bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climatology and trends of the Adriatic Sea wind waves: analysis of a 37‐year long instrumental data set
Authors: Pomaro Angela , Cavaleri Luigi , Lionello Piero 
Published: April 2017

ABSTRACTThis study concerns the analysis of a 37‐year long directional wave time series recorded since 1979 at the CNR‐ISMAR oceanographic research tower, located in the Northern Adriatic Sea. The length of the time series allows to describe the wave climate in the North Adriatic and to identify trends and links with large‐scale climate patterns. The northern part of the Adriatic Sea is characterized by two main wind and correspondingly wave regimes, strongly forced by the regional orography: the long‐fetch south‐easterly ‘sirocco’ and the short‐fetch strong north‐easterly ‘bora’ wind generated waves, blowing along the major and minor axis of the basin, respectively. Bora is the most frequent regime, but high waves are mostly associated to sirocco. A clear decrease of the significant wave height 99th percentile is evident, paralleled by a smaller, but distributed along the annual cycle, increase of the 50th and 75th ones. The estimated trend of the frequency of events above a certain threshold confirms an increase of the average storm frequency, with a shift from both the lower and the higher to the central part of the distribution, paralleled by a decrease of the maximum Hs values. In particular, a distributed decrease of the bora significant wave height is recognized. For sirocco the tendency is less pronounced, but with an evident increase of the frequency of the mean values. The high sensitivity of this particular area to even small variations of large‐scale climate allows to explore possible links of the local wave, hence wind, activity with large‐scale Northern Hemisphere circulation patterns or weather regimes. Our main interest is on the storm tracks and jet stream location/intensity over vast areas, which led us to choose four reference patterns: the North Atlantic Oscillation and the East Atlantic (EA), EA/Western Russia and Scandinavian patterns.
A multiplex culture system for the long‐term growth of fission yeast cells
Authors: Callens Céline , Coelho Nelson C. , Miller Aaron W. , Sananes Maria Rosa Domingo , Dunham Maitreya J. , Denoual Matthieu , Coudreuse Damien 
Published: April 2017

AbstractMaintenance of long‐term cultures of yeast cells is central to a broad range of investigations, from metabolic studies to laboratory evolution assays. However, repeated dilutions of batch cultures lead to variations in medium composition, with implications for cell physiology. In Saccharomyces cerevisiae, powerful miniaturized chemostat setups, or ministat arrays, have been shown to allow for constant dilution of multiple independent cultures. Here we set out to adapt these arrays for continuous culture of a morphologically and physiologically distinct yeast, the fission yeast Schizosaccharomyces pombe, with the goal of maintaining constant population density over time. First, we demonstrated that the original ministats are incompatible with growing fission yeast for more than a few generations, prompting us to modify different aspects of the system design. Next, we identified critical parameters for sustaining unbiased vegetative growth in these conditions. This requires deletion of the gsf2 flocculin‐encoding gene, along with addition of galactose to the medium and lowering of the culture temperature. Importantly, we improved the flexibility of the ministats by developing a piezo‐pump module for the independent regulation of the dilution rate of each culture. This made it possible to easily grow strains that have different generation times in the same assay. Our system therefore allows for maintaining multiple fission yeast cultures in exponential growth, adapting the dilution of each culture over time to keep constant population density for hundreds of generations. These multiplex culture systems open the door to a new range of long‐term experiments using this model organism. © 2017 The Authors. Yeast published by John Wiley & Sons, Ltd.
THE TWILIGHT OF OTTOMAN SUFISM: ANTIQUITY, IMMORALITY, AND NATION IN YAKUP KADRI KARAOSMANOĞLU'SNUR BABA
Authors: Wilson M. Brett 
Published: April 2017

