bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond quantification: in situ analysis of transcriptome and pre‐mRNA alternative splicing at the nanoscale
Authors: Cui Yi , Liu Jing , Irudayaraj Joseph 
Published: November 2016

In situ analysis offers a venue for dissecting the complex transcriptome in its natural context to tap into cellular processes that could explain the phenotypic physiology and pathology yet to be understood. Over the past decades, enormous progress has been made to improve the resolution, sensitivity, and specificity of single‐cell technologies. The continued efforts in RNA research not only facilitates mechanistic studies of molecular biology but also provides state‐of‐the‐art strategies for diagnostic purposes. The implementation of novel bio‐imaging platforms has yielded valuable information for inspecting gene expression, mapping regulatory networks, and classifying cell types. In this article, we discuss the merits and technical challenges in single‐molecule in situ RNA profiling. Advanced in situ hybridization methodologies developed for a variety of detection modalities are reviewed. Considering the fact that in mammalian cells the number of protein products immensely exceeds that of the actual coding genes due to pre‐mRNA alternative splicing, tools capable of elucidating this process in intact cells are highlighted. To conclude, we point out future directions for in situ transcriptome analysis and expect a plethora of opportunities and discoveries in this field. WIREs Nanomed Nanobiotechnol 2017, 9:e1443. doi: 10.1002/wnan.1443This article is categorized under:

Nanotechnology Approaches to Biology > Cells at the Nanoscale
Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
Multiple resonances of a moving oscillating surface disturbance on a shear current
Authors: Li Yan , Ellingsen Simen Å. 
Published: November 2016

We consider waves radiated by a disturbance of oscillating strength moving at constant velocity along the free surface of a shear flow, which, when undisturbed, has uniform horizontal vorticity of magnitude$S$. When no current is present the problem is a classical one and much studied, and in deep water a resonance is known to occur when$\unicode[STIX]{x1D70F}=|\boldsymbol{V}|\unicode[STIX]{x1D714}_{0}/g$equals the critical value$1/4$($\boldsymbol{V}$: velocity of disturbance,$\unicode[STIX]{x1D714}_{0}$: oscillation frequency,$g$: gravitational acceleration). We show that the presence of a subsurface shear current can change this picture radically. Not only does the resonant value of$\unicode[STIX]{x1D70F}$depend strongly on the angle between$\boldsymbol{V}$and the current’s direction and the ‘shear-Froude number’$\mathit{Fr}_{s}=|\boldsymbol{V}|S/g$; when$\mathit{Fr}_{s}>1/3$, multiple resonant values – as many as four – can occur for some directions of motion. At sufficiently large values of$\mathit{Fr}_{s}$, the smallest resonance frequency tends to zero, representing the phenomenon of critical velocity for ship waves. We provide a detailed analysis of the dispersion relation for the moving oscillating disturbance, in both finite and infinite water depth, including for the latter case an overview of the different far-field waves which exist in different sectors of wave-vector space under different conditions. Owing to the large number of parameters, a detailed discussion of the structure of resonances is provided for infinite depth only, where analytical results are available.
Response of antioxidant enzymes inMythimna separata(Lepidoptera: Noctuidae) exposed to thermal stress
Authors: Ali A. , Rashid M. A. , Huang Q. Y. , Wong C. , Lei C.-L. 
Published: November 2016

AbstractThe oriental army wormMythimna separata(Lepidoptera: Noctuidae) is a migratory pest in Eastern Asia and China. Seasonal high temperatures in Southern China and low temperatures in Northern China are pressures favouring the annual migration of this species, while cold tolerance determines the northern limit of its overwintering range. A number of physiological stress responses occur in insects as a result of variations in temperature. One reaction to thermal stress is the generation of reactive oxygen species (ROS), which can be harmful by causing oxidative damage. The time-related effects (durations of 1, 4 and 7 h) of thermal stress treatments ofM. separataat comparatively low (5, 10, 15 and 20°C) and high (30, 35, 40 and 45°C) temperatures on the activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POX) and glutathione S-transferases (GSTs), and total antioxidant capacity (T-AOC) were determined. Thermal stress resulted in significant elevation of the activities of SOD, CAT and GSTs, indicating that these enzymes contribute to defence mechanisms counteracting oxidative damage caused by an increase in ROS. However, at high-temperatures, POX and T-AOC were also found to contribute to scavenging ROS. Our results also indicate that extreme temperatures lead to elevated ROS production inM. separata. The present study confirms that thermal stress can be responsible for oxidative damage. To overcome such stress, antioxidant enzymes play key roles in diminishing oxidative damage inM. separata.
Sequence stratigraphy, chemostratigraphy and facies analysis of Cambrian Series 2 – Series 3 boundary strata in northwestern Scotland
Authors: FAGGETTER LUKE E. , WIGNALL PAUL B. , PRUSS SARA B. , SUN YADONG , RAINE ROBERT J. , NEWTON ROBERT J. , WIDDOWSON MIKE , JOACHIMSKI MICHAEL M. , SMITH PAUL M. 
Published: November 2016

