bluuebunny/crossref_metadata_2025 huggingface dataset:
Human brain patterns underlying vigilant attention: impact of sleep debt, circadian phase and attentional engagement
Authors: Maire Micheline , Reichert Carolin F. , Gabel Virginie , Viola Antoine U. , Phillips Christophe , Berthomier Christian , Borgwardt Stefan , Cajochen Christian , Schmidt Christina
Published: January 2018

Sleepiness and cognitive function vary over the 24-h day due to circadian and sleep-wake-dependent mechanisms. However, the underlying cerebral hallmarks associated with these variations remain to be fully established. Using functional magnetic resonance imaging (fMRI), we investigated brain responses associated with circadian and homeostatic sleep-wake-driven dynamics of subjective sleepiness throughout day and night. Healthy volunteers regularly performed a psychomotor vigilance task (PVT) in the MR-scanner during a 40-h sleep deprivation (high sleep pressure) and a 40-h multiple nap protocol (low sleep pressure). When sleep deprived, arousal-promoting thalamic activation during optimal PVT performance paralleled the time course of subjective sleepiness with peaks at night and troughs on the subsequent day. Conversely, task-related cortical activation decreased when sleepiness increased as a consequence of higher sleep debt. Under low sleep pressure, we did not observe any significant temporal association between PVT-related brain activation and subjective sleepiness. Thus, a circadian modulation in brain correlates of vigilant attention was only detectable under high sleep pressure conditions. Our data indicate that circadian and sleep homeostatic processes impact on vigilant attention via specific mechanisms; mirrored in a decline of cortical resources under high sleep pressure, opposed by a subcortical “rescuing” at adverse circadian times.
The early conversion of deep-sea wood falls into chemosynthetic hotspots revealed by in situ monitoring
Authors: Kalenitchenko D. , Péru E. , Contreira Pereira L. , Petetin C. , Galand P. E. , Le Bris N.
Published: January 2018

Wood debris on the ocean floor harbor flourishing communities, which include invertebrate taxa thriving in sulfide-rich habitats belonging to hydrothermal vent and methane seep deep-sea lineages. The formation of sulfidic niches from digested wood material produced by woodborers has been known for a long time, but the temporal dynamics and sulfide ranges encountered on wood falls remains unknown. Here, we show that wood falls are converted into sulfidic hotpots, before the colonization by xylophagaid bivalves. Less than a month after immersion at a depth of 520 m in oxygenated seawater the sulfide concentration increased to millimolar levels inside immersed logs. From in situ experiments combining high-frequency chemical and video monitoring, we document the rapid development of a microbial sulfur biofilm at the surface of wood. These findings highlight the fact that sulfide is initially produced from the labile components of wood and supports chemosynthesis as an early pathway of energy transfer to deep-sea wood colonists, as suggested by recent aquarium studies. The study furthermore reveals that woodborers promote sulfide-oxidation at the periphery of their burrows, thus, not only facilitating the development of sulfidic zones in the surrounding of degraded wood falls, but also governing sulfur-cycling within the wood matrix.
Effects of straw application on nitrate leaching in fields in the Yellow River irrigation zone of Ningxia, China
Authors: Yang Shiqi , Wang Yongsheng , Liu Ruliang , Li Quanxin , Yang Zhengli
Published: January 2018

A five-year field experiment was conducted to investigate the effects of straw application on nitrate leaching loss. Treatments included soil that was not treated (control), soil treated with straw at a low rate (4,500 kg ha−2, T1) and soil treated with straw at a high rate (9,000 kg ha−2, T2). Nitrate-nitrogen leaching in the 10, 20, 30, 60, and 90 cm soil layers was measured using the resin-core method. The results indicated that straw application could reduce soil nitrate leaching losses in the 0–30 cm layer. In this layer, the nitrate leaching values for T1 (13.76 kg ha−2) and T2 (13.74 kg ha−2) were both significantly lower than those of the control (15.76 kg ha−2) (P < 0.05); the soil nitrate leaching losses decreased by 12.71% and 12.84% for those two treatments, respectively. However, no significant differences in losses were observed (P > 0.05) between T1 and T2. The effects of straw application were apparent only in the ploughing layer (30 cm-depth soil layer). In the deeper layers (60 and 90 cm), no significant differences were observed between the treatments and the control, and the same results were observed in the topsoil layers (10 and 20 cm).
Impact of Concurrent Genomic Alterations Detected by Comprehensive Genomic Sequencing on Clinical Outcomes in East-Asian Patients with EGFR-Mutated Lung Adenocarcinoma
Authors: Sato Seijiro , Nagahashi Masayuki , Koike Terumoto , Ichikawa Hiroshi , Shimada Yoshifumi , Watanabe Satoshi , Kikuchi Toshiaki , Takada Kazuki , Nakanishi Ryota , Oki Eiji , Okamoto Tatsuro , Akazawa Kouhei , Lyle Stephen , Ling Yiwei , Takabe Kazuaki , Okuda Shujiro , Wakai Toshifumi , Tsuchida Masanori
Published: January 2018