AbstractThis article examines modernist-nationalist thought on Sufi lodges during the late Ottoman Empire and early Turkish Republic via the controversial novelNur Baba(1922) by Yakup Kadri Karaosmanoğlu. Widely translated and the basis of the first-ever Turkish motion picture,Nur Babadepicts a debauched Sufi lodge in turn-of-the-century Istanbul where drug use, alcoholism, and illicit amorous liaisons run amok. The novel played an important role in shaping public perceptions of Sufi lodges in the twilight years of the Ottoman Empire. This piece explores the novel's place among early 20th-century critiques of Sufism, its approach to national history, its historical setting (during the reign of Sultan Abdülhamid II), and its close relationship to the intellectual concerns of the Second Constitutional Period (1908–18). It argues for a revised understanding of the novel's historical setting and contends that the novel employs a combination of moralistic critique and romantic nostalgia that is central to modernist-nationalist treatments of Sufism that instrumentalize Sufi culture for nation-building purposes.
Influence of opacification in the frontal recess on frontal sinusitis
Authors: Hashimoto K , Tsuzuki K , Okazaki K , Sakagami M 
Published: April 2017

AbstractObjectives:This study aimed to radiologically evaluate the influence of inflammatory changes in frontal recess cells on frontal sinusitis.Methods:A total of 93 patients (186 sides) who underwent primary sinonasal surgery at Hyogo College of Medicine were enrolled in 2015 and 2016. Opacification of agger nasi, fronto-ethmoidal, ethmoid bulla, suprabullar and frontal bulla cells was determined by pre-operative computed tomography and its influence on frontal sinusitis was investigated.Results:In all, 42 per cent of 186 sides were affected by frontal sinusitis. Agger nasi, ethmoid bulla, fronto-ethmoidal, suprabullar and frontal bulla cells were identified in 99 per cent, 100 per cent, 38 per cent, 69 per cent, and 16 per cent of sides, respectively. The presence of frontal recess cells and frontal ostium size did not significantly influence frontal sinusitis development. However, opacification of agger nasi, type 1 fronto-ethmoidal and suprabullar cells significantly influenced frontal sinusitis development.Conclusion:Frontal sinusitis is caused by inflammatory changes in frontal recess cells.
Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation
Authors: Gigante Crystal M. , Dibattista Michele , Dong Frederick N. , Zheng Xiaobin , Yue Sibiao , Young Stephen G. , Reisert Johannes , Zheng Yixian , Zhao Haiqing 
Published: April 2017

AbstractB-type lamins are major constituents of the nuclear lamina in all metazoan cells, yet have specific roles in the development of certain cell types. Although they are speculated to regulate gene expression in developmental contexts, a direct link between B-type lamins and developmental gene expression in an in vivo system is currently lacking. Here, we identify lamin B1 as a key regulator of gene expression required for the formation of functional olfactory sensory neurons. By using targeted knockout in olfactory epithelial stem cells in adult mice, we show that lamin B1 deficient neurons exhibit attenuated response to odour stimulation. This deficit can be explained by decreased expression of genes involved in mature neuron function, along with increased expression of genes atypical of the olfactory lineage. These results support that the broadly expressed lamin B1 regulates expression of a subset of genes involved in the differentiation of a specific cell type.
Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Authors: Hillion Melanie , Bernhardt Jörg , Busche Tobias , Rossius Martina , Maaß Sandra , Becher Dörte , Rawat Mamta , Wirtz Markus , Hell Rüdiger , Rückert Christian , Kalinowski Jörn , Antelmann Haike 
Published: April 2017

AbstractMycothiol (MSH) is the major low molecular weight (LMW) thiol in Actinomycetes. Here, we used shotgun proteomics, OxICAT and RNA-seq transcriptomics to analyse protein S-mycothiolation, reversible thiol-oxidations and their impact on gene expression in Mycobacterium smegmatis under hypochlorite stress. In total, 58 S-mycothiolated proteins were identified under NaOCl stress that are involved in energy metabolism, fatty acid and mycolic acid biosynthesis, protein translation, redox regulation and detoxification. Protein S-mycothiolation was accompanied by MSH depletion in the thiol-metabolome. Quantification of the redox state of 1098 Cys residues using OxICAT revealed that 381 Cys residues (33.6%) showed >10% increased oxidations under NaOCl stress, which overlapped with 40 S-mycothiolated Cys-peptides. The absence of MSH resulted in a higher basal oxidation level of 338 Cys residues (41.1%). The RseA and RshA anti-sigma factors and the Zur and NrdR repressors were identified as NaOCl-sensitive proteins and their oxidation resulted in an up-regulation of the SigH, SigE, Zur and NrdR regulons in the RNA-seq transcriptome. In conclusion, we show here that NaOCl stress causes widespread thiol-oxidation including protein S-mycothiolation resulting in induction of antioxidant defense mechanisms in M. smegmatis. Our results further reveal that MSH is important to maintain the reduced state of protein thiols.
Expandable Mg-based Helical Stent Assessment using Static, Dynamic, and Porcine Ex Vivo Models
Authors: Koo Youngmi , Tiasha Tarannum , Shanov Vesselin N. , Yun Yeoheung 
Published: April 2017

