Visualization of lithium-ion transport and phase evolution within and between manganese oxide nanorods.

Multiple lithium-ion transport pathways and local phase changes upon lithiation in silver hollandite are revealed via in situ microscopy including electron diffraction, imaging and spectroscopy, coupled with density functional theory and phase field calculations. We report unexpected inter-nanorod lithium-ion transport, where the reaction fronts and kinetics are maintained within the neighbouring nanorod. Notably, this is the first time-resolved visualization of lithium-ion transport within and between individual nanorods, where the impact of oxygen deficiencies is delineated. Initially, fast lithium-ion transport is observed along the long axis with small net volume change, resulting in two lithiated silver hollandite phases distinguishable by orthorhombic distortion. Subsequently, a slower reaction front is observed, with formation of polyphase lithiated silver hollandite and face-centred-cubic silver metal with substantial volume expansion. These results indicate lithium-ion transport is not confined within a single nanorod and may provide a paradigm shift for one-dimensional tunnelled materials, particularly towards achieving high-rate capability

Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion.

The advent of cell culture-based methods for the establishment and expansion of human corneal endothelial cells (CEnC) has provided a source of transplantable corneal endothelium, with a significant potential to challenge the one donor-one recipient paradigm. However, concerns over cell identity remain, and a comprehensive characterization of the cultured CEnC across serial passages has not been performed. To this end, we compared two established CEnC culture methods by assessing the transcriptomic changes that occur during in vitro expansion. In confluent monolayers, low mitogenic culture conditions preserved corneal endothelial cell state identity better than culture in high mitogenic conditions. Expansion by continuous passaging induced replicative cell senescence. Transcriptomic analysis of the senescent phenotype identified a cell senescence signature distinct for CEnC. We identified activation of both classic and new cell signaling pathways that may be targeted to prevent senescence, a significant barrier to realizing the potential clinical utility of in vitro expansion

Rationale, design, and protocol for the prevention of low back pain in the military (POLM) trial (NCT00373009)

<p>Abstract</p> <p>Background</p> <p>There are few effective strategies reported for the primary prevention of low back pain (LBP). Core stabilization exercises targeting the deep abdominal and trunk musculature and psychosocial education programs addressing patient beliefs and coping styles represent the current best evidence for secondary prevention of low back pain. However, these programs have not been widely tested to determine if they are effective at preventing the primary onset and/or severity of LBP. The purpose of this cluster randomized clinical trial is to determine if a combined core stabilization exercise and education program is effective in preventing the onset and/or severity of LBP. The effect of the combined program will be compared to three other standard programs.</p> <p>Methods/Design</p> <p>Consecutive Soldiers participating in advanced individual training (AIT) will be screened for eligibility requirements and consented to study participation, as appropriate. Companies of Soldiers will be randomly assigned to receive the following standard prevention programs; a core stabilization exercise program (CSEP) alone, a CSEP with a psychosocial education (PSEP), a traditional exercise (TEP), or a TEP with a PSEP. Proximal outcome measures will be assessed at the conclusion of AIT (a 12 week training period) and include imaging of deep lumbar musculature using real-time ultrasound imaging and beliefs about LBP by self-report questionnaire. We are hypothesizing that Soldiers receiving the CSEP will have improved thickness of selected deep lumbar musculature (transversus abdominus, multifidi, and erector spinae muscles). We are also hypothesizing that Soldiers receiving the PSEP will have improved beliefs about the management of LBP. After AIT, Soldiers will be followed monthly to measure the distal outcomes of LBP occurrence and severity. This information will be collected during the subsequent 2 years following completion of AIT using a web-based data entry system. Soldiers will receive a monthly email that queries whether any LBP was experienced in the previous calendar month. Soldiers reporting LBP will enter episode-specific data related to pain intensity, pain-related disability, fear-avoidance beliefs, and pain catastrophizing. We are hypothesizing that Soldiers receiving the CSEP and PSEP will report the longest duration to first episode of LBP, the lowest frequency of LBP, and the lowest severity of LBP episodes. Statistical comparisons will be made between each of the randomly assigned prevention programs to test our hypotheses related to determining which of the 4 programs is most effective.</p> <p>Discussion</p> <p>We have presented the design and protocol for the POLM trial. Completion of this trial will provide important information on how to effectively train Soldiers for the prevention of LBP.</p> <p>Trial registration</p> <p>NCT00373009</p

Landscape of stimulation-responsive chromatin across diverse human immune cells.

A hallmark of the immune system is the interplay among specialized cell types transitioning between resting and stimulated states. The gene regulatory landscape of this dynamic system has not been fully characterized in human cells. Here we collected assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing data under resting and stimulated conditions for up to 32 immune cell populations. Stimulation caused widespread chromatin remodeling, including response elements shared between stimulated B and T cells. Furthermore, several autoimmune traits showed significant heritability in stimulation-responsive elements from distinct cell types, highlighting the importance of these cell states in autoimmunity. Allele-specific read mapping identified variants that alter chromatin accessibility in particular conditions, allowing us to observe evidence of function for a candidate causal variant that is undetected by existing large-scale studies in resting cells. Our results provide a resource of chromatin dynamics and highlight the need to characterize the effects of genetic variation in stimulated cells

Identification of novel host-oriented targets for Human Immunodeficiency Virus type 1 using Random Homozygous Gene Perturbation

<p>Abstract</p> <p>Background</p> <p>Human Immunodeficiency Virus (HIV) is a global threat to public health. Current therapies that directly target the virus often are rendered ineffective due to the emergence of drug-resistant viral variants. An emerging concept to combat drug resistance is the idea of targeting host mechanisms that are essential for the propagation of the virus, but have a minimal cellular effect.</p> <p>Results</p> <p>Herein, using Random Homozygous Gene Perturbation (RHGP), we have identified cellular targets that allow human MT4 cells to survive otherwise lethal infection by a wild type HIV-1_NL4-3. These gene targets were validated by the reversibility of the RHGP technology, which confirmed that the RHGP itself was responsible for the resistance to HIV-1 infection. We further confirmed by siRNA knockdowns that the RHGP-identified cellular pathways are responsible for resistance to infection by either CXCR4 or CCR5 tropic HIV-1 variants. We also demonstrated that cell clones with these gene targets disrupted by RHGP were not permissible to the replication of a drug resistant HIV-1 mutant.</p> <p>Conclusion</p> <p>These studies demonstrate the power of RHGP to identify novel host targets that are essential for the viral life cycle but which can be safely perturbed without overt cytotoxicity. These findings suggest opportunities for the future development of host-oriented therapeutics with the broad spectrum potential for safe and effective inhibition of HIV infection.</p

Targeted covalent inhibitors of MDM2 using electrophile-bearing stapled peptides.

Herein, we describe the development of a novel staple with an electrophilic warhead to enable the generation of stapled peptide covalent inhibitors of the p53-MDM2 protein-protein interaction (PPI). The peptide developed showed complete and selective covalent binding resulting in potent inhibition of p53-MDM2 PPI.Royal Society, Trinity College, A*STAR (IAF-PP H17/01/a0/010

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.

Background: Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment.Results: Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of&nbsp;the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA.Conclusions: Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA

Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed