Quantifying the impact of an inference model in Bayesian phylogenetics

Phylogenetic trees are currently routinely reconstructed from an alignment of character sequences (usually nucleotide sequences). Bayesian tools, such as MrBayes, RevBayes and BEAST2, have gained much popularity over the last decade, as they allow joint estimation of the posterior distribution of the phylogenetic trees and the parameters of the underlying inference model. An important ingredient of these Bayesian approaches is the species tree prior. In principle, the Bayesian framework allows for comparing different tree priors, which may elucidate the macroevolutionary processes underlying the species tree. In practice, however, only macroevolutionary models that allow for fast computation of the prior probability are used. The question is how accurate the tree estimation is when the real macroevolutionary processes are substantially different from those assumed in the tree prior. Here we present pirouette, a free and open-source r package that assesses the inference error made by Bayesian phylogenetics for a given macroevolutionary diversification model. pirouette makes use of BEAST2, but its philosophy applies to any Bayesian phylogenetic inference tool. We describe pirouette's usage providing full examples in which we interrogate a model for its power to describe another. Last, we discuss the results obtained by the examples and their interpretation

Preliminary characterization of residual biomass from Hibiscus sabdariffa Calyces

Hibiscus sabdariffa calyces are mainly used for different agro-food and beverages applications. The residual biomass generated contains various useful substances that were extracted and characterized. It contained 23% (w/w) soluble pectic material, a food additive, extracted with hot acidified water (80°C, pH = 1.5) and precipitated with ethanol. The molecular weight (28.5 and 109.7 kDa), the degree of methylation (70.6 and 44.3%) and the degree of acetylation (19.0 and 4.9%) were determined for two Senegalese cultivars (koor and vimto, respectively). The effect of the extraction method on these parameters was highlighted. The residual lignocellulosic material (LCM) was chemically degraded to monosaccharides and the amount of glucose and xylose (39% of dry LCM) determined to estimate its potential as feedstock for biofuels production. However, an enzymatic degradation test revealed a recalcitrant LCM, as only 50 to 55% of its polymeric glucose content was degraded to monosaccharides without pretreatment. Xylo-oligosaccharides (XOS) are functional foods with a real market potential as prebiotics, characterized by their degree of polymerization (DP). The production of XOS synthetized by the enzymatic degradation of LCM was monitored. The results of analyses performed showed that XOS produced had mainly DP3 and DP4 values.Key words: Pectin, lignocellulosic material, enzymatic degradation, xylo-oligosaccharides

The Viral Picture of Well-Being: Biggest Concerns, Losses, and Unintended Gifts of COVID-19 in the Philippines

The COVID-19 pandemic revealed more than anticipated about global human functioning and resiliency. This Philippines-based study replicated a recent U.S. COVID analysis on psychological well-being (PWB). Factors examined herein were grouped into categories for analysis: 1) predictors of PWB, 2) areas of greatest stress or worry (biggest concerns), 3) perceived or real losses across SES, and 4) identified “unintended gifts” across PWB. Participants (n = 1345) were volunteers who responded to an online survey from August to September 2021, peak of the Delta variant. Three general groups of predictors (biological, psychological, and socio-economic) contributed to PWB. A regression model containing a total of 11 variables was significant, F(11, 1092) = 116.02, p \u3c .00, explaining 53.9% of the variance. The model indicated PWB was significantly predicted by physical health, age, spirituality, emotional loneliness, social loneliness, sense of agency, and income. The strongest predictors of PWB were a sense of agency, social loneliness, and spirituality. Qualitative data analysis was conducted examining biggest concerns, losses due to COVID, and unintended gifts. Top ranking participant concerns were the health of family and friends, personal wellness, and governmental inefficiency/lack of concern. Losses compared to pre-COVID life were analyzed by SES group, with the most frequent responses being missing face-to-face interactions and the freedom to go/do what they please. Low SES groups were most likely to endorse missing everyday routine and experiencing changes in housing conditions due to the pandemic. Unintended gifts of COVID explored by PWB, high PWB individuals significantly appreciated intentional time with family and friends, deepening their spiritual lives, the ability to work from home, less pollution, and more time for physical exercise. Low PWB individuals reported nothing gained, except more time playing video games and watching TV. Those with higher PWB identified more unintended gifts of COVID and coped more actively

Anthracycline-trastuzumab regimens for HER2/neu-overexpressing breast cancer: current experience and future strategies

