bluuebunny/crossref_metadata_2025_split huggingface dataset:
Standardization of electroencephalography for multi-site, multi-platform and multi-investigator studies: insights from the canadian biomarker integration network in depression
Authors: Farzan Faranak , Atluri Sravya , Frehlich Matthew , Dhami Prabhjot , Kleffner Killian , Price Rae , Lam Raymond W. , Frey Benicio N. , Milev Roumen , Ravindran Arun , McAndrews Mary Pat , Wong Willy , Blumberger Daniel , Daskalakis Zafiris J. , Vila-Rodriguez Fidel , Alonso Esther , Brenner Colleen A. , Liotti Mario , Dharsee Moyez , Arnott Stephen R. , Evans Kenneth R. , Rotzinger Susan , Kennedy Sidney H. 
Published: August 2017

AbstractSubsequent to global initiatives in mapping the human brain and investigations of neurobiological markers for brain disorders, the number of multi-site studies involving the collection and sharing of large volumes of brain data, including electroencephalography (EEG), has been increasing. Among the complexities of conducting multi-site studies and increasing the shelf life of biological data beyond the original study are timely standardization and documentation of relevant study parameters. We present the insights gained and guidelines established within the EEG working group of the Canadian Biomarker Integration Network in Depression (CAN-BIND). CAN-BIND is a multi-site, multi-investigator, and multi-project network supported by the Ontario Brain Institute with access to Brain-CODE, an informatics platform that hosts a multitude of biological data across a growing list of brain pathologies. We describe our approaches and insights on documenting and standardizing parameters across the study design, data collection, monitoring, analysis, integration, knowledge-translation, and data archiving phases of CAN-BIND projects. We introduce a custom-built EEG toolbox to track data preprocessing with open-access for the scientific community. We also evaluate the impact of variation in equipment setup on the accuracy of acquired data. Collectively, this work is intended to inspire establishing comprehensive and standardized guidelines for multi-site studies.
Carriage frequency, phenotypic, and genotypic characteristics of methicillin-resistant Staphylococcus aureus isolated from dental health-care personnel, patients, and environment
Authors: Khairalla Ahmed S. , Wasfi Reham , Ashour Hossam M. 
Published: August 2017

AbstractThere is limited data on methicillin-resistant Staphylococcus aureus (MRSA) carriage in dental clinics. 1300 specimens from patients, health personnel, and environmental surfaces of a dental clinic in Egypt were tested for MRSA. Antibiotic susceptibility, biofilm formation, Staphylococcal protein A (spa) typing, SCCmec typing, and PCR-based assays were used to detect mecA, mecC, vanA, Panton-Valentine Leukocidin toxin (PVL), and toxic shock syndrome toxin-1 (tst) genes. Among 34 mecA-positive MRSA isolates, five (14.7%) were PVL-positive, seventeen (50%) were tst-positive, ten (29.4%) were vanA-positive, while none harboured mecC. MRSA hand carriage rates in patients, nurses, and dentists were 9.8%, 6.6%, and 5%. The respective nasal colonization rates were 11.1%, 6.7%, and 9.7%. 1.3% of the environmental isolates were MRSA-positive. Strong and moderate biofilm-forming isolates represented 23.5% and 29.4% of MRSA isolates. 24 MRSA isolates (70.6%) were multi-resistant and 18 (52.9%) harboured SCCmec IV. Among eight spa types, t223 (26.5%), t267 (23.5%), and t14339 (23.5%) were predominant. We noted an alarming genetic relatedness between 7 (20.6%) MRSA isolates and the epidemic EMRSA-15 clone, as well as a combined occurrence of tst and PVL in 3 (8.8%) isolates. Results suggest high MRSA pathogenicity in dental wards highlighting the need for more efficient surveillance/infection control strategies.
Neuromorphic photonic networks using silicon photonic weight banks
Authors: Tait Alexander N. , de Lima Thomas Ferreira , Zhou Ellen , Wu Allie X. , Nahmias Mitchell A. , Shastri Bhavin J. , Prucnal Paul R. 
Published: August 2017

