Spt5 Cooperates with Human Immunodeficiency Virus Type 1 Tat by Preventing Premature RNA Release at Terminator Sequences

The human immunodeficiency virus type 1 (HIV-1) Tat protein activates transcription elongation by stimulating the Tat-activated kinase (TAK/p-TEFb), a protein kinase composed of CDK9 and its cyclin partner, cyclin T1. CDK9 is able to hyperphosphorylate the carboxyl-terminal domain (CTD) of the large subunit of RNA polymerase during elongation. In addition to TAK, the transcription elongation factor Spt5 is required for the efficient activation of transcriptional elongation by Tat. To study the role of Spt5 in HIV transcription in more detail, we have developed a three-stage Tat-dependent transcription assay that permits the isolation of active preinitiation complexes, early-stage elongation complexes, and Tat-activated elongation complexes. Spt5 is recruited in the transcription complex shortly after initiation. After recruitment of Tat during elongation through the transactivation response element RNA, CDK9 is activated and induces hyperphosphorylation of Spt5 in parallel to the hyperphosphorylation of the CTD of RNA polymerase II. However, immunodepletion experiments demonstrate that Spt5 is not required for Tat-dependent activation of the kinase. Chase experiments using the Spt5-depleted extracts demonstrate that Spt5 is not required for early elongation. However, Spt5 plays an important role in late elongation by preventing the premature dissociation of RNA from the transcription complex at terminator sequences and reducing the amount of polymerase pausing at arrest sites, including bent DNA sequences. This novel biochemical function of Spt5 is analogous to the function of NusG, an elongation factor found in Escherichia coli that enhances RNA polymerase stability on templates and shows sequence similarity to Spt5

MR sequence design using digital twins of non-idealized hardware

MRI systems are traditionally engineered to produce close to idealized performance, enabling a simplified pulse sequence design philosophy. An example of this is control of eddy currents produced by gradient fields; usually these are compensated by pre-emphasizing demanded waveforms. This process typically happens invisibly to the pulse designer, allowing them to assume the achieved gradient waveform will be as desired. Whilst convenient, this imposes stricter limits on the sequence design than the hardware can handle (for example, pre-emphasis adds an additional overhead to amplifiers). This strategy can be undesirable particularly for lower performance or resource-limited hardware. Instead we explore the use of a 'digital twin' (i.e. an end-to-end model of the scanner system) to optimize control inputs, resulting in sequences that inherently compensate for known imperfections. We explore digital twin optimization specifically for gradient system imperfections as an exemplar. This is first explored in simulations using a simple exponential eddy current model, then experimentally using an empirical gradient impulse response function on a 7T MRI system. When unconstrained, digital twin optimization reproduces classic pre-emphasis. When strict hardware constraints are imposed (simulating lower performance hardware), it identifies novel sequences for scenarios where classic pre-emphasis would be unachievable. Experimentally, the optimization approach was demonstrated to substantially reduce ghosting effects in echo planar images on a 7T system. Digital twin optimization may allow more efficient use of hardware by taking a whole system approach. Ultimately this could enable the use of cheaper hardware without loss of performance.Comment: 33 pages, 14 figures (including supporting information

Caught on camera:a video assessment of suspected concussion and other injury events in women's rugby union

Objectives: The objective of this study was to identify and report the incidence and mechanisms of suspected injury and concussion in women's rugby union. Design: A cross-sectional video analysis study. Methods: Using video analysis of non-professional, single-angle footage, cases of suspected injury and concussion were identified and reported, based on content validation and consensus by eight rugby-specific researchers, therapists, and sport medicine physicians. Results: There were 225 suspected injuries recorded in 48 games [Suspected injury rate (IR) = 117.5/1000 h (95 % CI;102.6–133.9) or 4.7 suspected injuries per match]. The on-field medical attention IR was 95.0/1000 h (95 % CI;81.7–109.9: 3.8 per game). Suspected concussions accounted for 26 % of injuries (30.8/1000 h: 95 % CI;23.5–39.7: 1.2 per game). The attacking team sustained 64 % of suspected injuries. Permanent removal from play was observed for 29 % of suspected injuries. The most common suspected injury locations were head/neck (28.4 %) and lower extremity (27.6 %). The tackle accounted for 67.1 % of all suspected injuries, with a propensity of 11.2/1000 tackle events (95 % CI;9.5–13.2) or 3.1 tackle-related injuries/game. Of tackle-related injuries, 63.6 % were to the ball carrier while 52.2 % of tackle-related concussions were to the ball carrier. Conclusion: This study adds to the growing body of literature examining women's rugby. The rate of suspected injury is high compared with other studies. It is acknowledged that these are suspected injuries not supported by prospective injury surveillance. The high proportion of suspected injuries that are tackle-related warrants specific attention to identify tackle characteristics associated with injury and concussion.</p

Relationships between Larval and Juvenile Abundance of Winter-Spawned Fishes in North Carolina, USA

We analyzed the relationships between the larval and juvenile abundances of selected estuarine-dependent fishes that spawn during the winter in continental shelf waters of the U.S. Atlantic coast. Six species were included in the analysis based on their ecological and economic importance and relative abundance in available surveys: spot Leiostomus xanthurus, pinfish Lagodon rhomboides, southern flounder Paralichthys lethostigma, summer flounder Paralichthys dentatus, Atlantic croaker Micropogonias undulatus, and Atlantic menhaden Brevoortia tyrannus. Cross-correlation analysis was used to examine the relationships between the larval and juvenile abundances within species. Tests of synchrony across species were used to find similarities in recruitment dynamics for species with similar winter shelf-spawning life-history strategies. Positive correlations were found between the larval and juvenile abundances for three of the six selected species (spot, pinfish, and southern flounder). These three species have similar geographic ranges that primarily lie south of Cape Hatteras. There were no significant correlations between the larval and juvenile abundances for the other three species (summer flounder, Atlantic croaker, and Atlantic menhaden); we suggest several factors that could account for the lack of a relationship. Synchrony was found among the three southern species within both the larval and juvenile abundance time series. These results provide support for using larval ingress measures as indices of abundance for these and other species with similar geographic ranges and winter shelf-spawning life-history strategies

