bluuebunny/crossref_metadata_2025_split huggingface dataset:
Divalent metal-ion transporter 1 is decreased in intestinal epithelial cells and contributes to the anemia in inflammatory bowel disease
Authors: Wu Wei , Song Yang , He Chong , Liu Changqin , Wu Ruijin , Fang Leilei , Cong Yingzi , Miao Yinglei , Liu Zhanju 
Published: November 2015

AbstractDivalent metal-ion transporter 1 (DMT1) has been found to play an important role in the iron metabolism and hemogenesis. However, little is known about the potential role of DMT1 in the pathogenesis of anemia from patients with inflammatory bowel disease (IBD). Herein, we investigated expression of DMT1 in the intestinal mucosa by quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry and found that DMT1 was significantly decreased in the inflamed mucosa of active IBD patients compared with that in those patients at remission stage and healthy controls. To further study the mechanism, we cultured HCT 116 cell line in vitro. Expression of DMT1 in HCT116 was demonstrated to be markedly decreased under stimulation with TNF for 24 and 48 h, while JNK inhibitor (JNK-IN-7) could significantly reverse the decrease. Interestingly, anti-TNF therapy successfully improved anemia in clinical responsive Crohn’s disease patients and DMT1 was found to be markedly up-regulated in intestinal mucosa. Taken together, our studies demonstrate that decreased expression of DMT1 in intestinal mucosa leads to compromised absorption and transportation of iron and that blockade of TNF could rescue anemia and promote DMT1 expression in gut mucosa. This work provides a therapeutic approach in the management of anemia in IBD.
Association of specific frequency bands of functional MRI signal oscillations with motor symptoms and depression in Parkinson’s disease
Authors: Song Xiaopeng , Hu Xiao , Zhou Shuqin , Xu Yuanyuan , Zhang Yi , Yuan Yonggui , Liu Yijun , Zhu Huaiqiu , Liu Weiguo , Gao Jia-Hong 
Published: November 2015

AbstractA novel empirical mode decomposition method was adopted to investigate the dissociative or interactive neural impact of depression and motor impairments in Parkinson’s disease (PD). Resting-state fMRI data of 59 PD subjects were first decomposed into characteristic frequency bands and the main effects of motor severity and depression and their interaction on the energy of blood-oxygen-level-dependent signal oscillation in specific frequency bands were then evaluated. The results show that the severity of motor symptoms is negatively correlated with the energy in the frequency band of 0.10–0.25 Hz in the bilateral thalamus, but positively correlated with 0.01–0.027 Hz band energy in the bilateral postcentral gyrus. The severity of depression, on the other hand, is positively correlated with the energy of 0.10–0.25 Hz but negatively with 0.01–0.027 Hz in the bilateral subgenual gyrus. Notably, the interaction between motor and depressive symptoms is negatively correlated with the energy of 0.10–0.25 Hz in the substantia nigra, hippocampus, inferior orbitofrontal cortex and temporoparietal junction, but positively correlated with 0.02–0.05 Hz in the same regions. These findings indicate unique associations of fMRI band signals with motor and depressive symptoms in PD in specific brain regions, which may underscore the neural impact of the comorbidity and the differentiation between the two PD-related disorders.
Sustainable production of valuable compound 3-succinoyl-pyridine by genetically engineering Pseudomonas putida using the tobacco waste
Authors: Wang Weiwei , Xu Ping , Tang Hongzhi 
Published: November 2015

AbstractTreatment of solid and liquid tobacco wastes with high nicotine content remains a longstanding challenge. Here, we explored an environmentally friendly approach to replace tobacco waste disposal with resource recovery by genetically engineering Pseudomonas putida. The biosynthesis of 3-succinoyl-pyridine (SP), a precursor in the production of hypotensive agents, from the tobacco waste was developed using whole cells of the engineered Pseudomonas strain, S16dspm. Under optimal conditions in fed-batch biotransformation, the final concentrations of product SP reached 9.8 g/L and 8.9 g/L from aqueous nicotine solution and crude suspension of the tobacco waste, respectively. In addition, the crystal compound SP produced from aqueous nicotine of the tobacco waste in batch biotransformation was of high purity and its isolation yield on nicotine was 54.2%. This study shows a promising route for processing environmental wastes as raw materials in order to produce valuable compounds.
Superresolution imaging with optical fluctuation using speckle patterns illumination
Authors: Kim MinKwan , Park ChungHyun , Rodriguez Christophe , Park YongKeun , Cho Yong-Hoon 
Published: November 2015

