The Integration of marketing concepts within the graphic design process

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Complete RNA inverse folding: computational design of functional hammerhead ribozymes

Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis-cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/.Comment: 17 pages, 2 tables, 7 figures, final version to appear in Nucleic Acids Researc

CRLF2 rearrangement in Ph-like acute lymphoblastic leukemia predicts relative glucocorticoid resistance that is overcome with MEK or Akt inhibition.

Philadelphia chromosome-like (Ph-like) acute lymphoblastic leukemia (ALL) is a genetically heterogeneous subtype of B-cell ALL characterized by chromosomal rearrangements and mutations that result in aberrant cytokine receptor and kinase signaling. In particular, chromosomal rearrangements resulting in the overexpression of cytokine receptor-like factor 2 (CRLF2) occur in 50% of Ph-like ALL cases. CRLF2 overexpression is associated with particularly poor clinical outcomes, though the molecular basis for this is currently unknown. Glucocorticoids (GCs) are integral to the treatment of ALL and GC resistance at diagnosis is an important negative prognostic factor. Given the importance of GCs in ALL therapy and the poor outcomes for patients with CRLF2 overexpression, we hypothesized that the aberrant signal transduction associated with CRLF2 overexpression might mediate intrinsic GC insensitivity. To test this hypothesis, we exposed Ph-like ALL cells from patient-derived xenografts to GCs and found that CRLF2 rearranged (CRLF2R) leukemias uniformly demonstrated reduced GC sensitivity in vitro. Furthermore, targeted inhibition of signal transduction with the MEK inhibitor trametinib and the Akt inhibitor MK2206, but not the JAK inhibitor ruxolitinib, was sufficient to augment GC sensitivity. These data suggest that suboptimal GC responses may in part underlie the poor clinical outcomes for patients with CRLF2 overexpression and provide rationale for combination therapy involving GCs and signal transduction inhibitors as a means of enhancing GC efficacy

Gauging the Relationship Between Contextual Growth and Structural Neglect

Population and land use out-migrations from urban to peripheral areas can result in non-functional, unmaintained historic structures which deteriorate to the point where removal is cheaper than removal – or demolition by neglect. The increasing rate of neglected historic structures is a growing concern. There is a need for research investigating connections between urban growth management and its effect on neglect. This paper applies Newman\u27s (2013) conceptual model of measuring neglect to Geographic Information Systems, comparing rates of neglect in historic Doylestown, Quakertown, and Bristol boroughs in Pennsylvania, USA utilizing different amounts of peripheral agricultural preservation. Comparisons are made examining descriptive statistics on existing conditions, a Polychoric correlation evaluating relationships between drivers of neglect, and a cross-comparative GIS spatial analysis. Results indicate as amounts of peripheral preserved farmlands increase, neglect can be lowered

Frequency and Clinical Presentation of Mucocutaneous Disease Due to Mycoplasma pneumoniae Infection in Children With Community-Acquired Pneumonia

