Using hexamers to predict cis-regulatory motifs in Drosophila

BACKGROUND: Cis-regulatory modules (CRMs) are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upstream, downstream, and even within their target genes. Due to the difficulty of finding CRMs using biological and computational techniques, even well-studied regulatory systems may contain CRMs that have not yet been discovered. RESULTS: We present a simple, efficient method (HexDiff) based only on hexamer frequencies of known CRMs and non-CRM sequence to predict novel CRMs in regulatory systems. On a data set of 16 gap and pair-rule genes containing 52 known CRMs, predictions made by HexDiff had a higher correlation with the known CRMs than several existing CRM prediction algorithms: Ahab, Cluster Buster, MSCAN, MCAST, and LWF. After combining the results of the different algorithms, 10 putative CRMs were identified and are strong candidates for future study. The hexamers used by HexDiff to distinguish between CRMs and non-CRM sequence were also analyzed and were shown to be enriched in regulatory elements. CONCLUSION: HexDiff provides an efficient and effective means for finding new CRMs based on known CRMs, rather than known binding sites

Investigation of the lineâ pair pattern method for evaluating mammographic focal spot performance

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135107/1/mp7921.pd

Introduction: Dialogues about the local and the global in education

This issue of the journal is based on an OCIES-sponsored program for Early Career Researchers (ECRs). The program has established an academic alliance of ECRs to explore educational issues in Oceania and Asia through the lens of local knowledges, wisdoms and theories, helping us to de-centre ourselves from an obsession with the West and Western epistemologies. Philip Chan and Hongzhi Zhang are the conveners, and Bob Teasdale and Zane Ma Rhea have acted as mentors of the program

Characteristics of Cognitive Behavioral Therapy for Older Adults Living in Residential Care: Protocol for a Systematic Review

Background: The prevalence rates of depressive and anxiety disorders are high in residential aged care settings. Older adults in such settings might be prone to these disorders because of losses associated with transitioning to residential care, uncertainty about the future, as well as a decline in personal autonomy, health, and cognition. Cognitive behavioral therapy (CBT) is efficacious in treating late-life depression and anxiety. However, there remains a dearth of studies examining CBT in residential settings compared with community settings. Typically, older adults living in residential settings have higher care needs than those living in the community. To date, no systematic reviews have been conducted on the content and the delivery characteristics of CBT for older adults living in residential aged care settings. Objective: The objective of this paper is to describe the systematic review protocol on the characteristics of CBT for depression and/or anxiety for older adults living in residential aged care settings. Methods: This protocol was developed in compliance with the recommendations of the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P). Studies that fulfill the inclusion criteria will be identified by systematically searching relevant electronic databases, reference lists, and citation indexes. In addition, the PRISMA flowchart will be used to record the selection process. A pilot-tested data collection form will be used to extract and record data from the included studies. Two reviewers will be involved in screening the titles and abstracts of retrieved records, screening the full text of potentially relevant reports, and extracting data. Then, the delivery and content characteristics of different CBT programs of the included studies, where available, will be summarized in a table. Furthermore, the Downs and Black checklist will be used to assess the methodological quality of the included studies. Results: Systematic searches will commence in May 2018, and data extraction is expected to commence in July 2018. Data analyses and writing will happen in October 2018. Conclusions: In this section, the limitations of the systematic review will be outlined. Clinical implications for treating late-life depression and/or anxiety, and implications for residential care facilities will be discussed

Molecular analysis distinguishes metastatic disease from second cancers in patients with retinoblastoma

The pediatric ocular tumor retinoblastoma readily metastasizes, but these lesions can masquerade as histologically similar pediatric small round blue cell tumors. Since 98% of retinoblastomas have RB1 mutations and a characteristic genomic copy number “signature”, genetic analysis is an appealing adjunct to histopathology to distinguish retinoblastoma metastasis from second primary cancer in retinoblastoma patients. Here, we describe such an approach in two retinoblastoma cases. In patient one, allele-specific (AS)-PCR for a somatic nonsense mutation confirmed that a temple mass was metastatic retinoblastoma. In a second patient, a rib mass shared somatic copy number gains and losses with the primary tumor. For definitive diagnosis, however, an RB1 mutation was needed, but heterozygous promoter→exon 11 deletion was the only RB1 mutation detected in the primary tumor. We used a novel application of inverse PCR to identify the deletion breakpoint. Subsequently, AS-PCR designed for the breakpoint confirmed that the rib mass was metastatic retinoblastoma. These cases demonstrate that personalized molecular testing can confirm retinoblastoma metastases and rule out a second primary cancer, thereby helping to direct the clinical management

A Survey of PCN-Based Admission Control and Flow Termination

Pre-congestion notification (PCN) provides feedback\ud about load conditions in a network to its boundary nodes. The PCN working group of the IETF discusses the use of PCN to implement admission control (AC) and flow termination (FT) for prioritized realtime traffic in a DiffServ domain. Admission control (AC) is a well-known flow control function that blocks admission requests of new flows when they need to be carried over a link whose admitted PCN rate already exceeds an admissible rate. Flow termination (FT) is a new flow control function that terminates some already admitted flows when they are carried over a link whose admitted PCN rate exceeds a supportable rate. The latter condition can occur in spite of AC, e.g., when traffic is rerouted due to network failures.\ud This survey gives an introduction to PCN and is a primer for\ud this new technology. It presents and discusses the multitude of architectural design options in an early stage of the standardization process in a comprehensive and streamlined way before only a subset of them is standardized by the IETF. It brings PCN from the IETF to the research community and serves as historical record

Classification of compressed breast shapes for the design of equalization filters in xâ ray mammography

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134971/1/mp8272.pd