bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying multiple deep aquifers in the Bengal Basin: Implications for resource management
Authors: Ravenscroft Peter , McArthur John M. , Rahman Muhammad Saifur 
Published: August 2018

AbstractIn the Bengal Basin of Bangladesh and West Bengal (India), where arsenic (As) and salinity adversely affect groundwater in shallow aquifers (<150 m deep), consumers increasingly turn to “the deep aquifer” as a source of low‐As and low‐salinity water. We show that “the deep aquifer,” which has traditionally been regarded as a single entity, can be divided into at least eight deep aquifer units each with distinctive chemical, isotopic, hydraulic, and piezometric characteristics. Except in the rapidly subsiding Sylhet Basin, the deep aquifers are largely As‐safe (<50 μg/L and mostly <10 μg/L) but differ in terms of iron (Fe), manganese (Mn), salinity, stable isotopic composition, groundwater age, and in their piezometric response to pumping. We use isotopic data to identify recharge from five periods, of which two are quantitatively dominant: (a) from the Last Glacial Maximum, isotopically heavy water (δ18O >−3.5‰) with low As, Cl, and Fe concentrations occupies hydraulically trapped positions in the South‐Central, Southeast, Southwest, and Madhupur aquifer units and (b) terminal Pleistocene to Early Holocene recharge of isotopically lighter water (δ18O <−3.5‰) that has high Fe and slightly elevated Cl concentrations and was recharged along palaeochannels that facilitated deep circulation up to the mid‐Holocene. Piezometric responses to development change in style towards the coast. In the north, water levels at all depths tend to be coincident and transition through a seasonally divergent pattern to become parallel in the south with a near constant downward gradient. The delineation of the deep aquifer units provides a practical framework for the assessment and management of groundwater resources for water supply.
Information flows and stock market volatility
Authors: Chua Chew Lian , Tsiaplias Sarantis 
Published: August 2018

SummaryThis study examines how news is distributed across stocks. A model is developed that categorizes a stock's latent news into normal and nonnormal news, and allows both types of news to be filtered through to other stocks. This is achieved by formulating a model that jointly incorporates a multivariate lognormal‐Poisson jump process (for nonnormal news) and a multivariate GARCH process (for normal news), in addition to a news (or shock) transmission mechanism that allows the shocks from both processes to impact intertemporally on all stocks in the system. The relationship between news and the expected volatility surface is explored and a unique news impact surface is derived that depends on time, news magnitude, and news type. We find that the effect of nonnormal news on volatility expectations typically builds up before dissipating, with the news transmission mechanism effectively crowding‐out normal news and crowding‐in nonnormal news. Moreover, in contrast to the standard approach for measuring leverage effects using asymmetric generalized autoregressive conditional heteroskedasticity models, we find that leverage effects stem predominantly from nonnormal news. Finally, we find that the capacity to identify positively or negatively correlated stock returns is ambiguous in the short term, and depends heavily on the behavior of the nonnormal news component.
High molecular weight fibroblast growth factor 2 induces apoptosis by interacting with complement component 1 Q subcomponent–binding protein in vitro
Authors: Hong Xiaobing , Yu Zelin , Chen Zhonglin , Jiang Hongyan , Niu Yongdong , Huang Zhanqin 
Published: August 2018

AbstractFibroblast growth factor 2 (FGF2) is a multifunctional cell growth factor that regulates cell proliferation, differentiation, adhesion, migration, and apoptosis. FGF2 has multiple isoforms, including an 18‐kDa low molecular weight isoform (lo‐FGF2) and 22‐, 23‐, 24‐, and 34‐kDa high molecular weight isoforms (hi‐FGF2). Hi‐FGF2 overexpression induces chromatin compaction, which requires the mitochondria and leads to apoptosis. Complement component 1 Q subcomponent–binding protein (C1QBP) plays an important role in mitochondria‐dependent apoptosis by regulating the opening of the mitochondrial permeability transition pore. However, the interaction between C1QBP and hi‐FGF2 and its role in hi‐FGF2–mediated apoptosis remain unclear. Here, we found that hi‐FGF2 overexpression induced depolarization of the mitochondrial membrane, cytochrome c release into the cytosol, and a considerable increase in C1QBP messenger RNA and protein expression. Furthermore, coimmunoprecipitation results showed that the mitochondrial protein, C1QBP, interacts with hi‐FGF2. C1QBP knockdown using small interfering RNA significantly decreased the localization of hi‐FGF2 to the mitochondria and increased the rate of apoptosis. Our results highlight a novel mechanism underlying hi‐FGF2–induced, mitochondria‐driven cell death involving the direct interaction between hi‐FGF2 and C1QBP and the upregulation of C1QBP expression.
Retracted: Triptolide inhibits the proliferation and migration of medulloblastoma Daoy cells by upregulation of microRNA‐138
Authors: Zhang Haifang , Li Hui , Liu Zhenguo , Ge Ang , Guo Enyu , Liu Shuxia , Chen Zhiping 
Published: August 2018

