evoText: A new tool for analyzing the biological sciences

We introduce here evoText, a new tool for automated analysis of the literature in the biological sciences. evoText contains a database of hundreds of thousands of journal articles and an array of analysis tools for generating quantitative data on the nature and history of life science, especially ecology and evolutionary biology. This article describes the features of evoText, presents a variety of examples of the kinds of analyses that evoText can run, and offers a brief tutorial describing how to use it

Diabetes Self-Management Support Program in Predominantly Hispanic Faith Community Settings: A Pilot Study

Objectives: This study aimed to assess the feasibility, facilitators, barriers, and impact of adopting the Self-Management Resource Center Diabetes Self-Management Program (SMRC DSMP) on diabetes-related outcomes. Methods: The SMRC DSMP was implemented in five churches in San Antonio, Texas. A single group pre-post-test design was used to evaluate program effect on improving T2D outcomes. The primary outcome was glycohemoglobin (HbA1c) and secondary outcomes included Self-Efficacy for Diabetes, health-related quality of life (HRQOL), and patterns of eating and physical activity. Program feasibility, facilitators, and barriers were assessed through documentation and in-person interviews with participants. Results: A total of 96 participants were in the program with 87 completed endpoint surveys (91%). HbA1c level was significantly reduced by 0.73%. HRQL score increased by 2.6 days per month; stretching/strengthening activity increased by 36 minutes per week; and Self-Efficacy for Diabetes score significantly increased. The program was viewed as necessary for the community due to familiar environment with church acquaintances and ease of access to the program. Key barriers were a lack of facilitators’ competency in the Spanish language, short program length, and no ongoing support group / reunions. Conclusion: The DSMP program was feasible and effective when implemented in faith community settings for Hispanics

Coherent vortex dynamics in a strongly-interacting superfluid on a silicon chip

Two-dimensional superfluidity and quantum turbulence are directly connected to the microscopic dynamics of quantized vortices. However, surface effects have prevented direct observations of coherent vortex dynamics in strongly-interacting two-dimensional systems. Here, we overcome this challenge by confining a two-dimensional droplet of superfluid helium at microscale on the atomically-smooth surface of a silicon chip. An on-chip optical microcavity allows laser-initiation of vortex clusters and nondestructive observation of their decay in a single shot. Coherent dynamics dominate, with thermal vortex diffusion suppressed by six orders-of-magnitude. This establishes a new on-chip platform to study emergent phenomena in strongly-interacting superfluids, test astrophysical dynamics such as those in the superfluid core of neutron stars in the laboratory, and construct quantum technologies such as precision inertial sensors.Comment: Main text - 12 pages, 4 figures. Supplementary materials - 25 pages, 13 figure

Generation of Stable Pluripotent Stem Cells From NOD Mouse Tail-Tip Fibroblasts

OBJECTIVE: The NOD mouse strain has been widely used to investigate the pathology and genetic susceptibility for type 1 diabetes. Induced pluripotent stem cells (iPSCs) derived from this unique mouse strain would enable new strategies for investigating type 1 diabetes pathogenesis and potential therapeutic targets. The objective of this study was to determine whether somatic fibroblasts from NOD mice could be reprogrammed to become iPSCs, providing an alternative source of stem cells for the production of genetically modified NOD cells and mice. RESEARCH DESIGN AND METHODS: Adult tail-tip fibroblasts from male NOD mice were reprogrammed by retroviral transduction of the coding sequences of three transcription factors, OCT4, SOX2, and KLF4, in combination with a histone deacetylase inhibitor, valproic acid. RESULTS: Eighteen NOD iPSC lines were generated, and three of these cell lines were further characterized. All three cell lines exhibited silencing of the three reprogramming transgenes and reactivation of endogenous pluripotent markers (OCT4, SOX2, NANOG, REX1, and SSEA1). These NOD iPSCs readily differentiated in vitro to form embryoid bodies and in vivo by teratoma formation in immunodeficient mice. Moreover, NOD iPSCs were successfully transfected with a reporter transgene and were capable of contributing to the inner cell mass of C57BL/6 blastocysts, leading to the generation of a chimeric mouse. CONCLUSIONS: Adult tail-tip fibroblasts from NOD mice can be reprogrammed, without constitutive ectopic expression of transcription factors, to produce iPSCs that exhibit classic mouse embryonic stem cell (ESC) features. These NOD iPSCs can be maintained and propagated under normal ESC culture conditions to produce genetically altered cell lines, differentiated cells, and chimeric mice

A Late Maoist Industrial Revolution? Economic Growth in Jiangsu Province, 1966-1978

According to the conventional wisdom, the promise of the Chinese revolution of 1949 went unfulfilled in the Maoist era. Instead of taking-off, the economy grew slowly and widespread rural poverty persisted. The economic turning point was instead the famous political climacteric of 1976-78. But this metric of aggregates is the wrong criterion by which to judge China’s economic record because industrial revolutions have regional beginnings. They invariably take place against a backcloth of slow aggregate growth and stagnant material living standards. Accordingly, we should dwell neither on China’s slow overall growth nor its widespread poverty before 1978, but look instead for evidence of an emerging regional growth pole. This article argues that Jiangsu was such a growth pole in the late Maoist era, and that its record bears comparison with that of Lancashire and Yorkshire during the early years of Britain's industrial revolution. This holds out the intriguing possibility that a Chinese economic take-off, diffusing out of the Yangzi delta, would have occurred even without post-1978 policy changes

