bluuebunny/crossref_metadata_2025_split huggingface dataset:
A numerical treatment of radiative nanofluid 3D flow containing gyrotactic microorganism with anisotropic slip, binary chemical reaction and activation energy
Authors: Lu Dianchen , Ramzan M. , Ullah Naeem , Chung Jae Dong , Farooq Umer 
Published: November 2017

AbstractA numerical investigation of steady three dimensional nanofluid flow carrying effects of gyrotactic microorganism with anisotropic slip condition along a moving plate near a stagnation point is conducted. Additionally, influences of Arrhenius activation energy, joule heating accompanying binary chemical reaction and viscous dissipation are also taken into account. A system of nonlinear differential equations obtained from boundary layer partial differential equations is found by utilization of apposite transformations. RK fourth and fifth order technique of Maple software is engaged to acquire the solution of the mathematical model governing the presented fluid flow. A Comparison with previously done study is also made and a good agreement is achieved with existing results; hence reliable results are being presented. Evaluations are carried out for involved parameters graphically against velocity, temperature, concentration fields, microorganism distribution, density number, local Nusselt and Sherwood numbers. It is detected that microorganism distribution exhibit diminishing behavior for rising values of bio-convection Lewis and Peclet numbers.
Simultaneous multi-slice inverse imaging of the human brain
Authors: Hsu Yi-Cheng , Chu Ying-Hua , Tsai Shang-Yueh , Kuo Wen-Jui , Chang Chun-Yuan , Lin Fa-Hsuan 
Published: November 2017

AbstractUltrafast functional magnetic resonance imaging (fMRI) can measure blood oxygen level dependent (BOLD) signals with high sensitivity and specificity. Here we propose a novel method: simultaneous multi-slice inverse imaging (SMS-InI) — a combination of simultaneous multi-slice excitation, simultaneous echo refocusing (SER), blipped controlled aliasing in parallel imaging echo-planar imaging (EPI), and regularized image reconstruction. Using a 32-channel head coil array on a 3 T scanner, SMS-InI achieves nominal isotropic 5-mm spatial resolution and 10 Hz sampling rate at the whole-brain level. Compared with traditional inverse imaging, we found that SMS-InI has higher spatial resolution with lower signal leakage and higher time-domain signal-to-noise ratio with the optimized regularization parameter in the reconstruction. SMS-InI achieved higher effective resolution and higher detection power in detecting visual cortex activity than InI. SMS-InI also detected subcortical fMRI signals with the similar sensitivity and localization accuracy like EPI. The spatiotemporal resolution of SMS-InI was used to reveal that presenting visual stimuli with 0.2 s latency between left and right visual hemifield led to 0.2 s relative hemodynamic response latency between the left and right visual cortices. Together, these results indicate that SMS-InI is a useful tool in measuring cortical and subcortical hemodynamic responses with high spatiotemporal resolution.
Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers
Authors: Zhu Bin , Song Nan , Shen Ronglai , Arora Arshi , Machiela Mitchell J. , Song Lei , Landi Maria Teresa , Ghosh Debashis , Chatterjee Nilanjan , Baladandayuthapani Veera , Zhao Hongyu 
Published: November 2017

AbstractMultiple omic profiles have been generated for many cancer types; however, comprehensive assessment of their prognostic values across cancers is limited. We conducted a pan-cancer prognostic assessment and presented a multi-omic kernel machine learning method to systematically quantify the prognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, integratively, and in combination with clinical factors for 3,382 samples across 14 cancer types. We found that the prognostic performance varied substantially across cancer types. mRNA and miRNA expression profile frequently performed the best, followed by DNA methylation profile. Germline susceptibility variants displayed low prognostic performance consistently across cancer types. The integration of omic profiles with clinical variables can lead to substantially improved prognostic performance over the use of clinical variables alone in half of cancer types examined. Moreover, we showed that the kernel machine learning method consistently outperformed existing prognostic signatures, suggesting that including a large number of omic biomarkers may provide substantial improvement in prognostic assessment. Our study provides a comprehensive portrait of omic architecture for tumor prognosis across cancers, and highlights the prognostic value of genome-wide omic biomarker aggregation, which may facilitate refined prognostic assessment in the era of precision oncology.
Assessment of Concordance between 22C3 and SP142 Immunohistochemistry Assays regarding PD-L1 Expression in Non-Small Cell Lung Cancer
Authors: Xu Haipeng , Lin Gen , Huang Cheng , Zhu Weifeng , Miao Qian , Fan Xirong , Wu Biao , Zheng Xiaobing , Lin Xiandong , Jiang Kan , Hu Dan , Li Chao 
Published: November 2017

