bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of latitude, geographic distance, and habitat discontinuities on genetic variation in a high latitude montane species
Authors: Hindley J. A. , Graham B. A. , Pulgarin-R. P. C. , Burg T. M. 
Published: August 2018

AbstractExamining the factors that influence contemporary genetic patterns is important given the alarming rate at which natural environments are changing. In particular habitat fragmentation and climate change are expected to influence the distribution and diversity of natural populations. In this study we used both mitochondrial control region (mtDNA) and microsatellite data to answer the following questions about genetic diversity and divergence in mountain chickadees (Poecile gambeli) a resident bird species in western North America: (1) Do populations exhibit similar levels of genetic diversity across the range? (2) What is the genetic affinity of western populations in Oregon and Washington? (3) Do genetic patterns exhibit isolation by distance, or are genetic patterns more heavily influenced by habitat discontinuity? We tested the effects of isolation by distance and habitat distribution on genetic structure by analyzing 266 samples from 17 sites across western Canada and the United States. We found a near significant relationship between genetic diversity and latitude, however, our results indicate that overall, latitude is not a strong predictor of genetic diversity. Our analyses of populations in Oregon and Washington revealed a mismatch between patterns detected with mtDNA and microsatellite data. In particular, Washington clustered with the Coast Range/Cascades/Rocky Mountain mtDNA group, but with populations in southern Oregon/California based on microsatellite data. These results suggest the presence of a contact zone in Washington between the two mtDNA clades Coast Range/Cascades/Rocky Mountain and southern Oregon/California clades. Finally, our study revealed a greater effect of isolation by distance than isolation by habitat for both mtDNA and microsatellite data. Overall the isolation by distance signal was greater for mtDNA than microsatellite patterns. The greater signal of isolation by distance on mtDNA patterns likely reflects the strong effects of Pleistocene glaciations in shaping genetic patterns in western North America.
Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer
Authors: Chiu Alec M. , Mitra Mithun , Boymoushakian Lari , Coller Hilary A. 
Published: August 2018

AbstractTriple-negative breast cancers (TNBC) lack estrogen and progesterone receptors and HER2 amplification, and are resistant to therapies that target these receptors. Tumors from TNBC patients are heterogeneous based on genetic variations, tumor histology, and clinical outcomes. We used high throughput genomic data for TNBC patients (n = 137) from TCGA to characterize inter-tumor heterogeneity. Similarity network fusion (SNF)-based integrative clustering combining gene expression, miRNA expression, and copy number variation, revealed three distinct patient clusters. Integrating multiple types of data resulted in more distinct clusters than analyses with a single datatype. Whereas most TNBCs are classified by PAM50 as basal subtype, one of the clusters was enriched in the non-basal PAM50 subtypes, exhibited more aggressive clinical features and had a distinctive signature of oncogenic mutations, miRNAs and expressed genes. Our analyses provide a new classification scheme for TNBC based on multiple omics datasets and provide insight into molecular features that underlie TNBC heterogeneity.
Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics
Authors: Chaib De Mares Maryam , Jiménez Diego Javier , Palladino Giorgia , Gutleben Johanna , Lebrun Laura A. , Muller Emilie E. L. , Wilmes Paul , Sipkema Detmer , van Elsas Jan Dirk 
Published: August 2018

