A generic approach to infer community-level fitness of microbial genes.

The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.

Data-driven learning of structure augments quantitative prediction of biological responses.

Multi-factor screenings are commonly used in diverse applications in medicine and bioengineering, including optimizing combination drug treatments and microbiome engineering. Despite the advances in high-throughput technologies, large-scale experiments typically remain prohibitively expensive. Here we introduce a machine learning platform, structure-augmented regression (SAR), that exploits the intrinsic structure of each biological system to learn a high-accuracy model with minimal data requirement. Under different environmental perturbations, each biological system exhibits a unique, structured phenotypic response. This structure can be learned based on limited data and once learned, can constrain subsequent quantitative predictions. We demonstrate that SAR requires significantly fewer data comparing to other existing machine-learning methods to achieve a high prediction accuracy, first on simulated data, then on experimental data of various systems and input dimensions. We then show how a learned structure can guide effective design of new experiments. Our approach has implications for predictive control of biological systems and an integration of machine learning prediction and experimental design.

Horizontal gene transfer enables programmable gene stability in synthetic microbiota.

The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have been commonly hypothesized to explain such decoupling. Here, we proposed that dynamic mechanisms, mediated by horizontal gene transfer (HGT), also enable the independence of functions from the compositions of microbial communities. We combined theoretical analysis with numerical simulations to illustrate that HGT rates can determine the stability of gene abundance in microbial communities. We further validated these predictions using engineered microbial consortia of different complexities transferring one or more than a dozen clinically isolated plasmids, as well as through the reanalysis of data from the literature. Our results demonstrate a generalizable strategy to program the gene stability of microbial communities.

Modulation of microbial community dynamics by spatial partitioning.

Microbial communities inhabit spatial architectures that divide a global environment into isolated or semi-isolated local environments, which leads to the partitioning of a microbial community into a collection of local communities. Despite its ubiquity and great interest in related processes, how and to what extent spatial partitioning affects the structures and dynamics of microbial communities are poorly understood. Using modeling and quantitative experiments with simple and complex microbial communities, we demonstrate that spatial partitioning modulates the community dynamics by altering the local interaction types and global interaction strength. Partitioning promotes the persistence of populations with negative interactions but suppresses those with positive interactions. For a community consisting of populations with both positive and negative interactions, an intermediate level of partitioning maximizes the overall diversity of the community. Our results reveal a general mechanism underlying the maintenance of microbial diversity and have implications for natural and engineered communities.

Predicting plasmid persistence in microbial communities by coarse-grained modeling.

Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.

Identifying barriers and facilitators to palliative care integration in the management of hospitalized patients with COVID-19: A qualitative study.

BACKGROUND: Palliative care is well suited to support patients hospitalized with COVID-19, but integration into care has been variable and generally poor. AIM: To understand barriers and facilitators of palliative care integration for hospitalized patients with COVID-19. METHODS: Internists, Intensivists and palliative care physicians completed semi-structured interviews about their experiences providing care to patients with COVID-19. Results were analysed using thematic analysis. RESULTS: Twenty-three physicians (13 specialist palliative care, five intensivists, five general internists) were interviewed; mean ± SD age was 42 ± 11 years and 61% were female. Six thematic categories were described including: patient and family factors, palliative care knowledge, primary provider factors, COVID-19 specific factors, palliative care service factors, and leadership and culture factors. Patient and family factors included patient prognosis, characteristics that implied prognosis (i.e., age, etc.), and goals of care. Palliative care knowledge included confidence in primary palliative care skills, misperception that COVID-19 is not a 'palliative diagnosis', and the need to choose quantity or quality of life in COVID-19 management. Primary provider factors included available time, attitude, and reimbursement. COVID-19 specific factors were COVID-19 as an impetus to act, uncertain illness trajectory, treatments and outcomes, and infection control measures. Palliative care service factors were accessibility, adaptability, and previous successful relationships. Leadership and culture factors included government-mandated support, presence at COVID planning tables, and institutional and unit culture. CONCLUSION: The study findings highlight the need for leadership support for formal integrated models of palliative care for patients with COVID-19, a palliative care role in pandemic planning, and educational initiatives with primary palliative care providers.

