bluuebunny/crossref_metadata_2025_split huggingface dataset:
BinDash, software for fast genome distance estimation on a typical personal laptop
Authors: Zhao XiaoFei 
Published: July 2018

Abstract

Motivation
The number of genomes (including meta-genomes) is increasing at an accelerating pace. In the near future, we may need to estimate pairwise distances between millions of genomes. Even with the use of cloud computing, very few softwares can perform such estimation.

Results
The multi-threaded software BinDash can perform such estimation using only a typical personal laptop. BinDash implemented b-bit one-permutation rolling MinHash with optimal densification, an existing data-mining technique. BinDash empirically outperforms the state-of-the-art software in terms of precision, compression ratio, memory usage and runtime according to our evaluation. Our evaluation is performed with a Dell Inspiron 157 559 Notebook on all bacterial genomes in RefSeq.

Availability and implementation
BinDash is released under the Apache 2.0 license at https://github.com/zhaoxiaofei/BinDash.

Supplementary information
Supplementary data are available at Bioinformatics online.
European eel Anguilla anguilla compromise speed for safety in the early marine spawning migration
Authors: Lennox Robert J , Økland Finn , Mitamura Hiromichi , Cooke Steven J , Thorstad Eva B 
Published: July 2018

AbstractThere are substantial benefits to potential fitness conferred to animals that undertake migrations. However, animals must make compromises to maximize survival and compensate for the risks associated with long-distance movement. European eel (Anguilla anguilla), a migratory catadromous fish, has undergone population declines owing to changes in marine and freshwater habitat and interactions with human infrastructure, instigating research to investigate the mechanisms controlling their migration. Yellow-phase European eels from the local River Opo and silver-phase European eels transplanted from River Imsa, Norway, were implanted with acoustic transmitters and released within a network of receiver stations in the Hardangerfjord, Norway. Silver-phase eels exhibited more movement within the array than yellow-phase eels, signifying the onset of migration. Silver-phase eels moved through the fjord nocturnally, arriving at gates predominantly at night. Eels had slower rates of migration than expected based on models predicting continuous movement, suggesting that movement ceased during daylight hours. Reduced net rates of travel supported the hypothesis that eels compromise speed for safety during the early marine migration by avoiding predators and not actively migrating during daylight. The silver eels were capable of directed movement towards the ocean and were not recorded by receivers in bays or dead ends. European eels must successfully transit this coastal zone, where their residence is prolonged because of the relatively slow speeds. These results suggest that the early marine phase of the European eel spawning migration be a focal period for European eel conservation efforts.
Cell-Enhanced Acellular Nerve Allografts for Peripheral Nerve Reconstruction: A Systematic Review and a Meta-Analysis of the Literature
Authors: Pedrini Francesca Alice , Boriani Filippo , Bolognesi Federico , Fazio Nicola , Marchetti Claudio , Baldini Nicola 
Published: July 2018

Abstract

BACKGROUND
Peripheral nerve reconstruction is a difficult problem to solve. Acellular nerve allografts (ANAs) have been widely tested and are a promising alternative to the autologous gold standard. However, current reconstructive methods still yield unpredictable and unsuccessful results. Consequently, numerous studies have been carried out studying alternatives to plain ANAs, but it is not clear if nerve regeneration potential exists between current biological, chemical, and physical enrichment modes.

OBJECTIVE
To systematically review the effects of cell-enhanced ANAs on regeneration of peripheral nerve injuries.

METHODS
PubMed, ScienceDirect, Medline, and Scopus databases were searched for related articles published from 2007 to 2017. Inclusion criteria of selected articles consisted of (1) articles written in English; (2) the topic being cell-enhanced ANAs in peripheral nerve regeneration; (3) an in vivo study design; and (4) postgrafting neuroregenerative assessment of results. Exclusion criteria included all articles that (1) discussed central nervous system ANAs; (2) consisted of xenografts as the main topic; and (3) consisted of case series, case reports or reviews.

RESULTS
Forty papers were selected, and categorization included the animal model; the enhancing cell types; the decellularization method; and the neuroregenerative test performed. The effects of using diverse cellular enhancements combined with ANAs are discussed and also compared with the other treatments such as autologous nerve graft, and plain ANAs.

CONCLUSION
ANAs cellular enhancement demonstrated positive effects on recovery of nerve function. Future research should include clinical translation, in order to increase the level of evidence available on peripheral nerve reconstruction.
Thirdhand Smoke at Philip Morris
Authors: Whitlatch Adam , Schick Suzaynn 
Published: July 2018

Abstract

Introduction
Thirdhand cigarette smoke is the fraction of cigarette smoke that remains in the environment long after a cigarette is extinguished.

Methods
The Truth Tobacco Industry Documents collection at the University of California San Francisco was searched for information on thirdhand smoke.

Results
In 1991, scientists at Philip Morris Inc conducted some of the first studies on thirdhand cigarette smoke. For 110 days, 8 hours a day, they ran sidestream cigarette smoke through a 30 m3 room that contained carpet, curtain, and textured wallpaper. The room was ventilated with clean air every night. By comparing the chemicals in the air during the 8-hour smoking period and during the clean air ventilation period, they showed that some smoke chemicals persist in the air 12 hours after smoking. By extracting the nicotine and nitrosamines from samples of the carpet, curtain, and wallpaper, they found that high concentrations of nicotine and the carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) persisted in the room for more than 50 days; that surface chemistry affected nitrosamine concentrations; and that the concentration of NNK in the room, 110 days after the last cigarette was extinguished, could exceed the mass of NNK that entered the room as smoke.

Conclusions
These data, from a controlled environment where the total number of cigarettes smoked is known, provide further evidence that cigarette smoke chemicals remain in the environment for months after smoking, that they reemit back into the air, and that they react to form new toxins and carcinogens. Smoke-free policies are the best method to reduce exposure to thirdhand smoke.

Implications
This unpublished, original research from Philip Morris Inc demonstrates that majority of the nicotine and tobacco-specific nitrosamines in the secondhand smoke from each cigarette smoked indoors remains on indoor surfaces for months after the cigarette is extinguished. It also demonstrates that elevated concentrations of nicotine, ammonia, formaldehyde, and the gas-phase nitrosamine, N-nitrosopyrrolidine, can be found in the air for more than 12 hours after smoking; that surface chemistry affects nitrosamine formation and persistence; and that the amount of the carcinogenic nitrosamine NNK that persists months after smoking ends can exceed the amount that actually came out of the cigarettes.
Train Up a Child in the Way He Should Go
Authors: Larsen Timothy 
Published: July 2018

Abstract
This chapter presents Mill’s precocious learning as a child—he famously was reading Greek at the age of three—as well as his father’s and Jeremy Bentham’s interest in shaping the boy in the light of their theories and beliefs. It traces how much religious education Mill actually did receive, and what books he read that helped to form his views on religion and Christianity. Despite Alexander Bain’s claim to the contrary, Mill read theology throughout his life. He spoke approvingly of the religious works of a range of authors, especially liberal Anglicans such as F. D. Maurice, Charles Kingsley, Florence Nightingale, and Baden Powell, but also the Quaker John Woolman and even the Roman Catholic W. G. Ward. This chapter also argues that Mill lacked a devotional sense.
‘All is Returned’
Authors: Newton Hannah 
Published: July 2018

Abstract
This final chapter asks what it was like to resume ordinary life after serious illness: it traces the patient’s journey from the sickbed to the wider world of society and work. Organized around three areas—spatial, social, and working life—the overarching argument is that the return to normality was found to be physically liberating, socially bonding, and mentally stimulating. Ultimately, patients felt they regained not just their bodily faculties, but all the other aspects of life that they cherished, which sickness had rendered impossible, such as the enjoyment of company, the outdoors, and work. There were, however, significant downsides: residual weakness rendered daily tasks difficult for some patients, certain actions were thought to precipitate relapse, and for those who disliked socializing or working, returning to former employments could be troublesome. This argument challenges the entrenched notion that early modern people rarely retired from normal life during serious illness.
Objectcy and Agency
Authors: Walsh Denis M. 
Published: July 2018

Abstract
Organisms are like nothing else in the natural world. They are agents. Methodological vitalism is a view according to which the difference that organisms make to the natural world cannot be captured wholly if we treat them as mere objects. Understanding agency calls for a different kind of theory, an agent theory. Most of our scientific theories are object theories. The modern synthesis theory of evolution is a prominent example of object theory. Being the way it is, it cannot countenance the contribution to evolution that organisms make as agents. A comprehensive account of adaptive evolution requires an agent theory.
Symbiosis, Transient Biological Individuality, and Evolutionary Processes
Authors: Bouchard Frédéric 
Published: July 2018

Abstract
Whereas individual organisms have acted as the paradigm case to make us think about biological individuality, multi-organism assemblages such as colonies and communities force us to reconsider how biological individuality can emerge. Symbiosis research has given philosophers of biology tools for rethinking the nature of biological individuality. This chapter discusses how the adaptations linked to symbiotic communities highlight a new research dilemma: should we think of a biological ontology focused on individuals and their traits (even if this means positing non-orthodox individuals with non-standard properties)? Or should we move beyond individuals and focus instead on intersecting evolutionary processes? While reasons are offered to favour the former option, it is explained why this dilemma highlights the question of the different temporal scales at which evolution occurs and how this forces us to consider the transient and intermittent biological individuals generated by evolution, as well as the significance of the processes that generate them.
Measuring the World
Authors: Barwich Ann-Sophie 
Published: July 2018

Abstract
How much does stimulus input shape perception? The common-sense view is that our perceptions are representations of objects and their features and that the stimulus structures the perceptual object. The problem for this view concerns perceptual biases as responsible for distortions and the subjectivity of perceptual experience. These biases are increasingly studied as constitutive factors of brain processes in recent neuroscience. In neural network models the brain is said to cope with the plethora of sensory information by predicting stimulus regularities on the basis of previous experiences. Drawing on this development, this chapter analyses perceptions as processes. Looking at olfaction as a model system, it argues for the need to abandon a stimulus-centred perspective, where smells are thought of as stable percepts, computationally linked to external objects such as odorous molecules. Perception here is presented as a measure of changing signal ratios in an environment informed by expectancy effects from top-down processes.
Transient activation of AMPK preceding left ventricular pressure overload reduces adverse remodeling and preserves left ventricular function
Authors: Nam Deok Hwa , Kim Eunah , Benham Ashley , Park Hye-Kyung , Soibam Benjamin , Taffet George E. , Kaelber Jason T. , Suh Ji Ho , Taegtmeyer Heinrich , Entman Mark L. , Reineke Erin L. 
Published: July 2018

ABSTRACTCoordinated changes in signaling pathways and gene expression in hearts subjected to prolonged stress maintain cardiac function. Loss of steroid receptor coactivator‐2 (SRC‐2) results in a reversal to the fetal gene program and disrupts the response to pressure overload, accompanied by prominent effects on metabolism and growth signaling, including increased AMPK activation. We proposed that early metabolic stress driven by AMPK activation induces contractile dysfunction in mice lacking SRC‐2. We used 5‐aminoimidazole‐4‐carboxamide ribonucleotide (AICAR) to activate AMPK transiently before transverse aortic constriction (TAC) in wild‐type and cardiomyocyte‐specific SRC‐2 knockout (CKO) animals. In contrast to AMPK activities during stress, in unstressed hearts, AICAR induced a mild activation of Akt signaling, and, in SRC‐2–CKO mice, partially relieved an NAD+ deficiency and increased antioxidant signaling. These molecular changes translated to a mild hypertrophic response to TAC with decreased maladaptive remodeling, including markedly decreased fibrosis. Additionally, preactivation of AMPK in SRC‐2–CKO mice was accompanied by a dramatic improvement in cardiac function compared with saline‐treated SRC‐2–CKO mice. Our results show that altered molecular signaling before stress onset has extended effects on sustained cardiac stress responses, and prestress modulation of transient growth and metabolism pathways may control those effects.—Nam, D. H., Kim, E., Benham, A., Park, H.‐K., Soibam, B., Taffet, G. E., Kaelber, J. T., Suh, J. H., Taegtmeyer, H., Entman, M. L., Reineke, E. L. Transient activation of AMPK preceding left ventricular pressure overload reduces adverse remodeling and preserves left ventricular function. FASEB J. 33, 711–721 (2019). www.fasebj.org
A Collaborative Approach to Prepare Nursing Students to Implement Relationship-Based Care
Authors: Terry Allison J. 
Published: July 2018

Abstract
The author proposes the use of a collaborative approach to prepare nursing students to implement relationship-based care through the use of a dedicated education unit. This collaboration would use the phases of relationship-based care, Benner's novice-to-expert stages, and the semesters of the typical upper division nursing curriculum. The ways in which relationship-based care can enhance the learning process for nursing students are discussed.
Risk and Resilience in Pediatric Pain
Authors: Feinstein Amanda B. , Sturgeon John A. , Bhandari Rashmi P. , Yoon Isabel A. , Ross Alexandra C. , Huestis Samantha E. , Griffin Anya T. , Simons Laura E. 
Published: July 2018

Objectives:
Both pediatric and parent pain catastrophizing and pain acceptance are key factors associated with pediatric pain outcomes; however, the interactive effects of these factors within the parent-child dyad have yet to be tested. The aims of this study were to examine: (1) the mediating role of child catastrophizing between parent catastrophizing and child outcomes (pain interference and mobility), (2) the mediating role of child acceptance between parent acceptance and child outcomes, and (3) whether child acceptance buffers the relation between parent catastrophizing and child catastrophizing, which in turn impacts child outcomes.

Materials and Methods:
Cross-sectional data from 324 youth with chronic pain ages 10 to 17 years (mean age=14.72, [SD=2.12]; 73.1% female; 59% Caucasian) and their parents were collected. Participants completed measures assessing pediatric Patient-Reported Outcome Measurement Information System (PROMIS) domains (mobility and pain interference), pain catastrophizing, pain acceptance, and child pain intensity. Mediation was conducted via 1000-draw bootstrap–adjusted analyses in Mplus.

Results:
Parent pain catastrophizing was indirectly associated with child pain interference via child catastrophizing but was not associated with mobility difficulties in the mediation model. Parent pain acceptance was indirectly associated with both child pain interference and mobility via child acceptance. We did not find evidence of child acceptance-buffering parent and child pain catastrophizing.

Discussion:
The findings of this study highlight the need for caregiver involvement in multidisciplinary treatments to mitigate risk and enhance resilience in youth with chronic pain.
The Effect of Axial Torsion on the Mechanical Properties of the Annulus Fibrosus
Authors: Harvey-Burgess Maxine , Gregory Diane E. 
Published: July 2018

Study Design.
In-vitro study of the tissue mechanics of annulus fibrosus.

Objective.
To determine the effect of axial torsion on the mechanical properties of the inter- and intralamellar matrices.

Summary of Background Data.
Axial torsion, when combined with repetitive flexion, has been associated with an increased risk of intervertebral disc herniation. However, the mechanisms behind this relationship are poorly understood.

Methods.
Bovine intervertebral discs (IVDs) from the caudal region were exposed to a combination of either 0° or 12° of static axial torsion and 0 N or 1000 N of compression for 2 hours in an attempt to created micro-damage to the IVD. Following the loading protocol, one multilayered sample and two single layer samples were dissected from the annulus fibrosus to undergo tensile testing of the inter- and intralamellar matrices. Histological staining was also performed.

Results.
The strength of the interlamellar matrix was not affected by axial torsion or compression, suggesting that torsion did not damage the interlamellar matrix. However, intralamellar matrix strength of samples exposed to axial torsion, regardless of compressive loading magnitude, was 48% lower than those from samples that were not exposed to torsion (P < 0.001). Similarly, intralamellar matrix stiffness of samples exposed to axial torsion was 42% lower than from samples that were not exposed to torsion (P = 0.010). Additionally, histological analysis demonstrated more disruption within individual lamellae of the samples exposed to axial torsion compared with samples that were not.

Conclusion.
This study suggests that axial torsion damages the components of the intralamellar matrix as a result of the strain it puts on the matrix, thus making the intervertebral disc more susceptible to herniation.

Level of Evidence: N/A
The Association Between Inhaled Nitric Oxide Treatment and ICU Mortality and 28-Day Ventilator-Free Days in Pediatric Acute Respiratory Distress Syndrome*
Authors: Bhalla Anoopindar K. , Yehya Nadir , Mack Wendy J. , Wilson Melissa L. , Khemani Robinder G. , Newth Christopher J. L. 
Published: July 2018

Objectives:
To investigate the association between inhaled nitric oxide treatment and ICU mortality and 28-day ventilator-free days in pediatric acute respiratory distress syndrome.