AbstractDifferent anti-PD-1 and anti-PD-L1 antibodies bind different epitopes. However, whether the results from the SP142 and 22C3 immunochemistry (IHC) assays can be interchanged to determine patient eligibility for immunotherapy remains largely unknown. Histologic sections from 135 tumor samples were probed with both 22C3 and SP142 antibodies. The concordance of PD-L1 expression determined by the two assays was assessed. Additionally, we evaluated the association of PD-L1 expression detected by different assays with clinicopathological features and prognosis. In total, 105 (77.78%) of 135 samples evaluated by the 22C3-IHC platform produced the same results with the SP142-IHC platform (Kappa value: 0.481, p < 0.001). In addition, 69 (51.11%) of 135 samples evaluated by the SP142-IHC platform produced the same results with the 22C3-IHC platform (Kappa value: 0.324, p < 0.001). PD-L1 expression based on the 22C3-IHC assay was significantly correlated with smoking status, whereas that based on the SP142-IHC assay was correlated with smoking status, sex, and histology. Compared to the SP142-IHC assay, the 22C3-IHC assay usually resulted in an underestimation of PD-L1 expression in tumor cells and immune cells. Thus, the results from the two assays cannot be interchanged. Our data also suggest that the use of different reagents may account for inconsistencies in the literature regarding the association between PD-L1 expression and clinicopathological features.
Integrated mRNA and microRNA transcriptome analysis reveals miRNA regulation in response to PVA in potato
Authors: Li Yanlin , Hu Xinxi , Chen Jiren , Wang Wanxing , Xiong Xingyao , He Changzheng 
Published: November 2017

AbstractPotato (Solanum tuberosum L.) is the fourth most important crop worldwide. Potato virus A (PVA) is one of the most harmful viruses infecting potatoes. However, the molecular mechanisms governing the responses to PVA infection in potato at the transcriptional and post-transcriptional levels are not well understood. In this study, we performed both mRNA and small RNA sequencing in potato leaves to identify the genes and miRNAs involved in the response to PVA infection. A total of 2,062 differentially expressed genes (DEGs) and 201 miRNAs (DEMs) were identified, respectively. Gene ontology (GO) and KEGG analysis revealed that these DEGs were involved in the transduction of pathogen signals, transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related (PR) genes, and changes in secondary metabolism. Small RNA sequencing revealed 58 miRNA-mRNA interactions related to PVA infection. Some of the miRNAs (stu-miR482d-3p, stu-miR397-5p, etc) which target PR genes showed negative correlations between the DEMs and DEGs. Eight of the DEGs and three DEMs with their target genes were further validated by quantitative real time-PCR (qRT-PCR). Overall, this study provides a transcriptome-wide insight into the molecular basis of resistance to PVA infection in potato leaves and potenital candidate genes for improving resistance cultivars.
Enhanced CD25+Foxp3+ regulatory T cell development by amodiaquine through activation of nuclear receptor 4A
Authors: Won Hee Yeon , Shin Ji Hyun , Oh Sera , Jeong Hana , Hwang Eun Sook 
Published: November 2017

AbstractCD4+T cells play key roles in the regulation of immune responses against pathogenic infectious antigens via development into effector T helper and induced regulatory T (iTreg) cells. Particularly, CD4+CD25+Foxp3+iTreg cells are crucial for maintaining immune homeostasis and controlling inflammatory diseases. Anti-inflammatory drugs that enhance iTreg cell generation would be effective at preventing and treating inflammatory and autoimmune diseases. In this study, we examined whether anti-malarial and anti-arthritic amodiaquine (AQ) could affect iTreg cell development. Despite the anti-proliferative activity of AQ, AQ only moderately decreased iTreg cell proliferation but substantially increased IL-2 production by iTreg cells. Furthermore, AQ dose-dependently increased iTreg cell development and significantly upregulated iTreg cell markers including CD25. Interestingly, CD25 expression was decreased at later stages of iTreg cell development but was sustained in the presence of AQ, which was independent of IL-2 signaling pathway. AQ directly increased CD25 gene transcription by enhancing the DNA-binding and transcriptional activity of nuclear receptor 4 A. Most importantly,in vivoadministration of AQ attenuated inflammatory colitis, resulted in the increased iTreg cells and decreased inflammatory cytokines. The ability of anti-malarial AQ to potentiate iTreg cell development makes it a promising drug for preventing and treating inflammatory and autoimmune diseases.
Mitochondrial DNA Mutations Associated with Type 2 Diabetes Mellitus in Chinese Uyghur Population
Authors: Jiang Wenxi , Li Ronghui , Zhang Yongbiao , Wang Panpan , Wu Tingting , Lin Jinming , Yu Jun , Gu Mingliang 
Published: November 2017