AbstractGlobally, the Series 2 – Series 3 boundary of the Cambrian System coincides with a major carbon isotope excursion, sea-level changes and trilobite extinctions. Here we examine the sedimentology, sequence stratigraphy and carbon isotope record of this interval in the Cambrian strata (Durness Group) of NW Scotland. Carbonate carbon isotope data from the lower part of the Durness Group (Ghrudaidh Formation) show that the shallow-marine, Laurentian margin carbonates record two linked sea-level and carbon isotopic events. Whilst the carbon isotope excursions are not as pronounced as those expressed elsewhere, correlation with global records (Sauk I – Sauk II boundary andOlenellusbiostratigraphic constraint) identifies them as representing the local expression of the ROECE and DICE. The upper part of the ROECE is recorded in the basal Ghrudaidh Formation whilst the DICE is seen around 30m above the base of this unit. Both carbon isotope excursions co-occur with surfaces interpreted to record regressive–transgressive events that produced amalgamated sequence boundaries and ravinement/flooding surfaces overlain by conglomerates of reworked intraclasts. The ROECE has been linked with redlichiid and olenellid trilobite extinctions, but in NW Scotland,Olenellusis found after the negative peak of the carbon isotope excursion but before sequence boundary formation.
Electrocoagulation improving bone cement use in middle-ear surgery: short-term and middle-term results
Authors: Galy-Bernadoy C , Akkari M , Mondain M , Uziel A , Venail F 
Published: November 2016

AbstractBackground:Bone cement is used for ossicular chain repair and revision stapes surgery. Its efficient use requires cautious removal of mucosa from the ossicles. This paper reports a technique for easy, fast and safe removal of this mucosa prior to cement application. It consists of the application of monopolar electrocoagulation on the ossicles prior to bone cement application.Methods:The outcomes of six cases of revision stapes surgery and seven cases of partial ossiculoplasty, conducted between 2007 and 2012 using this new technique, were evaluated. Intra-operative reports and audiometric data were collected.Results:During the last assessment, reconstruction using bone cement resulted in mean post-operative air–bone gaps of 4.1 ± 6.5 dB in revision stapes surgery cases and 5.7 ± 5.5 dB in partial ossiculoplasty cases, reflecting a significant hearing improvement (p = 0.03). No complications were observed.Conclusion:Electrocoagulation allows the removal of mucosa from the ossicles in an easy, fast and safe manner, enabling the use of bone cement for ossicular chain reconstruction.
Hearing loss and its association with occupational noise exposure among Saudi dentists: a cross-sectional study
Authors: Alabdulwahhab Bander M , Alduraiby Raneem I , Ahmed May A , Albatli Lamya I , Alhumain Maram S , Softah Nada A , Saleh Shaza 
Published: November 2016

AbstractObjectives/Aims:Dental practitioners are prone to hearing loss due to noise exposure encountered in dental clinics. The aim of this study was to determine whether the persistent high-frequency sounds produced by the dental equipment could cause hearing decrement among the Saudi dental practitioners.Materials and Methods:This cross-sectional study included 38 randomly selected Saudi dentists from different specialties who were exposed to noise during working hours and 38 individuals as a control group. The participants underwent four audiometric tests that included an otoscopic examination, tympanometry, pure tone audiometry and the distortion product otoacoustic emissions (DPOAE) test.Results:The data revealed that ~15.8% of the dentists and 2.6% of the control group had some hearing loss. No significant difference was found between the two groups in the pure tone audiometry test; however, qualitative analysis revealed a higher percentage of hearing loss among the dentists’ group as compared with their control counterparts. A statistically significant difference was found in DPOAEs between the two groups in the left ear (P=0.002), and between the right and left ears (P=0.005).Discussion:In the present cross-sectional study, the prevalence of hearing loss among dentists as assessed with the pure tone audiometry test was 15.8%. Which was in accordance with a previous study performed by Khaimooket al., which revealed the prevalence of hearing loss in dental personnel to be 17.7%; however, no significant differences were observed compared to the control group in both studies. The otoacoustic emission test in the left ear exhibited significant changes. These changes could have been due to the presence and continuity of the sounds produced by high- and low-velocity suction devices on the left side of the dental unit knowing that 97% of the dentists are right handed.Conclusion:Evidence suggests that noise from dental clinics can cause hearing problems, which had a greater effect on the left ear than the right; however, these problems are not severe in nature. Noise-induced hearing loss was more prevalent among the dentists than the control group.
Tuning the chemiluminescence of a luminol flow using plasmonic nanoparticles
Authors: Karabchevsky Alina , Mosayyebi Ali , Kavokin Alexey V 
Published: November 2016