Next-generation sequencing (NGS) has enabled comprehensive detection of genomic alterations in lung cancer. Ethnic differences may play a critical role in the efficacy of targeted therapies. The aim of this study was to identify and compare genomic alterations of lung adenocarcinoma between Japanese patients and the Cancer Genome Atlas (TCGA), which majority of patients are from the US. We also aimed to examine prognostic impact of additional genomic alterations in patients harboring EGFR mutations. Genomic alterations were determined in Japanese patients with lung adenocarcinoma (N = 100) using NGS-based sequencing of 415 known cancer genes, and correlated with clinical outcome. EGFR active mutations, i.e., those involving exon 19 deletion or an L858R point mutation, were seen in 43% of patients. Some differences in driver gene mutation prevalence were observed between the Japanese cohort described in the present study and the TCGA. Japanese cohort had significantly more genomic alterations in cell cycle pathway, i.e., CDKN2B and RB1 than TCGA. Concurrent mutations, in genes such as CDKN2B or RB1, were associated with worse clinical outcome in patients with EGFR active mutations. Our data support the utility of comprehensive sequencing to detect concurrent genomic variations that may affect clinical outcomes in this disease.
Use of nanoparticle concentration as a tool to understand the structural properties of colloids
Authors: Ribeiro Lígia Nunes de Morais , Couto Verônica Muniz , Fraceto Leonardo Fernandes , de Paula Eneida
Published: January 2018

Elucidation of the structural properties of colloids is paramount for a successful formulation. However, the intrinsic dynamism of colloidal systems makes their characterization a difficult task and, in particular, there is a lack of physicochemical techniques that can be correlated to their biological performance. Nanoparticle tracking analysis (NTA) allows measurements of size distribution and nanoparticle concentration in real time. Its analysis over time also enables the early detection of physical instability in the systems not assessed by subtle changes in size distribution. Nanoparticle concentration is a parameter with the potential to bridge the gap between in vitro characterization and biological performance of colloids, and therefore should be monitored in stability studies of formulations. To demonstrate this, we have followed two systems: extruded liposomes exposed to increasing CHCl3 concentrations, and solid lipid nanoparticles prepared with decreasing amounts of poloxamer 188. NTA and dynamic light scattering (DLS) were used to monitor changes in nanoparticle number and size, and to estimate the number of lipid components per particle. The results revealed a strong negative correlation between particle size (determined by DLS) and concentration (assessed by NTA) in diluted samples, which should be adopted to monitor nanocolloidal stability, especially in drug delivery.
Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle
Authors: Villarreal-Ramos Bernardo , Berg Stefan , Whelan Adam , Holbert Sebastien , Carreras Florence , Salguero Francisco J. , Khatri Bhagwati L. , Malone Kerri , Rue-Albrecht Kevin , Shaughnessy Ronan , Smyth Alicia , Ameni Gobena , Aseffa Abraham , Sarradin Pierre , Winter Nathalie , Vordermeier Martin , Gordon Stephen V.
Published: January 2018

The Mycobacterium tuberculosis complex (MTBC) is the collective term given to the group of bacteria that cause tuberculosis (TB) in mammals. It has been reported that M. tuberculosis H37Rv, a standard reference MTBC strain, is attenuated in cattle compared to Mycobacterium bovis. However, as M. tuberculosis H37Rv was isolated in the early 1930s, and genetic variants are known to exist, we sought to revisit this question of attenuation of M. tuberculosis for cattle by performing a bovine experimental infection with a recent M. tuberculosis isolate. Here we report infection of cattle using M. bovis AF2122/97, M. tuberculosis H37Rv, and M. tuberculosis BTB1558, the latter isolated in 2008 during a TB surveillance project in Ethiopian cattle. We show that both M. tuberculosis strains caused reduced gross pathology and histopathology in cattle compared to M. bovis. Using M. tuberculosis H37Rv and M. bovis AF2122/97 as the extremes in terms of infection outcome, we used RNA-Seq analysis to explore differences in the peripheral response to infection as a route to identify biomarkers of progressive disease in contrast to a more quiescent, latent infection. Our work shows the attenuation of M. tuberculosis strains for cattle, and emphasizes the potential of the bovine model as a ‘One Health’ approach to inform human TB biomarker development and post-exposure vaccine development.
Electronic Properties of Synthetic Shrimp Pathogens-derived DNA Schottky Diodes
Authors: Rizan Nastaran , Yew Chan Yen , Niknam Maryam Rajabpour , Krishnasamy Jegenathan , Bhassu Subha , Hong Goh Zee , Devadas Sridevi , Din Mohamed Shariff Mohd , Tajuddin Hairul Anuar , Othman Rofina Yasmin , Phang Siew Moi , Iwamoto Mitsumasa , Periasamy Vengadesh
Published: January 2018

The exciting discovery of the semiconducting-like properties of deoxyribonucleic acid (DNA) and its potential applications in molecular genetics and diagnostics in recent times has resulted in a paradigm shift in biophysics research. Recent studies in our laboratory provide a platform towards detecting charge transfer mechanism and understanding the electronic properties of DNA based on the sequence-specific electronic response, which can be applied as an alternative to identify or detect DNA. In this study, we demonstrate a novel method for identification of DNA from different shrimp viruses and bacteria using electronic properties of DNA obtained from both negative and positive bias regions in current-voltage (I–V) profiles. Characteristic electronic properties were calculated and used for quantification and further understanding in the identification process. Aquaculture in shrimp industry is a fast-growing food sector throughout the world. However, shrimp culture in many Asian countries faced a huge economic loss due to disease outbreaks. Scientists have been using specific established methods for detecting shrimp infection, but those methods do have their significant drawbacks due to many inherent factors. As such, we believe that this simple, rapid, sensitive and cost-effective tool can be used for detection and identification of DNA from different shrimp viruses and bacteria.
Establishing a mental lexicon with cochlear implants: an ERP study with young children
Authors: Vavatzanidis Niki K. , Mürbe Dirk , Friederici Angela D. , Hahne Anja
Published: January 2018

