bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sedimentation in the floodplains of the Mekong Delta, Vietnam. Part I: suspended sediment dynamics
Authors: Hung Nguyen Nghia , Delgado José Miguel , Güntner Andreas , Merz Bruno , Bárdossy András , Apel Heiko 
Published: April 2013

AbstractSuspended sediment is the primary source for a sustainable agro‐ecosystem in the Mekong Delta by providing nutrient input for the subsequent cropping season. In addition, the suspended sediment concentration (SSC) plays an important role in the erosion and deposition processes in the Delta; that is, it influences the morphologic development and may counteract the deltaic subsidence and sea level rise. Despite this importance, little is known about the dynamics of suspended sediment in the floodplains of the Mekong Delta. In particular, quantitative analyses are lacking mainly because of data scarcity with respect to the inundation processes in the floodplains. In 2008, therefore, a comprehensive in situ system to monitor the dynamics of suspended sediment in a study area located in the Plain of Reeds was established, aiming at the characterization and quantification of suspended sediment dynamics in the deeply inundated parts of the Vietnamese part of the Mekong Delta. The monitoring system was equipped with seven water quality–monitoring stations. They have a robust design and autonomous power supply suitable for operation on inundated floodplains, enabling the collection of reliable data over a long period of time with a high temporal resolution. The data analysis shows that the general seasonal dynamics of suspended sediment transport in the Delta is controlled by two main mechanisms: the flood wave of the Mekong River and the tidal backwater influences from the coast. In the channel network, SSC decreases exponentially with distance from the Mekong River. The anthropogenic influence on SSC could also be identified for two periods: at the start of the floodplain inundation and at the end of the flood period, when subsequent paddy rice crops are prepared. Based on the results, we recommend an operation scheme for the sluice gates, which intends to distribute the sediment and thus the nutrients equally over the floodplain. Copyright © 2013 John Wiley & Sons, Ltd.
An Overview of Synergistic Data Tools for Biological Scrutiny
Authors: Olender Tsviya , Safran Marilyn , Edgar Ron , Stelzer Gil , Nativ Noam , Rosen Naomi , Shtrichman Ronit , Mazor Yaron , West Michael D. , Keydar Ifat , Rappaport Noa , Belinky Frida , Warshawsky David , Lancet Doron 
Published: April 2013

AbstractA network of biological databases is reviewed, supplying a framework for studies of human genes and the association of their genomic variations with human phenotypes. The network is composed of GeneCards, the human gene compendium, which provides comprehensive information on all known and predicted human genes, along with its suite members GeneDecks and GeneLoc. Two databases are shown that address genes and variations focusing on olfactory reception (HORDE) and transduction (GOSdb). In the realm of disease scrutiny, we portray MalaCards, a novel comprehensive database of human diseases and their annotations. Also shown is GeneKid, a tool aimed at generating novel kidney disease biomarkers using systems biology, as well as Xome, a database for whole‐exome next‐generation DNA sequences for human diseases in the Israeli population. Finally, we show LifeMap Discovery, a database of embryonic development, stem cell research and regenerative medicine, which links to both GeneCards and MalaCards.
Novel Multinuclear Cyclic and V‐shaped Cuprous Clusters with Short and Unsupported Cu(I)‐Cu(I) Separations
Authors: Ho Po‐Hsien , Tsai Ming‐Shih , Lee Gene‐Hsiang , Che Chi‐Ming , Peng Shie‐Ming 
Published: April 2013

