bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound Evaluation of Quadriceps Muscle Dysfunction in Respiratory Disease
Authors: Parry Selina M. , Burtin Chris , Denehy Linda , Puthucheary Zudin A. , Bear Danielle 
Published: December 2018

Purpose:
Peripheral muscle dysfunction can encompass reductions in muscle mass, strength, endurance, and fatigability, and is common in both critical illness and chronic respiratory diseases. There is growing interest in nonvolitional methods to quantify the severity of peripheral muscle dysfunction—in particular, the utility of ultrasonography. This review provides an up-to-date narrative synthesis of current knowledge around ultrasonography methodology and the quantitative and qualitative measures that can be obtained from ultrasound imaging. The application of ultrasonography in chronic respiratory disease and critical illness will be discussed alongside the need for standardized methodologies.

Summary:
Quadriceps muscle dysfunction is multifactorial with changes in muscle quantity and quality impacting on patient clinical outcomes. There is significant variability in ultrasonography image acquisition and analysis methodologies, which requires standardization. Ultrasound imaging is a promising evaluation tool that may enable identification of individuals at highest risk of muscle dysfunction and thus targeting of intervention resources.

Conclusion:
Ultrasonography is noninvasive and easily integrated at the bedside in clinical practice. A range of quantitative and qualitative parameters can be assessed to provide detail on severity of peripheral muscle dysfunction in respiratory disease. There is significant variability in the application of ultrasonography, in order for the field to progress standardized approach to ultrasonography needs to be developed.
Spontaneous bacterial peritonitis recurrence in patients with cirrhosis receiving secondary prophylaxis with norfloxacin
Authors: Marciano Sebastián , Dirchwolf Melisa , Diaz Juan M. , Bermudez Carla , Gutierrez-Acevedo Maria N. , Barcán Laura A. , Smud Astrid , Giunta Diego , Gadano Adrián C. 
Published: December 2018

Objective
Few studies carried out more than 20 years ago have evaluated spontaneous bacterial peritonitis (SBP) recurrence in patients receiving secondary antibiotic prophylaxis. These studies reported a 1-year recurrence rate of 20–26%. Changes in the bacteriology of SBP over the last few years might have negative effects on secondary prophylaxis. Our primary aim was to estimate the incidence of SBP recurrence in patients with cirrhosis receiving secondary prophylaxis with norfloxacin and to explore the factors associated with SBP recurrence.

Patients and methods
This was a retrospective cohort study of patients receiving norfloxacin for the secondary prophylaxis of SBP from 1 March 2003 to 31 March 2016. Follow-up was performed for 365 days after secondary prophylaxis was started. A competing risk analysis approach was used.

Results
A total of 115 patients were included. The prevalence of quinolone-resistant and multiresistant bacteria in the first episode of SBP among patients with culture-positive SBP was 70.96% [95% confidence interval (CI): 51.96–85.77%] and 12.90% (95% CI: 3.63–29.83%), respectively. The cumulative incidence of SBP recurrence was 28.53% (95% CI: 20.15–37.45%) after 365 days. Male patients showed an estimated subhazard ratio of SBP recurrence of 2.52 (95% CI: 1.07–5.91, P=0.034). No other risk factors for SBP recurrence were identified. The overall cumulative incidence of death after 365 days was 21.57% (95% CI: 14.14–30.04%), without significant differences among patients with or without SBP recurrence.

Conclusion
Even though changes in the bacteriology of SBP occurred over time, its recurrence rate in patients receiving norfloxacin remains similar to what was reported in the initial studies.
A Comparison of Acellular Dermal Matrices in Abdominal Wall Reconstruction
Authors: Maxwell Daniel W. , Hart Alexandra M. , Keifer Orion P. , Halani Sameer H. , Losken Albert 
Published: December 2018

Background
There is a growing literature of evidence that the use of acellular dermal matrices (ADMs) in abdominal wall reconstruction (AWR) for high-risk patients provides superior complication profiles when compared with standard synthetic mesh. Here we compare Fortiva, Strattice, and Alloderm ADMs in AWR.