In the present study we explore the implications of acquiring language when relying mainly or exclusively on input from a cochlear implant (CI), a device providing auditory input to otherwise deaf individuals. We focus on the time course of semantic learning in children within the second year of implant use; a period that equals the auditory age of normal hearing children during which vocabulary emerges and extends dramatically. 32 young bilaterally implanted children saw pictures paired with either matching or non-matching auditory words. Their electroencephalographic responses were recorded after 12, 18 and 24 months of implant use, revealing a large dichotomy: Some children failed to show semantic processing throughout their second year of CI use, which fell in line with their poor language outcomes. The majority of children, though, demonstrated semantic processing in form of the so-called N400 effect already after 12 months of implant use, even when their language experience relied exclusively on the implant. This is slightly earlier than observed for normal hearing children of the same auditory age, suggesting that more mature cognitive faculties at the beginning of language acquisition lead to faster semantic learning.
Microdosimetric Modeling of Biological Effectiveness for Boron Neutron Capture Therapy Considering Intra- and Intercellular Heterogeneity in 10B Distribution
Authors: Sato Tatsuhiko , Masunaga Shin-ichiro , Kumada Hiroaki , Hamada Nobuyuki
Published: January 2018

We here propose a new model for estimating the biological effectiveness for boron neutron capture therapy (BNCT) considering intra- and intercellular heterogeneity in 10B distribution. The new model was developed from our previously established stochastic microdosimetric kinetic model that determines the surviving fraction of cells irradiated with any radiations. In the model, the probability density of the absorbed doses in microscopic scales is the fundamental physical index for characterizing the radiation fields. A new computational method was established to determine the probability density for application to BNCT using the Particle and Heavy Ion Transport code System PHITS. The parameters used in the model were determined from the measured surviving fraction of tumor cells administrated with two kinds of 10B compounds. The model quantitatively highlighted the indispensable need to consider the synergetic effect and the dose dependence of the biological effectiveness in the estimate of the therapeutic effect of BNCT. The model can predict the biological effectiveness of newly developed 10B compounds based on their intra- and intercellular distributions, and thus, it can play important roles not only in treatment planning but also in drug discovery research for future BNCT.
Deep-Ultraviolet AlGaN/AlN Core-Shell Multiple Quantum Wells on AlN Nanorods via Lithography-Free Method
Authors: Kim Jinwan , Choi Uiho , Pyeon Jaedo , So Byeongchan , Nam Okhyun
Published: January 2018

We report deep ultraviolet (UVC) emitting core-shell-type AlGaN/AlN multiple quantum wells (MQWs) on the AlN nanorods which are prepared by catalyst/lithography free process. The MQWs are grown on AlN nanorods on a sapphire substrate by polarity-selective epitaxy and etching (PSEE) using high-temperature metal organic chemical vapor deposition. The AlN nanorods prepared through PSEE have a low dislocation density because edge dislocations are bent toward neighboring N-polar AlN domains. The core–shell-type MQWs grown on AlN nanorods have three crystallographic orientations, and the final shape of the grown structure is explained by a ball-and-stick model. The photoluminescence (PL) intensity of MQWs grown on AlN nanorods is approximately 40 times higher than that of MQWs simultaneously grown on a planar structure. This result can be explained by increased internal quantum efficiency, large active volume, and increase in light extraction efficiency based on the examination in this study. Among those effects, the increase of active volume on AlN nanorods is considered to be the main reason for the enhancement of the PL intensity.
Altered pattern of monocyte differentiation and monocyte-derived TGF-β1 in severe asthma
Authors: Hung Chih-Hsing , Wang Chin-Chou , Suen Jau-Ling , Sheu Chau-Chyun , Kuo Chang-Hung , Liao Wei-Ting , Yang Yi-Hsin , Wu Chao-Chien , Leung Sum-Yee , Lai Ruay-Sheng , Lin Chi-Cheng , Wei Yu-Feng , Lee Chong-Yeh , Huang Ming-Shyan , Huang Shau-Ku
Published: January 2018

CD14+ monocytes contain precursors for macrophages and fibrocytes, known to be involved in regulating airway remodeling in human asthma and distinguishable by the PM-2K marker. We sought to identify circulating subsets of PM-2K+ macrophage-like cells and evaluate their relationships to lung function, severity and control status. Circulating PM-2K+ macrophage-like cells and fibrocytes could be identified and distinguished between normal individuals (N = 152) and asthmatic subjects (N = 133) using multi-parametric flow cytometry. PM-2K+ macrophage-like cells were found to be significantly lower in asthmatic subjects, particularly noted for the CD14−PM-2K+ subset and PM-2K+CCR7−CD86+ cells in subjects with poor lung function (FEV%/FVC% < 80%) as compared to those of normal subjects and asthmatics with normal lung function, whereas the frequency of fibrocytes was higher in asthmatics and the CCR7−CD86+ subset distribution was significantly different in subjects with varying severity. Moreover, exogenous transforming growth factor beta 1 (TGF-β1) was found to inhibit the generation of PM-2K+ macrophage-like cells, but promote the growth of fibrocytes, from CD14+ monocytes, and monocyte-derived TGF-β1 was found to correlate with the lung function, severity and control status in asthmatic patients. Collectively, aberrant differentiation of monocytes into PM-2K+ macrophage-like cell subsets and fibrocytes, together with increased monocyte-derived TGF-β1, characterized patients with severe asthma.
First estimates of Greenland shark (Somniosus microcephalus) local abundances in Arctic waters
Authors: Devine Brynn M. , Wheeland Laura J. , Fisher Jonathan A. D.
Published: January 2018

