bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistence of Zika virus in conjunctival fluid of convalescence patients
Authors: Tan Jeslin J. L. , Balne Praveen K. , Leo Yee-Sin , Tong Louis , Ng Lisa F. P. , Agrawal Rupesh 
Published: September 2017

AbstractA widespread epidemic of Zika fever, caused by Zika virus (ZIKAV) has spread throughout the Pacific islands, the Americas and Southeast Asia. The increased incidences of ocular anomalies observed in ZIKAV-infected infants and adults may be associated with the rapid spread of ZIKAV. The objective of this study was to check if ZIKAV could be detected in human tears after the first week of infection. Twenty-nine patients with PCR confirmed ZIKAV infection during the Singapore August 2016 ZIKAV outbreak were enrolled for the study. Detection and quantification of ZIKAV RNA was performed on conjunctival swabs collected from both eyes of these patients at the late convalescent phase (30 days post-illness). Efficiency of viral isolation from swab samples was confirmed by the limit of detection (as low as 0.1 PFU/µL, equivalent to copy number of 4.9) in spiked swabs with different concentrations of ZIKAV (PFU/µL). Samples from three patients were found positive by qRT-PCR for ZIKAV and the viral RNA copy numbers detected in conjunctival swabs ranged from 5.2 to 9.3 copies respectively. ZIKAV could persist in the tears of infected patients for up to 30 days post-illness, and may therefore possess a potential public health risk of transmission.
A duality principle for the multi-block entanglement entropy of free fermion systems
Authors: Carrasco J. A. , Finkel F. , González-López A. , Tempesta P. 
Published: September 2017

AbstractThe analysis of the entanglement entropy of a subsystem of a one-dimensional quantum system is a powerful tool for unravelling its critical nature. For instance, the scaling behaviour of the entanglement entropy determines the central charge of the associated Virasoro algebra. For a free fermion system, the entanglement entropy depends essentially on two sets, namely the set A of sites of the subsystem considered and the set K of excited momentum modes. In this work we make use of a general duality principle establishing the invariance of the entanglement entropy under exchange of the sets A and K to tackle complex problems by studying their dual counterparts. The duality principle is also a key ingredient in the formulation of a novel conjecture for the asymptotic behavior of the entanglement entropy of a free fermion system in the general case in which both sets A and K consist of an arbitrary number of blocks. We have verified that this conjecture reproduces the numerical results with excellent precision for all the configurations analyzed. We have also applied the conjecture to deduce several asymptotic formulas for the mutual and r-partite information generalizing the known ones for the single block case.
Blood triglyceride levels are associated with DNA methylation at the serine metabolism gene PHGDH
Authors: Truong Vinh , Huang Siying , Dennis Jessica , Lemire Mathieu , Zwingerman Nora , Aïssi Dylan , Kassam Irfahan , Perret Claire , Wells Philip , Morange Pierre-Emmanuel , Wilson Michael , Trégouët David-Alexandre , Gagnon France 
Published: September 2017

AbstractEfficient interventions to reduce blood triglycerides are few; newer and more tolerable intervention targets are needed. Understanding the molecular mechanisms underlying blood triglyceride levels variation is key to identifying new therapies. To explore the role of epigenetic mechanisms on triglyceride levels, a blood methylome scan was conducted in 199 individuals from 5 French-Canadian families ascertained on venous thromboembolism, and findings were replicated in 324 French unrelated patients with venous thromboembolism. Genetic context and functional relevance were investigated. Two DNA methylation sites associated with triglyceride levels were identified. The first one, located in the ABCG1 gene, was recently reported, whereas the second one, located in the promoter of the PHGDH gene, is novel. The PHGDH methylation site, cg14476101, was found to be associated with variation in triglyceride levels in a threshold manner: cg14476101 was inversely associated with triglyceride levels only when triglyceride levels were above 1.12 mmol/L (discovery P-value = 8.4 × 10−6; replication P-value = 0.0091). Public databases findings supported a functional role of cg14476101 on PHGDH expression. PHGDH catalyses the first step in the serine biosynthesis pathway. These findings highlight the role of epigenetic regulation of the PHGDH gene in triglyceride metabolism, providing novel insights on putative intervention targets.
Description of two three-gendered nematode species in the new genus Auanema (Rhabditina) that are models for reproductive mode evolution
Authors: Kanzaki Natsumi , Kiontke Karin , Tanaka Ryusei , Hirooka Yuuri , Schwarz Anna , Müller-Reichert Thomas , Chaudhuri Jyotiska , Pires-daSilva Andre 
Published: September 2017

