Designing a Modern Software Engineering Training Program with Cloud Computing

The software engineering industry is trending towards cloud computing. For our project, we assessed the various tools and practices used in modern software development. The main goals of this project were to create a reference model for developing cloud-based applications, to program a functional cloud-based prototype, and to develop an accompanying training manual. These materials will be incorporated into the software engineering courses at WPI, namely CS 3733 and CS 509

A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells

Recent large-scale genomics efforts to characterize the cis-regulatory sequences that orchestrate genome-wide expression patterns have produced impressive catalogues of putative regulatory elements. Most of these sequences have not been functionally tested, and our limited understanding of the non-coding genome prevents us from predicting which sequences are bona fide cis-regulatory elements. Recently, massively parallel reporter assays (MPRAs) have been deployed to measure the activity of putative cis-regulatory sequences in several biological contexts, each with specific advantages and distinct limitations. We developed LV-MPRA, a novel lentiviral-based, massively parallel reporter gene assay, to study the function of genome-integrated regulatory elements in any mammalian cell type; thus, making it possible to apply MPRAs in more biologically relevant contexts. We measured the activity of 2,600 sequences in U87 glioblastoma cells and human neural progenitor cells (hNPCs) and explored how regulatory activity is encoded in DNA sequence. We demonstrate that LV-MPRA can be applied to estimate the effects of local DNA sequence and regional chromatin on regulatory activity. Our data reveal that primary DNA sequence features, such as GC content and dinucleotide composition, accurately distinguish sequences with high activity from sequences with low activity in a full chromosomal context, and may also function in combination with different transcription factor binding sites to determine cell type specificity. We conclude that LV-MPRA will be an important tool for identifying cis-regulatory elements and stimulating new understanding about how the non-coding genome encodes information

Tourism in the Tuapse Region

The Tuapse region of Russia has great potential appeal for tourists yet experiences less tourism than nearby regions. The purpose of this project was to evaluate tourism in the Tuapse region compared to nearby regions on the Black Sea coast. We collaborated with the Financial University under the Government of the Russian Federation to visit regions of interest to conduct surveys of tourists, interviews of business administrators, and to make observations about the places visited. From the results of this data, we organized our findings in a SWOT analysis to present ideas for increasing tourism in the Tuapse region

Work related musculoskeletal injuries sustained by Australian osteopaths: Qualitative analysis of effects on practitioner health, clinical practice, and patient care

Background: There is limited literature that explores the experiences of osteopaths injured while engaging in clinical practice. Evidence from other similar health professions has described the numerous effects of work-related musculoskeletal injuries (WRMI). Work-related musculoskeletal injury refers to trauma to joints, ligaments, muscles and tendons resulting from injury sustained while undertaking work duties. This research aimed to gain a contextualised understanding of the experiences of osteopaths who have sustained a work-related musculoskeletal injury while performing clinical practice. Method: This research used a descriptive qualitative design. Participants were recruited as part of a larger cross-sectional study. Thirteen Australian osteopaths who had sustained a work-related musculoskeletal injury consented to participate in semi-structured interviews during May and June 2016. Thematic analysis was used to elicit important themes from the interview transcripts that had been recorded and transcribed verbatim. The qualitative accounts provided by the participants were coded for the impacts of their injuries on work, home life and leisure activities. Results: The participants provided detailed, contextual information about their injuries, including the contributing factors and the experience of living with a WRMI. The findings indicate that injured osteopaths often continue working because of financial commitments and their dedication to patient care. The participants offered insights into the challenges they faced due to the injury and the management strategies they used to deal with the impact on their work and personal life. The injuries were mostly unreported, the burden being carried by the participants and their families. Conclusion: This is the first research that explores the experiences of osteopaths who have sustained a WRMI. We anticipate that this research will encourage a broad and constructive discussion within the profession of the issues associated with WRMIs, including risk minimisation and injury prevention. Further research is warranted to understand the relationship between osteopaths training in ergonomics and injury prevention. This would lead to the development of guidelines and educational curricula addressing safe work for osteopaths. © 2017 The Author(s)

