bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving visualization and quantitative assessment of choriocapillaris with swept source OCTA through registration and averaging applicable to clinical systems
Authors: Chu Zhongdi , Zhou Hao , Cheng Yuxuan , Zhang Qinqin , Wang Ruikang K. 
Published: November 2018

AbstractChoriocapillaris (CC) visualization and quantification remains challenging. We propose an innovative three-step registration and averaging approach using repeated swept source optical coherence tomography angiography (SS-OCTA) scans to conduct automatic quantitative assessment on CC. Six subjects were enrolled, each imaged at several locations with SS-OCTA from macular to equatorial regions using 3 mm × 3 mm scanning pattern. Five repeated volumes were collected for each subject. The complex optical microangiography (OMAG) algorithm was applied to identify blood flow in CC slab. An automatic three-step registration of translation, affine and B-Spline was applied to en face OCTA images of CC, followed with averaging. A fuzzy clustering approach was used to segment vasculature and flow deficits from the averaged images. The improvement in visualization of CC was evaluated and the average intercapillary distance was estimated by calculating the averaged capillary lumen spacing. A series of quantitative indices of flow deficit density, number, size, complexity index and aspect ratio index (FDD, FDN, FDS, FDCI and FDARI) were designed and validated with the increase of repeated scan numbers for averaging. Quantitative assessment was applied and compared on CC in macular and equatorial regions. The intercapillary distance was observed to be around 24 µm at macula and increased toward equatorial regions. All five quantitative indices (FDD, FDN, FDS, FDCI and FDARI) showed significant changes with multiple averaging and tend to become stable with repeated number of 4. Our proposed registration and averaging algorithm significantly improved the visualization of CC with SS-OCTA. The designed five indices for CC provide more options in the quantitative assessment of CC and are of great potentials in assisting the understanding of disease pathology, early diagnosis and treatment monitoring.
Radiation-induced premature cellular senescence involved in glomerular diseases in rats
Authors: Aratani Sae , Tagawa Masako , Nagasaka Shinya , Sakai Yukinao , Shimizu Akira , Tsuruoka Shuichi 
Published: November 2018

AbstractCurrently, cellular senescence has emerged as a fundamental contributor to chronic organ diseases. Radiation is one of the stress factors that induce cellular senescence. Although the kidney is known as a radiosensitive organ, whether and how radiation-induced cellular senescence is associated with kidney diseases remains unclear. In this study, we performed experiments on 7–8-week-old male rats that received a single dose of 18-Gy radiation in the unilateral kidney. The irradiated kidneys showed hallmarks of cellular senescence, including increased SA-β-gal activity, upregulation of cyclin-dependent kinase inhibitor (p53, p21, and p16), and absence of DNA proliferation marker (Ki-67). Furthermore, combined with in-vitro experiments, we demonstrated that radiation-induced senescent glomerular endothelial cells acquired altered gene expression, namely, senescence-associated secretory phenotype (particularly, IL-6), which might be triggered by NF-kB signaling pathway. Pathological analysis suggested severe glomerular endothelial cell injury, as evidenced by thrombotic microangiopathy, collapsing glomeruli, and reduced endothelial cell numbers. We suggested that glomerular endothelial cells were more susceptible to radiation-induced cellular senescence. In conclusion, the current study is the first to identify the important role of radiation-induced cellular senescence, mainly derived from glomerular endothelial cells, for the development of glomerular injury.
Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion
Authors: De Vrieze Jo , Ijaz Umer Z. , Saunders Aaron M. , Theuerl Susanne 
Published: November 2018

AbstractThe microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.
Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates
Authors: Arachchige Pavithra S. Pitumpe , Hettiarachchi Ganga M. , Rice Charles W. , Dynes James J. , Maurmann Leila , Wang Jian , Karunakaran Chithra , Kilcoyne A. L. David , Attanayake Chammi P. , Amado Telmo J. C. , Fiorin Jackson E. 
Published: November 2018

