Advanced Data Analysis - Lecture Notes

Lecture notes for Advanced Data Analysis (ADA1 Stat 427/527 and ADA2 Stat 428/528), Department of Mathematics and Statistics, University of New Mexico, Fall 2016-Spring 2017. Additional material including RMarkdown templates for in-class and homework exercises, datasets, R code, and video lectures are available on the course websites: https://statacumen.com/teaching/ada1 and https://statacumen.com/teaching/ada2 . Contents I ADA1: Software 0 Introduction to R, Rstudio, and ggplot II ADA1: Summaries and displays, and one-, two-, and many-way tests of means 1 Summarizing and Displaying Data 2 Estimation in One-Sample Problems 3 Two-Sample Inferences 4 Checking Assumptions 5 One-Way Analysis of Variance III ADA1: Nonparametric, categorical, and regression methods 6 Nonparametric Methods 7 Categorical Data Analysis 8 Correlation and Regression IV ADA1: Additional topics 9 Introduction to the Bootstrap 10 Power and Sample size 11 Data Cleaning V ADA2: Review of ADA1 1 R statistical software and review VI ADA2: Introduction to multiple regression and model selection 2 Introduction to Multiple Linear Regression 3 A Taste of Model Selection for Multiple Regression VII ADA2: Experimental design and observational studies 4 One Factor Designs and Extensions 5 Paired Experiments and Randomized Block Experiments 6 A Short Discussion of Observational Studies VIII ADA2: ANCOVA and logistic regression 7 Analysis of Covariance: Comparing Regression Lines 8 Polynomial Regression 9 Discussion of Response Models with Factors and Predictors 10 Automated Model Selection for Multiple Regression 11 Logistic Regression IX ADA2: Multivariate Methods 12 An Introduction to Multivariate Methods 13 Principal Component Analysis 14 Cluster Analysis 15 Multivariate Analysis of Variance 16 Discriminant Analysis 17 Classificationhttps://digitalrepository.unm.edu/unm_oer/1002/thumbnail.jp

Effect of soil fertilization on the incidence of berry shrivel and the quality of resulting wine

Berry shrivel is becoming an increasing concern for winegrowers all over the world. Until today, no single factor causing this physiological disorder has been determined. Studies concerning berry shrivel conducted in Austria have shown that an unbalanced ratio of K and Mg in the soil is a likely factor contributing to the disorder. The aims of the present study were to establish a better understanding of the causes and consequences of berry shrivel and observe the effects of K and Mg fertilization via the soil on the incidence of berry shrivel, the mineral composition of affected berries and the resulting wine quality. A two-year fertilization trial was conducted on two sites located within southern Germany with the varieties 'Zweigelt' and 'Pinot Blanc'. Different amounts of K and Mg were applied each year at both locations in order to generate different ratios of K and Mg in the soil. Before harvest, the incidences of berry shrivel of the different treatments were determined. In addition, macronutrients including K, Mg and Ca that were translocated in healthy berries and berries affected by berry shrivel were determined at harvest. To compare the quality of wine influenced by berry shrivel, different wines were produced consisting of shrivelled berries, berries affected by bunch stem necrosis and healthy berries. In the soil fertilization trials, no significant differences in the incidences of berry shrivel were observed in relation to the soil fertilization. Major differences were found in the wine qualities of the different wines. Wines produced from healthy berries were always rated as the best wines, whereas wines produced from shrivelled berries were always rated as the lowest quality. The low quality parameters found in the must did not improve in the wine making process. Wines produced from berries affected by bunch stem necrosis were rated better than berry-shrivel-wines, however, rated less than the wine produced from healthy berries. The determinations of macronutrients’ level in the berries showed significant differences regarding the concentration of Ca. In the variety 'Zweigelt' in 2009, an average of 36 mg∙L-1 of Ca were found in healthy berries and 107 mg∙L-1 in berries affected by berry shrivel. In 'Pinot Blanc' in 2010, the average of Ca in healthy berries was 46 mg∙L-1 and 70 mg∙L-1 in berries affected by berry shrivel. No significant differences were found for K and Mg in the berries.