Baited remote underwater video cameras were deployed in the Eastern Canadian Arctic, for the purpose of estimating local densities of the long-lived Greenland shark within five deep-water, data-poor regions of interest for fisheries development and marine conservation in Nunavut, Canada. A total of 31 camera deployments occurred between July-September in 2015 and 2016 during joint exploratory fishing and scientific cruises. Greenland sharks appeared at 80% of deployments. A total of 142 individuals were identified and no individuals were observed in more than one deployment. Estimates of Greenland shark abundance and biomass were calculated from averaged times of first arrival, video-derived swimming speed and length data, and local current speed estimates. Density estimates varied 1–15 fold among regions; being highest in warmer (>0 °C), deeper areas and lowest in shallow, sub-zero temperature regions. These baited camera results illustrate the ubiquity of this elusive species and suggest that Nunavut’s Lancaster Sound eco-zone may be of particular importance for Greenland shark, a potentially vulnerable Arctic species.
Effluent and serum protein N-glycosylation is associated with inflammation and peritoneal membrane transport characteristics in peritoneal dialysis patients
Authors: Ferrantelli Evelina , Farhat Karima , Ederveen Agnes L. Hipgrave , Reiding Karli R. , Beelen Robert H. J. , van Ittersum Frans J. , Wuhrer Manfred , Dotz Viktoria
Published: January 2018

Mass spectrometric glycomics was used as an innovative approach to identify biomarkers in serum and dialysate samples from peritoneal dialysis (PD) patients. PD is a life-saving treatment worldwide applied in more than 100,000 patients suffering from chronic kidney disease. PD treatment uses the peritoneum as a natural membrane to exchange waste products from blood to a glucose-based solution. Daily exposure of the peritoneal membrane to these solutions may cause complications such as peritonitis, fibrosis and inflammation which, in the long term, lead to the failure of the treatment. It has been shown in the last years that protein N-glycosylation is related to inflammatory and fibrotic processes. Here, by using a recently developed MALDI-TOF-MS method with linkage-specific sialic acid derivatisation, we showed that alpha2,6-sialylation, especially in triantennary N-glycans from peritoneal effluents, is associated with critical clinical outcomes in a prospective cohort of 94 PD patients. Moreover, we found an association between the levels of presumably immunoglobulin-G-related glycans as well as galactosylation of diantennary glycans with PD-related complications such as peritonitis and loss of peritoneal mesothelial cell mass. The observed glycomic changes point to changes in protein abundance and protein-specific glycosylation, representing candidate functional biomarkers of PD and associated complications.
Malaria infected red blood cells release small regulatory RNAs through extracellular vesicles
Authors: Babatunde Kehinde Adebayo , Mbagwu Smart , Hernández-Castañeda María Andrea , Adapa Swamy R. , Walch Michael , Filgueira Luis , Falquet Laurent , Jiang Rays H. Y. , Ghiran Ionita , Mantel Pierre-Yves
Published: January 2018

The parasite Plasmodium falciparum causes the most severe form of malaria. Cell communication between parasites is an important mechanism to control population density and differentiation. The infected red blood cells (iRBCs) release small extracellular vesicles (EVs) that transfer cargoes between cells. The EVs synchronize the differentiation of the asexual parasites into gametocytes to initiate the transmission to the mosquito. Beside their role in parasite communication, EVs regulate vascular function. So far, the exact cargoes responsible for cellular communication remain unknown. We isolated EVs from cultured iRBCs to determine their small RNA content. We identified several types of human and plasmodial regulatory RNAs. While the miRNAs and tRNA-derived fragments were the most abundant human RNAs, we also found Y-RNAs, vault RNAs, snoRNAs and piRNAs. Interestingly, we found about 120 plasmodial RNAs, including mRNAs coding for exported proteins and proteins involved in drug resistance, as well as non-coding RNAs, such as rRNAs, small nuclear (snRNAs) and tRNAs. These data show, that iRBC-EVs carry small regulatory RNAs. A role in cellular communication is possible since the RNAs were transferred to endothelial cells. Furthermore, the presence of Plasmodium RNAs, in EVs suggests that they may be used as biomarker to track and detect disease.
Moderate decline in select synaptic markers in the prefrontal cortex (BA9) of patients with Alzheimer’s disease at various cognitive stages
Authors: Poirel Odile , Mella Sébastien , Videau Catherine , Ramet Lauriane , Davoli Maria Antonietta , Herzog Etienne , Katsel Pavel , Mechawar Naguib , Haroutunian Vahram , Epelbaum Jacques , Daumas Stéphanie , El Mestikawy Salah
Published: January 2018

