bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription
Authors: Kim Eun Ji , Grant Gregory R. , Bowman Anita S. , Haider Naqi , Gudiseva Harini V. , Chavali Venkata Ramana Murthy 
Published: February 2018

AbstractAge-related macular degeneration (AMD) predominantly affects the retina and retinal pigment epithelium in the posterior eye. While there are numerous studies investigating the non-coding transcriptome of retina and RPE, few significant differences between AMD and normal tissues have been reported. Strand specific RNA sequencing of both peripheral retina (PR) and RPE-Choroid-Sclera (PRCS), in both AMD and matched normal controls were generated. The transcriptome analysis reveals a highly significant and consistent impact on anti-sense transcription as well as moderate changes in the regulation of non-coding (sense) RNA. Hundreds of genes that do not express anti-sense transcripts in normal PR and PRCS demonstrate significant anti-sense expression in AMD in all patient samples. Several pathways are highly enriched in the upregulated anti-sense transcripts—in particular the EIF2 signaling pathway. These results call for a deeper exploration into anti-sense and noncoding RNA regulation in AMD and their potential as therapeutic targets.
Transitional correlation between inner-membrane potential and ATP levels of neuronal mitochondria
Authors: Suzuki R. , Hotta K. , Oka K. 
Published: February 2018

AbstractThe importance of highly active mitochondria and their contribution to neuronal function has been of recent interest. In most cases, however, mitochondrial activity is estimated using measurements of mitochondrial inner membrane potential (IMPmito), and little is known about the dynamics of native mitochondrial ATP (ATPmito). This study conducted simultaneous imaging of IMPmito and ATPmito in neurons to explore their behaviour and their correlation during physiological mitochondrial/neuronal activity. We found that mitochondrial size, transport velocity and transport direction are not dependent on ATPmito or IMPmito. However, changes in ATPmito and IMPmito during mitochondrial fission/fusion were found; IMPmito depolarized via mitochondrial fission and hyperpolarized via fusion, and ATPmito levels increased after fusion. Because the density of mitochondria is higher in growth cones (GCs) than in axonal processes, integrated ATPmito signals (density × ATPmito) were higher in GCs. This integrated signal in GCs correlated with axonal elongation. However, while the averaged IMPmito was relatively hyperpolarized in GCs, there was no correlation between IMPmito in GCs and axonal elongation. A detailed time-course analysis performed to clarify the reason for these discrepancies showed that IMPmito and ATPmito levels did not always correlate accurately; rather, there were several correlation patterns that changed over time.
Mesoscopic physical removal of material using sliding nano-diamond contacts
Authors: Celano Umberto , Hsia Feng-Chun , Vanhaeren Danielle , Paredis Kristof , Nordling Torbjörn E. M. , Buijnsters Josephus G. , Hantschel Thomas , Vandervorst Wilfried 
Published: February 2018

AbstractWear mechanisms including fracture and plastic deformation at the nanoscale are central to understand sliding contacts. Recently, the combination of tip-induced material erosion with the sensing capability of secondary imaging modes of AFM, has enabled a slice-and-view tomographic technique named AFM tomography or Scalpel SPM. However, the elusive laws governing nanoscale wear and the large quantity of atoms involved in the tip-sample contact, require a dedicated mesoscale description to understand and model the tip-induced material removal. Here, we study nanosized sliding contacts made of diamond in the regime whereby thousands of nm3 are removed. We explore the fundamentals of high-pressure tip-induced material removal for various materials. Changes in the load force are systematically combined with AFM and SEM to increase the understanding and the process controllability. The nonlinear variation of the removal rate with the load force is interpreted as a combination of two contact regimes each dominating in a particular force range. By using the gradual transition between the two regimes, (1) the experimental rate of material eroded on each tip passage is modeled, (2) a controllable removal rate below 5 nm/scan for all the materials is demonstrated, thus opening to future development of 3D tomographic AFM.
Quantitative assessment of liver fibrosis (qFibrosis) reveals precise outcomes in Ishak “stable” patients on anti-HBV therapy
Authors: Sun Yameng , Zhou Jialing , Wu Xiaoning , Chen Yongpeng , Piao Hongxin , Lu Lungen , Ding Huiguo , Nan Yuemin , Jiang Wei , Wang Tailing , Liu Hui , Ou Xiaojuan , Wee Aileen , Theise Neil D. , Jia Jidong , You Hong 
Published: February 2018