Effectiveness of a Multiprofessional, Online and Simulation-Based Difficult Conversations Training Program on Self-Perceived Competence of Oncology Healthcare Provider Trainees.

Effective communication between healthcare providers (HCPs) and patients is important for HCP well-being, patient engagement, and health outcomes. Yet, HCPs do not receive adequate communication skills training and report feeling unprepared for difficult conversations. A needs assessment of 64 cancer HCP trainees in Toronto, Canada, found that a majority of trainees rated themselves with low competency in communication skills to support patients through difficult conversations, while nearly all rated these skills as important to their practice. A blended multiprofessional communications program was developed including online theoretical learning and reflective practice in addition to in-person simulation with standardised patient actors. Since communication skills mastery is highly unlikely to occur at the termination of a single training program, the goal of the program was to stimulate participants' motivational beliefs about difficult conversations communication skills in order to deepen their commitment to learning and mastery. The motivational beliefs assessed included self-efficacy (self-perceived competence), intent to use techniques learned, and confidence in task mastery. After completing the course, participants' self-perceived competence in dealing with difficult conversations significantly increased by an average of 25 points (p < 0.001) on a rating scale of 1-100 (n = 40). Participants' intent to use techniques did not change significantly and remained high with an overall average of 89 points. After the course, participants rated their confidence in mastering techniques learned at an average score of 71 points. Multiprofessional, simulation-based training is an effective way to improve HCP trainees' motivational beliefs around having difficult conversations.

Identification of low-dose multidrug combinations for sunitinib-naive and pre-treated renal cell carcinoma.

BACKGROUND: Combinations of drugs can improve the efficacy of cancer treatment, enable the reduction of side effects and the occurrence of acquired drug resistance. METHODS: We approached this challenge mathematically by using the validated technology called the Therapeutically Guided Multidrug Optimization (TGMO) method. In a set of genetically distinct human renal cell carcinoma (RCC) cell lines, either treated chronically with sunitinib (-ST) or sunitinib-naive, we identified cell line-specific low-dose-optimised drug combinations (ODC). RESULTS: Six cell-type-specific low-dose drug combinations for three sunitinib-naive as well as three sunitinib pre-treated cells were established. These ODCs effectively inhibited the RCC cell metabolic activity while being ineffective in non-cancerous cells. Based on a single screening test and three searches, starting with ten drugs, we identified highly efficacious drug mixtures containing four drugs. All ODCs contained AZD4547 (FGFR signalling pathway inhibitor) and pictilisib (pan-phosphatidylinositol 3-kinase inhibitor), but varied in the third and fourth drug. ODC treatment significantly decreased cell metabolic activity (up to 70%) and induced apoptosis, independent of the pretreatment with sunitinib. The ODCs outperformed sunitinib, the standard care for RCC. Moreover, short-term starvation potentiated the ODC activity. The translation of the 2D-based results to 3D heterotypic co-culture models revealed significant inhibition of the spheroid growth (up to 95%). CONCLUSION: We demonstrate a promising low-dose drug combination development to obtain drug combinations effective in naive as well as resistant tumours. Nevertheless, we emphasise the need for further mechanistic investigation and preclinical development.

Anti-angiogenic effects of crenolanib are mediated by mitotic modulation independently of PDGFR expression.

BACKGROUND: Crenolanib is a tyrosine kinase inhibitor targeting PDGFR-α, PDGFR-ß and Fms related tyrosine kinase-3 (FLT3) that is currently evaluated in several clinical trials. Although platelet-derived growth factor receptor (PDGFR) signalling pathway is believed to play an important role in angiogenesis and maintenance of functional vasculature, we here demonstrate a direct angiostatic activity of crenolanib independently of PDGFR signalling. METHODS: The activity of crenolanib on cell viability, migration, sprouting, apoptosis and mitosis was assessed in endothelial cells, tumour cells and fibroblasts. Alterations in cell morphology were determined by immunofluorescence experiments. Flow-cytometry analysis and mRNA expression profiles were used to investigate cell differentiation. In vivo efficacy was investigated in human ovarian carcinoma implanted on the chicken chorioallantoic membrane (CAM). RESULTS: Crenolanib was found to inhibit endothelial cell viability, migration and sprout length, and induced apoptosis independently of PDGFR expression. Treated cells  showed altered actin arrangement and nuclear aberrations. Mitosis was affected at several levels including mitosis entry and centrosome clustering. Crenolanib suppressed human ovarian carcinoma tumour growth and angiogenesis in the CAM model. CONCLUSIONS: The PDGFR/FLT3 inhibitor crenolanib targets angiogenesis and inhibits tumour growth in vivo unrelated to PDGFR expression. Based on our findings, we suggest a broad mechanism of action of crenolanib.

