bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pressure accelerates the circadian clock of cyanobacteria
Authors: Kitahara Ryo , Oyama Katsuaki , Kawamura Takahiro , Mitsuhashi Keita , Kitazawa Soichiro , Yasunaga Kazuhiro , Sagara Natsuno , Fujimoto Megumi , Terauchi Kazuki 
Published: August 2019

AbstractAlthough organisms are exposed to various pressure and temperature conditions, information remains limited on how pressure affects biological rhythms. This study investigated how hydrostatic pressure affects the circadian clock (KaiA, KaiB, and KaiC) of cyanobacteria. While the circadian rhythm is inherently robust to temperature change, KaiC phosphorylation cycles that were accelerated from 22 h at 1 bar to 14 h at 200 bars caused the circadian-period length to decline. This decline was caused by the pressure-induced enhancement of KaiC ATPase activity and allosteric effects. Because ATPase activity was elevated in the CI and CII domains of KaiC, while ATP hydrolysis had negative activation volumes (ΔV≠), both domains played key roles in determining the period length of the KaiC phosphorylation cycle. The thermodynamic contraction of the structure of the active site during the transition state might have positioned catalytic residues and lytic water molecules favourably to facilitate ATP hydrolysis. Internal cavities might represent sources of compaction and structural rearrangement in the active site. Overall, the data indicate that pressure differences could alter the circadian rhythms of diverse organisms with evolved thermotolerance, as long as enzymatic reactions defining period length have a specific activation volume.
Photonic scheme of discrete quantum Fourier transform for quantum algorithms via quantum dots
Authors: Heo Jino , Won Kitak , Yang Hyung-Jin , Hong Jong-Phil , Choi Seong-Gon 
Published: August 2019

AbstractWe propose an optical scheme of discrete quantum Fourier transform (DQFT) via ancillary systems using quantum dots (QDs) confined in single-sided cavities (QD-cavity systems). In our DQFT scheme, the main component is a controlled-rotation k (CRk) gate, which utilizes the interactions between photons and QDs, consisting of two QD-cavity systems. Since the proposed CRk gate can be experimentally implemented with high efficiency and reliable performance, the scalability of multi-qubit DQFT scheme can also be realized through the simple composition of the proposed CRk gates via the QD-cavity systems. Subsequently, in order to demonstrate the performance of the CRk gate, we analyze the interaction between a photon and a QD-cavity system, and then indicate the condition to be efficient CRk gate with feasibility under vacuum noise and sideband leakage.
PET/MRI in large-vessel vasculitis: clinical value for diagnosis and assessment of disease activity
Authors: Laurent Charlotte , Ricard Laure , Fain Olivier , Buvat Irene , Adedjouma Amir , Soussan Michael , Mekinian Arsène 
Published: August 2019

AbstractDiagnosis of large vessel vasculitis (LVV) and evaluation of its inflammatory activity can be challenging. Our aim was to investigate the value of hybrid positron-emission tomography/magnetic resonance imaging (PET/MRI) in LVV. All consecutive patients with LVV from the Department of Internal Medicine who underwent PET/MRI were included. Three PET/MRI patterns were defined: (i) “inflammatory,” with positive PET (>liver uptake) and abnormal MRI (stenosis and/or wall thickening); (ii) “fibrous”, negative PET (≤liver uptake) and abnormal MRI; and (iii) “normal”. Thirteen patients (10 female; median age: 67-years [range: 23–87]) underwent 18 PET/MRI scans. PET/MRI was performed at diagnosis (n = 4), at relapse (n = 7), or during remission (n = 7). Among the 18 scans, eight (44%) showed an inflammatory pattern and three (17%) a fibrous pattern; the other seven were normal. The distribution of the three patterns did not differ between patients with Takayasu arteritis (TA, n = 10 scans) and those with giant cell arteritis (GCA, n = 8 scans). PET/MRI findings were normal in 2/10 (20%) TA scans vs. 5/8 (62%) GCA scans (p = 0.3). Median SUVmax was 4.7 [2.1–8.6] vs. 2 [1.8–2.6] in patients with active disease vs. remission, respectively (p = 0.003). PET/MRI is a new hybrid imaging modality allowing comprehensive and multimodal analysis of vascular wall inflammation and the vascular lumen. This technique offers promising perspectives for the diagnosis and monitoring of LVV.
Albumin evokes Ca2+-induced cell oxidative stress and apoptosis through TRPM2 channel in renal collecting duct cells reduced by curcumin
Authors: Nazıroğlu Mustafa , Çiğ Bilal , Yazğan Yener , Schwaerzer Gerburg K. , Theilig Franziska , Pecze László 
Published: August 2019

