bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-density Mapping Guided Pulmonary Vein Isolation for Treatment of Atrial Fibrillation - Two-year clinical outcome of a single center experience
Authors: Siebermair J. , Neumann B. , Risch F. , Riesinger L. , Vonderlin N. , Koehler M. , Lackermaier K. , Fichtner S. , Rizas K. , Sattler S. M. , Sinner M. F. , Kääb S. , Estner H. L. , Wakili R. 
Published: June 2019

AbstractPulmonary vein isolation (PVI) as interventional treatment for atrial fibrillation (AF) aims to eliminate arrhythmogenic triggers from the PVs. Improved signal detection facilitating a more robust electrical isolation might be associated with a better outcome. This retrospective cohort study compared PVI procedures using a novel high-density mapping system (HDM) with improved signal detection vs. age- and sex-matched PVIs using a conventional 3D mapping system (COM). Endpoints comprised freedom from AF and procedural parameters. In total, 108 patients (mean age 63.9 ± 11.2 years, 56.5% male, 50.9% paroxysmal AF) were included (n = 54 patients/group). Our analysis revealed that HDM was not superior regarding freedom from AF (mean follow-up of 494.7 ± 26.2 days), with one- and two-year AF recurrence rates of 38.9%/46.5% (HDM) and 38.9%/42.2% (COM), respectively. HDM was associated with reduction in fluoroscopy times (18.8 ± 10.6 vs. 29.8 ± 13.4 min; p < 0.01) and total radiation dose (866.0 ± 1003.3 vs. 1731.2 ± 1978.4 cGy; p < 0.01) compared to the COM group. HDM was equivalent but not superior to COM with respect to clinical outcome after PVI and resulted in reduced fluoroscopy time and radiation exposure. These results suggest that HDM-guided PVI is effective and safe for AF ablation. Potential benefits in comparison to conventional mapping systems, e.g. arrhythmia recurrence rates, have to be addressed in randomized trials.
Eukaryotic and cyanobacterial communities associated with marine snow particles in the oligotrophic Sargasso Sea
Authors: Lundgreen Regitze B. C. , Jaspers Cornelia , Traving Sachia J. , Ayala Daniel J. , Lombard Fabien , Grossart Hans-Peter , Nielsen Torkel G. , Munk Peter , Riemann Lasse 
Published: June 2019

AbstractMarine snow aggregates represent heterogeneous agglomerates of dead and living organic matter. Composition is decisive for their sinking rates, and thereby for carbon flux to the deep sea. For oligotrophic oceans, information on aggregate composition is particularly sparse. To address this, the taxonomic composition of aggregates collected from the subtropical and oligotrophic Sargasso Sea (Atlantic Ocean) was characterized by 16S and 18S rRNA gene sequencing. Taxonomy assignment was aided by a collection of the contemporary plankton community consisting of 75 morphologically and genetically identified plankton specimens. The diverse rRNA gene reads of marine snow aggregates, not considering Trichodesmium puffs, were dominated by copepods (52%), cnidarians (21%), radiolarians (11%), and alveolates (8%), with sporadic contributions by cyanobacteria, suggesting a different aggregate composition than in eutrophic regions. Composition linked significantly with sampling location but not to any measured environmental parameters or plankton biomass composition. Nevertheless, indicator and network analyses identified key roles of a few rare taxa. This points to complex regulation of aggregate composition, conceivably affected by the environment and plankton characteristics. The extent to which this has implications for particle densities, and consequently for sinking rates and carbon sequestration in oligotrophic waters, needs further interrogation.
Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods
Authors: Drozdova Polina , Bedulina Daria , Madyarova Ekaterina , Rivarola-Duarte Lorena , Schreiber Stephan , Stadler Peter F. , Luckenbach Till , Timofeyev Maxim 
Published: June 2019