AbstractAplysina aerophoba is an emerging model marine sponge, with a well-characterized microbial community in terms of diversity and structure. However, little is known about the expressed functional capabilities of its associated microbes. Here, we present the first metaproteomics-based study of the microbiome of A. aerophoba. We found that transport and degradation of halogenated and chloroaromatic compounds are common active processes in the sponge microbiomes. Our data further reveal that the highest number of proteins were affiliated to a sponge-associated Tectomicrobium, presumably from the family Entotheonellaceae, as well as to the well-known symbiont “Candidatus Synechococcus spongiarium”, suggesting a high metabolic activity of these two microorganisms in situ. Evidence for nitric oxide (NO) conversion to nitrous oxide was consistently observed for Tectomicrobia across replicates, by production of the NorQ protein. Moreover, we found a potential energy-yielding pathway through CO oxidation by putative Chloroflexi bacteria. Finally, we observed expression of enzymes that may be involved in the transformation of chitin, glycoproteins, glycolipids and glucans into smaller molecules, consistent with glycosyl hydrolases predicted from analyses of the genomes of Poribacteria sponge symbionts. Thus, this study provides crucial links between expressed proteins and specific members of the A. aerophoba microbiome.
Seasonal variability of water characteristics in the Challenger Deep observed by four cruises
Authors: Huang Caijing , Xie Qiang , Wang Dongxiao , Shu Yeqiang , Xu Hongzhou , Xiao Jingen , Zu Tingting , Long Tong , Zhang Tiecheng 
Published: August 2018

AbstractThirty conductivity-temperature-depth profiler casts in the Challenger Deep were conducted during four cruises from December 2015 to February 2017. Two cruises took place in the summer, and two in the winter. The results demonstrated that water characteristics varied seasonally. The temperature minimum values were the same between the four cruises, but its depth was noticeably shallower in the winter than that in the summer. The θ-S diagram indicated that deep water is more saline in the summer than that in winter at the same potential temperature. Mixing is more intense between 5000 and 6800 m in the summer than that in the winter. The dissipation rate and eddy diffusivity vertically averaged between 5000 and 6800 m in the summer were εT = 3.277 × 10−8m2s−3 and KzT = 2.58 × 10−2m2s−1, respectively. The geostrophic flows below the reference level of 3000 dbar were cyclonic in the summer, travelling westwards in the northern and eastwards in the southern areas of the Challenger Deep.
Flexible Localized Surface Plasmon Resonance Sensor with Metal–Insulator–Metal Nanodisks on PDMS Substrate
Authors: Chang Chiao-Yun , Lin Hsiang-Ting , Lai Ming-Sheng , Shieh Teng-Yi , Peng Chien-Chung , Shih Min-Hsiung , Tung Yi-Chung 
Published: August 2018

AbstractThe small sized, flexible, high-performed and bio-compatible sensing devices are the critical elements to realize the bio-related detection or on-site health monitoring systems. In this work, the flexible localized surface plasmon resonance (LSPR) bio-sensors were demonstrated by integrating the metal–insulator–metal (MIM) nanodisks with bio-compatible polydimethylsiloxane (PDMS) substrate. The different geometries of MIM nanodisk sensors were investigated and optimized to enhance the spatial overlap of the LSPR waves with the environment, which lead to a high sensitivity of 1500 nm/RIU. The omni-directional characteristics of LSPR resonances were beneficial for maintaining the device sensitivity stable under various bending curvatures. Furthermore, the flexible MIM nanodisk LSPR sensor was applied to detect A549 cancer cells in PBS+ solution. The absorption peak of the MIM-disk LSPR sensor obviously redshift to easily distinguish between the phosphate buffered saline (PBS+) solution with A549 cancer cells and without cells. Therefore, the flexible MIM nanodisk LSPR sensor is suitable to develop on-chip microfluidic biosensors for detection of cancer cells on nonplanar surfaces.
Scalable Gastric Resident Systems for Veterinary Application
Authors: Hayward Alison , Bensel Taylor , Mazdiyasni Hormoz , Rogner Jaimie , Kirtane Ameya R. , Lee Young-Ah Lucy , Hua Tiffany , Bajpayee Ambika , Collins Joy , McDonnell Shane , Cleveland Cody , Lopes Aaron , Wahane Aniket , Langer Robert , Traverso Giovanni 
Published: August 2018