AbstractIn proteinuric nephropathies of chronic kidney disease, the epithelial cells of the nephron including the collecting duct are exposed to high concentrations of luminal albumin. Albumin is taken up from collecting duct cells by endocytosis causing excessive reactive oxygen species (ROS) production and a proinflammatory response. Curcumin used in the traditional medicine possesses anti-inflammatory and antioxidant effects. ROS and ADP-ribose (ADPR) activate the cation channel TRPM2. We hypothesize, that albumin-induced cell stress and proinflammatory response are mediated by Ca2+ and can be reduced by curcumin. The cortical collecting duct (CCD) cells mpkCCDc14 exhibit spontaneous and inducible Ca2+ oscillations, which can be blocked by pre-treatment with curcumin. Curcumin accumulates in plasma membrane and intracellular vesicles, where it interferes with TRPM2 and decreases the influx of Ca2+. Albumin reduces cell viability and increases apoptosis, NF-κB activation, and mitochondrial membrane depolarization via Ca2+-dependent signaling, which results in increased ROS production. Albumin-induced cell stress is diminished by the inhibition of TRPM2 after administration of curcumin and ADPR (PARP1) inhibitors. Curcumin did not reduce the Ca2+ elevation induced by thapsigargin in Ca2+-free medium, but it reduced the function of store-operated Ca2+ channels and ATP-evoked Ca2+ response. In conclusion, albumin-induced oxidative stress is mediated by Ca2+-dependent signaling via TRPM2 and leads to cell damage and a proinflammatory response, strengthening the role of CCD cells in the progression of chronic kidney disease.
RETRACTED ARTICLE: Investigating the Heteronjunction between ZnO/Fe2O3 and g-C3N4 for an Enhanced Photocatalytic H2 production under visible-light irradiation
Authors: Mao Na 
Published: August 2019

AbstractA series of ZnO/Fe2O3/g-C3N4 photocatalysts were synthetized by impregnation of g-C3N4 with Zn(NO3)2·6H2O, and Fe(NO3)2·9H2O followed by calcination. The morphology, chemical composition, and structure of the resulted materials were carefully analyzed by various characterization techniques. The photocatalytic performance of ZnO/Fe2O3/g-C3N4 composites was evaluated based on the H2 evolution from water splitting reaction. The results showed that the ZnO/Fe2O3/g-C3N4 composite can effectively produce more H2 than pure g-C3N4 when irradiated under visible-light. H2 production rate over 3-ZnO/Fe2O3/g-C3N4 composite was of 25 μmol·h−1, which is 4 times higher than that obtained in the presence of pure g-C3N4, clearly showing a significant improvement of the photocatalytic activity of the prepared nanocomposite. This result was attributed to the formation of a heterojunction between g-C3N4 and ZnO/Fe2O3, which delayed the recombination of holes-electrons pairs and resulted in a remarkable increase in photocatalytic performance.
SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages
Authors: Schroder Wayne A. , Hirata Thiago D. , Le Thuy T. , Gardner Joy , Boyle Glen M. , Ellis Jonathan , Nakayama Eri , Pathirana Dilan , Nakaya Helder I. , Suhrbier Andreas 
Published: August 2019