Methods
In a prospectively maintained database, all patients undergoing AWR between January 2003 and November 2016 were reviewed. Hernia recurrence and surgical site occurrence (SSO) were our primary and secondary endpoints. Kaplan-Meier survival curves and logistic regression models were used to evaluate risks for hernia recurrence and SSO.

Results
A total of 229 patients underwent AWR with 1 of 3 ADMs. Median follow-up time was 20.9 months (1–60 months). Cumulative recurrence rates for each mesh were 6.9%, 11.2%, and 22.0% (P = 0.04), for Fortiva, Strattice, and Alloderm groups. Surgical site occurrence for each mesh was 56.9%, 49.0%, and 49.2%, respectively. Seroma was significantly lower in the Fortiva group (1.4%; P = 0.02). Independent risk factors hernia recurrence included body mass index of 30 kg/m2 or higher and hypertension. Adjusted risk factors included oncologic resection for hernia recurrence (odds ratio, 5.3; confidence interval, 1.1–97.7; P = 0.11) and a wound class of contaminated or dirty/infected for SSO (odds ratio, 3.6; confidence interval, 1.0–16.6; P = 0.07).

Conclusions
Acellular dermal matrices provide a durable repair with low overall rate of recurrence and complications in AWR. The recurrence and complication profiles differ between brands. With proper patient selection and consideration, ADMs can be used confidently for a variety of indications and wound classifications.
Insoluble Aβ overexpression in an App knock-in mouse model alters microstructure and gamma oscillations in the prefrontal cortex, and social and anxiety-related behaviours
Authors: Pervolaraki Eleftheria , Hall Stephen P , Foresteire Denise , Saito Takashi , Saido Takaomi C , Whittington Miles A , Lever Colin , Dachtler James 
Published: December 2018

AbstractWe studied two new App knock-in mice models of Alzheimer’s disease (AppNL-F and AppNL-G-F), which generate elevated levels of Aβ40 and Aβ42 without the confounds associated with APP overexpression. This enabled us to assess changes in anxiety-related and social behaviours, and neural alterations potentially underlying such changes, driven specifically by Aβ accumulation. AppNL-G-F knock-in mice exhibited subtle deficits in tasks assessing social memory, but not in social motivation tasks. In anxiety-assessing tasks, AppNL-G-F knock-in mice exhibited: 1) increased thigmotaxis in the Open Field (OF), yet; 2) reduced closed-arm, and increased open-arm, time in the Elevated Plus Maze (EPM). Their ostensibly-anxiogenic OF profile, yet ostensibly-anxiolytic EPM profile, could hint at altered cortical mechanisms affecting decision-making (e.g. ‘disinhibition’), rather than simple core deficits in emotional motivation. Consistent with this possibility, alterations in microstructure, glutamatergic-dependent gamma oscillations, and glutamatergic gene expression were all observed in the prefrontal cortex, but not the amygdala, of AppNL-G-F knock-in mice. Thus, insoluble Aβ overexpression drives prefrontal cortical alterations, potentially underlying changes in social and anxiety-related behavioural tasks.HighlightsAppNL-G-F KI mice displayed differing anxiety behaviours in two tests of anxiety.Prefrontal gamma was no longer NMDA-receptor dependent in AppNL-G-F KI mice.Prefrontal expression of Grin2b was reduced in AppNL-G-F KI mice.DTI found structural alterations in the hippocampus and prefrontal cortex in AppNL-G-F KI mice.
opentsv prevents the corruption of scientific data by Excel
Authors: De Rijk Peter , D’Hert Svenn , Strazisar Mojca 
Published: December 2018