AbstractDirect evidence-based approaches are vital to evaluating newly proposed theories on the persistence of soil organic carbon and establishing the contributions of abiotic and biotic controls. Our primary goal was to directly identify the mechanisms of organic carbon stabilization in native-state, free soil microaggregates without disrupting the aggregate microstructure using scanning transmission x-ray microscopy coupled with near edge x-ray absorption fine structure spectroscopy (STXM-NEXAFS). The influence of soil management practices on microaggregate associated-carbon was also assessed. Free, stable soil microaggregates were collected from a tropical agro-ecosystem in Cruz Alta, Brazil. The long-term experimental plots (>25 years) comparing two tillage systems: no-till and till with a complex crop rotation. Based on simultaneously collected multi-elemental associations and speciation, STXM-NEXAFS successfully provided submicron level information on organo-mineral associations. Simple organic carbon sources were found preserved within microaggregates; some still possessing original morphology, suggesting that their stabilization was not entirely governed by the substrate chemistry. Bulk analysis showed higher and younger organic carbon in microaggregates from no-till systems than tilled systems. These results provide direct submicron level evidence that the surrounding environment is involved in stabilizing organic carbon, thus favoring newly proposed concepts on the persistence of soil organic carbon.
Evidence for mitigation of coral bleaching by manganese
Authors: Biscéré Tom , Ferrier-Pagès Christine , Gilbert Antoine , Pichler Thomas , Houlbrèque Fanny 
Published: November 2018

AbstractUnprecedented mass coral bleaching events due to global warming and overall seawater pollution have been observed worldwide over the last decades. Although metals are often considered as toxic substances for corals, some are essential at nanomolar concentrations for physiological processes such as photosynthesis and antioxidant defenses. This study was designed to elucidate, the individual and combined effects of nanomolar seawater enrichment in manganese (Mn) and iron (Fe), on the main physiological traits of Stylophora pistillata, maintained under normal growth and thermal stress conditions. We provide, for the first time, evidence that Mn is a key trace element for coral symbionts, enhancing cellular chlorophyll concentrations, photosynthetic efficiency and gross photosynthetic rates at ambient temperature. Our experiment also highlights the key role of Mn in increasing coral resistance to heat stress-induced bleaching. While Mn-enriched corals did not bleach and did not reduce their rates of photosynthesis and calcification, control corals experienced significant bleaching. On the contrary to Mn, Fe enrichment not only impaired calcification but induced significant bleaching. Such information is an important step towards a better understanding of the response of corals to seawater enrichment in metals. It can also explain, to some extent, species susceptibility to environmental stress.
NTG-101: A Novel Molecular Therapy that Halts the Progression of Degenerative Disc Disease
Authors: Matta Ajay , Karim Muhammad Zia , Gerami Hoda , Jun Peter , Funabashi Martha , Kawchuk Greg , Goldstein Alyssa , Foltz Warren , Sussman Marshall , Eek Bjorn C. , Erwin W. Mark 
Published: November 2018

AbstractThe tremendous cost, pain and disability associated with degenerative disc disease (DDD) makes the development of a biological agent that can mitigate the course of DDD, a critical unmet need. We have identified and reported that a single injection of a combination of recombinant human (rh) Transforming growth factor beta 1 (TGF-β1) and Connective tissue growth factor (CTGF) proteins into the injured intervertebral disc (IVD) nucleus pulposus (NP) can mediate DDD in a pre-clinical rodent model. In this study, we developed and evaluated the efficacy of a novel molecular therapy (NTG-101) containing rhTGF-β1 and rhCTGF proteins suspended in an excipient solution usingin vivomodels of DDD including rat-tail and chondrodystrophic (CD) canines. Needle puncture injury in CD-canine NPs resulted in loss of hydration, disc height and showed radiographic evidence of DDD like humans. However, NTG-101-injected IVDs maintained disc height and demonstrated retention of viscoelastic properties as compared to IVDs injected with phosphate buffer saline (PBS, 1X, pH = 7.2). In addition, a single intra-discal injection of NTG-101 into the injured IVD-NPs resulted in sustained expression of healthy extra-cellular matrix (ECM) proteins (aggrecan, collagen 2A1) and reduced expression of inflammation associated proteins and molecules (IL-1β, IL-6, IL-8, MMP-13, Cox-2 and PGE2) as compared to vehicle controls. In conclusion, we demonstrated that a single intra-discal injection of the novel formulation, NTG-101 confers a robust anti-inflammatory, anti-catabolic and pro-anabolic effects in pre-clinical models of DDD thereby restoring homeostasis. These findings suggest the therapeutic potential of NTG-101 for clinical use.
Revised role for Hfq bacterial regulator on DNA topology
Authors: Malabirade Antoine , Partouche David , El Hamoui Omar , Turbant Florian , Geinguenaud Frédéric , Recouvreux Pierre , Bizien Thomas , Busi Florent , Wien Frank , Arluison Véronique 
Published: November 2018

AbstractHfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNA. Besides these RNA-related functions, Hfq has also been described as one of the nucleoid associated proteins shaping the bacterial chromosome. Therefore, Hfq appears as a versatile nucleic acid-binding protein, which functions are probably even more numerous than those initially suggested. For instance, E. coli Hfq, and more precisely its C-terminal region (CTR), has been shown to induce DNA compaction into a condensed form. In this paper, we establish that DNA induces Hfq-CTR amyloidogenesis, resulting in a change of DNA local conformation. Furthermore, we clarify the effect of Hfq on DNA topology. Our results evidence that, even if the protein has a strong propensity to compact DNA thanks to its amyloid region, it does not affect overall DNA topology. We confirm however that hfq gene disruption influences plasmid supercoiling in vivo, indicating that the effect on DNA topology in former reports was indirect. Most likely, this effect is related to small regulatory sRNA-Hfq-based regulation of another protein that influences DNA supercoiling, possibly a nucleoid associated protein such as H-NS or Dps. Finally, we hypothesise that this indirect effect on DNA topology explains, at least partially, the previously reported effect of Hfq on plasmid replication efficiency.
Correlation between dynamic recrystallization and formation of rare earth texture in a Mg-Zn-Gd magnesium alloy during extrusion
Authors: Jiang M. G. , Xu C. , Yan H. , Lu S. H. , Nakata T. , Lao C. S. , Chen R. S. , Kamado S. , Han E. H. 
Published: November 2018

AbstractThe trace addition of rare earth (RE) elements in Mg alloys can modify the extrusion texture, leading to the formation of RE texture and thus improved formability. The interrupted extrusion experiment as well as electron back-scatter diffraction (EBSD) characterization was conducted in Mg-1.5Zn-0.5Gd (wt.%) alloy to unveil the dominant dynamic recrystallization (DRX) mechanism and its correlation with the formation of RE texture during extrusion. The results indicate that continuous DRX (CDRX) dominated the microstructural development. Fresh DRXed grains with 30° [0001] grain boundaries preferentially nucleated in unDRXed grains with [10$$\bar{{\bf{1}}}$$

1
¯

0] basal fiber orientation via CDRX, showing preferred selection of [2$$\bar{{\bf{1}}}$$

1
¯

$$\bar{{\bf{1}}}$$

1
¯

0] basal fiber orientation rather than RE texture orientation. Consequently, CDRX contributed to the weakening of [10$$\bar{{\bf{1}}}$$

1
¯

0] basal fiber texture and had a more significant effect on the formation of [2$$\bar{{\bf{1}}}$$

1
¯

$$\bar{{\bf{1}}}$$

1
¯

0] basal fiber component than that of RE texture component. Besides, the preferred growth of recrystallized grains with RE texture orientation was confirmed to occur during static annealing after extrusion, which is inferred as the key reason for the formation of RE texture in dilute Mg-RE alloys.
Non-mercaptalbumin, Oxidized Form of Serum Albumin, Significantly Associated with Renal Function and Anemia in Chronic Kidney Disease Patients
Authors: Nakatani Shinya , Yasukawa Keiko , Ishimura Eiji , Nakatani Ayumi , Toi Norikazu , Uedono Hideki , Tsuda Akihiro , Yamada Shinsuke , Ikeda Hitoshi , Mori Katsuhito , Emoto Masanori , Yatomi Yutaka , Inaba Masaaki 
Published: November 2018