AbstractCurrent widely used semiquantitative histological assessment methods are insensitive to identify subtle changes of liver fibrosis. Therefore, to precisely assess therapeutic efficacy on chronic hepatitis B (CHB), we explored the utility of qFibrosis (a fully-quantitative morphometric method employing second harmonic generation/two photon excitation fluorescence) in liver fibrosis evaluation. Fibrosis changes were evaluated by Ishak fibrosis scoring and qFibrosis in CHB patients with paired liver biopsies before and after 78 weeks’ antiviral therapy. A total of 162 patients with qualified paired biopsies were enrolled. Ishak fibrosis scoring revealed that 42.6% (69/162) of the patients achieved fibrosis regression (≥1-point decrease), 51.9% (84/162) remained stable, and 5.5% (9/162) showed progression (≥1-point increase). qFibrosis showed similar trends in the groups of regression and progression patients as evaluated by Ishak. However, in Ishak stable patients, qFibrosis revealed hitherto undetected changes, allowing for further subcategorization into regression (“Regression by qFibrosis”; 40/84, 47.6%), stable (29/84, 34.5%), and progression (“Progression by qFibrosis”; 15/84, 17.9%) groups. These newly fine-tuned categories were supported by changes of morphological parameters of fibrosis, collagen percentage area, and liver stiffness measurements. In conclusion, qFibrosis can be used to quantitatively identify subtle changes of liver fibrosis in CHB patients after antiviral therapy.
Tuning the Optical Properties of Silicon Quantum Dots via Surface Functionalization with Conjugated Aromatic Fluorophores
Authors: Abdelhameed Mohammed , Martir Diego Rota , Chen Shalimar , Xu William Z. , Oyeneye Olabode O. , Chakrabarti Subrata , Zysman-Colman Eli , Charpentier Paul A. 
Published: February 2018

AbstractSilicon Quantum Dots (SQDs) have recently attracted great interest due to their excellent optical properties, low cytotoxicity, and ease of surface modification. The size of SQDs and type of ligand on their surface has a great influence on their optical properties which is still poorly understood. Here we report the synthesis and spectroscopic studies of three families of unreported SQDs functionalized by covalently linking to the aromatic fluorophores, 9-vinylphenanthrene, 1-vinylpyrene, and 3-vinylperylene. The results showed that the prepared functionalized SQDs had a highly-controlled diameter by HR-TEM, ranging from 1.7–2.1 nm. The photophysical measurements of the assemblies provided clear evidence for efficient energy transfer from the fluorophore to the SQD core. Fӧrster energy transfer is the likely mechanism in these assemblies. As a result of the photogenerated energy transfer process, the emission color of the SQD core could be efficiently tuned and its emission quantum efficiency enhanced. To demonstrate the potential application of the synthesized SQDs for bioimaging of cancer cells, the water-soluble perylene- and pyrene-capped SQDs were examined for fluorescent imaging of HeLa cells. The SQDs were shown to be of low cytotoxicity
Holographic Traction Force Microscopy
Authors: Makarchuk Stanislaw , Beyer Nicolas , Gaiddon Christian , Grange Wilfried , Hébraud Pascal 
Published: February 2018

AbstractTraction Force Microscopy (TFM) computes the forces exerted at the surface of an elastic material by measuring induced deformations in volume. It is used to determine the pattern of the adhesion forces exerted by cells or by cellular assemblies grown onto a soft deformable substrate. Typically, colloidal particles are dispersed in the substrate and their displacement is monitored by fluorescent microscopy. As with any other fluorescent techniques, the accuracy in measuring a particule’s position is ultimately limited by the number of evaluated fluorescent photons. Here, we present a TFM technique based on the detection of probe particle displacements by holographic tracking microscopy. We show that nanometer scale resolutions of the particle displacements can be obtained and determine the maximum volume fraction of markers in the substrate. We demonstrate the feasibility of the technique experimentally and measure the three-dimensional force fields exerted by colorectal cancer cells cultivated onto a polyacrylamide gel substrate.
Interactions between predation and disturbances shape prey communities
Authors: Karakoç Canan , Radchuk Viktoriia , Harms Hauke , Chatzinotas Antonis 
Published: February 2018

