Miracle-dz/UniFAR-FTUs huggingface dataset:
Amplified fragment length polymorphism (AFLP) analysis of genetic variability in Phalaenopsis

Amplified fragment length polymorphism (AFLP) markers allow a rapid assessment of the level of genetic variation that would be difficult to evaluate using a limited number of morphological markers. AFLP was used to assess the level of genetic variation among 16 different Phalaenopsis species and hybrids. Ten AFLP primer combinations were used for genetic analysis of these Phalaenopsis and 95% of polymorphism in 16 Phalaenopsis species and hybrids was detected. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by UPGMA analysis clustered into two main groups. A significant linear relationship (r = 0.524, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results indicate that there is an abundance of genetic diversity among within Phalaenopsis and that AFLP can be used to distinguish morphologically similar genotypes. In a second study, the effect of gametophytic selection on genetic diversity in Phalaenopsis was examined by AFLP analysis. Sixteen F1 seedlings resulting from cross-pollination that occurred within high (30 oC) and low (14oC) temperature incubators between two hybrid Phalaenopsis [P. (Taisoco Windian × Sogo Yukidian) by P. hybrid unknown], were subjected to genetic analysis by AFLP. A total of 651 fragments ranging in size from 100 to 350 bp were detected using six primer combinations, of which 387 (59.4%) were polymorphic. Seedlings derived from different temperature treatments exhibited 25.5% to 35.9% polymorphism. The genetic similarity among 16 F1 seedlings ranged from 0.825 to 0.946 based on the Dice coefficient. A dendrogram based on 387 polymorphic markers was derived by UPGMA analysis resulting in three major groups and one subgroup. The dendrogram analysis showed clear clustering in Phalaenopsis hybrids pollinated under different temperature treatments, suggesting that several loci may have been
Dissolved organic carbon loss from Yedoma permafrost amplified by ice wedge thaw

Pleistocene Yedoma permafrost contains nearly a third of all organic matter (OM) stored in circum-arctic permafrost and is characterized by the presence of massive ice wedges. Due to its rapid formation by sediment accumulation and subsequent frozen storage, Yedoma OM is relatively well preserved and highly biologically available (biolabile) upon thaw. A better understanding of the processes regulating Yedoma degradation is important to improve estimates of the response and magnitude of permafrost carbon feedbacks to climate warming. In this study, we examine the composition of ice wedges and the influence of ice wedge thaw on the biolability of Yedoma OM. Incubation assays were used to assess OM biolability, fluorescence spectroscopy to characterize the OM composition, and potential enzyme activity rates to examine the controls and regulation of OM degradation. We show that increasing amounts of ice wedge melt water in Yedoma-leached incubations enhanced the loss of dissolved OM over time. This may be attributed to the presence of low-molecular weight compounds and low initial phenolic content in the OM of ice wedges, providing a readily available substrate that promotes the degradation of Yedoma OC. The physical vulnerability of ice wedges upon thaw (causing irreversible collapse), combined with the composition of ice wedge-engrained OM (co-metabolizing old OM), underlines the particularly strong potential of Yedoma to generate a positive feedback to climate warming relative to other forms of non-ice wedge permafrost.
Bayesian logistic regression analysis of the association of intimate partner violence and modern contraceptive use in the Philippines

This study employs data extracted from the 2008 Philippine National Demographic and Health Survey to examine the association between intimate partner violence and modern contraceptive use among married women in the Philippines. Instead of the classical approach of data analysis commonly used in many studies, the Bayesian approach for logistic regression analysis is used to estimate the association between intimate partner violence and modern contraceptive use. Important variables that can affect the association such as the woman's age, work status, education, place of residence and religion, the husband's education and work status, the household's wealth status, family size, and decision making control were considered in this study. This study revealed a significant association between intimate partner violence and modern contraceptive use with an odds ratio of 1.345 and a corresponding 90% credible interval of 1.201 to 1.502. Thus, the odds of using modern contraceptives for married women in the Philippines who had experienced intimate partner violence is 34.5% higher than the odds for those women who did not experience intimate partner violence. KEYWORDS: Bayesian logistic regression, bayesian data analysis, logistic regression, intimate partner violence, modern contraceptive use
Chimeric Allografts Induced by Short‐Term Treatment With Stem Cell Mobilizing Agents Result in Long‐Term Kidney Transplant Survival Without Immunosuppression: II, Study in Miniature Swine

