bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities
Authors: Aguayo Jaime , Fourrier-Jeandel Céline , Husson Claude , Ioos Renaud 
Published: March 2018

ABSTRACTTechniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.IMPORTANCEThe advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.
Implementation of Failure Mode and Effects Analysis to the specimens flow in a population-based colorectal cancer screening programme using immunochemical faecal occult blood tests: a quality improvement project in the Milan colorectal cancer screening programme
Authors: Deandrea Silvia , Tidone Enrica , Bellini Aldo , Bisanti Luigi , Leonardo Nico Gerardo , Silvestri Anna Rita , Consonni Dario 
Published: March 2018

BackgroundA multidisciplinary working group applied the Healthcare Failure Mode and Effects Analysis (HFMEA) approach to the flow of kits and specimens for the first-level test of a colorectal cancer screening programme using immunochemical faecal occult blood tests.MethodsHFMEA comprised four steps: (1) identification and mapping of the process steps (subprocesses); (2) analysis of failure modes and calculation of the risk priority numbers (RPNs); (3) identification of corrective actions; and (4) follow-up and evaluation of corrective actions.ResultsThe team identified 9 main failure modes, 12 effects and 34 associated causes. RPN scores ranged from 2 to 96. Failure modes within the first five positions in the ranking list ordered by RPN concerned: ‘degraded haemoglobin in the specimen’, ‘mixed-up kits’ and ‘anonymous specimen’. All of these could lead to false-negative results and/or subjects with positive tests not being recalled for assessment. The team planned corrective actions for those failure modes. As a result, the follow-up of corrective actions showed a significant decrease in the proportion of anonymous kits from 11.6 to 4.8 per 1000 (relative reduction of 59%). The HFMEA exercise led to a reduction in: missed positive tests; missed cancer and high-risk adenomas; complaints about the communication of test results to a person who never did the test; and false-negative results due either to haemoglobin degradation or an expired sampling tube.ConclusionsHFMEA is a useful tool for reducing errors in colorectal cancer screening programmes using faecal occult blood tests and is characterised by a straightforward interpretation of results and ease of communication to healthcare managers and decision makers.
Investigation of the 2016 Linux TCP Stack Vulnerability at Scale
Authors: Quach Alan , Wang Zhongjie , Qian Zhiyun 
Published: March 2018

To combat blind in-window attacks against TCP, changes proposed in RFC 5961 have been implemented by Linux since late 2012. While successfully eliminating the old vulnerabilities, the new TCP implementation was reported in August 2016 to have introduced a subtle yet serious security flaw. Assigned CVE-2016-5696, the flaw exploits the challenge ACK rate limiting feature that could allow an off-path attacker to infer the presence/absence of a TCP connection between two arbitrary hosts, terminate such a connection, and even inject payload into an unsecured TCP connection.
In this work, we perform a comprehensive measurement of the impact of the new vulnerability. This includes (1) tracking the vulnerable Internet servers, (2) monitoring the patch behavior over time, (3) picturing the overall security status of TCP stacks at scale. Towards this goal, we design a scalable measurement methodology to scan the Alexa top 1 million websites for almost 6 months. We also present how notifications impact the patching behavior, and compare the result with the Heartbleed and the Debian PRNG vulnerability. The measurement represents a valuable data point in understanding how Internet servers react to serious security flaws in the operating system kernel.
Disk Prefetching Mechanisms for Increasing HTTP Streaming Video Server Throughput
Authors: Cassell Benjamin , Szepesi Tyler , Summers Jim , Brecht Tim , Eager Derek , Wong Bernard 
Published: March 2018