RNR1, a 3′–5′ exoribonuclease belonging to the RNR superfamily, catalyzes 3′ maturation of chloroplast ribosomal RNAs in Arabidopsis thaliana

Arabidopsis thaliana chloroplasts contain at least two 3′ to 5′ exoribonucleases, polynucleotide phosphorylase (PNPase) and an RNase R homolog (RNR1). PNPase has been implicated in both mRNA and 23S rRNA 3′ processing. However, the observed maturation defects do not affect chloroplast translation, suggesting that the overall role of PNPase in maturation of chloroplast rRNA is not essential. Here, we show that this role can be largely ascribed to RNR1, for which homozygous mutants germinate only on sucrose-containing media, and have white cotyledons and pale green rosette leaves. Accumulation of chloroplast-encoded mRNAs and tRNAs is unaffected in such mutants, suggesting that RNR1 activity is either unnecessary or redundant for their processing and turnover. However, accumulation of several chloroplast rRNA species is severely affected. High-resolution RNA gel blot analysis, and mapping of 5′ and 3′ ends, revealed that RNR1 is involved in the maturation of 23S, 16S and 5S rRNAs. The 3′ extensions of the accumulating 5S rRNA precursors can be efficiently removed in vitro by purified RNR1, consistent with this view. Our data suggest that decreased accumulation of mature chloroplast ribosomal RNAs leads to a reduction in the number of translating ribosomes, ultimately compromising chloroplast protein abundance and thus plant growth and development

Flexible Bioelectronic Devices Based on Micropatterned Monolithic Carbon Fiber Mats

Polymer-derived carbon can serve as an electrode material in multimodal neural stimulation, recording, and neurotransmitter sensing platforms. The primary challenge in its applicability in implantable, flexible neural devices is its characteristic mechanical hardness that renders it difficult to fabricate the entire device using only carbon. A microfabrication technique is introduced for patterning flexible, cloth-like, polymer-derived carbon fiber (CF) mats embedded in polyimide (PI), via selective reactive ion etching. This scalable, monolithic manufacturing method eliminates any joints or metal interconnects and creates electrocorticography electrode arrays based on a single CF mat. The batch-fabricated CF/PI composite structures, with critical dimension of 12.5 µm, are tested for their mechanical, electrical, and electrochemical stability, as well as to chemicals that mimic acute postsurgery inflammatory reactions. Their recording performance is validated in rat models. Reported CF patterning process can benefit various carbon microdevices that are expected to feature flexibility, material stability, and biocompatibility

A New Multielement Method for LA-ICP-MS Data Acquisition From Glacier Ice Cores

To answer pressing new research questions about the rate and timing of abrupt climate transitions, a robust system for ultrahigh-resolution sampling of glacier ice is needed. Here, we present a multielement method of LA-ICP-MS analysis wherein an array of chemical elements is simultaneously measured from the same ablation area. Although multielement techniques are commonplace for high-concentration materials, prior to the development of this method, all LA-ICP-MS analyses of glacier ice involved a single element per ablation pass or spot. This new method, developed using the LA-ICP-MS system at the W. M. Keck Laser Ice Facility at the University of Maine Climate Change Institute, has already been used to shed light on our flawed understanding of natural levels of Pb in Earth?s atmospherepublishersversionPeer reviewe

Creating access to SARS-CoV-2 screening and testing through community-based COVID-19 case-finding, observations from cross-sectional studies in Lesotho and Zambia

BACKGROUND: The health impact of the COVID-19 pandemic largely depends on the ability of the healthcare systems to develop effective and adaptable preparedness and mitigation strategies. A collaborative initiative (BRCCH-EDCTP COVID-19 Initiative) was set up between Lesotho and Zambia early on in the pandemic, to jointly conduct a project to investigate creating access to SARS-CoV-2 screening and testing through community-based COVID-19 case-finding. METHODS: Two different community case-finding strategies were deployed. In Lesotho, an approach was implemented whereby a community (village) health worker screened community members at their home or during community gatherings for COVID-19 signs and symptoms. All community members who screened positive were then offered SARS-CoV-2 testing. In Zambia, so-called community hubs, staffed by community health care workers, were set up at different locations in the community for people to walk in and get tested for SARS-CoV-2. Hubs changed location from week-to-week and targeted transmission hotspots. All persons visiting the hubs were offered testing for SARS-CoV-2 irrespective of self-reported signs and symptoms of COVID-19 though information was collected on occurrence of these. Testing in both approaches was done using SARS-CoV-2 rapid antigen tests. RESULTS: Setting up testing in the community setting was feasible in both countries. In Lesotho in the village health worker approach, over a period of 46 weeks, 7221 persons were screened, and 49 (11.4%) SARS-COV-2 cases identified among 428 COVID-19 screen positive participants. In the community hubs among 3150 people tested, 166 (5.3%) SARS-CoV-2 cases were identified in a period of 26 weeks. From the community hubs approach, where all seen were offered COVID-19 testing it was learned that people screening positive for COVID-19 signs and symptoms were more likely to test SARS-COV-2 positive, especially those reporting classic COVID-19 symptoms like loss of sense/smell for a short period of time (1-3 days). CONCLUSIONS: In conclusion, in this project we learned that implementing COVID-19 screening and testing by lay health workers in the community is possible. Characteristics of the population screened, tested, and identified to have SARS-CoV-2 are described to help guide development of future testing strategies

