bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome alteration spectrum in rat lung induced by radiotherapy
Authors: Zhang Tao , Cheng Guowei , Sun Li , Deng Lei , Wang Xin , Bi Nan 
Published: December 2019

AbstractRadiation therapy is crucial for curative treatment of lung cancer, which frequently leads to lung injury. Long non-coding RNAs (lncRNAs) are a group of RNAs longer than 200 nucleotides and lack protein-coding capacity. Increasing evidences demonstrate the important roles of lncRNAs in biological processes. However, the mechanism underlying the association of ionizing radiation with alterations in mRNA and lncRNA expression and lung injury remains unclear. In our study, the male Sprague-Dawley (SD) rats were exposed to a dose of 18 Gy of 6 MV X-ray and the transcriptome spectrum was studied. To identify the differentially expressed mRNAs and lncRNAs induced by X-ray, the RNA sequencing data of lung tissues from irradiated and normal rats for 4, 8, and 16 weeks were analyzed, using |log2_ratio| ≥ 1 and q ≤ 0.05 as thresholds for significantly differential expression. The number of differentially expressed mRNAs was 1097 (686 up- and 411 down-) for 4-week radiotherapy group, 3006 (1935 up- and 1071 down-) for 8-week group and 1838 (1178 up- and 660 down-) for 16-week group. There were 606 (279 up- and 327 down-) differentially expressed lncRNAs in 4-week group, 1715 (831 up- and 884 down-) in 8-week group and 1043 (656 up- and 387 down-) in 16-week group. The differentially expressed mRNAs were mainly involved in cell cycle regulation and Fc receptor pathway, while the lncRNA target genes were significantly enriched in cellular stress response and regulation of cell migration. Moreover, compared with the control group, the irradiated group presented higher tissue specificity of lncRNAs. Radiation-induced lung injury, especially the dynamic network of lncRNAs and mRNAs, is worthy of study. Investigation on the regulatory details of related pathways is significant for the prevention of radiation-related lung injury, as well as the improvement of radiation therapy.
Long noncoding RNA AURKAPS1 potentiates malignant hepatocellular carcinoma progression by regulating miR-142, miR-155 and miR-182
Authors: Li Jianhua , Guo Wenzhi , Xue Wenping , Xu Pengfei , Deng Zhen , Zhang Danhua , Zheng Shouhua , Qiu Xinguang 
Published: December 2019

AbstractThe mitotic serine/threonine kinase aurora kinase-A (AURKA) has been identified as carcinogenic in hepatocellular carcinoma (HCC). AURKAPS1, a long non-coding RNA (lncRNA), is the pseudo-gene of AURKA, which play important roles in the cancer. Its underlying functions and mechanisms in liver cancer progression remain largely unknown. The mRNA expression of AURKAPS1 in HCC tumor tissues was significantly higher, which is associated with tumor size and TNM stage. The high expression of AURKAPS1 promotes cell movement, migration and invasion. AURKAPS1 can increases the protein expression of RAC1, promotes the activation of ERK, and enhance the formation of membrane ruffles by binding with miR-182, miR-155 and miR-142 competively. Thus, AURKAPS1 could be a useful marker, and the combination of AURKAPS1/miRNAs (miR-142, miR-155 and miR-182) may be a new theoretical basis for the treatment of HCC.
Land use affects lowland stream ecosystems through dissolved oxygen regimes
Authors: dos Reis Oliveira Paula C. , van der Geest Harm G. , Kraak Michiel H. S. , Verdonschot Piet F. M. 
Published: December 2019

AbstractThe aim of the present study was to assess the impact of surrounding land use on the structure and functioning of lowland stream ecosystems. To this end, five different land use types were selected (forest, extensive grassland, intensive grassland, cropland and wastewater treatment plant) each represented by four replicate streams, in which diel dissolved oxygen concentrations were recorded, sediment and water quality parameters were measured and macroinvertebrate community composition was determined. Chironomus sp., Oligochaeta and Gastropoda dominated the cropland and wastewater treatment plant (WWTP) streams, while Plecoptera and most Trichoptera only occurred in forest and extensive grassland streams. Forest streams communities were related to a high oxygen saturation, a high C/N ratio in the sediment and woody debris and coarse particulate organic matter (CPOM) substrate cover. Macroinvertebrate communities in cropland and WWTP streams were related to a low oxygen saturation in water and sediment and high concentrations of dissolved nitrogen, phosphorus and carbon. It is concluded that land use specific impacts on lowland streams are likely exerted via fine sediment accumulation in deposition zones, affecting oxygen regimes, sediment oxygen demand and stream metabolism, ultimately changing macroinvertebrate community composition. This study supports therefore the importance of including the catchment scale in ecological stream quality assessments, combining structural and functional endpoints.
Sulfur isotope analysis for representative regional background atmospheric aerosols collected at Mt. Lulin, Taiwan
Authors: Chung Chuan-Hsiung , You Chen-Feng , Hsu Shih-Chieh , Liang Mao-Chang 
Published: December 2019

