The Solar Flare Iron Abundance

The abundance of iron is measured from emission line complexes at 6.65 keV (Fe line) and 8 keV (Fe/Ni line) in {\em RHESSI} X-ray spectra during solar flares. Spectra during long-duration flares with steady declines were selected, with an isothermal assumption and improved data analysis methods over previous work. Two spectral fitting models give comparable results, viz. an iron abundance that is lower than previous coronal values but higher than photospheric values. In the preferred method, the estimated Fe abundance is $A({\rm Fe}) = 7.91 \pm 0.10$ (on a logarithmic scale, with $A({\rm H}) = 12$), or $2.6 \pm 0.6$ times the photospheric Fe abundance. Our estimate is based on a detailed analysis of 1,898 spectra taken during 20 flares. No variation from flare to flare is indicated. This argues for a fractionation mechanism similar to quiet-Sun plasma. The new value of $A({\rm Fe})$ has important implications for radiation loss curves, which are estimated.Comment: Accepted by Astrophysical Journa

Exploring the Reactions of Peer Learners to a New Model of Peer-Assisted Simulation-Based Learning Clinical Placement

In response to the paucity of clinical placements available in 2020 due to the COVID-19 pandemic, alternate options for prelicensure students were necessary in order for them to complete the fieldwork required for graduation. In response, Curtin University replaced a faculty-led fully-simulated placement with a peer-assisted learning model. This incorporated final-year students acting as peer teachers to penultimate-year students, thus creating new learning and teaching placements for the final-year students. To our knowledge, this had never been done on such a scale before. Considering the importance of meeting learner expectations in the tertiary setting, the perceptions of peer learners around the innovation were important but unknown. This study used a prospective qualitative observational design that utilized feedback from peer learners relating to learning using the peer-assisted model. Peer learners provided written reflections that were analysed thematically. During November and December 2020, 171 penultimate-year physiotherapy students participated in one of two three-week placements, and 170 consented to participate in data collection. Qualitative data reflected several enablers and barriers to learning during the experience. These related to the peer teacher attributes, the provision of performance feedback, the learning environment, and the facilitation of clinical reasoning. Peer learners enjoyed the peer-assisted model, found peer teachers able to facilitate learning, and provided useful insights that will shape future placements. The success of the model supports repeating it in the future. This will maintain a bilateral exchange of peer-led clinical learning and teaching with diminished faculty supervisory workload

Observational Study Exploring the Efficacy and Effectiveness of a New Model of Peer-Assisted Simulation-Based Learning Clinical Placement

(1) Background: Immersive simulation-based learning is relevant and effective in health care professional pre-licensure training. Peer-assisted learning has reciprocal benefit for the learner and the teacher. A fully simulated model of fieldwork placement has been utilised at [de-identified] University since 2014, historically employing full-time faculty supervisors. Due to the COVID-19 pandemic in 2020, traditional clinical placement availability diminished. (2) Methods: This mixed-methods prospective observational study aimed to translate the existing faculty-led placement for penultimate-year physiotherapy students to a peer-taught model, thereby creating new teaching placements for final-year students. Final-and penultimate-year physiotherapy students undertook the fully simulated fieldwork placement either as peer learners or peer teachers. The placement was then evaluated using four outcome measures: The ‘measure of quality of giving feedback scale’ (MQF) was used to assess peer learner satisfaction with peer-teacher supervision; plus/delta reflec-tions were provided by peer teachers and faculty supervisors; student pass/fail rates for the penul-timate-year physiotherapy students. (3) Results: For 10 weeks during November and December 2020, 195 students and 19 faculty participated in the placement. Mean MQF scores ranged from 6.4 (SD 0.86) to 6.8 (SD) out of 7; qualitative data reflected positive and negative aspects of the experience. There was a 4% fail rate for penultimate-year students for the placement. Results suggested that peer learners perceived peer-led feedback was of a high quality; there were both positives and challenges experienced using the model. (4) Conclusions: Physiotherapy students effectively adopted a peer-taught fully simulated fieldwork placement model with minimal faculty supervision, and comparable clinical competency outcomes

Electroless Nickel Deposition:An Alternative for Graphene Contacting

We report the first investigation into the potential of electroless nickel deposition to form ohmic contacts on single layer graphene. To minimize the contact resistance on graphene, a statistical model was used to improve metal purity, surface roughness, and coverage of the deposited film by controlling the nickel bath parameters (pH and temperature). The metalized graphene layers were patterned using photolithography and contacts deposited at temperatures as low as 60 °C. The contact resistance was 215 ± 23 ω over a contact area of 200 μm × 200 μm, which improved upon rapid annealing to 107 ± 9 ω. This method shows promise toward low-cost and large-scale graphene integration into functional devices such as flexible sensors and printed electronics

Jejunal gene expression patterns correlate with severity of systemic infection in chicken

<p>Abstract</p> <p>Background</p> <p>Not much is known about the effect of <it>Salmonella enteritidis</it> on changes in the developmental processes occurring in the intestine of young chicken. Therefore we investigated the correlation of intestinal gene expression patterns with the severity of systemic Salmonella infections.</p> <p>Methods</p> <p>The number of Salmonella colony forming units (CFUs) in the liver of infected chicken were plotted against the average intestinal expression profiles of previously identified gene expression clusters. The functional properties of all the genes taken together present in 3 clusters exhibiting positive correlation at early time-points were compared with the functional properties of the genes displaying antagonistic correlations in 1 cluster. The top 5 ranking functional groups were analysed in further detail.</p> <p>Results</p> <p>Three clusters showed gene expression profiles which were positively correlated with the severity of systemic disease as measured by the number of Salmonella colony forming units in the liver. In these clusters, genes involved in morphological processes were predominantly present. One cluster had a profile that was negatively correlated with the severity of systemic disease, as measured by numbers of CFUs in the liver. The genes in the latter cluster were mostly involved in cell turn-over and metabolism.</p> <p>Conclusions</p> <p>In the developing jejunum of young chicken, both stimulatory and inhibitory gene expression mechanisms are correlated with the severity of systemic Salmonella infections.</p