Epigenetic approach for angiostatic therapy: promising combinations for cancer treatment.

Cancer cells are often dependent on epigenetic pathways for their survival. Consequently, drugs that target the epigenome, rather than the underlying DNA sequence, are currently attracting considerable attention. In recent years, the first epigenetic drugs have been approved for cancer chemotherapy, mainly for hematological applications. Limitations in single-drug efficacies have thus far limited their application in the treatment of solid tumors. Nevertheless, promising activity for these compounds has been suggested when combined with other, distinctly targeted agents. In this review, we discuss the anti-angiogenic activity of histone deacetylase and DNA methyltransferase inhibitors and their combinations with other targeted (anti-angiogenic) therapeutics in treatment of solid tumors. The role that these inhibitors play in the inhibition of tumor angiogenesis, particularly in combination with other targeted agents, and the advantages they present over broad acting anticancer agents, are critically discussed.

Beyond Watches and Chocolate-Global Mental Health Elective in Switzerland.

Despite increasing interest in global mental health training opportunities, only a few psychiatry residency programs offer global mental health training experiences in developing countries and even fewer programs offer it in other first-world countries. The authors developed a global mental health elective giving US psychiatry residents the opportunity to visit Switzerland to study and experience the mental health care system in this European country. This elective focuses on four major learning objectives: (1) the system of training and curriculum of postgraduate psychiatry education in Switzerland, (2) clinical and organizational aspects of Swiss mental health, (3) administrative aspects of Swiss mental health care delivery, and (4) scholarly activity. This program was uniquely tailored for psychiatry residents. The preliminary experiences with US psychiatry residents show that they value this learning experience, the opportunity to access a different mental health care system, as well as the potential to build international connections with peers.

A Survey of American and Canadian Psychiatry Residents on Their Training, Teaching Practices, and Attitudes Toward Teaching.

OBJECTIVE: Formal training for residents-as-teachers in psychiatry is increasingly emphasized. However, little is known about the quantity and content of residents' teaching, their attitudes toward teaching, or the training received on how to teach. METHODS: An online survey was disseminated to American and Canadian psychiatry residents. RESULTS: Three hundred eighty-two residents from all postgraduate years (PGY) responded, representing about 7 % of all trainees. About half of PGY-1 have not received residents-as-teachers training, but by PGY-3 most have. The majority of respondents reported teaching, most commonly 1-5 h. Most found teaching enjoyable or rewarding (n = 304; 87 %); however, 40 % (n = 138) found teaching burdensome, 43 % (n = 151) lacked sufficient time to teach, and many (n = 226; 64 %) reported insufficient feedback from supervisors. CONCLUSIONS: Although the sampling methodology and low response rate limit the generalizability of findings, respondents typically seemed to value teaching, though the majority felt that they lacked feedback on their teaching skills.

Rapid optimization of drug combinations for the optimal angiostatic treatment of cancer.

Drug combinations can improve angiostatic cancer treatment efficacy and enable the reduction of side effects and drug resistance. Combining drugs is non-trivial due to the high number of possibilities. We applied a feedback system control (FSC) technique with a population-based stochastic search algorithm to navigate through the large parametric space of nine angiostatic drugs at four concentrations to identify optimal low-dose drug combinations. This implied an iterative approach of in vitro testing of endothelial cell viability and algorithm-based analysis. The optimal synergistic drug combination, containing erlotinib, BEZ-235 and RAPTA-C, was reached in a small number of iterations. Final drug combinations showed enhanced endothelial cell specificity and synergistically inhibited proliferation (p < 0.001), but not migration of endothelial cells, and forced enhanced numbers of endothelial cells to undergo apoptosis (p < 0.01). Successful translation of this drug combination was achieved in two preclinical in vivo tumor models. Tumor growth was inhibited synergistically and significantly (p < 0.05 and p < 0.01, respectively) using reduced drug doses as compared to optimal single-drug concentrations. At the applied conditions, single-drug monotherapies had no or negligible activity in these models. We suggest that FSC can be used for rapid identification of effective, reduced dose, multi-drug combinations for the treatment of cancer and other diseases.