AbstractA bioresorbable metallic helical stent was explored as a new device opportunity (magnesium scaffold), which can be absorbed by the body without leaving a trace and simultaneously allowing restoration of vasoreactivity with the potential for vessel remodeling. In this study, developed Mg-based helical stent was inserted and expanded in vessels with subsequent degradation in various environments including static, dynamic, and porcine ex vivo models. By assessing stent degradation in three different environments, we observed: (1) stress- and flow-induced degradation; (2) a high degradation rate in the dynamic reactor; (3) production of intermediate products (MgO/Mg(OH)2 and Ca/P) during degradation; and (4) intermediate micro-gas pocket formation in the neighboring tissue ex vivo model. Overall, the expandable Mg-based helical stent employed as a scaffold performed well, with expansion rate (>100%) in porcine ex vivo model.
Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella
Authors: Liao Zhiwei , Wan Quanyuan , Shang Xueying , Su Jianguo 
Published: April 2017

AbstractGrass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively. Comparative transcriptome analysis identified 413 and 832 grass carp reovirus (GCRV)-resistant-association SNPs as well as 1,381 and 1,606 GCRV-susceptible-association SNPs in individuals and cell lines, respectively. Integrated analysis indicated 22 genes with single SNP share common resistant/susceptible traits in two transcriptomes. Furthermore, we infected grass carp with GCRV, genotyping and association analyses were performed, and 9 in 22 SNPs were confirmed by PCR-RFLP. Meanwhile, mRNA expression profiles of 6 genes containing confirmed SNPs were examined by qRT-PCR. The results demonstrated that mRNA expressions were significant differences in resistant/susceptible individuals and cell lines. The present study develops an important strategy for high throughput screening of phenotype association genetic markers and the results will serve in grass carp breeding for GCRV resistance.
Resolution-enhanced Fourier ptychographic microscopy based on high-numerical-aperture illuminations
Authors: Sun Jiasong , Zuo Chao , Zhang Liang , Chen Qian 
Published: April 2017

AbstractHigh-resolution and wide field-of-view (FOV) microscopic imaging plays a central role in diverse applications such as high-throughput screening and digital pathology. However, conventional microscopes face inherent trade-offs between the spatial resolution and FOV, which are fundamental limited by the space-bandwidth product (SBP) of the optical system. The resolution-FOV tradeoff can be effectively decoupled in Fourier ptychography microscopy (FPM), however, to date, the effective imaging NA achievable with a typical FPM system is still limited to the range of 0.4–0.7. Herein, we report, for the first time, a high-NA illumination based resolution-enhanced FPM (REFPM) platform, in which a LED-array-based digital oil-immersion condenser is used to create high-angle programmable plane-wave illuminations, endowing a 10×, 0.4 NA objective lens with final effective imaging performance of 1.6 NA. With REFPM, we present the highest-resolution results with a unprecedented half-pitch resolution of 154 nm at a wavelength of 435 nm across a wide FOV of 2.34 mm2, corresponding to an SBP of 98.5 megapixels (~50 times higher than that of the conventional incoherent microscope with the same resolution). Our work provides an important step of FPM towards high-resolution large-NA imaging applications, generating comparable resolution performance but significantly broadening the FOV of conventional oil-immersion microscopes.
A common neonicotinoid pesticide, thiamethoxam, impairs honey bee flight ability
Authors: Tosi Simone , Burgio Giovanni , Nieh James C. 
Published: April 2017

