bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical symptoms and related risk factors in pulmonary embolism patients and cluster analysis based on these symptoms
Authors: Ji Qiao-ying , Wang Mao-feng , Su Cai-min , Yang Qiong-fang , Feng Lan-fang , Zhao Lan-yan , Fang Shuang-yan , Zhao Fen-hua , Li Wei-min 
Published: October 2017

AbstractPulmonary embolism (PE) remains largely underdiagnosed due to nonspecific symptoms. This study aims to evaluate typical symptoms of PE patients, their related predictors, and to differentiate typical clusters of patients and principal components of PE symptoms. Clinical data from a total of 551 PE patients between January 2012 and April 2016 were retrospectively reviewed. PE was diagnosed according to the European Society of Cardiology Guidelines. Logistic regression models, system clustering method, and principal component analysis were used to identify potential risk factors, different clusters of the patients, and principal components of PE symptoms. The most common symptoms of PE were dyspnea, cough, and tachypnea in more than 60% of patients. Some combined chronic conditions, laboratory and clinical indicators were found to be related to these clinical symptoms. Our study also suggested that PE is associated with a broad list of symptoms and some PE patients might share similar symptoms, and some PE symptoms were usually cooccurrence. Based on ten symptoms generated from our sample, we classified the patients into five clusters which represent five groups of PE patients during clinical practice, and identified four principal components of PE symptoms. These findings will improve our understanding of clinical symptoms and their potential combinations which are helpful for clinical diagnosis of PE.
Structural Insight into Inhibition of CsrA-RNA Interaction Revealed by Docking, Molecular Dynamics and Free Energy Calculations
Authors: Ren Xiaodong , Zeng Rui , Tortorella Micky , Wang Jinming , Wang Changwei 
Published: October 2017

AbstractThe carbon storage regulator A (CsrA) and its homologs play an important role in coordinating the expression of bacterial virulence factors required for successful host infection. In addition, bacterial pathogens with deficiency of CsrA are typically attenuated for virulence. In 2016, the first series of small-molecule inhibitors of CsrA-RNA interaction were identified, which were found to achieve the CsrA-RNA inhibition by binding to the CsrA, without interfering with the RNA. However, the binding mechanism of these inhibitors of CsrA is not known. Herein, we applied molecular docking, molecular dynamics and binding free energy calculations to investigate the binding mode of inhibitors to CsrA. We found that the G11(RNA)-binding site is the most important binding site for CsrA inhibitors. An inhibitor with the proper size range can bind to that site and form a stable complex. We also found that inhibitors with larger size ranges bind to the entire CsrA-RNA interface, but have loose binding. However, this loose binding still resulted in inhibitory activity. The calculated binding free energy from MM/GBSA has a good correlation with the derived experimental binding energy, which might be used as a tool to further select CsrA inhibitors after a first-round of high-throughput virtual screening.
Dynamics of coral-associated bacterial communities acclimated to temperature stress based on recent thermal history
Authors: Shiu Jia-Ho , Keshavmurthy Shashank , Chiang Pei-Wen , Chen Hsing-Ju , Lou Shueh-Ping , Tseng Ching-Hung , Justin Hsieh Hernyi , Allen Chen Chaolun , Tang Sen-Lin 
Published: October 2017

AbstractSeasonal variation in temperature fluctuations may provide corals and their algal symbionts varying abilities to acclimate to changing temperatures. We hypothesized that different temperature ranges between seasons may promote temperature-tolerance of corals, which would increase stability of a bacterial community following thermal stress. Acropora muricata coral colonies were collected in summer and winter (water temperatures were 23.4–30.2 and 12.1–23.1 °C, respectively) from the Penghu Archipelago in Taiwan, then exposed to 6 temperature treatments (10–33 °C). Changes in coral-associated bacteria were determined after 12, 24, and 48 h. Based on 16S rRNA gene amplicons and Illumina sequencing, bacterial communities differed between seasons and treatments altered the dominant bacteria. Cold stress caused slower shifts in the bacterial community in winter than in summer, whereas a more rapid shift occurred under heat stress in both seasons. Results supported our hypothesis that bacterial community composition of corals in winter are more stable in cold temperatures but changed rapidly in hot temperatures, with opposite results for the bacterial communities in summer. We infer that the thermal tolerance ranges of coral-associated bacteria, with a stable community composition, are associated with their short-term (3 mo) seawater thermal history. Therefore, seasonal acclimation may increase tolerance of coral-associated bacteria to temperature fluctuations.
High-Mobility and High-Optical Quality Atomically Thin WS
2
Authors: Reale Francesco , Palczynski Pawel , Amit Iddo , Jones Gareth F. , Mehew Jake D. , Bacon Agnes , Ni Na , Sherrell Peter C. , Agnoli Stefano , Craciun Monica F. , Russo Saverio , Mattevi Cecilia 
Published: October 2017

