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Abstract Background Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue microenvironments. However, the sources of technical and biological variation in primary solid tumor tissues and patient-derived mouse xenografts for scRNA-seq are not well understood. Results We use low temperature (6 °C) protease and collagenase (37 °C) to identify the transcriptional signatures associated with tissue dissociation across a diverse scRNA-seq dataset comprising 155,165 cells from patient cancer tissues, patient-derived breast cancer xenografts, and cancer cell lines. We observe substantial variation in standard quality control metrics of cell viability across conditions and tissues. From the contrast between tissue protease dissociation at 37 °C or 6 °C, we observe that collagenase digestion results in a stress response. We derive a core gene set of 512 heat shock and stress response genes, including FOS and JUN, induced by collagenase (37 °C), which are minimized by dissociation with a cold active protease (6 °C). While induction of these genes was highly conserved across all cell types, cell type-specific responses to collagenase digestion were observed in patient tissues. Conclusions The method and conditions of tumor dissociation influence cell yield and transcriptome state and are both tissue- and cell-type dependent. Interpretation of stress pathway expression differences in cancer single-cell studies, including components of surface immune recognition such as MHC class I, may be especially confounded. We define a core set of 512 genes that can assist with the identification of such effects in dissociated scRNA-seq experiments.

Spatial clustering is thought to favour the evolution of cooperation because it puts cooperators in a position to help each other. However, clustering also increases competition. The fate of cooperation may depend on how much cooperators cluster relative to defectors, but these clustering differences have not been the focus of previous models and experiments. By competing siderophore-producing cooperator and defector strains of the opportunistic pathogen Pseudomonas aeruginosa in experimental microhabitats, we found that at the spatial scale of individual interactions, cooperator clustering lowers cooperation, but defector clustering favours cooperation. A theoretical model and individual-based simulations show these counterintuitive effects can arise when competition and cooperation occur at a single resource-determined scale, with population dynamics crucially allowing cooperators and defectors to cluster differently. The results suggest that cooperation relies on the regulation of sufficient defector clustering relative to cooperator clustering, which may be important in bacteria, social amoeba and cancer inhibition.

Abstract Background Patients and families want their healthcare to be delivered by healthcare providers that are both competent and compassionate. While compassion training has begun to emerge in healthcare education, there may be factors that facilitate or inhibit the uptake and implementation of training into practice. This review identified the attributes that explain the successes and/or failures of compassion training programs offered to practicing healthcare providers. Methods Realist review methodology for knowledge synthesis was used to consider the contexts, mechanisms (resources and reasoning), and outcomes of compassion training for practicing healthcare providers to determine what works, for whom, and in what contexts. Results Two thousand nine hundred ninety-one articles underwent title and abstract screening, 53 articles underwent full text review, and data that contributed to the development of a program theory were extracted from 45 articles. Contexts included the clinical setting, healthcare provider characteristics, current state of the healthcare system, and personal factors relevant to individual healthcare providers. Mechanisms included workplace-based programs and participatory interventions that impacted teaching, learning, and the healthcare organization. Contexts were associated with certain mechanisms to effect change in learners’ attitudes, knowledge, skills and behaviors and the clinical process. Conclusions In conclusion this realist review determined that compassion training may engender compassionate healthcare practice if it becomes a key component of the infrastructure and vision of healthcare organizations, engages institutional participation, improves leadership at all levels, adopts a multimodal approach, and uses valid measures to assess outcomes.