AbstractOxidative stress plays a major role in development of cardiovascular disease in patients with chronic kidney disease (CKD). Human mercaptalbumin (HMA), a reduced form of serum albumin, and non-mercaptalbumin (HNA), an oxidized form of serum albumin, are known as indicators for evaluating oxidative stress in systemic circulation, including end-stage renal disease cases. We investigated factors associated with fraction of HNA [f(HNA)] in 112 pre-dialysis CKD patients (63.6 ± 14.0 years old; 59 males, 53 females) using a newly established anion-exchange column packed with hydrophilic polyvinyl alcohol gel as well as high performance liquid chromatography. Mean f(HNA) in our CKD patients was 30.0 ± 6.1%, higher than that previously reported for healthy subjects. In multiple regression analysis, age (β = 0.200, p = 0.014), eGFR (β = −0.238, p = 0.009), hemoglobin (β = −0.346, p < 0.001), and ferritin (β = 0.200, p = 0.019) were significantly and independently associated with f(HNA) (R2 = 0.356, p < 0.001). In addition, factors related to CKD-mineral and bone disorder (CKD-MBD), including intact-PTH (β = 0.218, p = 0.049) and 1,25-dihydroxyvitamin D (1,25(OH)2D) (β = −0.178, p = 0.040), were significantly and independently associated with serum f(HNA) (R2 = 0.339, p < 0.001), whereas fibroblast growth factor-23 was not. These findings indicate the importance of management of hemoglobin and ferritin levels, as well as appropriate control of CKD-MBD factors for a better redox state of serum albumin in CKD patients.
Source evaluation of 137Cs in foodstuffs based on trace 134Cs radioactivity measurements following the Fukushima nuclear accident
Authors: Hori Mayumi , Saito Takuya , Shozugawa Katsumi 
Published: November 2018

AbstractWe performed gamma-ray analysis to determine the amount of radioactive cesium-134 (134Cs) and cesium-137 (137Cs) in 259 foodstuffs five years after the Fukushima nuclear accident of 2011. Using measurements of trace 134Cs radioactivity, we investigated the contribution ratio of 137Cs derived from the Fukushima accident on 2011 and pre-Fukushima. The median detected concentration of radiocesium (134Cs + 137Cs) in foodstuffs was 0.33 Bq/kg-raw, a much lower radioactivity than the Japanese regulatory limit. However, a few samples had particularly high radioactivity, including some dried mushrooms sold in Iwate Prefecture that had a 137Cs radioactivity concentration as high as 441 Bq/kg. Our analysis showed that 75.5% of the 137Cs detected in these mushrooms originated from the Fukushima accident, and 24.5% was originated before the Fukushima event. Our study clarified the 137Cs contamination in 75 of all 259 food samples before and after the Fukushima nuclear accident, showing that not only mushrooms but also fish had been contaminated before the Fukushima accident.
Cerebral Motor Functional Connectivity at the Acute Stage: An Outcome Predictor of Ischemic Stroke
Authors: Chi Nai-Fang , Ku Hsiao-Lun , Chen David Yen-Ting , Tseng Ying-Chi , Chen Chi-Jen , Lin Ying-Chin , Hsieh Yi-Chen , Chan Lung , Chiou Hung-Yi , Hsu Chung Y. , Hu Chaur-Jong 
Published: November 2018