AbstractThe rise of atomically thin materials has the potential to enable a paradigm shift in modern technologies by introducing multi-functional materials in the semiconductor industry. To date the growth of high quality atomically thin semiconductors (e.g. WS2) is one of the most pressing challenges to unleash the potential of these materials and the growth of mono- or bi-layers with high crystal quality is yet to see its full realization. Here, we show that the novel use of molecular precursors in the controlled synthesis of mono- and bi-layer WS2 leads to superior material quality compared to the widely used direct sulfidization of WO3-based precursors. Record high room temperature charge carrier mobility up to 52 cm2/Vs and ultra-sharp photoluminescence linewidth of just 36 meV over submillimeter areas demonstrate that the quality of this material supersedes also that of naturally occurring materials. By exploiting surface diffusion kinetics of W and S species adsorbed onto a substrate, a deterministic layer thickness control has also been achieved promoting the design of scalable synthesis routes.
Fragment-based screening identifies novel targets for inhibitors of conjugative transfer of antimicrobial resistance by plasmid pKM101
Authors: Casu Bastien , Arya Tarun , Bessette Benoit , Baron Christian 
Published: October 2017

AbstractThe increasing frequency of antimicrobial resistance is a problem of global importance. Novel strategies are urgently needed to understand and inhibit antimicrobial resistance gene transmission that is mechanistically related to bacterial virulence functions. The conjugative transfer of plasmids by type IV secretion systems is a major contributor to antimicrobial resistance gene transfer. Here, we present a structure-based strategy to identify inhibitors of type IV secretion system-mediated bacterial conjugation. Using differential scanning fluorimetry we screened a fragment library and identified molecules that bind the essential TraE protein of the plasmid pKM101 conjugation machinery. Co-crystallization revealed that fragments bind two alternative sites of the protein and one of them is a novel inhibitor binding site. Based on the structural information on fragment binding we designed novel small molecules that have improved binding affinity. These molecules inhibit the dimerization of TraE, bind to both inhibitor binding sites on TraE and inhibit the conjugative transfer of plasmid pKM101. The strategy presented here is generally applicable for the structure-based design of inhibitors of antimicrobial resistance gene transfer and of bacterial virulence.
TDP-43 accelerates age-dependent degeneration of interneurons
Authors: Tsuiji Hitomi , Inoue Ikuyo , Takeuchi Mari , Furuya Asako , Yamakage Yuko , Watanabe Seiji , Koike Masato , Hattori Mitsuharu , Yamanaka Koji 
Published: October 2017

AbstractTDP-43 is an RNA-binding protein important for many aspects of RNA metabolism. Abnormal accumulation of TDP-43 in the cytoplasm of affected neurons is a pathological hallmark of the neurodegenerative diseases frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Several transgenic mouse models have been generated that recapitulate defects in TDP-43 accumulation, thus causing neurodegeneration and behavioural impairments. While aging is the key risk factor for neurodegenerative diseases, the specific effect of aging on phenotypes in TDP-43 transgenic mice has not been investigated. Here, we analyse age-dependent changes in TDP-43 transgenic mice that displayed impaired memory. We found the accumulation of abundant poly-ubiquitinated protein aggregates in the hippocampus of aged TDP-43 transgenic mice. Intriguingly, the aggregates contained some interneuron-specific proteins such as parvalbumin and calretinin, suggesting that GABAergic interneurons were degenerated in these mice. The abundance of aggregates significantly increased with age and with the overexpression of TDP-43. Gene array analyses in the hippocampus and other brain areas revealed dysregulation in genes linked to oxidative stress and neuronal function in TDP-43 transgenic mice. Our results indicate that the interneuron degeneration occurs upon aging, and TDP-43 accelerates age-dependent neuronal degeneration, which may be related to the impaired memory of TDP-43 transgenic mice.
Marked bias towards spontaneous synaptic inhibition distinguishes non-adapting from adapting layer 5 pyramidal neurons in the barrel cortex
Authors: Popescu Ion R. , Le Kathy Q. , Palenzuela Rocío , Voglewede Rebecca , Mostany Ricardo 
Published: October 2017

