bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three newly identified Immediate Early Genes of Bovine herpesvirus 1 lack the characteristic Octamer binding motif- 1
Authors: Pokhriyal Mayank , Ratta Barkha , Yadav Brijesh Singh , Kumar Ajay , Saxena Meeta , Verma Om Prakash , Sharma Bhaskar 
Published: July 2018

AbstractOnly three immediate early genes (IE) BICP0, BICP4 and BICP22 of Bovine herpesvirus 1 (BoHV-1) are known. These genes are expressed coordinately and their promoters are well characterized. We provide evidence for expression of three additional IE genes of BoHV-1 i.e. UL21, UL33 and UL34. These genes are expressed in the presence of cycloheximide (CH) at the same time as known IE genes. Surprisingly, the promoters of newly identified IE genes (UL21, UL33, UL34) lack the OCT-1 binding site, a considered site of transactivation of the BoHV-1 IE genes. The other difference in the promoters of the newly identified IE genes is the presence of TATA box at near optimal site. However, all the IE genes have similar spatial placements of C/EBPα, DPE and INR elements.
Sleep and light exposure across different levels of urbanisation in Brazilian communities
Authors: Pilz Luísa K. , Levandovski Rosa , Oliveira Melissa A. B. , Hidalgo Maria Paz , Roenneberg Till 
Published: July 2018

AbstractQuilombos are settlements originally founded by Africans and African descendants (Quilombolas) in remote parts of Brazil to escape slavery. Due to individual histories, Quilombos nowadays exhibit different states of industrialisation, making them ideal for studying the influence of electrification on daily behaviour. In a comparative approach, we aimed to understand whether and how human sleep changes with the introduction of artificial light. We investigated daily rest-activity-rhythms and sleep-patterns in the Quilombolas’ by both wrist actimetry and the Munich ChronoType Questionnaire (MCTQ; the results of these two instruments correlated highly). Seven communities (MCTQ: N = 213/actimetry: N = 125) were compared in this study. Light exposure, phase of activity, sleep timing and duration differ across communities with various levels of urbanisation and histories of access to electricity. People living without electricity and those, who acquired it only very recently on average sleep earlier than those in more urbanised communities (mid-sleep about 1 hour earlier); sleep duration tends to be longer. Our results and those of others show that use of electricity and modern lifestyles have changed sleep behaviour. To understand the consequences of these changes for health, further studies are warranted.
Vitamin K supplementation during pregnancy for improving outcomes: a systematic review and meta-analysis
Authors: Shahrook Sadequa , Ota Erika , Hanada Nobutsugu , Sawada Kimi , Mori Rintaro 
Published: July 2018

AbstractTo study supplementation effect of vitamin K (VK) alone or combined with other nutrients administered to pregnant women, we searched Cochrane Pregnancy and Childbirth Group’s Trials Register (till 22 January 2016, updated on 28 February 2018) including other resources. Two review authors independently assessed randomised or quasi-randomised controlled trials for inclusion, data extraction, accuracy, and risk of bias. We included older trials from high-income countries (six; 21,493 women-newborns), judged mostly as high or unclear bias risk. We could not assess high-risk e.g. epileptic women, but healthy women (different gestational ages) received varying VK dosages and duration. We meta-analysed neonatal bleeding (RR 1.16, 95% CI 0.59 to 2.29; P = 0.67) and maternal plasma VK1 (MD 2.46, 95% CI 0.98 to 3.93; P = 0.001). We found many outcomes were un-assessed e.g. perinatal death, maternal bleeding, healthcare utilization. Mostly newborns were included where VK found significantly effective for e.g. serum VK (mother-newborn), maternal breast milk VK. Few trials reported neonatal adverse side effects. The GRADE evidence quality was very low i.e. neonatal bleeding, neonatal jaundice, maternal plasma VK1. The intervention was favourable for maternal sera VK1 but remained uncertain for neonatal bleeding and other outcomes. The existing literature gaps warrant future investigations on un-assessed or inadequately reported outcomes.
Highly-Sensitive Refractive Index Sensing by Near-infrared Metatronic Nanocircuits
Authors: Rashed A. R. , Gudulluoglu B. , Yun H. W. , Habib M. , Boyaci I. H. , Hong S. H. , Ozbay E. , Caglayan H. 
Published: July 2018

AbstractIn this work, we present a highly-sensitive refractive index sensor based on metatronic nanocircuits operating at near-infrared spectral range. The structure is designed based on simple nanorod geometry and fabricated by nanopatterning of transparent conducting oxides. The functionality of these polarization dependent metatronic nanocircuits is enhanced by applying tunable response. This feature is investigated by depositing NH2 (Amine) groups via plasma polymerization technique on top of indium-tin-oxide nanorods. The dielectric constant of Amine groups is a function of their thickness, which can be controlled by the RF power and the time duration of the applied plasma polymerization process. The resonance wavelengths of nanocircuits shift to higher wavelength, as the dielectric constant of the deposited material increases. An excellent agreement between the design and experimental results are obtained. Our metatronic based nanosensor offers a high-sensitive performance of 1587 nm/RIU with a satisfactory figure of merit for this class of sensors.
Growth kinetics of endosymbiont Wolbachia in the common bed bug, Cimex lectularius
Authors: Fisher Michael L. , Watson David W. , Osborne Jason A. , Mochizuki Hiroyuki , Breen Matthew , Schal Coby 
Published: July 2018

AbstractThe common bed bug, Cimex lectularius harbors the endosymbiotic microorganism, Wolbachia (wCle), in a gonad-associated bacteriome as an obligate nutritional mutualist. The obligatory nature of this association suggests that all individuals in C. lectularius populations would be infected with wCle. However, studies spanning the past several decades have reported variation in both infection frequency and relative abundance of wCle in field-collected samples of bed bugs. Since the growth kinetics of wCle is poorly understood, the objective of this study was to quantify wCle over the life cycle of two strains of C. lectularius. Our results highlight that wCle is dynamic during bed bug development, changing relative to life stage, intermolt stage, and blood-fed status. These results suggest new hypotheses about the coordination of Wolbachia growth and regression with its host’s physiology and endocrine events. The observed quantitative modulation of wCle during the bed bug life cycle and during periods of starvation may explain the disparities in wCle infections reported in field-collected C. lectularius.
A multi-scale flow model for production performance analysis in shale gas reservoirs with fractal geometry
Authors: Wang Lei , Dong Zhenzhen , Li Xiang , Xia Zunyi 
Published: July 2018

AbstractShale gas reservoirs can be divided into three regions, including hydraulic fracture regions, stimulating reservoir volume regions (SRV regions), and outer stimulating reservoir volume regions (OSRV regions). Due to the impact of hydraulic fracturing, induced fractures in SRV regions are often irregular. In addition, a precise description of secondary fractures in SRV regions is of critical importance for production analysis and prediction. In this work, the following work is achieved: (1) the complex fracture network in the SRV region is described with fractal theory; (2) a dual inter-porosity flow mechanism with sorption and diffusion behaviors is considered in both SRV and OSRV regions; and (3) both multi-rate and multi-pressure solutions are proposed for history matching based on fractal models and Duhamel convolution theory. Compared with previous numerical and analytic methods, the developed model can provide more accurate dynamic parameter estimates for production analysis in a computationally efficient manner. In this paper, type curves are also established to delineate flow characteristics of the system. It is found that the flow can be classified as six stages, including a bi-linear flow regime, a linear flow regime, a transition flow regime, an inter-porosity flow regime from the matrix to the fractures in the inner region, inter-porosity flow regime from matrix to fractures in the outer region, and a boundary dominant flow regime. The effects of the fracture and matrix properties, fractal parameters, inter-porosity flow coefficients, and sorption characteristics on type curves and production performance were studied in detail. Finally, production performance was analyzed for Marcellus and Fuling shale gas wells, in the U.S.A. and China, respectively.
Rice Defensin OsAFP1 is a New Drug Candidate against Human Pathogenic Fungi
Authors: Ochiai Akihito , Ogawa Kodai , Fukuda Minami , Ohori Masahiro , Kanaoka Takumi , Tanaka Takaaki , Taniguchi Masayuki , Sagehashi Yoshiyuki 
Published: July 2018

