Removing batch effects for prediction problems with frozen surrogate variable analysis

Batch effects are responsible for the failure of promising genomic prognos- tic signatures, major ambiguities in published genomic results, and retractions of widely-publicized findings. Batch effect corrections have been developed to re- move these artifacts, but they are designed to be used in population studies. But genomic technologies are beginning to be used in clinical applications where sam- ples are analyzed one at a time for diagnostic, prognostic, and predictive applica- tions. There are currently no batch correction methods that have been developed specifically for prediction. In this paper, we propose an new method called frozen surrogate variable analysis (fSVA) that borrows strength from a training set for individual sample batch correction. We show that fSVA improves prediction ac- curacy in simulations and in public genomic studies. fSVA is available as part of the sva Bioconductor package

Engaging Elementary Students of Color in Culturally Relevant Teaching

The United States population has and is continuing to become more diverse. This is evident in our country’s schools as there is an increasing number of students of color in our classrooms. The problem is that national standardized assessment data shows students of color perform significantly lower than their white peers across all content areas. Numerous factors have been studied as possible reasons for the persisting gap. This project focuses on some of the in-school contributing factors, such as teacher diversity, inadequate curriculum, and the lack of diversity found in curriculum and children’s literature. As the gap in achievement has been studied for decades, researchers have also focused on studying the mismatch between school and students’ home culture. While researchers have coined varying terms, the theory of ‘culturally relevant teaching’ from Gloria Ladson-Billings is the backbone of this project. Culturally relevant teaching stands on three principles--- academic success, cultural competence, and critical consciousness. This project aims to engage elementary students of color in daily lessons that will connect to their identity, as well as having them critically think about the ways in which oppression and racism are present in our society, all while teaching academic skills. A professional development, in the format of a learning lab, will take place as lessons are being taught. This professional development will grow teachers\u27 knowledge and experience in implementing culturally relevant teaching. Children of color deserve an education that values and empowers them, while preparing them for better opportunities to be successful in life

Uses and Potentials of Wikis in the Classroom

As Prensky (2001) observes, "Our students have changed radically. Today's students are no longer the people our educational system was designed to teach " (1). Prensky sees today's students as digital natives while most of today's teachers remain digital immigrants. In particular, today's educators are acculturated to a print paradigm while students are increasingly products of a digitally-based secondary-oral paradigm. Happily for educators, electronic and cyber technologies can potentially combine the best aspects of both print and secondary-oral paradigms, allowing educators to move freely across the print-oral continuum. One cyber technology enabling this movement is the wiki, a unique interface where information is not fixed (as in a print model) but fluid and flexible to meet the needs of the community (as in the pre-literate age). In this article we describe how teaching and learning have changed across oral, print, and secondary-oral paradigms; in turn, after addressing some controversies over the use of wikis as scholarly and educational resources, we advocate the use of wikis as a teaching and learning tool. Technology and Learning Paradigms As technologies have changed through the millennia, so have teaching methods. From the one-to-one oral teaching style of the early agrarian age (pre-writing and pre-printing cultures) to the apprenticeship system and one-to-many lectures of the pre-industrial ages (writing and print cultures), teaching was predominantl

International students’ experiences of informed learning: a pedagogical case study

This case study explores the theory and practice of informed learning (Bruce, 2008) in a culturally diverse higher education context. It presents research findings about learning and teaching in a postgraduate unit of study entitled Personalised Language Development, an elective in the Master of TESOL and TEFL programs at Queensland University of Technology (QUT). This unit aims to enable international students to extend their disciplinary knowledge of English language teaching, their academic and linguistic fluency and awareness of their own information using processes. The paper outlines the case study research approach; describes the design and implementation of the unit; demonstrates how informed learning principles and characteristics underpin the unit design; presents findings about the international students’ experiences of informed learning through their reflections; and finally the paper discusses the implications of the findings for educators, including the potential transferability of informed learning across higher education disciplines

SIMULATED SODOMY AND OTHER FORMS OF HETEROSEXUAL HORSEPLAY: SAME SEX SEXUAL HARASSMENT, WORKPLACE GENDER HIERARCHIES, AND THE MYTH OF THE GENDER MONOLITH BEFORE AND AFTER ONCALE