AbstractA series of novel cyclic and V‐shaped cuprous clusters, (HNEt3)2 [Cu6(bmsapy)4] (1), [Cu8(banlny)4] (2) and [Cu6(ansny)4Cl] (CF3SO3) (3), were synthesized. Compounds (1) and (2) possess a similar cyclic metal structural arrangement, and the metallic arrangement of compound (2) is as in (1) with an insertion of a pair of ligand‐unbridged Cu(I) atoms. Compounds (1) and (2) both have unusual ligand‐unbridged Cu(I)‐Cu(I) separations, but compound (3) does not. The ligand‐unbridged Cu(I)‐Cu(I) distances in (2) are shorter than those in (1). In absorption spectra, compound (2) displayed red shifts from (1) due to the increase in nuclearity and the number of the aromatic rings in ligands. TDDFT calculations suggest that in HOMOs, the major molecular orbital contribution is from the six Cu(I) atoms implying that the photoluminescent property of (1) is dependent on the cyclic hexacopper arrangement rather than that of (HNEt3) [Cu3(btsapy)2] (4).
Differentiation of human adipose stem cells into neural phenotype by neuroblastoma‐ or olfactory ensheathing cells‐conditioned medium
Authors: Lo Furno Debora , Pellitteri Rosalia , Graziano Adriana C.E. , Giuffrida Rosario , Vancheri Carlo , Gili Elisa , Cardile Venera 
Published: April 2013

AbstractOlfactory ensheathing cells (OECs) are known to be capable of continuous neurogenesis throughout lifetime and are a source of multiple trophic factors important in central nervous system regeneration. B104 neuroblastoma cells are recognized to induce differentiation of neural stem cells into oligodendrocyte precursor cells. Therefore, the aim of this study was to verify if conditioned medium (CM) obtained from OECs or B104 cells was capable of inducing differentiation of adipose tissue‐derived mesenchymal stem cells (AT‐MSCs) to a neuronal phenotype. In order to this goal, immunocytochemical procedures and flow cytometry analysis were used and some neural markers, as nestin, protein gene product 9.5 (PGP 9.5), microtubule‐associated protein 2 (MAP2), glial fibrillary acidic protein (GFAP), and neuron cell surface antigen (A2B5) were examined 24 h and 7 days after the treatment. The results showed that both OECs‐ or B104‐CM treated AT‐MSCs express markers of progenitor and mature neurons (nestin, PGP 9.5 and MAP2) in time‐dependent manner, display morphological features resembling neuronal cells, and result negative for GFAP and A2B5, astrocyte and oligodendrocyte markers, respectively. This study demonstrated that AT‐MSCs can be influenced by the environment, indicating that these cells can respond to environmental cues also versus a neuronal phenotype. J. Cell. Physiol. 228: 2109–2118, 2013. © 2013 Wiley Periodicals, Inc.
1α,25‐dihydroxyvitamin D3 stimulates activin A production to fine‐tune osteoblast‐induced mineralization
Authors: Woeckel V.J. , van der Eerden B.C.J. , Schreuders‐Koedam M. , Eijken M. , Van Leeuwen J.P.T.M. 
Published: April 2013

AbstractIn healthy bones, mineralization has to be tightly controlled to avoid pathological phenotypes. In this study, we investigated interactions between 1α,25(OH)2D3 (1,25D3) and activin A in the regulation of osteoblast induced mineralization. In human osteoblast cultures, we demonstrated that besides stimulation of mineralization, 1,25D3 also induced activin A, a strong inhibitor of mineralization. Simultaneously, follistatin (FST), the natural antagonist of activin A, was down‐regulated by1,25D3. This resulted in an increase in activin A activity during 1,25D3 treatment. We also showed that in 1,25D3‐treated osteoblasts, mineralization can be further increased when activin A activity was abrogated by adding exogenous FST. This observation implies that, besides stimulation of mineralization, 1,25D3 also controls activin A‐mediated inhibition of mineralization. Besides activin A, 1,25D3 also induces osteocalcin (BGLAP), another inhibitor of mineralization. Warfarin, which has been shown to inactivate osteocalcin, increased 1,25D3‐induced mineralization. Interaction between these two systems became evident from the synergistic increase in BGLAP expression upon blocking activin activity in 1,25D3‐treated cultures. In conclusion, we demonstrate that 1,25D3 stimulation of mineralization by human osteoblasts is suppressed by concomitant induction of inhibitors of mineralization. Mineralization induction by 1,25D3 may actually be controlled via interplay with activin A and osteocalcin. Finally, this complex regulation of mineralization substantiates the significance of tight control of mineralization to prevent excessive mineralization and consequently reduction in bone quality and strength. J. Cell. Physiol. 228: 2167–2174, 2013. © 2013 Wiley Periodicals, Inc.
Culture under low physiological oxygen conditions improves the stemness and quality of induced pluripotent stem cells
Authors: Guo Chao‐Wan , Kawakatsu Miho , Idemitsu Marie , Urata Yoshishige , Goto Shinji , Ono Yusuke , Hamano Kimikazu , Li Tao‐Sheng 
Published: April 2013