AbstractGastric resident dosage forms have been used successfully in farm animals for the delivery of a variety of drugs helping address the challenge of extended dosing. Despite these advances, there remains a significant challenge across the range of species with large variation in body size. To address this, we investigate a scalable gastric resident platform capable of prolonged retention. We investigate prototypes in dimensions consistent with administration and retention in the stomachs of two species (rabbit and pig). We investigate sustained gastric retention of our scalable dosage form platform, and in pigs show the capacity to modulate drug release kinetics of a model drug in veterinary practice, meloxicam, with our dosage form. The ability to achieve gastric residence and thereby enable sustained drug levels across different species may have a significant impact in the welfare of animals in both research, agricultural, zoological, and clinical practice settings.
Highly Stable Persistent Photoconductivity with Suspended Graphene Nanoribbons
Authors: Suzuki Hiroo , Ogura Noritada , Kaneko Toshiro , Kato Toshiaki 
Published: August 2018

AbstractGraphene nanoribbon (GNR), also known as 1-dimensional graphene, with a non-zero band gap has a huge potential for various electrical and optoelectrical applications because of its high transparency, flexibility, controllable band gap, and unique edge states. Recent advances in the synthesis of GNR enable us to show the possibility of GNRs as future high performance electrical devices. However, the applicability of GNRs to optoelectrical devices is unclear. Here we report that suspended GNR devices can show persistent photoconductivity (PPC) with long decay time (over 72 h) and adequate environmental stability. Repeated non-volatile memory operation is also demonstrated with an integrated PPC device using GNRs. This very stable PPC device can be applied to a wide variety of fields such as ultra-low-power non-volatile memory, nanoscale imaging, and biological sensors. Our results have opened the door to advance the study of GNRs in novel directions such as optoelectrical applications.
A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens
Authors: Mehbub Mohammad F. , Tanner Jason E. , Barnett Stephen J. , Bekker Jan , Franco Christopher M. M. , Zhang Wei 
Published: August 2018

AbstractSponge-bacteria interactions are very important due to their ecological and biological significance. To understand the impact of interactions between sponges and bacteria (both associated with and external to sponges) on sponge-associated microbial diversity, sponge metabolite profiles and bioactivity, we used a controlled aquarium system and designed an experimental approach that allows the study of sponge-bacteria interactions in a well-defined manner. To test the feasibility of this approach, this system was used to study the interaction between a spongeAplysilla roseaand a marine bacterium commonly found in seawater,Vibrio natriegens. Sponge explants were exposed toV.natriegens, at 5 × 106cfu/ml, and changes were monitored for 48 hours. Pyro-sequencing revealed significant shifts in microbial communities associated with the sponges after 24 to 48 hours. Both the control (sponge only without added bacteria) andVibrio-exposed sponges showed a distinct shift in bacterial diversity and abundance with time.Vibrioexposure significantly increased bacterial diversity, the abundance of a number of taxa compared to control sponges. The result experimentally supports the notion of dynamic and concerted responses by the sponge when interacting with a bacterium, and demonstrates the feasibility of using this controlled aquarium system for the study of sponge-bacteria interactions.
Comparative effect of immunotherapy and standard therapy in patients with high grade glioma: a meta-analysis of published clinical trials
Authors: Artene Stefan-Alexandru , Turcu-Stiolica Adina , Ciurea Marius Eugen , Folcuti Catalin , Tataranu Ligia Gabriela , Alexandru Oana , Purcaru Oana Stefana , Tache Daniela Elise , Boldeanu Mihail Virgil , Silosi Cristian , Dricu Anica 
Published: August 2018

AbstractImmunotherapy holds great promise in the treatment of high grade glioma (HGG). We performed a comprehensive meta-analysis of clinical trials involving dendritic cell (DC) therapy and viral therapy (VT) for the treatment of HGG, in order to assess their clinical impact in comparison to standard treatments in terms of overall survival (OS) and progression-free survival (PFS). To our knowledge, this is the first meta-analysis to evaluate VT for the treatment of HGG, allowing comparison of different immunotherapeutic approaches. Thirteen eligible studies of 1043 cases were included in the meta-analysis. For DC vaccination, in terms of OS, both newly diagnosed patients (HR, 0.65) and patients who suffered from recurrent HGGs (HR = 0.63) presented markedly improved results compared to the control groups. PFS was also improved (HR = 0.49) but was not statistically significant (p = 0.1). A slight improvement was observed for newly diagnosed patients receiving VT in terms of OS (HR = 0.88) while PFS was inferior for patients in the experimental arm (HR = 1.16). Our results show that DC therapy greatly improves OS for patients with both newly diagnosed and recurrent HGGs. VT, however, did not provide any statistically significant improvements in terms of OS and PFS for patients with newly diagnosed HGGs.
ACR11 modulates levels of reactive oxygen species and salicylic acid-associated defense response in Arabidopsis
Authors: Singh Shashi Kant , Sung Tzu-Ying , Chung Tsui-Yun , Lin Shao-Yu , Lin Sang-Chu , Liao Jo-Chien , Hsieh Wei-Yu , Hsieh Ming-Hsiun 
Published: August 2018