Rickettsia parkeri in Amblyomma americanum Ticks, Tennessee and Georgia, USA

To determine the geographic distribution of the newly recognized human pathogen Rickettsia parkeri, we looked for this organism in ticks from Tennessee and Georgia, USA. Using PCR and sequence analysis, we identified R. parkeri in 2 Amblyomma americanum ticks. This rickettsiosis may be underdiagnosed in the eastern United States

Infected Cell Killing by HIV-1 Protease Promotes NF-κB Dependent HIV-1 Replication

Acute HIV-1 infection of CD4 T cells often results in apoptotic death of infected cells, yet it is unclear what evolutionary advantage this offers to HIV-1. Given the independent observations that acute T cell HIV-1 infection results in (1) NF-κB activation, (2) caspase 8 dependent apoptosis, and that (3) caspase 8 directly activates NF-κB, we questioned whether these three events might be interrelated. We first show that HIV-1 infected T cell apoptosis, NF-κB activation, and caspase 8 cleavage by HIV-1 protease are coincident. Next we show that HIV-1 protease not only cleaves procaspase 8, producing Casp8p41, but also independently stimulates NF-κB activity. Finally, we demonstrate that the HIV protease cleavage of caspase 8 is necessary for optimal NF-κB activation and that the HIV-1 protease specific cleavage fragment Casp8p41 is sufficient to stimulate HIV-1 replication through NF-κB dependent HIV-LTR activation both in vitro as well as in cells from HIV infected donors. Consequently, the molecular events which promote death of HIV-1 infected T cells function dually to promote HIV-1 replication, thereby favoring the propagation and survival of HIV-1

Auditory Selective Attention to Speech Modulates Activity in the Visual Word Form Area

Selective attention to speech versus nonspeech signals in complex auditory input could produce top-down modulation of cortical regions previously linked to perception of spoken, and even visual, words. To isolate such top-down attentional effects, we contrasted 2 equally challenging active listening tasks, performed on the same complex auditory stimuli (words overlaid with a series of 3 tones). Instructions required selectively attending to either the speech signals (in service of rhyme judgment) or the melodic signals (tone-triplet matching). Selective attention to speech, relative to attention to melody, was associated with blood oxygenation level–dependent (BOLD) increases during functional magnetic resonance imaging (fMRI) in left inferior frontal gyrus, temporal regions, and the visual word form area (VWFA). Further investigation of the activity in visual regions revealed overall deactivation relative to baseline rest for both attention conditions. Topographic analysis demonstrated that while attending to melody drove deactivation equivalently across all fusiform regions of interest examined, attending to speech produced a regionally specific modulation: deactivation of all fusiform regions, except the VWFA. Results indicate that selective attention to speech can topographically tune extrastriate cortex, leading to increased activity in VWFA relative to surrounding regions, in line with the well-established connectivity between areas related to spoken and visual word perception in skilled readers

Preferred reporting items for journal and conference abstracts of systematic reviews and meta-analyses of diagnostic test accuracy studies (PRISMA-DTA for Abstracts):checklist, explanation, and elaboration

For many users of the biomedical literature, abstracts may be the only source of information about a study. Hence, abstracts should allow readers to evaluate the objectives, key design features, and main results of the study. Several evaluations have shown deficiencies in the reporting of journal and conference abstracts across study designs and research fields, including systematic reviews of diagnostic test accuracy studies. Incomplete reporting compromises the value of research to key stakeholders. The authors of this article have developed a 12 item checklist of preferred reporting items for journal and conference abstracts of systematic reviews and meta-analyses of diagnostic test accuracy studies (PRISMA-DTA for Abstracts). This article presents the checklist, examples of complete reporting, and explanations for each item of PRISMA-DTA for Abstracts