AbstractMicrosoft Excel is widely used by researchers to edit tab- or comma-separated data files. However, Excel often corrupts the data when opening these files, most notably by changing some gene names to a date. Although this problem was cautioned against earlier, we show that every year hundreds of published papers still come with supplementary data files containing these errors. Opentsv was developed to effectively circumvent this problem at the root by providing an easy and transparent way to open delimited data files in Excel without these conversions. Opentsv is freely available at https://github.com/derijkp/opentsv.
Conformational changes in Apolipoprotein N-acyltransferase (Lnt)
Authors: Wiseman Benjamin , Högbom Martin 
Published: December 2018

SUMMARYIn bacteria, lipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three essential integral membrane enzymes. The last step of this process, unique to Gram negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of this enzyme. In one form the enzyme crystallized with two molecules in the asymmetric unit. In one of those molecules the thioester acyl-intermediate is observed. In the other molecule, the crystal packing suggests one potential mode of apolipoprotein docking to Lnt. In the second crystal form the enzyme crystallized with one molecule in the asymmetric unit in an apparent apo-state remarkably devoid of any bound molecules in the large open substrate entry portal. Taken together, these structures suggest that the movement of the essential W237 is triggered by substrate binding and could help direct and stabilize the interaction between Lnt and the incoming substrate apolipoprotein.Graphical Abstract
Using Flow Cytometry and Multistage Machine Learning to Discover Label-Free Signatures of Algal Lipid Accumulation
Authors: Tanhaemami Mohammad , Alizadeh Elaheh , Sanders Claire , Marrone Babetta L. , Munsky’ Brian 
Published: December 2018

Abstract—Most applications of flow cytometry or cell sorting rely on the conjugation of fluorescent dyes to specific biomarkers. However, labeled biomarkers are not always available, they can be costly, and they may disrupt natural cell behavior. Label-free quantification based upon machine learning approaches could help correct these issues, but label replacement strategies can be very difficult to discover when applied labels or other modifications in measurements inadvertently modify intrinsic cell properties. Here we demonstrate a new, but simple approach based upon feature selection and linear regression analyses to integrate statistical information collected from both labeled and unlabeled cell populations and to identify models for accurate label-free single-cell quantification. We verify the method’s accuracy to predict lipid content in algal cells(Picochlorum soloecismus)during a nitrogen starvation and lipid accumulation time course. Our general approach is expected to improve label-free single-cell analysis for other organisms or pathways, where biomarkers are inconvenient, expensive, or disruptive to downstream cellular processes.
OCT4 expression regulated apoptosis and cell cycle in myeloma cells
Authors: Niknamian Sorush 
Published: December 2018

AbstractPurposeOCT4 gene is specifically expressed in embryonic stem cells and plays a very important role in the proliferation, differentiation, and self-renewal of these cells. The abnormal expression of the OCT4 gene has been observed in most malignancies. Expression of this gene can affect the proliferation and apoptosis of malignant cells by activating various signaling pathways. The proliferation and excessive accumulation of myeloma cells in the bone marrow causes the essential complications of multiple myeloma. Genetic changes and mutations play a role in unscheduled proliferation and diminishing of the apoptosis of the myeloma cells.Material and methodsIn this study, the expression of the OCT4 gene by quantitative PCR and its effects on proliferation, apoptosis, and cell cycle of the myeloma cells by flow cytometry was investigated.ResultsThe results of our study indicated that the myeloma cells express the OCT4 gene; and inhibition of the OCT4 gene by siRNA reduced its expression. The siRNA treated myeloma cells indicated decreased proliferation and increased apoptosis.ConclusionAs with studies in other malignancies, our study also revealed that the OCT4 gene was expressed in the myeloma cells, with evidences of increased proliferation and reduced apoptosis in these cells.
Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data
Authors: Paissoni Cristina , Jussupow Alexander , Camilloni Carlo 
Published: December 2018