AbstractSuperresolution fluorescence microscopy possesses an important role for the study of processes in biological cells with subdiffraction resolution. Recently, superresolution methods employing the emission properties of fluorophores have rapidly evolved due to their technical simplicity and direct applicability to existing microscopes. However, the application of these methods has been limited to samples labeled with fluorophores that can exhibit intrinsic emission properties at a restricted timescale, especially stochastic blinking. Here, we present a superresolution method that can be performed using general fluorophores, regardless of this intrinsic property. Utilizing speckle patterns illumination, temporal emission fluctuation of fluorophores is induced and controlled, from which a superresolution image can be obtained exploiting its statistical property. Using this method, we demonstrate, theoretically and experimentally, the capability to produce subdiffraction resolution images. A spatial resolution of 500 nm, 300 nm and 140 nm with 0.4, 0.5 and 1.4 NA objective lenses respectively was achieved in various samples with an enhancement factor of 1.6 compared to conventional fluorescence microscopy.
Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase
Authors: Kusakabe Yoshio , Ishihara Masaaki , Umeda Tomonobu , Kuroda Daisuke , Nakanishi Masayuki , Kitade Yukio , Gouda Hiroaki , Nakamura Kazuo T. , Tanaka Nobutada 
Published: November 2015

AbstractS-adenosyl-L-homocysteine hydrolase (SAH hydrolase or SAHH) is a highly conserved enzyme that catalyses the reversible hydrolysis of SAH to L-homocysteine (HCY) and adenosine (ADO). High-resolution crystal structures have been reported for bacterial and plant SAHHs, but not mammalian SAHHs. Here, we report the first high-resolution crystal structure of mammalian SAHH (mouse SAHH) in complex with a reaction product (ADO) and with two reaction intermediate analogues—3’-keto-aristeromycin (3KA) and noraristeromycin (NRN)—at resolutions of 1.55, 1.55 and 1.65 Å. Each of the three structures constitutes a structural snapshot of one of the last three steps of the five-step process of SAH hydrolysis by SAHH. In the NRN complex, a water molecule, which is an essential substrate for ADO formation, is structurally identified for the first time as the candidate donor in a Michael addition by SAHH to the 3’-keto-4’,5’-didehydroadenosine reaction intermediate. The presence of the water molecule is consistent with the reaction mechanism proposed by Palmer & Abeles in 1979. These results provide insights into the reaction mechanism of the SAHH enzyme.
The influence of whispering gallery modes on the far field of ring lasers
Authors: Szedlak Rolf , Holzbauer Martin , MacFarland Donald , Zederbauer Tobias , Detz Hermann , Andrews Aaron Maxwell , Schwarzer Clemens , Schrenk Werner , Strasser Gottfried 
Published: November 2015

AbstractWe introduce ring lasers with continuous π-phase shifts in the second order distributed feedback grating. This configuration facilitates insights into the nature of the modal outcoupling in an optical cavity. The grating exploits the asymmetry of whispering gallery modes and induces a rotation of the far field pattern. We find that this rotation can be connected to the location of the mode relative to the grating. Furthermore, the direction of rotation depends on the radial order of the whispering gallery mode. This enables a distinct identification and characterization of the mode by simple analysis of the emission beam.
Targeted Proteomics Enables Simultaneous Quantification of Folate Receptor Isoforms and Potential Isoform-based Diagnosis in Breast Cancer
Authors: Yang Ting , Xu Feifei , Fang Danjun , Chen Yun 
Published: November 2015