AbstractThe ex vivo expansion of stem cells under low physiological oxygen (O2) conditions has been demonstrated to improve the stemness and genomic stability of the cells. We investigated whether low‐oxygen culture would be beneficial for the culture of induced pluripotent stem (iPS) cells. Two human iPS cell lines (201B7 and 253G1) were used for the experiments. Cells expanded from a single colony of each cell line were initiated for culture in 2.5% O2, 5% O2, or 20% O2 and maintained for 2 months in parallel. The levels of intracellular and mitochondrial reactive oxygen species did not differ between the cells cultured under different conditions. More colonies of uniformly smaller size were observed at 2.5% and 5% O2 than at 20% O2. All of these iPS colonies that expanded under the various oxygen conditions stained positively for Oct3/4, Nanog, SSEA‐4, and ALP. However, Western blot analysis showed that the iPS cells cultured at 2.5% and 5% O2 expressed significantly more Nanog but less 53BP1 than those cultured at 20% O2. Data from an array CGH showed no significant chromosomal abnormalities, although some genes involved in cellular and metabolic processes were amplified in the low oxygen culture, particularly at 2.5% O2. Our data suggest that low physiological oxygen culture could improve the stemness and quality of iPS cells, a result that might be associated with the amplification of genes involved in metabolic and cellular processes. Long‐term culture will be necessary to confirm whether low physiological oxygen levels also improve genomic stability. J. Cell. Physiol. 228: 2159–2166, 2013. © 2013 Wiley Periodicals, Inc.
Regulation of the delta and alpha epithelial sodium channel (ENaC) by ubiquitination and Nedd8
Authors: Ly Kevin , McIntosh C. Joy , Biasio Wolfgang , Liu Yongfeng , Ke Ying , Olson Diane R. , Miller John H. , Page Rachel , Snyder Peter M. , McDonald Fiona J. 
Published: April 2013

AbstractThe δ epithelial sodium channel (δENaC) is a proton‐activated, sodium‐selective, amiloride‐sensitive ion channel in the ENaC/degenerin family of ion channels involved in blood pressure regulation and mechanosensation. Other ENaC family members are subject to ubiquitin modification leading to internalization from the cell surface, and degradation of the channel. Here, we show that δENaC is also modified by ubiquitin on three intracellular lysine residues. Absence of these lysines abolished ubiquitin modification of δENaC and increased cell surface levels of δENaC. Although the HECT‐domain ubiquitin ligase Nedd4‐2 reduced amiloride‐sensitive current generated by δβγENaC‐containing channels, δENaC does not contain a binding site for Nedd4‐2; therefore, this effect is probably mediated by the βγENaC subunits. Nedd8, a ubiquitin‐like protein that regulates RING‐domain E3 ubiquitin ligases, promoted δENaC ubiquitination, decreased both the intracellular and cell surface δENaC populations, and decreased δβγENaC amiloride‐sensitive short circuit current (Isc‐amiloride) in a mammalian epithelium. Nedd8 also promoted α− and γENaC ubiquitination, decreased the cell surface pools, and decreased αβγENaC Isc‐amiloride. Conversely, XIAP, a single subunit RING E3 ligase, decreased ubiquitinated δENaC, increased the δENaC cell surface pool and increased δβγENaC Isc‐amiloride. Therefore δ− and α − βγENaC channel function may be influenced by RING‐domain E3 ubiquitin ligases. J. Cell. Physiol. 228: 2190–2201, 2013. © 2013 Wiley Periodicals, Inc.
Markers of cochlear inflammation using MRI
Authors: Floc'h Johann Le , Tan Winston , Telang Ravindra S. , Vlajkovic Srdjan M. , Nuttall Alfred , Rooney William D. , Pontré Beau , Thorne Peter R. 
Published: April 2013