Abstract Background High quality genetic material is an essential pre-requisite when analyzing gene expression using microarray technology. Peripheral blood mononuclear cells (PBMC) are frequently used for genomic analyses, but several factors can affect the integrity of nucleic acids prior to their extraction, including the methods of PBMC collection and isolation. Due to the lack of the relevant data published, we compared the Ficoll-Paque density gradient centrifugation and BD Vacutainer cell preparation tube (CPT) protocols to determine if either method offered a distinct advantage in preparation of PBMC-derived immune cell subsets for their use in gene expression analysis. We evaluated the yield and purity of immune cell subpopulations isolated from PBMC derived by both methods, the quantity and quality of extracted nucleic acids, and compared gene expression in PBMC and individual immune cell types from Ficoll and CPT isolation protocols using Affymetrix microarrays. Results The mean yield and viability of fresh PBMC acquired by the CPT method (1.16 × 106 cells/ml, 93.3 %) were compatible to those obtained with Ficoll (1.34 × 106 cells/ml, 97.2 %). No differences in the mean purity, recovery, and viability of CD19+ (B cells), CD8+ (cytotoxic T cells), CD4+ (helper T cell) and CD14+ (monocytes) positively selected from CPT- or Ficoll-isolated PBMC were found. Similar quantities of high quality RNA and DNA were extracted from PBMC and immune cells obtained by both methods. Finally, the PBMC isolation methods tested did not impact subsequent recovery and purity of individual immune cell subsets and, importantly, their gene expression profiles. Conclusions Our findings demonstrate that the CPT and Ficoll PBMC isolation protocols do not differ in their ability to purify high quality immune cell subpopulations. Since there was no difference in the gene expression profiles between immune cells obtained by these two methods, the Ficoll isolation can be substituted by the CPT protocol without conceding phenotypic changes of immune cells and compromising the gene expression studies. Given that the CPT protocol is less elaborate, minimizes cells’ handling and processing time, this method offers a significant operating advantage, especially in large-scale clinical studies aiming at dissecting gene expression in PBMC and PBMC-derived immune cell subpopulations.

Additional file 2: Figure S2. Simulated degree used as the generating distribution for the simulated networked populations. The full range of reported degrees is shown in A, and a reduced range of degree

Abstract Background The North American opioid crisis is driven by opioid-related mortality and morbidity, including opioid use-associated infections (OUAIs), resulting in a substantial burden for society. Users of legal and illegal opioids are at an increased risk of OUAIs compared to individuals not using opioids. As reported for hepatitis C virus (HCV), human immunodeficiency virus (HIV), bacterial, fungal, and other infections, OUAIs transmission and acquisition risks may be modifiable. Several systematic reviews (SRs) synthetized data regarding interventions to prevent infections in persons using drugs (e.g., opioid substitution therapy, needle and syringes exchange programs, psycho-social interventions); however, their conclusions varied. Therefore, SR of published SRs is needed to synthesize the highest level of evidence on the scope and effectiveness of interventions to prevent OUAIs in people using opioids legally or illegally. Methods We will comprehensively search for SRs in the PubMed, Embase, PsycINFO, Cochrane Database of Systematic Reviews, Epistemonikos, and Google Scholar databases from inception to November 2020. Data selection and extraction for each SR will be performed independently by two researchers, with disagreements resolved by consensus. All SRs regarding interventions with evaluated effectiveness to prevent OUAI in legal and/or illegal opioid users will be eligible. Risk of bias assessment will be performed using the AMSTAR2 tool. The results will be qualitatively synthesized, and a typology of interventions��� effectiveness with a statement on the strength of evidence for each category will be created. Discussion Our pilot search of PubMed resulted in 379 SRs analyzing the effectiveness of interventions to prevent HCV and HIV in persons who inject different types of drugs, including opioids. Of these 379 SRs, 8 evaluated primary studies where participants used opioids and would therefore be eligible for inclusion. The search results thus justify the application of SR of SRs approach. Comprehensive data on the scope and effectiveness of existing interventions to prevent OUAIs will help policy-makers to plan and implement preventive interventions and will assist clinicians in the guidance for their patients using opioids. Systematic review registration Registered in PROSPERO on 30 July 2020 ( #195929 ).

A novel 3D photoacoustic imaging technique is experimentally demonstrated using a 64×64 element bias-sensitive crossed-electrode relaxor array. This technique allows for large 2D arrays to receive across all elements while using minimal channel counts. Hadamard-bias patterns are applied to column electrodes while signals are measured from row electrodes. Photoacoustic signals are measured from a crossed-wire phantom in an intralipid scattering medium. The Hadamard-bias encoded imaging scheme showed an SNR of 25.3 dB while the single-column biasing strategy (or identity matrix bias pattern) showed an SNR of 8.8 dB.

Additional file 2. Supplemental Table 2: DEPICT genetic association in pathways.