A video presentation on the cover test concepts & case examples

An instructional video on the cover test demonstrating the concepts and techniques involved with performing a cover test as well as clinical case examples

An EUV Study of the Intermediate Polar EX Hydrae

On 2000 May 5, we began a large multi-wavelength campaign to study the intermediate polar, EX Hydrae. The simultaneous observations from six satellites and four telescopes were centered around a one million second observation with EUVE. Although EX Hydrae has been studied previously with EUVE, our higher signal-to-noise observations present new results and challenge the current IP models. Previously unseen dips in the light curve are reminiscent of the stream dips seen in polar light curves. Also of interest is the temporal extent of the bulge dip; approximately 0.5 in phase, implying that the bulge extends over half of the accretion disk. We propose that the magnetic field in EX Hydrae is strong enough (a few MG) to begin pulling material directly from the outer edge of the disk, thereby forming a large accretion curtain which would produce a very broad bulge dip. This would also result in magnetically controlled accretion streams originating from the outer edge of the disk. We also present a period analysis of the photometric data which shows numerous beat frequencies with strong power and also intermittent and wandering frequencies, an indication that physical conditions within EX Hya changed over the course of the observation. Iron spectral line ratios give a temperature of log T=6.5-6.9 K for all spin phases and a poorly constrained density of n_e=10^10-10^11 cm^-3 for the emitting plasma. This paper is the first in a series detailing our results from this multi-wavelength observational campaign.Comment: 27 pages, 7 figures, accepted for publication in Ap

Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface (GUI) toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.Peer reviewe

Bidirectional switch of the valence associated with a hippocampal contextual memory engram

The valence of memories is malleable because of their intrinsic reconstructive property. This property of memory has been used clinically to treat maladaptive behaviours. However, the neuronal mechanisms and brain circuits that enable the switching of the valence of memories remain largely unknown. Here we investigated these mechanisms by applying the recently developed memory engram cell- manipulation technique. We labelled with channelrhodopsin-2 (ChR2) a population of cells in either the dorsal dentate gyrus (DG) of the hippocampus or the basolateral complex of the amygdala (BLA) that were specifically activated during contextual fear or reward conditioning. Both groups of fear-conditioned mice displayed aversive light-dependent responses in an optogenetic place avoidance test, whereas both DG- and BLA-labelled mice that underwent reward conditioning exhibited an appetitive response in an optogenetic place preference test. Next, in an attempt to reverse the valence of memory within a subject, mice whose DG or BLA engram had initially been labelled by contextual fear or reward conditioning were subjected to a second conditioning of the opposite valence while their original DG or BLA engram was reactivated by blue light. Subsequent optogenetic place avoidance and preference tests revealed that although the DG-engram group displayed a response indicating a switch of the memory valence, the BLA-engram group did not. This switch was also evident at the cellular level by a change in functional connectivity between DG engram-bearing cells and BLA engram-bearing cells. Thus, we found that in the DG, the neurons carrying the memory engram of a given neutral context have plasticity such that the valence of a conditioned response evoked by their reactivation can be reversed by re-associating this contextual memory engram with a new unconditioned stimulus of an opposite valence. Our present work provides new insight into the functional neural circuits underlying the malleability of emotional memory.RIKEN Brain Science InstituteHoward Hughes Medical InstituteJPB FoundationNational Institutes of Health (U.S.) (Pre-doctoral Training Grant T32GM007287

FLUXNET: A New Tool to Study the Temporal and Spatial Variability of Ecosystem-Scale Carbon Dioxide, Water Vapor, and Energy Flux Densities

FLUXNET is a global network of micrometeorological flux measurement sites that measure the exchanges of carbon dioxide, water vapor, and energy between the biosphere and atmosphere. At present over 140 sites are operating on a long–term and continuous basis. Vegetation under study includes temperate conifer and broadleaved (deciduous and evergreen) forests, tropical and boreal forests, crops, grasslands, chaparral, wetlands, and tundra. Sites exist on five continents and their latitudinal distribution ranges from 70°N to 30°S. FLUXNET has several primary functions. First, it provides infrastructure for compiling, archiving, and distributing carbon, water, and energy flux measurement, and meteorological, plant, and soil data to the science community. (Data and site information are available online at the FLUXNET http://www–eosdis.ornl.gov/FLUXNET/.) Second, the project supports calibration and flux intercomparison activities. This activity ensures that data from the regional networks are intercomparable. And third, FLUXNET supports the synthesis, discussion, and communication of ideas and data by supporting project scientists, workshops, and visiting scientists. The overarching goal is to provide information for validating computations of net primary productivity, evaporation, and energy absorption that are being generated by sensors mounted on the NASA Terra satellite. Data being compiled by FLUXNET are being used to quantify and compare magnitudes and dynamics of annual ecosystem carbon and water balances, to quantify the response of stand–scale carbon dioxide and water vapor flux densities to controlling biotic and abiotic factors, and to validate a hierarchy of soil–plant–atmosphere trace gas exchange models. Findings so far include 1) net CO2 exchange of temperate broadleaved forests increases by about 5.7 g C m–2 day–1 for each additional day that the growing season is extended; 2) the sensitivity of net ecosystem CO2 exchange to sunlight doubles if the sky is cloudy rather than clear; 3) the spectrum of CO2 flux density exhibits peaks at timescales of days, weeks, and years, and a spectral gap exists at the month timescale; 4) the optimal temperature of net CO2 exchange varies with mean summer temperature; and 5) stand age affects carbon dioxide and water vapor flux densities

