Miracle-dz/UniFAR-FTUs huggingface dataset:
Undergraduate Honors Theses Honors Program Spring 2013 Using Rule Induction to Elucidate Co-Occurrence Patterns in Microbial Data

Hundreds of studies have addressed whether the presence or absence of certain bacteria are linked with a particular phenotype. However, it is plausible that the causative agent (or the consequence) of a given phenotype is not a single type of microbe, but groups of them, perhaps in specific combinations. Rule Induction is a commonly used machine learning method to infer structure within observational data, and build rules to represent these structures. In this thesis I introduce the application of a method, Rule Induction, to infer co-occurrence patterns in microbial data. First, I benchmark the methods within Rule Induction, to assess how rules are generated with regards to several parameters such as table density, support and confidence. I then subsample data over multiple iterations to understand the robustness of the rules being produced to verify due to sampling. Next, I provide insight into different biological variables and examine their effect on rules produced. I compare 16S rRNA region, specifically V1-3 and V3-5 regions. I compare different sequencing technology, specifically 454 and Illumina. I finally compare time, specifically looking over a time frame of 400 days. Within all these comparisons I aim to understand the differences, but more importantly what is conserved when these samples are stratified by these variables in terms of the generated rules. Finally, I explore Rule Induction using two microbial datasets, and compare the rules to already-known associations. The first dataset I interpret identifies a correlation between HIV and the Gut Microbiome. The second dataset distinguishes the Gut Microbiome over varying geographical locations. I link each of these rules iv produced from each dataset with taxonomic information and consolidate those rules to give rise to the underlying structure within the biological data. Dedication To my family and friends. Acknowledgements First and foremost, I would like to thank Rob Knight for letting me be a part of his lab. He has been a fantastic mentor and someone who I look up to very much. His passion for research is contagious, and I have learned so much in my time here. I am very fascinated and intrigued by the research being done in this lab in addition to the microbiome field at large. I would like to thank Mike Mozer for being a great mentor as well, by giving me great advice specific to this project as well as general life advice. My final committee member, Anne Dougherty, has been …
Vitellogenin expression in the oilseed rape pest Meligethes aeneus

When investigating insecticide resistance of pest insects, for example, the pollen beetle Meligethes aeneus, it is relevant to differentiate toxicological and molecular genetic data between male and female specimens. A molecular sex determination method would allow resistance testing to be run without prior sorting of the samples. A one‐step quantitative RT‐PCR method for quantification of the yolk protein vitellogenin expression in the pollen beetle was established. The expression level of vitellogenin relative to tubulin was determined. Pollen beetles were tested at different time points during their development to determine if vitellogenin is a reliable molecular marker for detection of sexually mature females. The differentiation between females and males by relative expression of vitellogenin to tubulin is conditional regarding the life cycle. Sexually mature females and males could easily be distinguished, whereas immature specimens could not be seperated. Vitellogenin expression is a successful marker for identification of sexually mature pollen beetles. Females from the spring populations showed vitellogenin expression when the temperature was above 10.2°C. Further, detailed observations of vitellogenin throughout the spring indicated a strong relationship between daily temperatures and vitellogenin expression, which is an indicator of oviposition ability.
Shatterbelts and conflict behaviour: The effect of globalisation on ‘high risk’ states

This article ties together seemingly disparate literatures (those of globalisation and ‘shatterbelt states') as a means of investigating the changing conflict behaviour of high‐risk states. The objective of this research is to ascertain empirically whether the circumstances that generate aggression by high‐risk states are the same as those for others. In addition, by examining how conflict behaviour has changed over time, and in conjunction with trade openness, these tests speak to the importance of economic interdependence as a mitigating counterforce to aggressive tendencies. The results indicate that domestic instability and fragmentation are more directly tied to high‐risk state behaviour than are systemic influences. In contrast, the probability that low‐risk states originate or participate in conflicts, and resort to violence, is tied to international factors. Surprisingly, increased repression seems to result from the opposite circumstances. For high‐risk states, changes in repressive behaviour are tied to the external environment while low‐risk states seem prone to change levels of repression in conjunction with their internal conditions. Lastly, and most importantly, trade openness has an important pacifying effect on high‐risk states, but appears to be irrelevant to the conflict behaviour of all others. Globalisation, it appears, mitigates the violence that is often initiated by high‐risk states. These results offer important preliminary evidence for understanding high risk‐states and the strategies that may reduce their aggressiveness.
The Effectiveness of a Home Care Program for Supporting Caregivers of Persons with Dementia in Developing Countries: A Randomised Controlled Trial from Goa, India