Low-dose angiostatic tyrosine kinase inhibitors improve photodynamic therapy for cancer: lack of vascular normalization.

Photodynamic therapy (PDT) is an effective clinical treatment for a number of different cancers. PDT can induce hypoxia and inflammation, pro-angiogenic side effects, which may counteract its angio-occlusive mechanism. The combination of PDT with anti-angiogenic drugs offers a possibility for improved anti-tumour outcome. We used two tumour models to test the effects of the clinically approved angiostatic tyrosine kinase inhibitors sunitinib, sorafenib and axitinib in combination with PDT, and compared these results with the effects of bevacizumab, the anti-VEGF antibody, for the improvement of PDT. Best results were obtained from the combination of PDT and low-dose axitinib or sorafenib. Molecular analysis by PCR revealed that PDT in combination with axitinib suppressed VEGFR-2 expression in tumour vasculature. Treatment with bevacizumab, although effective as monotherapy, did not improve PDT outcome. In order to test for tumour vessel normalization effects, axitinib was also applied prior to PDT. The absence of improved PDT outcome in these experiments, as well as the lack of increased oxygenation in axitinib-treated tumours, suggests that vascular normalization did not occur. The current data imply that there is a future for certain anti-angiogenic agents to further improve the efficacy of photodynamic anti-cancer therapy.

The emerging quest for the optimal angiostatic combination therapy.

Angiostatic therapies are now routinely embedded in the daily clinical management of cancer. Although these agents clearly benefit patient survival rates, the effect is only moderate with sometimes considerable side effects. A major cause of failure in this respect is the induction of resistance and tolerability against these drugs. Most angiostatic drugs are tyrosine kinase inhibitors that aim to inhibit or neutralize the activity of tumour-produced growth factors. Frustrating the tumour cells in this way results in genetic adaptations in the cells, turning them into mutants that are dependent on other growth mechanisms. It may therefore be necessary to shift to another class of drugs that directly target the tumour vasculature. It is evident that improvement of future angiogenesis inhibitors can only arise from two efforts. First, through the identification of better targets, preferably specifically expressed in the tumour vasculature. Secondly, through the development of combination therapies. The present review highlights the current efforts and challenges in trying to develop effective angiostatic combination therapies.

Discovery of a low order drug-cell response surface for applications in personalized medicine.

The cell is a complex system involving numerous components, which may often interact in a non-linear dynamic manner. Diseases at the cellular level are thus likely to involve multiple cellular constituents and pathways. As some drugs, or drug combinations, may act synergistically on these multiple pathways, they might be more effective than the respective single target agents. Optimizing a drug mixture for a given disease in a particular patient is particularly challenging due to both the difficulty in the selection of the drug mixture components to start out with, and the all-important doses of these drugs to be applied. For n concentrations of m drugs, in principle, n(m) combinations will have to be tested. As this may lead to a costly and time-consuming investigation for each individual patient, we have developed a Feedback System Control (FSC) technique which can rapidly select the optimal drug-dose combination from the often millions of possible combinations. By testing this FSC technique in a number of experimental systems representing different disease states, we found that the response of cells to multiple drugs is well described by a low order, rather smooth, drug-mixture-input/drug-effect-output multidimensional surface. The main consequences of this are that optimal drug combinations can be found in a surprisingly small number of tests, and that translation from in vitro to in vivo is simplified. This points to the possibility of personalized optimal drug mixtures in the near future. This unexpectedly simple input-output relationship may also lead to a simple solution for handling the issue of human diversity in cancer therapeutics.

Diffuse age-related lumbar mri changes confound diagnosis of single (L5) root lesions.