AbstractSerpinB2 (plasminogen activator inhibitor type 2) has been called the “undecided serpin” with no clear consensus on its physiological role, although it is well described as an inhibitor of urokinase plasminogen activator (uPA). In macrophages, pro-inflammatory stimuli usually induce SerpinB2; however, expression is constitutive in Gata6+ large peritoneal macrophages (LPM). Interrogation of expression data from human macrophages treated with a range of stimuli using a new bioinformatics tool, CEMiTool, suggested that SerpinB2 is most tightly co- and counter-regulated with genes associated with cell movement. Using LPM from SerpinB2−/− and SerpinB2R380A (active site mutant) mice, we show that migration on Matrigel was faster than for their wild-type controls. Confocal microscopy illustrated that SerpinB2 and F-actin staining overlapped in focal adhesions and lamellipodia. Genes associated with migration and extracellular matrix interactions were also identified by RNA-Seq analysis of migrating RPM from wild-type and SerpinB2R380A mice. Subsequent gene set enrichment analyses (GSEA) suggested SerpinB2 counter-regulates many Gata6-regulated genes associated with migration. These data argue that the role of SerpinB2 in macrophages is inhibition of uPA-mediated plasmin generation during cell migration. GSEA also suggested that SerpinB2 expression (likely via ensuing modulation of uPA-receptor/integrin signaling) promotes the adoption of a resolution phase signature.
Euler-Lagrange Prediction of Diesel-Exhaust Polydisperse Particle Transport and Deposition in Lung: Anatomy and Turbulence Effects
Authors: Islam Mohammad S. , Saha Suvash C. , Gemci Tevfik , Yang Ian A. , Sauret Emilie , Ristovski Zoran , Gu Y. T. 
Published: August 2019

AbstractIn clinical assessments, the correlation between atmospheric air pollution and respiratory damage is highly complicated. Epidemiological studies show that atmospheric air pollution is largely responsible for the global proliferation of pulmonary disease. This is particularly significant, since most Computational Fluid Dynamics (CFD) studies to date have used monodisperse particles, which may not accurately reflect realistic inhalation patterns, since atmospheric aerosols are mostly polydisperse. The aim of this study is to investigate the anatomy and turbulent effects on polydisperse particle transport and deposition (TD) in the upper airways. The Euler-Lagrange approach is used for polydisperse particle TD prediction in both laminar and turbulent conditions. Various anatomical models are adopted to investigate the polydisperse particle TD under different flow conditions. Rossin-Rammler diameter distribution is used for the distribution of the initial particle diameter. The numerical results illustrate that airflow rate distribution at the right lung of a realistic model is higher than a non-realistic model. The CFD study also shows that turbulence effects on deposition are higher for larger diameter particles than with particles of smaller diameter. A significant amount of polydisperse particles are also shown to be deposited at the tracheal wall for CT-based model, whereas particles are mostly deposited at the carinal angle for the non-realistic model. A comprehensive, polydisperse particle TD analysis would enhance understanding of the realistic deposition pattern and decrease unwanted therapeutic aerosol deposition at the extrathoracic airways.
Prediction of future gastric cancer risk using a machine learning algorithm and comprehensive medical check-up data: A case-control study
Authors: Taninaga Junichi , Nishiyama Yu , Fujibayashi Kazutoshi , Gunji Toshiaki , Sasabe Noriko , Iijima Kimiko , Naito Toshio 
Published: August 2019

AbstractA comprehensive screening method using machine learning and many factors (biological characteristics, Helicobacter pylori infection status, endoscopic findings and blood test results), accumulated daily as data in hospitals, could improve the accuracy of screening to classify patients at high or low risk of developing gastric cancer. We used XGBoost, a classification method known for achieving numerous winning solutions in data analysis competitions, to capture nonlinear relations among many input variables and outcomes using the boosting approach to machine learning. Longitudinal and comprehensive medical check-up data were collected from 25,942 participants who underwent multiple endoscopies from 2006 to 2017 at a single facility in Japan. The participants were classified into a case group (y = 1) or a control group (y = 0) if gastric cancer was or was not detected, respectively, during a 122-month period. Among 1,431 total participants (89 cases and 1,342 controls), 1,144 (80%) were randomly selected for use in training 10 classification models; the remaining 287 (20%) were used to evaluate the models. The results showed that XGBoost outperformed logistic regression and showed the highest area under the curve value (0.899). Accumulating more data in the facility and performing further analyses including other input variables may help expand the clinical utility.
Homogeneous sulfur isotope signature in East Antarctica and implication for sulfur source shifts through the last glacial-interglacial cycle
Authors: Ishino Sakiko , Hattori Shohei , Savarino Joel , Legrand Michel , Albalat Emmanuelle , Albarede Francis , Preunkert Susanne , Jourdain Bruno , Yoshida Naohiro 
Published: August 2019