AbstractWe have discovered a strong increase in the intensity of the chemiluminescence of a luminol flow and a dramatic modification of its spectral shape in the presence of metallic nanoparticles. We observed that pumping gold and silver nanoparticles into a microfluidic device fabricated in polydimethylsiloxane prolongs the glow time of luminol. We have demonstrated that the intensity of chemiluminescence in the presence of nanospheres depends on the position along the microfluidic serpentine channel. We show that the enhancement factors can be controlled by the nanoparticle size and material. Spectrally, the emission peak of luminol overlaps with the absorption band of the nanospheres, which maximizes the effect of confined plasmons on the optical density of states in the vicinity of the luminol emission peak. These observations, interpreted in terms of the Purcell effect mediated by nano-plasmons, form an essential step toward the development of microfluidic chips with gain media. Practical implementation of the discovered effect will include improving the detection limits of chemiluminescence for forensic science, research in biology and chemistry, and a number of commercial applications.
Acetylation of histone H4 lysine 5 and 12 is required for CENP-A deposition into centromeres
Authors: Shang Wei-Hao , Hori Tetsuya , Westhorpe Frederick G. , Godek Kristina M. , Toyoda Atsushi , Misu Sadahiko , Monma Norikazu , Ikeo Kazuho , Carroll Christopher W. , Takami Yasunari , Fujiyama Asao , Kimura Hiroshi , Straight Aaron F. , Fukagawa Tatsuo 
Published: November 2016

AbstractCentromeres are specified epigenetically through the deposition of the centromere-specific histone H3 variant CENP-A. However, how additional epigenetic features are involved in centromere specification is unknown. Here, we find that histone H4 Lys5 and Lys12 acetylation (H4K5ac and H4K12ac) primarily occur within the pre-nucleosomal CENP-A–H4–HJURP (CENP-A chaperone) complex, before centromere deposition. We show that H4K5ac and H4K12ac are mediated by the RbAp46/48–Hat1 complex and that RbAp48-deficient DT40 cells fail to recruit HJURP to centromeres and do not incorporate new CENP-A at centromeres. However, C-terminally-truncated HJURP, that does not bind CENP-A, does localize to centromeres in RbAp48-deficient cells. Acetylation-dead H4 mutations cause mis-localization of the CENP-A–H4 complex to non-centromeric chromatin. Crucially, CENP-A with acetylation-mimetic H4 was assembled specifically into centromeres even in RbAp48-deficient DT40 cells. We conclude that H4K5ac and H4K12ac, mediated by RbAp46/48, facilitates efficient CENP-A deposition into centromeres.
Circulating vitamin D in relation to cancer incidence and survival of the head and neck and oesophagus in the EPIC cohort
Authors: Fanidi Anouar , Muller David C. , Midttun Øivind , Ueland Per Magne , Vollset Stein Emil , Relton Caroline , Vineis Paolo , Weiderpass Elisabete , Skeie Guri , Brustad Magritt , Palli Domenico , Tumino Rosario , Grioni Sara , Sacerdote Carlotta , Bueno-de-Mesquita H. B. , Peeters Petra H. , Boutron-Ruault Marie-Christine , Kvaskoff Marina , Cadeau Claire , Huerta José María , Sánchez Maria-José , Agudo Antonio , Lasheras Cristina , Quirós J. Ramón , Chamosa Saioa , Riboli Elio , Travis Ruth C. , Ward Heather , Murphy Neil , Khaw Kay-Tee , Trichopoulou Antonia , Lagiou Pagona , Papatesta Eleni-Maria , Boeing Heiner , Kuehn Tilman , Katzke Verena , Steffen Annika , Johansson Anders , Brennan Paul , Johansson Mattias 
Published: November 2016