Most video streaming traffic is delivered over HTTP using standard web servers. While traditional web server workloads consist of requests that are primarily for small files that can be serviced from the file system cache, HTTP video streaming workloads often service a long tail of large infrequently requested videos. As a result, optimizing disk accesses is critical to obtaining good server throughput.
In this article we explore serialized, aggressive disk prefetching, a technique that can be used to improve the throughput of HTTP streaming video web servers. We identify how serialization and aggressive prefetching affect performance, and, based on our findings, we construct and evaluate Libception, an application-level shim library that implements both techniques. By dynamically linking against Libception at runtime, applications are able to transparently obtain benefits from serialization and aggressive prefetching without needing to change their source code. In contrast to other approaches that modify applications, make kernel changes, or attempt to optimize kernel tuning, Libception provides a portable and relatively simple system in which techniques for optimizing I/O in HTTP video streaming servers can be implemented and evaluated.
We empirically evaluate the efficacy of serialization and aggressive prefetching both with and without Libception, using three web servers (Apache, nginx, and the userver) running on two operating systems (FreeBSD and Linux). We find that, by using Libception, we can improve streaming throughput for all three web servers by at least a factor of 2 on FreeBSD and a factor of 2.5 on Linux. Additionally, we find that with significant tuning of Linux kernel parameters, we can achieve similar performance to Libception by globally modifying Linux’s disk prefetch behaviour. Finally, we demonstrate Libception’s ability to reduce the completion time of a microbenchmark involving two applications competing for disk resources.
Influence of long-term treatment with glyceryl trinitrate on remote ischemic conditioning
Authors: Hauerslev Marie , Mørk Sivagowry Rasalingam , Pryds Kasper , Contractor Hussain , Hansen Jan , Jespersen Nichlas Riise , Johnsen Jacob , Heusch Gerd , Kleinbongard Petra , Kharbanda Rajesh , Bøtker Hans Erik , Schmidt Michael Rahbek 
Published: March 2018

Remote ischemic conditioning (RIC) protects against sustained myocardial ischemia. Because of overlapping mechanisms, this protection may be altered by glyceryl trinitrate (GTN), which is commonly used in the treatment of patients with chronic ischemic heart disease. We investigated whether long-term GTN treatment modifies the protection by RIC in the rat myocardium and human endothelium. We studied infarct size (IS) in rat hearts subjected to global ischemia-reperfusion (I/R) in vitro and endothelial function in healthy volunteers subjected to I/R of the upper arm. In addition to allocated treatment, rats were coadministered with reactive oxygen species (ROS) or nitric oxide (NO) scavengers. Rats and humans were randomized to 1) control, 2) RIC, 3) GTN, and 4) GTN + RIC. In protocols 3 and 4, rats and humans underwent long-term GTN treatment for 7 consecutive days, applied subcutaneously or 2 h daily transdermally. In rats, RIC and long-term GTN treatment reduced mean IS (18 ± 12%, P = 0.007 and 15 ± 5%, P = 0.002) compared with control (35 ± 13%). RIC and long-term GTN treatment in combination did not reduce IS (29 ± 12%, P = 0.55 vs. control). ROS and NO scavengers both attenuated IS reduction by RIC and long-term GTN treatment. In humans, I/R reduced endothelial function ( P = 0.01 vs. baseline). Separately, RIC and long-term GTN prevented the reduction in endothelial function caused by I/R; given in combination, prevention was lost. RIC and long-term GTN treatment both protect against rat myocardial and human endothelial I/R injury through ROS and NO-dependent mechanisms. However, when given in combination, RIC and long-term GTN treatment fail to confer protection. NEW & NOTEWORTHY Remote ischemic conditioning (RIC) and long-term glyceryl trinitrate (GTN) treatment protect against ischemia-reperfusion injury in both human endothelium and rat myocardium. However, combined application of RIC and long-term GTN treatment abolishes the individual protective effects of RIC and GTN treatment on ischemia-reperfusion injury, suggesting an interaction of clinical importance.
Humoral transfer and intramyocardial signal transduction of protection by remote ischemic perconditioning in pigs, rats, and mice
Authors: Skyschally Andreas , Kleinbongard Petra , Lieder Helmut , Gedik Nilgün , Stoian Leanda , Amanakis Georgios , Elbers Etienne , Heusch Gerd 
Published: March 2018