AbstractSulfate aerosol (SO42−) preserved in Antarctic ice cores is discussed in the light of interactions between marine biological activity and climate since it is mainly sourced from biogenic emissions from the surface ocean and scatters solar radiation during traveling in the atmosphere. However, there has been a paradox between the ice core record and the marine sediment record; the former shows constant non-sea-salt (nss-) SO42− flux throughout the glacial-interglacial changes, and the latter shows a decrease in biogenic productivity during glacial periods compared to interglacial periods. Here, by ensuring the homogeneity of sulfur isotopic compositions of atmospheric nss-SO42− (δ34Snss) over East Antarctica, we established the applicability of the signature as a robust tool for distinguishing marine biogenic and nonmarine biogenic SO42−. Our findings, in conjunction with existing records of nss-SO42− flux and δ34Snss in Antarctic ice cores, provide an estimate of the relative importance of marine biogenic SO42− during the last glacial period to be 48 ± 10% of nss-SO42−, slightly lower than 59 ± 11% during the interglacial periods. Thus, our results tend to reconcile the ice core and sediment records, with both suggesting the decrease in marine productivity around Southern Ocean under the cold climate.
Non-diagnostic Results of Percutaneous Transthoracic Needle Biopsy: A Meta-analysis
Authors: Chae Kum Ju , Hong Hyunsook , Yoon Soon Ho , Hahn Seokyung , Jin Gong Yong , Park Chang Min , Goo Jin Mo 
Published: August 2019

AbstractNon-diagnostic results can affect the diagnostic performance of percutaneous transthoracic needle biopsy (PTNB) but have not been critically meta-analyzed yet. To meta-analyze the incidence and malignancy rate of non-diagnostic results, 3-by-2 table approaches rather than the conventional 2-by-2 approaches are needed to know its impact on the diagnostic performance of PTNB. A systematic literature search identified studies evaluating the diagnostic performance of PTNB with extractable outcomes. A total of 143 studies with 35,059 biopsies were included. The pooled incidence of non-diagnostic results was 6.8% (95% CI, 6.0–7.6%; I2 = 0.91). The pooled malignancy rate of non-diagnostic results was 59.3% (95% CI, 51.7–66.8%; I2 = 0.80), and was correlated with the prevalence of malignancy (correlation coefficient, 0.66; 95% CI, 0.42–0.91). Pooled percentage decrease of sensitivity and specificity due to non-diagnostic results were 4.5% (95% CI, 3.2–5.7%; I2 = 0.64) and 10.7% (95% CI, 7.7–13.7%; I2 = 0.70), respectively, and the pooled incidence of non-diagnostic results was 4.4% (95% CI, 3.2–5.8%; I2 = 0.83) in lesions ultimately diagnosed as malignancies and 10.4% (95% CI, 7.5–13.8%; I2 = 0.74) in benign disease. In conclusion, non-diagnostic results averagely occurred in 6.8% of PTNB and more than half of the results were malignancies. The non-diagnostic results decreased specificity and sensitivity by 10.7% and 4.5%, respectively, demanding efforts to minimize the non-diagnostic results in PTNB.
Principles of open source bioinstrumentation applied to the poseidon syringe pump system
Authors: Booeshaghi A. Sina , Beltrame Eduardo da Veiga , Bannon Dylan , Gehring Jase , Pachter Lior 
Published: August 2019

AbstractThe poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.io/poseidon. We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, safety, simplicity, modularity, benchmarking, and documentation.
Association between visual function and the integrity of residual ellipsoid zone in resolved central serous chorioretinopathy
Authors: Fujita Asahi , Aoyama Yurika , Tsuneyoshi Saori , Sugiura Aya , Azuma Keiko , Asano-Shimizu Kimiko , Soga Hirotsugu , Hashimoto Yohei , Asaoka Ryo , Inoue Tatsuya , Obata Ryo 
Published: August 2019