AbstractMedulloblastoma is a primitive neuroectodermal‐derived brain tumor and the most common malignant brain tumor in children. Triptolide (TPL) is the major active component extracted from Tripterygium wilfordii Hook F. This study aimed to explore the effects of TPL on medulloblastoma cell proliferation, migration, and apoptosis, as well as the underlying possible molecular mechanism. Viability, proliferation, and apoptosis of Daoy cells were measured using cell counting kit‐8 assay, 5‐bromo‐2′‐deoxyuridine incorporation assay, and Guava Nexin assay, respectively. Cell migration was detected using two‐chamber transwell assay and wound healing assay. Quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was performed to determine the relative expression of microRNA‐138 (miR‐138) in Daoy cells. Cell transfection was used to change the expression of miR‐138 in cells. Western blot analysis was used to analyze the expression of key factors involved in cell apoptosis, cell migration, the phosphatidylinositol 3‐kinase (PI3K)/protein kinase 3 (AKT) pathway, and the Notch pathway in Daoy cells. We found that TPL significantly inhibited the viability, proliferation, and migration of Daoy cells but promoted Daoy cell apoptosis. The expression levels of matrix metalloproteinases (MMP)‐2 and MMP‐9 after TPL treatment were decreased. The expression of miR‐138 in Daoy cells after TPL treatment was increased. Suppression of miR‐138 obviously reversed the TPL‐induced Daoy cell proliferation, migration inhibition, and cell apoptosis enhancement, as well as the inactivation of the PI3K/AKT and Notch pathways. Cyclin‐dependent kinase 6 (CDK6) was a direct target gene of miR‐138, which might be involved in the antitumor effects of TPL on Daoy cells. In conclusion, our study verified that TPL exerted anticancer effects on medulloblastoma cells possibly via upregulating miR‐138 and inactivating the PI3K/AKT and Notch pathways.
Med19 is involved in chemoresistance by mediating autophagy through HMGB1 in breast cancer
Authors: Liu Beibei , Qi Xiaowei , Zhang Xiufen , Gao Danfeng , Fang Kai , Guo Zijian , Li Lihua 
Published: August 2018

AbstractAdriamycin (ADM)‐based regimens are the most effective chemotherapeutic treatments for breast cancer. However, intrinsic and acquired chemoresistance is a major therapeutic problem. Our goal was to clarify the role of mediator complex subunit 19 (Med19) in chemotherapy resistance and to elucidate the related molecular mechanisms. In this study, ADM‐resistant human cells (MCF‐7/ADM) and tissues exhibited increased Med19 expression and autophagy levels relative to the corresponding control groups. Additionally, MCF‐7/ADM cells showed changes in two selective markers of autophagy. There was a dose‐dependent increase in the light chain 3 (LC3)‐II/LC3‐I ratio and a decrease in sequestosome 1 (P62/SQSTMl) expression. Furthermore, lentivirus‐mediated Med19 inhibition significantly attenuated the LC3‐II/LC3‐I ratio, autophagy‐related gene 3 (Atg3) and autophagy‐related gene 5 (Atg5) expression, P62 degradation, and red fluorescent protein‐LC3 dot formation after treatment with ADM or rapamycin, an autophagy activator. Furthermore, the antiproliferative effects of ADM, cisplatin (DDP), and taxol (TAX) were significantly enhanced after suppressing Med19 expression. Notably, the effects of Med19 on autophagy were mediated through the high‐mobility group box‐1 (HMGB1) pathway. Our findings suggest that Med19 suppression increased ADM chemosensitivity by downregulating autophagy through the inhibition of HMGB1 signaling in human breast cancer cells. Thus, the regulatory mechanisms of Med19 in autophagy should be investigated to reduce tumor resistance to chemotherapy.
Affinity maturation and characterization of the ofatumumab monoclonal antibody
Authors: Payandeh Zahra , Rajabibazl Masoumeh , Mortazavi Yousef , Rahimpour Azam , Taromchi Amir Hossein , Dastmalchi Siavoush 
Published: August 2018