AbstractThe distinct roles of protein isoforms in cancer are becoming increasingly evident. FRα and FRβ, two major isoforms of the folate receptor family, generally have different cellular distribution and tissue specificity. However, the presence of FRβ in breast tumors, where FRα is normally expressed, complicates this situation. Prior to applying any FR isoform-based diagnosis and therapeutics, it is essential to monitor the expression profile of FR isoforms in a more accurate manner. An LC-MS/MS-based targeted proteomics assay was developed and validated in this study because of the lack of suitable methodology for the simultaneous and specific measurement of highly homologous isoforms occurring at low concentrations. FRα and FRβ monitoring was achieved by measuring their surrogate isoform-specific peptides. Five human breast cell lines, isolated macrophages and 60 matched pairs of breast tissue samples were subjected to the analysis. The results indicated that FRβ was overexpressed in tumor-associated macrophages (TAMs) but not epithelial cells, in addition to an enhanced level of FRα in breast cancer cells and tissue samples. Moreover, the levels of the FR isoforms were evaluated according to the histology, histopathological features and molecular subtypes of breast cancer. Several positive associations with PR/ER and HER2 status and metastasis were revealed.
Unobtrusive ambulatory EEG using a smartphone and flexible printed electrodes around the ear
Authors: Debener Stefan , Emkes Reiner , De Vos Maarten , Bleichner Martin 
Published: November 2015

AbstractThis study presents first evidence that reliable EEG data can be recorded with a new cEEGrid electrode array, which consists of ten electrodes printed on flexible sheet and arranged in a c-shape to fit around the ear. Ten participants wore two cEEGrid systems for at least seven hours. Using a smartphone for stimulus delivery and signal acquisition, resting EEG and auditory oddball data were collected in the morning and in the afternoon six to seven hours apart. Analysis of resting EEG data confirmed well-known spectral differences between eyes open and eyes closed conditions. The ERP results confirmed the predicted condition effects with significantly larger P300 amplitudes for target compared to standard tones and a high test-retest reliability of the P300 amplitude (r > = .74). Moreover, a linear classifier trained on data from the morning session revealed similar performance in classification accuracy for the morning and the afternoon sessions (both > 70%). These findings demonstrate the feasibility of concealed and comfortable brain activity acquisition over many hours.
Alterations in Circulating Immune Cells in Neovascular Age-Related Macular Degeneration
Authors: Lechner Judith , Chen Mei , Hogg Ruth E. , Toth Levente , Silvestri Giuliana , Chakravarthy Usha , Xu Heping 
Published: November 2015

AbstractNeovascular age-related macular degeneration (nAMD) is the leading cause of irreversible blindness in developed countries. Recent advances have highlighted the essential role of inflammation in the development of the disease. In addition to local retinal chronic inflammatory response, systemic immune alterations have also been observed in AMD patients. In this study we investigated the association between the frequency of circulating leukocyte populations and the prevalence as well as clinical presentations of nAMD. Leukocyte subsets of 103 nAMD patients (most of them were receiving anti-VEGF therapy prior to enrolment) and 26 controls were analysed by flow cytometry by relative cell size, granularity and surface markers. Circulating CD11b+ cells and CD16hiHLA-DR− neutrophils were significantly increased (P = 0.015 and 0.009 respectively) in nAMD when compared to controls. The percentage of circulating CD4+ T-cells was reduced in nAMD patients without subretinal fibrosis (P = 0.026) compared to patients with subretinal fibrosis. There was no correlation between the percentage of circulating leukocytes and the responsiveness to anti-VEGF therapy in nAMD patients. Our results suggest that higher levels of circulating CD11b+ cells and neutrophils are associated with nAMD and that reduced levels of CD4+ T-cells are associated with the absence of subretinal fibrosis in nAMD.
What determines positive, neutral and negative impacts of Solidago canadensis invasion on native plant species richness?
Authors: Dong Li-Jia , Yu Hong-Wei , He Wei-Ming 
Published: November 2015

AbstractWhether plant invasions pose a great threat to native plant diversity is still hotly debated due to conflicting findings. More importantly, we know little about the mechanisms of invasion impacts on native plant richness. We examined how Solidago canadensis invasion influenced native plants using data from 291 pairs of invaded and uninvaded plots covering an entire invaded range and quantified the relative contributions of climate, recipient communities and S. canadensis to invasion impacts. There were three types of invasion consequences for native plant species richness (i.e., positive, neutral and negative impacts). Overall, the relative contributions of recipient communities, S. canadensis and climate to invasion impacts were 71.39%, 21.46% and 7.15%, respectively; furthermore, the roles of recipient communities, S. canadensis and climate were largely ascribed to plant diversity, density and cover and precipitation. In terms of direct effects, invasion impacts were negatively linked to temperature and native plant communities and positively to precipitation and soil microbes. Soil microbes were crucial in the network of indirect effects on invasion impacts. These findings suggest that the characteristics of recipient communities are the most important determinants of invasion impacts and that invasion impacts may be a continuum across an entire invaded range.
Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity
Authors: Mitra A. , MacIntyre D. A. , Lee Y. S. , Smith A. , Marchesi J. R. , Lehne B. , Bhatia R. , Lyons D. , Paraskevaidis E. , Li J. V. , Holmes E. , Nicholson J. K. , Bennett P. R. , Kyrgiou M. 
Published: November 2015