AbstractAir pollution resulted from fossil fuel burning has been an environmental issue in developing countries in Asia. Sulfur-bearing compounds, in particular, are species that are regulated and monitored routinely. To assess how the species affect at local and global scales, regional background level has to be defined. Here, we report analysis of sulfur isotopes in atmospheric sulfate, the oxidation end product of sulfur species, in particulate phase collected at the Lulin observatory located at 2862 m above mean sea level in 2010. The averaged sulfate concentration for 44 selected samples is 2.7 ± 2.3 (1-σ standard deviation) μg m−3, and the averaged δ34S is 2.2 ± 1.6‰, with respect to the international standard Vienna Canyon Diablo Troilite. Regardless of the origins of air masses, no noticeable difference between the low-altitude Pacific and high-altitude free troposphere sulfate aerosols is observed. Also, no identifiable seasonal cycle in seen. Correlation analysis with respect to coal burning tracers such as lead and oil industry tracers such as vanadium shows sulfate concentration is in better correlation with vanadium (R2 = 0.86, p-value < 0.001) than with lead (R2 = 0.45, p-value < 0.001) but no statistically significant correlation is found in δ34S with any of physical quantities measured. We suggest the sulfate collected at Lulin can best represent the regional background level in the Western Pacific, a quantity that is needed in order to quantitatively assess the budget of sulfur in local to country scales.
Metagenomic analysis of dental calculus in ancient Egyptian baboons
Authors: Ottoni Claudio , Guellil Meriam , Ozga Andrew T. , Stone Anne C. , Kersten Oliver , Bramanti Barbara , Porcier Stéphanie , Van Neer Wim 
Published: December 2019

AbstractDental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals’ oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th–6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons’ oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.
Electron Tomography Analysis of Thylakoid Assembly and Fission in Chloroplasts of a Single-Cell C4 plant, Bienertia sinuspersici
Authors: Mai Keith Ka Ki , Yeung Wai-Tsun , Han Sang-Yun , Cai Xiaohao , Hwang Inhwan , Kang Byung-Ho 
Published: December 2019

AbstractBienertia sinuspersici is a single-cell C4 plant species of which chlorenchyma cells have two distinct groups of chloroplasts spatially segregated in the cytoplasm. The central vacuole encloses most chloroplasts at the cell center and confines the rest of the chloroplasts near the plasma membrane. Young chlorenchyma cells, however, do not have large vacuoles and their chloroplasts are homogenous. Therefore, maturing Bienertia chlorenchyma cells provide a unique opportunity to investigate chloroplast proliferation in the central cluster and the remodeling of chloroplasts that have been displaced by the vacuole to the cell periphery. Chloroplast numbers and sizes increased, more notably, during later stages of maturation than the early stages. Electron tomography analyses indicated that chloroplast enlargement is sustained by thylakoid growth and that invaginations from the inner envelope membrane contributed to thylakoid assembly. Grana stacks acquired more layers, differentiating them from stroma thylakoids as central chloroplasts matured. In peripheral chloroplasts, however, grana stacks stretched out to a degree that the distinction between grana stacks and stroma thylakoids was obscured. In central chloroplasts undergoing division, thylakoids inside the cleavage furrow were kinked and severed. Grana stacks in the division zone were disrupted, and large complexes in their membranes were dislocated, suggesting the existence of a thylakoid fission machinery.
Reciprocal connectivity between secondary auditory cortical field and amygdala in mice
Authors: Tsukano Hiroaki , Hou Xubin , Horie Masao , Kitaura Hiroki , Nishio Nana , Hishida Ryuichi , Takahashi Kuniyuki , Kakita Akiyoshi , Takebayashi Hirohide , Sugiyama Sayaka , Shibuki Katsuei 
Published: December 2019