Importance The diagnosis of Mycoplasma pneumoniae infection as the cause of mucocutaneous disease is challenging because current diagnostic tests are not able to differentiate M pneumoniae infection from carriage. Objective To examine the frequency and clinical presentation of M pneumoniae-induced mucocutaneous disease in children with community-acquired pneumonia (CAP) using improved diagnostics. Design, Setting, and Participants This prospective, longitudinal cohort study included 152 children aged 3 to 18 years with CAP enrolled in a CAP study from May 1, 2016, to April 30, 2017, at the University Children's Hospital Zurich. Children were inpatients or outpatients with clinically defined CAP according to the British Thoracic Society guidelines. Data analysis was performed from July 10, 2017, to June 29, 2018. Main Outcomes and Measures Frequency and clinical presentation of M pneumoniae-induced mucocutaneous disease in childhood CAP. Mycoplasma pneumoniae infection was diagnosed by polymerase chain reaction (PCR) of oropharyngeal samples and confirmed with the measurement of specific peripheral blood IgM antibody-secreting cells by enzyme-linked immunospot assay to differentiate M pneumoniae-infected patients from carriers with CAP caused by other pathogens. Mucocutaneous disease was defined as any eruptive lesion that involved skin and/or mucous membranes occurring during the CAP episode. Results Among 152 enrolled children with CAP (median [interquartile range] age, 5.7 [4.3-8.9] years; 84 [55.3%] male), 44 (28.9%) tested positive for M pneumoniae by PCR; of these, 10 children (22.7%) developed mucocutaneous lesions. All 10 patients with mucocutaneous eruptions tested positive for specific IgM antibody-secreting cells. Skin manifestations were found in 3 cases (2.8%) of M pneumoniae PCR-negative CAP (P < .001). The spectrum of M pneumoniae-induced mucocutaneous disease included M pneumoniae-induced rash and mucositis (3 cases [6.8%]), urticaria (2 cases [4.5%]), and maculopapular skin eruptions (5 cases [11.4%]). Two patients had ocular involvement as the sole mucosal manifestation (bilateral anterior uveitis and nonpurulent conjunctivitis). Patients with M pneumoniae-induced mucocutaneous disease had longer duration of prodromal fever (median [interquartile range], 10.5 [8.3-11.8] vs 7.0 [5.5-9.5] days; P = .02) and higher C-reactive protein levels (median [interquartile range], 31 [22-59] vs 16 [7-23] mg/L; P = .04) than patients with CAP due to M pneumoniae without mucocutaneous manifestations. They were also more likely to require oxygen (5 [50%] vs 1 [5%]; P = .007), to require hospitalization (7 [70%] vs 4 [19%]; P = .01), and to develop long-term sequelae (3 [30%] vs 0; P = .03). Conclusions and Relevance Mucocutaneous disease occurred significantly more frequently in children with CAP due to M pneumoniae than in children with CAP of other origins. Mycoplasma pneumoniae-induced mucocutaneous disease was associated with increased systemic inflammation, morbidity, and a higher risk of long-term sequelae

Epithelial laminin α5 is necessary for distal epithelial cell maturation, VEGF production, and alveolization in the developing murine lung

AbstractLaminin α5 is prominent in the basement membrane of alveolar walls, airways, and pleura in developing and adult lung. Targeted deletion of laminin α5 in mice causes developmental defects in multiple organs, but embryonic lethality has precluded examination of the latter stages of lung development. To identify roles for laminin α5 in lung development, we have generated an inducible lung epithelial cell-specific Lama5 null (SP-CLama5fl/−) mouse through use of the Cre/loxP system, the human surfactant protein C promoter, and the reverse tetracycline transactivator. SP-CLama5fl/− embryos exposed to doxycycline from E6.5 died a few hours after birth. Compared to control littermates, SP-CLama5fl/− lungs had dilated, enlarged distal airspaces, but basement membrane ultrastructure was preserved. Distal epithelial cell differentiation was perturbed, with a marked reduction of alveolar type II cells and a virtual absence of type I cells. Cell proliferation was reduced and apoptosis was increased. Capillary density was diminished, and this was associated with a decrease in total lung VEGF production. Overall, these findings indicate that epithelial laminin α5, independent of its structural function, is necessary for murine lung development, and suggest a role for laminin α5 in signaling pathways that promote alveolar epithelial cell differentiation and VEGF expression

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

<p>Abstract</p> <p>Background</p> <p>Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of '<it>Candidatus </it>Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.</p> <p>Results</p> <p>To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of '<it>Cand</it>. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from '<it>Cand</it>. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely <it>cis</it>-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data.</p> <p>Conclusion</p> <p>This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.</p

Weaving Academic Grace into the Fabric of Online Courses and Faculty Training: First-Year Engineering Student Advice for Online Faculty During the COVID-19 Pandemic and Faculty Responses