AbstractA hospital-based case-control study was conducted to investigate potential association between mitochondrial DNA and Type 2 diabetes mellitus (T2DM) in Chinese Uyghur population. We sequenced mitochondrial DNA from 210 Uyghur individuals including 88 T2DM patients and 122 controls. Using haplogroup classification and association test, we found that haplogroup H (odds ratio [OR] = 1.40; 95% confidence interval [CI]: 1.20–1.64; P = 0.0005138) and D4 (odds ratio = 1.47; 95% CI: 1.22–1.77; P = 0.001064) were associated with an increased risk of T2DM in Chinese Uyghur population. Two markers of haplogroup D4 and H, MT-ATP8 m.8414 T > G (p.Leu17Phe) and m.2706 G > A encoding 16S rRNA in mitochondria, were predicted to affect the structure of MT-ATP8 and 16S RNA, respectively, and may be involved in the pathogenesis of T2DM. Our study provides a new clue for mitochondrial DNA in the etiology of T2DM in Chinese Uyghur population.
Relativistic inverse Compton scattering of photons from the early universe
Authors: Malu Siddharth , Datta Abhirup , Colafrancesco Sergio , Marchegiani Paolo , Subrahmanyan Ravi , Narasimha D. , Wieringa Mark H. 
Published: November 2017

AbstractElectrons at relativistic speeds, diffusing in magnetic fields, cause copious emission at radio frequencies in both clusters of galaxies and radio galaxies through non-thermal radiation emission called synchrotron. However, the total power radiated through this mechanism is ill constrained, as the lower limit of the electron energy distribution, or low–energy cutoffs, for radio emission in galaxy clusters and radio galaxies, have not yet been determined. This lower limit, parametrized by the lower limit of the electron momentum – pmin – is critical for estimating the total energetics of non-thermal electrons produced by cluster mergers or injected by radio galaxy jets, which impacts the formation of large–scale structure in the universe, as well as the evolution of local structures inside galaxy clusters. The total pressure due to the relativistic, non–thermal population of electrons can be measured using the Sunyaev-Zel’dovich Effect, and is critically dependent on pmin, making the measurement of this non–thermal pressure a promising technique to estimate the electron low–energy cutoff. We present here the first unambiguous detection of this Sunyaev-Zel’dovich Effect for a non–thermal population of electrons in a radio galaxy jet/lobe, located at a significant distance away from the center of the Bullet cluster of galaxies.
Experimental maturation of Archaea encrusted by Fe-phosphates
Authors: Miot J. , Bernard S. , Bourreau M. , Guyot F. , Kish A. 
Published: November 2017

AbstractBurial is generally detrimental to the preservation of biological signals. It has often been assumed that (bio)mineral-encrusted microorganisms are more resistant to burial-induced degradation than non-encrusted ones over geological timescales. For the present study, we submitted Sulfolobus acidocaldarius experimentally encrusted by amorphous Fe phosphates to constrained temperature conditions (150 °C) under pressure for 1 to 5 days, thereby simulating burial-induced processes. We document the molecular and mineralogical evolution of these assemblages down to the sub-micrometer scale using X-ray diffraction, scanning and transmission electron microscopies and synchrotron-based X-ray absorption near edge structure spectroscopy at the carbon K-edge. The present results demonstrate that the presence of Fe-phosphates enhances the chemical degradation of microbial organic matter. While Fe-phosphates remained amorphous in abiotic controls, crystalline lipscombite (FeIIxFeIII3−x(PO4)2(OH)3−x) entrapping organic matter formed in the presence of S. acidocaldarius cells. Lipscombite textures (framboidal vs. bipyramidal) appeared only controlled by the initial level of encrustation of the cells, suggesting that the initial organic matter to mineral ratio influences the competition between nucleation and crystal growth. Altogether these results highlight the important interplay between minerals and organic matter during fossilization, which should be taken into account when interpreting the fossil record.
Repurposing an inhibitor of ribosomal biogenesis with broad anti-fungal activity
Authors: Sun Nuo , Li Dongmei , Zhang Yuhan , Killeen Kyle , Groutas William , Calderone Richard 
Published: November 2017