AbstractHeat shock proteins/cognates 70 are chaperones essential for proper protein folding. This protein family comprises inducible members (Hsp70s) with expression triggered by the increased concentration of misfolded proteins due to protein-destabilizing conditions, as well as constitutively expressed cognate members (Hsc70s). Previous works on non-model amphipod species Eulimnogammarus verrucosus and Eulimnogammarus cyaneus, both endemic to Lake Baikal in Eastern Siberia, have only revealed a constitutively expressed form, expression of which was moderately further induced by protein-destabilizing conditions. Here we describe heat-inducible hsp70s in these species. Contrary to the common approach of using sequence similarity with hsp/hsc70 of a wide spectrum of organisms and some characteristic features, such as absence of introns within genes and presence of heat shock elements in their promoter areas, the present study is based on next-generation sequencing for the studied or related species followed by differential expression analysis, quantitative PCR validation and detailed investigation of the predicted polypeptide sequences. This approach allowed us to describe a novel type of hsp70 transcripts that overexpress in response to heat shock. Moreover, we propose diagnostic sequence features of this Hsp70 type for amphipods. Phylogenetic comparisons with different types of Hsp/Hsc70s allowed us to suggest that the hsp/hsc70 gene family in Amphipoda diversified into cognate and heat-inducible paralogs independently from other crustaceans. Thus, the cognate and inducible hsp70 types in distant taxa may not be recognized by sequence similarity.
Evaluation of six blood-based age prediction models using DNA methylation analysis by pyrosequencing
Authors: Daunay Antoine , Baudrin Laura G. , Deleuze Jean-François , How-Kit Alexandre 
Published: June 2019

AbstractDNA methylation has been identified as the most promising molecular biomarker for the prediction of age. Several DNA methylation-based models have been proposed for age prediction based on blood samples, using mainly pyrosequencing. These methods present different performances for age prediction and have rarely, if ever, been evaluated and intercompared in an independent validation study. Here, for the first time, we evaluate and compare six blood-based age prediction models (Bekaert1, Park2, Thong3, Weidner4, and the Zbiec-Piekarska 15 and Zbiec-Piekarska 26), using DNA methylation analysis by pyrosequencing on 100 blood samples from French individuals aged between 19–65 years. For each model, we perform correlation analysis and evaluate age-prediction performance (mean absolute deviation (MAD) and standard error of the estimate (SEE)). The best age-prediction performances were found with the Bekaert and Thong models (MAD of 4.5–5.2, SEE of 6.8–7.2), followed by the Zbiec-Piekarska 1 model (MAD of 6.8 and SEE of 9.2), while the Park, Weidner and Zbiec-Piekarska 2 models presented lower performances (MAD of 7.2–8.7 and SEE of 9.2–10.3). Given these results, we recommend performing systematic, independent evaluation of all age prediction models on a same cohort to validate the different models and compare their performance.
A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells
Authors: Nguyen Chi D. L. , Malchow Sebastian , Reich Stefan , Steltgens Sascha , Shuvaev Konstantin V. , Loroch Stefan , Lorenz Christin , Sickmann Albert , Knobbe-Thomsen Christiane B. , Tews Björn , Medenbach Jan , Ahrends Robert 
Published: June 2019

AbstractMany cellular events are driven by changes in protein expression, measurable by mass spectrometry or antibody-based assays. However, using conventional technology, the analysis of transcription factor or membrane receptor expression is often limited by an insufficient sensitivity and specificity. To overcome this limitation, we have developed a high-resolution targeted proteomics strategy, which allows quantification down to the lower attomol range in a straightforward way without any prior enrichment or fractionation approaches. The method applies isotope-labeled peptide standards for quantification of the protein of interest. As proof of principle, we applied the improved workflow to proteins of the unfolded protein response (UPR), a signaling pathway of great clinical importance, and could for the first time detect and quantify all major UPR receptors, transducers and effectors that are not readily detectable via antibody-based-, SRM- or conventional PRM assays. As transcription and translation is central to the regulation of UPR, quantification and determination of protein copy numbers in the cell is important for our understanding of the signaling process as well as how pharmacologic modulation of these pathways impacts on the signaling. These questions can be answered using our newly established workflow as exemplified in an experiment using UPR perturbation in a glioblastoma cell lines.
Truels and strategies for survival
Authors: Dorraki Mohsen , Allison Andrew , Abbott Derek 
Published: June 2019