Low Energy Analyzing Powers in Pion-Proton Elastic Scattering

Analyzing powers of pion-proton elastic scattering have been measured at PSI with the Low Energy Pion Spectrometer LEPS as well as a novel polarized scintillator target. Angular distributions between 40 and 120 deg (c.m.) were taken at 45.2, 51.2, 57.2, 68.5, 77.2, and 87.2 MeV incoming pion kinetic energy for pi+ p scattering, and at 67.3 and 87.2 MeV for pi- p scattering. These new measurements constitute a substantial extension of the polarization data base at low energies. Predictions from phase shift analyses are compared with the experimental results, and deviations are observed at low energies.Comment: 15 pages, 4 figure

A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of nonredundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansion and plant growth

Cytochromes P450 monooxygenases from the CYP98 family catalyze the meta-hydroxylation step in the phenylpropanoid biosynthetic pathway. The ref8 Arabidopsis (Arabidopsis thaliana) mutant, with a point mutation in the CYP98A3 gene, was previously described to show developmental defects, changes in lignin composition, and lack of soluble sinapoyl esters. We isolated a T-DNA insertion mutant in CYP98A3 and show that this mutation leads to a more drastic inhibition of plant development and inhibition of cell growth. Similar to the ref8 mutant, the insertion mutant has reduced lignin content, with stem lignin essentially made of p-hydroxyphenyl units and trace amounts of guaiacyl and syringyl units. However, its roots display an ectopic lignification and a substantial proportion of guaiacyl and syringyl units, suggesting the occurrence of an alternative CYP98A3-independent meta-hydroxylation mechanism active mainly in the roots. Relative to the control, mutant plantlets produce very low amounts of sinapoyl esters, but accumulate flavonol glycosides. Reduced cell growth seems correlated with alterations in the abundance of cell wall polysaccharides, in particular decrease in crystalline cellulose, and profound modifications in gene expression and homeostasis reminiscent of a stress response. CYP98A3 thus constitutes a critical bottleneck in the phenylpropanoid pathway and in the synthesis of compounds controlling plant development. CYP98A3 cosuppressed lines show a gradation of developmental defects and changes in lignin content (40% reduction) and structure (prominent frequency of p-hydroxyphenyl units), but content in foliar sinapoyl esters is similar to the control. The purple coloration of their leaves is correlated to the accumulation of sinapoylated anthocyanins

Sunitinib induced pyoderma gangrenosum-like ulcerations

Pyoderma gangrenosum is a non-infectious neutrophilic skin disease commonly associated with underlying systemic diseases. Histopathological and laboratory diagnostics are unspecific in the majority of the cases and the diagnosis is made in accordance with the clinical picture. Here, we report the case of a 69-year old man with progredient pyoderma gangrenosum-like ulcerations under treatment with sunitinib due to hepatocellular carcinoma. A conventional ulcer therapy did not lead to a regression of the lesions. Solely cessation of sunitinib therapy resulted in an improvement of the ulcerations. Sunitinib is a multikinase inhibitor that targets the PDGF-α - and -β-, VEGF-1-3-, KIT-, FLT3-, CSF-1- and RET-receptor, thereby impairing tumour proliferation, pathological angiogenesis and metastasation. Here, we demonstrate that pyoderma gangrenosum-like ulcers may represent a serious side effect of sunitinib-based anti-cancer treatment

Photoluminescence investigations of 2D hole Landau levels in p-type single Al_{x}Ga_{1-x}As/GaAs heterostructures

We study the energy structure of two-dimensional holes in p-type single Al_{1-x}Ga_{x}As/GaAs heterojunctions under a perpendicular magnetic field. Photoluminescence measurments with low densities of excitation power reveal rich spectra containing both free and bound-carrier transitions. The experimental results are compared with energies of valence-subband Landau levels calculated using a new numerical procedure and a good agreement is achieved. Additional lines observed in the energy range of free-carrier recombinations are attributed to excitonic transitions. We also consider the role of many-body effects in photoluminescence spectra.Comment: 13 pages, 10 figures, accepted to Physical Review