Remote ischemic perconditioning (RPER) during ongoing myocardial ischemia reduces infarct size. The signal transduction of RPER's cardioprotection is still largely unknown. Anesthetized pigs were therefore subjected to RPER by 4 × 5 min/5 min of hindlimb ischemia-reperfusion during 60 min of coronary occlusion before 3 h of reperfusion. Pigs without RPER served as placebo (PLA). The phosphorylation of Akt and ERK [reperfusion injury salvage kinase (RISK) pathway] and STAT3 [survivor activating factor enhancement (SAFE) pathway] in the area at risk was determined by Western blot analysis. Wortmannin/U0126 or AG490 was used for pharmacological RISK or SAFE blockade, respectively. Pig plasma/plasma dialysate sampled after RPER or PLA, respectively, was transferred to isolated rat and mouse hearts subjected to 30 min/120 min of global ischemia-reperfusion. Mitochondria were isolated from rat hearts at early reperfusion. Isolated mouse cardiomyocytes were subjected to 1 h of hypoxia/5 min of reoxygenation without and with prior plasma dialysate incubation. RPER reduced infarct size in pigs to 21 ± 15% versus 44 ± 9% in PLA (percentage of the area at risk, mean ± SD, P < 0.05) and increased STAT3 phosphorylation at early reperfusion. AG490 but not RISK blockade abolished the protection. RPER plasma/plasma dialysate reduced infarct size in rat (22 ± 3% of ventricular mass vs. 40 ± 11% with PLA plasma, P < 0.05) and mouse (29 ± 4% vs. 63 ± 8% with PLA plasma dialysate, P < 0.05) hearts and improved mitochondrial function (e.g., increased respiration, ATP formation, and calcium retention capacity and decreased reactive oxygen species formation). RPER dialysate also improved the viability of mouse cardiomyocytes after hypoxia/reoxygenation. RISK or SAFE blockade each abrogated these beneficial effects. NEW & NOTEWORTHY Remote ischemic perconditioning salvages the myocardium in patients with acute infarction. We identified a signal transduction with humoral transfer and STAT3 activation in pigs and an involvement of reperfusion injury salvage kinases and STAT3 in rat and mouse hearts, along with better cardiomyocyte viability and mitochondrial function.
Noninvasive assessment of the common carotid artery hemodynamics with increasing exercise work rate using wave intensity analysis
Authors: Pomella N. , Wilhelm E. N. , Kolyva C. , González-Alonso J. , Rakobowchuk M. , Khir A. W. 
Published: March 2018

Noninvasively determined local wave speed ( c) and wave intensity (WI) parameters provide insights into arterial stiffness and cardiac-vascular interactions in response to physiological perturbations. However, the effects of incremental exercise and subsequent recovery on c and WI have not been fully established. We examined the changes in c and WI parameters in the common carotid artery (CCA) during exercise and recovery in eight young, healthy male athletes. Ultrasound measurements of CCA diameter and blood flow velocity were acquired at rest, during five stages of incremental exercise (up to 70% maximum work rate), and throughout 1 h of recovery, and noninvasive WI analysis [diameter-velocity ( DU) approach] was performed. During exercise, c increased (+136%), showing increased stiffness with work rate. All peak and area of forward compression, backward compression, and forward expansion waves increased during exercise (+452%, +700%, and +900%, respectively). However, WI reflection indexes and CCA resistance did not significantly change from rest to exercise. Furthermore, wave speed and the magnitude of all waves returned to baseline within 5 min of recovery, suggesting that the effects of exercise in the investigated parameters of young, healthy individuals were transient. In conclusion, incremental exercise was associated with an increase in local CCA stiffness and increases in all wave parameters, indicative of enhanced ventricular contractility and improved late-systolic blood flow deceleration. NEW & NOTEWORTHY We examined hemodynamics of the common carotid artery using noninvasive application of wave intensity analysis during exercise and recovery. The hemodynamic adjustments to exercise were associated with increases in local common carotid artery stiffness and all waves’ parameters, with the latter indicating enhanced ventricular contractility and improved late systolic blood flow deceleration.
A microRNA’s journey to the center of the mitochondria
Authors: Macgregor-Das Anne M. , Das Samarjit 
Published: March 2018