Objectives To develop and evaluate the effectiveness of a home based intervention in reducing caregiver burden, promoting caregiver mental health and reducing behavioural problems in elderly persons with dementia. Methodology and Principal Findings This was a randomised controlled trial in which the person with dementia-caregiver dyad was randomly allocated either to receive the intervention immediately or to a waiting list group which received the intervention after 6 months. It was carried out in communities based in two talukas (administrative blocks) in Goa, India. Mild to moderate cases with dementia (diagnosed using the DSM IV criteria and graded using the Clinical Dementia Rating scale) and their caregivers were included in the trial. Community based intervention provided by a team consisting of Home Care Advisors who were supervised by a counselor and a psychiatrist, focusing on supporting the caregiver through information on dementia, guidance on behaviour management, a single psychiatric assessment and psychotropic medication if needed. We measured caregiver mental health (General Health Questionnaire), caregiver burden (Zarit Burden Score), distress due to behavioural disturbances (NPI-D), behavioural problems in the subject (NPI-S) and activities of daily living in the elder with dementia (EASI). Outcome evaluations were masked to the allocation status. We analysed each outcome with a mixed effects model. 81 families enrolled in the trial; 41 were randomly allocated to the intervention. 59 completed the trial and 18 died during the trial. The intervention led to a significant reduction of GHQ (−1.12, 95% CI −2.07 to −0.17) and NPI-D scores (−1.96, 95%CI −3.51 to −0.41) and non-significant reductions in the ZBS, EASI and NPI-S scores. We also observed a non-significant reduction in the total number of deaths in people with dementia in the intervention arm (OR 0.34, 95% CI 0.01 to 1.03). Conclusion Home based support for caregivers of persons with dementia, which emphasizes the use of locally available, low-cost human resources, is feasible, acceptable and leads to significant improvements in caregiver mental health and burden of caring. ClinicalTrials.gov NCT00479271
A Multifunctional Four-Leg Grid-Connected Compensator

There has been a growing demand for using active power filters (APFs) for grid-connected converter systems based on nonconventional energy sources such as solar, wind, and fuel cells. In addition to power quality conditioning, the APF can also be used for bidirectional active power exchange with the three-phase four-wire grid and, therefore, acts as a multifunctional compensator. This paper presents a four-leg shunt multifunctional grid-connected power quality compensator. The compensator reference currents are generated using the instantaneous p-q-r theory. This paper proposes a simple modification to the conventional theory to eliminate the source neutral current from the three-phase four-wire power system. A digital controller is used to implement dead-beat current control. The outputs of the digital current controller are used as reference voltages for a 3-D space vector modulator (3D-SVM). A new approach for pulse width modulation waveform generation in 3D-SVM is proposed. All the intermediate steps are discussed from the viewpoint of implementation on a digital signal processor field-programmable gate array platform. The multifunctional compensator is analyzed, simulated, and tested experimentally for the most practical conditions in the power system, and the results are presented.
The European Union as a Leader in International Multilateral Negotiations — a Problematic Aspiration?