AbstractFungal infections, such as candidiasis and aspergillosis, are some of the most frequent infections in humans. Although antifungal drugs are available for the treatment of these infections, antifungal agents with new mechanisms of action should be developed because of the increasing incidence of drug-resistant pathogens in recent years. In this study, a basic functional analysis of rice defensin OsAFP1, a novel antifungal drug candidate, was conducted. OsAFP1 exerted fungicidal activity against Candida albicans, the most common pathogenic fungus in humans, at 4 μM concentration, but it did not inhibit the growth of human pathogenic bacteria. In addition, OsAFP1 retained structural stability after heat treatment at 100 °C for 10 min and after serum treatment at 37 °C for 24 h. A propidium iodide (PI) uptake assay and mutational analysis revealed that amino acid residues within the C-terminal γ-core motif of OsAFP1, particularly Leu-39 and Lys-41, play an important role in its antifungal activity. Further, PI uptake and apoptosis assays suggested that OsAFP1 exerts its antifungal activity by inducing apoptosis of target cells. Immunohistochemistry showed that the OsAFP1 target molecule was located in the cell wall. These findings indicate that OsAFP1 may be developed into a potent antifungal drug.
The role of sedimentation and natural compaction in a prograding delta: insights from the mega Mekong delta, Vietnam
Authors: Zoccarato Claudia , Minderhoud Philip S. J. , Teatini Pietro 
Published: July 2018

AbstractThe Vietnamese Mekong Delta was formed by rapid transgression during the second half of the Holocene by deposition of mainly unconsolidated, fine-grained (clayey) sediments undergoing high compaction rates. The natural subsidence can seriously impact the already vulnerable delta plain as its low elevation exposes the delta to global sea level rise, flooding, salinization. Human activities such as groundwater pumping, infrastructural loading, sand mining and dam construction have exacerbated the effects of natural consolidation. Here we present a novel modeling study that has allowed to reproduce the formation and evolution of the Mekong delta over the past 4000 years. Using an adaptive finite-element mesh, the model properly simulates accretion and natural consolidation characterizing the delta evolution. Large soil grain motion and the delayed dissipation of pore-water overpressure are accounted for. We find that natural compaction of Holocene deposits following delta evolution exceeds predicted values of absolute sea level rise. The unprecedented high rates (up to ~20 mm/yr) threaten the lower delta plain with permanent inundation and inevitably reduce the designed service life of flood defense structures along the coast. Total subsidence and sediment delivery to the delta plain will determine its future elevation and vulnerability to relative sea level rise.
Magnetic Drug Targeting: A Novel Treatment for Intramedullary Spinal Cord Tumors
Authors: Kheirkhah Pouyan , Denyer Steven , Bhimani Abhiraj D. , Arnone Gregory D. , Esfahani Darian R. , Aguilar Tania , Zakrzewski Jack , Venugopal Indu , Habib Nazia , Gallia Gary L. , Linninger Andreas , Charbel Fady T. , Mehta Ankit I. 
Published: July 2018

AbstractMost applications of nanotechnology in cancer have focused on systemic delivery of cytotoxic drugs. Systemic delivery relies on accumulation of nanoparticles in a target tissue through enhanced permeability of leaky vasculature and retention effect of poor lymphatic drainage to increase the therapeutic index. Systemic delivery is limited, however, by toxicity and difficulty crossing natural obstructions, like the blood spine barrier. Magnetic drug targeting (MDT) is a new technique to reach tumors of the central nervous system. Here, we describe a novel therapeutic approach for high-grade intramedullary spinal cord tumors using magnetic nanoparticles (MNP). Using biocompatible compounds to form a superparamagnetic carrier and magnetism as a physical stimulus, MNP-conjugated with doxorubicin were successfully localized to a xenografted tumor in a rat model. This study demonstrates proof-of-concept that MDT may provide a novel technique for effective, concentrated delivery of chemotherapeutic agents to intramedullary spinal cord tumors without the toxicity of systemic administration.
Transcriptome profiling of whisker follicles in methamphetamine self-administered rats
Authors: Song Sang-Hoon , Jang Won-Jun , Hwang Jihye , Park Byoungduck , Jang Jung-Hee , Seo Young-Ho , Yang Chae Ha , Lee Sooyeun , Jeong Chul-Ho 
Published: July 2018