AbstractEcological disturbances are important drivers of biodiversity patterns. Many biodiversity studies rely on endpoint measurements instead of following the dynamics that lead to those outcomes and testing ecological drivers individually, often considering only a single trophic level. Manipulating multiple factors (biotic and abiotic) in controlled settings and measuring multiple descriptors of multi-trophic communities could enlighten our understanding of the context dependency of ecological disturbances. Using model microbial communities, we experimentally tested the effects of imposed disturbances (i.e. increased dilution simulating density-independent mortality as press or pulse disturbances coupled with resource deprivation) on bacterial abundance, diversity and community structure in the absence or presence of a protist predator. We monitored the communities immediately before and after imposing the disturbance and four days after resuming the pre-disturbance dilution regime to infer resistance and recovery properties. The results highlight that bacterial abundance, diversity and community composition were more affected by predation than by disturbance type, resource loss or the interaction of these factors. Predator abundance was strongly affected by the type of disturbance imposed, causing temporary relief of predation pressure. Importantly, prey community composition differed significantly at different phases, emphasizing that endpoint measurements are insufficient for understanding the recovery of communities.
Atrial Fibrillation Characteristics in Patients on Haemodialysis vs. Peritoneal Dialysis
Authors: Abuhasira Ran , Mizrakli Yuval , Shimony Avi , Novack Victor , Shnaider Alla , Haviv Yosef S. 
Published: February 2018

AbstractAtrial fibrillation (AF) is highly prevalent in dialysis patients, however whether its impact differs between patients on haemodialysis (HD) vs. peritoneal dialysis (PD) is unknown. We aimed to compare the association of AF and clinical outcomes in different dialysis modalities. We performed a population based retrospective cohort study, including adult patients who initiated dialysis between the years 2002 and 2015. Clinical, echocardiographic and laboratory data were reviewed and correlated with outcomes in HD vs. PD. During the study period, 1,130 patients began dialysis. Of the 997 patients without AF before dialysis initiation, 17% developed new-onset AF after the initiation of dialysis (17.3% of HD vs. 13.7% of PD patients, p = 0.27). Using multivariate analysis, only enlarged left atrium at dialysis initiation (hazard ratio (HR) 2.82, CI95% 2.00–3.99) and age (HR 1.04, CI95% 1.03–1.06) were significantly associated with AF. Dialysis modality was not a significant predictor of AF in either univariate or multivariate analysis. In conclusion, our study demonstrated that AF is common in dialysis patients irrespective of modality. In our cohort, the risk factors associated with AF were older age and enlarged left atrium. AF was associated with increased rates of heart failure and mortality, but not stroke.
Remodeling of the Actin/Spectrin Membrane-associated Periodic Skeleton, Growth Cone Collapse and F-Actin Decrease during Axonal Degeneration
Authors: Unsain Nicolas , Bordenave Martin D. , Martinez Gaby F. , Jalil Sami , von Bilderling Catalina , Barabas Federico M. , Masullo Luciano A. , Johnstone Aaron D. , Barker Philip A. , Bisbal Mariano , Stefani Fernando D. , Cáceres Alfredo O. 
Published: February 2018

AbstractAxonal degeneration occurs in the developing nervous system for the appropriate establishment of mature circuits, and is also a hallmark of diverse neurodegenerative diseases. Despite recent interest in the field, little is known about the changes (and possible role) of the cytoskeleton during axonal degeneration. We studied the actin cytoskeleton in an in vitro model of developmental pruning induced by trophic factor withdrawal (TFW). We found that F-actin decrease and growth cone collapse (GCC) occur early after TFW; however, treatments that prevent axonal fragmentation failed to prevent GCC, suggesting independent pathways. Using super-resolution (STED) microscopy we found that the axonal actin/spectrin membrane-associated periodic skeleton (MPS) abundance and organization drop shortly after deprivation, remaining low until fragmentation. Fragmented axons lack MPS (while maintaining microtubules) and acute pharmacological treatments that stabilize actin filaments prevent MPS loss and protect from axonal fragmentation, suggesting that MPS destruction is required for axon fragmentation to proceed.
On the origins of transport inefficiencies in mesoscopic networks
Authors: Toussaint Sébastien , Martins Frederico , Faniel Sébastien , Pala Marco G. , Desplanque Ludovic , Wallart Xavier , Sellier Hermann , Huant Serge , Bayot Vincent , Hackens Benoit 
Published: February 2018