AbstractPhotonic systems for high-performance information processing have attracted renewed interest. Neuromorphic silicon photonics has the potential to integrate processing functions that vastly exceed the capabilities of electronics. We report first observations of a recurrent silicon photonic neural network, in which connections are configured by microring weight banks. A mathematical isomorphism between the silicon photonic circuit and a continuous neural network model is demonstrated through dynamical bifurcation analysis. Exploiting this isomorphism, a simulated 24-node silicon photonic neural network is programmed using “neural compiler” to solve a differential system emulation task. A 294-fold acceleration against a conventional benchmark is predicted. We also propose and derive power consumption analysis for modulator-class neurons that, as opposed to laser-class neurons, are compatible with silicon photonic platforms. At increased scale, Neuromorphic silicon photonics could access new regimes of ultrafast information processing for radio, control, and scientific computing.
Bronchoalveolar Lavage Fluid Protein Expression in Acute Respiratory Distress Syndrome Provides Insights into Pathways Activated in Subjects with Different Outcomes
Authors: Bhargava Maneesh , Viken Kevin , Wang Qi , Jagtap Pratik , Bitterman Peter , Ingbar David , Wendt Chris 
Published: August 2017

AbstractAcute respiratory distress syndrome (ARDS) is associated with high mortality. We sought to identify biological pathways in ARDS that differentiate survivors from non-survivors. We studied bronchoalveolar lavage fluid (BALF) from 36 patients with ARDS (20 survivors, 16 non-survivors). Each sample, obtained within seven days of ARDS onset, was depleted of high abundance proteins and labeled for iTRAQ LC-MS/MS separately. Protein identification and relative quantification was performed employing a target-decoy strategy. A variance weighted t-test was used to identify differential expression. Ingenuity Pathway Analysis was used to determine the canonical pathways that differentiated survivors from non-survivors. We identified 1115 high confidence proteins in the BALF out of which 142 were differentially expressed between survivors and non-survivors. These proteins mapped to multiple pathways distinguishing survivors from non-survivors, including several implicated in lung injury and repair such as coagulation/thrombosis, acute phase response signaling and complement activation. We also identified proteins assigned to fibrosis and ones involved in detoxification of lipid peroxide-mediated oxidative stress to be different in survivors and non-survivors. These results support our previous findings demonstrating early differences in the BALF protein expression in ARDS survivors vs. non-survivors, including proteins that counter oxidative stress and canonical pathways associated with fibrosis.
Combinations of isoform-targeted histone deacetylase inhibitors and bryostatin analogues display remarkable potency to activate latent HIV without global T-cell activation
Authors: Albert Brice J. , Niu Austin , Ramani Rashmi , Marshall Garland R. , Wender Paul A. , Williams Robert M. , Ratner Lee , Barnes Alexander B. , Kyei George B. 
Published: August 2017

AbstractCurrent antiretroviral therapy (ART) for HIV/AIDS slows disease progression by reducing viral loads and increasing CD4 counts. Yet ART is not curative due to the persistence of CD4+ T-cell proviral reservoirs that chronically resupply active virus. Elimination of these reservoirs through the administration of synergistic combinations of latency reversing agents (LRAs), such as histone deacetylase (HDAC) inhibitors and protein kinase C (PKC) modulators, provides a promising strategy to reduce if not eradicate the viral reservoir. Here, we demonstrate that largazole and its analogues are isoform-targeted histone deacetylase inhibitors and potent LRAs. Significantly, these isoform-targeted HDAC inhibitors synergize with PKC modulators, namely bryostatin-1 analogues (bryologs). Implementation of this unprecedented LRA combination induces HIV-1 reactivation to unparalleled levels and avoids global T-cell activation within resting CD4+ T-cells.
Bio-implant as a novel restoration for tooth loss
Authors: Lee Dong-Joon , Lee Jong-Min , Kim Eun-Jung , Takata Takashi , Abiko Yoshihiro , Okano Teruo , Green David W. , Shimono Masaki , Jung Han-Sung 
Published: August 2017

AbstractA dental implant is used to replace a missing tooth. Fixing the implant in its natural position requires the engineering of a substantial amount of conformal bone growth inside the implant socket, osseointegration. However, this conventional implant attachment does not include the periodontal ligament (PDL), which has a fundamental role in cushioning high mechanical loads. As a result, tooth implants have a shorter lifetime than the natural tooth and have a high chance of infections. We have engineered a “bio-implant” that provides a living PDL connection for titanium implants. The bio-implant consists of a hydroxyapatite coated titanium screw, ensheathed in cell sheets made from immortalized human periodontal cells. Bio-implants were transplanted into the upper first molar region of a tooth-extraction mouse model. Within 8 weeks the bio-implant generated fibrous connective tissue, a localised blood vessel network and new bone growth fused into the alveolar bone socket. The study presents a bio-implant engineered with human cells, specialised for the root connection, and resulted in the partial reconstruction of a naturalised tooth attachment complex (periodontium), consisting of all the principal tissue types, cementum, PDL and alveolar bone.
Knockdown of Tlr4 in the Arcuate Nucleus Improves Obesity Related Metabolic Disorders
Authors: Zhao Yongli , Li Guohua , Li Ying , Wang Yuchuan , Liu Zhengjuan 
Published: August 2017

