bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome
Authors: Kokosar Milana , Benrick Anna , Perfilyev Alexander , Nilsson Emma , Källman Thomas , Ohlsson Claes , Ling Charlotte , Stener-Victorin Elisabet 
Published: January 2018

AbstractA single bout of electroacupuncture results in muscle contractions and increased whole body glucose uptake in women with polycystic ovary syndrome (PCOS). Women with PCOS have transcriptional and epigenetic alterations in the adipose tissue and we hypothesized that electroacupuncture induces epigenetic and transcriptional changes to restore metabolic alterations. Twenty-one women with PCOS received a single bout of electroacupuncture, which increased the whole body glucose uptake. In subcutaneous adipose tissue biopsies, we identified treatment-induced expression changes of 2369 genes (Q < 0.05) and DNA methylation changes of 7055 individual genes (Q = 0.11). The largest increase in expression was observed for FOSB (2405%), and the largest decrease for LOC100128899 (54%). The most enriched pathways included Acute phase response signaling and LXR/RXR activation. The DNA methylation changes ranged from 1–16%, and 407 methylation sites correlated with gene expression. Among genes known to be differentially expressed in PCOS, electroacupuncture reversed the expression of 80 genes, including PPARγ and ADIPOR2. Changes in the expression of Nr4a2 and Junb are reversed by adrenergic blockers in rats demonstrating that changes in gene expression, in part, is due to activation of the sympathetic nervous system. In conclusion, low-frequency electroacupuncture with muscle contractions remodels epigenetic and transcriptional changes that elicit metabolic improvement.
An efficient copper-based magnetic nanocatalyst for the fixation of carbon dioxide at atmospheric pressure
Authors: Sharma Rakesh Kumar , Gaur Rashmi , Yadav Manavi , Goswami Anandarup , Zbořil Radek , Gawande Manoj B. 
Published: January 2018

AbstractIn the last few decades, the emission of carbon dioxide (CO2) in the environment has caused havoc across the globe. One of the most promising strategies for fixation of CO2 is the cycloaddition reaction between epoxides and CO2 to produce cyclic carbonates. For the first time, we have fabricated copper-based magnetic nanocatalyst and have applied for the CO2 fixation. The prepared catalyst was thoroughly characterized using various techniques including XRD, FT-IR, TEM, FE-SEM, XPS, VSM, ICP-OES and elemental mapping. The reactions proceeded at atmospheric pressure, relatively lower temperature, short reaction time, solvent- less and organic halide free reaction conditions. Additionally, the ease of recovery through an external magnet, reusability of the catalyst and excellent yields of the obtained cyclic carbonates make the present protocol practical and sustainable.
Resilience management during large-scale epidemic outbreaks
Authors: Massaro Emanuele , Ganin Alexander , Perra Nicola , Linkov Igor , Vespignani Alessandro 
Published: January 2018

AbstractAssessing and managing the impact of large-scale epidemics considering only the individual risk and severity of the disease is exceedingly difficult and could be extremely expensive. Economic consequences, infrastructure and service disruption, as well as the recovery speed, are just a few of the many dimensions along which to quantify the effect of an epidemic on society’s fabric. Here, we extend the concept of resilience to characterize epidemics in structured populations, by defining the system-wide critical functionality that combines an individual’s risk of getting the disease (disease attack rate) and the disruption to the system’s functionality (human mobility deterioration). By studying both conceptual and data-driven models, we show that the integrated consideration of individual risks and societal disruptions under resilience assessment framework provides an insightful picture of how an epidemic might impact society. In particular, containment interventions intended for a straightforward reduction of the risk may have net negative impact on the system by slowing down the recovery of basic societal functions. The presented study operationalizes the resilience framework, providing a more nuanced and comprehensive approach for optimizing containment schemes and mitigation policies in the case of epidemic outbreaks.
Neuroprotective Drug for Nerve Trauma Revealed Using Artificial Intelligence
Authors: Romeo-Guitart David , Forés Joaquim , Herrando-Grabulosa Mireia , Valls Raquel , Leiva-Rodríguez Tatiana , Galea Elena , González-Pérez Francisco , Navarro Xavier , Petegnief Valerie , Bosch Assumpció , Coma Mireia , Mas José Manuel , Casas Caty 
Published: January 2018