MicroRNAs (miRNAs) are known as the master regulators of gene expression, and for the last two decades our knowledge of their functional reach keeps expanding. Recent studies have shown that a miRNA’s role in regulation extends to extracellular and intracellular organelles. Several studies have shown a role for miRNA in regulating the mitochondrial genome in normal and disease conditions. Mitochondrial dysfunction occurs in many human pathologies, such as cardiovascular disease, diabetes, cancer, and neurological diseases. These studies have shed some light on regulation of the mitochondrial genome as well as helped to explain the role of miRNA in altering mitochondrial function and the ensuing effects on cells. Although the field has grown in recent years, many questions still remain. For example, little is known about how nuclear-encoded miRNAs translocate to the mitochondrial matrix. Knowledge of the mechanisms of miRNA transport into the mitochondrial matrix is likely to provide important insights into our understanding of disease pathophysiology and could represent new targets for therapeutic intervention. For this review, our focus will be on the role of a subset of miRNAs, known as MitomiR, in mitochondrial function. We also discuss the potential mechanisms used by these nuclear-encoded miRNAs for import into the mitochondrial compartment. Listen to this article’s corresponding podcast at http://ajpheart.podbean.com/e/microrna-translocation-into-the-mitochondria/ .
Ablation Outcomes and Predictors of Mortality Following Catheter Ablation for Ventricular Tachycardia: Data From the German Multicenter Ablation Registry
Authors: Tilz Roland Richard , Lin Tina , Eckardt Lars , Deneke Thomas , Andresen Dietrich , Wieneke Heinrich , Brachmann Johannes , Kääb Stefan , Chun K. R. Julian , Münkler Paula , Lewalter Thorsten , Hochadel Matthias , Senges Jochen , Kuck Karl‐Heinz 
Published: March 2018

Background

Ventricular tachycardia (
VT
) causes significant morbidity and mortality. Implantable cardioverter‐defibrillator shocks terminate
VT
but confer a significant morbidity and mortality risk. Therefore,
VT
ablation is increasingly common. Patients with structural heart disease (
SHD
) and patients with structurally normal hearts as well as the subgroup with and without ischemic heart disease were assessed for predictors of mortality and nonfatal
VT
recurrence. We present the first multicenter, prospective German
VT
registry.

Methods and Results

In 334 patients, 118 structurally normal hearts and 216
SHD
(74.5% ischemic heart disease), referred for
VT
ablation in 38 centers, long‐term follow‐up was assessed for a minimum of 12 months and analyzed for factors predicting
VT
recurrence rates and mortality. The
VT
s in
SHD
patients were more frequently hemodynamically unstable (34.7% versus 12.7%,
P
<0.0001) or incessant (9.7% versus 2.7%,
P
<0.05). More
SHD
patients underwent substrate modification than patients with structurally normal hearts who had more focal ablations. Ablation failure was 9% in both groups. Two‐year mortality was higher in patients with
SHD
(18.7% versus 3.5%,
P
<0.001). Predictors of mortality include age >60 years, incessant
VT
, left ventricular ejection fraction ≤30%, procedural failure, and Class I and
III
anti‐arrhythmic drug use at discharge. Only procedural failure is a predictor of nonfatal
VT
recurrence.

