bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRI change metrics of facioscapulohumeral muscular dystrophy: Stir and T1
Authors: Ferguson Mark R. , Poliachik Sandra L. , Budech Christopher B. , Gove Nancy E. , Carter Gregory T. , Wang Leo H. , Miller Daniel G. , Shaw Dennis W.W. , Friedman Seth D. 
Published: December 2017

ABSTRACTIntroduction: MRI evaluation in facioscapulohumeral muscular dystrophy (FSHD) demonstrates fatty replacement and inflammation/edema in muscle. Our previous work demonstrated short T1 inversion recovery (STIR)‐hyperintense (STIR+) signal in muscle 2 years before fatty replacement. We evaluated leg muscle STIR changes and fatty replacement within 14 months. Methods: FSHD subjects received 2 MRI scans of thigh and calf over a 6.9‐ to 13.8‐month interval. Quality of life measures were collected. One Radiologist rated muscle changes on a semi‐quantitative scale. Results: Fifteen subjects completed longitudinal imaging. Four STIR + muscles and 3 STIR‐normal (STIR−) muscles were rated as progressing to fatty tissue over the study period. Discussion: STIR + muscles with confluent regions of fat at baseline increased more in fat, while STIR− muscles had increases in septal‐fat over the study period. These changes may reflect two phases of FSHD, demonstrating MRI sensitivity is weighted toward gross pathological phases of the disease. Muscle Nerve 57: 905–912, 2018
Theoretical design on a new double functional device of 2,2′‐bipyridine‐embedded N‐(9‐pyrenyl methyl)aza‐15‐crown‐5
Authors: Li Zhongliang , Li Weiwei , Liu Fan , Wang Xueye 
Published: December 2017

AbstractTheoretical design on a new molecular switch and fluorescent chemosensor double functional device of aza‐crown ether (2,2′‐dipyridine‐embedded N‐(9‐anthraceneyl(pyrenyl)methyl)aza‐15‐crown‐5) was explored. The interactions between ligands and a series of alkaline earth metal cations (Mg2+, Ca2+, Sr2+, and Ba2+) were investigated. The fully optimized geometry structures of the free ligands (L1, L2) and their metal cation complexes (L1/M2+, L2/M2+) were calculated with the B3LYP/6‐31G(d) method. The natural bond orbital analysis, which is based on optimized geometric structures, was used to explore the interaction of L1/M2+, L2/M2+ molecules. The absorption spectra of L1, L2, L1/M2+, and L2/M2+, and their excited states were studied by time‐dependent density functional theory. A new type molecular device L2(2,2′‐dipyridine‐embedded N‐(9‐pyrenyl methyl)aza‐15‐crown‐5) is designed, which not only has the selectivity for Sr2+, and construct allosteric switch, but also has fluorescent sensor performance.
Development of METAL‐ACTIVE SITE and ZINCCLUSTER tool to predict active site pockets
Authors: Ajitha M. , Sundar K. , Arul Mugilan S. , Arumugam S. 
Published: December 2017

AbstractThe advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in Protein Data Bank, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low‐preferential combination of endogenous ligands for 49 metal ions. User can also gain information about the residues present in the first and second coordination sphere as it plays a major role in maintaining the structure and function of metalloproteins in biological system. In this paper, a novel computational tool (ZINCCLUSTER) is developed, which can predict the zinc metal binding sites of proteins even if only the primary sequence is known. The purpose of this tool is to predict the active site cluster of an uncharacterized protein based on its primary sequence or a 3D structure. The tool can predict amino acids interacting with a metal or vice versa. This tool is based on the occurrence of significant triplets and it is tested to have higher prediction accuracy when compared to that of other available techniques.
The effect of green tea ointment on episiotomy pain and wound healing in primiparous women: A randomized, double‐blind, placebo‐controlled clinical trial
Authors: Shahrahmani Hadis , Kariman Nourossadat , Jannesari Sharareh , Rafieian‐Kopaei Mahmoud , Mirzaei Moghadameh , Ghalandari Sahar , Shahrahmani Nasim , Mardani Gashtasb 
Published: December 2017