AbstractRecent studies have examined the feedback pathway from the amygdala to the auditory cortex in conjunction with the feedforward pathway from the auditory cortex to the amygdala. However, these connections have not been fully characterized. Here, to visualize the comprehensive connectivity between the auditory cortex and amygdala, we injected cholera toxin subunit b (CTB), a bidirectional tracer, into multiple subfields in the mouse auditory cortex after identifying the location of these subfields using flavoprotein fluorescence imaging. After injecting CTB into the secondary auditory field (A2), we found densely innervated CTB-positive axon terminals that were mainly located in the lateral amygdala (La), and slight innervations in other divisions such as the basal amygdala. Moreover, we found a large number of retrogradely-stained CTB-positive neurons in La after injecting CTB into A2. When injecting CTB into the primary auditory cortex (A1), a small number of CTB-positive neurons and axons were visualized in the amygdala. Finally, we found a near complete absence of connections between the other auditory cortical fields and the amygdala. These data suggest that reciprocal connections between A2 and La are main conduits for communication between the auditory cortex and amygdala in mice.
Controllable symmetry breaking solutions for a nonlocal Boussinesq system
Authors: Fei Jinxi , Ma Zhengyi , Cao Weiping 
Published: December 2019

AbstractThe generalized Boussinesq equation is a useful model to describe the water wave. In this paper, with the coupled Alice-Bob (AB) systems, the nonlocal Boussinesq system can be obtained via the parity and time reversal symmetry reduction. By introducing an extended Bäcklund transformation, the symmetry breaking rogue wave, symmetry breaking soliton and symmetry breaking breather solutions for a nonlocal Boussinesq system are obtained through the derived Hirota bilinear form. The residual symmetry and finite symmetry transformation of the nonlocal AB-Boussinesq system are also studied.
Impact of iterative reconstruction with resolution recovery in myocardial perfusion SPECT: phantom and clinical studies
Authors: Okuda Koichi , Nakajima Kenichi , Yoneyama Hiroto , Shibutani Takayuki , Onoguchi Masahisa , Matsuo Shinro , Hashimoto Mitsumasa , Kinuya Seigo 
Published: December 2019

AbstractThe corrections of photon attenuation, scatter, and depth-dependent blurring improve image quality in myocardial perfusion single-photon emission computed tomography (SPECT) imaging; however, the combined corrections induce artifacts. Here, we present the single correction method of depth-dependent blurring and its impact for myocardial perfusion distribution in phantom and clinical studies. The phantom and clinical patient images were acquired with two conditions: circular and noncircular orbits of gamma cameras yielded constant and variable depth-dependent blurring, respectively. An iterative reconstruction with the correction method of depth-dependent was used to reconstruct the phantom and clinical patient images. We found that the single correction method improved the robustness of phantom images whether the images contained constant or variable depth-dependent blurring. The myocardial perfusion databases generated from 72 normal patients exhibited uniform perfusion distribution of whole myocardium. In summary, the single correction method of depth-dependent blurring with iterative reconstruction is helpful for myocardial perfusion SPECT.
Predictive factors for inadequate bowel preparation using low-volume polyethylene glycol (PEG) plus ascorbic acid for an outpatient colonoscopy
Authors: Shin Seung Yong , Ga Kyeong Seon , Kim In Young , Park Yoo Mi , Jung Da Hyun , Kim Jie-Hyun , Youn Young Hoon , Park Hyojin , Park Jae Jun 
Published: December 2019