AbstractPersistent infection with oncogenic Human Papillomavirus (HPV) is necessary for cervical carcinogenesis. Although evidence suggests that the vaginal microbiome plays a functional role in the persistence or regression of HPV infections, this has yet to be described in women with cervical intra-epithelial neoplasia (CIN). We hypothesised that increasing microbiome diversity is associated with increasing CIN severity. llumina MiSeq sequencing of 16S rRNA gene amplicons was used to characterise the vaginal microbiota of women with low-grade squamous intra-epithelial lesions (LSIL; n = 52), high-grade (HSIL; n = 92), invasive cervical cancer (ICC; n = 5) and healthy controls (n = 20). Hierarchical clustering analysis revealed an increased prevalence of microbiomes characterised by high-diversity and low levels of Lactobacillus spp. (community state type-CST IV) with increasing disease severity, irrespective of HPV status (Normal = 2/20,10%; LSIL = 11/52,21%; HSIL = 25/92,27%; ICC = 2/5,40%). Increasing disease severity was associated with decreasing relative abundance of Lactobacillus spp. The vaginal microbiome in HSIL was characterised by higher levels of Sneathia sanguinegens (P < 0.01), Anaerococcus tetradius (P < 0.05) and Peptostreptococcus anaerobius (P < 0.05) and lower levels of Lactobacillus jensenii (P < 0.01) compared to LSIL. Our results suggest advancing CIN disease severity is associated with increasing vaginal microbiota diversity and may be involved in regulating viral persistence and disease progression.
Chronic corticosterone-mediated dysregulation of microRNA network in prefrontal cortex of rats: relevance to depression pathophysiology
Authors: Dwivedi Y , Roy B , Lugli G , Rizavi H , Zhang H , Smalheiser N R 
Published: November 2015

AbstractStress plays a major role in inducing depression, which may arise from interplay between complex cascades of molecular and cellular events that influence gene expression leading to altered connectivity and neural plasticity. In recent years, microRNAs (miRNAs) have carved their own niche owing to their innate ability to induce disease phenotype by regulating expression of a large number of genes in a cohesive and coordinated manner. In this study, we examined whether miRNAs and associated gene networks have a role in chronic corticosterone (CORT; 50 mg kg−1 × 21 days)-mediated depression in rats. Rats given chronic CORT showed key behavioral features that resembled depression phenotype. Expression analysis revealed differential regulation of 26 miRNAs (19 upregulated, 7 downregulated) in prefrontal cortex of CORT-treated rats. Interaction between altered miRNAs and target genes showed dense interconnected molecular network, in which multiple genes were predicated to be targeted by the same miRNA. A majority of altered miRNAs showed binding sites for glucocorticoid receptor element, suggesting that there may be a common regulatory mechanism of miRNA regulation by CORT. Functional clustering of predicated target genes yielded disorders such as developmental, inflammatory and psychological that could be relevant to depression. Prediction analysis of the two most prominently affected miRNAs miR-124 and miR-218 resulted into target genes that have been shown to be associated with depression and stress-related disorders. Altogether, our study suggests miRNA-mediated novel mechanism by which chronic CORT may be involved in depression pathophysiology.
PXR stimulates growth factor-mediated hepatocyte proliferation by cross-talk with the FOXO transcription factor
Authors: Shizu Ryota , Abe Taiki , Benoki Satoshi , Takahashi Miki , Kodama Susumu , Miayata Masaaki , Matsuzawa Atsushi , Yoshinari Kouichi 
Published: November 2015

