Importance of tissue sampling, laboratory methods, and patient characteristics for detection of Pneumocystis in autopsied lungs of non-immunosuppressed individuals

To understand the epidemiological significance of Pneumocystis detection in a lung tissue sample of non-immunosuppressed individuals, we examined sampling procedures, laboratory methodology, and patient characteristics of autopsy series reported in the literature. Number of tissue specimens, DNA-extraction procedures, age and underlying diagnosis highly influence yield and are critical to understand yield differences of Pneumocystis among reports of pulmonary colonization in immunocompetent individuals.publishersversionpublishe

Harmonized Soil Database of Ecuador (HESD): data from 2009 to 2015

One of the largest challenges with soil information around the world is how to harmonize archived soil data from different sources and how to make it accessible to soil scientist. In Ecuador, there have been two major projects that have provided soil information, but the methodology of these projects, although comparable, did not coincide, especially with respect to how information was reported. Here, we present a new soil database for Ecuador, comprising 13 542 soil profiles with 51 713 measured soil horizons, including 92 different edaphic variables. The original data were in a non-editable format (i.e., PDF), which made it difficult to access and process the information. Our study provides an integrated framework that combines multiple analytic tools for automatically converting legacy soil information from an analog format into usable digital soil mapping inputs across Ecuador. This framework allowed us to incorporate quantitative information on a broad set of soil properties and retrieve qualitative information on soil morphological properties collected in the profile description phase, which is rarely included in soil databases. We present a new harmonized national soil database using a specific methodology to preserve relevant information. The national representativeness of soil information has been enhanced compared with other international databases, and this new database contributes to filling the gaps in publicly available soil information across the country. The database is freely available at https://doi.org/10.6073/pasta/1560e803953c839e7aedef78ff7d3f6c (Armas et al., 2022).</p

Proposing environmental flows based on physical habitat simulation for five fish species in the Lower Duero River Basin, Mexico

The concept of “environmental flow” is defined as hydrologic regimes that are required to sustain ecosystem health and functions in rivers. In Mexico, it has become an important topic, not least because a 2012 legal standard (NMX-AA-159-SCFI-2012), establishes procedures for determining instream flow requirements. Goals. The aim of this paper is to propose an acceptable environmental flow requirement for a regulated river segment in the Duero River Basin in, Michoacan, Mexico. Methods. Of the many methods of establishing environmental flows in rivers, this article is concerned with the habitat simulation method. This is based on the IFIM theoretical framework and the PHABSIM mathematical model, by which the WUA-Q curves were obtained for five species of fish. Results. From these curves, we determined that the Goodea atripinnis species has the greater habitat area and reached a maximum of 4338 m2/km for a flow of 5 m3/s; Alloophorus robustus maintained a constant habitat of 2000 m2/km between flow rates of 5 to 15 m3/s. With smaller area, Menidia jordani had a maximum habitat of 1323 m2/km for 4.5 m3/s; and with WUA less than 500 m2/km the curves of the species Algansea tincella and Aztecula sallaei were obtained. Conclusions. The average regulation in March and April was 3.61 and 3.44 m3/s and with the EFR proposal it was 5.11 and 5.00 m3/s for March and April, respectively. In general, the monthly environmental regime is to maintain 80% of the natural flow regime, generating an increase in habitat during the dry season of 24% for A. robustus and 23% for A. sallaei

A Quantitative Approach to the Watershed Governance Prism: The Duero River Basin, Mexico

Advances have been made in water resource investigation due to the implementation of mathematical models, the development of theoretical frameworks, and the evaluation of sustainability indices. Together, they improve and make integrated water resource management more efficient. In this paper, in the study area of the Duero River Basin, located in Michoacan, Mexico, we schematize a series of numerical indices of the Watershed Governance Prism to determine the quantitative status of water governance in a watershed. The results, presented as axes, perspectives, and prisms in the Axis Index, Water Governance Index, and Watershed Governance Prism Index, provide the conclusion that it is possible to establish and evaluate the Watershed Governance Prism Index using our numerical implementation of the Watershed Governance Prism theoretical framework. Thus, it is possible to define a quantitative status and evoke how water governance is being designed and implemented in a watershed

BlackCAT: A catalogue of stellar-mass black holes in X-ray transients

During the last ~50 years, the population of black hole candidates in X-ray binaries has increased considerably with 59 Galactic objects detected in transient low-mass X-ray binaries, plus a few in persistent systems (including ~5 extragalactic binaries). We collect near-infrared, optical and X-ray information spread over hundreds of references in order to study the population of black holes in X-ray transients as a whole. We present the most updated catalogue of black hole transients, which contains X-ray, optical and near-infrared observations together with their astrometric and dynamical properties. It provides new useful information in both statistical and observational parameters providing a thorough and complete overview of the black hole population in the Milky Way. Analysing the distances and spatial distribution of the observed systems, we estimate a total population of ~1300 Galactic black hole transients. This means that we have already discovered less than ~5% of the total Galactic distribution. The complete version of this catalogue will be continuously updated online and in the Virtual Observatory, including finding charts and data in other wavelengths.Comment: http://www.astro.puc.cl/BlackCAT - Accepted for publication in Astronomy & Astrophysics. 20 pages, 8 figures, 5 Table