AbstractThe co-existence of males, females and hermaphrodites, a rare mating system known as trioecy, has been considered as an evolutionarily transient state. In nematodes, androdioecy (males/hermaphrodites) as found in Caenorhabditis elegans, is thought to have evolved from dioecy (males/females) through a trioecious intermediate. Thus, trioecious species are good models to understand the steps and requirements for the evolution of new mating systems. Here we describe two new species of nematodes with trioecy, Auanema rhodensis and A. freiburgensis. Along with molecular barcodes, we provide a detailed analysis of the morphology of these species, and document it with drawings and light and SEM micrographs. Based on morphological data, these free-living nematodes were assigned to a new genus, Auanema, together with three other species described previously. Auanema species display convergent evolution in some features with parasitic nematodes with complex life cycles, such as the production of few males after outcrossing and the obligatory development of dauers into self-propagating adults.
Induction of high titred, non-neutralising antibodies by self-adjuvanting peptide epitopes derived from the respiratory syncytial virus fusion protein
Authors: Jaberolansar Noushin , Chappell Keith J. , Watterson Daniel , Bermingham Imogen M. , Toth Istvan , Young Paul R. , Skwarczynski Mariusz 
Published: September 2017

AbstractRespiratory syncytial virus (RSV) causes severe lower respiratory tract illness in infants and young children. The significant morbidity and mortality rates associated with RSV infection make an effective RSV vaccine development a priority. Two neutralising antibody binding sites, Ø and II, located on the pre-fusion RSV F glycoprotein are prime candidates for epitope-focused vaccine design. We report on a vaccine strategy that utilises a lipid core peptide (LCP) delivery system with self-adjuvanting properties in conjunction with either the antigenic site Ø or II (B cell epitopes) along with PADRE as a T helper cell epitope. These LCP constructs adopted the desired helical conformation in solution and were recognised by their cognate antibodies D25 and Motavizumab, specific for site Ø and II on RSV F protein, respectively. The LCP constructs were capable of eliciting higher levels of antigen specific antibodies than those induced by antigens administered with complete Freund’s adjuvant, demonstrating the potent adjuvanting properties of LCP delivery. However, the antibodies induced failed to recognise native F protein or neutralise virus infectivity. These results provide a note of caution in assuming that peptide vaccines, successfully designed to structurally mimic minimal linear B cell epitopes, will necessarily elicit the desired immune response.
Soluble intercellular adhesion molecule-1 is associated with hepatocellular carcinoma risk: multiplex analysis of serum markers
Authors: Chen Vincent L. , Le An K. , Podlaha Ondrej , Estevez Jacqueline , Li Biao , Vutien Philip , Chang Ellen T. , Rosenberg-Hasson Yael , Pflanz Stefan , Jiang Zhaoshi , Ge Dongliang , Gaggar Anuj , Nguyen Mindie H. 
Published: September 2017

AbstractIndividualized assessment of hepatocellular carcinoma (HCC) risk in chronic liver disease remains challenging. Serum biomarkers including cytokines may offer helpful adjuncts to standard parameters for risk prediction. Our aim was to identify markers associated with increased HCC incidence. This was a prospective cohort study of 282 patients with both viral or non-viral chronic liver disease. Baseline serum cytokines and other markers were measured in multiplex with a commercially-available Luminex-based system. Patients were followed until death or HCC diagnosis. We performed Lasso-based survival analysis to determine parameters associated with HCC development. Cytokine mean florescence intensity (MFI) was the primary predictor and HCC development the primary outcome. 25 patients developed HCC with total follow-up of 1,363 person-years. Parameters associated with increased HCC incidence were cirrhosis, hepatic decompensation, and soluble serum intercellular adhesion molecule 1 (sICAM-1) MFI. No other molecules increased predictive power for HCC incidence. On univariate analysis, the parameters associated with HCC incidence in patients with cirrhosis were age, antiviral treatment, and high sICAM-1 MFI; on multivariate analysis, sICAM-1 remained associated with HCC development (adjusted HR = 2.75). On unbiased screening of serum cytokines and other markers in a diverse cohort, baseline sICAM-1 MFI is associated with HCC incidence.
Microbial colonization is required for normal neurobehavioral development in zebrafish
Authors: Phelps Drake , Brinkman Nichole E. , Keely Scott P. , Anneken Emily M. , Catron Tara R. , Betancourt Doris , Wood Charles E. , Espenschied Scott T. , Rawls John F. , Tal Tamara 
Published: September 2017