PathEx: a novel multi factors based datasets selector web tool

<p>Abstract</p> <p>Background</p> <p>Microarray experiments have become very popular in life science research. However, if such experiments are only considered independently, the possibilities for analysis and interpretation of many life science phenomena are reduced. The accumulation of publicly available data provides biomedical researchers with a valuable opportunity to either discover new phenomena or improve the interpretation and validation of other phenomena that partially understood or well known. This can only be achieved by intelligently exploiting this rich mine of information.</p> <p>Description</p> <p>Considering that technologies like microarrays remain prohibitively expensive for researchers with limited means to order their own experimental chips, it would be beneficial to re-use previously published microarray data. For certain researchers interested in finding gene groups (requiring many replicates), there is a great need for tools to help them to select appropriate datasets for analysis. These tools may be effective, if and only if, they are able to re-use previously deposited experiments or to create new experiments not initially envisioned by the depositors. However, the generation of new experiments requires that all published microarray data be completely annotated, which is not currently the case. Thus, we propose the PathEx approach.</p> <p>Conclusion</p> <p>This paper presents PathEx, a human-focused web solution built around a two-component system: one database component, enriched with relevant biological information (expression array, omics data, literature) from different sources, and another component comprising sophisticated web interfaces that allow users to perform complex dataset building queries on the contents integrated into the PathEx database.</p

Amplified engagement of prefrontal cortex during control of voluntary action in Tourette syndrome

Tourette syndrome is characterized by ‘unvoluntary’ tics, which are compulsive, yet often temporarily suppressible. The inferior frontal gyrus is implicated in motor control, including inhibition of pre-potent actions through influences on downstream subcortical and motor regions. Although tic suppression in Tourette syndrome also engages the inferior frontal gyrus, it is unclear whether such prefrontal control of action is also dysfunctional: Tic suppression studies do not permit comparison with control groups, and neuroimaging studies of motor inhibition can be confounded by the concurrent expression or suppression of tics. Here, patients with Tourette syndrome were directly compared to control participants when performing an intentional inhibition task during functional MRI. Tic expression was recorded throughout for removal from statistical models. Participants were instructed to make a button press in response to Go cues, withhold responses to NoGo cues, and decide whether to press or withhold to ‘Choose’ cues. Overall performance was similar between groups, for both intentional inhibition rates (% Choose-Go) and reactive NoGo inhibition commission errors. A subliminal face prime elicited no additional effects on intentional or reactive inhibition. Across participants, the task activated prefrontal and motor cortices and subcortical nuclei, including pre-supplementary motor area, inferior frontal gyrus, insula, caudate nucleus, thalamus and primary motor cortex. In Tourette syndrome, activity was elevated in the inferior frontal gyrus, insula and basal ganglia, most notably within the right inferior frontal gyrus during voluntary action and inhibition (Choose-Go and Choose-NoGo), and reactive inhibition (NoGo-correct). Anatomically, the locus of this inferior frontal gyrus hyperactivation during control of voluntary action matched that previously reported for tic suppression. In Tourette syndrome, activity within the caudate nucleus was also enhanced during both intentional (Choose-NoGo) and reactive (NoGo-correct) inhibition. Strikingly, despite the absence of overt motor behaviour, primary motor cortex activity increased in patients with Tourette syndrome but decreased in controls during both reactive and intentional inhibition. Additionally, severity of premonitory sensations scaled with functional connectivity of the pre-supplementary motor area to the caudate nucleus, globus pallidus and thalamus when choosing to respond (Choose-Go). Together, these results suggest that patients with Tourette syndrome use equivalent prefrontal mechanisms to suppress tics and withhold non-tic actions, but require greater inferior frontal gyrus engagement than controls to overcome motor drive from hyperactive downstream regions, notably primary motor cortex. Moreover, premonitory sensations may cue midline motor regions to generate tics through interactions with the basal ganglia

Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures

Comparing independent high-throughput gene-expression experiments can generate hypotheses about which gene-expression programs are shared between particular biological processes. Current techniques to compare expression profiles typically involve choosing a fixed differential expression threshold to summarize results, potentially reducing sensitivity to small but concordant changes. We present a threshold-free algorithm called Rank–rank Hypergeometric Overlap (RRHO). This algorithm steps through two gene lists ranked by the degree of differential expression observed in two profiling experiments, successively measuring the statistical significance of the number of overlapping genes. The output is a graphical map that shows the strength, pattern and bounds of correlation between two expression profiles. To demonstrate RRHO sensitivity and dynamic range, we identified shared expression networks in cancer microarray profiles driving tumor progression, stem cell properties and response to targeted kinase inhibition. We demonstrate how RRHO can be used to determine which model system or drug treatment best reflects a particular biological or disease response. The threshold-free and graphical aspects of RRHO complement other rank-based approaches such as Gene Set Enrichment Analysis (GSEA), for which RRHO is a 2D analog. Rank–rank overlap analysis is a sensitive, robust and web-accessible method for detecting and visualizing overlap trends between two complete, continuous gene-expression profiles. A web-based implementation of RRHO can be accessed at http://systems.crump.ucla.edu/rankrank/

Linking microarray reporters with protein functions

<p>Abstract</p> <p>Background</p> <p>The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways.</p> <p>Results</p> <p>This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways.</p> <p>Conclusion</p> <p>Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/.</p