PurposeTo quantify spatial and temporal inflammation‐induced changes in vascular permeability and macrophage infiltration in guinea‐pig (GP) cochlea using MRI.Materials and MethodsGPs were injected with lipopolysaccharide (LPS) to induce cochlear inflammation. One group was injected with a gadolinium based contrast agent (GBCA) and dynamic contrast enhanced (DCE)‐MRI was performed at 4, 7, and 10 days after LPS treatment. A two‐compartment pharmacokinetic model was used to determine the apparent rate constant of GBCA extravasation (Ktrans). A second group was injected with ultrasmall superparamagnetic iron oxide particles (USPIOs) and studied at 2, 3, and 7 days after LPS treatment to detect tissue USPIO uptake and correlate with histology. For both groups, control GPs were scanned similarly.ResultsThe signal enhancement increased substantially and more rapidly at day 4 in LPS‐treated than in control cochlea shortly following GBCA injection. Ktrans of LPS‐treated cochlea was maximum on day 4 at 0.0218 ± 0.0032 min−1 and then decreased to control level at 0.0036 ± 0.0004 min−1 by day 10. In the second group, the relative signal intensity and T2 in cochlear perilymphatic spaces on day 2 decreased, on average, by 54% and 45%, respectively, compared with baseline and then remained under control levels by day 7. This suggests the infiltration of inflammatory cells, although unconfirmed by histology.ConclusionThis provides the first measurement of cochlear vascular permeability using MRI and a quantitative evaluation of the development of cochlear inflammation. MRI holds considerable potential for the assessment of disease processes such as clinical diagnosis of conditions such as labyrinthitis. J. Magn. Reson. Imaging 2014;39:150–161. © 2013 Wiley Periodicals, Inc.
MR elastography for noninvasive assessment of hepatic fibrosis: Reproducibility of the examination and reproducibility and repeatability of the liver stiffness value measurement
Authors: Lee Ye ji , Lee Jeong Min , Lee Jeong Eun , Lee Kyung Bun , Lee Eun Sun , Yoon Jeong‐Hee , Yu Mi Hye , Baek Jee Hyun , Shin Cheong Il , Han Joon Koo , Choi Byung Ihn 
Published: April 2013

PurposeTo determine the reproducibility of MR elastography (MRE) and the reproducibility and repeatability of the stiffness measurement of MRE in the staging of liver fibrosis.Materials and MethodsNinety‐four patients, who underwent liver MRE, were included in this study. The patients were classified into group 1 (n = 47) and group 2 (n = 47) according to our knowledge of their histologic hepatic fibrosis (HF) stage. To analyze the reproducibility of MRE, the group 1 patients underwent MRE twice. In addition, to evaluate the repeatability and reproducibility of the stiffness measurement of MRE, a single observer measured the stiffness values of the second MREs in group 1 twice, and two observers independently measured the stiffness values of MRE in group 2. A 95% Bland‐Altman limits of agreement and intraclass correlation coefficients (ICCs) were used to evaluate the reproducibility and repeatability of MRE.ResultsIn group I, there was no significant difference in the mean liver stiffness values of the first and second MRE examinations, i.e., 3.45 ± 0.25 kPa vs. 3.35 ± 0.23 kPa (p = 0.22). The reproducibility of the MRE examination and the reproducibility and repeatability of the stiffness measurement were high, i.e., the ICCs of each parameter were 0.945, 0.827, and 0.963, respectively, and the 95% limits of agreement were 25.3%, 35.35%, and 18.0%, respectively.ConclusionMRE is a promising tool for evaluating HF and has high reproducibility of the examination as well as reproducibility and repeatability of the stiffness measurements. J. Magn. Reson. Imaging 2014;39:326–331. © 2013 Wiley Periodicals, Inc.
MRI for acute chest pain: Current state of the Art
Authors: François Christopher J. , Hartung Michael P. , Reeder Scott B. , Nagle Scott K. , Schiebler Mark L. 
Published: April 2013