AbstractChanges in resident microbiota may have wide-ranging effects on human health. We investigated whether early life microbial disruption alters neurodevelopment and behavior in larval zebrafish. Conventionally colonized, axenic, and axenic larvae colonized at 1 day post fertilization (dpf) were evaluated using a standard locomotor assay. At 10 dpf, axenic zebrafish exhibited hyperactivity compared to conventionalized and conventionally colonized controls. Impairment of host colonization using antibiotics also caused hyperactivity in conventionally colonized larvae. To determine whether there is a developmental requirement for microbial colonization, axenic embryos were serially colonized on 1, 3, 6, or 9 dpf and evaluated on 10 dpf. Normal activity levels were observed in axenic larvae colonized on 1–6 dpf, but not on 9 dpf. Colonization of axenic embryos at 1 dpf with individual bacterial species Aeromonas veronii or Vibrio cholerae was sufficient to block locomotor hyperactivity at 10 dpf. Exposure to heat-killed bacteria or microbe-associated molecular patterns pam3CSK4 or Poly(I:C) was not sufficient to block hyperactivity in axenic larvae. These data show that microbial colonization during early life is required for normal neurobehavioral development and support the concept that antibiotics and other environmental chemicals may exert neurobehavioral effects via disruption of host-associated microbial communities.
Room temperature self-assembled growth of vertically aligned columnar copper oxide nanocomposite thin films on unmatched substrates
Authors: Wang Y. , Ghanbaja J. , Bruyère S. , Soldera F. , Horwat D. , Mücklich F. , Pierson J. F. 
Published: September 2017

AbstractIn this work, we report the self-assembled growth of vertically aligned columnar Cu2O + Cu4O3 nanocomposite thin films on glass and silicon substrates by reactive sputtering at room temperature. Microstructure analyses show that each phase in nanocomposite films has the columnar growth along the whole thickness, while each column exhibits the single phase characteristics. The local epitaxial growth behavior of Cu2O is thought to be responsible for such an unusual microstructure. The intermediate oxygen flow rate between those required to synthesize single phase Cu2O and Cu4O3 films produces some Cu2O nuclei, and then the local epitaxial growth provides a strong driving force to promote Cu2O nuclei to grow sequentially, giving rise to Cu2O columns along the whole thickness. Lower resistivity has been observed in such kind of nanocomposite thin films than that in single phase thin films, which may be due to the interface coupling between Cu2O and Cu4O3 columns.
Elongation factor Tu is a multifunctional and processed moonlighting protein
Authors: Widjaja Michael , Harvey Kate Louise , Hagemann Lisa , Berry Iain James , Jarocki Veronica Maria , Raymond Benjamin Bernard Armando , Tacchi Jessica Leigh , Gründel Anne , Steele Joel Ricky , Padula Matthew Paul , Charles Ian George , Dumke Roger , Djordjevic Steven Philip 
Published: September 2017

AbstractMany bacterial moonlighting proteins were originally described in medically, agriculturally, and commercially important members of the low G + C Firmicutes. We show Elongation factor Tu (Ef-Tu) moonlights on the surface of the human pathogens Staphylococcus aureus (SaEf-Tu) and Mycoplasma pneumoniae (MpnEf-Tu), and the porcine pathogen Mycoplasma hyopneumoniae (MhpEf-Tu). Ef-Tu is also a target of multiple processing events on the cell surface and these were characterised using an N-terminomics pipeline. Recombinant MpnEf-Tu bound strongly to a diverse range of host molecules, and when bound to plasminogen, was able to convert plasminogen to plasmin in the presence of plasminogen activators. Fragments of Ef-Tu retain binding capabilities to host proteins. Bioinformatics and structural modelling studies indicate that the accumulation of positively charged amino acids in short linear motifs (SLiMs), and protein processing promote multifunctional behaviour. Codon bias engendered by an A + T rich genome may influence how positively-charged residues accumulate in SLiMs.
The role of the secretin/secretin receptor axis in inflammatory cholangiocyte communication via extracellular vesicles
Authors: Sato Keisaku , Meng Fanyin , Venter Julie , Giang Thao , Glaser Shannon , Alpini Gianfranco 
Published: September 2017

