bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase field simulation of grain growth in Al2O3-based composite ceramic cutting tool materials containing second phase nanoparticles and pores
Authors: Zhou Youxin , Peng Bin
Published: November 2020

A phase field model was established to simulate the grain growth of Al2O3-based composite ceramic tool materials containing second phase nanoparticles and pores. The free energy parameters of the model are directly related to the surface and grain boundary energies of Al2O3 such that the grain growth process can be quantitatively analysed. The model was used to investigate the effects of the volume fraction and size of second phase particles on grain growth in Al2O3 with a certain initial pore volume fraction. Findings show that pores and second phase particles jointly hinder grain growth. When the radii of second phase nanoparticles are the same, as the number of particles increase, most of the grain boundaries occur as straight lines in the microstructure, and grain size decreases. It is beneficial to obtain fine and uniform microstructure. However, when the particles content reaches a certain level, the second phase particles tend to agglomerate at the grain boundary of matrix grains, which will result in a decrease in the properties of nanocomposite ceramic tool materials. The study also found that, at a constant volume fraction of particles, with the decrease of particle radius, the grain size decreases. When the second phase particle size is reduced to 50 nm, relatively more intragranular microstructure was observed, which is considered to be the main reason for increasing the toughness of nano composite ceramic tool materials. Through analyzing the simulation results, the optimal combination of the content and size of the second phase particles can provide theoretical guidance for Al2O3 nano composite ceramic tool materials design and preparation.
Influence of graphene oxide filler content on the dentin bond integrity, degree of conversion and bond strength of experimental adhesive. A SEM, micro-Raman, FTIR and microtensile study
Authors: Bin-Shuwaish Mohammed S , Maawadh Ahmed M , Al-Hamdan Rana S , Alresayes Saad , Ali Thamer , Almutairi Basil , Vohra Fahim , Abduljabbar Tariq
Published: November 2020

The study aimed to evaluate the effect of graphene oxide (GO) nano-filler content in experimental dental adhesive on its degree of conversion (DC), microtensile bond strength (μTBS) and structural reliability, using Fourier transform infrared spectroscopy (FTIR), Micro-Raman spectroscopy and Scanning electron microscopy (SEM). A resin adhesive was fabricated (control adhesive - CA) and fabricated GO nano-particles were added at 0.5% and 2.0% (m/m) to produce adhesives GOA1 and GOA2 respectively. One hundred and two teeth (specimens) were prepared for dentin exposure and conditioned with 36% phosphoric acid. Specimens in each group (n = 34) were treated with formulated adhesives (CA, GOA1 & GOA2) and photo-polymerized for 20 s followed by composite build up. Sixty specimens were used forμTBS testing in the adhesive groups (CA, GOA1 & GOA2), with half exposed to thermocycling (TC) whereas the remaining half (n = 10) stored in distilled water. Seven specimens each were assessed using SEM and Micro-Raman spectroscopy, in each adhesive group (n = 7). DC for the adhesives was assessed using FTIR. The means ofμTBS and DC were analyzed using ANOVA and post hoc Tukey multiple comparisons test. GO nano-filler content showed significant influence on the adhesiveμTBS in comparison to controls (p < 0.01). Ageing (TC) revealed significant reduction in theμTBS, except in GOA2 specimens, which showed comparable outcomes among TC and non-TC specimens (p > 0.05). DC was significantly higher in control adhesive [46.8 (3.6)%] compared to GOA2 [37.7 (4.2)%] specimens, however DC was comparable among GOA1 [42.3 (2.9)%] and GOA2 [37.7 (4.2)%] specimens (p > 0.05) respectively. GO exhibited interaction within adhesive and tooth dentin comparable to control adhesive. Increasing GO content showed increase inμTBS of adhesive to dentin, but a decrease in degree of conversion. Under ideal conditions, experimental adhesive with 2% GO content showed acceptable bond strength and DC; and should be further assessed under dynamic conditions to recommend clinical use.
Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files
Authors: Du Lianming , Liu Qin , Fan Zhenxin , Tang Jie , Zhang Xiuyue , Price Megan , Yue Bisong , Zhao Kelei
Published: November 2020

FASTA and FASTQ are the most widely used biological data formats that have become the de facto standard to exchange sequence data between bioinformatics tools. With the avalanche of next-generation sequencing data, the amount of sequence data being deposited and accessed in FASTA/Q formats is increasing dramatically. However, the existing tools have very low efficiency at random retrieval of subsequences due to the requirement of loading the entire index into memory. In addition, most existing tools have no capability to build index for large FASTA/Q files because of the limited memory. Furthermore, the tools do not provide support to randomly accessing sequences from FASTA/Q files compressed by gzip, which is extensively adopted by most public databases to compress data for saving storage. In this study, we developed pyfastx as a versatile Python package with commonly used command-line tools to overcome the above limitations. Compared to other tools, pyfastx yielded the highest performance in terms of building index and random access to sequences, particularly when dealing with large FASTA/Q files with hundreds of millions of sequences. A key advantage of pyfastx over other tools is that it offers an efficient way to randomly extract subsequences directly from gzip compressed FASTA/Q files without needing to uncompress beforehand. Pyfastx can easily be installed from PyPI (https://pypi.org/project/pyfastx) and the source code is freely available at https://github.com/lmdu/pyfastx.
Autoregressive modeling and diagnostics for qPCR amplification
Authors: Hsu Benjamin , Sherina Valeriia , McCall Matthew N
Published: November 2020