AbstractHigh-fat diet-induced hypothalamic metabolic inflammation is emerging as a cause for the development of obesity. It is acknowledged that Toll-like receptor4 (TLR4) signaling plays a crucial role in triggering of the hypothalamic metabolic inflammation during the course of diet-induced obesity. Whether hypothalamic arcuate nucleus (ARC)-restricted TLR4 knockdown improves obesity-related metabolic disorders remains unexplored. In this study, we used TLR4 shRNA lentiviral particles to suppress the TLR4 expression in the hypothalamic ARC of diet-induced obese rat model by stereotaxic injection. Our results demonstrate that ARC-restricted TLR4 knockdown protects obese rats from diet-induced weight gain and energy intake, from diet-induced impaired glucose homeostasis and peripheral insulin resistance, and from high-fat diet-induced hepatic steatosis and adipocyte hypertrophy. Thus, we define ARC-restricted TLR4 knockdown as a potential strategy to combat metabolic disorders associated with obesity.
Phylodynamics of Yellow Fever Virus in the Americas: new insights into the origin of the 2017 Brazilian outbreak
Authors: Mir Daiana , Delatorre Edson , Bonaldo Myrna , Lourenço-de-Oliveira Ricardo , Vicente Ana Carolina , Bello Gonzalo 
Published: August 2017

AbstractYellow fever virus (YFV) strains circulating in the Americas belong to two distinct genotypes (I and II) that have diversified into several concurrent enzootic lineages. Since 1999, YFV genotype I has spread outside endemic regions and its recent (2017) reemergence in non-endemic Southeastern Brazilian states fuels one of the largest epizootic of jungle Yellow Fever registered in the country. To better understand this phenomenon, we reconstructed the phylodynamics of YFV American genotypes using sequences from nine countries sampled along 60 years, including strains from Brazilian 2017 outbreak. Our analyses reveals that YFV genotypes I and II follow roughly similar evolutionary and demographic dynamics until the early 1990s, when a dramatic change in the diversification process of the genotype I occurred associated with the emergence and dissemination of a new lineage (here called modern). Trinidad and Tobago was the most likely source of the YFV modern-lineage that spread to Brazil and Venezuela around the late 1980s, where it replaced all lineages previously circulating. The modern-lineage caused all major YFV outbreaks detected in non-endemic South American regions since 2000, including the 2017 Brazilian outbreak, and its dissemination was coupled to the accumulation of several amino acid substitutions particularly within non-structural viral proteins.
Inhibition of glycogen synthase kinase-3 by BTA-EG4 reduces tau abnormalities in an organotypic brain slice culture model of Alzheimer’s disease
Authors: Croft Cara L. , Kurbatskaya Ksenia , Hanger Diane P. , Noble Wendy 
Published: August 2017

AbstractOrganotypic brain slice culture models provide an alternative to early stage in vivo studies as an integrated tissue system that can recapitulate key disease features, thereby providing an excellent platform for drug screening. We recently described a novel organotypic 3xTg-AD mouse brain slice culture model with key Alzheimer’s disease-like changes. We now highlight the potential of this model for testing disease-modifying agents and show that results obtained following in vivo treatment are replicated in brain slice cultures from 3xTg-AD mice. Moreover, we describe novel effects of the amyloid-binding tetra (ethylene glycol) derivative of benzothiazole aniline, BTA-EG4, on tau. BTA-EG4 significantly reduced tau phosphorylation in the absence of any changes in the amounts of amyloid precursor protein, amyloid-β or synaptic proteins. The reduction in tau phosphorylation was associated with inactivation of the Alzheimer’s disease-relevant major tau kinase, GSK-3. These findings highlight the utility of 3xTg-AD brain slice cultures as a rapid and reliable in vitro method for drug screening prior to in vivo testing. Furthermore, we demonstrate novel tau-directed effects of BTA-EG4 that are likely related to the ability of this agent to inactivate GSK-3. Our findings support the further exploration of BTA-EG4 as a candidate therapeutic for Alzheimer’s disease.
Emergence of unusual coexistence states in cyclic game systems
Authors: Park Junpyo , Do Younghae , Jang Bongsoo , Lai Ying-Cheng 
Published: August 2017