The delayed healing of episiotomy wound and its associated pain is a major problem in obstetrics. Because green tea has analgesic and wound‐healing properties, the present study was conducted to determine the effect of green tea ointment on episiotomy pain and wound‐healing. The green tea extract was also standardized by measuring its Phenolic and flavonoid compounds, antioxidant activity, and one of its active components, that is, Epigallocatechin gallate. The present clinical trial was conducted on 99 primiparous women visiting Afzalipour Hospital in Kerman in 2015. The subjects were randomly divided into 3 groups, including a green tea ointment group, a placebo ointment group, and a routine care group. The 2 ointment groups smeared 2 cm of the green tea or placebo ointments onto their sutured area twice daily for a total of 10 days. The severity of pain was assessed in the subjects using the visual pain scale and wound‐healing using the Redness, Edema, Ecchymosis, Discharge, Approximation (REEDA) scale before the intervention and on the 5th and 10th days after delivery. To standardize the extract, Epigallocatechin gallate was measured by high‐performance liquid chromatography (HPLC). Phenolic and flavonoid compounds, as well as antioxidant activity of the extract were also determined by spectrometry methods. Before the intervention, no significant differences were observed between the 3 groups in terms of their personal and obstetric details (p > .05), the severity of pain (p = .118), and the REEDA score (p = .212). On the 5th and 10th days after delivery, the severity of pain was significantly lower in the green tea group than in the other 2 groups (p < .0001). The mean REEDA score on the 5th and 10th days showed a better and faster healing in the green tea group compared to the other 2 groups (p < .0001). Total content of phenolic and flavonoids contents of green tea were 74.2 mg/g Gallic acid equivalent and 16.3 mg/g Rutin equivalent, respectively, and its antioxidant capacity was 46% of b‐carotene. Green tea ointment appears to be effective in relieving episiotomy pain and improving wound‐healing in this study. Further studies are recommended to be conducted on the effectiveness and safety of the different doses of green tea ointment.
Remote sampling mass spectrometry for dry samples: Sheath‐flow probe electrospray ionization (PESI) using a gel‐loading tip inserted with an acupuncture needle
Authors: Usmanov Dilshadbek T. , Ashurov Khatam B. , Ninomiya Satoshi , Hiraoka Kenzo , Wada Hiroshi , Nakano Hiroshi , Matsumura Masaya , Sanada‐Morimura Sachiyo , Nonami Hiroshi 
Published: December 2017

RationaleProbe electrospray ionization (PESI) is only applicable to liquid or wet samples. In this study, a sheath‐flow PESI method for remote sampling mass spectrometry that can be applied to dry samples was developed.MethodsAn acupuncture needle (0.12 mm outer diameter, 700 nm tip diameter) was inserted into a gel‐loading tip with a 0.1 mm protrusion out of the tip. Analytes were extracted by filling the latter tip with solvent and softly touching the sample surface for a short time (<1 s). A high voltage was applied to the acupuncture needle, and mass spectra of analytes were obtained by self‐aspirating electrospray.ResultsDry samples, such as lines of ballpoint pen ink on paper, pharmaceutical tablets, instant coffee, brown rice, and narcotics, gave strong ion signals. The sample carryover was negligible. The sequential electrospray was observed to be similar to conventional PESI. The limits of detection (LODs) for morphine and rhodamine B were found to be of the order of picograms.ConclusionsBecause of its simplicity and versatility, sheath‐flow PESI is a promising technique for on‐site and nondestructive profile analysis of dry samples with bulky and complicated shapes, with a spatial resolution of ~0.3 mm.
The case of extreme hydrologic drought downstream from reservoirs in Quebec (Canada): The intermittent flow
Authors: Azouaoui O. , Assani A. A. 
Published: December 2017

AbstractIntermittent flow is a hydrological phenomenon observed at all latitudes. This phenomenon is characterized by a complete or partial interruption of flow in time and/or space in channels. In Quebec, even though the climate is humid, intermittent flow occurs downstream from headwater reservoirs. These reservoirs store water during spring and summer (from April to September) and release it in winter to supply hydroelectric power plants located downstream. During the water storage period, intermittent flow is common (discharges falling to <1 L/s/km2). The goal of the study is to analyse the characteristics (magnitude, frequency, and duration) of this flow downstream from 3 reservoirs built in the Saint‐Maurice River watershed, during the period from 1930 to 2010. Downstream, the contribution (magnitude) of intermittent flow to total altered flow is less than 2%. Intermittent flow frequency ranges from 24 to 65 days per year downstream from the 3 reservoirs. As far as duration is concerned, intermittent flow persists on average from 40 to 128 consecutive days. Canonical correlation analysis revealed that the frequency of intermittent flow is correlated with the North Atlantic Oscillation and its magnitude and negatively correlated with the Southern Oscillation.
Reversible Cu4O3 Phase Formation in CuO Nanoplate Anodes for High Capacity and High Coulombic Efficiency
Authors: Radhakrishnan Arya , Gangaja Binitha , Nair Shantikumar , Santhanagopalan Dhamodaran 
Published: December 2017

