bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC) loss to activation of the MAPK signalling cascade
Authors: LeBlanc Veronique G , Firme Marlo , Song Jungeun , Chan Susanna Y , Lee Min Hye , Yip Stephen , Chittaranjan Suganthi , Marra Marco A 
Published: March 2017

AbstractCIC encodes a transcriptional repressor, capicua (CIC), whose disrupted activity appears to be involved in several cancer types, including type I low‐grade gliomas (LGGs) and stomach adenocarcinomas (STADs). To explore human CIC's transcriptional network in an isogenic background, we developed novel isogenic CIC knockout cell lines as model systems, and used these in transcriptome analyses to study the consequences of CIC loss. We also compared our results with analyses of transcriptome data from TCGA for type I LGGs and STADs. We identified 39 candidate targets of CIC transcriptional regulation, and confirmed seven of these as direct targets. We showed that, although many CIC targets appear to be context‐specific, the effects of CIC loss converge on the dysregulation of similar biological processes in different cancer types. For example, we found that CIC deficiency was associated with disruptions in the expression of genes involved in cell–cell adhesion, and in the development of several cell and tissue types. We also showed that loss of CIC leads to overexpression of downstream members of the mitogen‐activated protein kinase (MAPK) signalling cascade, indicating that CIC deficiency may present a novel mechanism for activation of this oncogenic pathway. © 2017 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Measuring perceived morphological relatedness
Authors: Hall Kathleen Currie , Allen Claire , Fairburn Tess , Fry Michael , McAuliffe Michael , McMullin Kevin 
Published: March 2017

AbstractThis paper provides a metric for determining whether a given pair of English words is perceived to be morphologically related, based on objective measurements of the words’ orthographic, phonetic, and semantic similarity to each other. The metric is developed on the basis of results from a behavioural study in which participants were asked to judge the relative similarity of pairs of words. The metric is intended to help researchers determine which forms in a language plausibly have segments that alternate; as an example, it is applied to the lexicon of English to illustrate its utility in calculating the frequency of alternation of [s] and [ʃ].
THE EXPECTED JAGGEDNESS OF ORDER IDEALS
Authors: CHAN MELODY , HADDADAN SHAHRZAD , HOPKINS SAM , MOCI LUCA 
Published: March 2017

Thejaggednessof an order ideal$I$in a poset$P$is the number of maximal elements in$I$plus the number of minimal elements of$P$not in$I$. A probability distribution on the set of order ideals of$P$istoggle-symmetricif for every$p\in P$, the probability that$p$is maximal in$I$equals the probability that$p$is minimal not in$I$. In this paper, we prove a formula for the expected jaggedness of an order ideal of $P$under any toggle-symmetric probability distribution when$P$is the poset of boxes in a skew Young diagram. Our result extends the main combinatorial theorem of Chan–López–Pflueger–Teixidor [Trans. Amer. Math. Soc., forthcoming. 2015,arXiv:1506.00516], who used an expected jaggedness computation as a key ingredient to prove an algebro-geometric formula; and it has applications to homomesies, in the sense of Propp–Roby, of the antichain cardinality statistic for order ideals in partially ordered sets.
Tensor veli palatini electromyography for monitoring Eustachian tube rehabilitation in otitis media
Authors: Picciotti P M , Della Marca G , D'Alatri L , Lucidi D , Rigante M , Scarano E 
Published: March 2017

AbstractBackground:The pathogenesis of otitis media is related to Eustachian tube dysfunction. The tensor veli palatini muscle actively opens the Eustachian tube and promotes middle-ear ventilation. This study describes a technique for paratubal electromyography that uses a surface, non-invasive electrode able to record tensor veli palatini muscle activity during swallowing.Methods:Twenty otitis media patients and 10 healthy patients underwent tensor veli palatini electromyography. Activity of this muscle before and after Eustachian tube rehabilitation was also assessed.Results:In 78.5 per cent of patients, the electromyography duration phase and/or amplitude were reduced in the affected side. The muscle action potential was impaired in all patients who underwent Eustachian tube rehabilitation.Conclusion:This study confirmed that Eustachian tube muscle dysfunction has a role in otitis media pathogenesis and showed that muscle activity increases after Eustachian tube rehabilitation therapy.
Energy use and carbon footprints differ dramatically for diverse wastewater-derived carbonaceous substrates: An integrated exploration of biokinetics and life-cycle assessment
Authors: Li Yanbo , Wang Xu , Butler David , Liu Junxin , Qu Jiuhui 
Published: March 2017

