Seasonal distribution of genetic types of planktonic foraminifer morphospecies in the Santa Barbara Channel and its paleoceanographic implications

We present data on the temporal distribution of planktonic foraminifer genotypes (small subunit (SSU) ribosomal (r) RNA gene) and morphospecies (sediment traps) collected during 1999 in the Santa Barbara Channel. The sampling was undertaken with special emphasis on paleoceanographically important morphospecies, predominantly Globigerina bulloides. We found the same genotype of G. bulloides (type IId) in all the changing hydrographic regimes associated with this region throughout the annual cycle with the exception of January, when we recorded the additional presence of the high-latitude G. bulloides type IIa. We identified three new genotypes: Neogloboquadrina dutertrei type Ic, N. pachyderma dextral type II, and Turborotalita quinqueloba type IId. Our data suggest that G. bulloides type IId and possibly even the new genotypes listed above may be associated specifically with the complex hydrography or other environmental features characteristic of this area. Since G. bulloides type IId occurs throughout the year and its peak fluxes are related to different hydrographic regimes, we argue that the physical properties of the water column are not the major factor influencing the distribution and growth of this genotype. In sediment trap samples we found a skewed coiling ratio for G. bulloides (most likely representing type IId), which is related neither to sea surface temperature nor to genotypic difference. This study illustrates the necessity to map both the spatial and temporal distribution of the genetic types, especially in areas of paleoceanographic interest, where geochemical and paleontological proxies are being calibrated

Engaging and partnering with Aboriginal and Torres Strait Islander parents and caregivers

The Engaging and partnering with Aboriginal and Torres Strait Islander parents and caregivers two-year project has culminated in a unique interactive website (see www.yourstoryourjourney.net) that houses a number of learning and teaching tools, strategies and resources designed to support all those working to improve the educational success of Aboriginal and Torres Strait Islander students in schools, Australia’s First Nations peoples. It is intended to be used in teacher education programs (pre-service and in-service), by teachers and school leaders, and by Aboriginal and Torres Strait Islander communities. The resource has been created to help all educators form relationships and partnerships with local communities, parents and caregivers to achieve better educational outcomes for all Aboriginal and Torres Strait Islander students. The resource positions educators as powerful agents of change

A Historical Perspective on Presentations of Hypertensive Acute Heart Failure

BACKGROUND: The initial systolic blood pressure (SBP) in patients presenting to the hospital with acute heart failure (AHF) informs prognosis, diagnosis, and guides initial treatment. However, over time AHF presentations with elevated SBP appear to have declined. The present study examined whether the frequency of AHF presentations with systolic hypertension (SBP \u3e 160 mmHg) declined over a nearly two-decade time interval. METHODS: This study compares four historical, cross-sectional cohorts with AHF who were admitted to tertiary care medical centres in the North-eastern USA in 1995, 2000, 2006, and 2011-13. The main outcome was the proportion of AHF patients presenting with an initial SBP \u3e 160 mmHg. RESULTS: 2,366 patients comprised the study sample. The average age was 77 years, 55% were female, 94% white, and 75% had prior heart failure. In 1995, 34% of AHF patients presented with an initial SBP \u3e 160 mmHg compared to 20% in 2011-2013 (p \u3c 0.01). Multivariate logistic regression demonstrated reduced odds of presenting with a SBP \u3e 160 mmHg in 2006 (0.64, 95% CI 0.42-0.96) and 2011-13 (0.46, 95% CI 0.28-0.74) compared with patients in 1995. CONCLUSION: The proportion of patients with AHF and initial SBP \u3e 160 mmHg significantly declined over the study time period. There are several potential reasons for this observation and these findings highlight the need for ongoing surveillance of patients with AHF as changing clinical characteristics can impact early treatment decisions

Know Your Epidemic, Know Your Response: COVID-19 in the United States

We document that during the week of March 10-16, the Covid-19 pandemic fundamentally affected the perceptions of U.S. residents about the health risks and socioeconomic consequences entailed by the pandemic. During this week, it seems, everything changed. Not only did the pandemic progress rapidly across the United States, but U.S. residents started to realize that the threat was real: increasing Covid-19 caseloads heightened perceptions of infection risks and excess mortality risks, concerns about the economic implications increased substantially, and behavioral responses became widespread as the pandemic expanded rapidly in the U.S. In early to mid-March 2020, average perceptions about the coronavirus infection risks are broadly consistent with projections about the pandemic, while expectations about dying conditional on infection and expectations about Covid-19-related excess mortality during the next months are possibly too pessimistic. However, some aspects of Covid-19 perceptions are disconcerting from the perspective of implementing and sustaining an effective societal response to the pandemic. For instance, the education gradient in expected infection risks entails the possibility of having different perceptions of the reality of the pandemic between people with and without a college education, potentially resulting in two different levels of behavioral and policy-responses across individuals and regions. Unless addressed by effective health communication that reaches individuals across all social strata, some of the misperceptions about Covid-19 epidemic raise concerns about the ability of the United States to implement and sustain the widespread and harsh policies that are required to curtail the pandemic. Our analyses also reveal perceptions of becoming infected with the virus, and dying from Covid-19, were driven upwards by a rapidly increasing national caseload, and perceptions of the economic consequences and the adaptation of social distancing were affected by both national and state-level cases

Apicomplexan Parasites Co-Opt Host Calpains to Facilitate Their Escape from Infected Cells