AbstractHere we used a systems biology approach and artificial intelligence to identify a neuroprotective agent for the treatment of peripheral nerve root avulsion. Based on accumulated knowledge of the neurodegenerative and neuroprotective processes that occur in motoneurons after root avulsion, we built up protein networks and converted them into mathematical models. Unbiased proteomic data from our preclinical models were used for machine learning algorithms and for restrictions to be imposed on mathematical solutions. Solutions allowed us to identify combinations of repurposed drugs as potential neuroprotective agents and we validated them in our preclinical models. The best one, NeuroHeal, neuroprotected motoneurons, exerted anti-inflammatory properties and promoted functional locomotor recovery. NeuroHeal endorsed the activation of Sirtuin 1, which was essential for its neuroprotective effect. These results support the value of network-centric approaches for drug discovery and demonstrate the efficacy of NeuroHeal as adjuvant treatment with surgical repair for nervous system trauma.
Changes in Distribution of Dry Eye Disease by the New 2016 Diagnostic Criteria from the Asia Dry Eye Society
Authors: Inomata Takenori , Shiang Tina , Iwagami Masao , Sakemi Fumika , Fujimoto Keiichi , Okumura Yuichi , Ohno Mizu , Murakami Akira 
Published: January 2018

AbstractDry eye disease (DED) is a disorder of the tear film. Here, we delineate the changes in distribution of DED after diagnostic criteria changes from the 2006 Japanese Diagnostic Criteria to the 2016 Asia Dry Eye Society criteria. We included 250 right eyes of 250 patients and all patients completed ophthalmic assessments for DED. The 2006 criteria classified patients into definite DED, probable DED, and non-DED based on subjective symptoms, tear function, and/or vital staining. The 2016 criteria eliminated probable DED and classified patients into definite DED or non-DED based on subjective symptoms and decreased tear break-up time. We examined how probable DED patients were reclassified by the 2016 criteria. By the 2006 criteria, 38.8% (97/250) of patients had definite DED, 35.6% (89/250) had probable DED, and 25.6% (64/250) had non-DED. By the 2016 criteria, 66.8% (167/250) had definite DED and 33.2% (83/250) had non-DED. Among patients with probable DED using the 2006 criteria, 79.8% (71/89) were reclassified as definite DED and 20.2% (18/89) were reclassified as non-DED using the 2016 criteria. Our data revealed that prevalence of definite DED increased because most probable DED patients were reclassified as definite DED after changes in the diagnostic criteria.
Early bone tissue aging in human auditory ossicles is accompanied by excessive hypermineralization, osteocyte death and micropetrosis
Authors: Rolvien Tim , Schmidt Felix N. , Milovanovic Petar , Jähn Katharina , Riedel Christoph , Butscheidt Sebastian , Püschel Klaus , Jeschke Anke , Amling Michael , Busse Björn 
Published: January 2018

AbstractWithin the mineralized bone, osteocytes form a multifunctional mechanosensitive network orchestrating bone remodelling. A preserved osteocyte population is a crucial determinant of bone quality. In human auditory ossicles, the early decrease in osteocyte numbers but maintained integrity remains an unexplained phenomenon that might serve for sound transmission from air to the labyrinth. Here we analysed the frequency, size and composition of osteocyte lacunae in the auditory ossicles of 22 individuals from early postnatal period to old age. Mineralization of the bone matrix was determined using backscattered electron imaging. No signs of bone remodelling were observed above the age of 1 year. We detected characteristics of early bone tissue aging, such as decrease in osteocytes, lower total lacunar density and lacunar area, as well as high matrix mineralization accompanied by distinct accumulation of micropetrotic lacunae and decreased indentation depths. The majority of these changes took place in the first months and years of life, while afterwards only minor reorganization was present. With osteocyte apoptosis potentially being a consequence of low mechanical stimuli, the early loss of osteocytes without initiation of bone remodelling indicates an adaptive response conserving the architecture of the auditory ossicles and ensuring stable sound transmission throughout life.
Dynamical Transitions and Diffusion Mechanism in DODAB Bilayer
Authors: Dubey P. S. , Srinivasan H. , Sharma V. K. , Mitra S. , Sakai V. Garcia , Mukhopadhyay R. 
Published: January 2018