AbstractCentral serous chorioretinopathy (CSC) usually resolves spontaneously; however, in some patients, it can be chronic and visual impairment remains even after resolution of the serous retinal detachment. The impaired photoreceptor cells often present with disrupted ellipsoid zone (EZ) on optical coherence tomography (OCT). In this study, the integrity of EZ was quantified by calculating the index of residual EZ, identified on binarized OCT images from 25 eyes of 23 patients with resolved CSC. To estimate residual EZ, integrity of residual EZ with the central horizontal line on the fovea (rEZc) and average integrity of residual EZ within 3 × 3-mm macular area (rEZave) were investigated. The interrater reliability of the method was assessed using the intraclass correlation coefficient (ICC). The relationship between LogMAR VA and age, central retinal thickness, central choroidal thickness, rEZc, and rEZave were evaluated using the linear mixed model. Retinal sensitivity was measured with the MP-3 microperimeter and similar analyses were iterated for mean retinal sensitivity (MS). ICC values were 0.938 with rEZc and 0.979 with rEZave. rEZc was significantly related to LogMAR VA (p = 0.039). rEZave was significantly related to MS (p < 0.001). These results suggested potential usefulness of residual EZ to predict visual function in resolved CSC.
SQUID-based ultralow-field MRI of a hyperpolarized material using signal amplification by reversible exchange
Authors: Lee Seong-Joo , Jeong Keunhong , Shim Jeong Hyun , Lee Hyun Joon , Min Sein , Chae Heelim , Namgoong Sung Keon , Kim Kiwoong 
Published: August 2019

AbstractThe signal amplification by reversible exchange (SABRE) technique is a very promising method for increasing magnetic resonance (MR) signals. SABRE can play a particularly large role in studies with a low or ultralow magnetic field because they suffer from a low signal-to-noise ratio. In this work, we conducted real-time superconducting quantum interference device (SQUID)-based nuclear magnetic resonance (NMR)/magnetic resonance imaging (MRI) studies in a microtesla-range magnetic field using the SABRE technique after designing a bubble-separated phantom. A maximum enhancement of 2658 for 1H was obtained for pyridine in the SABRE-NMR experiment. A clear SABRE-enhanced MR image of the bubble-separated phantom, in which the para-hydrogen gas was bubbling at only the margin, was successfully obtained at 34.3 μT. The results show that SABRE can be successfully incorporated into an ultralow-field MRI system, which enables new SQUID-based MRI applications. SABRE can shorten the MRI operation time by more than 6 orders of magnitude and establish a firm basis for future low-field MRI applications.
Spontaneous mutations of the Zpld1 gene in mice cause semicircular canal dysfunction but do not impair gravity receptor or hearing functions
Authors: Vijayakumar Sarath , Jones Sherri M. , Jones Timothy A. , Tian Cong , Johnson Kenneth R. 
Published: August 2019

AbstractThe cupula is a gelatinous membrane overlying the crista ampullaris of the semicircular canal, important for sensing rotation of the head and critical for normal balance. Recently the zona pellucida like domain containing 1 protein (ZPLD1, also known as cupulin) was identified in the cupula of fish. Here, we describe two new spontaneous mutations in the mouse Zpld1 gene, which were discovered by the circling behavior of mutant mice, an indicator of balance dysfunction. The Zpld1 mutant mice exhibited normal hearing function as assessed by auditory brainstem response (ABR) measurements, and their otolithic organs appeared normal. In the inner ear, Zpld1 mRNA expression was detected only in the hair cells and supporting cells of the crista ampullaris. Normal vestibular sensory evoked potential (VsEP) responses and abnormal vestibulo-ocular reflex (VOR) responses demonstrated that the vestibular dysfunction of the Zpld1 mutant mice is caused by loss of sensory input for rotary head movements (detected by cristae ampullaris) and not by loss of input for linear head translations (detected by maculae of the utricle and saccule). Taken together, these results are consistent with ZPLD1 being an important functional component of the cupula, but not tectorial or otoconial membranes.
Live-cell STED nanoscopy of mitochondrial cristae
Authors: Stephan Till , Roesch Axel , Riedel Dietmar , Jakobs Stefan 
Published: August 2019

AbstractMitochondria are highly dynamic organelles that exhibit a complex inner architecture. They exhibit a smooth outer membrane and a highly convoluted inner membrane that forms invaginations called cristae. Imaging cristae in living cells poses a formidable challenge for super-resolution light microscopy. Relying on a cell line stably expressing the mitochondrial protein COX8A fused to the SNAP-tag and using STED (stimulated emission depletion) nanoscopy, we demonstrate the visualization of cristae dynamics in cultivated human cells. We show that in human HeLa cells lamellar cristae are often arranged in groups separated by voids that are generally occupied by mitochondrial nucleoids.