Synaptic loss, plaques and neurofibrillary tangles are viewed as hallmarks of Alzheimer’s disease (AD). This study investigated synaptic markers in neocortical Brodmann area 9 (BA9) samples from 171 subjects with and without AD at different levels of cognitive impairment. The expression levels of vesicular glutamate transporters (VGLUT1&2), glutamate uptake site (EAAT2), post-synaptic density protein of 95 kD (PSD95), vesicular GABA/glycine transporter (VIAAT), somatostatin (som), synaptophysin and choline acetyl transferase (ChAT) were evaluated. VGLUT2 and EAAT2 were unaffected by dementia. The VGLUT1, PSD95, VIAAT, som, ChAT and synaptophysin expression levels significantly decreased as dementia progressed. The maximal decrease varied between 12% (synaptophysin) and 42% (som). VGLUT1 was more strongly correlated with dementia than all of the other markers (polyserial correlation = −0.41). Principal component analysis using these markers was unable to differentiate the CDR groups from one another. Therefore, the status of the major synaptic markers in BA9 does not seem to be linked to the cognitive status of AD patients. The findings of this study suggest that the loss of synaptic markers in BA9 is a late event that is only weakly related to AD dementia.
Increasing conversion efficiency of two-step photon up-conversion solar cell with a voltage booster hetero-interface
Authors: Asahi Shigeo , Kusaki Kazuki , Harada Yukihiro , Kita Takashi
Published: January 2018

Development of high-efficiency solar cells is one of the attractive challenges in renewable energy technologies. Photon up-conversion can reduce the transmission loss and is one of the promising concepts which improve conversion efficiency. Here we present an analysis of the conversion efficiency, which can be increased by up-conversion in a single-junction solar cell with a hetero-interface that boosts the output voltage. We confirm that an increase in the quasi-Fermi gap and substantial photocurrent generation result in a high conversion efficiency.
Mercury sodium exospheric emission as a proxy for solar perturbations transit
Authors: Orsini Stefano , Mangano Valeria , Milillo Anna , Plainaki Christina , Mura Alessandro , Raines Jim M. , De Angelis Elisabetta , Rispoli Rosanna , Lazzarotto Francesco , Aronica Alessandro
Published: January 2018

The first evidence at Mercury of direct relation between ICME transit and Na exosphere dynamics is presented, suggesting that Na emission, observed from ground, could be a proxy of planetary space weather at Mercury. The link existing between the dayside exosphere Na patterns and the solar wind-magnetosphere-surface interactions is investigated. This goal is pursued by analyzing the Na intensity hourly images, as observed by the ground-based THEMIS solar telescope during 10 selected periods between 2012 and 2013 (with seeing, σ < = 2″), when also MESSENGER data were available. Frequently, two-peak patterns of variable intensity are observed, located at high latitudes in both hemispheres. Occasionally, Na signal is instead diffused above the sub-solar region. We compare these different patterns with the in-situ time profiles of proton fluxes and magnetic field data from MESSENGER. Among these 10 cases, only in one occasion the Na signal is diffused above the subsolar region, when the MESSENGER data detect the transit of two ICMEs. The selected cases suggest that the Na emission patterns are well related to the solar wind conditions at Mercury. Hence, the exospheric Na emission patterns, observed from ground, could be considered as a ‘natural monitor’ of solar disturbances when transiting near Mercury.
Significantly High Modulation Efficiency of Compact Graphene Modulator Based on Silicon Waveguide
Authors: Shu Haowen , Su Zhaotang , Huang Le , Wu Zhennan , Wang Xingjun , Zhang Zhiyong , Zhou Zhiping
Published: January 2018

We theoretically and experimentally demonstrate a significantly large modulation efficiency of a compact graphene modulator based on a silicon waveguide using the electro refractive effect of graphene. The modulation modes of electro-absorption and electro-refractive can be switched with different applied voltages. A high extinction ratio of 25 dB is achieved in the electro-absorption modulation mode with a driving voltage range of 0 V to 1 V. For electro-refractive modulation, the driving voltage ranges from 1 V to 3 V with a 185-pm spectrum shift. The modulation efficiency of 1.29 V · mm with a 40-μm interaction length is two orders of magnitude higher than that of the first reported graphene phase modulator. The realisation of phase and intensity modulation with graphene based on a silicon waveguide heralds its potential application in optical communication and optical interconnection systems.
Counting Caenorhabditis elegans: Protocol Optimization and Applications for Population Growth and Toxicity Studies in Liquid Medium
Authors: Scanlan Leona D. , Lund Steven P. , Coskun Sanem Hosbas , Hanna Shannon K. , Johnson Monique E. , Sims Christopher M. , Brignoni Karina , Lapasset Patricia , Petersen Elijah J. , Elliott John T. , Nelson Bryant C.
Published: January 2018

The nematode Caenorhabditis elegans is used extensively in molecular, toxicological and genetics research. However, standardized methods for counting nematodes in liquid culture do not exist despite the wide use of nematodes and need for accurate measurements. Herein, we provide a simple and affordable counting protocol developed to maximize count accuracy and minimize variability in liquid nematode culture. Sources of variability in the counting process were identified and tested in 14 separate experiments. Three variables resulted in significant effects on nematode count: shaking of the culture, priming of pipette tips, and sampling location within a microcentrifuge tube. Between-operator variability did not have a statistically significant effect on counts, even among differently-skilled operators. The protocol was used to assess population growth rates of nematodes in two different but common liquid growth media: axenic modified Caenorhabditis elegans Habitation and Reproduction medium (mCeHR) and S-basal complete. In mCeHR, nematode populations doubled daily for 10 d. S-basal complete populations initially doubled every 12 h, but slowed within 7 d. We also detected a statistically significant difference between embryo-to-hatchling incubation period of 5 d in mCeHR compared to 4 d in S-basal complete. The developed counting method for Caenorhabditis elegans reduces variability and allows for rigorous and reliable experimentation.
Focal hyperintensity in the dorsal brain stem of patients with cerebellopontine angle tumor: A high-resolution 3 T MRI study
Authors: Yamamoto Hirotaka , Fujita Atsushi , Imahori Taichiro , Sasayama Takashi , Hosoda Kohkichi , Nibu Ken-ichi , Kohmura Eiji
Published: January 2018