Transplantation is now lifesaving therapy for patients with end‐stage organ failure but requires lifelong immunosuppression with resultant morbidity. Current immunosuppressive strategies inhibit T cell activation and prevent donor–recipient engagement. Therefore, it is not surprising that few host cells are demonstrated in donor grafts. However, our recent small animal studies found large numbers of recipient stem cells present after transplantation and pharmacological mobilization, resulting in a chimeric, repopulated organ. We now confirm these findings in a well‐characterized large animal preclinical model. Here, we show that AMD3100 and FK506 mobilization of endogenous stem cells immediately post kidney transplantation combined with repeat therapy at 1, 2, and 3 months led to drug‐free long‐term survival in maximally immunologically mismatched swine. Three long‐term recipients have stable chimeric transplants, preserved antidonor skin graft responses, and normal serum creatinine levels despite withdrawal of all medication for 3 years.
A multicore system using NoC communication for parallel coarse-grain data processing

We design a Multicores System On-Chip (MPSoC) that uses Network-on-Chip (NoC) as the communication interconnect between the cores. The system is designed to perform parallel coarse-grain data processing. As a comparison, we also build a bus-based system that contains the same number of cores. UVM based cycle accurate test is created to measure the performance of bothsystems and to show the advantages of the NoC interconnect.
Properties of spinal lamina III GABAergic neurons in naïve and in neuropathic mice

Nerve injury leads to Aβ‐fibre‐mediated mechanical allodynia that is in part due to an impaired GABAergic inhibition in the spinal cord dorsal horn. The properties and function of GABAergic neurons in spinal cord lamina III, an area where low‐threshold mechanosensitive Aβ‐fibres terminate are, however, largely unknown.
The Feasibility of Incentivizing Participation in an Online Social Network Weight Loss Program

Engagement in online social network-delivered weight loss interventions is a predictor of weight loss. Incentivizing engagement in a subset of participants may increase group engagement and subsequent weight loss. In a pilot feasibility trial, 56 adults with obesity were randomized to two Facebook-delivered weight loss interventions, one had 10% users incentivized to engage daily and the other did not. We compared conditions on engagement and weight loss, and then compared incentivized users and natural high engagers on weight loss. Participants were 46.3 (SD: 10.3) years and 89% female. The incentivized user condition had greater total engagement (p=0.0361), but weight loss did not differ (p=0.2096). Three natural superusers emerged in each condition. Natural superusers lost more weight than incentivized users (p=0.0358). Natural superusers’ posts elicited more comments than incentivized superusers (p=0.0107). Incentivized superusers may engage differently than natural superusers. Future studies should explore ways to promote engagement in online interventions.
Determinants of the human immunodeficiency virus type 1 p15NC-RNA interaction that affect enhanced cleavage by the viral protease