AbstractThe ACT domain (aspartate kinase, chorismate mutase and TyrA), an allosteric effector binding domain, is commonly found in amino acid metabolic enzymes. In addition to ACT domain-containing enzymes, plants have a novel family of ACT domain repeat (ACR) proteins, which do not contain any recognizable catalytic domain. Arabidopsis has 12 ACR proteins, whose functions are largely unknown. To study the functions of Arabidopsis ACR11, we have characterized two independent T-DNA insertion mutants, acr11-2 and acr11-3. RNA gel-blot analysis revealed that the expression of wild-type ACR11 transcripts was not detectable in the acr11 mutants. Interestingly, a lesion-mimic phenotype occurs in some rosette leaves of the acr11 mutants. In addition, high levels of reactive oxygen species (ROS), salicylic acid (SA), and callose accumulate in the mutant leaves when grown under normal conditions. The expression of several SA marker genes and the key SA biosynthetic gene ISOCHORISMATE SYNTHASE1 is up-regulated in the acr11 mutants. Furthermore, the acr11 mutants are more resistant to the infection of bacterial pathogen Pseudomonas syringae pathovar tomato DC3000. These results suggest that ACR11 may be directly or indirectly involved in the regulation of ROS and SA accumulation, which in turn modulates SA-associated defense responses and disease resistance in Arabidopsis.
Identifying individuals with attention deficit hyperactivity disorder based on temporal variability of dynamic functional connectivity
Authors: Wang Xun-Heng , Jiao Yun , Li Lihua 
Published: August 2018

AbstractAttention deficit hyperactivity disorder (ADHD) is a common disorder that emerges in school-age children. The diagnostic model based on neuroimaging features could be beneficial for ADHD in twofold: identifying individuals with ADHD and discovering the discriminative patterns for patients. The dynamic functional connectivity of ADHD remains unclear. Towards this end, 100 children with ADHD and 140 normal controls were obtained from the ADHD-200 Consortium. The raw features were derived from the temporal variability between intrinsic connectivity networks (ICNs) as well as the demographic and covariate variables. The diagnostic model was based on the support vector machines (SVMs). The performance of diagnostic model was analyzed using leave-one-out cross-validation (LOOCV) and 10-folds cross-validations (CVs). The diagnostic model based on inter-ICN variability outperformed that based on inter-ICN functional connectivity and inter-ICN phase synchrony. The LOOCV achieved total accuracy of 78.75%, the sensitivity of 76%, and the specificity of 80.71%. The 10-folds CVs achieved average prediction accuracy of 75.54% ± 1.34%, average sensitivity of 70.5% ± 2.34%, and average specificity of 77.44% ± 1.47%. In addition, the discriminative patterns for ADHD were discovered using SVMs. The discriminative patterns confirmed with previous findings. In summary, individuals with ADHD could be identified through inter-ICN variability, which could be potential biomarkers for diagnostic model of ADHD.
Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia
Authors: Orsini Paola , Minervini Crescenzio F. , Cumbo Cosimo , Anelli Luisa , Zagaria Antonella , Minervini Angela , Coccaro Nicoletta , Tota Giuseppina , Casieri Paola , Impera Luciana , Parciante Elisa , Brunetti Claudia , Giordano Annamaria , Specchia Giorgina , Albano Francesco 
Published: August 2018