Anthracycline-trastuzumab-containing regimens demonstrate significant clinical activity in human epidermal growth factor receptor 2 (HER2)-positive breast cancer; however, the utility of this strategy is limited by unacceptably high rates of significant cardiotoxicity, particularly with concurrent administration. Anthracycline-induced cardiotoxicity is thought to be mediated primarily through increased myocardial oxidative stress, modified partly by the activity of neuregulins. Trastuzumab-induced cardiotoxicity is thought to be mediated by the ErbB/neuregulin system, with exposure to trastuzumab partly blocking the protective effect of neuregulins on the myocardium. As a result, trastuzumab increases the risk of anthracycline-induced cardiotoxicity. Several strategies have been adopted in attempts to minimize cardiotoxicity, including patient selection on the basis of preexisting cardiac risk, monitoring of cardiac function during treatment, and early management of cardiac dysfunction. The use of less cardiotoxic anthracyclines may be one strategy to lessen the risk of cardiotoxicity. Liposomal doxorubicin products offer similar efficacy compared with conventional doxorubicin, with significantly less cardiotoxicity, and have been successfully used in combination with trastuzumab in the metastatic and neo-adjuvant setting. Clinical trials are currently underway to assess the safety of pegylated liposomal doxorubicin during concurrent administration with trastuzumab compared with standard sequential treatment using conventional doxorubicin in the adjuvant settin

Vascular Endothelial Growth Factor in the Circulation in Cancer Patients May Not Be a Relevant Biomarker

Levels of circulating vascular endothelial growth factor (VEGF) have widely been used as biomarker for angiogenic activity in cancer. For this purpose, non-standardized measurements in plasma and serum were used, without correction for artificial VEGF release by platelets activated ex vivo. We hypothesize that "true" circulating (c)VEGF levels in most cancer patients are low and unrelated to cancer load or tumour angiogenesis. We determined VEGF levels in PECT, a medium that contains platelet activation inhibitors, in citrate plasma, and in isolated platelets in 16 healthy subjects, 18 patients with metastatic non-renal cancer (non-RCC) and 12 patients with renal cell carcinoma (RCC). In non-RCC patients, circulating plasma VEGF levels were low and similar to VEGF levels in controls if platelet activation was minimized during the harvest procedure by PECT medium. In citrate plasma, VEGF levels were elevated in non-RCC patients, but this could be explained by a combination of increased platelet activation during blood harvesting, and by a two-fold increase in VEGF content of individual platelets (controls: 3.4 IU/10(6), non-RCC: 6.2 IU/10(6) platelets, p = 0.001). In contrast, cVEGF levels in RCC patients were elevated (PECT plasma: 64 pg/ml vs. 21 pg/ml, RCC vs. non-RCC, p<0.0001), and not related to platelet VEGF concentration. Our findings suggest that "true" freely cVEGF levels are not elevated in the majority of cancer patients. Previously reported elevated plasma VEGF levels in cancer appear to be due to artificial release from activated platelets, which in cancer have an increased VEGF content, during the blood harvest procedure. Only in patients with RCC, which is characterized by excessive VEGF production due to a specific genetic defect, were cVEGF levels elevated. This observation may be related to limited and selective success of anti-VEGF agents, such as bevacizumab and sorafenib, as monotherapy in RCC compared to other forms of cance

HIGH SPIN ISOMERIC STATES IN 197Pb

High spin isomeric states in 197Pb have been investigated by in-beam gamma ray technics. These states are produced in (heavy ion, xn) reactions. various experiments performed are summarized in table I

High-dose carboplatin, thiotepa and cyclophosphamide (CTC) with peripheral blood stem cell support in the adjuvant therapy of high-risk breast cancer: a practical approach.

In 29 chemotherapy-naive patients with stage II-III breast cancer, peripheral blood stem cells (PBSCs) were mobilised following fluorouracil 500 mg m-2, epirubicin 90-120 mg m-2 and cyclophosphamide 500 mg m-2 (FEC) and granulocyte colony-stimulating factor (G-CSF; Filgrastim) 300 microgram s.c. daily. In all but one patient, mobilisation was successful, requiring three or fewer leucocytopheresis sessions in 26 patients; 28 patients subsequently underwent high-dose chemotherapy consisting of carboplatin 1600 mg m-2, thiotepa 480 mg m-2 and cyclophosphamide 6 g m-2 (CTC) followed by PBSC transplantation. Haemopoietic engraftment was rapid with a median time to neutrophils of 500 x 10(6) l(-1) of 9 days (range 8-10) in patients who received G-CSF after PBSC-transplantation; platelet transfusion independence was reached within a median of 10 days (range 7-16). Neutropenic fever occurred in 96% of patients. Gastrointestinal toxicity was substantial but reversible. Renal, neural or ototoxicity was not observed. Complications related to the central venous catheter were encountered in 64% of patients, with major vein thrombosis occurring in 18%. High-dose CTC-chemotherapy with PBSC-transplantation, harvested after mobilisation with FEC and G-CSF, is reasonably well tolerated without life-threatening toxicity and is a suitable high-dose strategy for the adjuvant treatment of breast cancer

UvA-DARE (Digital Academic Repository) Vascular Endothelial Growth Factor in the Circulation in Cancer Patients May Not Be a Relevant Biomarker

Abstract Background: Levels of circulating vascular endothelial growth factor (VEGF) have widely been used as biomarker for angiogenic activity in cancer. For this purpose, non-standardized measurements in plasma and serum were used, without correction for artificial VEGF release by platelets activated ex vivo. We hypothesize that &apos;&apos;true&apos;&apos; circulating (c)VEGF levels in most cancer patients are low and unrelated to cancer load or tumour angiogenesis