AbstractDioctadecyldimethylammonium bromide (DODAB), a potential candidate for applications in drug transport or DNA transfection, forms bilayer in aqueous media exhibiting a rich phase behavior. Here, we report the detailed dynamical features of DODAB bilayer in their different phases (coagel, gel and fluid) as studied by neutron scattering techniques. Elastic intensity scans show dynamical transitions at 327 K in the heating and at 311 K and 299 K during cooling cycle. These results are consistent with calorimetric studies, identified as coagel-fluid phase transition during heating, and fluid-gel and gel-coagel phase transitions during cooling. Quasielastic Neutron Scattering (QENS) data analysis showed presence of only localized internal motion in the coagel phase. However, in the gel and fluid phases, two distinct motions appear, namely lateral motion of the DODAB monomers and a faster localized internal motion of the monomers. The lateral motion of the DODAB molecule is described by a continuous diffusion model and is found to be about an order of magnitude slower in the gel phase than in the fluid phase. To gain molecular insights, molecular dynamics simulations of DODAB bilayer have also been carried out and the results are found to be in agreement with the experiment.
Genetic diversity and kelp forest vulnerability to climatic stress
Authors: Wernberg Thomas , Coleman Melinda A. , Bennett Scott , Thomsen Mads S. , Tuya Fernando , Kelaher Brendan P. 
Published: January 2018

AbstractGenetic diversity confers adaptive capacity to populations under changing conditions but its role in mediating impacts of climate change remains unresolved for most ecosystems. This lack of knowledge is particularly acute for foundation species, where impacts may cascade throughout entire ecosystems. We combined population genetics with eco-physiological and ecological field experiments to explore relationships among latitudinal patterns in genetic diversity, physiology and resilience of a kelp ecosystem to climate stress. A subsequent ‘natural experiment’ illustrated the possible influence of latitudinal patterns of genetic diversity on ecosystem vulnerability to an extreme climatic perturbation (marine heatwave). There were strong relationships between physiological versatility, ecological resilience and genetic diversity of kelp forests across latitudes, and genetic diversity consistently outperformed other explanatory variables in contributing to the response of kelp forests to the marine heatwave. Population performance and vulnerability to a severe climatic event were thus strongly related to latitudinal patterns in genetic diversity, with the heatwave extirpating forests with low genetic diversity. Where foundation species control ecological structure and function, impacts of climatic stress can cascade through the ecosystem and, consequently, genetic diversity could contribute to ecosystem vulnerability to climate change.
Integrated transcriptomic and proteomic analyses reveal potential mechanisms linking thermal stress and depressed disease resistance in the turbot Scophthalmus maximus
Authors: Yue Xin , Huan Pin , Hu Yonghua , Liu Baozhong 
Published: January 2018

AbstractA worldwide increase in the reports of diseases affecting marine organisms has paralleled the climate warming over the past few decades. In this study, we applied omics to explore the mechanisms underlying thermo-linked epizootics, by comparing both the transcriptome- and proteome-wide response of turbots to a mimic pathogen (poly I:C) between high temperature and low temperature using a time-course approach. Our results showed that myeloperoxidase (MPO) and insulin were differentially expressed transcripts shared by all five time-points post poly I:C-injection between high and low temperature and also had a consistent expression trend as differentially expressed proteins at 24 h post injection. Combined with other data, it was suggested that the elevated temperature enhanced neutrophil-mediated immunity and the resultant MPO-mediated oxidative stress, which lasted for at least 5 days. The contents of malondialdehyde and protein carbonyls, markers of oxidative damage for lipids and proteins, respectively, were compared between different temperature groups, and the results further implied the emergence of oxidative damage under high temperature. It was also suggested that metabolism disorder likely occur considering the sustained expression changes of insulin. Hence, prolonged MPO-mediated oxidative stress and metabolic disorder might be involved in the thermo-linked epizootic.
Proactive Locomotor Adjustments Are Specific to Perturbation Uncertainty in Below-Knee Prosthesis Users
Authors: Major Matthew J. , Serba Chelsi K. , Chen Xinlin , Reimold Nicholas , Ndubuisi-Obi Franklyn , Gordon Keith E. 
Published: January 2018