Narrowband UVB treatment is highly effective and causes a strong reduction in the use of steroid and other creams in psoriasis patients in clinical practice

Narrowband NB-UVB phototherapy (NB-UVB) is an effective treatment for psoriasis, as demonstrated by clinical trials. However, due to required infrastructure and need for treatment attendance opinions on the value of offering this treatment in routine practice vary. AIMS: To provide high quality large-scale and long-term data on the efficacy of NB-UVB for psoriasis under real-world conditions in order to assist in management decisions.The following resources were employed: (1) complete and prospectively recorded prescription drug records for a population of 420,000 marked by low demographic mobility, (2) prospectively recorded clinical treatment outcomes for all NB-UVB treatment episodes occurring in the local population; (3) complete dermatology electronic treatment records of all psoriasis patients, allowing cross-validation of diagnoses and treatment records. Using these data sets, we analysed all first-ever initial NB-UVB treatment episodes occurring over 79 months (n = 1749) for both clinical outcomes and the effect of NB-UVB on the use of topical treatments for psoriasis.Around 75% of patients both achieved a status of "clear/minimal disease" and used fewer topical treatments. NB-UVB treatment led to a strong reduction for both steroid creams (25%) and psoriasis-specific topicals, e.g. vitamin-D products (30%) during the 12-month period following NB-UVB treatment. The effects measured were specific as no effect of NB-UVB was noted on drug prescriptions unrelated to psoriasis. Results were independent of individuals administering and/or scoring treatment, as they were highly similar between four geographically separate locations.NB-UVB treatment is highly effective and leads to a remarkable reduction in the need for topical cream treatments for a period of at least 12 months

Toward cyberinfrastructure to facilitate collaboration and reproducibility for marine integrated ecosystem assessments

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Earth Science Informatics 10 (2017): 85-97, doi:10.1007/s12145-016-0280-4.There is a growing need for cyberinfrastructure to support science-based decision making in management of natural resources. In particular, our motivation was to aid the development of cyberinfrastructure for Integrated Ecosystem Assessments (IEAs) for marine ecosystems. The IEA process involves analysis of natural and socio-economic information based on diverse and disparate sources of data, requiring collaboration among scientists of many disciplines and communication with other stakeholders. Here we describe our bottom-up approach to developing cyberinfrastructure through a collaborative process engaging a small group of domain and computer scientists and software engineers. We report on a use case evaluated for an Ecosystem Status Report, a multi-disciplinary report inclusive of Earth, life, and social sciences, for the Northeast U.S. Continental Shelf Large Marine Ecosystem. Ultimately, we focused on sharing workflows as a component of the cyberinfrastructure to facilitate collaboration and reproducibility. We developed and deployed a software environment to generate a portion of the Report, retaining traceability of derived datasets including indicators of climate forcing, physical pressures, and ecosystem states. Our solution for sharing workflows and delivering reproducible documents includes IPython (now Jupyter) Notebooks. We describe technical and social challenges that we encountered in the use case and the importance of training to aid the adoption of best practices and new technologies by domain scientists. We consider the larger challenges for developing end-to-end cyberinfrastructure that engages other participants and stakeholders in the IEA process.Support for this research was provided by the U. S. National Science Foundation #0955649 with additional support to SB by the Investment in Science Fund at Woods Hole Oceanographic Institution

An optimised tissue disaggregation and data processing pipeline for characterising fibroblast phenotypes using single-cell RNA sequencing

Single-cell RNA sequencing (scRNA-Seq) provides a valuable platform for characterising multicellular ecosystems. Fibroblasts are a heterogeneous cell type involved in many physiological and pathological processes, but remain poorly-characterised. Analysis of fibroblasts is challenging: these cells are difficult to isolate from tissues, and are therefore commonly under-represented in scRNA-seq datasets. Here, we describe an optimised approach for fibroblast isolation from human lung tissues. We demonstrate the potential for this procedure in characterising stromal cell phenotypes using scRNA-Seq, analyse the effect of tissue disaggregation on gene expression, and optimise data processing to improve clustering quality. We also assess the impact of in vitro culture conditions on stromal cell gene expression and proliferation, showing that altering these conditions can skew phenotypes

The Effect of Condensates on the Characterization of Transiting Planet Atmospheres with Transmission Spectroscopy

Through a simple physical argument we show that the slant optical depth through the atmosphere of a "hot Jupiter" planet is 35-90 times greater than the normal optical depth. This not unexpected result has direct consequences for the method of transmission spectroscopy for characterizing the atmospheres of transiting giant planets. The atmospheres of these planets likely contain minor condensates and hazes which at normal viewing geometry have negligible optical depth, but at slant viewing geometry have appreciable optical depth that can obscure absorption features of gaseous atmospheric species. We identify several possible condensates. We predict that this is a general masking mechanism for all planets, not just for HD 209458b, and will lead to weaker than expected or undetected absorption features. Constraints on an atmosphere from transmission spectroscopy are not the same as constraints on an atmosphere at normal viewing geometry.Comment: 6 pages. MNRAS, in press. New version fixes some incorrect numbers in Table 1. References update