AbstractA counter-intuitive behavior analogous to the Braess paradox is encountered in a two-terminal mesoscopic network patterned in a two-dimensional electron system (2DES). Decreasing locally the electron density of one channel of the network paradoxically leads to an increased network electrical conductance. Our low temperature scanning gate microscopy experiments reveal different occurrences of such puzzling conductance variations, thanks to tip-induced localized modifications of electron flow throughout the network’s channels in the ballistic and coherent regime of transport. The robustness of the puzzling behavior is inspected by varying the global 2DES density, magnetic field and the tip-surface distance. Depending on the overall 2DES density, we show that either Coulomb Blockade resonances due to disorder-induced localized states or Fabry-Perot interferences tuned by the tip-induced electrostatic perturbation are at the origin of transport inefficiencies in the network, which are lifted when gradually closing one channel of the network with the tip.
Iron Overload Accelerates the Progression of Diabetic Retinopathy in Association with Increased Retinal Renin Expression
Authors: Chaudhary Kapil , Promsote Wanwisa , Ananth Sudha , Veeranan-Karmegam Rajalakshmi , Tawfik Amany , Arjunan Pachiappan , Martin Pamela , Smith Sylvia B. , Thangaraju Muthusamy , Kisselev Oleg , Ganapathy Vadivel , Gnana-Prakasam Jaya P. 
Published: February 2018

AbstractDiabetic retinopathy (DR) is a leading cause of blindness among working-age adults. Increased iron accumulation is associated with several degenerative diseases. However, there are no reports on the status of retinal iron or its implications in the pathogenesis of DR. In the present study, we found that retinas of type-1 and type-2 mouse models of diabetes have increased iron accumulation compared to non-diabetic retinas. We found similar iron accumulation in postmortem retinal samples from human diabetic patients. Further, we induced diabetes in HFE knockout (KO) mice model of genetic iron overload to understand the role of iron in the pathogenesis of DR. We found increased neuronal cell death, vascular alterations and loss of retinal barrier integrity in diabetic HFE KO mice compared to diabetic wildtype mice. Diabetic HFE KO mouse retinas also exhibited increased expression of inflammation and oxidative stress markers. Severity in the pathogenesis of DR in HFE KO mice was accompanied by increase in retinal renin expression mediated by G-protein-coupled succinate receptor GPR91. In light of previous reports implicating retinal renin-angiotensin system in DR pathogenesis, our results reveal a novel relationship between diabetes, iron and renin-angiotensin system, thereby unraveling new therapeutic targets for the treatment of DR.
Individual and combined effects of herbicide tribenuron-methyl and fungicide tebuconazole on soil earthworm Eisenia fetida
Authors: Chen Jiqiang , Saleem Muhammad , Wang Caixia , Liang Wenxing , Zhang Qingming 
Published: February 2018

AbstractEarthworms are soil engineers that alter the soil bio-physical properties to favor plant growth whereas pesticides represent a significant threat to their abundance and soil health. Thus, we investigated the toxic effects of tribenuron-methyl (TBM) and tebuconazole (TEB) on the soil earthworm, Eisenia fetida. The TBM demonstrated low toxicity to E. fetida in the contact filter paper and artificial soil tests, with median lethal concentrations (LC50) of 135.6 μg cm−2 at 48 h and 511 mg kg−1 on day 14, respectively. Similarly, TEB also showed low toxicity to E. fetida in the artificial soil test with LC50 of 287 mg kg−1 on day 14. However, TEB was highly toxic to earthworm in the contact filter paper test with LC50 of 5.7 μg cm−2 at 48 h. The mixture of two pesticides had an antagonistic effect on the earthworm. Under 0.1 LC50 of TBM and TEB, either single or combined application of pesticides induced oxidative stress and inhibited cellulase activity in early days of the earthworm exposure. However, both pesticides did not damage the earthworm DNA. Our results suggest that pesticides can negatively affect soil earthworms and provide valuable information regarding the responses of soil biological engineers to the lethal agrochemicals.
Species-specified VOC emissions derived from a gridded study in the Pearl River Delta, China
Authors: Mo Ziwei , Shao Min , Liu Ying , Xiang Yang , Wang Ming , Lu Sihua , Ou Jiamin , Zheng Junyu , Li Meng , Zhang Qiang , Wang Xuemei , Zhong Liuju 
Published: February 2018