From August to November 1991, Joseph Oncale, a married, heterosexual father of two, worked on an oil platform in the Gulf of Mexico. He quit his job, however, after two of his co-workers restrained him in the shower and forced a bar of soap into his anus while threatening to rape him.\u27 An automotive mechanic named Mark McWilliams reported to work each day to face not only constant teasing about his sex life and inability to get a woman, but also physical harassment. His co-workers exposed their genitals to him, placed a condom in his food, flicked their tongues at him while saying, I love you, I love you, tied his hands behind his back, blindfolded him, forced him to his knees, and simulated sexual acts by inserting a finger in his mouth and a broomstick between his buttocks. Over the course of two years, Phil Quick, a welder and machine operator at a plant in Iowa, was subjected to a practice of bagging, common in his workplace, in which men would grab and squeeze other men\u27s testicles. Quick, a heterosexual, endured repeated homophobic epithets and over one hundred bagging incidents, including one in which a coworker restrained Quick\u27s arms while another grabbed and squeezed Quick\u27s testicles hard enough to produce bruising and swelling. During the summer of 1992, the city of Belleville, Illinois, hired J. Doe and H. Doe, two heterosexual, sixteen-year-old twin brothers, for summer maintenance jobs. When they arrived, Jeff Dawe, a heterosexual former Marine of imposing stature, began picking on H. Doe, who wore an earring. He called him queer, fag, and bitch; questioned whether he was a boy or a girl; threatened to take H. out to the woods and get him in the ass; and on one occasion grabbed H.\u27s testicles

It’s MORe exciting than mu: crosstalk between mu opioid receptors and glutamatergic transmission in the mesolimbic dopamine system

Opioids selective for the G protein-coupled mu opioid receptor (MOR) produce potent analgesia and euphoria. Heroin, a synthetic opioid, is considered one of the most addictive substances, and the recent exponential rise in opioid addiction and overdose deaths has made treatment development a national public health priority. Existing medications (methadone, buprenorphine, and naltrexone), when combined with psychosocial therapies, have proven efficacy in reducing aspects of opioid addiction. Unfortunately, these medications have critical limitations including those associated with opioid agonist therapies (e.g., sustained physiological dependence and opioid withdrawal leading to high relapse rates upon discontinuation), non-adherence to daily dosing, and non-renewal of monthly injection with extended-release naltrexone. Furthermore, current medications fail to ameliorate key aspects of addiction such as powerful conditioned associations that trigger relapse (e.g., cues, stress, the drug itself). Thus, there is a need for developing novel treatments that target neural processes corrupted with chronic opioid use. This requires a basic understanding of molecular and cellular mechanisms underlying effects of opioids on synaptic transmission and plasticity within reward-related neural circuits. The focus of this review is to discuss how crosstalk between MOR-associated G protein signaling and glutamatergic neurotransmission leads to immediate and long-term effects on emotional states (e.g., euphoria, depression) and motivated behavior (e.g., drug-seeking, relapse). Our goal is to integrate findings on how opioids modulate synaptic release of glutamate and postsynaptic transmission via α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid and N-methyl-D-aspartate receptors in the nucleus accumbens and ventral tegmental area with the clinical (neurobehavioral) progression of opioid dependence, as well as to identify gaps in knowledge that can be addressed in future studies

Triggering of microearthquakes in Iceland by volatiles released from a dyke intrusion