AbstractSmall and large intrahepatic bile ducts consist of small and large cholangiocytes, respectively, and these cholangiocytes have different morphology and functions. The gastrointestinal peptide hormone, secretin (SCT) that binds to secretin receptor (SR), is a key mediator in cholangiocyte pathophysiology. Extracellular vesicles (EVs) are membrane-bound vesicles and cell-cell EV communication is recognized as an important factor in liver pathology, although EV communication between cholangiocytes is not identified to date. Cholangiocytes secrete proinflammatory cytokines during bacterial infection leading to biliary inflammation and hyperplasia. We demonstrate that cholangiocytes stimulated with lipopolysaccharide (LPS), which is a membrane component of gram-negative bacteria, secrete more EVs than cholangiocytes incubated with vehicle. These LPS-derived EVs induce inflammatory responses in other cholangiocytes including elevated cytokine production and cell proliferation. Large but not small cholangiocytes show inflammatory responses against large but not small cholangiocyte-derived EVs. Large cholangiocytes with knocked down either SCT or SR by short hairpin RNAs show reduced EV secretion during LPS stimulation, and EVs isolated from SCT or SR knocked down cholangiocytes fail to induce inflammatory reactions in control large cholangiocytes. This study identifies cholangiocyte EV communication during LPS stimulation, and demonstrates that the SCT/SR axis may be important for this event.
In silico prediction of drug-target interaction networks based on drug chemical structure and protein sequences
Authors: Li Zhengwei , Han Pengyong , You Zhu-Hong , Li Xiao , Zhang Yusen , Yu Haiquan , Nie Ru , Chen Xing 
Published: September 2017

AbstractAnalysis of drug–target interactions (DTIs) is of great importance in developing new drug candidates for known protein targets or discovering new targets for old drugs. However, the experimental approaches for identifying DTIs are expensive, laborious and challenging. In this study, we report a novel computational method for predicting DTIs using the highly discriminative information of drug-target interactions and our newly developed discriminative vector machine (DVM) classifier. More specifically, each target protein sequence is transformed as the position-specific scoring matrix (PSSM), in which the evolutionary information is retained; then the local binary pattern (LBP) operator is used to calculate the LBP histogram descriptor. For a drug molecule, a novel fingerprint representation is utilized to describe its chemical structure information representing existence of certain functional groups or fragments. When applying the proposed method to the four datasets (Enzyme, GPCR, Ion Channel and Nuclear Receptor) for predicting DTIs, we obtained good average accuracies of 93.16%, 89.37%, 91.73% and 92.22%, respectively. Furthermore, we compared the performance of the proposed model with that of the state-of-the-art SVM model and other previous methods. The achieved results demonstrate that our method is effective and robust and can be taken as a useful tool for predicting DTIs.
Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients
Authors: Ticinesi Andrea , Milani Christian , Lauretani Fulvio , Nouvenne Antonio , Mancabelli Leonardo , Lugli Gabriele Andrea , Turroni Francesca , Duranti Sabrina , Mangifesta Marta , Viappiani Alice , Ferrario Chiara , Maggio Marcello , Ventura Marco , Meschi Tiziana 
Published: September 2017

