bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complications Following Arthroscopic Rotator Cuff Tear Repair
Authors: Audigé Laurent , Blum Raphael , Müller Andreas M. , Flury Matthias , Durchholz Holger 
Published: June 2015

Background Valid comparison of outcomes after surgical procedures requires consensus on which instruments and parameters should be used, including the recording and evaluation of surgical complications. An international standard outlining the terminology and definitions of surgical complications in orthopaedics is lacking. Purpose This study systematically reviewed the literature for terms and definitions related to the occurrence of negative events or complications after arthroscopic rotator cuff repair (ARCR) with specific focus on shoulder stiffness. Study Design Systematic review; Level of evidence, 4. Methods PubMed, EMBASE, Cochrane Library, and Scopus databases were searched for reviews, clinical studies, and case reports of complications associated with ARCR. Reference lists of selected articles were also screened. The terminology of complications and their definitions were extracted from all relevant original articles by a single reviewer and verified by a second reviewer. Definitions of shoulder stiffness or equivalent terms were tabulated. Results Of 654 references published after 2007 and obtained from the search, 233 full-text papers (44 reviews, 155 studies, 31 case reports, and 3 surgical technique presentations) were reviewed. Twenty-two additional references cited for a definition were checked. One report defined the term surgical complication. There were 242 different terms used to describe local events and 64 to describe nonlocal events. Furthermore, 16 definitions of terms such as frozen shoulder, shoulder stiffness, or stiff painful shoulder were identified. Diagnosis criteria for shoulder stiffness differed widely; 12 various definitions for restriction in range of motion were noted. One definition included a gradation of stiffness severity, whereas another considered the patient’s subjective assessment of motion. Conclusion The literature does not consistently report on complications after ARCR, making valid comparison of the incidence of these events among published reports impossible. Specifically, the variation in criteria used to diagnose shoulder stiffness is problematic for valid and accurate reporting of this event. A standard for reporting this event and other complications after ARCR is needed. Clinical Relevance This review serves as the basis for the development of a uniform documentation process for shoulder stiffness and the standardization of complication definitions in ARCR following international consensus.
Early dynamic left intraventricular obstruction is associated with hypovolemia and high mortality in septic shock patients
Authors: Chauvet Jean-Louis , El-Dash Shari , Delastre Olivier , Bouffandeau Bernard , Jusserand Dominique , Michot Jean-Baptiste , Bauer Fabrice , Maizel Julien , Slama Michel 
Published: June 2015

AbstractIntroductionBased on previously published case reports demonstrating dynamic left intraventricular obstruction (IVO) triggered by hypovolemia or catecholamines, this study aimed to establish: (1) IVO occurrence in septic shock patients; (2) correlation between the intraventricular gradient and volume status and fluid responsiveness; and (3) mortality rate.MethodWe prospectively analyzed patients with septic shock admitted to a general ICU over a 28-month period who presented Doppler signs of IVO. Clinical characteristics and hemodynamic parameters as well as echocardiographic data regarding left ventricular function, size, and calculated mass, and left ventricular outflow Doppler pattern and velocity before and after fluid infusions were recorded.ResultsDuring the study period, 218 patients with septic shock were admitted to our ICU. IVO was observed in 47 (22 %) patients. Mortality rate at 28 days was found to be higher in patients with than in patients without IVO (55 % versus 33 %,p< 0.01). Small, hypercontractile left ventricles (end-diastolic left ventricular surface 4.7 ± 2.1 cm2/m2and ejection fraction 82 ± 12 %), and frequent pseudohypertrophy were found in these patients. A rise ≥12 % in stroke index was found in 87 % of patients with IVO, with a drop of 47 % in IVO after fluid infusion.ConclusionLeft IVO is a frequent event in septic shock patients with an important correlation with fluid responsiveness. The mortality rate was found to be higher in these patients in comparison with patients without obstruction.
Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits
Authors: Pal Bhupinder , Chen Yunshun , Bert Andrew , Hu Yifang , Sheridan Julie M. , Beck Tamara , Shi Wei , Satterley Keith , Jamieson Paul , Goodall Gregory J. , Lindeman Geoffrey J. , Smyth Gordon K. , Visvader Jane E. 
Published: June 2015

Abstract
Introduction
MicroRNAs (miRNAs) have been implicated in governing lineage specification and differentiation in multiple organs; however, little is known about their specific roles in mammopoiesis. We have determined the global miRNA expression profiles of functionally distinct epithelial subpopulations in mouse and human mammary tissue, and compared these to their cognate transcriptomes and epigenomes. Finally, the human miRNA signatures were used to interrogate the different subtypes of breast cancer, with a view to determining miRNA networks deregulated during oncogenesis.