Growth factor-mediated hepatocyte proliferation is crucial in liver regeneration and the recovery of liver function after injury. The nuclear receptor, pregnane X receptor (PXR), is a key transcription factor for the xenobiotic-induced expression of genes associated with various liver functions. Recently, we reported that PXR activation stimulates xenobiotic-induced hepatocyte proliferation. In the present study, we investigated whether PXR activation also stimulates growth factor-mediated hepatocyte proliferation. In G0 phase-synchronized, immortalized mouse hepatocytes, serum or epidermal growth factor treatment increased cell growth and this growth was augmented by the expression of mouse PXR and co-treatment with pregnenolone 16α-carbonitrile (PCN), a PXR ligand. In a liver regeneration model using carbon tetrachloride, PCN treatment enhanced the injury-induced increase in the number of Ki-67-positive nuclei as well as Ccna2 and Ccnb1 mRNA levels in wild-type (WT) but not Pxr-null mice. Chronological analysis of this model demonstrated that PCN treatment shifted the maximum cell proliferation to an earlier time point and increased the number of M-phase cells at those time points. In WT but not Pxr-null mice, PCN treatment reduced hepatic mRNA levels of genes involved in the suppression of G0/G1- and G1/S-phase transition, e.g. Rbl2, Cdkn1a and Cdkn1b. Analysis of the Rbl2 promoter revealed that PXR activation inhibited its Forkhead box O3 (FOXO3)-mediated transcription. Finally, the PXR-mediated enhancement of hepatocyte proliferation was inhibited by the expression of dominant active FOXO3 in vitro. The results of the present study suggest that PXR activation stimulates growth factor-mediated hepatocyte proliferation in mice, at least in part, through inhibiting FOXO3 from accelerating cell-cycle progression.
pH ISFET sensor with PVTA compensation
Authors: Carrillo‐Martínez L.A. , Espinosa Flores‐Verdad G. , Pérez B.M. , Molina Reyes J. 
Published: November 2015

Sensory system performance and variability depend on the compensation degree against fabrication process, voltage, temperature and ageing (PVTA) variations. A pH ion sensitive field‐effect transistor sensor with PVTA compensation is presented; stages for calibration and sensitivity adjustment were also included. To validate its performance, the proposed sensor was compared with a non‐compensated sensor; the results showed that PVTA variations were reduced by 81.50% for fabrication process and ageing, 87.91% for voltage and 80.30% for temperature. The maximum resolution achieved was 833.33 mV/pH.
Global impacts of energy demand on the freshwater resources of nations
Authors: Holland Robert Alan , Scott Kate A. , Flörke Martina , Brown Gareth , Ewers Robert M. , Farmer Elizabeth , Kapos Valerie , Muggeridge Ann , Scharlemann Jörn P. W. , Taylor Gail , Barrett John , Eigenbrod Felix 
Published: November 2015

Significance
Understanding the role of international trade in driving pressures on freshwater resources is key to meeting challenges at the water–energy nexus. A coupled trade and hydrological model is used to examine pressures on freshwater resources associated with energy production across the global economy. While the electric and gas sectors induce freshwater consumption predominantly within countries where demand originates (91% and 81%, respectively), the petroleum sector exhibits a high international footprint (56%). Critical geographic areas and economic sectors are identified, providing focus for resource-management actions to ensure energy and freshwater security. Our analysis demonstrates the importance of broadening the discourse on energy policy to address issues including freshwater scarcity, the role of international trade, and wider environmental and societal considerations.
Rad51 recombinase prevents Mre11 nuclease-dependent degradation and excessive PrimPol-mediated elongation of nascent DNA after UV irradiation
Authors: Vallerga María Belén , Mansilla Sabrina F. , Federico María Belén , Bertolin Agustina P. , Gottifredi Vanesa 
Published: November 2015

Significance
Pathways that promote DNA replication across replication barriers are central for cell survival. Herein, we report that in UV-irradiated cells lacking the Rad51 recombinase (Rad51), the DNA replication choreography is profoundly altered. We detected excessive degradation of nascent DNA followed by dysregulated elongation of DNA across UV barriers. PrimPol, a DNA polymerase with primase activity, promoted excessive elongation of nascent DNA, thus suggesting the accumulation of discontinuous replication tracks in Rad51-depleted cells. The altered DNA replication choreography in Rad51-knockdown samples resulted in the accumulation of replication stress markers and cell death. Hence, Rad51 promotes multiple, biologically relevant events at ongoing forks that encounter UV-damaged replication templates.