Conclusions

Procedural failure was the sole independent predictor for nonfatal
VT
recurrence for our study cohort. This emphasizes the importance of a successful ablation procedure in experienced hands to reduce long‐term mortality and nonfatal
VT
recurrence.
Left Atrial Epicardial Fat Volume Is Associated With Atrial Fibrillation: A Prospective Cardiovascular Magnetic Resonance 3D Dixon Study
Authors: Nakamori Shiro , Nezafat Maryam , Ngo Long H. , Manning Warren J. , Nezafat Reza 
Published: March 2018

Background

Recent studies demonstrated a strong association between atrial fibrillation (
AF
) and epicardial fat around the left atrium (
LA
). We sought to assess whether epicardial fat volume around the
LA
is associated with
AF
, and to determine the additive value of
LA
‐epicardial fat measurements to
LA
structural remodeling for identifying patients with
AF
using 3‐dimensional multi‐echo Dixon fat–water separated cardiovascular magnetic resonance.

Methods and Results

A total of 105 subjects were studied: 53 patients with a history of
AF
and 52 age‐matched patients with other cardiovascular diseases but no history of
AF
. The 3‐dimensional multi‐echo Dixon fat‐water separated sequence was performed for
LA
‐epicardial fat measurements.
AF
patients had significantly greater
LA
‐epicardial fat (28.9±12.3 and 14.2±7.3 mL for
AF
and non‐
AF
, respectively;
P
<0.001) and
LA
volume (110.8±38.2 and 89.7±30.3 mL for
AF
and non‐
AF
, respectively;
P
=0.002).
LA
‐epicardial fat adjusted for
LA
volume was still higher in patients with
AF
compared with those without
AF
(
P
<0.001).
LA
‐epicardial fat and hypertension were independently associated with the risk of
AF
(odds ratio, 1.17; 95% confidence interval, 1.10%–1.25%,
P
<0.001, and odds ratio, 3.29; 95% confidence interval, 1.17%–9.27%,
P
=0.03, respectively). In multivariable logistic regression analysis adjusted for body surface area,
LA
‐epicardial fat remained significant and an increase per mL was associated with a 42% increase in the odds of
AF
presence (odds ratio, 1.42; 95% confidence interval, 1.23%–1.62%,
P
<0.001). Combined assessment of
LA
‐epicardial fat and
LA
volume provided greater discriminatory performance for detecting
AF
than
LA
volume alone (c‐statistic=0.88 and 0.74, respectively, DeLong test;
P
<0.001).

Conclusions

Cardiovascular magnetic resonance 3‐dimensional Dixon‐based
LA
‐epicardial fat volume is significantly increased in
AF
patients.
LA
‐epicardial fat measured by 3‐dimensional Dixon provides greater performance for detecting
AF
beyond
LA
structural remodeling.
Religion, Cognition, and the Myth of Conscious Will
Authors: Nicholson Hugh 
Published: March 2018

AbstractCharacteristic of the recent cognitive approach to religion (CSR) is the thesis that religious discourse and practice are rooted in an inveterate human propensity to explain events in terms of agent causality. This thesis readily lends itself to the critical understanding of religious belief as “our intuitive psychology run amok.” This effective restriction of the scientific critique of agent causality to notions of supernatural agency appears arbitrary, however, in light of evidence from cognitive and social psychology that our sense of human agency, including our own, is interpretive in nature. In this paper I argue that a cognitive approach to religion that extends the critique of agent causality to the folk psychological experience of conscious will is able to shed light on several characteristically religious phenomena, such as spirit possession, ritual action, and spontaneous action in Zen Buddhism.
War and the Military in Rabbi Shlomo Zalman Auerbach’s Halakhic Decisions
Authors: Mashiach Amir 
Published: March 2018

Abstract
Rabbi Shlomo Zalman Auerbach (1910–1995) was one of the most influential Halakhic authorities of the twentieth century. Although he was an ultra-Orthodox rabbi, Rabbi Auerbach dealt with the complexity of army and military life. This article shows that he possessed of a clear “operational way of thinking,” reflecting deeply on the unique needs of the military of the Jewish State. Additionally, the article examines various approaches of filling the normative gap in issues of war and the military. Rabbi Auerbach based his specification of the Halakhah on his personal understanding and his own S’vara, that is, Halakhic logic.