Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison.

BACKGROUND: Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several expressed sequence tag (EST) libraries were generated from a variety of U. maydis cell types. In addition to utility in the context of gene identification and structure annotation, the ESTs were analyzed to identify differentially abundant transcripts and to detect evidence of alternative splicing and anti-sense transcription. RESULTS: Four cDNA libraries were constructed using RNA isolated from U. maydis diploid teliospores (U. maydis strains 518 x 521) and haploid cells of strain 521 grown under nutrient rich, carbon starved, and nitrogen starved conditions. Using the genome sequence as a scaffold, the 15,901 ESTs were assembled into 6,101 contiguous expressed sequences (contigs); among these, 5,482 corresponded to predicted genes in the MUMDB (MIPS Ustilago maydis database), while 619 aligned to regions of the genome not yet designated as genes in MUMDB. A comparison of EST abundance identified numerous genes that may be regulated in a cell type or starvation-specific manner. The transcriptional response to nitrogen starvation was assessed using RT-qPCR. The results of this suggest that there may be cross-talk between the nitrogen and carbon signalling pathways in U. maydis. Bioinformatic analysis identified numerous examples of alternative splicing and anti-sense transcription. While intron retention was the predominant form of alternative splicing in U. maydis, other varieties were also evident (e.g. exon skipping). Selected instances of both alternative splicing and anti-sense transcription were independently confirmed using RT-PCR. CONCLUSION: Through this work: 1) substantial sequence information has been provided for U. maydis genome annotation; 2) new genes were identified through the discovery of 619 contigs that had previously escaped annotation; 3) evidence is provided that suggests the regulation of nitrogen metabolism in U. maydis differs from that of other model fungi, and 4) Alternative splicing and anti-sense transcription were identified in U. maydis and, amid similar observations in other basidiomycetes, this suggests these phenomena may be widespread in this group of fungi. These advances emphasize the importance of EST analysis in genome annotation

EST analysis of gene expression in early cleavage-stage sea urchin embryos

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts

Association of ABC (HbA1c, Blood Pressure, LDL-Cholesterol) Goal Attainment with Depression and Health-Related Quality of Life among Adults with Type 2 Diabetes

Aims: To determine the relationship between ABC goal attainment, depression, and health-related quality of life (HRQoL) among a national sample of patients with type 2 diabetes (T2DM). Methods: A retrospective, cross-sectional analysis was performed examining 808 non-pregnant patients ≥ 20 years old with T2DM from the National Health and Nutrition Examination Survey (NHANES) 2007-2012. ABC goals were defined as HbA1c \u3c 7%, BP \u3c 130/80mmHg, and LDL-C \u3c 100mg/dL. Patient characteristics associated with ABC goal attainment were examined. Results: Overall, 23.7% of participants achieved simultaneous ABC goals. Severe depression was significantly associated with lower rates of ABC goal attainment compared to those with no depression (5.0% vs. 25.4%, p = 0.048). ABC goal attainment rates were lower among females, Hispanic and non-Hispanic Black minority groups, and patients with a duration of diabetes over five years, while increased visits with health care professionals was significantly associated with meeting all three ABC goals for patients with T2DM. Conclusions: The relationship between simultaneous ABC goal attainment, depression and HRQoL is complex. Patients with T2DM unable to meet ABC goals may benefit from increased contact with health care professionals