Motivation

Current methods used to analyze real-time quantitative polymerase chain reaction (qPCR) data exhibit systematic deviations from the assumed model over the progression of the reaction. Slight variations in the amount of the initial target molecule or in early amplifications are likely responsible for these deviations. Commonly used 4- and 5-parameter sigmoidal models appear to be particularly susceptible to this issue, often displaying patterns of autocorrelation in the residuals. The presence of this phenomenon, even for technical replicates, suggests that these parametric models may be misspecified. Specifically, they do not account for the sequential dependent nature of the amplification process that underlies qPCR fluorescence measurements.

Results

We demonstrate that a Smooth Transition Autoregressive (STAR) model addresses this limitation by explicitly modeling the dependence between cycles and the gradual transition between amplification regimes. In summary, application of a STAR model to qPCR amplification data improves model fit and reduces autocorrelation in the residuals.

Availability and implementation

R scripts to reproduce all the analyses and results described in this manuscript can be found at: https://github.com/bhsu4/GAPDH.SO.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fast detection of differential chromatin domains with SCIDDO
Authors: Ebert Peter , Schulz Marcel H
Published: November 2020

Motivation

The generation of genome-wide maps of histone modifications using chromatin immunoprecipitation sequencing is a standard approach to dissect the complexity of the epigenome. Interpretation and differential analysis of histone datasets remains challenging due to regulatory meaningful co-occurrences of histone marks and their difference in genomic spread. To ease interpretation, chromatin state segmentation maps are a commonly employed abstraction combining individual histone marks. We developed the tool SCIDDO as a fast, flexible and statistically sound method for the differential analysis of chromatin state segmentation maps.

Results

We demonstrate the utility of SCIDDO in a comparative analysis that identifies differential chromatin domains (DCD) in various regulatory contexts and with only moderate computational resources. We show that the identified DCDs correlate well with observed changes in gene expression and can recover a substantial number of differentially expressed genes (DEGs). We showcase SCIDDO’s ability to directly interrogate chromatin dynamics, such as enhancer switches in downstream analysis, which simplifies exploring specific questions about regulatory changes in chromatin. By comparing SCIDDO to competing methods, we provide evidence that SCIDDO’s performance in identifying DEGs via differential chromatin marking is more stable across a range of cell-type comparisons and parameter cut-offs.

Availability and implementation

The SCIDDO source code is openly available under github.com/ptrebert/sciddo.

Supplementary information

Supplementary data are available at Bioinformatics online.
Negative impact of high doses of follicle-stimulating hormone during superovulation on the ovulatory follicle function in small ovarian reserve dairy heifers
Authors: Karl Kaitlin R , Jimenez-Krassel Fermin , Gibbings Emily , Ireland Janet L H , Clark Zaramasina L , Tempelman Robert J , Latham Keith E , Ireland James J
Published: November 2020

When women with small ovarian reserves are subjected to assisted reproductive technologies, high doses of gonadotropins are linked to high oocyte and embryo wastage and low live birth rates. We hypothesized that excessive follicle-stimulating hormone (FSH) doses during superovulation are detrimental to ovulatory follicle function in individuals with a small ovarian reserve. To test this hypothesis, heifers with small ovarian reserves were injected twice daily for 4 days, beginning on Day 1 of the estrous cycle with 35, 70, 140, or 210 IU doses of Folltropin-V (FSH). Each heifer (n = 8) was superovulated using a Williams Latin Square Design. During each superovulation regimen, three prostaglandin F2α injections were given at 12-h interval, starting at the seventh FSH injection to regress the newly formed corpus luteum (CL). Human chorionic gonadotropin was injected 12 h after the last (8th) FSH injection to induce ovulation. Daily ultrasonography and blood sampling were used to determine the number and size of follicles and corpora lutea, uterine thickness, and circulating concentrations of estradiol, progesterone, and anti-Müllerian hormone (AMH). The highest doses of FSH did not increase AMH, progesterone, number of ovulatory-size follicles, uterine thickness, or number of CL. However, estradiol production and ovulation rate were lower for heifers given high FSH doses compared to lower doses, indicating detrimental effects on ovulatory follicle function.
Associations between dyspnoea, coronary atherosclerosis, and cardiovascular outcomes: results from the long-term follow-up CONFIRM registry
Authors: van Rosendael Alexander R , Bax A Maxim , van den Hoogen Inge J , Smit Jeff M , Al’Aref Subhi J , Achenbach Stephan , Al-Mallah Mouaz H , Andreini Daniele , Berman Daniel S , Budoff Matthew J , Cademartiri Filippo , Callister Tracy Q , Chang Hyuk-Jae , Chinnaiyan Kavitha , Chow Benjamin J W , Cury Ricardo C , DeLago Augustin , Feuchtner Gudrun , Hadamitzky Martin , Hausleiter Joerg , Kaufmann Philipp A , Kim Yong-Jin , Leipsic Jonathon A , Maffei Erica , Marques Hugo , de Araújo Gonçalves Pedro , Pontone Gianluca , Raff Gilbert L , Rubinshtein Ronen , Villines Todd C , Gransar Heidi , Lu Yao , Peña Jessica M , Lin Fay Y , Shaw Leslee J , Narula Jagat , Min James K , Bax Jeroen J
Published: November 2020