AbstractSmall-angle X-ray scattering (SAXS) use in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speed up by using a coarse grain representation of the structure. Here following the work of Niebling, et al. (J. Appl. Cryst., (2014), 47, 1190) we derived the Martini beads form factors for nucleic acids and we implemented them, together with those previously determined for proteins, in the publicly available PLUMED library. We also implemented a hybrid multi-resolution strategy to perform SAXS restrained simulations at atomic resolution by calculating on-the-fly the virtual position of the Martini beads and using them for the calculation of SAXS. The accuracy and efficiency of the method is demonstrated by refining the structure of two protein/nucleic acid complexes. Instrumental for this result is the use of metainference that allows considering and alleviating the approximations at play in our SAXS calculation.
Blood vessels guide Schwann cell migration in the adult demyelinated CNS through Eph/ephrin signaling
Authors: Garcia-Diaz Beatriz , Bachelin Corinne , Coulpier Fanny , Gerschenfeld Gaspard , Deboux Cyrille , Zujovic Violetta , Charnay Patrick , Topilko Piotr , Baron-Van Evercooren Anne 
Published: December 2018

ABSTRACTSchwann cells (SC) enter the central nervous system (CNS) in pathophysiological conditions. However, how SC invade the CNS to remyelinate central axons remains undetermined. We studied SC migratory behaviorex vivoandin vivoafter exogenous transplantation in the demyelinated spinal cord. Data highlight for the first time that SC migrate preferentially along blood vessel in perivascular ECM, avoiding CNS myelin. We demonstratein vitroandin vivothat this migration route occurs by virtue of a dual mode of action of Eph/ephrin receptor. Indeed, EphrinB3, enriched in myelin, interacts with SC Eph receptors, to drive SC away from CNS myelin, and triggers their preferential adhesion to ECM components, such as fibronectin via integrinβ1 interactions. This complex interplay enhances SC migration along the blood vessel network and together with lesion-induced vascular remodeling facilitates their timely invasion of the lesion site. These novel findings elucidate the mechanism by which SC invade and contribute to spinal cord repair.
A Heuristic Derived from Analysis of the Ion Channel Structural Proteome Permits the Rapid Identification of Hydrophobic Gates
Authors: Rao Shanlin , Klesse Gianni , Stansfeld Phillip J. , Tucker Stephen J. , Sansom Mark S.P. 
Published: December 2018

AbstractIon channel proteins control ionic flux across biological membranes through conformational changes in their transmembrane pores. An exponentially increasing number of channel structures captured in different conformational states are now being determined. However, these newly-resolved structures are commonly classified as either open or closed based solely on the physical dimensions of their pore and it is now known that more accurate annotation of their conductive state requires an additional assessment of the effect of pore hydrophobicity. A narrow hydrophobic gate region may disfavour liquid-phase water, leading to local de-wetting which will form an energetic barrier to water and ion permeation without steric occlusion of the pore. Here we quantify the combined influence of radius and hydrophobicity on pore de-wetting by applying molecular dynamics simulations and machine learning to nearly 200 ion channel structures. This allows us to propose a simple simulation-free heuristic model that rapidly and accurately predicts the presence of hydrophobic gates. This not only enables the functional annotation of new channel structures as soon as they are determined, but may also facilitate the design of novel nanopores controlled by hydrophobic gates.Significance statementIon channels are nanoscale protein pores in cell membranes. An exponentially increasing number of structures for channels means that computational methods for predicting their functional state are needed. Hydrophobic gates in ion channels result in local de-wetting of pores which functionally closes them to water and ion permeation. We use simulations of water behaviour within nearly 200 different ion channel structures to explore how the radius and hydrophobicity of pores determine their hydration vs. de-wetting behaviour. Machine learning-assisted analysis of these simulations enables us to propose a simple model for this relationship. This allows us to present an easy method for the rapid prediction of the functional state of new channel structures as they emerge.
Flexibility, variability and constraint in energy management patterns across vertebrate taxa revealed by long‐term heart rate measurements
Authors: Halsey Lewis G. , Green Jonathan A. , Twiss Sean D. , Arnold Walter , Burthe Sarah J. , Butler Patrick J. , Cooke Steven J. , Grémillet David , Ruf Thomas , Hicks Olivia , Minta Katarzyna J. , Prystay Tanya S. , Wascher Claudia A. F. , Careau Vincent 
Published: December 2018