Electromagnetic Forces in a Hybrid Magnetic-Bearing Switched-Reluctance Motor

Analysis and experimental measurement of the electromagnetic force loads on the hybrid rotor in a novel hybrid magnetic-bearing switched-reluctance motor (MBSRM) have been performed. A MBSRM has the combined characteristics of a switched-reluctance motor and a magnetic bearing. The MBSRM discussed in this report has an eight-pole stator and a six-pole hybrid rotor, which is composed of circular and scalloped lamination segments. The hybrid rotor is levitated using only one set of four stator poles, while a second set of four stator poles imparts torque to the scalloped portion of the rotor, which is driven in a traditional switched reluctance manner by a processor. Static torque and radial force analysis were done for rotor poles that were oriented to achieve maximum and minimum radial force loads on the rotor. The objective is to assess whether simple one-dimensional magnetic circuit analysis is sufficient for preliminary evaluation of this machine, which may exhibit strong three-dimensional electromagnetic field behavior. Two magnetic circuit geometries, approximating the complex topology of the magnetic fields in and around the hybrid rotor, were employed in formulating the electromagnetic radial force equations. Reasonable agreement between the experimental and the theoretical radial force loads predictions was obtained with typical magnetic bearing derating factors applied to the predictions

Far-Ultraviolet Cooling Features of the Antlia Supernova Remnant

We present far-ultraviolet observations of the Antlia supernova remnant obtained with Far-ultraviolet IMaging Spectrograph (FIMS, also called SPEAR). The strongest lines observed are C IV 1548,1551 and C III 977. The C IV emission of this mixed-morphology supernova remnant shows a clumpy distribution, and the line intensity is nearly constant with radius. The C III 977 line, though too weak to be mapped over the whole remnant, is shown to vary radially. The line intensity peaks at about half the radius, and drops at the edge of the remnant. Both the clumpy distribution of C IV and the rise in the C IV to C III ratio towards the edge suggest that central emission is from evaporating cloudlets rather than thermal conduction in a more uniform, dense medium.Comment: 9 pages, 4 figures, will be published in ApJ December 1, 2007, v670n2 issue. see http://astro.snu.ac.kr/~jhshinn/ms.pd

Implementation of an Accelerated Physical Examination Course in a Doctor of Pharmacy Program

Objective. To describe the implementation of a 1-day accelerated physical examination course for a doctor of pharmacy program and to evaluate pharmacy students’ knowledge, attitudes, and confi- dence in performing physical examination. Design. Using a flipped teaching approach, course coordinators collaborated with a physician faculty member to design and develop the objectives of the course. Knowledge, attitude, and confidence survey questions were administered before and after the practical laboratory. Assessment. Following the practical laboratory, knowledge improved by 8.3% (p,0.0001). Students’ perceived ability and confidence to perform a physical examination significantly improved (p,0.0001). A majority of students responded that reviewing the training video (81.3%) and reading material (67.4%) prior to the practical laboratory was helpful in learning the physical examination. Conclusion. An accelerated physical examination course using a flipped teaching approach was successful in improving students’ knowledge of, attitudes about, and confidence in using physical examination skills in pharmacy practice

Toward a neuroscience of interactive parent–infant dyad empathy

In accord with social neuroscience's progression to include interactive experimental paradigms, parents' brains have been activated by emotionally charged infant stimuli - especially of their own infant - including baby cry and picture. More recent research includes the use of brief video clips and opportunities for maternal response. Among brain systems important to parenting are those involved in empathy. This research may inform recent studies of decreased societal empathy, offer mechanisms and solutions

Towards Hierarchical Cluster Analysis Heatmaps as Visual Data Analysis of Entire Student Cohort Longitudinal Trajectories and Outcomes from Grade 9 through College

Research on data use and school Early Warning Systems (EWS) notes a central practice of researchers and practitioners is to search for patterns in student data to predict outcomes so schools can support success when students experience challenges. Yet, the domain lacks a means to visualize the rich longitudinal data that schools collect. Here, we use visual data analytic hierarchical cluster analysis (HCA) heatmaps to pattern and visualize entire longitudinal grading histories of a national sample of n=14,290 students from grade 9 to college in every enrolled subject and year, visualizing 6,728,920 individual datapoints. We provide both the open access code in R and an open-access online tool allowing anyone to upload their data and create a HCA heatmap, providing support for visual data analytic and data science practice for both education researchers and schooling organizations. Keywords: cluster analysis, heatmap, early warning indicator, early warning system, data use, education data mining, education data science, visual data analytics, longitudinal data, grades, dropout, high school, post-secondary, degree, STE