Aims 

The relationship between dyspnoea, coronary artery disease (CAD), and major cardiovascular events (MACE) is poorly understood. This study evaluated (i) the association of dyspnoea with the severity of anatomical CAD by coronary computed tomography angiography (CCTA) and (ii) to which extent CAD explains MACE in patients with dyspnoea.

Methods and results 

From the international COronary CT Angiography EvaluatioN for Clinical Outcomes: An InteRnational Multicenter (CONFIRM) registry, 4425 patients (750 with dyspnoea) with suspected but without known CAD were included and prospectively followed for ≥5 years. First, the association of dyspnoea with CAD severity was assessed using logistic regression analysis. Second, the prognostic value of dyspnoea for MACE (myocardial infarction and death), and specifically, the interaction between dyspnoea and CAD severity was investigated using Cox proportional-hazard analysis. Mean patient age was 60.3 ± 11.9 years, 63% of patients were male and 592 MACE events occurred during a median follow-up duration of 5.4 (IQR 5.1–6.0) years. On uni- and multivariable analysis (adjusting for age, sex, body mass index, chest pain typicality, and risk factors), dyspnoea was associated with two- and three-vessel/left main (LM) obstructive CAD. The presence of dyspnoea increased the risk for MACE [hazard ratio (HR) 1.57, 95% confidence interval (CI): 1.29–1.90], which was modified after adjusting for clinical predictors and CAD severity (HR 1.26, 95% CI: 1.02–1.55). Conversely, when stratified by CAD severity, dyspnoea did not provide incremental prognostic value in one-, two-, or three-vessel/LM obstructive CAD, but dyspnoea did provide incremental prognostic value in non-obstructive CAD.

Conclusion 

In patients with suspected CAD, dyspnoea was independently associated with severe obstructive CAD on CCTA. The severity of obstructive CAD explained the elevated MACE rates in patients presenting with dyspnoea, but in patients with non-obstructive CAD, dyspnoea portended additional risk.
Live fast, die young and sleep later
Authors: Dishakjian Vahe , Fessler Daniel M T , Sparks Adam Maxwell
Published: November 2020

Background and objectives

Life History Theory (LHT) describes trade-offs that organisms make with regard to three investment pathways: growth, maintenance and reproduction. In light of the reparative functions of sleep, we examine sleep behaviors and corresponding attitudes as proximate manifestations of an individual’s underlying relative prioritization of short-term reproduction versus long-term maintenance.

Methodology

We collected survey data from 568 participants across two online studies having different participant pools. We use a mixture of segmented and hierarchical regression models, structural equation modeling and machine learning to infer relationships between sleep duration/quality, attitudes about sleep and biodemographic/psychometric measures of life history strategy (LHS).

Results

An age-mediated U- or V-shaped relationship appears when LHS is plotted against habitual sleep duration, with the fastest strategies occupying the sections of the curve with the highest mortality risk: < 6.5 hr (short sleep) and > 8.5 hr (long sleep). LH ‘fastness’ is associated with increased sleepiness and worse overall sleep quality: delayed sleep onset latency, more wakefulness after sleep onset, higher sleep–wake instability and greater sleep duration variability. Hedonic valuations of sleep may mediate the effects of LHS on certain sleep parameters.

Conclusions and implications

The costs of deprioritizing maintenance can be parameterized in the domain of sleep, where ‘life history fastness’ corresponds with sleep patterns associated with greater senescence and mortality. Individual differences in sleep having significant health implications can thus be understood as components of lifelong trajectories likely stemming from calibration to developmental circumstances. Relatedly, hedonic valuations of sleep may constitute useful avenues for non-pharmacological management of chronic sleep disorders.

