The Iron Range Engineering PBL Curriculum: How Students Adapt to and Function within PBL

Iron Range Engineering is a unique complete-PBL curriculum for upper division students. Rather than studying about engineering in traditional engineering courses, IRE students solve complex and ill-structured industry problems in mining, milling, and manufacturing industries. To support students’ transition to PBL and to facilitate deep approaches to learning technical and professional competencies required for the engineers of the future, faculty have created a variety of structures. This paper describes IRE’s PBL implementation and reports the results of a qualitative study of their students

Alternative Pathways To Engineering Success –Using Academic And Social Integration To Understand Two-Year Engineering Student Success

The need for educating engineers in the United States continues as the projected demand is still rising as the number of high school seniors planning to enter engineering careers has remained relatively stable (Sargent, 2014). Additionally, figures show that attrition rates in undergraduate engineering continue to be an area of concern, (Sargent, 2014; Gibbons, 2005; NSF, 2004). Given the projected increased demand for engineers, the engineering education community must explore a variety of pathways for engineering students to be successful. Organizations such as National Science Foundation (Laanan, Jackson, Darrow, 2010) have noted that beginning engineering study at a two-year campus and then transferring to an engineering bachelor’s degree-granting institution is an important path and source for additional engineering students. Although some have explored the logistical issues and curricular design components of two-year campuses that enables engineering students to complete their bachelor degrees elsewhere, there is very little that explores the non-curricular factors on these campuses that help such students successfully progress (Laanan, et al., 2010). Using Tinto’s theory of integration (1975, 1993), this study examines the relationship between student entry characteristics and measures of social and academic integration to engineering learning outcomes. Understanding how integration factors on two-year campuses impact engineering student success can be used to inform the design of curricular and campus-based experiences that support the success of engineering students on two-year campuses.  Results indicate the social and academic integration factors significantly predict engineering students’ learning outcomes, especially their commitment to engineering studies

Average luminosity distance in inhomogeneous universes

The paper studies the correction to the distance modulus induced by inhomogeneities and averaged over all directions from a given observer. The inhomogeneities are modeled as mass-compensated voids in random or regular lattices within Swiss-cheese universes. Void radii below 300 Mpc are considered, which are supported by current redshift surveys and limited by the recently observed imprint such voids leave on CMB. The averaging over all directions, performed by numerical ray tracing, is non-perturbative and includes the supernovas inside the voids. Voids aligning along a certain direction produce a cumulative gravitational lensing correction that increases with their number. Such corrections are destroyed by the averaging over all directions, even in non-randomized simple cubic void lattices. At low redshifts, the average correction is not zero but decays with the peculiar velocities and redshift. Its upper bound is provided by the maximal average correction which assumes no random cancelations between different voids. It is described well by a linear perturbation formula and, for the voids considered, is 20% of the correction corresponding to the maximal peculiar velocity. The average correction calculated in random and simple cubic void lattices is severely damped below the predicted maximal one after a single void diameter. That is traced to cancellations between the corrections from the fronts and backs of different voids. All that implies that voids cannot imitate the effect of dark energy unless they have radii and peculiar velocities much larger than the currently observed. The results obtained allow one to readily predict the redshift above which the direction-averaged fluctuation in the Hubble diagram falls below a required precision and suggest a method to extract the background Hubble constant from low redshift data without the need to correct for peculiar velocities.Comment: 34 pages, 21 figures, matches the version accepted in JCA

Allelic Ratios and the Mutational Landscape Reveal Biologically Significant Heterozygous SNVs

The issue of heterozygosity continues to be a challenge in the analysis of genome sequences. In this article, we describe the use of allele ratios to distinguish biologically significant single-nucleotide variants from background noise. An application of this approach is the identification of lethal mutations in Caenorhabditis elegans essential genes, which must be maintained by the presence of a wild-type allele on a balancer. The h448 allele of let-504 is rescued by the duplication balancer sDp2. We readily identified the extent of the duplication when the percentage of read support for the lesion was between 70 and 80%. Examination of the EMS-induced changes throughout the genome revealed that these mutations exist in contiguous blocks. During early embryonic division in self-fertilizing C. elegans, alkylated guanines pair with thymines. As a result, EMS-induced changes become fixed as either G→A or C→T changes along the length of the chromosome. Thus, examination of the distribution of EMS-induced changes revealed the mutational and recombinational history of the chromosome, even generations later. We identified the mutational change responsible for the h448 mutation and sequenced PCR products for an additional four alleles, correlating let-504 with the DNA-coding region for an ortholog of a NFκB-activating protein, NKAP. Our results confirm that whole-genome sequencing is an efficient and inexpensive way of identifying nucleotide alterations responsible for lethal phenotypes and can be applied on a large scale to identify the molecular basis of essential genes

A two-neuron system for adaptive goal-directed decision-making in Lymnaea

During goal-directed decision-making, animals must integrate information from the external environment and their internal state to maximize resource localization while minimizing energy expenditure. How this complex problem is solved by the nervous system remains poorly understood. Here, using a combined behavioural and neurophysiological approach, we demonstrate that the mollusc Lymnaea performs a sophisticated form of decision-making during food-searching behaviour, using a core system consisting of just two neuron types. The first reports the presence of food and the second encodes motivational state acting as a gain controller for adaptive behaviour in the absence of food. Using an in vitro analogue of the decision-making process, we show that the system employs an energy management strategy, switching between a low- and high-use mode depending on the outcome of the decision. Our study reveals a parsimonious mechanism that drives a complex decision-making process via regulation of levels of tonic inhibition and phasic excitation

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Distributed network organization underlying feeding behavior in the mollusk Lymnaea

The aim of the work reviewed here is to relate the properties of individual neurons to network organization and behavior using the feeding system of the gastropod mollusk, Lymnaea. Food ingestion in this animal involves sequences of rhythmic biting movements that are initiated by the application of a chemical food stimulus to the lips and esophagus. We investigated how individual neurons contribute to various network functions that are required for the generation of feeding behavior such as rhythm generation, initiation ('decision making'), modulation and hunger and satiety. The data support the view that feeding behavior is generated by a distributed type of network organization with individual neurons often contributing to more than one network function, sharing roles with other neurons. Multitasking in a distributed type of network would be 'economically' sensible in the Lymnaea feeding system where only about 100 neurons are available to carry out a variety of complex tasks performed by millions of neurons in the vertebrate nervous system. Having complementary and potentially alternative mechanisms for network functions would also add robustness to what is a 'noisy' network where variable firing rates and synaptic strengths are commonly encountered in electrophysiological recording experiments

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN