Reporting on novel complex intervention development for adults with social communication impairments after acquired brain injury

Purpose: Interventions are often poorly described in published controlled trials, with relatively little information regarding intervention development, content and fidelity. This makes it difficult to conduct replication studies, interpret and compare findings across studies and for therapists to deliver the intervention in clinical practice. Complete reporting of interventions (including fidelity) is now recommended for treatment studies, and this standardised approach is achieved using the Template for Intervention Description and Replication (TIDieR). The aim of this paper is to describe the multi-phase process of developing a novel intervention for adults with acquired brain injury (ABI), and report on the findings from involving practicing therapists in this process. Methods: Phase 1 involved a review of relevant literature and specifying the intervention as a prototype intervention manual. Phase 2 comprised a focus group with eight practicing therapists exploring their experiences and perceptions of the intervention, potential active components, and essential elements; it also included review of the prototype manual. Data from the focus group discussion was transcribed and analysed thematically. Phase 3 investigated actual fidelity of the intervention undertaken, achieved by observers viewing videoed sessions and appraising against the fidelity checklist, which was then analysed using Cohen’s kappa. Results: Project-based intervention was defined as having six essential elements: a project or tangible end product focus; group-based intervention; individualised communication-based goals; communication partner involvement; acknowledgement and support of participants’ cognitive ability; and consideration and plan to address impaired awareness. Analysis of focus group data revealed four themes of essential elements; group context; therapeutic skills; and manual core components and informed the development of a fidelity checklist with 13 essential and 6 desirable criteria. Fidelity assessed using percent agreement was acceptable for almost all rater pairs; where significant, Kappa coefficients had values ranging from poor to excellent (k=0.34 – 1.0) depending on rater pair and session. Discussion: The TIDieR framework provided a clear systematic approach for the complete description and reporting of a complex communication intervention for people with ABI. This paper comprehensively described the development and manualisation of an intervention in collaboration with practicing therapists which can be used for future testing. In addition, the process undertaken has the potential to inform rehabilitation researchers in other fields on the development of complex interventions

Low pH immobilizes and kills human leukocytes and prevents transmission of cell-associated HIV in a mouse model

BACKGROUND: Both cell-associated and cell-free HIV virions are present in semen and cervical secretions of HIV-infected individuals. Thus, topical microbicides may need to inactivate both cell-associated and cell-free HIV to prevent sexual transmission of HIV/AIDS. To determine if the mild acidity of the healthy vagina and acid buffering microbicides would prevent transmission by HIV-infected leukocytes, we measured the effect of pH on leukocyte motility, viability and intracellular pH and tested the ability of an acidic buffering microbicide (BufferGel(®)) to prevent the transmission of cell-associated HIV in a HuPBL-SCID mouse model. METHODS: Human lymphocyte, monocyte, and macrophage motilities were measured as a function of time and pH using various acidifying agents. Lymphocyte and macrophage motilities were measured using video microscopy. Monocyte motility was measured using video microscopy and chemotactic chambers. Peripheral blood mononuclear cell (PBMC) viability and intracellular pH were determined as a function of time and pH using fluorescent dyes. HuPBL-SCID mice were pretreated with BufferGel, saline, or a control gel and challenged with HIV-1-infected human PBMCs. RESULTS: Progressive motility was completely abolished in all cell types between pH 5.5 and 6.0. Concomitantly, at and below pH 5.5, the intracellular pH of PBMCs dropped precipitously to match the extracellular medium and did not recover. After acidification with hydrochloric acid to pH 4.5 for 60 min, although completely immotile, 58% of PBMCs excluded ethidium homodimer-1 (dead-cell dye). In contrast, when acidified to this pH with BufferGel, a microbicide designed to maintain vaginal acidity in the presence of semen, only 4% excluded dye at 10 min and none excluded dye after 30 min. BufferGel significantly reduced transmission of HIV-1 in HuPBL-SCID mice (1 of 12 infected) compared to saline (12 of 12 infected) and a control gel (5 of 7 infected). CONCLUSION: These results suggest that physiologic or microbicide-induced acid immobilization and killing of infected white blood cells may be effective in preventing sexual transmission of cell-associated HIV

PHDcleav: A SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors

Background: Dicer, an RNase III enzyme, plays a vital role in the processing of pre-miRNAs for generating the miRNAs. The structural and sequence features on pre-miRNA which can facilitate position and efficiency of cleavage are not well known. A precise cleavage by Dicer is crucial because an inaccurate processing can produce miRNA with different seed regions which can alter the repertoire of target genes.Results: In this study, a novel method has been developed to predict Dicer cleavage sites on pre-miRNAs using Support Vector Machine. We used the dataset of experimentally validated human miRNA hairpins from miRBase, and extracted fourteen nucleotides around Dicer cleavage sites. We developed number of models using various types of features and achieved maximum accuracy of 66% using binary profile of nucleotide sequence taken from 5p arm of hairpin. The prediction performance of Dicer cleavage site improved significantly from 66% to 86% when we integrated secondary structure information. This indicates that secondary structure plays an important role in the selection of cleavage site. All models were trained and tested on 555 experimentally validated cleavage sites and evaluated using 5-fold cross validation technique. In addition, the performance was also evaluated on an independent testing dataset that achieved an accuracy of ~82%.Conclusion: Based on this study, we developed a webserver PHDcleav (http://www.imtech.res.in/raghava/phdcleav/) to predict Dicer cleavage sites in pre-miRNA. This tool can be used to investigate functional consequences of genetic variations/SNPs in miRNA on Dicer cleavage site, and gene silencing. Moreover, it would also be useful in the discovery of miRNAs in human genome and design of Dicer specific pre-miRNAs for potent gene silencing.Peer reviewedBiochemistry and Molecular Biolog

Silver-rich telluride mineralization at Mount Charlotte and Au-Ag zonation in the giant Golden Mile deposit, Kalgoorlie, Western Australia

The gold deposits at Kalgoorlie in the 2. 7-Ga Eastern Goldfields Province of the Yilgarn Craton, Western Australia, occur adjacent to the D2 Golden Mile Fault over a strike of 8 km within a district-scale zone marked by porphyry dykes and chloritic alteration. The late Golden Pike Fault separates the older (D2) shear zone system of the Golden Mile (1,500 t Au) in the southeast from the younger (D4) quartz vein stockworks at Mt Charlotte (126 t Au) in the northwest. Both deposits occur in the Golden Mile Dolerite sill and display inner sericite-ankerite alteration and early-stage gold-pyrite mineralization replacing the wall rocks. Late-stage tellurides account for 20 % of the total gold in the first, but for &1 % in the second deposit. In the Golden Mile, the main telluride assemblage is coloradoite + native gold (898-972 fine) + calaverite + petzite ± krennerite. Telluride-rich ore (>30 g/t Au) is characterized by Au/Ag = 2. 54 and As/Sb = 2. 6-30, the latter ratio caused by arsenical pyrite. Golden Mile-type D2 lodes occur northwest of the Golden Pike Fault, but the Hidden Secret orebody, the only telluride bonanza mined (10,815 t at 44 g/t Au), was unusually rich in silver (Au/Ag = 0. 12-0. 35) due to abundant hessite. We describe another array of silver-rich D2 shear zones which are part of the Golden Mile Fault exposed on the Mt Charlotte mine 22 level. They are filled with crack-seal and pinch-and-swell quartz-carbonate veins and are surrounded by early-stage pyrite + pyrrhotite disseminated in a sericite-ankerite zone more than 6 m wide. Gold grade (0. 5-0. 8 g/t) varies little across the zone, but Au/Ag (0. 37-2. 40) and As/Sb (1. 54-13. 9) increase away from the veins. Late-stage telluride mineralization (23 g/t Au) sampled in one vein has a much lower Au/Ag (0. 13) and As/Sb (0. 48) and comprises scheelite, pyrite, native gold (830-854 fine), hessite, and minor pyrrhotite, altaite, bournonite, and boulangerite. Assuming 250-300 °C, gold-hessite compositions indicate a fluid log fTe2 of -11. 5 to -10, values well below the stability of calaverite. The absence of calaverite and the dominance of hessite in the D2 lodes of the Mt Charlotte area point to a kilometer-scale mineral and Au/Ag zonation along the Golden Mile master fault, which is attributed to a lateral decrease in peak tellurium fugacity of the late-stage hydrothermal fluid. The As/Sb ratio may be similarly zoned to lower values at the periphery. The D4 gold-quartz veins constituting the Mt Charlotte orebodies represent a younger hydrothermal system, which did not contribute to metal zonation in the older one. © 2012 Springer-Verlag

Mutations in MEGF10, a regulator of satellite cell myogenesis, cause early onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD).

Infantile myopathies with diaphragmatic paralysis are genetically heterogeneous, and clinical symptoms do not assist in differentiating between them. We used phased haplotype analysis with subsequent targeted exome sequencing to identify MEGF10 mutations in a previously unidentified type of infantile myopathy with diaphragmatic weakness, areflexia, respiratory distress and dysphagia. MEGF10 is highly expressed in activated satellite cells and regulates their proliferation as well as their differentiation and fusion into multinucleated myofibers, which are greatly reduced in muscle from individuals with early onset myopathy, areflexia, respiratory distress and dysphagia