AbstractWe report a customized gene panel assay based on multiplex long-PCR followed by third generation sequencing on nanopore technology (MinION), designed to analyze five frequently mutated genes in chronic lymphocytic leukemia (CLL): TP53, NOTCH1, BIRC3, SF3B1 and MYD88. For this purpose, 12 patients were selected according to specific cytogenetic and molecular features significantly associated with their mutational status. In addition, simultaneous analysis of the targets genes was performed by molecular assays or Sanger Sequencing. Data analysis included mapping to the GRCh37 human reference genome, variant calling and annotation, and average sequencing depth/error rate analysis. The sequencing depth resulted on average higher for smaller amplicons, and the final breadth of coverage of the panel was 94.1%. The error rate was about 6% and 2% for insertions/deletions and single nucleotide variants, respectively. Our gene panel allows analysis of the prognostically relevant genes in CLL, with two PCRs per patient. This strategy offers an easy and affordable workflow, although further advances are required to improve the accuracy of the technology and its use in the clinical field. Nevertheless, the rapid and constant development of nanopore technology, in terms of chemistry advances, more accurate basecallers and analysis software, offers promise for a wide use of MinION in the future.
Use of user-centered design to create a smartphone application for patient-reported outcomes in atopic dermatitis
Authors: Gracey Lia E. , Zan Shiyi , Gracz Joseph , Miner John J. , Moreau Jacqueline F. , Sperber Jodi , Jethwani Kamal , Hale Timothy M. , Kvedar Joseph C. 
Published: August 2018

AbstractThe ubiquity and convenience of smartphones carries great potential for collecting patient-reported data to address many gaps in research, especially those that rely on ongoing, real-time data collection. Health care apps have often suffered from low utility due to lack of consideration of the needs of multiple stakeholders. We employed an iterative user-centered design approach to create the myEczema smartphone application (app) to study the burden of disease of atopic dermatitis. We outline below the steps we took for developing myEczema for multiple stakeholders, including patients, clinicians, and researchers.
Smartphone measures of day-to-day behavior changes in children with autism
Authors: Jones Rebecca M. , Tarpey Thaddeus , Hamo Amarelle , Carberry Caroline , Lord Catherine 
Published: August 2018

AbstractSmartphones offer a flexible tool to collect data about mental health, but less is known about their effectiveness as a method to assess variability in children’s problem behaviors. Caregivers of children with autism completed daily questions about irritability, anxiety and mood delivered via smartphones across 8-weeks. Smartphone questions were consistent with subscales on standard caregiver questionnaires. Data collection from 7 to 10 days at the beginning and 7 to 10 days at the end of the study were sufficient to capture similar amounts of variance as daily data across 8-weeks. Other significant findings included effects of caregiver socioeconomic status and placebo-like effects from participation even though the study included no specific treatment. Nevertheless, single questions via smartphones collected over relatively brief periods reliably represent subdomains in standardized behavioral questionnaires, thereby decreasing burden on caregivers.
Bioluminescence resonance energy transfer-based biosensors allow monitoring of ligand- and transducer-mediated GPCR conformational changes
Authors: Picard Louis-Philippe , Schönegge Anne Marie , Lohse Martin J. , Bouvier Michel 
Published: August 2018

AbstractG protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate a variety of cellular response which make them a target of choice for drug development in many indications. It is now well established that GPCRs can adopt several distinct conformations that can be differentially stabilized by various ligands resulting in different biological outcomes, a concept known as functional selectivity. However, due to the highly hydrophobic nature of GPCRs, tools to monitor these conformational ensembles are limited and addressing their conformation dynamics remains a challenge with current structural biology approaches. Here we describe new bioluminescent resonance energy transfer-based biosensors that can probe the conformational rearrangement promoted by ligands with different signaling efficacies as well as the impact of transducers such as G proteins and β-arrestin on these conformational transitions. The design of such sensors for other receptors should be useful to further explore the structural determinants of GPCR functional selectivity.