AbstractSixty-seven patients with first acute ischemic stroke onset between 3 to 7 days and 25 age- and sex- matched controls were analyzed for the performance of a resting-state functional MRI to investigate whether the functional connectivity (FC) of the motor network in acute ischemic stroke is independently associated with functional outcomes. The FC of cortical motor network and default mode network was analyzed. The FC was compared between controls, patients with favorable outcomes (modified Rankin Scale, mRS ≤1), and patients with unfavorable outcomes (mRS ≥2) at 3 months. Of the 67 patients, 23 (34%) exhibited unfavorable outcomes. In multivariate analysis, the FC between ipsilesional primary motor cortex (M1) and contralesional dorsal premotor area (PMd) ≤0.63, were independently associated with unfavorable outcomes (odds ratio = 6.32,P = 0.032), whereas the FC of default mode network was not different between groups. The interhemispheric FC of the motor network is an independent predictor of functional outcomes in patients with acute ischemic stroke.
Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects
Authors: Sundin Johanna , Stridsberg Mats , Tap Julien , Derrien Muriel , Le Nevé Boris , Doré Joël , Törnblom Hans , Simrén Magnus , Öhman Lena 
Published: November 2018

AbstractAltered fecal levels of chromogranins (Cg) and secretogranins (Sg) are demonstrated in irritable bowel syndrome (IBS), but their role in IBS pathophysiology remains unknown. This study aimed to determine if granins are associated with bacterial composition, immune activation and IBS symptoms. Protein levels of fecal granins (CgA, CgB, SgII and SgIII) were analysed with immunoassays. Mucosal mRNA expression of granins, TPH1 and immune markers were evaluated with RT-qPCR. 16S rRNA gene sequencing was performed on fecal and mucosal bacteria. The intestinal granin profile, based on fecal protein levels and mucosal mRNA expression, could not discriminate between IBS patients (n = 88) and healthy subjects (HS, n = 33). IBS patients dominated by high fecal or mucosal granin levels, respectively, did not differ in symptom or immune profiles. Fecal-dominated and mucosal-dominated granin clusters of IBS patients and HS, demonstrated separate fecal and mucosal bacterial profiles and high fecal abundance of granins were associated with a less diverse bacterial composition and the Bacteroides enterotype. The intestinal granin profiles of IBS patients and HS are linked to the intestinal bacterial composition, diversity and enterotypes. These findings suggest that granins may be one of several host-produced factors regulating the microbiota composition of the intestine.
Transcriptomic analysis of hepatocellular carcinoma reveals molecular features of disease progression and tumor immune biology
Authors: Okrah K. , Tarighat S. , Liu B. , Koeppen H. , Wagle M. C. , Cheng G. , Sun C. , Dey A. , Chang M. T. , Sumiyoshi T. , Mounir Z. , Cummings C. , Hampton G. , Amler L. , Fridlyand J. , Hegde P. S. , Turley S. J. , Lackner M. R. , Huang S. M. 
Published: November 2018

AbstractHepatocellular carcinoma (HCC) develops in the context of chronic inflammatory liver disease and has an extremely poor prognosis. An immunosuppressive tumor microenvironment may contribute to therapeutic failure in metastatic HCC. Here, we identified unique molecular signatures pertaining to HCC disease progression and tumor immunity by analyzing genome-wide RNA-Seq data derived from HCC patient tumors and non-tumor cirrhotic tissues. Unsupervised clustering of gene expression data revealed a gradual suppression of local tumor immunity that coincided with disease progression, indicating an increasingly immunosuppressive tumor environment during HCC disease advancement. IHC examination of the spatial distribution of CD8+ T cells in tumors revealed distinct intra- and peri-tumoral subsets. Differential gene expression analysis revealed an 85-gene signature that was significantly upregulated in the peri-tumoral CD8+ T cell-excluded tumors. Notably, this signature was highly enriched with components of underlying extracellular matrix, fibrosis, and epithelial–mesenchymal transition (EMT). Further analysis condensed this signature to a core set of 23 genes that are associated with CD8+ T cell localization, and were prospectively validated in an independent cohort of HCC specimens. These findings suggest a potential association between elevated fibrosis, possibly modulated by TGF-β, PDGFR, SHH or Notch pathway, and the T cell-excluded immune phenotype. Indeed, targeting fibrosis using a TGF-β neutralizing antibody in the STAM™ model of murine HCC, we found that ameliorating the fibrotic environment could facilitate redistribution of CD8+ lymphocytes into tumors. Our results provide a strong rationale for utilizing immunotherapies in HCC earlier during treatment, potentially in combination with anti-fibrotic therapies.