AbstractPyramidal neuron subtypes differ in intrinsic electrophysiology properties and dendritic morphology. However, do different pyramidal neuron subtypes also receive synaptic inputs that are dissimilar in frequency and in excitation/inhibition balance? Unsupervised clustering of three intrinsic parameters that vary by cell subtype – the slow afterhyperpolarization, the sag, and the spike frequency adaptation – split layer 5 barrel cortex pyramidal neurons into two clusters: one of adapting cells and one of non-adapting cells, corresponding to previously described thin- and thick-tufted pyramidal neurons, respectively. Non-adapting neurons presented frequencies of spontaneous inhibitory postsynaptic currents (sIPSCs) and spontaneous excitatory postsynaptic currents (sEPSCs) three- and two-fold higher, respectively, than those of adapting neurons. The IPSC difference between pyramidal subtypes was activity independent. A subset of neurons were thy1-GFP positive, presented characteristics of non-adapting pyramidal neurons, and also had higher IPSC and EPSC frequencies than adapting neurons. The sEPSC/sIPSC frequency ratio was higher in adapting than in non-adapting cells, suggesting a higher excitatory drive in adapting neurons. Therefore, our study on spontaneous synaptic inputs suggests a different extent of synaptic information processing in adapting and non-adapting barrel cortex neurons, and that eventual deficits in inhibition may have differential effects on the excitation/inhibition balance in adapting and non-adapting neurons.
MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation
Authors: Iquebal M. A. , Jaiswal Sarika , Mahato Ajay Kumar , Jayaswal Pawan K. , Angadi U. B. , Kumar Neeraj , Sharma Nimisha , Singh Anand K. , Srivastav Manish , Prakash Jai , Singh S. K. , Khan Kasim , Mishra Rupesh K. , Rajan Shailendra , Bajpai Anju , Sandhya B. S. , Nischita Puttaraju , Ravishankar K. V. , Dinesh M. R. , Rai Anil , Kumar Dinesh , Sharma Tilak R. , Singh Nagendra K. 
Published: October 2017

AbstractMango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world’s first web-based genomic resources for genetic improvement and germplasm management of mango.
Quality of medical therapy in heart failure patients undergoing elective revascularisation: A protective effect of disease modifying therapy at discharge
Authors: Wurm Raphael , Huelsmann Martin , Hienert Marius , Seidl Veronika , Wiedemann Dominik , Laufer Guenther , Kocher Alfred , Adlbrecht Christopher , Andreas Martin 
Published: October 2017

AbstractThe STICH(-ES) trial showed that coronary artery bypass grafting was superior to medical therapy alone in treating ischemic heart failure. However, dosages of disease modifying drugs were not reported. We included 128 (84% male, mean age 66 ± 11 years) consecutive patients with ischemic heart failure and an ejection fraction ≤35% undergoing isolated elective coronary artery bypass grafting. We defined optimal medical therapy (OMT) as prescription of ≥50% dosages of guideline recommended medications (i.e. beta-blocker (BB) and renin angiotensin system (RAS) antagonist) plus prescription of a mineralocorticoid receptor antagonist (MRA). The mean logistic EuroSCORE was 12.3 ± 13.8%. The five year survival was 74%. At discharge, 111 patients (87%) were on a BB and 106 (83%) were on a RAS antagonist. Forty-nine patients (38%) received an MRA. Only 8 patients (6%) received OMT. A Cox regression analysis revealed EuroSCORE (p < 0.001) and the use of MRA (p = 0.003) and BB (p = 0.037) at discharge as significant predictors of 5 year survival. Prescription rates of heart failure medication are comparable to those reported in the STICH trial, but rates of OMT are very low at admission and discharge. Prescription of BB and MRA was associated with improved survival, highlighting the need for disease management programs and rigorous discharge management.
A damping circadian clock drives weak oscillations in metabolism and locomotor activity of aphids (Acyrthosiphon pisum)
Authors: Beer Katharina , Joschinski Jens , Arrazola Sastre Alazne , Krauss Jochen , Helfrich-Förster Charlotte 
Published: October 2017