Lay Summary: Sleep is essential because it allows the body to repair and maintain itself. But time spent sleeping is time that cannot be spent doing other things. People differ in how much they prioritize immediate rewards, including sociosexual opportunities, versus long-term goals. In this research, we show that individual differences in sleep behaviors, and attitudes toward sleep, correspond with psychological and behavioral differences reflecting such differing priorities. Orientation toward sleep can thus be understood as part of the overall lifetime strategies that people pursue.
Severe aortic stenosis in the young, with or without bicuspid valve: is transcatheter aortic valve implantation the first choice?
Authors: Belluschi Igor , Buzzatti Nicola , Castiglioni Alessandro , De Bonis Michele , Montorfano Matteo , Alfieri Ottavio
Published: November 2020

During the last decade, transcatheter aortic valve implantation (TAVI) has represented a valid alternative to surgical aortic valve replacement in patients with aortic stenosis and elevated surgical risk. Recent randomized clinical trials reported excellent results also for patients at low surgical risk, but in clinical practice, the mean age of the patients treated remain over 75 years, and the presence of a bicuspid aortic valve still represents an important exclusion criteria. Today, aortic valve replacement with a mechanical prosthesis remains the treatment of choice for young adults with aortic stenosis, although the desire to avoid oral anticoagulants drives more patients younger than 65 years of age towards biological prostheses. Furthermore, despite the follow-up of patients after TAVI is still limited to a few years, the opportunity of a second percutaneous treatment (TAVI-in-TAVI), extends the scope of percutaneous strategy. In the next few years, TAVI has to face many challenges to become a valid alternative to surgery in the younger patients as well.
Myths to debunk: the non-compacted myocardium
Authors: Di Toro Alessandro , Giuliani Lorenzo , Smirnova Alexandra , Favalli Valentina , Serio Alessandra , Urtis Mario , Grasso Maurizia , Arbustini Eloisa
Published: November 2020

Left ventricular non-compaction (LVNC) is defined by the triad: prominent trabecular anatomy, thin compacted layer, and deep inter-trabecular recesses. No person, sick or healthy, demonstrates identical anatomy of the trabeculae; their configuration represents a sort of individual dynamic ‘cardiac fingerprinting’. LVNC can be observed in healthy subjects with normal left ventricular (LV) size and function, in athletes, in pregnant women, as well as in patients with haematological disorders, neuromuscular diseases, and chronic renal failure; it can be acquired and potentially reversible. When LVNC is observed in patients with dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy, restrictive cardiomyopathy, or arrhythmogenic cardiomyopathy, the risk exists of misnaming the cardiomyopathy as ‘LVNC cardiomyopathy’ rather than properly describe, i.e. a ‘DCM associated with LVNC’. In rare infantile CMPs (the paradigm is tafazzinopathy or Barth syndrome), the non-compaction (NC) is intrinsically part of the cardiac phenotype. The LVNC is also common in congenital heart disease (CHD) as well as in chromosomal disorders with systemic manifestations. The high prevalence of LVNC in healthy athletes, its possible reversibility or regression, and the increasing detection in healthy subjects suggest a cautious use of the term ‘LVNC cardiomyopathy’, which describes the morphology, but not the functional profile of the cardiac disease. Genetic testing, when positive, usually reflects the genetic causes of an underlying cardiomyopathy rather than that of the NC, which often does not segregate with CMP phenotype in families. Therefore, when associated with LV dilation and dysfunction, hypertrophy, or CHD, the leading diagnosis is cardiomyopathy or CHD followed by the descriptor LVNC.
Timing of cardioversion in atrial fibrillation: the sooner the better?
Authors: Capranzano Piera , Calvi Valeria
Published: November 2020

Management of recent-onset (<36 h) atrial fibrillation (AF) in the emergency room is highly variable, particularly concerning the type and timing of cardioversion, and the logistics of the treatment pathway. In clinical practice, it is fairly common for patients with recent-onset AF an attempt at re-establishing sinus rhythm, either with electric or pharmacologic cardioversion, as soon as feasible. Nonetheless, a ‘wait-and-see’ approach, and potentially delayed cardioversion, could represent a valid alternative to early cardioversion, considering that, often, in recent-onset AF, sinus rhythm is re-established spontaneously, thus repealing the need for active cardioversion, hence avoiding the possible risks of treatment. These concepts form the rationale for a recent multicentric randomized trial, Rate Control vs. Electrical Cardioversion Trial 7 – Acute Cardioversion vs. Wait and See (RACE 7 ACWAS), comparing the efficacy of delayed cardioversion, within 48 h from symptoms onset, in case of lack of spontaneous conversion, with early cardioversion in symptomatic patients with recent-onset AF. In patients presenting to the emergency department with recent-onset, symptomatic AF, a wait-and-see approach was non-inferior to early cardioversion in maintaining the sinus rhythm at 4 weeks. Nonetheless a system employing a delayed cardioversion strategy increases the costs of treatment, complicates the treatment pathway, and could represent a psychological burden for the patients. Accordingly, delayed cardioversion could not represent a practical choice for many hospitals with limited resources and without an adequate outpatient organization.
How should the ticagrelor be used? The point after the TWILIGHT and THEMIS-PCI studies
Authors: Gatto Laura , Prati Francesco
Published: November 2020

The ticagrelor represents a cornerstone of antiplatelet therapy and its use has been supported, over the years, by several clinical trials that have enrolled thousands of patients; while the PLATO study initially demonstrated its effectiveness in the immediate treatment of acute coronary syndromes, the PEGASUS study documented the benefit of prolonging this treatment beyond 12 months from the heart attack. Over the past few months, two new randomized clinical trials have been published that have seen the use of ticagrelor in different clinical settings. The TWILIGHT study showed that in high-risk patients who completed 3 months of double antiplatelet drugs after coronary angioplasty, ticagrelor monotherapy is associated with a 44% reduction in the risk of clinically relevant bleeding in the absence of an increase in the ischaemic risk. The THEMIS study instead concluded that in the population of diabetics with stable coronary artery disease, but without a history of heart attack or stroke, a strategy that involves the addition of ticagrelor to the acetylsalicylic acid is not advisable as in the face of a benefit in the prevention of events ischaemic an increased risk of bleeding has been observed. Only in the subgroup of diabetic patients with a history of previous angioplasty would a more powerful antithrombotic therapy seem to be advantageous.
The treatment of mitral insufficiency in refractory heart failure
Authors: Cammertoni Federico , Bruno Piergiorgio , Mazza Andrea , Massetti Massimo
Published: November 2020

Secondary mitral insufficiency (SMI) is caused by dilatation and left ventricular dysfunction and is a frequent finding in patients with heart failure (HF). It is associated with a mortality of between 40% and 50% at 3 years. The first-line treatment is represented by medical therapy, possibly associated, when indicated, with cardiac re-synchronization. If the patient remains symptomatic, corrective action should be considered. Surgery is indicated in cases of severe SMI with ejection fraction >30% and the need for myocardial revascularization. The management of patients in whom revascularization is not an option remains extremely complex and the evidence in this field is extremely limited. Percutaneous transcatheter therapies, reparative or replacement, are rapidly emerging as valid alternatives in cases of patients at high surgical risk. In particular, edge-to-edge repair (MitraClip) has proven effective in improving symptoms and reducing hospitalizations for HF. However, neither transcatheter nor surgical mitral repair or replacement has been shown to significantly improve prognosis, with mortality remaining high (14–20% at 1 year). Randomized trials aimed at assessing the effect of these treatments and establishing their long-term outcomes are urgently required.
The management of non-culprit coronary lesions in patients with acute coronary syndrome
Authors: Montone Rocco A , Meucci Maria Chiara , Niccoli Giampaolo
Published: November 2020

About 50% of patients diagnosed with ST-segment elevation myocardial infarction have multivessel disease on coronary angiography. Recent evidence has shown that a staged percutaneous coronary intervention (PCI) strategy of non-culprit lesions, achieving complete revascularization, significantly reduces the rate of recurrent cardiovascular events compared with a PCI strategy limited to culprit lesion. Although functional evaluation of intermediate coronary stenoses by functional flow reserve (FFR) or instantaneous wave-free ratio (iFR) is widely used to detect residual myocardial ischaemia, the reliability of the study of non-culprit lesions in the acute phase of heart attack is controversial. On the other hand, the excess of new events in patients with acute coronary syndrome in whom PCI was deferred on the basis of FFR/iFR compared to patients with stable CAD could be due to both an inadequate functional evaluation and an intrinsic higher risk, related to the presence of untreated vulnerable plaques. In this context, intra-coronary imaging has shown that the presence of vulnerability features in non-culprit plaques is associated with an increased rate of ischaemic recurrence.
Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR
Authors: Defosset Audrey , Kress Arnaud , Nevers Yannis , Ripp Raymond , Thompson Julie D , Poch Olivier , Lecompte Odile
Published: November 2020

In the multiomics era, comparative genomics studies based on gene repertoire comparison are increasingly used to investigate evolutionary histories of species, to study genotype–phenotype relations, species adaptation to various environments, or to predict gene function using phylogenetic profiling. However, comparisons of orthologs have highlighted the prevalence of sequence plasticity among species, showing the benefits of combining protein and subprotein levels of analysis to allow for a more comprehensive study of genotype/phenotype correlations. In this article, we introduce a new approach called BLUR (BLAST Unexpected Ranking), capable of detecting genotype divergence or specialization between two related clades at different levels: gain/loss of proteins but also of subprotein regions. These regions can correspond to known domains, uncharacterized regions, or even small motifs. Our method was created to allow two types of research strategies: 1) the comparison of two groups of species with no previous knowledge, with the aim of predicting phenotype differences or specializations between close species or 2) the study of specific phenotypes by comparing species that present the phenotype of interest with species that do not. We designed a website to facilitate the use of BLUR with a possibility of in-depth analysis of the results with various tools, such as functional enrichments, protein–protein interaction networks, and multiple sequence alignments. We applied our method to the study of two different biological pathways and to the comparison of several groups of close species, all with very promising results. BLUR is freely available at http://lbgi.fr/blur/.
GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets
Authors: Kratochvíl Miroslav , Hunewald Oliver , Heirendt Laurent , Verissimo Vasco , Vondrášek Jiří , Satagopam Venkata P , Schneider Reinhard , Trefois Christophe , Ollert Markus
Published: November 2020

Background

The amount of data generated in large clinical and phenotyping studies that use single-cell cytometry is constantly growing. Recent technological advances allow the easy generation of data with hundreds of millions of single-cell data points with >40 parameters, originating from thousands of individual samples. The analysis of that amount of high-dimensional data becomes demanding in both hardware and software of high-performance computational resources. Current software tools often do not scale to the datasets of such size; users are thus forced to downsample the data to bearable sizes, in turn losing accuracy and ability to detect many underlying complex phenomena.