AbstractMethamphetamine (MA) is a highly addictive psychostimulant that disturbs the central nervous system; therefore, diagnosis of MA addiction is important in clinical and forensic toxicology. In this study, a MA self-administration rat model was used to illustrate the gene expression profiling of the rewarding effect caused by MA. RNA-sequencing was performed to examine changes in gene expression in rat whisker follicles collected before self-administration, after MA self-administration, and after withdrawal sessions. We identified six distinct groups of genes, with statistically significant expression patterns. By constructing the functional association network of these genes and performing the subsequent topological analysis, we identified 43 genes, which have the potential to regulate MA reward and addiction. The gene pathways were then analysed using the Reactome and Knowledgebase for Addiction-Related Gene database, and it was found that genes and pathways associated with Alzheimer’s disease and the heparan sulfate biosynthesis were enriched in MA self-administration rats. The findings suggest that changes of the genes identified in rat whisker follicles may be useful indicators of the rewarding effect of MA. Further studies are needed to provide a comprehensive understanding of MA addiction.
Effects of human-driven water stress on river ecosystems: a meta-analysis
Authors: Sabater Sergi , Bregoli Francesco , Acuña Vicenç , Barceló Damià , Elosegi Arturo , Ginebreda Antoni , Marcé Rafael , Muñoz Isabel , Sabater-Liesa Laia , Ferreira Verónica 
Published: July 2018

AbstractHuman appropriation of water resources may induce water stress in freshwater ecosystems when ecosystem needs are not met. Intensive abstraction and regulation cause river ecosystems to shift towards non-natural flow regimes, which might have implications for their water quality, biological structure and functioning. We performed a meta-analysis of published studies to assess the potential effects of water stress on nutrients, microcontaminants, biological communities (bacteria, algae, invertebrates and fish), and ecosystem functions (organic matter breakdown, gross primary production and respiration). Despite the different nature of the flow regime changes, our meta-analysis showed significant effects of human-driven water stress, such as significant increases in algal biomass and metabolism and reduced invertebrate richness, abundance and density and organic matter decomposition. Water stress also significantly decreased phosphate concentration and increased the concentration of pharmaceutical compounds. The magnitude of significant effects was dependent on climate, rainfall regime, period of the year, river size and type of water stress. Among the different causes of water stress, flow regulation by dams produced the strongest effects, followed by water abstraction and channelization.
Dual Mechanism for the Emergence of Synchronization in Inhibitory Neural Networks
Authors: Chauhan Ashok S. , Taylor Joseph D. , Nogaret Alain 
Published: July 2018

AbstractDuring cognitive tasks cortical microcircuits synchronize to bind stimuli into unified perception. The emergence of coherent rhythmic activity is thought to be inhibition-driven and stimulation-dependent. However, the exact mechanisms of synchronization remain unknown. Recent optogenetic experiments have identified two neuron sub-types as the likely inhibitory vectors of synchronization. Here, we show that local networks mimicking the soma-targeting properties observed in fast-spiking interneurons and the dendrite-projecting properties observed in somatostatin interneurons synchronize through different mechanisms which may provide adaptive advantages by combining flexibility and robustness. We probed the synchronization phase diagrams of small all-to-all inhibitory networks in-silico as a function of inhibition delay, neurotransmitter kinetics, timings and intensity of stimulation. Inhibition delay is found to induce coherent oscillations over a broader range of experimental conditions than high-frequency entrainment. Inhibition delay boosts network capacity (ln2)−N-fold by stabilizing locally coherent oscillations. This work may inform novel therapeutic strategies for moderating pathological cortical oscillations.
Improved phosphoproteomic analysis for phosphosignaling and active-kinome profiling in Matrigel-embedded spheroids and patient-derived organoids
Authors: Abe Yuichi , Tada Asa , Isoyama Junko , Nagayama Satoshi , Yao Ryoji , Adachi Jun , Tomonaga Takeshi 
Published: July 2018

AbstractMany attempts have been made to reproduce the three-dimensional (3D) cancer behavior. For that purpose, Matrigel, an extracellular matrix from Engelbreth-Holm-Swarm mouse sarcoma cell, is widely used in 3D cancer models such as scaffold-based spheroids and patient-derived organoids. However, severe ion suppression caused by contaminants from Matrigel hampers large-scale phosphoproteomics. In the present study, we successfully performed global phosphoproteomics from Matrigel-embedded spheroids and organoids. Using acetone precipitations of tryptic peptides, we identified more than 20,000 class 1 phosphosites from HCT116 spheroids. Bioinformatic analysis revealed that phosphoproteomic status are significantly affected by the method used for the recovery from the Matrigel, i.e., Dispase or Cell Recovery Solution. Furthermore, we observed the activation of several phosphosignalings only in spheroids and not in adherent cells which are coincident with previous study using 3D culture. Finally, we demonstrated that our protocol enabled us to identify more than 20,000 and nearly 3,000 class 1 phosphosites from 1.4 mg and 150 μg of patient-derived organoid, respectively. Additionally, we were able to quantify phosphosites with high reproducibility (r = 0.93 to 0.95). Our phosphoproteomics protocol is useful for analyzing the phosphosignalings of 3D cancer behavior and would be applied for precision medicine with patient-derived organoids.
Texture Analysis as Imaging Biomarker for recurrence in advanced cervical cancer treated with CCRT
Authors: Meng Jie , Liu Shunli , Zhu Lijing , Zhu Li , Wang Huanhuan , Xie Li , Guan Yue , He Jian , Yang Xiaofeng , Zhou Zhengyang 
Published: July 2018