AbstractSensory-motor deficits associated with below-knee amputation impair reactions to external perturbations. As such, below-knee prosthesis users rely on proactive control strategies to maintain locomotor stability. However, there are trade-offs (metabolic, comfort, etc.) associated with proactive strategies. We hypothesize that because proactive control strategies are costly, prosthesis users and non-impaired participants will use a priori knowledge (timing, direction) of an impending lateral perturbation to make specific gait adaptations only when the timing of the perturbation is known and the adaptation can be temporally-limited. This hypothesis was partially supported. When the perturbation timing was predictable, only prosthesis users, and only on their impaired side, increased their lateral margin of stability during the steps immediately preceding the perturbation when perturbation direction was either unknown or known to be directed towards their impaired side. This strategy should reduce the likelihood of requiring a corrective step to maintain stability. However, neither group exhibited substantial proactive adaptations compared to baseline walking when perturbation timing was unpredictable, independent of perturbation direction knowledge. The absence of further proactive stabilization behaviors observed in prosthesis users in anticipation of a certain but temporally unpredictable perturbation may be partially responsible for impaired balance control.
Role of P2X4 Receptor in Mouse Voiding Function
Authors: Yu Weiqun , Hill Warren G. , Robson Simon C. , Zeidel Mark L. 
Published: January 2018

AbstractPurinergic signalling plays an important role in the regulation of bladder smooth muscle (BSM) contractility, and P2X4 receptor is expressed in the bladder wall, where it may act by forming heteromeric receptors with P2X1, the major purinergic force-generating muscle receptor. To test this hypothesis, we examined mouse BSM contractile properties in the absence and presence of selective P2X1 (NF449 & NF279) and P2X4 antagonists (5-BDBD). These drugs inhibited BSM purinergic contraction only partially, suggesting the possibility of a heteromeric receptor. However, carefully controlled co-immunoprecipitation experiments indicated that P2X1 and P2X4 do not form physically linked heteromers. Furthermore, immunofluorescence staining showed that P2X4 is not present in mouse BSM per se, but in an unknown cellular structure among BSM bundles. To investigate whether deletion of P2X4 could impact voiding function in vivo, P2X4 null mice were characterized. P2X4 null mice had normal bladder weight and morphology, normal voiding spot size and number by voiding spot assay, normal voiding interval, pressure and compliance by cystometrogram, and normal BSM contractility by myography. In conclusion, these data strongly suggest that P2X4 is not present in mouse BSM cells, does not affect smooth muscle contractility and that mice null for P2X4 exhibit normal voiding function.
Peach RNA viromes in six different peach cultivars
Authors: Jo Yeonhwa , Lian Sen , Chu Hyosub , Cho Jin Kyong , Yoo Su-Hyun , Choi Hoseong , Yoon Ju-Yeon , Choi Seung-Kook , Lee Bong Choon , Cho Won Kyong 
Published: January 2018

AbstractMany recent studies have demonstrated that several known and unknown viruses infect many horticultural plants. However, the elucidation of a viral population and the understanding of the genetic complexity of viral genomes in a single plant are rarely reported. Here, we conducted metatranscriptome analyses using six different peach trees representing six individual peach cultivars. We identified six viruses including five viruses in the family Betaflexiviridae and a novel virus belonging to the family Tymoviridae as well as two viroids. The number of identified viruses and viroids in each transcriptome ranged from one to six. We obtained 18 complete or nearly complete genomes for six viruses and two viroids using transcriptome data. Furthermore, we analyzed single nucleotide variations for individual viral genomes. In addition, we analyzed the amount of viral RNA and copy number for identified viruses and viroids. Some viruses or viroids were commonly present in different cultivars; however, the list of infected viruses and viroids in each cultivar was different. Taken together, our study reveals the viral population in a single peach tree and a comprehensive overview for the diversities of viral communities in different peach cultivars.
Pre-revascularization coronary wedge pressure as marker of adverse long-term left ventricular remodelling in patients with acute ST-segment elevation myocardial infarction
Authors: Marc Mãdãlin Constantin , Iancu Adrian Corneliu , Ober Camelia Diana , Homorodean Cãlin , Bãlãnescu Şerban , Sitar Adela Viviana , Bolboacã Sorana , Dregoesc Ioana Mihaela 
Published: January 2018