AbstractLow-volume polyethylene glycol (PEG) plus ascorbic acid solutions are widely used for bowel cleansing before colonoscopy. This study aimed to investigate the pre-endoscopic predictive factors for inadequate preparation in subjects receiving low-volume PEG plus ascorbic acid. A prospective study was performed at Gangnam Severance Hospital, Korea, from June 2016 to December 2016. All participants received low-volume PEG plus ascorbic acid solutions for outpatient colonoscopy. The split-dose bowel preparation was administered in subject with morning colonoscopy while same day bowel preparation was used for afternoon colonoscopy. 715 patients were enrolled (mean age 56.1 years, 54.4% male), of which 138 (19.3%) had an inadequate bowel preparation. In multivariable analysis, cirrhosis (OR 4.943, 95% CI 1.191–20.515), low (less than 70%) compliance for three-day low-residual diet (OR 2.165, 95% CI 1.333–3.515), brown liquid rectal effluent (compared with clear or semi-clear effluent) (OR 7.604, 95% CI, 1.760–32.857), and longer time interval (≥2 hours) between last defecation and colonoscopic examination (OR 1.841, 95% CI, 1.190–2.849) were found as an independent predictors for inadequate preparation. These predictive factors may be useful in guiding additional intervention to improve quality of bowel preparation.
An Effect of Chronic Stress on Prospective Memory via Alteration of Resting-State Hippocampal Subregion Functional Connectivity
Authors: Chen Jierong , Wei Zhen , Han Hongying , Jin Lili , Xu Chuanyong , Dong Dan , Lu Jianping , Wan Guobin , Peng Ziwen 
Published: December 2019

AbstractThe alteration of hippocampal function by chronic stress impairs higher order cognitive functions such as prospective memory (PM). However, how chronic stress affects hippocampal subregions related to PM remains largely unknown. In this study, the altered functional network of hippocampal subregions related to PM in chronic stress was explored. College students (N = 21) completed PM tasks and resting-state functional magnetic resonance imaging scans one month prior to (baseline) and during the final examination week (chronic stress). Hippocampal subregions’ seed-based functional connectivity (FC) and PM were compared between baseline and chronic stress. PM performance declined in chronic stress. The FC of the cornu ammonis 2, 3 and dentate gyrus (CA23DG) with the bilateral caudate and precuneus was increased in chronic stress, while the FC of the subicular complex (SUBC) with the left middle frontal gyrus, the left inferior parietal gyrus and the right supramarginal gyrus was decreased. There was a negative correlation between PM performance and the FC of hippocampal subregions. We found chronic stress impairs PM by decreasing the FC of SUBC and increasing the FC of CA23DG. These findings suggest functional changes in hippocampal subregion networks as a mechanism underlying the impairment of PM in chronic stress.
An In Vivo Mouse Model of Pelvic Recurrence of Human Colorectal Cancer
Authors: Yamamoto Masashi , Taniguchi Kohei , Masubuchi Shinsuke , Tominaga Tomo , Inomata Yosuke , Miyamoto Akiko , Ishizuka Taka-Aki , Murakami Takashi , Osumi Wataru , Hamamoto Hiroki , Tanaka Keitaro , Okuda Junji , Uchiyama Kazuhisa 
Published: December 2019

AbstractPelvic recurrence of colorectal cancer is a crucial problem because radical surgery can lead to excessive invasion. Novel therapeutic strategies are required instead of surgery. However, there are few suitable models because of the difficulty in transplanting and observing tumors in the pelvis. We have established an appropriate injection site suitable for the establishment of colorectal cancer pelvic recurrence that allows for the observation of tumor growth. DLD-1 cells stably expressing luciferase (DLD-1 clone#1-Luc) were inoculated into various points of female BALB/c nude mice and the engrafted cells were analyzed with an imaging system employing bioluminescent signals and computed tomography. Weekly analysis with the imaging system showed that a triangular area defined by the vagina, the anus, and the ischial spine was suitable for the engraftment of pelvic tumors. The imaging system was able to detect the engrafted tumor 7 days after the inoculation of cells. Weight loss was observed in our model, and overall survival was 21–42 days. Tumor involvement of adjacent organs was detected histopathologically, as is the case in the clinical situation. These findings suggest that this model is valid for evaluations of the therapeutic effects of novel treatments under development. It is hoped that this model will be used in preclinical research.
Rapid, CRISPR-Based, Field-Deployable Detection Of White Spot Syndrome Virus In Shrimp
Authors: Sullivan Timothy J. , Dhar Arun K. , Cruz-Flores Roberto , Bodnar Andrea G. 
Published: December 2019