AbstractExperimental and epidemiological data suggest that vitamin D play a role in pathogenesis and progression of cancer, but prospective data on head and neck cancer (HNC) and oesophagus cancer are limited. The European Prospective Investigation into Cancer and Nutrition (EPIC) study recruited 385,747 participants with blood samples between 1992 and 2000. This analysis includes 497 case-control pairs of the head and neck and oesophagus, as well as 443 additional controls. Circulating 25(OH)D3 were measured in pre-diagnostic samples and evaluated in relation to HNC and oesophagus cancer risk and post-diagnosis all-cause mortality. After controlling for risk factors, a doubling of 25(OH)D3 was associated with 30% lower odds of HNC (OR 0.70, 95% confidence interval [95% CI] 0.56–0.88, Ptrend = 0.001). Subsequent analyses by anatomical sub-site indicated clear inverse associations with risk of larynx and hypopharynx cancer combined (OR 0.55, 95CI% 0.39–0.78) and oral cavity cancer (OR 0.60, 95CI% 0.42–0.87). Low 25(OH)D3 concentrations were also associated with higher risk of death from any cause among HNC cases. No clear association was seen with risk or survival for oesophageal cancer. Study participants with elevated circulating concentrations of 25(OH)D3 had decreased risk of HNC, as well as improved survival following diagnosis.
Differential diagnosis of lung cancer, its metastasis and chronic obstructive pulmonary disease based on serum Vegf, Il-8 and MMP-9
Authors: Balla Murali M. S. , Desai Sejal , Purwar Pallavi , Kumar Amit , Bhandarkar Prashant , Shejul Yogesh K. , Pramesh C. S. , Laskar S. , Pandey Badri N. 
Published: November 2016

AbstractChronic obstructive pulmonary disease (COPD) patients are at higher risk of developing lung cancer and its metastasis, but no suitable biomarker has been reported for differential diagnosis of these patients. Levels of serum biomarkers (VEGF, IL-8, MMP-9 and MMP-2) were analyzed in these patients, which were compared with healthy donors (HD). Levels of VEGF (P < 0.005) and MMP-9 (P < 0.05) were significantly higher in COPD patients than HD. Compared to HD, a decrease in IL-8 (~8.1 folds; P < 0.0001) but an increase in MMP-9 (~1.6 folds; P < 0.05) levels were observed in the lung cancer patients. Cancer patients showed significantly (P < 0.005) lower levels of serum VEGF (1.9 folds) and IL-8 (~9 folds) than the COPD patients. VEGF level was significantly higher (2.6 folds; P < 0.0005) in metastatic than non-metastatic cancer patients. However, MMP-2 didn’t show significant variation in these patients. The Youden’s index (YI) values for lung cancer diagnosis in HD using IL-8 was 0.55 with 83.3% overall accuracy. VEGF was able to diagnose COPD in HD with better YI (0.38) and overall accuracy (70.6%). IL-8 was able to diagnose cancer in COPD patients and HD with YI values of 0.35, 0.55 with 71% and 83.3% overall accuracy, respectively.
Regulation of the MDM2-p53 pathway by the nucleolar protein CSIG in response to nucleolar stress
Authors: Xie Nan , Ma Liwei , Zhu Feng , Zhao Wenhui , Tian Feng , Yuan Fuwen , Fu Jingxuan , Huang Daoyuan , Lv Cuicui , Tong Tanjun 
Published: November 2016

AbstractNucleolar proteins play an important role in the regulation of the MDM2–p53 pathway, which coordinates cellular response to stress. However, the mechanism underlying this regulation remains poorly understood. Here, we report that the nucleolar protein CSIG is a novel and crucial regulator of the MDM2–p53 pathway. We demonstrate that CSIG translocates from the nucleolus to the nucleoplasm in response to nucleolar stress. Moreover, knockdown of CSIG attenuates the induction of p53 and abrogates G1 phase arrest in response to nucleolar stress. CSIG interacts directly with the MDM2 RING finger domain and inhibits MDM2 E3 ubiquitin ligase activity, thus resulting in a decrease in MDM2-mediated p53 ubiquitination and degradation. Our results suggest that the CSIG–MDM2–p53 regulatory pathway plays an important role in the cellular response to nucleolar stress.
Power-efficient low-temperature woven coiled fibre actuator for wearable applications
Authors: Hiraoka Maki , Nakamura Kunihiko , Arase Hidekazu , Asai Katsuhiko , Kaneko Yuriko , John Stephen W. , Tagashira Kenji , Omote Atsushi 
Published: November 2016