Methods
RNA from sorted mouse and human mammary cell subpopulations was subjected to miRNA expression analysis using the TaqMan MicroRNA Array. Differentially expressed (DE) miRNAs were correlated with gene expression and histone methylation profiles. Analysis of miRNA signatures of the intrinsic subtypes of breast cancer in The Cancer Genome Atlas (TCGA) database versus those of normal human epithelial subpopulations was performed.

Results
Unique miRNA signatures characterized each subset (mammary stem cell (MaSC)/basal, luminal progenitor, mature luminal, stromal), with a high degree of conservation across species. Comparison of miRNA and transcriptome profiles for the epithelial subtypes revealed an inverse relationship and pinpointed key developmental genes. Interestingly, expression of the primate-specific miRNA cluster (19q13.4) was found to be restricted to the MaSC/basal subset. Comparative analysis of miRNA signatures with H3 lysine modification maps of the different epithelial subsets revealed a tight correlation between active or repressive marks for the top DE miRNAs, including derepression of miRNAs in Ezh2-deficient cellular subsets. Interrogation of TCGA-identified miRNA profiles with the miRNA signatures of different human subsets revealed specific relationships.

Conclusions
The derivation of global miRNA expression profiles for the different mammary subpopulations provides a comprehensive resource for understanding the interplay between miRNA networks and target gene expression. These data have highlighted lineage-specific miRNAs and potential miRNA–mRNA networks, some of which are disrupted in neoplasia. Furthermore, our findings suggest that key developmental miRNAs are regulated by global changes in histone modification, thus linking the mammary epigenome with genome-wide changes in the expression of genes and miRNAs. Comparative miRNA signature analyses between normal breast epithelial cells and breast tumors confirmed an important linkage between luminal progenitor cells and basal-like tumors.
Organisation of the motor cortex differs between people with and without knee osteoarthritis
Authors: Shanahan Camille J. , Hodges Paul W. , Wrigley Tim V. , Bennell Kim L. , Farrell Michael J. 
Published: June 2015

Abstract
Introduction
The aim of this study was to investigate possible differences in the organisation of the motor cortex in people with knee osteoarthritis (OA) and whether there is an association between cortical organisation and accuracy of a motor task.

Methods
fMRI data were collected while 11 participants with moderate/severe right knee OA (6 male, 69 ± 6 (mean ± SD) years) and seven asymptomatic controls (5 male, 64 ± 6 years) performed three visually guided, variable force, force matching motor tasks involving isolated isometric muscle contractions of: 1) quadriceps (knee), 2) tibialis anterior (ankle) and, 3) finger/thumb flexor (hand) muscles. fMRI data were used to map the loci of peak activation in the motor cortex during the three tasks and to assess whether there were differences in the organisation of the motor cortex between the groups for the three motor tasks. Root mean square of the difference between target and generated forces during muscle contraction quantified task accuracy.

Results
A 4.1 mm anterior shift in the representation of the knee (p = 0.03) and swap of the relative position of the knee and ankle representations in the motor cortex (p = 0.003) were found in people with knee OA. Poorer performance of the knee task was associated with more anterior placement of motor cortex loci in people with (p = 0.05) and without (p = 0.02) knee OA.

Conclusions
Differences in the organisation of the motor cortex in knee OA was demonstrated in relation to performance of knee and ankle motor tasks and was related to quality of performance of the knee motor task. These results highlight the possible mechanistic link between cortical changes and modified motor behavior in people with knee OA.
Diffusion imaging changes in grey matter in Alzheimer’s disease: a potential marker of early neurodegeneration
Authors: Weston Philip S.J. , Simpson Ivor J.A. , Ryan Natalie S. , Ourselin Sebastien , Fox Nick C. 
Published: June 2015

AbstractAlzheimer’s disease (AD) is recognized to have a long presymptomatic period, during which there is progressive accumulation of molecular pathology, followed by inexorable neuronal damage. The ability to identify presymptomatic individuals with evidence of neurodegenerative change, to stage their disease, and to track progressive changes will be important for early diagnosis and for prevention trials. Despite recent advances, particularly in magnetic resonance imaging, our ability to identify early neurodegenerative changes reliably is limited. The development of diffusion-weighted magnetic resonance imaging, which is sensitive to microstructural changes not visible with conventional volumetric techniques, has led to a number of diffusion imaging studies in AD; these have largely focused on white matter changes. However, in AD cerebral grey matter is affected very early, with pathological studies suggesting that grey matter changes predate those in white matter. In this article we review the growing number of studies that assess grey matter diffusivity changes in AD. Although use of the technique is still at a relatively early stage, results so far have been promising. Initial studies identified changes in diffusion measures in the hippocampi of patients with mild cognitive impairment, which predated macroscopic volume loss, with positive predictive value for progression to AD dementia. More recent studies have identified abnormalities in multiple neocortical areas (particularly the posterior cingulate) at various stages of disease progression. Studies of patients who carry genetic mutations predisposing to autosomal dominant familial AD have shown cortical and subcortical grey matter diffusivity changes several years before the expected onset of the first clinical symptoms. The technique is not without potential methodological difficulties, especially relating to partial volume effects, although recent advances appear to be reducing such issues. Going forward, further utilization of grey matter diffusion measurements in AD may improve our understanding with regards to the timing and nature of the earliest presymptomatic neurodegenerative changes. This imaging technique may also be useful in comparing and contrasting subtle variations in different disease subgroups, and as a sensitive outcome measure for presymptomatic clinical trials in AD and other neurodegenerative diseases.
Toward a 3D coupled atomistic and discrete dislocation dynamics simulation: dislocation core structures and Peierls stresses with several character angles in FCC aluminum
Authors: Cho Jaehyun , Junge Till , Molinari Jean-François , Anciaux Guillaume 
Published: June 2015