AbstractThe truel is a three person competition that generalises the classic duel. In this game three players try to eliminate each other in a series of one-to-one duels until there is only one survivor. The players’ marksmanship, shooting order and strategies for choosing a target play a significant role in individual’s survival probability. Strategies such as shooting into the air (abstention), shooting at the strongest opponent, and shooting at the weakest opponent have been analysed in the previous literature. In this paper, for the first time, we consider suicidal and random strategies that can be chosen by the weaker player. We show that although there is no possible highest probability region for weakest player adopting suicidal strategy, the player may increase the survival probability via switching between suicidal and abstention strategies randomly. In addition, we demonstrate that there is a narrow survival area for the weakest player when the player aims randomly at two other opponents, and eventually the area fades away if the player fires randomly at himself or the other two opponents.
The 2017–19 activity at Mount Agung in Bali (Indonesia): Intense unrest, monitoring, crisis response, evacuation, and eruption
Authors: Syahbana D. K. , Kasbani K. , Suantika G. , Prambada O. , Andreas A. S. , Saing U. B. , Kunrat S. L. , Andreastuti S. , Martanto M. , Kriswati E. , Suparman Y. , Humaida H. , Ogburn S. , Kelly P. J. , Wellik J. , Wright H. M. N. , Pesicek J. D. , Wessels R. , Kern C. , Lisowski M. , Diefenbach A. , Poland M. , Beauducel F. , Pallister J. , Vaughan R. G. , Lowenstern J. B. 
Published: June 2019

AbstractAfter 53 years of quiescence, Mount Agung awoke in August 2017, with intense seismicity, measurable ground deformation, and thermal anomalies in the summit crater. Although the seismic unrest peaked in late September and early October, the volcano did not start erupting until 21 November. The most intense explosive eruptions with accompanying rapid lava effusion occurred between 25 and 29 November. Smaller infrequent explosions and extrusions continue through the present (June 2019). The delay between intense unrest and eruption caused considerable challenges to emergency responders, local and national governmental agencies, and the population of Bali near the volcano, including over 140,000 evacuees. This paper provides an overview of the volcanic activity at Mount Agung from the viewpoint of the volcano observatory and other scientists responding to the volcanic crisis. We discuss the volcanic activity as well as key data streams used to track it. We provide evidence that magma intruded into the mid-crust in early 2017, and again in August of that year, prior to intrusion of an inferred dike between Mount Agung and Batur Caldera that initiated an earthquake swarm in late September. We summarize efforts to forecast the behavior of the volcano, to quantify exclusion zones for evacuations, and to work with emergency responders and other government agencies to make decisions during a complex and tense volcanic crisis.
A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance
Authors: Taylor Tracy , Lee Emma R. , Nykoluk Mikaela , Enns Eric , Liang Binhua , Capina Rupert , Gauthier Marie-Krystel , Domselaar Gary Van , Sandstrom Paul , Brooks James , Ji Hezhao 
Published: June 2019

AbstractConventional HIV drug resistance (HIVDR) genotyping utilizes Sanger sequencing (SS) methods, which are limited by low data throughput and the inability of detecting low abundant drug resistant variants (LADRVs). Here we present a next generation sequencing (NGS)-based HIVDR typing platform that leverages the advantages of Illumina MiSeq and HyDRA Web. The platform consists of a fully validated sample processing protocol and HyDRA web, an open web portal that allows automated customizable NGS-based HIVDR data processing. This platform was characterized and validated using a panel of HIV-spiked plasma representing all major HIV-1 subtypes, pedigreed plasmids, HIVDR proficiency specimens and clinical specimens. All examined major HIV-1 subtypes were consistently amplified at viral loads of ≥1,000 copies/ml. The gross error rate of this platform was determined at 0.21%, and minor variations were reliably detected down to 0.50% in plasmid mixtures. All HIVDR mutations identifiable by SS were detected by the MiSeq-HyDRA protocol, while LADRVs at frequencies of 1~15% were detected by MiSeq-HyDRA only. As compared to SS approaches, the MiSeq-HyDRA platform has several notable advantages including reduced cost and labour, and increased sensitivity for LADRVs, making it suitable for routine HIVDR monitoring for both patient care and surveillance purposes.
Inducible knockout of CHUK/IKKα in adult chondrocytes reduces progression of cartilage degradation in a surgical model of osteoarthritis
Authors: Culley Kirsty L. , Lessard Samantha G. , Green Jordan D. , Quinn Justin , Chang Jun , Khilnani Tyler , Wondimu Elisabeth B. , Dragomir Cecilia L. , Marcu Kenneth B. , Goldring Mary B. , Otero Miguel 
Published: June 2019