AbstractEnergy neutrality and reduction of carbon emissions are significant challenges to the enhanced sustainability of wastewater treatment plants (WWTPs). Harvesting energy from wastewater carbonaceous substrates can offset energy demands and enable net power generation; yet, there is limited research about how carbonaceous substrates influence energy and carbon implications of WWTPs with integrated energy recovery at systems-level. Consequently, this research uses biokinetics modelling and life cycle assessment philology to explore this notion, by tracing and assessing the quantitative flows of energy embodied or captured, and by exploring the carbon footprint throughout an energy-intensive activated sludge process with integrated energy recovery facilities. The results indicate that energy use and carbon footprint per cubic meter of wastewater treated, varies markedly with the carbon substrate. Compared with systems driven with proteins, carbohydrates or other short-chain fatty acids, systems fed with acetic acid realized energy neutrality with maximal net gain of power from methane combustion (0.198 kWh) and incineration of residual biosolids (0.153 kWh); and also achieved a negative carbon footprint (72.6 g CO2). The findings from this work help us to better understand and develop new technical schemes for improving the energy efficiency of WWTPs by repurposing the stream of carbon substrates across systems.
NMR monitoring of the SELEX process to confirm enrichment of structured RNA
Authors: Amano Ryo , Aoki Kazuteru , Miyakawa Shin , Nakamura Yoshikazu , Kozu Tomoko , Kawai Gota , Sakamoto Taiichi 
Published: March 2017

AbstractRNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.
Complete Genomic and Ultrastructural Analysis of a Nam Dinh Virus Isolated from Culex pipiens quinquefasciatus in China*
Authors: Zhou Jianming , Jin Yujuan , Chen Yingjian , Li Jingmei , Zhang Qiwen , Xie Xianqing , Gan Liping , Liu Qu 
Published: March 2017

AbstractThe Nam Dinh virus (NDiV) was isolated from Culex quinquefasciatus in Shenzhen, China, for the first time, in 2011. In this study, we characterized the ultrastructure of NDiV, determined its complete genome sequence and made comparisons with other known nidoviruses. Electron microscopic observation revealed that the NDiV strain isolated in China produced viral nucleocapsid-like particles and vesicles in host cells. The extracellular virions were enveloped and were spherical with short spikes. The complete genome sequence of the newly isolated NDiV was submitted to the GenBank database (GenBank accession number KF522691). Sequencing of the viral genome showed that the homologies of NDiV isolated in China and Vietnam were greater than 94.0% and 89.0% at the nucleotide and amino acid sequence levels, respectively. Moreover, gene substitution was detected, whereas insertions and deletions were not. A phylogenetic tree analysis showed that these viruses belong to the genus Alphamesonivirus1 of the family Mesoniviridae. The similarity between the two viruses regarding morphological and molecular biological characteristics indicates that the molecular genetics of NDiV are conservative and that the regional differences are unlikely to have a significant effect. This is the first report of the isolation and complete sequencing of a mesonivirus in mainland China.
Electric-field-driven magnetic domain wall as a microscale magneto-optical shutter
Authors: Khokhlov Nikolai E. , Khramova Anastasiya E. , Nikolaeva Elena P. , Kosykh Tatyana B. , Nikolaev Alexey V. , Zvezdin Anatoly K. , Pyatakov Alexander P. , Belotelov Vladimir I. 
Published: March 2017