Abstract

Background
We present a robust method to obtain the displacement field of a dislocation core, which is one of the building blocks for the development of a direct multiscale method coupling an atomistic domain to a discrete dislocation dynamics engine in 3D (e.g. CADD3D).

Methods
The core structure is achieved by modeling of a straight dislocation with an arbitrary mixed angle using atomistic simulation. In order to validate the obtained atomistic core structures, a variational Peierls-Nabarro method is extended to include arbitrary characters.

Results
Both methods show comparable dislocation core structures for all studied angles. We provide also the Peierls stress for a wide range of character angles.

Conclusions
The obtained displacement fields for the dislocation cores were fully validated. These can consequently be employed to construct the described CADD3D coupling scheme.
Long-term in vitro and in vivo effects of γ-irradiated BCG on innate and adaptive immunity
Authors: Arts Rob J W , Blok Bastiaan A , Aaby Peter , Joosten Leo A B , de Jong Dirk , van der Meer Jos W M , Benn Christine Stabell , van Crevel Reinout , Netea Mihai G 
Published: June 2015

AbstractBCG vaccination is associated with a reduced mortality from nonmycobacterial infections. This is likely to be mediated by a combination of innate-immune memory (“trained immunity”) and heterologous effects on adaptive immunity. As such, BCG could be used to boost host immunity but not in immunocompromised hosts, as it is a live, attenuated vaccine. Therefore, we assessed whether killed γBCG has similar potentiating effects. In an in vitro model of trained immunity, human monocytes were incubated with γBCG for 24 h and restimulated after 6 d. Cytokine production and the role of pattern recognition receptors and histone methylation markers were assessed. The in vivo effects of γBCG vaccination were studied in a proof-of-principle trial in 15 healthy volunteers. γBCG induced trained immunity in vitro via the NOD2 receptor pathway and up-regulation of H3K4me3 histone methylation. However, these effects were less strong than those induced by live BCG. γBCG vaccination in volunteers had only minimal effects on innate immunity, whereas a significant increase in heterologous Th1/Th17 immunity was observed. Our results indicate that γBCG induces long-term training of innate immunity in vitro. In vivo, γBCG induces mainly heterologous effects on the adaptive-immune system, whereas effects on innate cytokine production are limited.
Transcriptomic responses to environmental temperature in eurythermal and stenothermal fishes
Authors: Logan Cheryl A. , Buckley Bradley A. 
Published: June 2015

ABSTRACTEctothermic species like fishes differ greatly in the thermal ranges they tolerate; some eurythermal species may encounter temperature ranges in excess of 25°C, whereas stenothermal species in polar and tropical waters live at essentially constant temperatures. Thermal specialization comes with fitness trade-offs and as temperature increases due to global warming, the physiological basis of specialization and thermal plasticity has become of great interest. Over the past 50 years, comparative physiologists have studied the physiological and molecular differences between stenothermal and eurythermal fishes. It is now well known that many stenothermal fishes have lost an inducible heat shock response (HSR). Recent advances in transcriptomics have now made it possible to examine genome-wide changes in gene expression (GE) in non-model ecologically important fish, broadening our view beyond the HSR to regulation of genes involved in hundreds of other cellular processes. Here, we review the major findings from transcriptomic studies of extreme eurythermal and stenothermal fishes in response to acute and long-term exposure to temperature, both time scales being critically important for predicting climate change responses. We consider possible molecular adaptations that underlie eurythermy and stenothermy in teleosts. Furthermore, we highlight the challenges that still face the field of comparative environmental genomics and suggest fruitful paths of future investigation.
Biochemical adaptation to ocean acidification
Authors: Stillman Jonathon H. , Paganini Adam W. 
Published: June 2015