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

Albiglutide and cardiovascular outcomes in patients with type 2 diabetes and cardiovascular disease (Harmony Outcomes): a double-blind, randomised placebo-controlled trial

Background: Glucagon-like peptide 1 receptor agonists differ in chemical structure, duration of action, and in their effects on clinical outcomes. The cardiovascular effects of once-weekly albiglutide in type 2 diabetes are unknown. We aimed to determine the safety and efficacy of albiglutide in preventing cardiovascular death, myocardial infarction, or stroke. Methods: We did a double-blind, randomised, placebo-controlled trial in 610 sites across 28 countries. We randomly assigned patients aged 40 years and older with type 2 diabetes and cardiovascular disease (at a 1:1 ratio) to groups that either received a subcutaneous injection of albiglutide (30–50 mg, based on glycaemic response and tolerability) or of a matched volume of placebo once a week, in addition to their standard care. Investigators used an interactive voice or web response system to obtain treatment assignment, and patients and all study investigators were masked to their treatment allocation. We hypothesised that albiglutide would be non-inferior to placebo for the primary outcome of the first occurrence of cardiovascular death, myocardial infarction, or stroke, which was assessed in the intention-to-treat population. If non-inferiority was confirmed by an upper limit of the 95% CI for a hazard ratio of less than 1·30, closed testing for superiority was prespecified. This study is registered with ClinicalTrials.gov, number NCT02465515. Findings: Patients were screened between July 1, 2015, and Nov 24, 2016. 10 793 patients were screened and 9463 participants were enrolled and randomly assigned to groups: 4731 patients were assigned to receive albiglutide and 4732 patients to receive placebo. On Nov 8, 2017, it was determined that 611 primary endpoints and a median follow-up of at least 1·5 years had accrued, and participants returned for a final visit and discontinuation from study treatment; the last patient visit was on March 12, 2018. These 9463 patients, the intention-to-treat population, were evaluated for a median duration of 1·6 years and were assessed for the primary outcome. The primary composite outcome occurred in 338 (7%) of 4731 patients at an incidence rate of 4·6 events per 100 person-years in the albiglutide group and in 428 (9%) of 4732 patients at an incidence rate of 5·9 events per 100 person-years in the placebo group (hazard ratio 0·78, 95% CI 0·68–0·90), which indicated that albiglutide was superior to placebo (p&lt;0·0001 for non-inferiority; p=0·0006 for superiority). The incidence of acute pancreatitis (ten patients in the albiglutide group and seven patients in the placebo group), pancreatic cancer (six patients in the albiglutide group and five patients in the placebo group), medullary thyroid carcinoma (zero patients in both groups), and other serious adverse events did not differ between the two groups. There were three (&lt;1%) deaths in the placebo group that were assessed by investigators, who were masked to study drug assignment, to be treatment-related and two (&lt;1%) deaths in the albiglutide group. Interpretation: In patients with type 2 diabetes and cardiovascular disease, albiglutide was superior to placebo with respect to major adverse cardiovascular events. Evidence-based glucagon-like peptide 1 receptor agonists should therefore be considered as part of a comprehensive strategy to reduce the risk of cardiovascular events in patients with type 2 diabetes. Funding: GlaxoSmithKline

Online conformance checking using behavioural patterns

New and compelling regulations (e.g., the GDPR in Europe) impose tremendous pressure on organizations, in order to adhere to standard procedures, processes, and practices. The field of conformance checking aims to quantify the extent to which the execution of a process, captured within recorded corresponding event data, conforms to a given reference process model. Existing techniques assume a post-mortem scenario, i.e. they detect deviations based on complete executions of the process. This limits their applicability in an online setting. In such context, we aim to detect deviations online (i.e., in-vivo), in order to provide recovery possibilities before the execution of a process instance is completed. Also, current techniques assume cases to start from the initial stage of the process, whereas this assumption is not feasible in online settings. In this paper, we present a generic framework for online conformance checking, in which the underlying process is represented in terms of behavioural patterns and no assumption on the starting point of cases is needed. We instantiate the framework on the basis of Petri nets, with an accompanying new unfolding technique. The approach is implemented in the process mining tool ProM, and evaluated by means of several experiments including a stress-test and a comparison with a similar technique.Peer Reviewe