AbstractNowadays, spintronics considers magnetic domain walls as a kind of nanodeviсe that demands for switching much less energy in comparison to homogeneous process. We propose and demonstrate a new concept for the light control via electric field applied locally to a magnetic domain wall playing the role of nanodevice. In detail, we charged a 15-μm-thick metallic tip to generate strong non-uniform electric field in the vicinity of the domain wall in the iron garnet film. The electric field influences the domain wall due to flexomagnetoelectric effect and causes the domain wall shift. The resulting displacement of the domain wall is up to 1/3 of domain width and allows to demonstrate a novel type of the electrically controlled magneto-optical shutter. Polarized laser beam focused on the electric-field-driven domain wall was used to demonstrate the concept of a microscale Faraday modulator. We obtained different regimes of the light modulation – linear, nonlinear and tri-stable – for the same domain wall with corresponding controllable displacement features. Such variability to control of domain wall’s displacement with spatial scale of about 10 μm makes the proposed concept very promising for nanophotonics and spintronics.
Persistent DNA methylation changes associated with prenatal mercury exposure and cognitive performance during childhood
Authors: Cardenas Andres , Rifas-Shiman Sheryl L. , Agha Golareh , Hivert Marie-France , Litonjua Augusto A. , DeMeo Dawn L. , Lin Xihong , Amarasiriwardena Chitra J. , Oken Emily , Gillman Matthew W. , Baccarelli Andrea A. 
Published: March 2017

AbstractPrenatal exposure to mercury, a known neurotoxic metal, is associated with lower cognitive performance during childhood. Disruption of fetal epigenetic programming could explain mercury’s neurodevelopmental effects. We screened for epigenome-wide methylation differences associated with maternal prenatal blood mercury levels in 321 cord blood DNA samples and examined the persistence of these alterations during early (n = 75; 2.9–4.9 years) and mid-childhood (n = 291; 6.7–10.5 years). Among males, prenatal mercury levels were associated with lower regional cord blood DNA methylation at the Paraoxonase 1 gene (PON1) that persisted in early childhood and was attenuated in mid-childhood blood. Cord blood methylation at thePON1locus predicted lower cognitive test scores measured during early childhood. Methylation at thePON1locus was associated with PON1 expression in an independent set of cord blood samples. The observed persistent epigenetic disruption of thePON1gene may modulate mercury toxicity in humans and might serve as a biomarker of exposure and disease susceptibility.
Inosine attenuates spontaneous activity in the rat neurogenic bladder through an A2B pathway
Authors: Doyle Claire , Cristofaro Vivian , Sack Bryan S. , Lukianov Stefan N. , Schäfer Mattias , Chung Yeun Goo , Sullivan Maryrose P. , Adam Rosalyn M. 
Published: March 2017

AbstractNeurogenic detrusor overactivity (NDO) is among the most challenging complications of spinal cord injury (SCI). A recent report by us demonstrated an improvement in NDO in SCI rats following chronic systemic treatment with the purine nucleoside inosine. The objective of this study was to investigate the mechanism of action of inosine underlying improvement of NDO. Male Sprague-Dawley rats underwent complete spinal cord transection at T8. Inosine (1 mM) delivered intravesically to SCI rats during conscious cystometry significantly decreased the frequency of spontaneous non-voiding contractions. In isolated tissue assays, inosine (1 mM) significantly decreased the amplitude of spontaneous activity (SA) in SCI bladder muscle strips. This effect was prevented by a pan-adenosine receptor antagonist CGS15943, but not by A1 or A3 receptor antagonists. The A2A antagonist ZM241385 and A2B antagonist PSB603 prevented the effect of inosine. The effect of inosine was mimicked by the adenosine receptor agonist NECA and the A2B receptor agonist BAY60-6583. The inhibition of SA by inosine was not observed in the presence of the BK antagonist, iberiotoxin, but persisted in the presence of KATP and SK antagonists. These findings demonstrate that inosine acts via an A2B receptor-mediated pathway that impinges on specific potassium channel effectors.
Immune complexes in chronic Chagas disease patients are formed by exovesicles from Trypanosoma cruzi carrying the conserved MASP N-terminal region
Authors: Díaz Lozano Isabel María , De Pablos Luis Miguel , Longhi Silvia Andrea , Zago María Paola , Schijman Alejandro Gabriel , Osuna Antonio 
Published: March 2017