ABSTRACTThe change in oceanic carbonate chemistry due to increased atmospheric PCO2 has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2. From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid–base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the external environment, such as epithelial tissues, may be susceptible to changes in external pH. Such biochemical systems could be adapted to a reduced pH environment by adjustment of weak bonds in an analogous fashion to biochemical adaptation to temperature. Whether such biochemical adaptation to OA exists remains to be discovered.
Animal ice-binding (antifreeze) proteins and glycolipids: an overview with emphasis on physiological function
Authors: Duman John G. 
Published: June 2015

ABSTRACT
Ice-binding proteins (IBPs) assist in subzero tolerance of multiple cold-tolerant organisms: animals, plants, fungi, bacteria etc. IBPs include: (1) antifreeze proteins (AFPs) with high thermal hysteresis antifreeze activity; (2) low thermal hysteresis IBPs; and (3) ice-nucleating proteins (INPs). Several structurally different IBPs have evolved, even within related taxa. Proteins that produce thermal hysteresis inhibit freezing by a non-colligative mechanism, whereby they adsorb onto ice crystals or ice-nucleating surfaces and prevent further growth. This lowers the so-called hysteretic freezing point below the normal equilibrium freezing/melting point, producing a difference between the two, termed thermal hysteresis. True AFPs with high thermal hysteresis are found in freeze-avoiding animals (those that must prevent freezing, as they die if frozen) especially marine fish, insects and other terrestrial arthropods where they function to prevent freezing at temperatures below those commonly experienced by the organism. Low thermal hysteresis IBPs are found in freeze-tolerant organisms (those able to survive extracellular freezing), and function to inhibit recrystallization – a potentially damaging process whereby larger ice crystals grow at the expense of smaller ones – and in some cases, prevent lethal propagation of extracellular ice into the cytoplasm. Ice-nucleator proteins inhibit supercooling and induce freezing in the extracellular fluid at high subzero temperatures in many freeze-tolerant species, thereby allowing them to control the location and temperature of ice nucleation, and the rate of ice growth. Numerous nuances to these functions have evolved. Antifreeze glycolipids with significant thermal hysteresis activity were recently identified in insects, frogs and plants.
Physiological mechanisms used by fish to cope with salinity stress
Authors: Kültz Dietmar 
Published: June 2015

ABSTRACTSalinity represents a critical environmental factor for all aquatic organisms, including fishes. Environments of stable salinity are inhabited by stenohaline fishes having narrow salinity tolerance ranges. Environments of variable salinity are inhabited by euryhaline fishes having wide salinity tolerance ranges. Euryhaline fishes harbor mechanisms that control dynamic changes in osmoregulatory strategy from active salt absorption to salt secretion and from water excretion to water retention. These mechanisms of dynamic control of osmoregulatory strategy include the ability to perceive changes in environmental salinity that perturb body water and salt homeostasis (osmosensing), signaling networks that encode information about the direction and magnitude of salinity change, and epithelial transport and permeability effectors. These mechanisms of euryhalinity likely arose by mosaic evolution involving ancestral and derived protein functions. Most proteins necessary for euryhalinity are also critical for other biological functions and are preserved even in stenohaline fish. Only a few proteins have evolved functions specific to euryhaline fish and they may vary in different fish taxa because of multiple independent phylogenetic origins of euryhalinity in fish. Moreover, proteins involved in combinatorial osmosensing are likely interchangeable. Most euryhaline fishes have an upper salinity tolerance limit of approximately 2× seawater (60 g kg−1). However, some species tolerate up to 130 g kg−1 salinity and they may be able to do so by switching their adaptive strategy when the salinity exceeds 60 g kg−1. The superior salinity stress tolerance of euryhaline fishes represents an evolutionary advantage favoring their expansion and adaptive radiation in a climate of rapidly changing and pulsatory fluctuating salinity. Because such a climate scenario has been predicted, it is intriguing to mechanistically understand euryhalinity and how this complex physiological phenotype evolves under high selection pressure.
The emerging role of RNA editing in plasticity
Authors: Rosenthal Joshua J. C. 
Published: June 2015

ABSTRACT
All true metazoans modify their RNAs by converting specific adenosine residues to inosine. Because inosine binds to cytosine, it is a biological mimic for guanosine. This subtle change, termed RNA editing, can have diverse effects on various RNA-mediated cellular pathways, including RNA interference, innate immunity, retrotransposon defense and messenger RNA recoding. Because RNA editing can be regulated, it is an ideal tool for increasing genetic diversity, adaptation and environmental acclimation. This review will cover the following themes related to RNA editing: (1) how it is used to modify different cellular RNAs, (2) how frequently it is used by different organisms to recode mRNA, (3) how specific recoding events regulate protein function, (4) how it is used in adaptation and (5) emerging evidence that it can be used for acclimation. Organismal biologists with an interest in adaptation and acclimation, but with little knowledge of RNA editing, are the intended audience.