AbstractThe lack of new antifungal compounds with unique mechanisms of action is a concern for therapeutic management of patients. To identify inhibitors against human pathogenic fungi, we screened ~3000 compounds provided by the Developmental Therapeutics Program of NIH/NCI against a panel of pathogenic fungi including Candida species, Aspergillus fumigatus, and Cryptococcus neoformans. NSC319726 (a thiosemicarbazone) had broad antifungal activity in the range of 0.1–2.0 µg/ml and was also inhibitory to fluconazole-resistant isolates of Candida species. Synergy was demonstrated with NSC319726 and azoles, as well as caspofungin. The inhibitory concentration 50% (IC50) of NSC319726 was 35–800-fold higher than the Minimum Inhibitory Concentration 50% (MIC50 values), which indicates low compound toxicity to human cells in vitro. Transcriptome analysis of treated and untreated C. albicans using Gene Ontology (GO) revealed a large cluster of down regulated genes that encode translational proteins, especially those with ribosome biogenesis functions. As NSC319726 was first shown to have anti-cancer activity, its affects against human pathogenic fungi establish NSC319726 as a repurposed, off-patent compound that has potential antifungal activity. The minimal in vitro toxicity of lead optimized NSC319726 and its reasonable inhibitory activity against pathogens suggest advancing this compound to in vivo toxicity testing and protection studies against candidiasis.
Free SepF interferes with recruitment of late cell division proteins
Authors: Gao Yongqiang , Wenzel Michaela , Jonker Martijs J. , Hamoen Leendert W. 
Published: November 2017

AbstractThe conserved cell division protein SepF aligns polymers of FtsZ, the key cell division protein in bacteria, during synthesis of the (Fts)Z-ring at midcell, the first stage in cytokinesis. In addition, SepF acts as a membrane anchor for the Z-ring. Recently, it was shown that SepF overexpression in Mycobacterium smegmatis blocks cell division. Why this is the case is not known. Surprisingly, we found in Bacillus subtilis that SepF overproduction does not interfere with Z-ring assembly, but instead blocks assembly of late division proteins responsible for septum synthesis. Transposon mutagenesis suggested that SepF overproduction suppresses the essential WalRK two-component system, which stimulates expression of ftsZ. Indeed, it emerged that SepF overproduction impairs normal WalK localization. However, transcriptome analysis showed that the WalRK activity was in fact not reduced in SepF overexpressing cells. Further experiments indicated that SepF competes with EzrA and FtsA for binding to FtsZ, and that binding of extra SepF by FtsZ alleviates the cell division defect. This may explain why activation of WalRK in the transposon mutant, which increases ftsZ expression, counteracts the division defect. In conclusion, our data shows that an imbalance in early cell division proteins can interfere with recruitment of late cell division proteins.
CEA but not CA19-9 is an independent prognostic factor in patients undergoing resection of cholangiocarcinoma
Authors: Loosen Sven H. , Roderburg Christoph , Kauertz Katja L. , Koch Alexander , Vucur Mihael , Schneider Anne T. , Binnebösel Marcel , Ulmer Tom F. , Lurje Georg , Schoening Wenzel , Tacke Frank , Trautwein Christian , Longerich Thomas , Dejong Cornelis H. , Neumann Ulf P. , Luedde Tom 
Published: November 2017

AbstractCholangiocarcinoma (CCA) represents a rare form of primary liver cancer with increasing incidence but dismal prognosis. Surgical treatment has remained the only potentially curative treatment option, but it remains unclear which patients benefit most from liver surgery, highlighting the need for new preoperative stratification strategies. In clinical routine, CA19-9 represents the most widely used tumor marker in CCA patients. However, data on the prognostic value of CA19-9 in CCA patients are limited and often inconclusive, mostly due to small cohort sizes. Here, we investigated the prognostic value of CA19-9 in comparison with other standard laboratory markers in a large cohort of CCA patients that underwent tumor resection. Of note, while CA19-9 and CEA were able to discriminate between CCA and healthy controls, CEA showed a higher accuracy for the differentiation between CCA and patients with primary sclerosing cholangitis (PSC) compared to CA19-9. Furthermore, patients with elevated levels of C-reactive protein (CRP), CA19-9 or CEA showed a significantly impaired survival in Kaplan-Meier curve analysis, but surprisingly, only CEA but not CA19-9 represented an independent predictor of survival in multivariate Cox-regression analysis. Our data suggest that CEA might help to identify CCA patients with an unfavourable prognosis after tumor resection.
Preoperative serum thyroglobulin predicts initial distant metastasis in patients with differentiated thyroid cancer
Authors: Kim Hosu , Kim Young Nam , Kim Hye In , Park So Young , Choe Jun-Ho , Kim Jung-Han , Kim Jee Soo , Chung Jae Hoon , Kim Tae Hyuk , Kim Sun Wook 
Published: November 2017