AbstractConversion materials with high specific capacity are of interest to improve energy density of Li‐ion batteries. Here, we present results concerning hydrothermally synthesized CuO nanoplates that exhibit high specific capacity of 800 and 698 mAh/g at C/2 and 1C rates respectively and 180 mAh/g at a high rate of 30C. The electrodes exhibit high Coulombic efficiencies of about 66% and 60% at C/2 and 1C rate respectively, these are high efficiency values compared to the ones reported in the literature at respective rates. To understand the high performance, ex situ x‐ray diffraction at different states of first discharge/charge is utilized that shine light on the lithiation/delithiation pathways of the CuO nanoplates. Lithiation proceeds through multiple phase transition CuO → Cu4O3 → Cu2O → Cu and it was found that Cu4O3 is reversible at the end of first charge. Cu and residual Cu2O was observed at the end of lithiation along with Li2O and Li2O2 phases. At the end of first charge, Cu4O3 phase along with CuO was observed as a major end‐product with relatively minor concentrations of Cu2O. Cu4O3 as a major constituent observed in composite electrode seems to be the key information that can explain good reversibility and high Coulombic efficiency reported in the present work.
Hybrid Method Based on Information Gain and Support Vector Machine for Gene Selection in Cancer Classification
Authors: Gao Lingyun , Ye Mingquan , Lu Xiaojie , Huang Daobin 
Published: December 2017

Abstract
It remains a great challenge to achieve sufficient cancer classification accuracy with the entire set of genes, due to the high dimensions, small sample size, and big noise of gene expression data. We thus proposed a hybrid gene selection method, Information Gain-Support Vector Machine (IG-SVM) in this study. IG was initially employed to filter irrelevant and redundant genes. Then, further removal of redundant genes was performed using SVM to eliminate the noise in the datasets more effectively. Finally, the informative genes selected by IG-SVM served as the input for the LIBSVM classifier. Compared to other related algorithms, IG-SVM showed the highest classification accuracy and superior performance as evaluated using five cancer gene expression datasets based on a few selected genes. As an example, IG-SVM achieved a classification accuracy of 90.32% for colon cancer, which is difficult to be accurately classified, only based on three genes including CSRP1, MYL9, and GUCA2B.
Rapid regression of large cardiac rhabdomyomas in neonates after sirolimus therapy
Authors: Weiland M. David , Bonello Kristin , Hill Kevin D. 
Published: December 2017

AbstractCardiac rhabdomyomas are the most common tumours in children and are typically seen in association with the tuberous sclerosis complex. Although benign and often associated with spontaneous regression, in rare circumstances surgical resection is indicated to relieve obstruction or other mass-related effects. Recent clinical trials have demonstrated the benefits of mammalian target of rapamycin inhibitors for the treatment of other tumour sub-types associated with tuberous sclerosis. Here we report rapid regression of several massive cardiac rhadomyomas in two neonates with the use of the mammalian target of rapamycin inhibitor sirolimus.
Thinness in young schoolchildren in Serbia: another case of the double burden of malnutrition?
Authors: Djordjic Visnja , Jorga Jagoda , Radisavljevic Snezana , Milanovic Ivana , Bozic Predrag , Ostojic Sergej M 
Published: December 2017