This article analyses the leadership role of the European Union (EU) in international multilateral negotiations. The purpose is to problematize the role of the EU as a multilateral leader by contrasting its self-images as an active initiator with other negotiating actors' perceptions of the Union. This is done by comparing the role conceptions presented by EU representatives with the images presented by delegates from non-member states in three different multilateral negotiating contexts. My results present a picture of the EU as a `restricted leader'. The undisputable great power status that the EU is claimed to hold is not necessarily transformed into a leadership role. The causes vary: in two cases it is internal disunity and co-ordination problems that create obstacles to intellectual leadership; in the third case it is perceived role conflicts that make the EU less than credible in its leadership aspirations. The existing potential for structural leadership is therefore not translated into practice.
A fast higher-order time-domain finite element-boundary integral method for 3-D electromagnetic scattering analysis

We present a hybrid time-domain finite element-boundary integral (FE-BI) method for analyzing 3D electromagnetic open-region transient scattering phenomena. This method has three unique features. The first is the hybridization scheme that combines the FE and BI representations of the fields. Instead of following the standard hybridization scheme used in the frequency domain, we propose a novel scheme that preserves the sparsity of the finite element matrix and that yields solutions free of spurious modes associated with interior BI resonances. The second feature is the use of a fast algorithm, the multilevel plane-wave time-domain (PWTD) method, for evaluating the BI. Invoking this scheme greatly reduces the computational expense when an object of large electrical dimensions is considered. Third, the FE component of the solver employs curvilinear tetrahedral elements to precisely model the scatterer's geometry and higher-order vector basis functions to accurately represent the fields.
Cholesterol gallstone formation in overweight mice establishes that obesity per se is not linked directly to cholelithiasis risk DOI 10.1194/jlr.M200102-JLR200

The relationship between obesity and cholesterol cholelithiasis is not well understood at physiologic or genetic levels. To clarify whether obesity per se leads to increased prevalence of cholelithiasis, we examined cholesterol gallstone susceptibility in three polygenic (KK/H1J, NON/LtJ, NOD/LtJ) and five monogenic [carboxypeptidase E (Cpe fat), agouti yellow (Ay), tubby (tub), leptin (Lepob), leptin receptor (Lepr db)] murine models of obesity during in-gestion of a lithogenic diet containing dairy fat, cholesterol, and cholic acid. At 8 weeks on the diet, one strain of polygenic obese mice was resistant whereas the others revealed low or intermediate prevalence rates of cholelithiasis. Monogenic obese mice showed distinct patterns with either high or low gallstone prevalence rates depending upon the mutation. Dysfunction of the leptin axis, as evidenced by the Lepob and the Lepr db mutations, markedly reduced gallstone formation in a genetically susceptible background strain, indicating that in mice with this genetic background, physiologic leptin homeostasis is a requisite for cholesterol cholelithogenesis. In contrast, the Cpe fat mutation enhanced the prevalence of cholelithiasis markedly when compared with the background strain. Since CPE converts many prohormones to hormones, a deficiency of biologically active cholecystokinin is a likely contributor to enhanced susceptibility to cholelithiasis through compromising gallbladder contractility and small intestinal motility. Because some murine models of obesity increased, whereas others decreased cholesterol gallstone susceptibility, we establish that cholesterol cholelithiasis in mice is not simply a secondary consequence of obesity per se. Rather, specific genes and distinct pathophysiological pathways are responsible for the shared susceptibility to both of these common diseases.
A Rare case of Guillain-Barré syndrome in pregnancy treated with plasma exchange

Guillain-Barre syndromé (GBS) is an autoimmune disorder. It is rare in pregnancy as there is a decrease in cell-mediated immunity. A case of 28-year-old pregnant woman who presented with acute flaccid quadriplegia suffering from GBS is discussed in this study. She was treated with plasma exchange in her immediate post-partum period. The management of GBS in pregnancy has been discussed.
Differences in Methadone Metabolism by CYP2B6 Variants