During human immunodeficiency virus type 1 (HIV-1) virion assembly, cleavage of the Gag precursor by the viral protease results in the transient appearance of a nucleocapsid-p1-p6 intermediate product designated p15NC. Utilizing the p15NC precursor protein produced with an in vitro transcription-translation system or purified after expression in Escherichia coli, we have demonstrated that RNA is required for efficient cleavage of HIV p15NC. Gel mobility shift and nitrocellulose filter binding experiments indicate that purified p15NC protein specifically binds its corresponding mRNA with an estimated Kd of 1.5 nM. Binding was not affected by the presence or absence of zinc or EDTA. Moreover, mutagenesis of the cysteine residues within either of the two Cys-His arrays had no effect on RNA binding or on RNA-dependent cleavage by the viral protease. In contrast, decreased binding of RNA and diminished susceptibility to cleavage in vitro were observed with p15NC-containing mutations in one or more residues within the triplet of basic amino acids present in the region between the two zinc fingers. In addition, we found that 21- to 24-base DNA and RNA oligonucleotides of a particular sequence and secondary structure could substitute for p15 RNA in the enhancement of p15NC cleavage. Virus particles carrying a mutation in the triplet of NC basic residues (P3BE) show delayed cleavage of p15NC and a defect in core formation despite the eventual appearance of fully processed virion protein. These results define determinants of the p15NC-RNA interaction that lead to enhanced protease-mediated cleavage and demonstrate the importance of the triplet of basic residues in formation of the virus core.
Pharmacokinetics of Antiretroviral Drugs in Anatomical Sanctuary Sites: The Fetal Compartment (Placenta and Amniotic Fluid)

HIV resides within anatomical ‘sanctuary sites’ where local drug exposure and viral dynamics may differ significantly from the systemic compartment. Widespread implementation of antiretroviral therapy has seen a significant decline in the incidence of mother-to-child transmission (MTCT) of HIV. In addition to suppression of maternal plasma/genital viral loads, antiretroviral agents that cross the placenta and achieve adequate concentrations in the fetal compartment may exert a greater prophylactic effect. Penetration of antiretrovirals in the fetal compartment is expressed by accumulation ratios derived from the measurement of drug concentrations in paired maternal plasma and umbilical cord samples. The nucleoside analogues and nevirapine accumulate extensively in cord blood and in the surrounding amniotic fluid, whereas the protease inhibitors (PIs) exhibit low-to-moderate placental accumulation. Early data suggest that high placental/neonatal concentrations are achieved with raltegravir, but to a lesser extent with etravirine and maraviroc (rank order of accumulation: raltegravir/nucleoside reverse transcriptase inhibitor [tenofovir > zidovudine/lamivudine/emtricitabine/stavudine/abacavir] > non-nucleoside reverse transcriptase inhibitor [nevirapine > etravirine] > PI > maraviroc/enfuvirtide). More comprehensive in vivo pharmacokinetic data are required to justify the potential use of these agents as safe and effective options during pregnancy.
Immigrant status and unmet health care needs.

OBJECTIVES To compare whether unmet health needs differ between immigrants and non-immigrants, and examine whether help-seeking characteristics account for any unmet needs disparities. METHODS The data are from the Canadian Community Health Survey Cycle 1.1, conducted by Statistics Canada in 2000-2001. The study sample includes 16,046 immigrants and 102,173 non-immigrants aged 18 and older from across Canada. The study employs logistic regression models to examine whether help-seeking behaviours explain unmet needs differences. RESULTS Logistic regression analysis indicates that immigrants have a 12% (95% CI: 6-18) lower all-cause unmet needs risk (odds ratio) than non-immigrants after controlling for differences in help-seeking characteristics. The unmet needs risk among long-term immigrants (15 years of residence and more), however, is similar to non-immigrants after considering these characteristics. We found differences between immigrants and non-immigrants in reasons for unmet needs, with more immigrants believing that the care would be inadequate, not knowing where to access health care, and having foreign language problems. CONCLUSIONS The Canadian health care system delivers sufficient health care to immigrants, even though the poverty rate and proportion of visible minorities are comparatively higher within this subpopulation. Nonetheless, these results indicate that some immigrant-specific health care access barriers may exist.
Imputation of DNA Methylation Levels in the Brain Implicates a Risk Factor for Parkinson’s Disease