AbstractCD20 molecule, a phosphoprotein with 297 amino acids and four transmembrane domains, is a member of MS4A protein family. Anti‐CD20 antibodies such as ofatumumab, which have been developed for cancer treatment and has demonstrated efficacy in relapsed/refractory chronic lymphocytic leukemia, are among the most successful therapies to date. Rational engineering methods can be applied with reasonable success to improve functional characteristics of antibodies. Considering the importance of this issue, we have used in silico modeling approach for the improvement of ofatumumab monoclonal antibody. Four mutated variants of ofatumumab were developed and expressed in Chinese hamster ovary (CHO) cells along with the unmodified antibody. Analysis of affinity of the purified antibodies with CD20 showed significant improvement in antigen‐binding characteristics of one of the variants compared with the control antibody. This study represents the first step toward development of the second generation ofatumumab antibody with improved affinity.
Potential roles of microRNAs in redox state: An update
Authors: Yaribeygi Habib , Atkin Stephen L. , Sahebkar Amirhossein 
Published: August 2018

AbstractOxidative stress is an important underlying cause of many disease processes and may arise due to either increasing free radical generation or decreasing antioxidant defense systems. MicroRNAs (miRs) are 22‐nucleotide non‐coding RNAs that may regulate many intracellular processes; and, more recently, they have been implicated in the pathways for free radical generation leading to oxidative stress. However, conversely, there is evidence that miRs may have an antioxidant effect, thus miR expression may be critical for the maintenance of the normal redox state and cell homeostasis. This review addresses these discrepant and opposing miR actions on how they may modify and regulate the oxidative balance.
Genipin induces cell death via intrinsic apoptosis pathways in human glioblastoma cells
Authors: Ahani Narges , Sangtarash Mohammad Hossein , Houshmand Massoud , Eskandani Majid Alipour 
Published: August 2018

AbstractGenipin, a compound derived from Gardenis jasminoides Ellis fruits, was demonstrated to be the specific uncoupling protein 2 (UCP2) inhibitor. UCP2 is a mitochondrial carrier protein that creates proton leaks across the inner mitochondrial membrane, thus uncoupling oxidative phosphorylation from adenosine triphosphate (ATP) synthesis. Several studies revealed that UCP2 is broadly over‐expressed in leukemia, colorectal, lung, ovarian, prostate, testicular, and bladder cancers. However, the effect of genipin still needs to be elucidated in neurological malignancies. In this study, we investigated the anticancer effect of genipin in U87MG and A172 cell lines. The anticancer effect of genipin on these cell lines was measured by microculture tetrazoliumtest (MTT), Trypan blue exclusion, and colony formation assays, in the presence of various concentrations of genipin at different time intervals. We assessed apoptosis and measure intracellular reactive oxygen species (ROS) by flow cytometry. Expression of UCP2 and some of the genes involved in apoptosis was analyzed by real‐time quantitative polymerase chain reaction (PCR). Results of the MTT assay showed that genipin moderately reduced metabolic activity of both cell lines in dose‐ and time‐dependent manner. Result of Trypan blue exclusion test indicated that the viable cell count decreased in the treated group in a concentration‐dependent manner. Genipin also significantly decreased colony formation ability of these cells in a concentration‐dependent manner. Result of morphological changes showed that there were significant differences in cell number and morphology in treated groups as compared with the untreated groups. Flow cytometric analysis of U87MG and A172 cells with annexin V/propidium iodide staining, 48 hours after treatment with genipin, displays 22.4% and 26.1% apoptotic population, respectively, in treated cells, in comparison to 7.42% and 9.31% apoptotic cells of untreated cells. After treatment, UCP2 and B‐cell lymphoma 2 (BCL
2) genes are downregulated, and BCL
2 associated X protein, BCL
2 antagonist/killer, BCL
2 interacting killer, and Cytochrome c genes are upregulated. Genipin treatment increased mitochondrial ROS levels and also induced apoptosis through caspase‐3 upregulation. In conclusion, the antiproliferative effects of genipin on the growth of both glioblastoma cell lines have been shown in all of these assays, and genipin profoundly induced apoptosis in both cell lines via the UCP2‐related mitochondrial pathway through the induction of intracellular ROS.
Circular RNA of vimentin expression as a valuable predictor for acute myeloid leukemia development and prognosis
Authors: Yi Yun‐Yun , Yi Jing , Zhu Xin , Zhang Jing , Zhou Jiao , Tang Xi , Lin Jiang , Wang Peng , Deng Zhao‐Qun 
Published: August 2018