Focal hyperintensity (FHI) in the dorsal brain stem on T2-weighted images of patients with cerebellopontine angle (CPA) tumor was thought to indicate degeneration of the vestibular nucleus and to be specific to vestibular schwannoma. The purpose of this study was to evaluate FHI by using high-resolution 3 Tesla magnetic resonance imaging (3 T MRI) and the relation to clinical characteristics. We retrospectively reviewed the clinical data and MRI of 45 patients with CPA tumors (34 vestibular schwannomas and 11 other tumors). FHI in the dorsal brain stem was found in 25 (55.6%) patients (20 vestibular schwannomas and 5 other tumors). For the vestibular schwannomas, the factors contributing to positive FHI were age (p = 0.025), max CPA (p =  < 0.001), hearing ability (P = 0.005), and canal paresis (p =  < 0.001) in the univariate analysis. Multivariate regression analysis showed that max CPA (p = 0.029) was a significant factor of positive FHI. In other CPA tumors, these factors were not significant predictors. With the use of 3 T MRI, FHI was observed more frequently than previously reported. Our results suggest that FHI is not a specific indicator of vestibular schwannoma and is related to not only vestibular function but also other factors.
Experimental and Numerical Investigation on Dragonfly Wing and Body Motion during Voluntary Take-off
Authors: Li Qiushi , Zheng Mengzong , Pan Tianyu , Su Guanting
Published: January 2018

We present a detailed analysis of the voluntary take-off procedure of a dragonfly. The motions of the body and wings are recorded using two high-speed cameras at Beihang University. The experimental results show that the dragonfly becomes airborne after approximately one wingbeat and then leaves the ground. During this process, the maximum vertical acceleration could reach 20 m/s2. Evidence also shows that acceleration is generated only by the aerodynamic force induced by the flapping of wings. The dragonfly voluntary take-off procedure is divided into four phases with distinctive features. The variation in phase difference between the forewing and hindwing and angle of attack in the down-stroke are calculated to explain the different features of the four phases. In terms of the key parameters of flapping, the phase difference increases from approximately 0 to 110 degrees; the angle of attack in down-stroke reaches the maximum at first and then decreases in the following take-off procedure. Due to experimental limitations, 2-D simulations are conducted using the immersed boundary method. The results indicate that the phase difference and the angle of attack are highly correlated with the unsteady fluid field around the dragonfly’s wings and body, which determines the generation of aerodynamic forces.
Sac7 and Rho1 regulate the white-to-opaque switching in Candida albicans
Authors: Yang Siwy Ling , Zeng Guisheng , Chan Fong Yee , Wang Yan-Ming , Yang Dongliang , Wang Yue
Published: January 2018

Candida albicans cells homozygous at the mating-type locus stochastically undergo the white-to-opaque switching to become mating-competent. This switching is regulated by a core circuit of transcription factors organized through interlocking feedback loops around the master regulator Wor1. Although a range of distinct environmental cues is known to induce the switching, the pathways linking the external stimuli to the central control mechanism remains largely unknown. By screening a C. albicans haploid gene-deletion library, we found that SAC7 encoding a GTPase-activating protein of Rho1 is required for the white-to-opaque switching. We demonstrate that Sac7 physically associates with Rho1-GTP and the constitutively active Rho1G18V mutant impairs the white-to-opaque switching while the inactive Rho1D124A mutant promotes it. Overexpressing WOR1 in both sac7Δ/Δ and rho1
G18V
cells suppresses the switching defect, indicating that the Sac7/Rho1 module acts upstream of Wor1. Furthermore, we provide evidence that Sac7/Rho1 functions in a pathway independent of the Ras/cAMP pathway which has previously been positioned upstream of Wor1. Taken together, we have discovered new regulators and a signaling pathway that regulate the white-to-opaque switching in the most prevalent human fungal pathogen C. albicans.
A novel microRNA, hsa-miR-6852 differentially regulated by Interleukin-27 induces necrosis in cervical cancer cells by downregulating the FoxM1 expression
Authors: Poudyal Deepak , Herman Andrew , Adelsberger Joseph W. , Yang Jun , Hu Xiaojun , Chen Qian , Bosche Marjorie , Sherman Brad T. , Imamichi Tomozumi
Published: January 2018

We have previously demonstrated that Interleukin-27 differentially regulates the expression of seven novel microRNAs. Here we elucidate the functional significance of these novel microRNAs. Of the seven microRNAs, over expression of miRNA-6852 (miR-SX4) mimic induces cell cycle arrest at G2/M phase and induces necrosis in HEK293 and panel of cervical cancer cells (Human Papilloma Virus (HPV) infected cell lines; HeLa, CaSki and SiHa cells). To define the mechanism of the miR-SX4-mediated G2/M arrest, a microarray gene chip array and western blot analysis were performed. FoxM1, a transcription factor is identified as a key protein down-regulated by miR-SX4, even though the miR-SX4 does not target 3’UTR of FoxM1. Knock down of FoxM1 using si-RNA demonstrate that FoxM1 silenced cell induces G2/M cell cycle arrest and necrosis. Our data demonstrated for the first time that miR-SX4 could be a potent anti-cancer microRNA.
Loss induced coherent combining in InP-Si3N4 hybrid platform
Authors: Zhu Yeyu , Zhao Yunsong , Zhu Lin
Published: January 2018