AbstractReduced biodiversity and increased representation of opportunistic pathogens are typical features of gut microbiota composition in aging. Few studies have investigated their correlation with polypharmacy, multimorbidity and frailty. To assess it, we analyzed the fecal microbiota from 76 inpatients, aged 83 ± 8. Microbiome biodiversity (Chao1 index) and relative abundance of individual bacterial taxa were determined by next-generation 16S rRNA microbial profiling. Their correlation with number of drugs, and indexes of multimorbidity and frailty were verified using multivariate linear regression models. The impact of gut microbiota biodiversity on mortality, rehospitalizations and incident sepsis was also assessed after a 2-year follow-up, using Cox regression analysis. We found a significant negative correlation between the number of drugs and Chao1 Index at multivariate analysis. The number of drugs was associated with the average relative abundance of 15 taxa. The drug classes exhibiting the strongest association with single taxa abundance were proton pump inhibitors, antidepressants and antipsychotics. Conversely, frailty and multimorbidity were not significantly associated with gut microbiota biodiversity. Very low Chao1 index was also a significant predictor of mortality, but not of rehospitalizations and sepsis, at follow-up. In aging, polypharmacy may thus represent a determinant of gut microbiota composition, with detrimental clinical consequences.
Perinatal Malnutrition Leads to Sexually Dimorphic Behavioral Responses with Associated Epigenetic Changes in the Mouse Brain
Authors: Nätt Daniel , Barchiesi Riccardo , Murad Josef , Feng Jian , Nestler Eric J. , Champagne Frances A. , Thorsell Annika 
Published: September 2017

AbstractChildhood malnutrition is a risk factor for mental disorders, such as major depression and anxiety. Evidence shows that similar early life adversities induce sex-dependent epigenetic reprogramming. However, little is known about how genes are specifically affected by early malnutrition and the implications for males and females respectively. One relevant target is neuropeptide Y (NPY), which regulates both stress and food-intake. We studied maternal low protein diet (LPD) during pregnancy/lactation in mice. Male, but not female, offspring of LPD mothers consistently displayed anxiety- and depression-like behaviors under acute stress. Transcriptome-wide analysis of the effects of acute stress in the amygdala, revealed a list of transcription factors affected by either sex or perinatal LPD. Among these immediate early genes (IEG), members of theEarly growth responsefamily (Egr1/2/4) were consistently upregulated by perinatal LPD in both sexes. EGR1 also bound theNPY receptor Y1gene (Npy1r), which co-occurred with sex-specific effects of perinatal LPD on bothNpy1rDNA-methylation and gene transcription. Our proposed pathway connecting early malnutrition, sex-independent regulatory changes inEgr1, and sex-specific epigenetic reprogramming of its effector gene,Npy1r, represents the first molecular evidence of how early life risk factors may generate sex-specific epigenetic effects relevant for mental disorders.
Generative Models for Global Collaboration Relationships
Authors: Ciftcioglu Ertugrul Necdet , Ramanathan Ram , Basu Prithwish 
Published: September 2017

AbstractWhen individuals interact with each other and meaningfully contribute toward a common goal, it results in a collaboration. The artifacts resulting from collaborations are best captured using a hypergraph model, whereas the relation of who has collaborated with whom is best captured via an abstract simplicial complex (SC). We propose a generative algorithm GENESCs for SCs modeling fundamental collaboration relations. The proposed network growth process favors attachment that is preferential not to an individual’s degree, i.e., how many people has he/she collaborated with, but to his/her facet degree, i.e., how many maximal groups or facets has he/she collaborated within. Based on our observation that several real-world facet size distributions have significant deviation from power law–mainly since larger facets tend to subsume smaller ones–we adopt a data-driven approach. We prove that the facet degree distribution yielded by GENESCs is power law distributed for large SCs and show that it is in agreement with real world co-authorship data. Finally, based on our intuition of collaboration formation in domains such as collaborative scientific experiments and movie production, we propose two variants of GENESCs based on clamped and hybrid preferential attachment schemes, and show that they perform well in these domains.
A Chinese Pane-Like 2D Metal-Organic Framework Showing Magnetic Relaxation and Luminescence Dual-Functions
Authors: Liu Cai-Ming , Zhang De-Qing , Hao Xiang , Zhu Dao-Ben 
Published: September 2017

AbstractThe discovery of graphene kicked off the curtain of atom-type two-dimensional (2D) materials. Layered metal-organic frameworks (MOFs) as parallel molecule-based 2D materials are more designable and more diverse, and magnetism may be induced by their metal ion nodes. However, the multifunctional 2D plane-like MOFs are very difficult to obtain. Here we describe a Chinese pane-like 2D MOF constructed from the Ln3+ cation and the nanoscale luminescent tritopic ligand tris(4′-carboxybiphenyl)-amine, responding to the slow magnetic relaxation and luminescence properties, respectively. Notably, the Dy-Dy distances separated by the tritopic ligand are up to 2 nm. Such a 2D molecular material is expected to have potential applications in optoelectronics and multimodal sensing.