AbstractThe exovesicles (EVs) are involved in pathologic host-parasite immune associations and have been recently used as biomarkers for diagnosis of infectious diseases. The release of EVs byTrypanosoma cruzi, the causative agent of Chagas disease, has recently been described, with different protein cargoes including the MASP multigene family of proteins MASPs are specific to this parasite and characterized by a conserved C-terminal (C-term) region and an N-terminal codifying for a signal peptide (SP). In this investigation, we identified immature MASP proteins containing the MASP SP in EVs secreted by the infective forms of the parasite. Those EVs are responsible for the formation of immune complexes (ICs) containing anti-MASP SP IgGs in patients with different (cardiac, digestive and asymptomatic) chronic Chagas disease manifestations. Moreover, purified EVs as well as the MASP SP inhibit the action of the complement system and also show a significant association with the humoral response in patients with digestive pathologies. These findings reveal a new route for the secretion of MASP proteins inT. cruzi, which uses EVs as vehicles for immature and misfolded proteins, forming circulating immune complexes. Such complexes could be used in the prognosis of digestive pathologies of clinical forms of Chagas disease.
Improved shear wave motion detection using coded excitation for transient elastography
Authors: He Xiao-Nian , Diao Xian-Fen , Lin Hao-Ming , Zhang Xin-Yu , Shen Yuan-Yuan , Chen Si-Ping , Qin Zheng-Di , Chen Xin 
Published: March 2017

AbstractTransient elastography (TE) is well adapted for use in studying liver elasticity. However, because the shear wave motion signal is extracted from the ultrasound signal, the weak ultrasound signal can significantly deteriorate the shear wave motion tracking process and make it challenging to detect the shear wave motion in a severe noise environment, such as within deep tissues and within obese patients. This paper, therefore, investigated the feasibility of implementing coded excitation in TE for shear wave detection, with the hypothesis that coded ultrasound signals can provide robustness to weak ultrasound signals compared with traditional short pulse. The Barker 7, Barker 13, and short pulse were used for detecting the shear wave in the TE application. Two phantom experiments and one in vitro liver experiment were done to explore the performances of the coded excitation in TE measurement. The results show that both coded pulses outperform the short pulse by providing superior shear wave signal-to-noise ratios (SNR), robust shear wave speed measurement, and higher penetration intensity. In conclusion, this study proved the feasibility of applying coded excitation in shear wave detection for TE application. The proposed method has the potential to facilitate robust shear elasticity measurements of tissue.
Structural insights into the γ-lactamase activity and substrate enantioselectivity of an isochorismatase-like hydrolase from Microbacterium hydrocarbonoxydans
Authors: Gao Shuaihua , Zhou Yu , Zhang Weiwei , Wang Wenhe , Yu You , Mu Yajuan , Wang Hao , Gong Xinqi , Zheng Guojun , Feng Yue 
Published: March 2017

Abstract(+)-γ-lactamase catalyzes the specific hydrolysis of (+)-γ-lactam out of the racemic γ-lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one) to leave optically pure (−)-γ-lactam, which is the key building block of antiviral drugs such as carbovir and abacavir. However, no structural data has been reported on how the enzymes bind the γ-lactams and achieve their enantioselectivities. We previously identified an isochorismatase-like hydrolase (IHL, Mh33H4-5540) with (+)-γ-lactamase activity, which constitutes a novel family of γ-lactamase. Here, we first discovered that this enzyme actually hydrolyzed both (+)- and (−)-γ-lactam, but with apparently different specificities. We determined the crystal structures of the apo-form, (+)-γ-lactam bound, and (−)-γ-lactam bound forms of the enzyme. The structures showed that the binding sites of both (+) and (−)-γ-lactam resemble those of IHLs, but the “cover” loop conserved in IHLs is lacking in the enzyme, probably resulting in its incomplete enantioselectivity. Structural, biochemical, and molecular dynamics simulation studies demonstrated that the steric clash caused by the binding-site residues, especially the side-chain of Cys111 would reduce the binding affinity of (−)-γ-lactam and possibly the catalytic efficiency, which might explain the different catalytic specificities of the enantiomers of γ-lactam. Our results would facilitate the directed evolution and application of Mh33H4-5540 in antiviral drug synthesis.
Rational Design of Protein C Activators
Authors: Barranco-Medina Sergio , Murphy Mary , Pelc Leslie , Chen Zhiwei , Di Cera Enrico , Pozzi Nicola 
Published: March 2017