Results

We present GigaSOM.jl, a fast and scalable implementation of clustering and dimensionality reduction for flow and mass cytometry data. The implementation of GigaSOM.jl in the high-level and high-performance programming language Julia makes it accessible to the scientific community and allows for efficient handling and processing of datasets with billions of data points using distributed computing infrastructures. We describe the design of GigaSOM.jl, measure its performance and horizontal scaling capability, and showcase the functionality on a large dataset from a recent study.

Conclusions

GigaSOM.jl facilitates the use of commonly available high-performance computing resources to process the largest available datasets within minutes, while producing results of the same quality as the current state-of-art software. Measurements indicate that the performance scales to much larger datasets. The example use on the data from a massive mouse phenotyping effort confirms the applicability of GigaSOM.jl to huge-scale studies.
Potential use of a magnetic compass during long-distance dispersal in a subterranean rodent
Authors: Finn Kyle T
Published: November 2020

Geomagnetic sensitivity is present in a variety of vertebrates, but only recently has attention focused on subterranean mammals. We report the potential use of a magnetic compass in wild Damaraland mole-rats (Fukomys damarensis) during dispersal at two sites in the Kalahari region of South Africa. When the distance traveled was greater than 250 m, males and females dispersed in opposite directions and females preferentially chose a predominantly northeastern direction. This directional choice likely is due to the differing dispersal tactics between sexes. This evidence suggests that Damaraland mole-rats employ a magnetic compass during aboveground dispersal to assist in locating mates or a new territory. This study provides evidence to show how magnetic compass use could be useful in dispersal, an important ecological process for mammals.
Variation in diet and activity of river otters (Lontra canadensis) by season and aquatic community
Authors: Cosby Hilary , Szykman Gunther Micaela
Published: November 2020

Keystone predators can impact many prey species, including those that are endangered. A requisite to assess the impact predators have on different prey populations is to identify the species being consumed in different types of communities, while accounting for possible seasonal variation in consumption. Here we used analysis of North American river otter (Lontra canadensis) scat to assess the impact river otters have on their prey populations, particularly endangered salmonids and migrating birds. We analyzed the prey composition of 1,411 river otter scats collected from 10 sites in Humboldt County, California, between 2011 and 2012. Analysis of prey items in scat placed study sites into four distinct clusters based on diet. Fish, mostly from the families Gasterosteidae, Cottidae, and Pholidae, formed the primary prey component, and crustaceans, birds, amphibians, and insects, also were important components of river otter diet. Salmonids constituted < 5% of overall diet, but river otters consumed the largest percentage of salmon during salmon spawning season at the inland cluster where salmonids spawn. Scat marking intensity varied between clusters and seasons, with the most scats collected in the autumn and the fewest in the winter/spring, except at the inland cluster where the pattern of marking activity was reversed. River otters may be responding to seasonal migrations of endangered and threatened salmonids. Diet surveys of this type are useful for monitoring resource use by top predators in aquatic ecosystems.
Correlation of organelle dynamics between light microscopic live imaging and electron microscopic 3D architecture using FIB-SEM
Authors: Ohta Keisuke , Hirashima Shingo , Miyazono Yoshihiro , Togo Akinobu , Nakamura Kei-ichiro
Published: November 2020

Correlative light and electron microscopy (CLEM) methods combined with live imaging can be applied to understand the dynamics of organelles. Although recent advances in cell biology and light microscopy have helped in visualizing the details of organelle activities, observing their ultrastructure or organization of surrounding microenvironments is a challenging task. Therefore, CLEM, which allows us to observe the same area as an optical microscope with an electron microscope, has become a key technique in cell biology. Unfortunately, most CLEM methods have technical drawbacks, and many researchers face difficulties in applying CLEM methods. Here, we propose a live three-dimensional CLEM method, combined with a three-dimensional reconstruction technique using focused ion beam scanning electron microscopy tomography, as a solution to such technical barriers. We review our method, the associated technical limitations and the options considered to perform live CLEM.
A Cluster of Neonatal Infections Caused by Candida auris at a Large Referral Center in Colombia
Authors: Alvarado-Socarras Jorge L , Vargas-Soler José A , Franco-Paredes Carlos , Villegas-Lamus Katty Carolina , Rojas-Torres Juan Pablo , Rodriguez-Morales Alfonso J
Published: November 2020

Background

Globally, Candida auris is an emerging pathogen that poses an essential threat in healthcare settings presenting as outbreaks requiring significant allocation of infection control interventions to curb transmission. This fungal pathogen was initially identified in 2009 in Japan, but it has spread to all continents. Candida auris poses significant diagnostic and treatment challenges. Conventional microbiology laboratories often misidentify this pathogen as Candida haemulonii or as other Candida spp., Rhodoturola glutinis, and even with some bacterial pathogens, including Neisseria meningitidis serogroup A. Furthermore, C. auris displays distinct mechanisms of antifungal resistance to azoles and amphotericin B formulations. Most of the case series and outbreak reports have included invasive infections in adult populations.

Methods

Herein, we present a cluster of neonatal infections caused by Candida auris at a large referral center in Colombia.

Results

We report a case series of 8 neonates and infant patients who were seen at a large referral center in Colombia and who develop invasive infections caused by C. haemulonii and C. auris.

Discussion

Our report highlights the diagnostic challenges in identifying this fungal pathogen correctly, its clinical spectrum of disease, recommendations for empiric antifungal therapy, and it is not always associated with a high case fatality rate.
Qualifying the green city: professional moral practices of trying urban rainwater forms
Authors: Meilvang Marie
Published: November 2020

This article explores how the green, sustainable city is built in situations of uncertainty though professional practical engagements of testing and trying, and how these are formed by moral investments in professional work. Following recent studies investigating professional work and moral agency, the article engages with Terence Halliday’s famous distinction between science-based and normative professions. Contrary to this argument, the article argues that the practice of engineers, the clearest example of the so-called ‘science-based’ profession, is fraught with moral questions and practices. By drawing on French pragmatic sociology, the article conceptualizes the different ways engineers and others work in situations of uncertainty as different modes of trying. In these modes, professionals rely on different moral principles and ideas for evaluating and judging the professional solutions. As such, the article contributes to the sociology of professions by suggesting a new analytical frame for analyzing moral work as fundamental to professional practice in situations of uncertainty. Empirically, the article builds on fieldwork observations and interviews with professionals from an ongoing research project on Danish climate adaptation in cities and urban rainwater management.
When ‘Self-Sufficiency’ Is Not Sufficient: Refugee Integration Discourses of US Resettlement Actors and the Offer of Refuge
Authors: Frazier Emily , van Riemsdijk Micheline
Published: November 2020

Resettlement in a third country is fundamental in the protection of displaced persons, yet the offer of refuge encompasses more than mere admission into a country. In the US, various resettlement organizations provide arrival services; however, the resettlement programme’s ability to support long-term integration is restricted by an emphasis on economic self-sufficiency. Resettlement practices are shaped by the integration discourses of multiple resettlement actors, a term encompassing expectations, aspirations, and conceptions of ‘ideal’ refugee integration. This article explores the work of resettlement agencies and refugee ‘third sector’ organizations (RTSOs) by examining three organizations in a southeastern US city. Contesting government expectations of rapid ‘self-sufficiency’, RTSOs expand the offer of refuge provided in resettlement. They provide opportunities for social contact between volunteers and refugees and prioritize the formation of community and relationships. However, these organizations also reproduce neoliberal discourses of integration, ultimately constraining possibilities for expanded refugee integration.
Medical Student Experiences in Operation Bushmaster 2019: “I Now See Myself as Equal Parts Physician and Leader.”
Authors: Barron Johanna , Randall Virginia F , Villareal Charisse , Ramirez Valentina , Vojta Leslie
Published: November 2020

Introduction

Operation Bushmaster, a 5-day high-fidelity medical practicum bringing together fourth-year medical students, graduate nursing students, international students, and physicians and other medical professionals in emergency and operational medicine from across the world, is the capstone event of the Uniformed Services University of the Health Sciences’s Military Unique Curriculum. It is designed to simultaneously test students’ medical knowledge, leadership skills, and grace under fire. For many students, this experience represents one of the first times that they concurrently inhabit the dual roles of military officer and (soon-to-be) physician. This is likely the most “tactical” and stressful military simulation that many students have experienced.

Methods

In this qualitative study, we analyzed a data set of 49 de-identified reflective articles written by fourth-year medical students following the completion of Bushmaster, in order to understand what students gained from the experience. Additionally, we evaluated students’ responses through the lens of the threshold concept, looking for ontological shifts, integration, discursiveness, and troublesomeness during students’ Bushmaster experiences.

Results

We identified 10 themes throughout the essays that highlighted the lessons learned during the Bushmaster experience, including its importance in guiding professional identity formation and students’ deepened understanding of the unique responsibilities and pressures of the role of military physician.

Conclusion

One of the resulting themes, “the military physician,” met our criteria for a threshold concept, in that it was transformative, integrative, and troublesome. Before Bushmaster, many of the students saw themselves simply as medical students rather than as almost doctors. Following the field practicum, some identified more strongly with the role of military physician, while others continued to overestimate the amount of time remaining to complete the transformation from student to doctor or to integrate the roles of physician and military officer. Moreover, we identified the entirety of Bushmaster as a threshold experience. This work serves to further describe the liminal space in which military medical students reside on their journey to physician, as well as the moment of realization by many that becoming a military physician encompasses more than simply the sum of the roles of physician and military officer.
Neuromodulation for Chronic Pelvic Pain: A Single-Institution Experience With a Collaborative Team
Authors: Bridger Cheyanne , Prabhala Tarun , Dawson Rachael , Khazen Olga , MacDonell Jacquelyn , DiMarzio Marisa , Staudt Michael D , De Elise J B , Argoff Charles , Pilitsis Julie G
Published: November 2020

BACKGROUND

Secondary to the complex care, involved specialty providers, and various etiologies, chronic pelvic pain patients do not receive holistic care.