AbstractEvolutionary games of cyclic competitions have been extensively studied to gain insights into one of the most fundamental phenomena in nature: biodiversity that seems to be excluded by the principle of natural selection. The Rock-Paper-Scissors (RPS) game of three species and its extensions [e.g., the Rock-Paper-Scissors-Lizard-Spock (RPSLS) game] are paradigmatic models in this field. In all previous studies, the intrinsic symmetry associated with cyclic competitions imposes a limitation on the resulting coexistence states, leading to only selective types of such states. We investigate the effect of nonuniform intraspecific competitions on coexistence and find that a wider spectrum of coexistence states can emerge and persist. This surprising finding is substantiated using three classes of cyclic game models through stability analysis, Monte Carlo simulations and continuous spatiotemporal dynamical evolution from partial differential equations. Our finding indicates that intraspecific competitions or alternative symmetry-breaking mechanisms can promote biodiversity to a broader extent than previously thought.
Stability of volcanic ash aggregates and break-up processes
Authors: Mueller Sebastian B. , Kueppers Ulrich , Ametsbichler Jonathan , Cimarelli Corrado , Merrison Jonathan P. , Poret Matthieu , Wadsworth Fabian B. , Dingwell Donald B. 
Published: August 2017

AbstractNumerical modeling of ash plume dispersal is an important tool for forecasting and mitigating potential hazards from volcanic ash erupted during explosive volcanism. Recent tephra dispersal models have been expanded to account for dynamic ash aggregation processes. However, there are very few studies on rates of disaggregation during transport. It follows that current models regard ash aggregation as irrevocable and may therefore overestimate aggregation-enhanced sedimentation. In this experimental study, we use industrial granulation techniques to artificially produce aggregates. We subject these to impact tests and evaluate their resistance to break-up processes. We find a dependence of aggregate stability on primary particle size distribution and solid particle binder concentration. We posit that our findings could be combined with eruption source parameters and implemented in future tephra dispersal models.
The Transcription Factor DAF-16 is Essential for Increased Longevity in C. elegans Exposed to Bifidobacterium longum BB68
Authors: Zhao Liang , Zhao Yang , Liu Ruihai , Zheng Xiaonan , Zhang Min , Guo Huiyuan , Zhang Hao , Ren Fazheng 
Published: August 2017

AbstractThe longevity-promoting benefits of lactobacilli were hypothesized as early as 1907. Although the anti-aging effects of lactic acid bacteria (LAB) have been observed in nematodes, rodents and humans for over a century, the mechanisms underlying the effects of probiotics on aging have rarely been assessed. Using the Caenorhabditis elegans (C. elegans) model, various studies have elucidated the role of different signaling cascades, especially the DAF-16 cascade, on lifespan extension by LAB. In this study, the mechanisms through which Bifidobacterium longum strain BB68 affects the longevity of C. elegans were assessed. The lifespan of nematodes increased by 28% after worms were fed BB68, and this extension of lifespan was completely lost in backgrounds containing a mutated DAF-16 gene. High levels of DAF-16 (in the daf-16 (mu86); muIs61 strain) nuclear accumulation and high expression of the SOD-3 gene (a DAF-16-specific target gene) were observed as a result of BB68 treatment. Immunofluorescence microscopy revealed that TIR-1 and JNK-1 are involved in the phosphorylation and activation of DAF-16. Thus, BB68 increased the longevity of nematodes by activating the TIR-1 – JNK-1 – DAF-16 signaling pathway, and the cell wall component of BB68 contributed to longevity.
Dielectric study on mixtures of ionic liquids
Authors: Thoms E. , Sippel P. , Reuter D. , Weiß M. , Loidl A. , Krohns S. 
Published: August 2017