AbstractThis prospective study explored the application of texture features extracted from T2WI and apparent diffusion coefficient (ADC) maps in predicting recurrence of advanced cervical cancer patients treated with concurrent chemoradiotherapy (CCRT). We included 34 patients with advanced cervical cancer who underwent pelvic MR imaging before, during and after CCRT. Radiomic feature extraction was performed by using software at T2WI and ADC maps. The performance of texture parameters in predicting recurrence was evaluated. After a median follow-up of 31 months, eleven patients (32.4%) had recurrence. At four weeks after CCRT initiated, the most textural parameters (four T2 textural parameters and two ADC textural parameters) showed significant difference between the recurrence and nonrecurrence group (P values range, 0.002~0.046). Among them, RunLengthNonuniformity (RLN) from T2 and energy from ADC maps were the best selected predictors and together yield an AUC of 0.885. The support vector machine (SVM) classifier using ADC textural parameters performed best in predicting recurrence, while combining T2 textural parameters may add little value in prognosis. T2 and ADC textural parameters have potential as non-invasive imaging biomarkers in early predicting recurrence in advanced cervical cancer treated with CCRT.
In situ phase contrast X-ray brain CT
Authors: Croton Linda C. P. , Morgan Kaye S. , Paganin David M. , Kerr Lauren T. , Wallace Megan J. , Crossley Kelly J. , Miller Suzanne L. , Yagi Naoto , Uesugi Kentaro , Hooper Stuart B. , Kitchen Marcus J. 
Published: July 2018

AbstractPhase contrast X-ray imaging (PCXI) is an emerging imaging modality that has the potential to greatly improve radiography for medical imaging and materials analysis. PCXI makes it possible to visualise soft-tissue structures that are otherwise unresolved with conventional CT by rendering phase gradients in the X-ray wavefield visible. This can improve the contrast resolution of soft tissues structures, like the lungs and brain, by orders of magnitude. Phase retrieval suppresses noise, revealing weakly-attenuating soft tissue structures, however it does not remove the artefacts from the highly attenuating bone of the skull and from imperfections in the imaging system that can obscure those structures. The primary causes of these artefacts are investigated and a simple method to visualise the features they obstruct is proposed, which can easily be implemented for preclinical animal studies. We show that phase contrast X-ray CT (PCXI-CT) can resolve the soft tissues of the brain in situ without a need for contrast agents at a dose ~400 times lower than would be required by standard absorption contrast CT. We generalise a well-known phase retrieval algorithm for multiple-material samples specifically for CT, validate its use for brain CT, and demonstrate its high stability in the presence of noise.
Decreased signalling of EphA4 improves functional performance and motor neuron survival in the SOD1G93A ALS mouse model
Authors: Zhao J. , Cooper L. T. , Boyd A. W. , Bartlett P. F. 
Published: July 2018

AbstractAmyotrophic lateral sclerosis (ALS) is an untreatable, progressive, neurodegenerative disease specifically affecting motor neurons. Recently, the tyrosine kinase receptor EphA4 was directly implicated in ALS disease progression. We report that a long-lived mutated form of the EphA4 antagonist EphA4-Fc (mutEphA4-Fc), which blocks EphA4 binding to its ligands and inhibits its function, significantly improved functional performance in SOD1G93AALS model mice, as assessed by rotarod and hind-limb grip strength tests. Further, heterozygous motor neuron-specificEphA4gene deletion in SOD1G93Amice promoted significant improvement in functional performance during the disease course and a delay in disease onset relative to control mice. Importantly, mice in the heterozygous deletion group showed significantly improved survival of motor neurons and architecture of endplates of neuromuscular junctions compared with control and homozygousEphA4-deletion groups. Our novel results show that EphA4 signalling directly regulates motor neuron survival and that mutEphA4-Fc is a promising therapeutic candidate to slow disease progression in ALS.