AbstractIn addition to its procoagulant and proinflammatory functions mediated by cleavage of fibrinogen and PAR1, the trypsin-like protease thrombin activates the anticoagulant protein C in a reaction that requires the cofactor thrombomodulin and the endothelial protein C receptor. Once in the circulation, activated protein C functions as an anticoagulant, anti-inflammatory and regenerative factor. Hence, availability of a protein C activator would afford a therapeutic for patients suffering from thrombotic disorders and a diagnostic tool for monitoring the level of protein C in plasma. Here, we present a fusion protein where thrombin and the EGF456 domain of thrombomodulin are connected through a peptide linker. The fusion protein recapitulates the functional and structural properties of the thrombin-thrombomodulin complex, prolongs the clotting time by generating pharmacological quantities of activated protein C and effectively diagnoses protein C deficiency in human plasma. Notably, these functions do not require exogenous thrombomodulin, unlike other anticoagulant thrombin derivatives engineered to date. These features make the fusion protein an innovative step toward the development of protein C activators of clinical and diagnostic relevance.
Mitigation Effect of Proanthocyanidin on Secondary Heart Injury in Rats Caused by Mechanical Trauma
Authors: Ma Shuo , Chen Chong , Cao Tingting , Bi Yue , Zhou Jicheng , Li Xintao , Yu Deqin , Li Shuzhuang 
Published: March 2017

AbstractMultiple organ dysfunctional syndrome secondary to mechanical trauma (MT) has attracted considerable research attention. The heart is one of the most important organs of the body, and secondary cardiac insufficiency caused by MT seriously affects the quality of life. This study aims to investigate whether proanthocyanidin can alleviate myocardial injury and improve heart function in the process of MT leading to secondary cardiac insufficiency. Noble-Collip drum wasused to prepare MT model in rats. And myocardial apoptosis index was calculated after TUNEL staining. Ventricular intubation was employed to detect heart function. Changes in myocardial ultrastructure were observed using an electron microscope. ELISA was used to detect the content of TNF-α and reactive oxygen species generated from monocytes and cardiomyocytes. The changes in Ca2+ concentration in cardiomyocyte were observed by confocal microscope. Compared with trauma group, the administration group had a decreased apoptosis index of cardiomyocytes, and increased ±dp/dtmax. Meanwhile, proanthocyanidin can inhibit monocytes’ TNF-α production, and reduce plasma TNF-α concentration. Moreover, proanthocyanidin can attenuate the excessive oxidative stress reaction of cardiomyocyte, and inhibit calcium overload in cardiomyocytes. In conclusion, proanthocyanidin can effectively ease myocardial damage and improve cardiac function, through anti-inflammatory and antioxidant effects in secondary cardiac insufficiency caused by MT.
Microstructural changes are coincident with the improvement of clinical symptoms in surgically treated compressed nerve roots
Authors: Wu Weifei , Liang Jie , Chen Ying , Chen Aihua , Wu Yongde , Yang Zong 
Published: March 2017

AbstractDiffusion tensor imaging (DTI) has been widely used to visualize peripheral nerves, but the microstructure of compressed nerve roots can be assessed using DTI. However, there are no data regarding the association among microstructural changes evaluated using DTI, the symptoms assessed using the Oswestry Disability Index (ODI) and the duration of symptoms after surgery in patients with lumbar disc herniation (LDH). Thirty patients with unilateral radiculopathy were investigated using DTI. The changes in the mean fractional anisotropy (FA) and the apparent diffusion coefficient (ADC) values as well as the correlation between these changes and the severity and duration of the clinical symptoms were investigated before and at least one month after surgery. The FA values were significantly increased after surgical treatment (p < 0.0001). Both the ADC and ODI values were noticeably decreased (p < 0.0001). A strong positive correlation between the preoperative and postoperative DTI parameters (p < 0.0001) as well as between the preoperative ODI and postoperative ODI/ODI changes (p < 0.0001) were found. In addition, there was a significant positive correlation between the changes in the DTI parameters and changes in the ODI (p < 0.0001). This preliminary study suggests it may be possible to use DTI to diagnose, quantitatively evaluate and follow-up patients with LDH.