Methadone is a long-acting opioid with considerable unexplained interindividual variability in clearance. Cytochrome P450 2B6 (CYP2B6) mediates clinical methadone clearance and metabolic inactivation via N-demethylation to 2-ethyl-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP). Retrospective studies suggest that individuals with the CYP2B6*6 allelic variant have higher methadone plasma concentrations. Catalytic activities of CYP2B6 variants are highly substrate- and expression-system dependent. This investigation evaluated methadone N-demethylation by expressed human CYP2B6 allelic variants in an insect cell coexpression system containing P450 reductase. Additionally, the influence of coexpressing cytochrome b5, whose role in metabolism can be inhibitory or stimulatory depending on the P450 isoform and substrate, on methadone metabolism, was evaluated. EDDP formation from therapeutic (0.25–1 μM) R- and S-methadone concentrations was CYP2B6.4 ≥ CYP2B6.1 ≥ CYP2B6.5 >> CYP2B6.9 ≈ CYP2B6.6, and undetectable from CYP2B6.18. Coexpression of b5 had small and variant-specific effects at therapeutic methadone concentrations but at higher concentrations stimulated EDDP formation by CYP2B6.1, CYP2B6.4, CYP2B6.5, and CYP2B6.9 but not CYP2B6.6. In vitro intrinsic clearances were generally CYP2B6.4 ≥ CYP2B6.1 > CYP2B6.5 > CYP2B6.9 ≥ CYP2B6.6. Stereoselective methadone metabolism (S>R) was maintained with all CYP2B6 variants. These results show that methadone N-demethylation by CYP2B6.4 is greater compared with CYP2B6.1, whereas CYP2B6.9 and CYP2B6.6 (which both contain the 516G>T, Q172H polymorphism), are catalytically deficient. The presence or absence of b5 in expression systems may explain previously reported disparate catalytic activities of CYP2B6 variants for specific substrates. Differences in methadone metabolism by CYP2B6 allelic variants provide a mechanistic understanding of pharmacogenetic variability in clinical methadone metabolism and clearance.
Periodic breathing and apnea in preterm infants. I. Evidence for hypoventilation possibly due to central respiratory depression.

We made 84 studies on 20 "healthy" preterm infants during the first 34 days of life to discover whether infants breathing periodically hypoventilate or hyperventilate and whether the major defect is at the central or peripheral chemoreceptors. Six infants breathed periodically (n = 26) and seven regularly (n = 27) at all times; seven infants breathed periodically (n = 15) or regularly (n = 16) in different studies. In these three groups (periodic, regular, and intermediate), we compared respiratory minute volume and frequency, heart rate, alveolar oxygen tension (PAO2) and alveolar carbon dioxide tension (PACO2) and PO2, PCO2 and pH of arterialized capillary blood, alveolar-capillary differences for PO2 and PCO2, peripheral chemoreceptor sensitivity and CO2 responses. We measured ventilation with a nosepiece and a screen flowmeter. The mean values for the intermediate and periodic groups were similar. There were major differences between the periodic and regular groups. The infants breathing periodically (1) hypoventilated, (2) showed a significant shift of the CO2 response curve to the right with a 22% decrease in slope, and (3) had an increased response to O2. However, the two groups had similar alveolar-capillary PO2 and PCO2 differences. These findings suggest that the major defect is not in the lungs or at the peripheral chemoreceptors but at the respiratory center (or central receptors).
Frequency of Antibiotic-Producing Pseudomonas spp. in Natural Environments

The antibiotics phenazine-1-carboxylic acid (PCA) and 2,4-diacetylphloroglucinol (Phl) are major determinants of biological control of soilborne plant pathogens by various strains of fluorescent Pseudomonas spp. In this study, we described primers and probes that enable specific and efficient detection of a wide variety of fluorescent Pseudomonas strains that produce various phenazine antibiotics or Phl. PCR analysis and Southern hybridization demonstrated that specific genes within the biosynthetic loci for Phl and PCA are conserved among various Pseudomonas strains of worldwide origin. The frequency of Phl- and PCA-producing fluorescent pseudomonads was determined on roots of wheat grown in three soils suppressive to take-all disease of wheat and four soils conducive to take-all by colony hybridization followed by PCR. Phenazine-producing strains were not detected on roots from any of the soils. However, Phl-producing fluorescent pseudomonads were isolated from all three take-all-suppressive soils at densities ranging from approximately 5 x 10(sup5) to 2 x 10(sup6) CFU per g of root. In the complementary conducive soils, Phl-producing pseudomonads were not detected or were detected at densities at least 40-fold lower than those in the suppressive soils. We speculate that fluorescent Pseudomonas spp. that produce Phl play an important role in the natural suppressiveness of these soils to take-all disease of wheat.
Investigating Risk Factors for Cataract Using the Cerner Health FactsÂ® Database