AbstractRapid, sensitive, point-of-care diagnostics are critical for managing infectious diseases. Here we adapt the CRISPR-based SHERLOCK method to develop a rapid, accurate, single copy detection assay for White Spot Syndrome Virus, the most devastating virus impacting global shrimp aquaculture. Further, we combine paper matrix nucleic acid extraction and lateral flow colorimetric reporting to create a fully field-deployable, next-generation diagnostic with potential to transform veterinary pathology, disease ecology, and animal production.
Identification of miR-328-3p as an endogenous reference gene for the normalization of miRNA expression data from patients with Diabetic Retinopathy
Authors: Prado Marcelle SanJuan Ganem , de Goes Thaline Cunha , de Jesus Mirthz Lemos , Mendonça Lucilla Silva Oliveira , Nascimento Jadson Santos , Kaneto Carla Martins 
Published: December 2019

AbstractDiabetic Retinopathy, the main cause of visual loss and blindness among working population, is a complication of Diabetes mellitus (DM), which has been described as a major public health challenge, so it is important to identify biomarkers to predict and to stratify patient´s possibility for developing DR. MicroRNAs (miRNAs) are small non-coding RNA molecules that have showed to be promising disease biomarkers and association of miRNAs with the possibility to develop DR has been reported. However, evaluating miRNA expression involves normalization of RT-qPCR data using internal reference genes that should be properly determined, considering their impact on expression levels calculation and, until date, there is no unanimity on reference miRNAs for the investigation of circulating miRNAs in DR. We aimed to estimate the appropriateness of a group of miRNAs as normalizers to identify which might be considered steady internal reference genes in expression studies on DR plasma samples. Expression levels of candidates were analyzed in 60 healthy controls, 48 DM without DR patients and 62 DR patients with two statistical tools: NormFinder and RefFinder. MiR-328-3p was the most stable gene and we also investigated the effect of gene normalization, demonstrating that different normalization strategies have important implications for accurate data interpretation.
Generation of polarization singularities with geometric metasurfaces
Authors: Zhang Yuchao , Yang Xiaodong , Gao Jie 
Published: December 2019

AbstractThe polarization singularities are directly generated by using plasmonic metasurfaces with the geometric phase profiles designed to form the Poincaré beams. Different morphologies of polarization topological structures of lemon, star, monstar, spiral, dipole and quadrupole are created by the superpositions of Laguerre–Gauss modes with different orders under orthogonal circular or linear polarization basis. The polarization ellipse patterns and topological features of the produced optical vector fields are analyzed to reveal the properties of the polarization singularities of C-points and L-lines, and the orbital angular momentum states are also measured. The demonstrated polarization singularities generated from the geometric metasurfaces will promise many potential applications related to optical polarization imaging, metrology, optical trapping and quantum information processing.
Diffusion-weighted Renal MRI at 9.4 Tesla Using RARE to Improve Anatomical Integrity
Authors: Periquito Joāo dos Santos , Paul Katharina , Huelnhagen Till , Ku Min-Chi , Ji Yiyi , Cantow Kathleen , Gladytz Thomas , Grosenick Dirk , Flemming Bert , Seeliger Erdmann , Waiczies Sonia , Niendorf Thoralf , Pohlmann Andreas 
Published: December 2019

AbstractDiffusion-weighted magnetic resonance imaging (DWI) is a non-invasive imaging technique sensitive to tissue water movement. By enabling a discrimination between tissue properties without the need of contrast agent administration, DWI is invaluable for probing tissue microstructure in kidney diseases. DWI studies commonly make use of single-shot Echo-Planar Imaging (ss-EPI) techniques that are prone to suffering from geometric distortion. The goal of the present study was to develop a robust DWI technique tailored for preclinical magnetic resonance imaging (MRI) studies that is free of distortion and sensitive to detect microstructural changes. Since fast spin-echo imaging techniques are less susceptible to B0 inhomogeneity related image distortions, we introduced a diffusion sensitization to a split-echo Rapid Acquisition with Relaxation Enhancement (RARE) technique for high field preclinical DWI at 9.4 T. Validation studies in standard liquids provided diffusion coefficients consistent with reported values from the literature. Split-echo RARE outperformed conventional ss-EPI, with ss-EPI showing a 3.5-times larger border displacement (2.60 vs. 0.75) and a 60% higher intra-subject variability (cortex = 74%, outer medulla = 62% and inner medulla = 44%). The anatomical integrity provided by the split-echo RARE DWI technique is an essential component of parametric imaging on the way towards robust renal tissue characterization, especially during kidney disease.