Loss, as a time-reversed counterpart of gain, can also be used to control lasing in an optical system with coupled cavities. In this study, by manipulating mirror losses at different output ports of coupled Fabry-Perot cavities, an integrated coherently combined laser system is proposed and experimentally demonstrated in the InP-Si3N4 hybrid platform. Two InP-based reflective semiconductor amplifiers are coherently combined through an adiabatic 50:50 directional coupler in silicon nitride. The combining efficiency is ~92% at ~2× threshold. The novel system not only realizes the miniaturization of coherent laser beam combining but also provides a chip-scale platform to study the coherent coupling between coupled laser cavities.
A high throughput approach for the generation of orthogonally interacting protein pairs
Authors: Lawrie Justin , Song Xi , Niu Wei , Guo Jiantao
Published: January 2018

In contrast to the nearly error-free self-assembly of protein architectures in nature, artificial assembly of protein complexes with pre-defined structure and function in vitro is still challenging. To mimic nature’s strategy to construct pre-defined three-dimensional protein architectures, highly specific protein-protein interacting pairs are needed. Here we report an effort to create an orthogonally interacting protein pair from its parental pair using a bacteria-based in vivo directed evolution strategy. This high throughput approach features a combination of a negative and a positive selection. The newly developed negative selection from this work was used to remove any protein mutants that retain effective interaction with their parents. The positive selection was used to identify mutant pairs that can engage in effective mutual interaction. By using the cohesin-dockerin protein pair that is responsible for the self-assembly of cellulosome as a model system, we demonstrated that a protein pair that is orthogonal to its parent pair could be readily generated using our strategy. This approach could open new avenues to a wide range of protein-based assembly, such as biocatalysis or nanomaterials, with pre-determined architecture and potentially novel functions and properties.
Widespread persistent changes to temperature extremes occurred earlier than predicted
Authors: Li Chao , Fang Yuanyuan , Caldeira Ken , Zhang Xuebin , Diffenbaugh Noah S. , Michalak Anna M.
Published: January 2018

A critical question for climate mitigation and adaptation is to understand when and where the signal of changes to climate extremes have persistently emerged or will emerge from the background noise of climate variability. Here we show observational evidence that such persistent changes to temperature extremes have already occurred over large parts of the Earth. We further show that climate models forced with natural and anthropogenic historical forcings underestimate these changes. In particular, persistent changes have emerged in observations earlier and over a larger spatial extent than predicted by models. The delayed emergence in the models is linked to a combination of simulated change (‘signal’) that is weaker than observed, and simulated variability (‘noise’) that is greater than observed. Over regions where persistent changes had not occurred by the year 2000, we find that most of the observed signal-to-noise ratios lie within the 16–84% range of those simulated. Examination of simulations with and without anthropogenic forcings provides evidence that the observed changes are more likely to be anthropogenic than nature in origin. Our findings suggest that further changes to temperature extremes over parts of the Earth are likely to occur earlier than projected by the current climate models.
An improved method of crafting a multi-electrode spiral cuff for the selective stimulation of peripheral nerves
Authors: Rozman Janez , Pečlin Polona , Ribarič Samo , Godec Matjaž , Burja Jaka
Published: January 2018

This article reviews an improved methodology and technology for crafting a multi-electrode spiral cuff for the selective activation of nerve fibres in particular superficial regions of a peripheral nerve. The analysis, structural and mechanical properties of the spot welds used for the interconnections between the stimulating electrodes and stainless-steel lead wires are presented. The cuff consisted of 33 platinum electrodes embedded within a self-curling 17-mm-long silicone spiral sheet with a nominal internal diameter of 2.5 mm. The weld was analyzed using scanning electron microscopy and nanohardness tests, while the interconnection was investigated using destructive load tests. The functionality of the cuff was tested in an isolated porcine vagus nerve. The results of the scanning electron microscopy show good alloying and none of the typical welding defects that occur between the wire and the platinum foil. The results of the destructive load tests show that the breaking loads were between 3.22 and 5 N. The results of the nanohardness testing show that the hardness of the weld was different for the particular sites on the weld sample. Finally, the results of the functional testing show that for different stimulation intensities both the compound action potential deflection and the shape are modulated.
Developmental pathways inferred from modularity, morphological integration and fluctuating asymmetry patterns in the human face
Authors: Quinto-Sánchez Mirsha , Muñoz-Muñoz Francesc , Gomez-Valdes Jorge , Cintas Celia , Navarro Pablo , Cerqueira Caio Cesar Silva de , Paschetta Carolina , de Azevedo Soledad , Ramallo Virginia , Acuña-Alonzo Victor , Adhikari Kaustubh , Fuentes-Guajardo Macarena , Hünemeier Tábita , Everardo Paola , de Avila Francisco , Jaramillo Claudia , Arias Williams , Gallo Carla , Poletti Giovani , Bedoya Gabriel , Bortolini Maria Cátira , Canizales-Quinteros Samuel , Rothhammer Francisco , Rosique Javier , Ruiz-Linares Andres , Gonzalez-Jose Rolando
Published: January 2018