Title: Investigating Risk Factors for Cataract Using the Cerner Health Facts® Database Background: A retrospective study was performed using the Cerner Health Facts® database, a HIPAA compliant and deidentified database, to evaluate risk factors associated with cataract. Methods and Findings: Using ICD-9 codes, a study group population was determined by selecting all patients in the database who visited the eye clinic. A data-driven approach was used to select multiple variables and odds ratio analysis was performed to determine the association of the risk factors with cataract formation. Odds ratio analysis indicated that 7 variables out of 18 were at a 20% or higher odds for developing of cataract. These include gentamicin, hypertension, lipid metabolism disorder, obesity, steroids and type-two diabetes and lacrimal disorder. Conclusion: This is the first study to show a link between lacrimal disorders and the development of cataract.
Provenance Aware Linked Sensor Data

Provenance, from the French word “provenir”, describes the lineage or history of a data entity. Provenance is critical information in the sensors domain to identify a sensor and analyze the observation data over time and geographical space. In this paper, we present a framework to model and query the provenance information associated with the sensor data exposed as part of the Web of Data using the Linked Open Data conventions. This is accomplished by developing an ontology-driven provenance management infrastructure that includes a representation model and query infrastructure. This provenance infrastructure, called Sensor Provenance Management System (PMS), is underpinned by a domain specific provenance ontology called Sensor Provenance (SP) ontology. The SP ontology extends the Provenir upper level provenance ontology to model domain-specific provenance in the sensor domain. In this paper, we describe the implementation of the Sensor PMS for provenance tracking in the Linked Sensor
Constructing ontology-driven protein family databases

MOTIVATION Protein family databases provide a central focus for scientific communities as well as providing useful resources to aide research. However, such resources require constant curation and often become outdated and discontinued. We have developed an ontology-driven system for capturing and managing protein family data that addresses the problems of maintenance and sustainability. RESULTS Using protein phosphatases and ABC transporters as model protein families, we constructed two protein family database resources around a central DAML+OIL ontology. Each resource contains specialist information about each protein family, providing specialized domain-specific resources based on the same template structure. The formal structure, combined with the extraction of biological data using GO terms, allows for automated update strategies. Despite the functional differences between the two protein families, the ontology model was equally applicable to both, demonstrating the generic nature of the system. AVAILABILITY The protein phosphatase resource, PhosphaBase, is freely available on the internet (http://www.bioinf.man.ac.uk/phosphabase). The DAML+OIL ontology for the protein phosphatases and the ABC transporters is available on request from the authors. CONTACT kwolstencroft@cs.man.ac.uk.
First evidence of a bipartite medial cuneiform in the hominin fossil record: a case report from the Early Pleistocene site of Dmanisi

A medial cuneiform exhibiting complete bipartition was discovered at the Early Pleistocene site of Dmanisi, Georgia. The specimen is the oldest known instance of this anatomical variant in the hominin fossil record. Here we compare developmental variation of the medial cuneiform in fossil hominins, extant humans and great apes, and discuss potential implications of bipartition for hominin foot phylogeny and function. Complete bipartition is rare among modern humans (< 1%); incomplete bipartition was found in 2 of 200 examined great ape specimens and also appears in the form of a divided distal articular surface in the Stw573c Australopithecus africanus specimen. Although various developmental pathways lead to medial cuneiform bipartition, it appears that the bipartite bone does not deviate significantly from normal overall morphology. Together, these data indicate that bipartition represents a phyletically old developmental variant of the medial cuneiform, which does not, however, affect the species‐specific morphology and function of this bone.