Understanding how genetic variation affects intermediate phenotypes, like DNA methylation or gene expression, and how these in turn vary with complex human disease provides valuable insight into disease etiology. However, intermediate phenotypes are typically tissue and developmental stage specific, making relevant phenotypes difficult to assay. Assembling large case–control cohorts, necessary to achieve sufficient statistical power to assess associations between complex traits and relevant intermediate phenotypes, has therefore remained challenging. Imputation of such intermediate phenotypes represents a practical alternative in this context. We used a mixed linear model to impute DNA methylation (DNAm) levels of four brain tissues at up to 1826 methylome-wide sites in 6259 patients with Parkinson’s disease and 9452 controls from across five genome-wide association studies (GWAS). Six sites, in two regions, were found to associate with Parkinson’s disease for at least one tissue. While a majority of identified sites were within an established risk region for Parkinson’s disease, suggesting a role of DNAm in mediating previously observed genetic effects at this locus, we also identify an association with four CpG sites in chromosome 16p11.2. Direct measures of DNAm in the substantia nigra of 39 cases and 13 control samples were used to independently replicate these four associations. Only the association at cg10917602 replicated with a concordant direction of effect (P = 0.02). cg10917602 is 87 kb away from the closest reported GWAS hit. The employed imputation methodology implies that variation of DNAm levels at cg10917602 is predictive for Parkinson’s disease risk, suggesting a possible causal role for methylation at this locus. More generally this study demonstrates the feasibility of identifying predictive epigenetic markers of disease risk from readily available data sets.
Mitogen-Activated Protein/Extracellular Signal-Regulated Kinase Kinase Inhibition Results in Biphasic Alteration of Epidermal Homeostasis with Keratinocytic Apoptosis and Pigmentation Disorders

Purpose: Raf/mitogen-activated protein/extracellular signal-regulated kinase (ERK) kinase (MEK)/ERK signaling pathway is constitutively activated in melanoma. AZD6244 blocks MEK1/2, inhibiting ERK phosphorylation. We focus on associated cutaneous toxicity and we attempt to understand the underlying pathophysiology and design treatment strategies. Experimental Design: Dermatologic conditions of 22 patients with unresectable melanoma stage III/IV in a phase II trial were evaluated. Thirteen patients received AZD6244 initially, and nine patients were treated with AZD6244 following tumor progression with temozolomide. Biopsies were compared with matched controls in normal skin. Immunohistochemistry was performed. Half-side treatment of acute skin toxicity compared therapeutic options. Results: Nineteen of 22 (86%) AZD6244-treated patients presented with cutaneous eruptions. Seventeen patients (77%) developed acute papulopustular rash. Chronic skin changes included xerosis, paronychia, and fissured fingertips, resembling cutaneous toxicity of epidermal growth factor receptor inhibition. In addition, we observed reduced pigmentation of hair and skin. Histology of acute skin lesions revealed a significant increase of apoptotic keratinocytes (P = 0.0008), focal neutrophilic infiltrates, destruction of the adnexal structures by neutrophils, and reduced cytokeratins. A significant proliferation shift from basal to suprabasal keratinocytes was shown in acute and chronic lesions. The number and viability of melanocytes was not affected. Corticosteroids plus antibacterial topical therapy ameliorate acute skin toxicity. Conclusions: AZD6244-associated skin reactions partly overlap with those observed upon epidermal growth factor receptor inhibition. Additionally, pigmentation of skin and hair is affected. The interruption of the MEK signaling pathway results in an acute keratinocyte stress response with disturbed epidermal homeostasis, inflammation, and tissue damage. Chronic adaptation controls inflammatory tissue damage but leads to cutaneous malfunctions that explain chronic skin toxicity. Clin Cancer Res; 16(3); 1058–64
Personality and intimate partner aggression in Gorakhpur, Uttar Pradesh, India