Abstract

Animals are expected to be judicious in the use of the energy they gain due to the costs and limits associated with its intake. The management of energy expenditure (EE) exhibited by animals has previously been considered in terms of three patterns: the constrained, independent and performance patterns of energy management. These patterns can be interpreted by regressing daily EE against maintenance EE measured over extended periods. From the multiple studies on this topic, there is equivocal evidence about the existence of universal patterns in certain aspects of energy management.

The implicit assumption that animals exhibit specifically one of three discrete energy management patterns, and without variation, seems simplistic. We suggest that animals can exhibit gradations of different energy management patterns and that the exact pattern will fluctuate as their environmental context changes.

To investigate these ideas, and for possible large‐scale patterns in energy management, we analysed long‐term heart rate data—a strong proxy for EE—across and within individuals in 16 species of birds, mammals and fish.

Our analyses of 292 individuals representing 46,539 observation‐days suggest that vertebrates typically exhibit predominantly the independent or performance energy patterns at the across‐individual level, and that the pattern does not associate with taxonomic group. Within individuals, however, animals generally exhibit some degree of energy constraint. Together, these findings indicate that across diverse species, some individuals supply more energy to all aspects of their life than do others, however all individuals must trade‐off deployment of their available energy between competing functions. This demonstrates that within‐individual analyses are essential for the interpretation of energy management patterns.

We also found that species do not necessarily exhibit a fixed energy management pattern but rather temporal variation in their energy management over the year. Animals’ energy management exhibited stronger energy constraint during periods of higher EE, which typically coincided with clear and key life cycle events such as reproduction, suggesting an adaptive plasticity to respond to fluctuating energy demands.

A plain language summary is available for this article.
The meaning of the term ‘function’ in ecology: A coral reef perspective
Authors: Bellwood David R. , Streit Robert P. , Brandl Simon J. , Tebbett Sterling B. 
Published: December 2018

Abstract

The inherent complexity of high‐diversity systems can make them particularly difficult to understand. The relatively recent introduction of functional approaches, which seek to infer ecosystem functioning based on species’ ecological traits, has revolutionized our understanding of these high‐diversity systems. Today, the functional structure of an assemblage is widely regarded as a key indicator of the status or resilience of an ecosystem. Indeed, functional evaluations have become a mainstay of monitoring and management approaches. But is the heavy focus on broad metrics of functional structure grounded in empirical research?

On tropical coral reefs, the ocean’s most diverse ecosystems, remarkably few studies directly quantify ecosystem functions and the term ‘function’ is widely used but rarely defined, especially when applied to reef fishes. Our review suggests that most ‘functional’ studies do not study function as it relates to ecological processes. Rather, they look at easy‐to‐measure traits or proxies that are thought to have functional significance. However, these links are rarely tested empirically, severely limiting our capacity to extend results from community structure to the dynamic processes operating within high‐diversity ecosystems such as coral reefs.

With rapid changes in global ecosystems, and in their capacity to deliver ecosystem services, there is an urgent need to understand and empirically measure the role of organisms in various ecosystem functions. We suggest that if we are to understand and manage transitioning coral reefs in the Anthropocene, a broad definition of the word ‘function’ is needed along with a focus on ecological processes and the empirical quantification of functional roles.

In this review, we propose a universal operational definition of the term ‘function’ that works from a cellular to a global level. Specifically, it is the movement or storage of energy or material. Within this broad definitional framework, all functions are part of a continuum that is tied together by the process‐based unifier of material fluxes. With this universal definition at hand, we then present a path forward that will allow us to fully harness the power of functional approaches in understanding and managing high‐diversity systems such as coral reefs.

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