AbstractA fibre actuator that generates a large strain with high specific power represents a promising strategy to develop novel wearable devices and robotics. We propose a new coiled-fibre actuator based on highly drawn, hard linear low-density polyethylene (LLDPE) fibres. Driven by resistance heating, the actuator can be operated at temperatures as low as 60 °C and uses only 20% of the power consumed by previously coiled fibre actuators when generating 20 MPa of stress at 10% strain. In this temperature range, 1600 W kg−1 of specific work (8 times that of a skeletal muscle) at 69 MPa of tensile stress (230 times that of a skeletal muscle) with a work efficiency of 2% is achieved. The actuator generates strain as high as 23% at 90 °C. Given the low driving temperature, the actuator can be combined with common fabrics or stretchable conductive elastomers without thermal degradation, allowing for easy use in wearable systems. Nanostructural analysis implies that the lamellar crystals in drawn LLDPE fibres are weakly bridged with each other, which allows for easy deformation into compact helical shapes via twisting and the generation of large strain with high work efficiency.
Remote Sensing of the Water Storage Dynamics of Large Lakes and Reservoirs in the Yangtze River Basin from 2000 to 2014
Authors: Cai Xiaobin , Feng Lian , Hou Xuejiao , Chen Xiaoling 
Published: November 2016

AbstractBasin-scale water volumes of lakes and reservoirs are difficult to obtain due to a number of challenges. In this study, area-based water storage estimation models are proposed for large lakes and reservoirs in the Yangtze River Basin (YRB). The models are subsequently applied to Moderate Resolution Imaging Spectroradiometer (MODIS) observations of 128 large lakes and 108 reservoirs between 2000 and 2014, and the first comprehensive map of the temporal and spatial dynamics of water storage in large water bodies in the YRB is provided. The results show that 53.91% of the lakes experienced significant decreasing trends in water storage during this period, and the total water storage in lakes showed a decreasing trend of 14 million m3 month−1. By contrast, a monthly mean increase of 177 million m3 was observed for water storage in reservoirs. Our analysis revealed that the pronounced increase in reservoirs was primarily due to the rapid water level increase in the Three Gorges Reservoir in recent years, while understanding the water loss in lakes requires additional studies. The long-term data presented in this study provide critical baseline information for future water resource monitoring and regulation in the YRB and China.
Enrichment of 13C in diacids and related compounds during photochemical processing of aqueous aerosols: New proxy for organic aerosols aging
Authors: Pavuluri Chandra Mouli , Kawamura Kimitaka 
Published: November 2016

AbstractTo investigate the applicability of compound specific stable carbon isotope ratios (δ13C) of organics in assessment of their photochemical aging in the atmosphere, batch UV irradiation experiments were conducted on two ambient (anthropogenic and biogenic) aerosol samples in aqueous phase for 0.5–120 h. The irradiated samples were analyzed for δ13C of diacids, glyoxylic acid (ωC2) and glyoxal. δ13C of diacids and related compounds became larger with irradiation time (i.e., aging), except for few cases. In general, δ13C of C2-C4 diacids showed an increasing trend with decreasing chain length. Based on δ13C of diacids and related compounds and their relations to their concentrations, we found that C2 and C3 are enriched with 13C during the photochemical decomposition and production from their higher homologues and oxoacids. Photochemical breakdown of higher (≥C3) to lower diacids is also important in the enrichment of 13C in C3-C9 diacids whereas their production from primary precursors causes depletion of 13C. In case of ωC2 and glyoxal, their photochemical production and further oxidation to highly oxygenated compounds both cause the enrichment of 13C. This study reveals that δ13C of diacids and related compounds can be used as a proxy to trace the aging of organic aerosols during long-range atmospheric transport.
Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains
Authors: Yang Guang Li , Hou Shu Gui , Le Baoge Ri , Li Zhi Guo , Xu Hao , Liu Ya Ping , Du Wen Tao , Liu Yong Qin 
Published: November 2016

AbstractA detailed understanding of microbial ecology in different supraglacial habitats is important due to the unprecedented speed of glacier retreat. Differences in bacterial diversity and community structure between glacial snow and glacial soil on the Chongce Ice Cap were assessed using 454 pyrosequencing. Based on rarefaction curves, Chao1, ACE, and Shannon indices, we found that bacterial diversity in glacial snow was lower than that in glacial soil. Principal coordinate analysis (PCoA) and heatmap analysis indicated that there were major differences in bacterial communities between glacial snow and glacial soil. Most bacteria were different between the two habitats; however, there were some common bacteria shared between glacial snow and glacial soil. Some rare or functional bacterial resources were also present in the Chongce Ice Cap. These findings provide a preliminary understanding of the shifts in bacterial diversity and communities from glacial snow to glacial soil after the melting and inflow of glacial snow into glacial soil.