AbstractThis article reviews the magnetic resonance imaging (MRI) and angiography (MRA) techniques, imaging findings, and evidence for evaluating patients with acute chest pain due to acute pulmonary embolus (PE), aortic dissection (AD), and myocardial infarction (MI). When computed tomographic angiography (CTA) is contraindicated, MRI and MRA are important alternative imaging modalities for diagnosis and management of patients with acute PE, AD, and MI. Familiarity with the techniques, imaging findings, and evidence is critical to safely and appropriately managing patients presenting with acute chest pain. J. Magn. Reson. Imaging 2013;37:1290–1300. © 2013 Wiley Periodicals, Inc.
From the mobile proton to wandering hydride ion: mechanistic aspects of gas‐phase ion chemistry
Authors: Bouchoux Guy 
Published: April 2013

Structural characterization of molecular species by mass spectrometry supposes the knowledge of the type of ions generated and the mechanism by which they dissociate. In this context, a need for a rationalization of electrospray ionization(+)(−) mass spectra of small molecules has been recently expressed. Similarly, at the other end of the mass scale, efforts are currently made to interpret the major fragmentation processes of protonated and deprotonated peptides and their reduced forms produced in electron capture or electron transfer experiments.Most fragmentation processes of molecular and pseudo‐molecular ions produced in the ion source of a mass spectrometer may be described by a combination of several key mechanistic steps: simple bond dissociation, formation of ion‐neutral complex intermediates, hydrogen atom, hydride ion or proton migrations and nucleophilic attack. Selected crucial aspects of these elementary reactions, occurring inside positively charged ions, will be recalled and illustrated by examples taken in recent mass spectrometry literature. Emphasis will be given on the protonation process and its consequence in terms of structure and energetic. Copyright © 2013 John Wiley & Sons, Ltd.
Specificity of squamous cell carcinoma antigen (SCCA)‐IgM detection in patients with HCV infection and rheumatoid factor seropositivity
Authors: Biasiolo Alessandra , Tono Natascia , Zaninotto Martina , Merkel Carlo , Fassina Giorgio , Plebani Mario , Gatta Angelo , Pontisso Patrizia 
Published: April 2013

AbstractIgM antibodies bound to different cancer antigens have shown recently a higher diagnostic value, compared with the corresponding free molecule, giving rise to a new family of biomarkers. High or increasing levels of Squamous Cell Carcinoma Antigen (SCCA)‐IgM immune complexes were associated with more advanced liver disease and increased risk of development of HCC. Rheumatoid factor (RF) represents a long‐standing problem of interference for immunometric assays. The aim of the present study was to examine the specificity of SCCA‐IgM in relation to the presence of RF reactivity in patients infected with hepatitis C virus (HCV). Sera of 73 patients with cirrhosis, infected with HCV, (mean age ± SD: 66 ± 13 years; M/F: 45/28), including 21 patients with HCC, were studied. SCCA‐IgM immune complexes levels were measured by a commercial ELISA. To evaluate the possible interfering effect of RF, the standard calibrator, positive for SCCA‐IgM, was spiked with serial dilutions of a RF positive or negative serum. SCCA‐IgM immune complexes were positive in 35 out of 73 (48%) patients, while RF activity was found in 10 out of 73 (14%) patients. Patients with cirrhosis with RF activity had significantly higher levels of SCCA‐IgM, compared to RF negative cases; however, no significant correlation between SCCA‐IgM and RF values was observed. In samples created artificially the same results in terms of reactivity for SCCA‐IgM were obtained, regardless of the presence of RF activity. These findings support the lack of correlation between the two parameters found in sera of patients infected with HCV. J. Med. Virol. 85: 1005–1008, 2013. © 2013 Wiley Periodicals, Inc.
Seroprevalence of neutralizing antibodies to human adenoviruses type‐5 and type‐26 and chimpanzee adenovirus type‐68 in healthy Chinese adults
Authors: Zhang Shujun , Huang Wenxiang , Zhou Xiangyang , Zhao Qiquan , Wang Qun , Jia Bei 
Published: April 2013