AbstractPesticides can pose environmental risks, and a common neonicotinoid pesticide, thiamethoxam, decreases homing success in honey bees. Neonicotinoids can alter bee navigation, but we present the first evidence that neonicotinoid exposure alone can impair the physical ability of bees to fly. We tested the effects of acute or chronic exposure to thiamethoxam on the flight ability of foragers in flight mills. Within 1 h of consuming a single sublethal dose (1.34 ng/bee), foragers showed excitation and significantly increased flight duration (+78%) and distance (+72%). Chronic exposure significantly decreased flight duration (−54%), distance (−56%), and average velocity (−7%) after either one or two days of continuous exposure that resulted in bees ingesting field-relevant thiamethoxam doses of 1.96–2.90 ng/bee/day. These results provide the first demonstration that acute or chronic exposure to a neonicotinoid alone can significantly alter bee flight. Such exposure may impair foraging and homing, which are vital to normal colony function and ecosystem services.
Inkjet Printing of High Performance Transistors with Micron Order Chemically Set Gaps
Authors: Grubb Peter Mack , Subbaraman Harish , Park Saungeun , Akinwande Deji , Chen Ray T. 
Published: April 2017

AbstractThis paper reports a 100% inkjet printed transistor with a short channel of approximately 1 µm with an operating speed up to 18.21 GHz. Printed electronics are a burgeoning area in electronics development, but are often stymied by the large minimum feature size. To combat this, techniques were developed to allow for the printings of much shorter transistor channels. The small gap size is achieved through the use of silver inks with different chemical properties to prevent mixing. The combination of the short channel and semiconducting carbon nanotubes (CNT) allows for an exceptional experimentally measured on/off ratio of 106. This all inkjet printed transistor allows for the fabrication of devices using roll-to-roll methodologies with no additional overhead compared to current state of the art production methods.
Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools
Authors: Schleusener Viola , Köser Claudio U. , Beckert Patrick , Niemann Stefan , Feuerriegel Silke 
Published: April 2017

AbstractWhole-genome sequencing (WGS) has the potential to accelerate drug-susceptibility testing (DST) to design appropriate regimens for drug-resistant tuberculosis (TB). Several recently developed automated software tools promise to standardize the analysis and interpretation of WGS data. We assessed five tools (CASTB, KvarQ, Mykrobe Predictor TB, PhyResSE, and TBProfiler) with regards to DST and phylogenetic lineage classification, which we compared with phenotypic DST, Sanger sequencing, and traditional typing results for a collection of 91 strains. The lineage classifications by the tools generally only differed in the resolution of the results. However, some strains could not be classified at all and one strain was misclassified. The sensitivities and specificities for isoniazid and rifampicin resistance of the tools were high, whereas the results for ethambutol, pyrazinamide, and streptomycin resistance were more variable. False-susceptible DST results were mainly due to missing mutations in the resistance catalogues that the respective tools employed for data interpretation. Notably, we also found cases of false-resistance because of the misclassification of polymorphisms as resistance mutations. In conclusion, the performance of current WGS analysis tools for DST is highly variable. Sustainable business models and a shared, high-quality catalogue of resistance mutations are needed to ensure the clinical utility of these tools.
2D-DIGE as a strategy to identify serum biomarkers in Mexican patients with Type-2 diabetes with different body mass index
Authors: Gómez-Cardona Erik E. , Hernández-Domínguez Eric E. , Velarde-Salcedo Aída J. , Pacheco Alberto-Barrera- , Diaz-Gois Agustín , De León-Rodríguez Antonio , Barba de la Rosa Ana P. 
Published: April 2017