AbstractIonic liquids are promising candidates for electrolytes in energy-storage systems. We demonstrate that mixing two ionic liquids allows to precisely tune their physical properties, like the dc conductivity. Moreover, these mixtures enable the gradual modification of the fragility parameter, which is believed to be a measure of the complexity of the energy landscape in supercooled liquids. The physical origin of this index is still under debate; therefore, mixing ionic liquids can provide further insights. From the chemical point of view, tuning ionic liquids via mixing is an easy and thus an economic way. For this study, we performed detailed investigations by broadband dielectric spectroscopy and differential scanning calorimetry on two mixing series of ionic liquids. One series combines an imidazole based with a pyridine based ionic liquid and the other two different anions in an imidazole based ionic liquid. The analysis of the glass-transition temperatures and the thorough evaluations of the measured dielectric permittivity and conductivity spectra reveal that the dynamics in mixtures of ionic liquids are well defined by the fractions of their parent compounds.
Pathological features and their prognostic impacts on oral cavity cancer patients among different subsites – A singe institute’s experience in Taiwan
Authors: Liu Shih-An , Wang Chen-Chi , Jiang Rong-San , Lee Fang-Yi , Lin Wen-Jiun , Lin Jin-Ching 
Published: August 2017

AbstractWe investigated the relationship of different primary subsites together with their pathological features on the survival of oral cavity squamous cell carcinoma (OCSCC) patients. We retrospectively reviewed OCSCC patients and documented their demographic data, pathological features and clinical outcome. The Cox proportional hazard model was used to examine the influence of various pathological features on the prognosis in different subsites of oral cavity. There were totally 1,383 OCSCC patients enrolled for final analysis. Perineural invasion had a poor prognosis at the early stage of OCSCC patients especially those with primary at the tongue. In addition, lymphovascular invasion was associated with poor survival at the late stage especially those with primary at the buccal mucosa and the tongue. The impact of pathological features on the survival of OCSCC patients varied in different subsites. Further investigation is warranted to validate our finding in a multicenter study. Grouping the different markers to establish a prognostic scoring system may provide more accurate evaluation of the prognosis in OCSCC patients.
AOD: the antioxidant protein database
Authors: Feng Pengmian , Ding Hui , Lin Hao , Chen Wei 
Published: August 2017

AbstractAn antioxidant is a molecule that can prevent free radicals from causing damages in organisms. The increasing studies on antioxidants calls for a specialized database that is not readily available yet. To this end, in the present study, theAntioxidantDatabase (AOD) was developed to help researchers understand and reveal the biological functions of antioxidant proteins. AOD is freely available athttp://lin.uestc.edu.cn/AODdatabase/index.aspx. The current release of AOD consists of 710 antioxidant proteins. Information including taxonomy, source organism, subcellular location, gene ontology, catalytic activity and function of antioxidant proteins are all extracted from UniProtKB/Swiss-Prot and captured in AOD. In addition, two web-based tools for performing sequence similarity search and computationally identification of antioxidants were also integrated in AOD. We believe that AOD will greatly facilitate the researches on antioxidants.
Commensal microbiota maintains alveolar macrophages with a low level of CCL24 production to generate anti-metastatic tumor activity
Authors: Cheng Min , Chen Yongyan , Wang Liang , Chen Wen , Yang Ling , Shen Guodong , Xu Tingjuan , Shen Gan , Tian Zhigang , Hu Shilian 
Published: August 2017

AbstractMicrobiota maintains host tissue homeostasis and influences tissue-resident macrophages. However, the mechanisms by which commensal bacteria in regulating the alveolar macrophages remain unclear. Here, by using an antibiotic-treated (Abt) mouse model, we found commensal bacteria depletion induced lower frequencies and numbers of alveolar macrophages. This effect was accompanied by the altered levels of genes involved in several biological pathways, including M2 macrophage polarization, as determined by gene expression analysis. Alveolar macrophages from the Abt mice had higher protein and gene levels of Arg1, CCL24, IL-13, IL-10, IL-6 and IL-1β, which could be recovered to normal levels by reconstructing commensal bacteria in the upper respiratory of Abt mice. Moreover, alveolar macrophages performed significant enhancement of M2 functions, especially CCL24 secretion, in the Abt mice challenged with B16/F10 melanoma. Adoptive transfer of normal alveolar macrophages or antibody neutralization of CCL24 significantly recovered the decrease of γδT17 cells and rescued the defect anti-tumor response of Abt mice, indicating the elevated amount of alveolar macrophage-derived CCL24 inhibited γδT cell mediated anti-tumor response. In conclusion, we demonstrated the ability of commensal bacteria to maintain alveolar macrophages with a low level of CCL24 production, which was necessary for the normal anti-tumor response in the lung.