AbstractDifferentiated thyroid cancer (DTC) generally has a favorable prognosis. However, a small percentage of patients suffer from initial distant metastasis (DM). To date, there is no effective predictor for the presence of initial DM. The aim of this study was to determine if preoperative serum thyroglobulin (Tg) level could predict initial DM in DTC. We reviewed an institutional thyroid cancer database from October 1994 to February 2016. To determine the Tg cutoff for predicting initial DM, 4,735 patients who were diagnosed with DTC were included in this study. Fifty-seven patients (1.2%) were identified as having DTC with initial DM. Median preoperative Tg level was 328.4 ng/ml in the initial DM group and 10.0 ng/ml in the non-DM group. Initial DM was the most important factor affecting serum Tg level (β = 2,049.32 ± 103.40;P < 0.001). The Tg cutoff level that distinguished overall DM with the greatest accuracy was 63.4 ng/ml [area under the ROC curve 0.914, sensitivity 84.2%, specificity 90.6%, negative likelihood ratio (LR) 0.17, and positive LR 8.97]. Preoperative Tg levels were useful for predicting initial DM of DTC. Measurement of serum Tg in patients with DTC may guide preoperative staging evaluation and initial treatment.
Novel Mechanism of the Pericyte-Myofibroblast Transition in Renal Interstitial Fibrosis: Core Fucosylation Regulation
Authors: Wang Nan , Deng Yiyao , Liu Anqi , Shen Nan , Wang Weidong , Du Xiangning , Tang Qingzhu , Li Shuangxin , Odeh Zach , Wu Taihua , Lin Hongli 
Published: November 2017

AbstractPericytes have been identified as a major source of myofibroblasts in renal interstitial fibrosis (RIF). The overactivation of several signaling pathways, mainly the TGF-β and PDGF pathways, initiates the pericyte-myofibroblast transition during RIF. Key receptors in these two pathways have been shown to be modified by fucosyltransferase 8 (FUT8), the enzyme that catalyzes core fucosylation. This study postulated that core fucosylation might play an important role in regulating the pericyte transition in RIF. The data showed that core fucosylation increased with the extent of RIF in patients with IgA nephropathy (IgAN). Similarly, core fucosylation of pericytes increased in both a unilateral ureteral occlusion (UUO) mouse model and an in vitro model of pericyte transition. Inhibition of core fucosylation by adenoviral-mediated FUT8 shRNA in vivo and FUT8 siRNA in vitro significantly reduced pericyte transition and RIF. In addition, the activation of both the TGF-β/Smad and PDGF/ERK pathways was blocked by core fucosylation inhibition. In conclusion, core fucosylation may regulate the pericyte transition in RIF by modifying both the TGF-β/Smad and PDGF/ERK pathways. Glycosylation might be a novel “hub” target to prevent RIF.
Association between nonspecific interstitial pneumonia and presence of CD20+ B lymphocytes within pulmonary lymphoid follicles
Authors: Peng Min , Wang Wenze , Qin Ling , Liu Hongrui , Qin Mingwei , Zheng Wenjie , Shi JuHong , Xu Wenbing , Zhu Yuanjue 
Published: November 2017

AbstractNonspecific interstitial pneumonia (NSIP) is characterised by interstitial infiltration of lymphocytes and varying amounts of interstitial fibrosis. B cells have been suggested to contribute to the pathogenesis of NSIP. However, the relationship between B-lymphocyte and the clinical outcomes of NSIP was unclear. In this study, 50 patients with histopathologically confirmed NSIP from Peking Union Medical College Hospital between April 2003 to December 2012 were retrospectively analyzed. Using immunohistochemical analyses, CD20+ B cells were counted in the lymphoid follicles, perivascular, interstitial, and peribronchiolar regions of lung tissure. The CD20+ lymphocytes were mainly present in the lymphoid follicles. The number of follicular CD20+ lymphocytes was higher in the fibrosing than cellular NSIP pattern [255.08 (132.92–449.71) vs. 121.33 (63.54–282.88)/0.1 mm2, p = 0.017]. After 1 year of therapy, the follicular CD20+ lymphocytes were significantly higher in patients whose forced vital capacity (FVC) worsened as compared to those who improved (p = 0.014). Additionally, follicular CD20+ lymphocytes were negatively correlated with the post-treatment percentage change in FVC (rho = −0.397, p = 0.004). However, follicular CD20+ lymphocytes were not correlated with survival. These results suggested that pulmonary follicular CD20+ lymphocytes were correlated with the fibrosing pattern of NSIP and predicted less clinical improvement after treatment.