. Palmicirrata) based on unbranched/bifurcate versus digitately branched tendrils are not supported because subgen. Tetrastigma is paraphyletic. However, the unbranched versus bifurcate/digitately branched tendril is of taxonomic utility to characterize some of the major clades. Inflorescences in Tetrastigma appear axillary, but are leaf‐opposed on a compressed axillary shoot. We found most of the species in Tetrastigma retained the ancestral compound dichasial inflorescence, except those of clade IV that have derived pseudo‐umbellate inflorescences. Other characters including habit, leaf organization, and berry shape provide additional morphological support for the major clades. Our morphological analysis and recent molecular study suggest each of the five major clades within Tetrastigma be treated as distinct taxonomic sections (five sections in the genus).
Enhanced Coenzyme Q10 Yield by Blocking Hopanoids Pathway

Coenzyme Q10 (CoQ10), otherwise known as ubiquinone (UQ), is a valuable bioactive compound used both medically and cosmetically [1]. Many studies focus on enhancing CoQ10 production in Escherichia coli (E.coli) by genetic engineering [29]. Agrobacterium tumefaciens also have been employed as the producers of CoQ10 [10,11]. Typical purple non-sulfur bacteria (PNSB) generally have a relatively high content of CoQ10, as ideal CoQ10 producers [12-16]. R. Palustris (Rhodopseudomonas palustris) is a PNSB with a high content of inherent CoQ10, whose fermentation processes have been well researched over the years [17,18]. Therefore, R. Palustris could be a potential host for CoQ10 production by metabolic engineering.
Human Herpes Virus 6 (HHV-6) - Pathogen or Passenger? A pilot study of clinical laboratory data and next generation sequencing

ABSTRACT Background Human herpes virus 6 (HHV-6) is a ubiquitous organism that can cause a variety of clinical syndromes ranging from short-lived rash and fever through to life-threatening encephalitis. Objectives We set out to generate observational data regarding the epidemiology of HHV-6 infection in clinical samples from a UK teaching hospital and to compare different diagnostic approaches. Study design First, we scrutinized HHV-6 detection in samples submitted to our hospital laboratory through routine diagnostic pathways. Second, we undertook a pilot study using Illumina next generation sequencing (NGS) to determine the frequency of HHV-6 in CSF and respiratory samples that were initially submitted to the laboratory for other diagnostic tests. Results Of 72 samples tested for HHV-6 by PCR at the request of a clinician, 24 (33%) were positive for HHV-6. The majority of these patients were under the care of the haematology team (30/41, 73%), and there was a borderline association between HHV-6 detection and both Graft versus Host Disease (GvHD) and Central nervous system (CNS) disease (p=0.05 in each case). We confirmed detection of HHV-6 DNA using NGS in 4/20 (20%) CSF and respiratory samples. Conclusions HHV-6 is common in clinical samples submitted from a high-risk haematology population, and enhanced screening of this group should be considered. NGS can be used to identify HHV-6 from a complex microbiomee, but further controls are required to define the sensitivity and specificity, and to correlate these results with clinical disease. Our results underpin ongoing efforts to develop NGS technology for viral diagnostics.
Glyphosate Efficacy as Influenced by Cultivation Practices on a Creeping Bentgrass Fairway Turf

Glyphosate is routinely used to eradicate existing turf in golf course fairway renovations. However, current label recommendations suggest delaying cultivation of glyphosate treated areas for 7 days. A 2-year ﬁeld study was conducted to assess how various seedbed preparation techniques (i.e., verticutting, core-cultivation, or verticutting + core-cultivation) inﬂuence glyphosate efﬁcacy on creeping bentgrass fairway turf when completed at various intervals shortly after application [0–7 days before cultivation (DBC)]. Percent green cover declined from initial values of ’’ 90% to £ 0.2% at the end of the study after glyphosate application at all timings, regardless of cultivation during both years. All cultivated plots had 37.9% to 72.3%, or 5.9% to 62.1% less green cover compared with noncultivated plots when glyphosate was applied £ 3 days before cultivation in 2014 and 2015, respectively. Generally, the number of days until green cover reached 1% (GC 1 ) ranged from 6.6 to 11.1 in 2014 and 5.2 to 6.9 in 2015. Within glyphosate application timings, no differences in GC 1 were observed between cultivated and noncultivated treatments in 2014, except at 0 DBC. The GC 1 for verticutting was 5.1 days longer than noncultivated plots; however, all other cultivation treatments were equivalent to noncultivated plots when glyphosate was applied 0 DBC. All cultivation treatments reduced GC 1 1.7 to 2.5 days compared with the no cultivation treatment, regardless of glyphosate application timing in 2015. Results from this study indicate that cultivation of creeping bentgrass fairway turf within 7 days of glyphosate application is not detrimental to long-term herbicide efﬁcacy, and in some cases may actually enhance the rate of decline of glyphosate treated creeping bentgrass.
OPTIMIZATION OF THE FORMULATION OF EMULSIONS PREPARED WITH A MIXTURE OF VITAMINS D AND E BY MEANS OF AN EXPERIMENTAL DESIGN SIMPLEX CENTROID AND ANALYSIS OF COLOCALIZATION OF ITS COMPONENTS

A suitable alternative for satisfying the demand of healthy and targeted compounds such as vitamins, is the preparation and consumption of capsules formed from emulsions The objective of the present work was the preparation of emulsions of vitamins D and E based on a simplex centroid mixture design, using three wall materials: gum arabic (GA) maltodextrin (MD) and modified starch (MS) that represented 20% of total solids as well as a colocalization analysis to know the distribution of compounds in the micelle. The most stable formulation according to three response variables: particle size (PS), zeta potential (ZP) and Turbiscan stability index (TSI) was obtained. Data were analysed by using an ANOVA test. Results showed that wall materials have a synergic influence on PS and TSI and antagonic for ZP. PS increased with proportion of GA while ZP and TSI were affected by the charge of the wall materials. Optimum emulsion resulted in a mixture of 3.28% GA, 13.33% MD and 3.37% MS; Predicted and experimental values of the response variables were very similar among them. Also, colocalization analysis showed that once emulsified, the vitamin D was distributed in the centre of the micelle and a minimum part on their surface.