AbstractTiming seasonal events, like reproduction or diapause, is crucial for the survival of many species. Global change causes phenologies worldwide to shift, which requires a mechanistic explanation of seasonal time measurement. Day length (photoperiod) is a reliable indicator of winter arrival, but it remains unclear how exactly species measure day length. A reference for time of day could be provided by a circadian clock, by an hourglass clock, or, as some newer models suggest, by a damped circadian clock. However, damping of clock outputs has so far been rarely observed. To study putative clock outputs ofAcyrthosiphon pisumaphids, we raised individual nymphs on coloured artificial diet, and measured rhythms in metabolic activity in light-dark illumination cycles of 16:08 hours (LD) and constant conditions (DD). In addition, we kept individuals in a novel monitoring setup and measured locomotor activity. We found thatA.pisumis day-active in LD, potentially with a bimodal distribution. In constant darkness rhythmicity of locomotor behaviour persisted in some individuals, but patterns were mostly complex with several predominant periods. Metabolic activity, on the other hand, damped quickly. A damped circadian clock, potentially driven by multiple oscillator populations, is the most likely explanation of our results.
Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration
Authors: Huang Xiaochang , Fang Shaoming , Yang Hui , Gao Jun , He Maozhang , Ke Shanlin , Zhao Yuanzhang , Chen Congying , Huang Lusheng 
Published: October 2017

AbstractSerum glucose and lipids are important indicators for host metabolic condition. Interaction of host and gut microbes regulates the metabolism process. However, how much the gut microbiome contributes to the variance of serum glucose and lipids is largely unknown. Here we carried out a 16S rRNA gene based association study between cecum microbiome and the concentration of serum glucose and lipids in 240 Chinese Erhualian pigs. We identified tens of bacterial taxa associated with serum glucose and lipids. The butyrate-producing bacteria were significantly associated with serum glucose level. The pathogenic bacteria belonging to Proteobacteria and Fusobacteria showed significant associations with increased serum lipid levels, while the bacteria Lactobacillus and Bacilli had negative correlations with serum lipids. Cross-validation analysis revealed that 23.8% variation of serum glucose and 1.6%~6.0% variations of serum lipids were explained by gut microbiome. Furthermore, predicted function capacities related to nutrition intake, transport and carbohydrate metabolism were significantly associated with serum glucose level, while the pathways related to antioxidant metabolism and bile synthesis tended to be associated with serum lipid level. The results provide meaningful information to get insight into the effect of gut microbiome on serum glucose and lipid levels in pigs.
Antibody PEGylation in bioorthogonal pretargeting with trans-cyclooctene/tetrazine cycloaddition: in vitro and in vivo evaluation in colorectal cancer models
Authors: Rondon Aurélie , Ty Nancy , Bequignat Jean-Baptiste , Quintana Mercedes , Briat Arnaud , Witkowski Tiffany , Bouchon Bernadette , Boucheix Claude , Miot-Noirault Elisabeth , Pouget Jean-Pierre , Chezal Jean-Michel , Navarro-Teulon Isabelle , Moreau Emmanuel , Degoul Françoise 
Published: October 2017

