Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach

Psychological and psychiatric aspects of care

Serious psychological symptoms often accompany a progressive and/or life-threatening illness. It is well established that unrelieved suffering of any kind is associated with poor quality of life and care outcomes. Several barriers to psychiatric involvement with this population exist; however, mental health specialists have increasingly developed ways to provide their expertise to the care of seriously ill patients. Palliative care psychiatry is an emerging subspecialty at the intersection of palliative care and psychiatry. Effective management of psychosocial and psychiatric issues often enables improvements in other domains, including physical distress, quality of life, and care outcomes. Physician assistants can contribute meaningfully to care for seriously ill patients by developing expertise in various aspects of mental health care. This chapter provides a practical examination of some of these behavioral health aspects that physician assistants can utilize in the care of seriously ill patients, their caregivers, and loved ones

Insights into complex nanopillar-bacteria interactions: Roles of nanotopography and bacterial surface proteins

Nanopillared surfaces have emerged as a promising strategy to combat bacterial infections on medicaldevices. However, the mechanisms that underpin nanopillar-induced rupture of the bacterial cell membraneremain speculative. In this study, we have tested three medically relevant poly(ethylene terephthalate)(PET) nanopillared-surfaces with well-defined nanotopographies against both Gram-negative andGram-positive bacteria. Focused ion beam scanning electron microscopy (FIB-SEM) and contact mechanicsanalysis were utilised to understand the nanobiophysical response of the bacterial cell envelope to asingle nanopillar. Given their importance to bacterial adhesion, the contribution of bacterial surface proteinsto nanotopography-mediated cell envelope damage was also investigated. We found that, whilstcell envelope deformation was affected by the nanopillar tip diameter, the nanopillar density affectedbacterial metabolic activities. Moreover, three different types of bacterial cell envelope deformation wereobserved upon contact of bacteria with the nanopillared surfaces. These were attributed to bacterialresponses to cell wall stresses resulting from the high intrinsic pressure caused by the engagement ofnanopillars by bacterial surface proteins. Such influences of bacterial surface proteins on the antibacterial action of nanopillars have not been previously reported. Our findings will be valuable to the improveddesign and fabrication of effective antibacterial surfaces

Outcome of Immediate Versus Early Antibiotics in Severe Sepsis and Septic Shock: A Systematic Review and Meta-analysis

Study objective: Debate exists about the mortality benefit of administering antibiotics within either 1 or 3 hours of sepsis onset. We performed this meta-analysis to analyze the effect of immediate (0 to 1 hour after onset) versus early (1 to 3 hours after onset) antibiotics on mortality in patients with severe sepsis or septic shock. Methods: This review was consistent with the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Searched databases included PubMed, EMBASE, Web of Science, and Cochrane Library, as well as gray literature. Included studies were conducted with consecutive adults with severe sepsis or septic shock who received antibiotics within each period and provided mortality data. Data were extracted by 2 independent reviewers and pooled with random effects. Two authors independently assessed quality of evidence across all studies with Cochrane's Grading of Recommendations Assessment, Development and Evaluation methodology and risk of bias within each study, using the Newcastle-Ottawa Scale. Results: Thirteen studies were included: 5 prospective longitudinal and 8 retrospective cohort ones. Three studies (23%) had a high risk of bias (Newcastle-Ottawa Scale). Overall, quality of evidence across all studies (Grading of Recommendations Assessment, Development and Evaluation) was low. Pooling of data (33,863 subjects) showed no difference in mortality between patients receiving antibiotics in immediate versus early periods (odds ratio 1.09; 95% confidence interval 0.98 to 1.21). Analysis of severe sepsis studies (8,595 subjects) found higher mortality in immediate versus early periods (odds ratio 1.29; 95% confidence interval 1.09 to 1.53). Conclusion: We found no difference in mortality between immediate and early antibiotics across all patients. Although the quality of evidence across studies was low, these findings do not support a mortality benefit for immediate compared with early antibiotics across all patients with sepsis

Association of ceramide metabolism with resistance to androgen receptor signalling inhibitors in metastatic prostate cancer

Background:Prostate cancer (Pca) is the second common cancer among male worldwide. In recent years, the incidence and mortality in China have gradually increased. Most tumours profiled in these studies were obtained from patients from Caucasians population, while conditions in other races remain unclear.Methods:Somatic and germ line mutations were identified via targeted next generation sequencing with Acornmed panel including 808 genes associated with tumor development. Sequencing data were analyzed to call tumor specific single nucleotide variants (SNV), small insertions and deletions (InDels), copy number alterations (CNA)and chromosomal rearrangements.Results:A total 3158 genomic alterations (GA) were identified in 429 Pca patients,including missense mutations(61%), followed by frame shift indel (22%), infra meshiftindel (2%),stop gain (6%) , copy number loss (6%) copy number gain (2%) and splicing(2%) stop loss (0.1%) mutations. Germline pathogenic or likely pathogenic mutationsoccurred in DNA damage repair genes 13%. The median age of patients with Pca was55 (range 31-59) in the patients who were<60 and 70 (range 60-91) in the patientswho were 60. The GA/sample in patients who were 60 were higher (3.8 in<60 vs.7.8 in 60). P/LP mutations in DDR genes were more common in early-onset Pca<60(23% in<60 vs. 12% in 60, p¼0.024). In addition, the somatic spectrum was different between patients who were<60 and 60 years of age. The most commonmutations detected in patients with early-onset Pca<60 were TP53 (25%), AR (17%),CDK12 (9%), FOXA1 (9%) and PTEN (9%) vs. FOXA1 (16%), AR (14%), TP53 (14%),CDK12 (11%) and SPOP (9%) in patients who were 60 years of age. Frequency ofTP53 mutations were significantly higher in patients<60 years of age (p¼0.04),while FOXA1 mutations were higher in patients60 years of age.Conclusions:To our knowledge, this is a first systematic comparison study in Pcapatients in the patients who were<60 and 60 years of age. At a population level,there were notable differences observed in germ line and somatic variants in two cohorts. Those molecular profiling may predict the benefit of targeted therapy and immunotherapy in patients with Pca and that could potentially be used in clinicaltrials.Y. Wang, Z. Liu, T. Yang, H. Wang, F. Lou, S. Cao, Y. N

Intelligent action guidance and the use of mixed representational formats

My topic is the intelligent guidance of action. In this paper I offer an empirically grounded case for four ideas: that [a] cognitive processes of practical reasoning play a key role in the intelligent guidance of action, [b] these processes could not do so without significant enabling work done by both perception and the motor system, [c] the work done by perceptual and motor systems can be characterized as the generation of information specialized for action guidance, which in turn suggests that [d] the cognitive processes of practical reasoning that play a key role in the guidance of intelligent action are not the abstract, syllogistic ones philosophers often treat as the paradigm of practical reasoning. Rather, these cognitive processes are constrained by, and work well with, the specialized concepts outputted by perception and the feedback outputted by sensorimotor processes