Cooperative Interaction of Transcription Termination Factors with the RNA Polymerase II C-terminal Domain

Phosphorylation of the C-terminal domain of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTDinteracting domains that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CTD-interacting domains of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single amino acid mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3′-end processing site in vivo. We suggest that this cooperativity provides a signal-response mechanism to ensure that its action is confined only to proper polyadenylation sites where Serine 2 phosphorylation density is highest

A variable stiffness soft gripper using granular jamming and biologically inspired pneumatic muscles

As the domains in which robots operate change the objects a robot may be required to grasp and manipulate are likely to vary significantly and often. Furthermore there is increasing likelihood that in the future robots will work collaboratively alongside people. There has therefore been interest in the development of biologically inspired robot designs which take inspiration from nature. This paper presents the design and testing of a variable stiffness, three fingered soft gripper which uses pneumatic muscles to actuate the fingers and granular jamming to vary their stiffness. This gripper is able to adjust its stiffness depending upon how fragile/deformable the object being grasped is. It is also lightweight and low inertia making it better suited to operation near people. Each finger is formed from a cylindrical rubber bladder filled with a granular material. It is shown how decreasing the pressure inside the finger increases the jamming effect and raises finger stiffness. The paper shows experimentally how the finger stiffness can be increased from 21 to 71 N/m. The paper also describes the kinematics of the fingers and demonstrates how they can be position-controlled at a range of different stiffness values

Prevalence of positive depression screen among post miscarriage women- A cross sectional study

Background: Miscarriages are a common pregnancy complication affecting about 10–15% of pregnancies. Miscarriages may be associated with a myriad of psychiatric morbidity at various timelines after the event. Depression has been shown to affect about 10–20% of all women following a miscarriage. However, no data exists in the local setting informing on the prevalence of post-miscarriage depression. We set out to determine the prevalence of positive depression screen among women who have experienced a miscarriage at the Aga Khan University hospital, Nairobi. Methods: The study was cross-sectional in design. Patients who had a miscarriage were recruited at the post-miscarriage clinic review at the gynecology clinics at Aga Khan University Hospital, Nairobi. The Edinburgh postpartum depression scale was used to screen for depression in the patients. Prevalence was calculated from the percentage of patients achieving the cut –off score of 13 over the total number of patients. Results: A total of 182 patients were recruited for the study. The prevalence of positive depression screen was 34.1% since 62 of the 182 patients had a positive depression screen. Moreover, of the patients who had a positive depression screen, 21(33.1%) had thoughts of self-harm. Conclusion: A positive depression screen is present in 34.1% of women in our population two weeks after a miscarriage. Thoughts of self-harm are present in about a third of these women (33.1%) hence pointing out the importance of screening these women using the EPDS after a miscarriage

FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data

The hallmarks of many haematological malignancies and solid tumours are chromosomal translocations, which may lead to gene fusions. Recently, next-generation sequencing techniques at the transcriptome level (RNA-Seq) have been used to verify known and discover novel transcribed gene fusions. We present FusionFinder, a Perl-based software designed to automate the discovery of candidate gene fusion partners from single-end (SE) or paired-end (PE) RNA-Seq read data. FusionFinder was applied to data from a previously published analysis of the K562 chronic myeloid leukaemia (CML) cell line. Using FusionFinder we successfully replicated the findings of this study and detected additional previously unreported fusion genes in their dataset, which were confirmed experimentally. These included two isoforms of a fusion involving the genes BRK1 and VHL, whose co-deletion has previously been associated with the prevalence and severity of renal-cell carcinoma. FusionFinder is made freely available for non-commercial use and can be downloaded from the project website (http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/)

Optogenetic stimulation of a hippocampal engram activates fear memory recall

A specific memory is thought to be encoded by a sparse population of neurons. These neurons can be tagged during learning for subsequent identification3 and manipulation. Moreover, their ablation or inactivation results in reduced memory expression, suggesting their necessity in mnemonic processes. However, the question of sufficiency remains: it is unclear whether it is possible to elicit the behavioural output of a specific memory by directly activating a population of neurons that was active during learning. Here we show in mice that optogenetic reactivation of hippocampal neurons activated during fear conditioning is sufficient to induce freezing behaviour. We labelled a population of hippocampal dentate gyrus neurons activated during fear learning with channelrhodopsin-2 (ChR2) and later optically reactivated these neurons in a different context. The mice showed increased freezing only upon light stimulation, indicating light-induced fear memory recall. This freezing was not detected in non-fear-conditioned mice expressing ChR2 in a similar proportion of cells, nor in fear-conditioned mice with cells labelled by enhanced yellow fluorescent protein instead of ChR2. Finally, activation of cells labelled in a context not associated with fear did not evoke freezing in mice that were previously fear conditioned in a different context, suggesting that light-induced fear memory recall is context specific. Together, our findings indicate that activating a sparse but specific ensemble of hippocampal neurons that contribute to a memory engram is sufficient for the recall of that memory. Moreover, our experimental approach offers a general method of mapping cellular populations bearing memory engrams.RIKEN Brain Science InstituteNational Institutes of Health (U.S.) (Grant R01-MH078821)National Institutes of Health (U.S.) (Grant P50-MH58880