AbstractCHUK/IKKα contributes to collagenase-driven extracellular matrix remodeling and chondrocyte hypertrophic differentiation in vitro, in a kinase-independent manner. These processes contribute to osteoarthritis (OA), where chondrocytes experience a phenotypic shift towards hypertrophy concomitant with abnormal matrix remodeling. Here we investigated the contribution of IKKα to OA in vivo. To this end, we induced specific IKKα knockout in adult chondrocytes in AcanCreERT2/+; IKKαf/f mice treated with tamoxifen (cKO). Vehicle-treated littermates were used as wild type controls (WT). At 12 weeks of age, WT and cKO mice were subjected to the destabilization of medial meniscus (DMM) model of post-traumatic OA. The cKO mice showed reduced cartilage degradation and collagenase activity and fewer hypertrophy-like features at 12 weeks after DMM. Interestingly, in spite of the protection from structural articular cartilage damage, the postnatal growth plates of IKKα cKO mice after DMM displayed abnormal architecture and composition associated with increased chondrocyte apoptosis, which were not as evident in the articular chondrocytes of the same animals. Together, our results provide evidence of a novel in vivo functional role for IKKα in cartilage degradation in post-traumatic OA, and also suggest intrinsic, cell-autonomous effects of IKKα in chondrocytes that control chondrocyte phenotype and impact on cell survival, matrix homeostasis, and remodeling.
Direct visualization of charge transport in suspended (or free-standing) DNA strands by low-energy electron microscopy
Authors: Latychevskaia Tatiana , Escher Conrad , Andregg William , Andregg Michael , Fink Hans-Werner 
Published: June 2019

AbstractLow-energy electrons offer a unique possibility for long exposure imaging of individual biomolecules without significant radiation damage. In addition, low-energy electrons exhibit high sensitivity to local potentials and thus can be employed for imaging charges as small as a fraction of one elementary charge. The combination of these properties makes low-energy electrons an exciting tool for imaging charge transport in individual biomolecules. Here we demonstrate the imaging of individual deoxyribonucleic acid (DNA) molecules at the resolution of about 1 nm with simultaneous imaging of the charging of the DNA molecules that is of the order of less than one elementary charge per nanometer. The cross-correlation analysis performed on different sections of the DNA network reveals that the charge redistribution between the two regions is correlated. Thus, low-energy electron microscopy is capable to provide simultaneous imaging of macromolecular structure and its charge distribution which can be beneficial for imaging and constructing nano-bio-sensors.
Adaptive adipose tissue stromal plasticity in response to cold stress and antibody-based metabolic therapy
Authors: Chang Joshua C. , Durinck Steffen , Chen Mark Z. , Martinez-Martin Nadia , Zhang Jingli A. , Lehoux Isabelle , Li Hong , Lin May , Wu Jiansheng , Bainbridge Travis W. , Ernst James A. , Ramani Sree R. , Paduchuri Sairupa , Kates Lance , Solon Margaret , Buechler Matthew B. , Castiglioni Alessandra , Thai Minh , Breart Beatrice , Modrusan Zora , Peterson Andrew S. , Turley Shannon J. , Sonoda Junichiro 
Published: June 2019

AbstractIn response to environmental and nutrient stress, adipose tissues must establish a new homeostatic state. Here we show that cold exposure of obese mice triggers an adaptive tissue remodeling in visceral adipose tissue (VAT) that involves extracellular matrix deposition, angiogenesis, sympathetic innervation, and adipose tissue browning. Obese VAT is predominated by pro-inflammatory M1 macrophages; cold exposure induces an M1-to-M2 shift in macrophage composition and dramatic changes in macrophage gene expression in both M1 and M2 macrophages. Antibody-mediated CSF1R blocking prevented the cold-induced recruitment of adipose tissue M2 macrophages, suggesting the role of CSF1R signaling in the process. These cold-induced effects in obese VAT are phenocopied by an administration of the FGF21-mimetic antibody, consistent with its action to stimulate sympathetic nerves. Collectively, these studies illuminate adaptive visceral adipose tissue plasticity in obese mice in response to cold stress and antibody-based metabolic therapy.
Verification of mathematical models of response threshold through statistical characterisation of the foraging activity in ant societies
Authors: Yamanaka Osamu , Shiraishi Masashi , Awazu Akinori , Nishimori Hiraku 
Published: June 2019