SuRVoS: Super-Region Volume Segmentation workbench

Segmentation of biological volumes is a crucial step needed to fully analyse their scientific content. Not having access to convenient tools with which to segment or annotate the data means many biological volumes remain under-utilised. Automatic segmentation of biological volumes is still a very challenging research field, and current methods usually require a large amount of manually-produced training data to deliver a high-quality segmentation. However, the complex appearance of cellular features and the high variance from one sample to another, along with the time-consuming work of manually labelling complete volumes, makes the required training data very scarce or non-existent. Thus, fully automatic approaches are often infeasible for many practical applications. With the aim of unifying the segmentation power of automatic approaches with the user expertise and ability to manually annotate biological samples, we present a new workbench named SuRVoS (Super-Region Volume Segmentation). Within this software, a volume to be segmented is first partitioned into hierarchical segmentation layers (named Super-Regions) and is then interactively segmented with the user's knowledge input in the form of training annotations. SuRVoS first learns from and then extends user inputs to the rest of the volume, while using Super-Regions for quicker and easier segmentation than when using a voxel grid. These benefits are especially noticeable on noisy, low-dose, biological datasets

Nonrandom processes maintain diversity in tropical forests

An ecological community\u27s species diversity tends to erode through time as a result of stochastic extinction, competitive exclusion, and unstable host-enemy dynamics. This erosion of diversity can be prevented over the short term if recruits are highly diverse as a result of preferential recruitment of rare species or, alternatively, if rare species survive preferentially, which increases diversity as the ages of the individuals increase. Here, we present census data from seven New and Old World tropical forest dynamics plots that all show the latter pattern. Within local areas, the trees that survived were as a group more diverse than those that were recruited or those that died. The larger (and therefore on average older) survivors were more diverse within local areas than the smaller survivors. When species were rare in a local area, they had a higher survival rate than when they were common, resulting in enrichment for rare species and increasing diversity with age and size class in these complex ecosystems

Identification of functional, endogenous programmed −1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae

In viruses, programmed −1 ribosomal frameshifting (−1 PRF) signals direct the translation of alternative proteins from a single mRNA. Given that many basic regulatory mechanisms were first discovered in viral systems, the current study endeavored to: (i) identify −1 PRF signals in genomic databases, (ii) apply the protocol to the yeast genome and (iii) test selected candidates at the bench. Computational analyses revealed the presence of 10 340 consensus −1 PRF signals in the yeast genome. Of the 6353 yeast ORFs, 1275 contain at least one strong and statistically significant −1 PRF signal. Eight out of nine selected sequences promoted efficient levels of PRF in vivo. These findings provide a robust platform for high throughput computational and laboratory studies and demonstrate that functional −1 PRF signals are widespread in the genome of Saccharomyces cerevisiae. The data generated by this study have been deposited into a publicly available database called the PRFdb. The presence of stable mRNA pseudoknot structures in these −1 PRF signals, and the observation that the predicted outcomes of nearly all of these genomic frameshift signals would direct ribosomes to premature termination codons, suggest two possible mRNA destabilization pathways through which −1 PRF signals could post-transcriptionally regulate mRNA abundance

CDCOCA: a statistical method to define complexity dependent co-occurring chromosomal aberrations

<p>Abstract</p> <p>Background</p> <p>Copy number alterations (CNA) play a key role in cancer development and progression. Since more than one CNA can be detected in most tumors, frequently co-occurring genetic CNA may point to cooperating cancer related genes. Existing methods for co-occurrence evaluation so far have not considered the overall heterogeneity of CNA per tumor, resulting in a preferential detection of frequent changes with limited specificity for each association due to the high genetic instability of many samples.</p> <p>Method</p> <p>We hypothesize that in cancer some linkage-independent CNA may display a non-random co-occurrence, and that these CNA could be of pathogenetic relevance for the respective cancer. We also hypothesize that the statistical relevance of co-occurring CNA may depend on the sample specific CNA complexity. We verify our hypotheses with a simulation based algorithm CDCOCA (complexity dependence of co-occurring chromosomal aberrations).</p> <p>Results</p> <p>Application of CDCOCA to example data sets identified co-occurring CNA from low complex background which otherwise went unnoticed. Identification of cancer associated genes in these co-occurring changes can provide insights of cooperative genes involved in oncogenesis.</p> <p>Conclusions</p> <p>We have developed a method to detect associations of regional copy number abnormalities in cancer data. Along with finding statistically relevant CNA co-occurrences, our algorithm points towards a generally low specificity for co-occurrence of regional imbalances in CNA rich samples, which may have negative impact on pathway modeling approaches relying on frequent CNA events.</p