AbstractThe focus of this study was to investigate the expression status of Circ‐vimentin (VIM) and further analyze its pathogenesis and clinical significance in acute myeloid leukemia (AML) patients. Real‐time quantitative polymerase chain reaction was carried on Circ‐VIM in 113 AML patients and 42 healthy controls. Circ‐VIM was significantly upregulated in AML compared with control and was positively correlated with white blood cells (WBC) count. Receiver operating characteristic curve analysis indicated that the performance of Circ‐VIM expression could serve as a promising biomarker for differentiating AML patients from controls. Significant correlations of Circ‐VIM expression were found with WBC and French–American–British classifications. Survival analyses further showed that over‐expressed Circ‐VIM were associated with markedly shorter overall survival (OS) and leukemia‐free survival (LFS) in whole‐cohort AML, nonacute promyelocytic leukemia AML and cytogenetically normal‐AML patients. Multivariate analysis also disclosed that Circ‐VIM over‐expression was an independent poor prognostic factor for OS and LFS in AML patients. Remarkably, Pearson correlation analysis evidenced that the expression of Circ‐VIM was positively correlated with VIM expression in all AML patients. These results indicated that overexpression Circ‐VIM could serve as a significant biomarker.
Segmentation pattern of zebrafish caudal fin is affected by developmental temperature and defined by multiple fusions between segments
Authors: Christou Maria , Iliopoulou Maria , Witten Paul Eckhard , Koumoundouros George 
Published: August 2018

AbstractCaudal‐fin lepidotrichia is composed of numerous segments, which are linked to each other by intersegmental joints. During fish growth, lepidotrichia elongate by the addition of new segments at their distal margin, whereas the length of each segment remains constant after it is formed. In the present paper, we examined whether the water temperature affects the segmentation pattern of the juvenile and adult caudal fin. For this purpose, zebrafish (Danio rerio) embryos and larvae were exposed to three different temperature conditions (24°C, 28°C, and 32°C) from the pharyngula stage (1 day postfertilization [dpf]) to metamorphosis, whereas the control temperature (28°C) was applied to all the groups before and after this period. Results demonstrated that water temperature had a significant effect on the length of the segments of each lepidotrichium, at both the juvenile and adult stages. Moreover, at higher temperatures, there was a significant proximal shift of the position of the first bifurcation of the second lepidotrichium of the dorsal lobe. At all the experimental conditions, the length of proximal segment was not constant during fish growth, but it followed a discontinuous saltatory growth. Histological analysis of the proximal lepidotrichia segments revealed that the observed apparent growth of segments is the result of fusions between segments. Fusion occurs not by mineralization of the intersegmental joints, but by bone deposition around the joints.
Arc index of spatial graphs
Authors: Lee Min Jung , No Sungjong , Oh Seungsang 
Published: August 2018

AbstractBae and Park found an upper bound on the arc index of prime links in terms of the minimal crossing number. In this paper, we extend the definition of the arc presentation to spatial graphs and find an upper bound on the arc index of any spatial graph as where is the minimal crossing number of , is the number of edges, and is the number of bouquet cut‐components. This upper bound is lowest possible.
CycloBranch: An open tool for fine isotope structures in conventional and product ion mass spectra
Authors: Novák Jiří , Škríba Anton , Zápal Jakub , Kuzma Marek , Havlíček Vladimír 
Published: August 2018