AbstractObjectiveThinness is rarely highlighted or regularly monitored among children in developed countries although it may be rather frequent and pose a significant risk to children’s health. We aimed to describe the prevalence of mild, moderate and severe thinness among young Serbian schoolchildren.DesignCross-sectional study of schoolchildren aged 6–9 years. Children were assessed for weight, height and BMI as part of the WHO European Childhood Obesity Surveillance Initiative in Serbia. Thinness grades were defined as gender- and age-specific cut-offs for BMI according to the International Obesity Task Force criteria.SettingSerbia, September to November 2015.SubjectsStudents (n 4861) in grades 2 and 3 (6–9 years, 2397 girls).ResultsOverall prevalence of thinness in Serbian schoolchildren was 9·6 %. Mild thinness was clearly the largest category with a prevalence of 7·6 %, moderate thinness was present in 1·7 % of children and severe thinness was found in 0·3 % of children. OR indicated a significant risk of being thin for girls (1·44 times higher compared with boys) and children attending schools with no health-focused educational programme (1·57 times more likely to be thin than peers enrolled in schools with such programmes). In addition, OR for thinness tended to be 1·23 times higher in children living in an economically disadvantaged region of Serbia (P=0·06).ConclusionsA rather high prevalence of thinness highlights this malnutrition disorder as an emerging health issue that should trigger public health policies to tackle thinness, especially in girls of young age and children living in economically disadvantaged areas.
Hippocampal-prefrontal theta-gamma coupling during performance of a spatial working memory task
Authors: Tamura Makoto , Spellman Timothy J. , Rosen Andrew M. , Gogos Joseph A. , Gordon Joshua A. 
Published: December 2017

AbstractCross-frequency coupling supports the organization of brain rhythms and is present during a range of cognitive functions. However, little is known about whether and how long-range cross-frequency coupling across distant brain regions subserves working memory. Here we report that theta–slow gamma coupling between the hippocampus and medial prefrontal cortex (mPFC) is augmented in a genetic mouse model of cognitive dysfunction. This increased cross-frequency coupling is observed specifically when the mice successfully perform a spatial working memory task. In wild-type mice, increasing task difficulty by introducing a long delay or by optogenetically interfering with encoding, also increases theta–gamma coupling during correct trials. Finally, epochs of high hippocampal theta–prefrontal slow gamma coupling are associated with increased synchronization of neurons within the mPFC. These findings suggest that enhancement of theta–slow gamma coupling reflects a compensatory mechanism to maintain spatial working memory performance in the setting of increased difficulty.
Revealing chiral cell motility by 3D Riesz transform-differential interference contrast microscopy and computational kinematic analysis
Authors: Tamada Atsushi , Igarashi Michihiro 
Published: December 2017

AbstractLeft–right asymmetry is a fundamental feature of body plans, but its formation mechanisms and roles in functional lateralization remain unclear. Accumulating evidence suggests that left–right asymmetry originates in the cellular chirality. However, cell chirality has not yet been quantitatively investigated, mainly due to the absence of appropriate methods. Here we combine 3D Riesz transform-differential interference contrast (RT-DIC) microscopy and computational kinematic analysis to characterize chiral cellular morphology and motility. We reveal that filopodia of neuronal growth cones exhibit 3D left-helical motion with retraction and right-screw rotation. We next apply the methods to amoeba Dictyostelium discoideum and discover right-handed clockwise cell migration on a 2D substrate and right-screw rotation of subcellular protrusions along the radial axis in a 3D substrate. Thus, RT-DIC microscopy and the computational kinematic analysis are useful and versatile tools to reveal the mechanisms of left–right asymmetry formation and the emergence of lateralized functions.
A circular white-light flare with impulsive and gradual white-light kernels
Authors: Hao Q. , Yang K. , Cheng X. , Guo Y. , Fang C. , Ding M. D. , Chen P. F. , Li Z. 
Published: December 2017

AbstractWhite-light flares are the flares with emissions visible in the optical continuum. They are thought to be rare and pose the most stringent requirements in energy transport and heating in the lower atmosphere. Here we present a nearly circular white-light flare on 10 March 2015 that was well observed by the Optical and Near-infrared Solar Eruption Tracer and Solar Dynamics Observatory. In this flare, there appear simultaneously both impulsive and gradual white-light kernels. The generally accepted thick-target model would be responsible for the impulsive kernels but not sufficient to interpret the gradual kernels. Some other mechanisms including soft X-ray backwarming or downward-propagating Alfvén waves, acting jointly with electron beam bombardment, provide a possible interpretation. However, the origin of this kind of white-light kernel is still an open question that induces more observations and researches in the future to decipher it.
Hyperstretching DNA
Authors: Schakenraad Koen , Biebricher Andreas S. , Sebregts Maarten , ten Bensel Brian , Peterman Erwin J. G. , Wuite Gijs J. L. , Heller Iddo , Storm Cornelis , van der Schoot Paul 
Published: December 2017