We suggest that carbon dioxide exsolved from a mid-crustal basaltic dyke intrusion in Iceland migrated upwards and triggered shallow seismicity by allowing failure on pre-existing fractures under the relatively low elastic stresses (100–200 kPa; 1–2 bar) generated by the dyke inflation. Intense swarms of microseismicity accompanied magmatic intrusion into a dyke at depths of 13–19 km in the crust of Iceland's Northern Volcanic Rift Zone during 2007–2008. Contemporaneously, a series of small normal earthquakes, probably triggered by elastic stresses imposed by the dyke intrusion, occurred in the uppermost 4 km of crust: fault plane solutions from these are consistent with failure along the extensional fabric and surface fissure directions mapped in the area, suggesting that the faults failed along existing rift zone fabric even though the mid-crustal dyke is highly oblique to it. Several months after the melt froze in the mid-crust and seismicity associated with the intrusion had ceased, an upsurge in shallow microseismicity began in the updip projection of the dyke near the brittle–ductile transition at 6–7 km depth below sea level. This seismicity is caused by failure on right-lateral strike-slip faults, with fault planes orientated 23 ± 3°, which are identical with the 24 ± 2° orientation in this area of surface fractures and fissures caused by plate spreading and extension of the volcanic rift zone. However, these earthquakes have T-axes approximately aligned with the opening direction of the dyke, and the right-lateral sense of failure is opposite that of regional strike-slip faults. We suggest that the fractures occurred along pre-existing weaknesses generated by the pervasive fabric of the rift zone, but that the dyke opening in the mid-crust beneath it caused right-lateral failure. The seismicity commenced after a temporal delay of several months and has persisted for over 3 yr. We propose that fluids exsolved from the magma in the dyke, primarily carbon dioxide, percolated updip and to shallower depths predominantly along pre-existing fractures. Increased pore pressure from the volatiles reduced the effective normal compressive stress on faults, increasing the likelihood of failure and allowing the modest stress changes generated by the intrusion to cause failure. Propagation of volatiles through the crust would also account for the observed time delay between the intrusion at depth and the shallow earthquake clusters. A further short-lived cluster of earthquakes at 2–4 km depth beneath the surface exhibits left-lateral strike-slip faulting with epicentres well orientated along a lineation which is identical with other subparallel strike-slip faults in the area that transfer motion between two adjacent spreading segments. These shallow earthquakes lie beyond lobes of significant positive Coulomb stress change caused by the intrusion, implying minimal modifications to the stress field in their vicinity; hence, they continue to respond to the regional stress field rather than the local stress field generated by the dyke intrusion

Research Needs and Learning Format Preferences of Graduate Students at a Large Public University: An Exploratory Study

This article reports on a study of research needs and learning preferences of graduate students at a public research university. A sequential exploratory mixed-method design was used, with a survey instrument developed from an initial qualitative stage. Significant differences were found between master’s and doctoral students’ and on-campus and online students’ confidence with several research skills. Graduate students overall prefer asynchronous online options and in-person workshops over synchronous online instruction and in-class presentations for learning research skills. The article concludes with a discussion of the value of the sequential exploratory mixed-method design for informing practice at an individual institution.Publisher allows immediate open acces

Identification and analysis of Single Nucleotide Polymorphisms (SNPs) in the mosquito Anopheles funestus, malaria vector

BACKGROUND: Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in eukaryotic species and have become an important marker for genetic studies. The mosquito Anopheles funestus is one of the major malaria vectors in Africa and yet, prior to this study, no SNPs have been described for this species. Here we report a genome-wide set of SNP markers for use in genetic studies on this important human disease vector. RESULTS: DNA fragments from 50 genes were amplified and sequenced from 21 specimens of An. funestus. A third of specimens were field collected in Malawi, a third from a colony of Mozambican origin and a third form a colony of Angolan origin. A total of 494 SNPs including 303 within the coding regions of genes and 5 indels were identified. The physical positions of these SNPs in the genome are known. There were on average 7 SNPs per kilobase similar to that observed in An. gambiae and Drosophila melanogaster. Transitions outnumbered transversions, at a ratio of 2:1. The increased frequency of transition substitutions in coding regions is likely due to the structure of the genetic code and selective constraints. Synonymous sites within coding regions showed a higher polymorphism rate than non-coding introns or 3' and 5'flanking DNA with most of the substitutions in coding regions being observed at the 3(rd )codon position. A positive correlation in the level of polymorphism was observed between coding and non-coding regions within a gene. By genotyping a subset of 30 SNPs, we confirmed the validity of the SNPs identified during this study. CONCLUSION: This set of SNP markers represents a useful tool for genetic studies in An. funestus, and will be useful in identifying candidate genes that affect diverse ranges of phenotypes that impact on vector control, such as resistance insecticide, mosquito behavior and vector competence