AbstractWithin the growing community of Fourier transform mass spectrometry users, the identification of fine isotope structure has become an indispensable method for molecular formula determination. In this work, the fine isotope envelopes for accessing the mutual ratio of 2 closely related pyoverdines in a mixture were used. Bacterial siderophores pyoverdines D and E cannot be easily separated via liquid chromatography‐mass spectrometry because their structures differ in (de)amidation at the respective chromophore parts only. Their mutual ratio was determined in a mixture via nuclear magnetic resonance spectroscopy and semiquantitative mass spectrometry using our open‐source software CycloBranch, which represents a genuine free tool supporting the determination of fine isotope structures in both conventional and product ion mass spectra. Native Bruker, Thermo, and Waters data formats are supported in addition to XML and plain text formats.
Changes in the Raman spectra of monolayer MoS2 upon thermal annealing
Authors: Kim Ho‐Jong , Kim Daehee , Jung Suyong , Bae Myung‐Ho , Yun Yong Ju , Yi Sam Nyung , Yu Jeong‐Seon , Kim Jong‐Hyun , Ha Dong Han 
Published: August 2018

AbstractDefects have crucial effects on the electronic and optoelectronic properties of two‐dimensional materials. In this work, we measured the changes in the Raman spectra and electrical conductance of monolayer molybdenum disulfide (MoS2) with increasing defects via thermal annealing in a reducing atmosphere. Raman spectra of the basal plane MoS2 on SiO2 differed from those of the edge and revealed intricate changes upon annealing up to 550°C due to the substitution of adsorbed molecules and the creation of highly concentrated defects. On the other hand, MoS2 on hexagonal boron nitride (h‐BN) presented homogenous Raman spectra over the entire area and showed no noticeable changes in its Raman spectra upon annealing. For MoS2 on h‐BN, the charge transfer between MoS2 and adsorbed molecules and the number of defects created by annealing up to 550°C are not sufficient to change the Raman spectra. The distinct behaviors of the two sample spectra are ascribed to different substrate‐induced doping and interfacial adhesion strengths.
Rapid quantification of aloin A and B in aloe plants and aloe‐containing beverages, and pharmaceutical preparations by microchip capillary electrophoresis with laser induced fluorescence detection
Authors: Xiao Meng‐Wei , Bai Xiao‐Lin , Liu Yi‐Ming , Yang Li , Hu Ya‐Dong , Liao Xun 
Published: August 2018

AbstractA microchip capillary electrophoresis coupled with laser induced fluorescence detection method for the fast determination of aloin was developed and comprehensively applied for the quantification of aloin A and B present in seven aloe plant species, 42 aloin‐containing crude drugs, ten aloe pharmaceutical preparations, and four aloe gel‐containing functional foods. The excitation and emission wavelengths for detection of both aloins were set at 473 and 520 nm, respectively. Sample analysis on a 35 mm length of glass microchip channel was completed within 40 s. An interference study indicated that the other main anthraquinones present in the samples did not interrupt with the target aloins detection, demonstrating the good selectivity of this method. It is demonstrated that this method is fast, facile, and specific for determination of aloin A and B from matrix samples which can be applied to the quality control of a wide varieties of aloe species and aloe‐derived products.
Molecularly imprinted polymer based diffusive gradients in thin‐films for in situ selective sampling and determination of ciprofloxacin
Authors: Li Yanan , Chen Hong , Zhu Yu , Zhang Tingting , Gu Jiali , Xu Yongxia , Li Jianrong 
Published: August 2018

AbstractA technique of diffusive gradients in thin films with ciprofloxacin‐molecularly imprinted polymers as the binding agent was developed for in situ selective sampling and measurement of ciprofloxacin in water. The ciprofloxacin uptake by the method increased linearly with time (r2 = 0.998) with a recovery of 96.8% in synthetic solution. The method performance was not dependent on solution pH over the pH range of 2–11 and ionic strength range from 1 × 10−4 to 0.5 mol/L sodium nitrate. The binding agent has a higher adsorption affinity for ciprofloxacin than for other drug residues, such as norfloxacin, chloramphenicol, and malachite green. The concentration of ciprofloxacin in river water determined by this method was 0.52 ± 0.3 μg/L, and the recoveries of ciprofloxacin were 96.1–102.0%.