Facial asymmetries are usually measured and interpreted as proxies to developmental noise. However, analyses focused on its developmental and genetic architecture are scarce. To advance on this topic, studies based on a comprehensive and simultaneous analysis of modularity, morphological integration and facial asymmetries including both phenotypic and genomic information are needed. Here we explore several modularity hypotheses on a sample of Latin American mestizos, in order to test if modularity and integration patterns differ across several genomic ancestry backgrounds. To do so, 4104 individuals were analyzed using 3D photogrammetry reconstructions and a set of 34 facial landmarks placed on each individual. We found a pattern of modularity and integration that is conserved across sub-samples differing in their genomic ancestry background. Specifically, a signal of modularity based on functional demands and organization of the face is regularly observed across the whole sample. Our results shed more light on previous evidence obtained from Genome Wide Association Studies performed on the same samples, indicating the action of different genomic regions contributing to the expression of the nose and mouth facial phenotypes. Our results also indicate that large samples including phenotypic and genomic metadata enable a better understanding of the developmental and genetic architecture of craniofacial phenotypes.
Prebiotic formation of cyclic dipeptides under potentially early Earth conditions
Authors: Ying Jianxi , Lin Rongcan , Xu Pengxiang , Wu Yile , Liu Yan , Zhao Yufen
Published: January 2018

Cyclic dipeptides, also known as 2,5-diketopiperazines (DKPs), represent the simplest peptides that were first completely characterized. DKPs can catalyze the chiral selection of reactions and are considered as peptide precursors. The origin of biochemical chirality and synthesis of peptides remains abstruse problem believed to be essential precondition to origin of life. Therefore, it is reasonable to believe that the DKPs could have played a key role in the origin of life. How the formation of the DKPs through the condensation of unprotected amino acids in simulated prebiotic conditions has been unclear. Herein, it was found that cyclo-Pro-Pro could be formed directly from unprotected proline in the aqueous solution of trimetaphosphate (P3m) under mild condition with the yield up to 97%. Other amino acids were found to form proline-containing DKPs under the same conditions in spite of lower yield. During the formation process of these DKPs, P3m promotes the formation of linear dipeptides in the first step of the mechanism. The above findings are helpful and significant for understanding the formation of DKPs in the process of chemical evolution of life.
Pharmacological targeting of BET proteins attenuates radiation-induced lung fibrosis
Authors: Wang Jian , Zhou Fangzheng , Li Zhenyu , Mei Hong , Wang Ye , Ma Hong , Shi Liangliang , Huang Ai , Zhang Tao , Lin Zhenyu , Wu Gang
Published: January 2018

Radiation-induced lung injury has restricted radiotherapy for thoracic cancer. The purpose of this study was to investigate the radioprotective effects of bromodomain and extra terminal (BET) inhibitor JQ1 in a murine model of pulmonary damage. Chest computed tomography (CT) was performed in a rat model after 20 Gy radiation of the right thorax. And histological evaluation and protein expressions of irradiated tissue were analyzed to confirm the potential anti-fibrosis effect of JQ1 and its underlying mechanisms. Moreover, colony formation assays were used to explore the effects of JQ1 on esophageal cancer Eca109 and breast cancer MCF7. JQ1 attenuated radiologic and histologic presentations of radiation-induced fibrosis, inflammatory reaction and pulmonary structural changes and the increase of Hounsfield units (HU) density and hydroxyproline content after radiation. Additionally, JQ1 suppressed BRD4, c-MYC, Collagen I, TGF-β, p-NF-κB p65, p-Smad2 and p-Smad3 expressions after irradiation, repressed proliferation and transdifferentiation of lung fibroblasts, and impaired clonogenic survival of thoracic cancer cells. Collectively, our study demonstrated for the first time that BET Bromodomain inhibitor JQ1 protected normal lung tissue after radiation, and exerted a radiosensitizing effect in thoracic cancer cells.
Reconstructing the gradient source position from steady-state fluxes to small receptors
Authors: Dobramysl Ulrich , Holcman David
Published: January 2018

Recovering the position of a source from the fluxes of diffusing particles through small receptors allows a biological cell to determine its relative position, spatial localization and guide it to a final target. However, how a source can be recovered from point fluxes remains unclear. Using the Narrow Escape approach for an open domain, we compute the diffusion fluxes of Brownian particles generated by a steady-state gradient from a single source through small holes distributed on a surface in two dimensions. We find that the location of a source can be recovered when there are at least 3 receptors and the source is positioned no further than 10 cell radii away, but this condition is not necessary in a narrow strip. The present approach provides a computational basis for the first step of direction sensing of a gradient at a single cell level.
AlGaInP Red LEDs with Hollow Hemispherical Polystyrene Arrays
Authors: Cheng Wen-Ching , Huang Shih-Yung , Chen Yi-Jiun , Wang Chia-Sheng , Lin Hoang Yan , Wu Tzong-Ming , Horng Ray-Hua
Published: January 2018

A hollow hemispherical polystyrene (HHPS) was fabricated to reduce total internal reflection in AlGaInP-based LEDs. At an injection current of 350 mA, the external quantum efficiencies of LED-I, LED-II, LED-III, and LED-IV are 20.92%, 24.65%, 27.28%, and 33.77% and the wall-plug efficiencies are 17.11%, 20%, 22.5%, and 27.33%, respectively. The enhanced performance is attributed to the light output power enhancement through the surface roughness, microlens-liked PS hemisphere, and scatter-liked HHPS array. In this paper, the rigorous coupled wave analysis (RCWA) numerical method was also conducted to demonstrate the HHPS array effectively enlarge the effective light cone.