INTRODUCTION: L5 radiculopathy has characteristic clinical and electrodiagnostic features including: radicular pain; weakness or denervation of hip abductors, ankle dorsiflexors, and inverters; and pre-ganglionic dorsal foot sensory loss. It is unknown how often patients with this distinctive clinical-electrodiagnostic presentation have isolated L5-root compression on neuroimaging or more widespread, possibly age-related, lumbar neuroforaminal or spinal stenosis. METHODS: A study-blinded neuroradiologist quantitated lumbosacral neuroforaminal, lateral recess, and spinal stenosis in 26 consecutive patients with unilateral, clinically and EMG-ascertained L5 monoradiculopathy, and quantitated a global neuroforaminal and spinal stenosis score (SSS). RESULTS: Only 9 patients (35%) had isolated L5-root compression, 14 (54%) had multi-root compression, and 3 (12%) had normal neuroimaging. Increasing age correlated with SSS, and the 9 patients with isolated L5-root compression were significantly younger than patients with multi-root involvement. CONCLUSIONS: This study underscores the role of clinical and electrodiagnostic data when interpreting lumbosacral neuroimaging, particularly in older patients.

The Tarrytown Chief Residents Leadership Conference: a long-term follow-up.

OBJECTIVE: Creating training opportunities for the development of effective leaders is an increasingly important goal in psychiatry residency training programs. This article examines the long-term perceived impact of the Tarrytown Chief Residents Leadership Conference on preparing psychiatric residents for future leadership positions. METHODS: Self-report surveys from attendees who participated in the conference between 1998 and 2011 were examined. RESULTS: Five hundred and forty-one completed surveys were returned (43 % response rate). Eighty-six percent of respondents reported moderate to extreme improvement in leadership confidence post-conference. Most respondents indicated at least moderate improvement in self-awareness (93 %), understanding of group process (92 %), and willingness to address conflict (89 %). Ninety percent felt the conference was important to their residency training, and 80 % indicated increased interest in leadership post-conference. CONCLUSIONS: Responders reported lasting improvements in their confidence in and perceived ability to utilize skills necessary for effective leadership, demonstrating the value of this experiential learning opportunity.

Antibiotic-mediated microbial community restructuring is dictated by variability in antibiotic susceptibility and population interactions.

It is widely known that faster-growing bacterial cells are more susceptible to antibiotics. Given this notion, it appears intuitive that antibiotic treatment would enrich slower-growing cells in a clonal population or slower-growing populations in a microbial community, which has been commonly observed. However, experimental observations also show the enrichment of faster-growing subpopulations under certain conditions. Does this apparent discrepancy suggest uniqueness about different growth environments or the role of additional confounding factors? If so, what could be the major determinant in antibiotic-mediated community restructuring? Combining modeling and quantitative measurements using a barcoded heterogeneous E. coli library, we show that the outcome of antibiotic-mediated community restructuring can be driven by two major factors. One is the variability among the clonal responses of different subpopulations to the antibiotic; the other is their interactions. Our results suggest the importance of quantitative measurements of antibiotic responses in individual clones in predicting community responses to antibiotics and addressing subpopulation interactions.

Angiogenesis inhibition for the improvement of photodynamic therapy: the revival of a promising idea.

Photodynamic therapy (PDT) is a minimally invasive form of treatment, which is clinically approved for the treatment of angiogenic disorders, including certain forms of cancer and neovascular eye diseases. Although the concept of PDT has existed for a long time now, it has never made a solid entrance into the clinical management of cancer. This is likely due to secondary tissue reactions, such as inflammation and neoangiogenesis. The recent development of clinically effective angiogenesis inhibitors has lead to the initiation of research on the combination of PDT with such angiostatic targeted therapies. Preclinical studies in this research field have shown promising results, causing a revival in the field of PDT. This review reports on the current research efforts on PDT and vascular targeted combination therapies. Different combination strategies with angiogenesis inhibition and vascular targeting approaches are discussed. In addition, the concept of increasing PDT selectivity by targeted delivery of photosensitizers is presented. Furthermore, the current insights on sequencing the therapy arms of such combinations will be discussed in light of vascular normalization induced by angiogenesis inhibition.