AbstractThis study provides a top-down approach to establish an emission inventory of volatile organic compounds (VOC) based on ambient measurements, by combining the box model and positive matrix factorization (PMF) model. Species-specified VOC emissions, source contributions, and spatial distributions are determined based on regional-scale gridded measurements between September 2008 to December 2009 in the Pearl River Delta (PRD), China. The most prevalent anthropogenic species in the PRD was toluene estimated by the box model to be annual emissions of 167.8 ± 100.5 Gg, followed by m,p-xylene (68.0 ± 45.0 Gg), i-pentane (49.2 ± 40.0 Gg), ethene (47.6 ± 27.6 Gg), n-butane (47.5 ± 40.7 Gg), and benzene (46.8 ± 29.0 Gg). Alkanes such as propane, i-butane, and n-pentane were 2–8 times higher in box model than emission inventories (EI). Species with fewer emissions were highly variable between EI and box model results. Hotspots of VOC emissions were identified in southwestern PRD and port areas, which were not reflected by bottom-up EI. This suggests more research is needed for VOC emissions in the EI, especially for fuel evaporation, industrial operations and marine vessels. The species-specified top-down method can help improve the quality of these emission inventories.
Progesterone Receptor Membrane Component 1 suppresses the p53 and Wnt/β-catenin pathways to promote human pluripotent stem cell self-renewal
Authors: Kim Ji Yea , Kim So Young , Choi Hong Seo , Kim Min Kyu , Lee Hyun Min , Jang Young-Joo , Ryu Chun Jeih 
Published: February 2018

AbstractProgesterone receptor membrane component 1 (PGRMC1) is a multifunctional heme-binding protein involved in various diseases, including cancers and Alzheimer’s disease. Previously, we generated two monoclonal antibodies (MAbs) 108-B6 and 4A68 against surface molecules on human pluripotent stem cells (hPSCs). Here we show that PGRMC1 is the target antigen of both MAbs, and is predominantly expressed on hPSCs and some cancer cells. PGRMC1 is rapidly downregulated during early differentiation of hPSCs. Although PGRMC1 knockdown leads to a spread-out morphology and impaired self-renewal in hPSCs, PGRMC1 knockdown hPSCs do not show apoptosis and autophagy. Instead, PGRMC1 knockdown leads to differentiation of hPSCs into multiple lineage cells without affecting the expression of pluripotency markers. PGRMC1 knockdown increases cyclin D1 expression and decreases Plk1 expression in hPSCs. PGRMC1 knockdown also induces p53 expression and stability, suggesting that PGRMC1 maintains hPSC self-renewal through suppression of p53-dependent pathway. Analysis of signaling molecules further reveals that PGRMC1 knockdown promotes inhibitory phosphorylation of GSK-3β and increased expression of Wnt3a and β-catenin, which leads to activation of Wnt/β-catenin signaling. The results suggest that PGRMC1 suppresses the p53 and Wnt/β-catenin pathways to promote self-renewal and inhibit early differentiation in hPSCs.
Kinesin 1 regulates cilia length through an interaction with the Bardet-Biedl syndrome related protein CCDC28B
Authors: Novas Rossina , Cardenas-Rodriguez Magdalena , Lepanto Paola , Fabregat Matías , Rodao Magela , Fariello María Inés , Ramos Mauricio , Davison Camila , Casanova Gabriela , Alfaya Lucía , Lecumberry Federico , González-Sapienza Gualberto , Irigoín Florencia , Badano Jose L. 
Published: February 2018

AbstractBardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinal degeneration, obesity, polydactyly, renal disease and mental retardation. CCDC28B is a BBS-associated protein that we have previously shown plays a role in cilia length regulation whereby its depletion results in shortened cilia both in cells and Danio rerio (zebrafish). At least part of that role is achieved by its interaction with the mTORC2 component SIN1, but the mechanistic details of this interaction and/or additional functions that CCDC28B might play in the context of cilia remain poorly understood. Here we uncover a novel interaction between CCDC28B and the kinesin 1 molecular motor that is relevant to cilia. CCDC28B interacts with kinesin light chain 1 (KLC1) and the heavy chain KIF5B. Notably, depletion of these kinesin 1 components results in abnormally elongated cilia. Furthermore, through genetic interaction studies we demonstrate that kinesin 1 regulates ciliogenesis through CCDC28B. We show that kinesin 1 regulates the subcellular distribution of CCDC28B, unexpectedly, inhibiting its nuclear accumulation, and a ccdc28b mutant missing a nuclear localization motif fails to rescue the phenotype in zebrafish morphant embryos. Therefore, we uncover a previously unknown role of kinesin 1 in cilia length regulation that relies on the BBS related protein CCDC28B.