The goals of the study were threefold: to examine, in a sample of Hindi-speaking Indian women, (1) the internal consistency reliability and psychometric validity of a broad assessment of intimate partner aggression (IPA) that previously has been used in multiple languages in the public-health domain; (2) the extent to which the trait structure of a widely used personality measure conforms in this sample to the personality structure that has been found in many other cultural and geographic groupings and across many languages; and (3) relations between personality traits and the experience of IPA, including physical, psychological and sexual IPA. A sample of rural, north Indian women were recruited and asked to complete several psychological measures, including one of personality and one of their experience as a recipient of IPA. The data suggest that the structure of IPA, but not personality, in this sample is consistent with that commonly found in western samples. Reasons for the lack of replication in personality structure are discussed. Nonetheless, the relations between personality and IPA domains found in this sample suggest that personality is related to these women’s experience of IPA, but in ways that differ somewhat from western samples. Abstract Approved: Thesis SupervisorApproved: Thesis Supervisor Title and Department
Autism and Dietary Therapy

We report the history of a child with autism and epilepsy who, after limited response to other interventions following her regression into autism, was placed on a gluten-free, casein-free diet, after which she showed marked improvement in autistic and medical symptoms. Subsequently, following pubertal onset of seizures and after failing to achieve full seizure control pharmacologically she was advanced to a ketogenic diet that was customized to continue the gluten-free, casein-free regimen. On this diet, while still continuing on anticonvulsants, she showed significant improvement in seizure activity. This gluten-free casein-free ketogenic diet used medium-chain triglycerides rather than butter and cream as its primary source of fat. Medium-chain triglycerides are known to be highly ketogenic, and this allowed the use of a lower ratio (1.5:1) leaving more calories available for consumption of vegetables with their associated health benefits. Secondary benefits included resolution of morbid obesity and improvement of cognitive and behavioral features. Over the course of several years following her initial diagnosis, the child’s Childhood Autism Rating Scale score decreased from 49 to 17, representing a change from severe autism to nonautistic, and her intelligence quotient increased 70 points. The initial electroencephalogram after seizure onset showed lengthy 3 Hz spike-wave activity; 14 months after the initiation of the diet the child was essentially seizure free and the electroencephalogram showed only occasional 1-1.5 second spike-wave activity without clinical accompaniments.
Nucleotide Sequence of Beet Necrotic Yellow Vein Virus RNA-2

Summary The complete nucleotide sequence of beet necrotic yellow vein virus (BNYVV) RNA-2 has been determined from a study of cloned cDNA. The RNA sequence is 4612 nucleotides in length, excluding the poly(A) tail. There are six long open reading frames (ORFs) in the sequence. The viral coat protein cistron is the ORF nearest to the 5′ terminus and the coat protein amber termination codon is followed by a long in-phase ORF. A corresponding readthrough polypeptide with the coat protein sequence at its N terminus has been detected in previous in vitro translation studies. Four additional ORFs encoding potential polypeptides of mol. wt. 42000 (42K), 12.5K, 14.8K and 14.4K are present in the sequence and evidence is presented that the 42K polypeptide is expressed, probably from a subgenomic messenger RNA. There is extensive homology between sequences near the 3′ termini of RNA-2, RNA-3 and RNA-4 of BNYVV.
Reserves and trade jointly determine exposure to food supply shocks

While a growing proportion of global food consumption is obtained through international trade, there is an ongoing debate on whether this increased reliance on trade benefits or hinders food security, and specifically, the ability of global food systems to absorb shocks due to local or regional losses of production. This paper introduces a model that simulates the short-term response to a food supply shock originating in a single country, which is partly absorbed through decreases in domestic reserves and consumption, and partly transmitted through the adjustment of trade flows. By applying the model to publicly-available data for the cereals commodity group over a 17 year period, we find that differential outcomes of supply shocks simulated through this time period are driven not only by the intensification of trade, but as importantly by changes in the distribution of reserves. Our analysis also identifies countries where trade dependency may accentuate the risk of food shortages from foreign production shocks; such risk could be reduced by increasing domestic reserves or importing food from a diversity of suppliers that possess their own reserves. This simulation-based model provides a framework to study the short-term, nonlinear and out-of-equilibrium response of trade networks to supply shocks, and could be applied to specific scenarios of environmental or economic perturbations.