Apicomplexan parasites, including Plasmodium falciparum and Toxoplasma gondii (the causative agents of malaria and toxoplasmosis, respectively), are responsible for considerable morbidity and mortality worldwide. These pathogenic protozoa replicate within an intracellular vacuole inside of infected host cells, from which they must escape to initiate a new lytic cycle. By integrating cell biological, pharmacological, and genetic approaches, we provide evidence that both Plasmodium and Toxoplasma hijack host cell calpain proteases to facilitate parasite egress. Immunodepletion or inhibition of calpain-1 in hypotonically lysed and resealed erythrocytes prevented the escape of P. falciparum parasites, which was restored by adding purified calpain-1. Similarly, efficient egress of T. gondii from mammalian fibroblasts was blocked by either small interfering RNA– mediated suppression or genetic deletion of calpain activity and could be restored by genetic complementation

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.This work was supported by the National Science Foundation [grant numbers DBI-0755048, DEB-0732920, DEB-1036448, DMS-0931642, EF-0331495, EF-0905606, EF-0949453]; the National Institutes of Health [grant numbers R01-HG006139, R01-GM037841, R01-GM078985, R01-GM086887, R01-NS063897]; the Biotechnology and Biological Sciences Research Council [grant number BB/H011285/1]; the Wellcome Trust [grant number WT092807MA]; and Google Summer of Code

Point-of-care assessment of platelet reactivity in the emergency department may facilitate rapid rule-out of acute coronary syndromes: a prospective cohort pilot feasibility study

Objective: Accurate, efficient and cost-effective disposition of patients presenting to emergency departments (EDs) with symptoms suggestive of acute coronary syndromes (ACS) is a growing priority. Platelet activation is an early feature in the pathogenesis of ACS; thus, we sought to obtain an insight into whether point-of-care testing of platelet function: (1) may assist in the rule-out of ACS; (2) may provide additional predictive value in identifying patients with non-cardiac symptoms versus ACS-positive patients and (3) is logistically feasible in the ED. Design: Prospective cohort feasibility study. Setting: Two urban tertiary care sites, one located in the USA and the second in Argentina. Participants: 509 adult patients presenting with symptoms of ACS. Main outcome measures Platelet reactivity was quantified using the Platelet Function Analyzer-100, with closure time (seconds required for blood, aspirated under high shear, to occlude a 150 µm aperture) serving as the primary endpoint. Closure times were categorised as ‘normal’ or ‘prolonged’, defined objectively as the 90th centile of the distribution for all participants enrolled in the study. Diagnosis of ACS was made using the standard criteria. The use of antiplatelet agents was not an exclusion criterion. Results: Closure times for the study population ranged from 47 to 300 s, with a 90th centile value of 138 s. The proportion of patients with closure times ≥138 s was significantly higher in patients with non-cardiac symptoms (41/330; 12.4%) versus the ACS-positive cohort (2/105 (1.9%); p=0.0006). The specificity of ‘prolonged’ closure times (≥138 s) for a diagnosis of non-cardiac symptoms was 98.1%, with a positive predictive value of 95.4%. Multivariate analysis revealed that the closure time provided incremental, independent predictive value in the rule-out of ACS. Conclusions: Point-of-care assessment of platelet reactivity is feasible in the ED and may facilitate the rapid rule-out of ACS in patients with prolonged closure times

Fast-growing pancreatic neuroendocrine carcinoma in a patient with multiple endocrine neoplasia type 1: a case report

<p>Abstract</p> <p>Introduction</p> <p>Predictive genetic screening and regular screening programs in patients with multiple endocrine neoplasia type 1 are intended to detect and treat malignant tumors at the earliest stage possible. Malignant neuroendocrine pancreatic tumors are the most frequent cause of death in these patients. However, the extent and intervals of screening in patients with multiple endocrine neoplasia type 1 are controversial as neuroendocrine tumors are usually slow growing. Here we report the case of a patient who developed a fast-growing neuroendocrine carcinoma within 15 months of a laparoscopic distal pancreatic resection.</p> <p>Case presentation</p> <p>We followed a group of 45 patients with multiple endocrine neoplasia type 1 by an annual screening program in the Department of Visceral, Thoracic, and Vascular Surgery at the University Hospital Marburg in cooperation with the Department of Radiology and the Division of Endocrinology. A man with multiple endocrine neoplasia type 1 who was diagnosed with a recurrent primary hyperparathyroidism underwent a distal pancreatic resection for a non-functional neuroendocrine tumor. In the context of our regular screening program, a large non-functional neuroendocrine tumor was diagnosed in the pancreatic head 15 months after the first pancreatic surgery. Therefore, we performed an enucleation and regional lymph node resection. At histology, the diagnosis of a neuroendocrine carcinoma with one lymph node metastasis was established. There was no evidence of recurrence 9 months after re-operation.</p> <p>Conclusion</p> <p>Fast-growing neuroendocrine tumors are rare in patients with multiple endocrine neoplasia type 1. The intervals, both postoperative and in newly diagnosed pancreatic lesions, in patients with multiple endocrine neoplasia type 1 should be reduced to 6 months to establish the early diagnosis of rapidly progressive disease in a small subset of patients.</p

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations

Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional regulation. By means of a novel multi-scale spatial aggregation analysis, we uncover the existence of contiguous clusters of nucleoid-perturbation sensitive genes along the genome, whose expression is affected by a combination of topological DNA state and nucleoid-shaping protein occupancy. The clusters correlate well with the macrodomain structure of the genome. The most significant of them lay symmetrically at the edges of the ter macrodomain and involve all of the flagellar and chemotaxis machinery, in addition to key regulators of biofilm formation, suggesting that the regulation of the physical state of the chromosome by the nucleoid proteins plays an important role in coordinating the transcriptional response leading to the switch between a motile and a biofilm lifestyle.Comment: Article: first 24 pages, 3 figures Supplementary methods: 1 page, 1 figure Supplementary results: 14 pages, 11 figure

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software