Background: In the spring of 2020, COVID-19 forced the majority of higher education online, resulting in a wave of new online students uniquely positioned to offer fresh perspectives and advice to faculty. Purpose: This study investigated the advice offered to online faculty by first-year engineering (FYE) students who were forced online during the pandemic and faculty ideas to address the student advice. Methods: This multi-methods study included qualitative data from 233 FYE students (in 67 teams across four class offerings) who provided advice for online faculty through an end-of-year team assignment, leveraging analytic induction methods for analysis. The Quality Matters Online Instructor Skill Set was used as the theoretical framework for viewing the student results (Quality Matters, 2016). After being presented with the student results, 41 faculty participants within two workshops brainstormed ways to respond to FYEs’ advice. Faculty workshop participants organized their own brainstorming/discussion results by themes within community documents. Results: Students forced online expressed the following needs/desires: instructional design practices appropriate for the online environment; understanding, flexibility, and patience from their faculty (which we defined as Academic Grace); instructor social presence; appropriate pedagogy for online learning environments; effective assessment; technologically capable instructors; and instructor understanding of their institutional context. Faculty advised responding to online students with more Academic Grace. Conclusions: This work reveals a new competency missing from traditional online instructor skills, that of Academic Grace. To embed Academic Grace within online courses, we propose that faculty consider a flexible bichronous model for online courses, in which students can choose to attend synchronous live lectures/classes or cover the material asynchronously at their own convenience. In this model, lecture/class recordings and supplemental asynchronous materials should be provided to foster fluid student movement between the learning modes. We also recommend online faculty training efforts include the components of Academic Grace: understanding, flexibility, and patience

Identifying behaviour change techniques in 287 randomized controlled trials of audit and feedback interventions targeting practice change among healthcare professionals

Background: Audit and feedback (A&F) is among the most widely used implementation strategies, providing healthcare professionals with summaries of their practice performance to prompt behaviour change and optimize care. Wide variability in effectiveness of A&F has spurred efforts to explore why some A&F interventions are more effective than others. Unpacking the variability of the content of A&F interventions in terms of their component behaviours change techniques (BCTs) may help advance our understanding of how A&F works best. This study aimed to systematically specify BCTs in A&F interventions targeting healthcare professional practice change. / Methods: We conducted a directed content analysis of intervention descriptions in 287 randomized trials included in an ongoing Cochrane systematic review update of A&F interventions (searched up to June 2020). Three trained researchers identified and categorized BCTs in all trial arms (treatment & control/comparator) using the 93-item BCT Taxonomy version 1. The original BCT definitions and examples in the taxonomy were adapted to include A&F-specific decision rules and examples. Two additional BCTs (‘Education (unspecified)’ and ‘Feedback (unspecified)’) were added, such that 95 BCTs were considered for coding. / Results: In total, 47/95 BCTs (49%) were identified across 360 treatment arms at least once (median = 5.0, IQR = 2.3, range = 129 per arm). The most common BCTs were ‘Feedback on behaviour’ (present 89% of the time; e.g. feedback on drug prescribing), ‘Instruction on how to perform the behaviour’ (71%; e.g. issuing a clinical guideline), ‘Social comparison’ (52%; e.g. feedback on performance of peers), ‘Credible source’ (41%; e.g. endorsements from respected professional body), and ‘Education (unspecified)’ (31%; e.g. giving a lecture to staff). A total of 130/287 (45%) control/comparator arms contained at least one BCT (median = 2.0, IQR = 3.0, range = 0–15 per arm), of which the most common were identical to those identified in treatment arms. / Conclusions: A&F interventions to improve healthcare professional practice include a moderate range of BCTs, focusing predominantly on providing behavioural feedback, sharing guidelines, peer comparison data, education, and leveraging credible sources. We encourage the use of our A&F-specific list of BCTs to improve knowledge of what is being delivered in A&F interventions. Our study provides a basis for exploring which BCTs are associated with intervention effectiveness. / Trial registrations: N/A