AbstractReplication‐defective adenoviruses have been utilized as candidate vaccine vectors. However, clinical application of the best‐studied human adenovirus type‐5 (AdHu5) is limited by the high prevalence of preexisting neutralizing antibodies resulting from natural infection. Therefore, rare adenovirus serotypes, such as human adenovirus type‐26 (AdHu26) and chimpanzee adenovirus type‐68 (AdC68), have been employed as substitutes for AdHu5. However, few studies have described the epidemiology of pre‐existing immunity to these adenoviruses in China. Thus, 1,154 participants from six regions in China were examined to assess the presence of neutralizing antibodies against AdHu5, AdHu26, and AdC68. The seroprevalence rates of neutralizing antibodies were as follows: AdHu5, 73.1% (844/1,154) (95% confidence interval: 70.5–75.6%); AdHu26, 35.3% (407/1,154) (95% confidence interval: 32.6–38.1%); and AdC68, 12.7% (147/1,154) (95% confidence interval: 10.9–14.8%), respectively. The most frequently detected and highest titer antibodies were specific for AdHu5. The results indicate that AdHu26 and AdC68 serve as more suitable vaccine vectors than AdHu5. J. Med. Virol. 85: 1077–1084, 2013. © 2013 Wiley Periodicals, Inc.
Low‐level viremia is associated with non‐B subtypes in patients infected with HIV with virological success following HAART introduction
Authors: Saison Julien , Tardy Jean‐Claude , Scholtes Caroline , Icard Vinca , Trabaud Mary‐Anne , Perpoint Thomas , Chidiac Christian , Ecochard René , André Patrice , Ferry Tristan ,   on behalf of the Lyon HIV Cohort Study
Published: April 2013

AbstractThis prospective study aimed to determine factors associated with detection of very low‐level viremia in patients infected with HIV‐1 with virological success following HAART introduction. Fifty‐seven patients, mostly (n = 51, 89%) treated with a protease inhibitor‐based regimen, were included and followed for 2 years. Viral loads were monitored by Abbott m2000 RealTime HIV‐1. Patients were classified as (i) HIV‐RNA‐negative if viral loads remained strictly undetectable (0 copies/ml), or (ii) HIV‐RNA‐positive if at least one HIV‐1 RNA could be detected in 1–49 copies/ml during follow‐up. At month 24, 44 patients (77%) were in the HIV‐RNA‐positive group, whereas 13 (23%) remained without very low‐level viremia. Univariate analysis, Kaplan–Meier curves and the Cox proportional hazard model revealed that B subtype was the only predictor of belonging to the HIV‐RNA‐negative group (HR 3.98; 95% CI 1.08–14.7). This association needs to be confirmed. Further study of the reservoir and the mechanisms of viral latency according to HIV‐subtype will also be necessary to develop new therapeutic strategies and eradicate HIV infection. J. Med. Virol. 85: 953–958, 2013. © 2013 Wiley Periodicals, Inc.