Design:
Retrospective cohort study. A propensity score for inhaled nitric oxide treatment was developed and used in the analysis.

Setting:
Two quaternary care PICUs.

Patients:
Children with pediatric acute respiratory distress syndrome.

Interventions:
None.

Measurements and Main Results:
There were 499 children enrolled in this study with 143 (28.7%) receiving inhaled nitric oxide treatment. Children treated with inhaled nitric oxide were more likely to have a primary diagnosis of pneumonia (72% vs 54.8%; p < 0.001), had a higher initial oxygenation index (median 16.9 [interquartile range, 10.1–27.3] vs 8.5 [interquartile range, 5.8–12.2]; p < 0.001), and had a higher 72-hour maximal Vasoactive-Inotrope Score (median 15 [interquartile range, 6–25] vs 8 [interquartile range, 0–17.8]; p < 0.001) than those not receiving inhaled nitric oxide. Mortality was higher in the inhaled nitric oxide treatment group (25.2% vs 16.3%; p = 0.02), and children in this group had fewer 28-day ventilator-free days (10 d [interquartile range, 0–18 d] vs 17 d (interquartile range 5.5–22 d]; p < 0.0001). We matched 176 children based on propensity score for inhaled nitric oxide treatment. In the matched cohort, inhaled nitric oxide treatment was not associated with mortality (odds ratio, 1.3 [95% CI, 0.56–3.0]) or 28-day ventilator-free days (incidence rate ratio, 0.91 [95% CI, 0.80–1.04]). These results remained consistent in the entire study cohort when the propensity score for inhaled nitric oxide treatment was used for either inverse probability weighting or stratification in regression modeling with the exception that subjects treated with inhaled nitric oxide were more likely to have 0 ventilator-free days (p ≤ 0.02). In secondary analysis stratified by oxygenation response, inhaled nitric oxide treatment was not associated with mortality or 28-day ventilator-free days in children with a positive oxygenation response (all p > 0.2)

Conclusions:
Treatment with inhaled nitric oxide in pediatric acute respiratory distress syndrome is not associated with improvement in either mortality or ventilator-free days and may be associated with harm. Further prospective trials are required to define the role of inhaled nitric oxide treatment in pediatric acute respiratory distress syndrome.
Emerging Nonsurgical Therapies for Locally Advanced and Metastatic Nonmelanoma Skin Cancer
Authors: Chen Leon , Aria Alexander B. , Silapunt Sirunya , Migden Michael R. 
Published: July 2018

BACKGROUNDLocally advanced and metastatic nonmelanoma skin cancer (NMSC) not amenable to surgical resection requires a different approach to therapy.OBJECTIVETo review the efficacy and adverse effects of emerging treatment options for locally advanced and metastatic NMSC.MATERIALS AND METHODSA comprehensive search on PubMed was conducted to identify relevant literature investigating the role of program cell death 1 (PD-1) inhibitor, cytotoxic T-lymphocyte–associated antigen 4 (CTLA-4) inhibitor, epidermal growth factor receptor (EGFR) inhibitor, and Hedgehog pathway inhibitors in the treatment of NMSC.RESULTSPD-1 inhibitor and CTLA-4 inhibitor have shown promising efficacy with tolerable side-effect profiles in the treatment of NMSC, although the number of cases reported is limited. Currently, 3 larger-scale clinical trials are investigating PD-1 inhibitor therapy for NMSC. Similarly, EGFR inhibitor demonstrated marginal success in unresectable cutaneous squamous cell carcinomas. Hedgehog pathway inhibitors were approved by the US FDA for treatment of locally advanced and metastatic basal cell carcinomas and have shown favorable efficacy. Common adverse effects included muscle spasm, alopecia, and dysgeusia.CONCLUSIONSystemic therapies including PD-1 inhibitors and CTLA-4 inhibitors have demonstrated early promising results for difficult-to-treat NMSC. Future studies are necessary to optimize treatment outcome.