OBJECTIVE

To compare our general and neuromodulation cohorts based on referrals, diagnosis, and therapy and describe our neuromodulation patients.

METHODS

A multidisciplinary team was established at our center. The intake coordinator assessed demographics and facilitated care of enrolled patients. Outcomes were compared using minimal clinical important difference of current Numerical Rating Scale (NRS) between patients with neuropathic pain who received neuromodulation and those who did not. The neuromodulation cohort completed outcome metrics at baseline and recent follow-up, including NRS score (best, worst, and current), Oswestry Disability Index (ODI), Beck Depression Inventory, and Pain Catastrophizing Scale.

RESULTS

Over 7 yr, 233 patients were referred to our consortium and 153 were enrolled. A total of 55 patients had neuropathic pain and 44 of those were managed medically. Eleven underwent neuromodulation. A total of 45.5% patients of the neuromodulation cohort were classified as responders by minimal clinically important difference compared to 26.6% responders in the control cohort at most recent follow-up (median 25 and 33 mo, respectively). Outcome measures revealed improvement in NRS at worst (P = .007) and best (P = .025), ODI (P = .014), and Pain Catastrophizing Scale Rumination (P = .043).

CONCLUSION

Eleven percent of patients were offered neuromodulation. There were more responders in the neuromodulation cohort than the conservatively managed neuropathic pain cohort. Neuromodulation patients showed significant improvement at 29 mo in NRS best and worst pain, disability, and rumination. We share our algorithm for patient management.
Beyond Overdose: Drug-Related Deaths in People With and Without HIV in San Francisco, 2007–2018
Authors: Appa Ayesha , Rowe Christopher , Hessol Nancy A , Coffin Phillip
Published: November 2020

Despite elevated mortality in people with HIV (PWH) using drugs, drug-related deaths are poorly characterized. Among 6764 drug-related deaths, methamphetamine was more common in PWH than others. One in 4 deaths in PWH involved acute infection. Combatting mortality in PWH who use drugs should include stimulant-specific and infection prevention efforts.
More than Ownership: The Importance of Relationships with Companion Dogs for the Psychological Adjustment of Fibromyalgia Patients
Authors: Silva Karine , Castro Luísa , Costa-Santos Cristina , Lourenco Antonio , Lima Mariely
Published: November 2020

Objective

This study explored the role of companion dogs for psychological adjustment to pain in patients with fibromyalgia with different levels of social support. It also considered the potential moderating effects of the quality of the owner-dog relationship and the use of interactions with dogs as a coping strategy.

Setting

A cross-sectional approach was followed using an online questionnaire.

Subjects and Methods

Linear regression analyses were performed on data obtained from 106 participants (dog owners and non-owners). Sub-analyses were performed on 64 dog owners.

Results

Complex associations were observed between human social support, dog ownership and anxiety/depression levels. For participants with low levels of social support, owning a dog was associated with higher levels of anxiety and depression. In contrast, for moderate and high levels of social support, owning a dog was associated with lower levels of anxiety and depression. Sub-analyses showed that participants in this study actively used interactions with companion dogs to manage their pain more frequently than other pain coping strategies. Among those interactions, patting and stroking the dog to cope with pain was associated with lower anxiety levels, even after adjusting for social support. Emotional closeness with the dog was associated with lower depression levels.

Conclusions

Obtained results highlight the importance to go beyond mere ownership when addressing the effects of companion dogs and suggest that the development of emotional ties with companion dogs and the active use of interactions with these animals to cope with pain may contribute to better psychological adjustment in patients with fibromyalgia, regardless of human social support.
The Returns to Nursing: Evidence from a Parental-Leave Program
Authors: Friedrich Benjamin U , Hackmann Martin B
Published: November 2020

In this article, we quantify the effects of nurses on health care delivery and patient health in the context of an unintended and policy-induced nurse shortage. Our empirical strategy takes advantage of a parental-leave program in Denmark, which offered any parent the opportunity to take up to one year’s absence per child aged 0–8. Combining the policy variation with administrative employer–employee match data, we document substantial program take-up among nurses, who could not be replaced on net despite public education and immigration expansion efforts to mitigate the employment effects. We find that the parental leave program reduced hospital and nursing home nurse employment by 15% and 10%, respectively. Using detailed patient health records, we find detrimental effects on hospital-care delivery as indicated by a large increase in 30-day readmission rates among acute myocardial infarction patients. We find no evidence for an increase in hospital mortality. In nursing homes, we estimate a large increase in mortality.