AbstractThe aim of this study was to investigate the relationship between coronary wedge pressure (CWP), measured as a marker of pre-procedural microvascular obstruction, and left ventricular remodelling in high-risk ST-segment elevation myocardial infarction (STEMI) patients. Pre-revascularization CWP was measured in 25 patients with high-risk anterior STEMI. Left ventricular volumes and ejection fraction were echocardiographically measured at discharge and at follow-up. A 20% increase in left ventricular volumes was used to define remodelling. Patients with CWP ≤ 38 mmHg were characterized by late ventricular remodelling. Patients with CWP > 38 mmHg developed a progressive remodelling process which was associated with a significant 60 months increase in left ventricular volumes (P = 0.01 for end-systolic volume and 0.03 for end-diastolic volume) and a significant decrease in left ventricular ejection fraction (P = 0.05). A significant increase in both left ventricular end-systolic (P = 0.009) and end-diastolic volume (P = 0.02) from baseline to 60 months follow-up was recorded in patients with extracted thrombus length ≥2 mm. Pre-revascularization elevated CWP was associated with increased left ventricular volumes and decreased ejection fraction at long-term follow-up. CWP was a predictor of severe left ventricular enlargement, besides extracted thrombus quantity.
Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients
Authors: Christensen Emil , Nordentoft Iver , Vang Søren , Birkenkamp-Demtröder Karin , Jensen Jørgen Bjerggaard , Agerbæk Mads , Pedersen Jakob Skou , Dyrskjøt Lars 
Published: January 2018

AbstractAnalysis of plasma cell-free DNA (cfDNA) may provide important information in cancer research, though the often small fraction of DNA originating from tumor cells makes the analysis technically challenging. Digital droplet PCR (ddPCR) has been utilized extensively as sufficient technical performance is easily achieved, but analysis is restricted to few mutations. Next generation sequencing (NGS) approaches have been optimized to provide comparable technical performance, especially with the introduction of unique identifiers (UIDs). However, the parameters influencing data quality when utilizing UIDs are not fully understood. In this study, we applied a targeted NGS approach to 65 plasma samples from bladder cancer patients. Laboratory and bioinformatics parameters were found to influence data quality when using UIDs. We successfully sequenced 249 unique DNA fragments on average per genomic position of interest using a 225 kb gene panel. Validation identified 24 of 38 mutations originally identified using ddPCR across several plasma samples. In addition, four mutations detected in associated tumor samples were detected using NGS, but not using ddPCR. CfDNA analysis of consecutively collected plasma samples from a bladder cancer patient indicated earlier detection of recurrence compared to radiographic imaging. The insights presented here may further the technical advancement of NGS mediated cfDNA analysis.
Human Skeletal Muscle Possesses an Epigenetic Memory of Hypertrophy
Authors: Seaborne Robert A. , Strauss Juliette , Cocks Matthew , Shepherd Sam , O’Brien Thomas D. , van Someren Ken A. , Bell Phillip G. , Murgatroyd Christopher , Morton James P. , Stewart Claire E. , Sharples Adam P. 
Published: January 2018

AbstractIt is unknown if adult human skeletal muscle has an epigenetic memory of earlier encounters with growth. We report, for the first time in humans, genome-wide DNA methylation (850,000 CpGs) and gene expression analysis after muscle hypertrophy (loading), return of muscle mass to baseline (unloading), followed by later hypertrophy (reloading). We discovered increased frequency of hypomethylation across the genome after reloading (18,816 CpGs) versus earlier loading (9,153 CpG sites). We also identified AXIN1, GRIK2, CAMK4, TRAF1 as hypomethylated genes with enhanced expression after loading that maintained their hypomethylated status even during unloading where muscle mass returned to control levels, indicating a memory of these genes methylation signatures following earlier hypertrophy. Further, UBR5, RPL35a, HEG1, PLA2G16, SETD3 displayed hypomethylation and enhanced gene expression following loading, and demonstrated the largest increases in hypomethylation, gene expression and muscle mass after later reloading, indicating an epigenetic memory in these genes. Finally, genes; GRIK2, TRAF1, BICC1, STAG1 were epigenetically sensitive to acute exercise demonstrating hypomethylation after a single bout of resistance exercise that was maintained 22 weeks later with the largest increase in gene expression and muscle mass after reloading. Overall, we identify an important epigenetic role for a number of largely unstudied genes in muscle hypertrophy/memory.