AbstractObesity and type 2 diabetes(T2D) are the most prevalent and serious metabolic diseases affecting people worldwide. However racial and ethnic disparities seems to be a risk factor for their development. Mexico has been named as one of the largest populations with the highest prevalence of diabetes and obesity. The aim of this study was to identify novel T2D-associated proteins in Mexican patients. Blood samples were collected from 62 Mexican patients with T2D and they were grouped according to their body mass index(BMI). A panel of 10 diabetes and obesity serum markers was determined using MAGPIX. A comparative proteomics study was performed using two-dimensional difference in-gel electrophoresis(2D-DIGE) followed by mass spectrometry(LC-MS/MS). We detected 113 spots differentially accumulated, in which 64 unique proteins were identified, proteins that were involved in metabolism pathways, molecular transport, and cellular signalling. Four proteins(14-3-3, ApoH, ZAG, and OTO3) showing diabetes-related variation and also changes in relation to obesity were selected for further validation by western blotting. Our results reveal new diabetes related proteins present in the Mexican population. These could provide additional insight into the understanding of diabetes development in Mexican population and may also be useful candidate biomarkers.
Oncogenic activity of SOX1 in glioblastoma
Authors: Garcia Idoia , Aldaregia Juncal , Marjanovic Vicentic Jelena , Aldaz Paula , Moreno-Cugnon Leire , Torres-Bayona Sergio , Carrasco-Garcia Estefania , Garros-Regulez Laura , Egaña Larraitz , Rubio Angel , Pollard Steven , Stevanovic Milena , Sampron Nicolas , Matheu Ander 
Published: April 2017

AbstractGlioblastoma remains the most common and deadliest type of brain tumor and contains a population of self-renewing, highly tumorigenic glioma stem cells (GSCs), which contributes to tumor initiation and treatment resistance. Developmental programs participating in tissue development and homeostasis re-emerge in GSCs, supporting the development and progression of glioblastoma. SOX1 plays an important role in neural development and neural progenitor pool maintenance. Its impact on glioblastoma remains largely unknown. In this study, we have found that high levels of SOX1 observed in a subset of patients correlate with lower overall survival. At the cellular level, SOX1 expression is elevated in patient-derived GSCs and it is also higher in oncosphere culture compared to differentiation conditions in conventional glioblastoma cell lines. Moreover, genetic inhibition of SOX1 in patient-derived GSCs and conventional cell lines decreases self-renewal and proliferative capacity in vitro and tumor initiation and growth in vivo. Contrarily, SOX1 over-expression moderately promotes self-renewal and proliferation in GSCs. These functions seem to be independent of its activity as Wnt/β-catenin signaling regulator. In summary, these results identify a functional role for SOX1 in regulating glioma cell heterogeneity and plasticity, and suggest SOX1 as a potential target in the GSC population in glioblastoma.
Video-Assisted Thoracic Surgical Right Upper Lobectomy with Bronchus-First and Simultaneous Vessel Stapling Technique
Authors: Zhang Linyou , Xu Hao 
Published: April 2017

AbstractA method of video-assisted thoracic surgical (VATS) right upper lobectomy with bronchus-first and simultaneous vessel stapling will be introduced. In this study, all cases underwent two-port VATS as follows: first, the right upper lobe bronchus was identified and stapled; then, all right upper lobe vessels were stapled simultaneously. This method was performed in 50 cases. There was no surgical mortality, hemorrhage, vascular injuries, or conversion. This technique can reduce wound size and operative time and make the operation safer and easier to accomplish.
From semigroups to subelliptic estimates for quadratic operators
Authors: Hitrik Michael , Pravda-Starov Karel , Viola Joe 
Published: April 2017

Using an approach based on the techniques of FBI transforms, we give a new simple proof of the global subelliptic estimates for non-self-adjoint nonelliptic quadratic differential operators, under a natural averaging condition on the Weyl symbols of the operators, established by the second author in Subelliptic estimates for quadratic differential operators (Amer. J. Math. 133 (2011), no. 1, 39–89). The loss of the derivatives in the subelliptic estimates depends directly on algebraic properties of the Hamilton maps of the quadratic symbols. Using the FBI point of view, we also give accurate smoothing estimates of Gelfand–Shilov type for the associated heat semigroup in the limit of small times.
Vital signs: the molecules of life
Authors: Ball Philip 
Published: April 2017

Abstract‘Vital signs: the molecules of life’ outlines the molecular basis of life. Understanding molecular life is as much about understanding interactions between molecules and their position within the hierarchical system as it is about identifying the actors. Proteins are a specific type of molecule that perform a huge number of processes inside a biological cell. They are formed by subunits, which in turn are formed from long chains of amino acids. The instructions for these chains are contained, transmitted, and effected using DNA and RNA, another species of long, repeating chains of molecules. The molecular processes and interactions involving these molecules are well understood, but molecular understanding will never give the full story.