AbstractThe three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely used in biophysical/chemical assays and drug treatments. We present single-molecule experiments and a three-state statistical mechanical model that provide a quantitative understanding of the interplay between B-DNA, overstretched DNA and intercalated DNA. The predictions of this model include a hitherto unconfirmed hyperstretched state, twice the length of B-DNA. Our force-fluorescence experiments confirm this hyperstretched state and reveal its sequence dependence. These results pin down the physical principles that govern DNA mechanics under the influence of tension and biochemical reactions. A predictive understanding of the possibilities and limitations of DNA extension can guide refined exploitation of DNA in, e.g., programmable soft materials and DNA origami applications.
Identification of new genes associated to senescent and tumorigenic phenotypes in mesenchymal stem cells
Authors: Medeiros Tavares Marques Joana Cristina , Cornélio Déborah Afonso , Nogueira Silbiger Vivian , Ducati Luchessi André , de Souza Sandro , Batistuzzo de Medeiros Silvia Regina 
Published: December 2017

AbstractAlthough human mesenchymal stem cells (hMSCs) are a powerful tool for cell therapy, prolonged culture times result in replicative senescence or acquisition of tumorigenic features. To identify a molecular signature for senescence, we compared the transcriptome of senescent and young hMSCs with normal karyotype (hMSCs/n) and with a constitutional inversion of chromosome 3 (hMSC/inv). Senescent and young cells from both lineages showed differentially expressed genes (DEGs), with higher levels in senescent hMSCs/inv. Among the 30 DEGs in senescent hMSC/inv, 11 are new candidates for biomarkers of cellular senescence. The functional categories most represented in senescent hMSCs were related to cellular development, cell growth/proliferation, cell death, cell signaling/interaction, and cell movement. Mapping of DEGs onto biological networks revealed matrix metalloproteinase-1, thrombospondin 1, and epidermal growth factor acting as topological bottlenecks. In the comparison between senescent hMSCs/n and senescent hMSCs/inv, other functional annotations such as segregation of chromosomes, mitotic spindle formation, and mitosis and proliferation of tumor lines were most represented. We found that many genes categorized into functional annotations related to tumors in both comparisons, with relation to tumors being highest in senescent hMSCs/inv. The data presented here improves our understanding of the molecular mechanisms underlying the onset of cellular senescence as well as tumorigenesis.
A Novel Cell Line Based Orthotopic Xenograft Mouse Model That Recapitulates Human Hepatoblastoma
Authors: Woodfield Sarah E. , Shi Yan , Patel Roma H. , Jin Jingling , Major Angela , Sarabia Stephen F. , Starosolski Zbigniew , Zorman Barry , Gupta Siddharth S. , Chen Zhenghu , Ibarra Aryana M. , Bissig Karl-Dimiter , Ghaghada Ketan B. , Sumazin Pavel , López-Terrada Dolores , Vasudevan Sanjeev A. 
Published: December 2017

AbstractCurrently, preclinical testing of therapies for hepatoblastoma (HB) is limited to subcutaneous and intrasplenic xenograft models that do not recapitulate the hepatic tumors seen in patients. We hypothesized that injection of HB cell lines into the livers of mice would result in liver tumors that resemble their clinical counterparts. HepG2 and Huh-6 HB cell lines were injected, and tumor growth was monitored with bioluminescence imaging (BLI) and magnetic resonance imaging (MRI). Levels of human α-fetoprotein (AFP) were monitored in the serum of animals. Immunohistochemical and gene expression analyses were also completed on xenograft tumor samples. BLI signal indicative of tumor growth was seen in 55% of HepG2- and Huh-6-injected animals after a period of four to seven weeks. Increased AFP levels correlated with tumor growth. MRI showed large intrahepatic tumors with active neovascularization. HepG2 and Huh-6 xenografts showed expression of β-catenin, AFP, and Glypican-3 (GPC3). HepG2 samples displayed a consistent gene expression profile most similar to human HB tumors. Intrahepatic injection of HB cell lines leads to liver tumors in mice with growth patterns and biologic, histologic, and genetic features similar to human HB tumors. This orthotopic xenograft mouse model will enable clinically relevant testing of novel agents for HB.