AbstractBioorthogonal chemistry represents a challenging approach in pretargeted radioimmunotherapy (PRIT). We focus here on mAb modifications by grafting an increase amount of trans-cyclooctene (TCO) derivatives (0 to 30 equivalents with respect to mAb) bearing different polyethylene glycol (PEG) linkers between mAb and TCO (i.e. PEG0 (1), PEG4 (2) and PEG12 (3)) and assessing their functionality. We used colorectal xenograft (HT29/Ts29.2) and peritoneal carcinomatosis (A431-CEA-Luc/35A7) as tumor cells/mAbs models and fluorescent tetrazines (TZ). MALDI-TOF MS shows that grafting with 2,3 increases significantly the number of TCO per mAb compared with no PEG. In vitro immunofluorescence showed that Ts29.2 and 35A7 labeling intensity is correlated with the number of TCO when using 1,3 while signals reach a maximum at 10 equivalents when using 2. Under 10 equivalents conditions, the capacity of resulting mAbs-1–3 for antigen recognition is similar when reported per grafted TCO and comparable to mAbs without TCO. In vivo, on both models, pretargeting with mAbs-2,3 followed by TZ injection induced a fluorescent signal two times lower than with mAbs-1. These findings suggest that while PEG linkers allow a better accessibility for TCO grafting, it might decrease the number of reactive TCO. In conclusion, mAb-1 represents the best candidate for PRIT.
Anatomy of the external branch of the superior laryngeal nerve in Asian population
Authors: Cha Yong Hoon , Moon Seo-Young , Jehoon O. , Tansatit Tanvaa , Yang Hun-Mu 
Published: October 2017

AbstractInjury to the external branch of the superior laryngeal nerve (eSLN) can cause a hoarse or weak voice with dysergia of the cricothyroid. The present study provided the topographic information of the eSLN in the Asian and verified anatomical validity of the landmarks previously recruited to localize the eSLN. Thirty specimens were dissected from 16 human embalmed cadavers (12 men and four women; mean age: 80.5 years). The vertical distance between the eSLN and the apical pole of the thyroid gland (AP) was 8.2 ± 4.2 mm. It descended over the AP with <1 cm distance in 51.7%, >1 cm distance in 27.6% and under the AP in 20.7%. The piercing point (PP) of the eSLN to the muscles located 26.0 ± 5.5 mm posterior and 14.7 ± 5.0 mm inferior to the laryngeal prominence. Generally, the PP located superoposterior to the midpoint of the joint between the joint of inferior constrictor and cricothyroid (ICJ). The distance between the PP and the midpoint was 8.7 ± 5.1 mm. We found that 1) the Asian had the eSLN located over the AP with <1 cm distance about half cases, 2) the PP can be a consistent reference for the eSLN identification, 3) the ICJ can be a useful landmark to preserve the eSLN at the PP.
Dual targeting improves capture of ultrasound microbubbles towards activated platelets but yields no additional benefit for imaging of arterial thrombosis
Authors: Günther F. , Heidt T. , Kramer M. , Khanicheh E. , Klibanov A. L. , Geibel-Zehender A. , Ferrante E. A. , Hilgendorf I. , Wolf D. , Zirlik A. , Reinöhl J. , Bode C. , Peter K. , Kaufmann B. A. , Mühlen C. von zur 
Published: October 2017

AbstractPlatelets can be found on the surface of inflamed and ruptured atherosclerotic plaques. Thus, targeting of activated platelets may allow for molecular imaging of vulnerable atherosclerotic lesions. We here investigated microbubbles (MB) functionalized with the selectin ligand sialyl Lewisa individually (MBsLea) or dually with sLea and an antibody targeting ligand-induced binding sites of the activated GPIIb/IIIa receptor (MBDual). Assessed by in vitro flow chamber, targeted MB exhibited increased adhesion to platelets as compared to MBControl. While MBsLea rolled slowly on the platelets’ surface, MBDual enhanced the percentage of firm adhesion. In vivo, MB were investigated by ultrasound in a model of ferric chloride induced non-occlusive carotid artery thrombosis. MBsLea and MBDual revealed a higher ultrasound mean acoustic intensity than MBControl (p < 0.05), however MBDual demonstrated no additional increase in mean signal intensity as compared to MBsLea. The degree of carotid artery stenosis on histology correlated well with the ultrasound acoustic intensity of targeted MB (p < 0.05). While dual targeting of MB using fast binding carbohydrate polymers and specific antibodies is a promising strategy to support adhesion to activated platelets under arterial shear stress, these advantages seem not readily translatable to in vivo models.