AbstractThe concept of response threshold (RT) has been developed to explain task allocation in social insect colonies, wherein individual workers engage in tasks depending on their responsiveness to the task-related stimulus. Moreover, a mathematical model of RT has been proposed to explain data obtained from task allocation experiments; however, its applicability range warrants clarification through adequate quantitative analysis. Hence, we used an automatic measuring system to count passage events between a nest chamber and a foraging arena in five colonies of ants, Camponotus japonicus. The events were measured using radio-frequency identification tags attached to all workers of each colony. Here, we examined the detailed forms of i) labour distribution during foraging among workers in each colony and ii) the persistence of rank-order of foraging among workers. We found that labour distribution was characterized by a generalized gamma-distribution, indicating that only few workers carried out a large part of the workload. The rank-order of foraging activity among workers in each colony was maintained for a month and collapsed within a few months. We compared the obtained data with testable predictions of the RT model. The comparison indicated that proper evaluation of the mathematical model is required based on the obtained data.
Gene knockout analysis reveals essentiality of estrogen receptor β1 (Esr2a) for female reproduction in medaka
Authors: Kayo Daichi , Zempo Buntaro , Tomihara Soma , Oka Yoshitaka , Kanda Shinji 
Published: June 2019

AbstractIn vertebrates, sex steroids play crucial roles in multiple systems related to reproduction. In females, estrogens and their receptor estrogen receptor (ER or Esr) play indispensable roles in the negative sex steroid feedback regulation of pituitary gonadotropin secretion, which prevents excessive development of ovarian follicles. However, the mechanism of this feedback regulation of a gonadotropin, follicle stimulating hormone (FSH), which is essential for folliculogenesis throughout vertebrates, is poorly understood. In the present study, we generated knockouts of all subtypes of nuclear estrogen receptors in a model teleost medaka, which is suitable for the study of endocrine control and behavioral assays, and analyzed fertility, behavior and functionality of estrogen feedback in each knockout line. Among the estrogen receptors, we revealed that an estrogen receptor Esr2a plays an essential role in this feedback regulation. In addition to this, we also found that esr2a−/− females showed oviduct atresia, which causes complete infertility. Interestingly, esr2a−/− females showed apparently normal sexual behavior but without oviposition in response to male courtship. This phenotype indicates that physical readiness and motivation of sexual behavior is independently controlled.
On the Relationship between MRI and Local Field Potential Measurements of Spatial and Temporal Variations in Functional Connectivity
Authors: Shi Zhaoyue , Wilkes Don M. , Yang Pai-Feng , Wang Feng , Wu Ruiqi , Wu Tung-Lin , Chen Li Min , Gore John C. 
Published: June 2019

AbstractCorrelations between fluctuations in resting state BOLD fMRI signals are interpreted as measures of functional connectivity (FC), but the neural basis of their origins and their relationships to specific features of underlying electrophysiologic activity, have not been fully established. In particular, the dependence of FC metrics on different frequency bands of local field potentials (LFPs), and the relationship of dynamic changes in BOLD FC to underlying temporal variations of LFP correlations, are not known. We compared the spatial profiles of resting state coherences of different frequency bands of LFP signals, with high resolution resting state BOLD FC measurements. We also compared the probability distributions of temporal variations of connectivity in both modalities using a Markov chain model-based approach. We analyzed data obtained from the primary somatosensory (S1) cortex of monkeys. We found that in areas 3b and 1 of S1 cortex, low frequency LFP signal fluctuations were the main contributions to resting state LFP coherence. Additionally, the dynamic changes of BOLD FC behaved most similarly to the LFP low frequency signal coherence. These results indicate that, within the S1 cortex meso-scale circuit studied, resting state FC measures from BOLD fMRI mainly reflect contributions from low frequency LFP signals and their dynamic changes.