bluuebunny/crossref_metadata_2025 huggingface dataset:
Quarkonium in-medium properties from realistic lattice NRQCD
Authors: Kim Seyong , Petreczky Peter , Rothkopf Alexander
Published: November 2018

Abstract

We present the final results of our high statistics study on the properties of bottomonium and charmonium at finite temperature. We focus on the temperature range around the crossover transition 150 ≤ T ≤ 410MeV, relevant for current heavy ion collision experiments. The QCD medium degrees of freedom, which consist of dynamical u,d, and s quarks and gluons are captured by realistic state-of-the art (m

π
≈ 161MeV) lattice QCD simulations of the HotQCD collaboration. For the heavy quarks we deploy the non-relativistic effective field theory of QCD, NRQCD. The in-medium properties of quarkonium are deduced from their spectral functions, which are reconstructed using improved and novel Bayesian approaches. Through a systematic analysis we shed light on the origin of the discrepancies in melting temperatures previously reported in the literature, showing that they are owed to underestimated methods uncertainties of the deployed spectral reconstructions. Our simulations corroborate a picture of sequential in-medium modification, ordered according to the vacuum binding energy of the states. As a central quantitative result, our study reveals how the mass of the heavy quarkonium ground state reduces as temperature increases. The observed spectral modifications are interpreted in the light of, and compared to previous studies based on the complex lattice potential for heavy quarkonium. Thus for the first time we provide a robust picture of in-medium heavy quarkonium modification in the quark-gluon plasma consistent among different non-relativistic methods. We also critically discuss the perspectives for improving on these results.
Genes Encoding Mammalian Oviductal Proteins Involved in Fertilization are Subjected to Gene Death and Positive Selection
Authors: Moros-Nicolás Carla , Fouchécourt Sophie , Goudet Ghylène , Monget Philippe
Published: November 2018

Oviductal proteins play an important role in mammalian fertilization, as proteins from seminal fluid. However, in contrast with the latter, their phylogenetic evolution has been poorly studied. Our objective was to study in 16 mammals the evolution of 16 genes that encode oviductal proteins involved in at least one of the following steps: (1) sperm–oviduct interaction, (2) acrosome reaction, and/or (3) sperm–zona pellucida interaction. Most genes were present in all studied mammals. However, some genes were lost along the evolution of mammals and found as pseudogenes: annexin A5 (ANXA5) and deleted in malignant brain tumor 1 (DMBT1) in tarsier; oviductin (OVGP1) in megabat; and probably progestagen-associated endometrial protein (PAEP) in tarsier, mouse, rat, rabbit, dolphin, and megabat; prostaglandin D2 synthase (PTGDS) in microbat; and plasminogen (PLG) in megabat. Four genes [ANXA1, ANXA4, ANXA5, and heat shock 70 kDa protein 5 (HSPA5)] showed branch-site positive selection, whereas for seven genes [ANXA2, lactotransferrin (LTF), OVGP1, PLG, S100 calcium-binding protein A11 (S100A11), Sperm adhesion molecule 1 (SPAM1), and osteopontin (SPP1)] branch-site model and model-site positive selection were observed. These results strongly suggest that genes encoding oviductal proteins that are known to be important for gamete fertilization are subjected to positive selection during evolution, as numerous genes encoding proteins from mammalian seminal fluid. This suggests that such a rapid evolution may have as a consequence that two isolated populations become separate species more rapidly.
GPU-warp based finite element matrices generation and assembly using coloring method
Authors: Kiran Utpal , Sharma Deepak , Gautam Sachin Singh
Published: November 2018

Finite element method has been successfully implemented on the graphics processing units to achieve a significant reduction in simulation time. In this paper, new strategies for the finite element matrix generation including numerical integration and assembly are proposed by using a warp per element for a given mesh. These strategies are developed using the well-known coloring method. The proposed strategies use a specialized algorithm to realize fine-grain parallelism and efficient use of on-chip memory resources. The warp shuffle feature of Compute Unified Device Architecture (CUDA) is used to accelerate numerical integration. The evaluation of elemental stiffness matrix is further optimized by adopting a partial parallel implementation of numerical integration. Performance evaluations of the proposed strategies are done for three-dimensional elasticity problem using the 8-noded hexahedral elements with three degrees of freedom per node. We obtain a speedup of up to 8.2× over the coloring based assembly by element strategy (using a single thread per element) on NVIDIA Tesla K40 GPU. Also, the proposed strategies achieve better arithmetic throughput and bandwidth.

Highlights CUDA Warp based strategies for FE matrix generation and assembly. Performed using coloring method and on linear hexahedral element meshing in 3D. Obtained speedup of 5.17×− 8.2× over single thread per element strategy on GPU. Strategies showed better arithmetic throughput and bandwidth through code profiling.
Evolution of X-pinch loads for pulsed power generators with current from 50 to 5000 kA
Authors: Shelkovenko T.A. , Pikuz S.A. , Tilikin I.N. , Mitchell M.D. , Bland S.N. , Hammer D.A.
Published: November 2018

A review of X-pinches of various configurations and of different materials as an X-ray source for various applications is presented. The advantages and disadvantages of different designs of X-pinches as a load for generators with a wide range of output parameters and as a source of X-ray radiation for X-ray point-projection imaging were analyzed.
Developing a Comprehensive Trauma- and Resiliency- Focused Program After Superstorm Sandy in New York City
Authors: Scigliano Maria , Roncaglione Virginia , Madrid Paula A.
Published: November 2018

To contribute to the ongoing discourse about successful programming supporting intermediate behavioral and mental health needs of vulnerable communities affected by disaster, this article presents the Children’s Health Fund (CHF) Sandy Recovery and Resiliency Program as a descriptive case study for a multifaceted, community-based approach to building resiliency, coping, and socioemotional skills in an underserved community in New York City that was affected by Superstorm Sandy. The case study involves retrospective review and analysis of qualitative and quantitative data that were collected as part of routine care and program implementation. From the analysis emerged a program consisting of 3 components: (1) delivery of workshops and community events to decrease stigma and build community-wide resilience, (2) delivery of workshops for students and educators in the local school to increase coping skills as well as referrals to clinical mental health care, and (3) provision of mental health care via a mobile mental health clinic. As a result, we found that following periods of excessive trauma, children and families require a broad-based approach to mental health support. Additionally, the use of the mobile clinic abated most common access barriers and served as a proxy of the concern of the organization for the community. (Disaster Med Public Health Preparedness. 2018;page 1 of 5)
The Chronology of the Late Bronze (LB)-Iron Age (IA) Transition in the Southern Levant: A Response to Finkelstein’s Critique
Authors: Boaretto Elisabetta , Asscher Yotam , Hitchcock Louise A , Lehmann Gunnar , Maeir Aren M , Weiner Steve
Published: November 2018

The question under discussion is whether the dates of the Late Bronze (LBIIB)-LBIII (Iron IA) transitions in three sites in the southern Levant, namely Megiddo, Tell es-Safi/Gath and Qubur el-Walaydah occur at the same time, as has been proposed by Israel Finkelstein in his article in 2016 in Egypt and Levant. Here we respond to Finkelstein’s comments. We add some new data, clarify the issues that were raised, and conclude that the Late Bronze (LBIIB)-LBIII (Iron IA) transitions occurred at different times in northern and southern Israel.
New insight into the diagnostic cut-off value of serum anti-ToxocaraIgG for ocular toxocariasis in uveitis patients
Authors: Abd El-Aal N.F. , Basha M.A.A. , Eid A.M.
Published: November 2018

Uveitis is one of the commonest causes of vision loss worldwide and its exact etiology is still not clarified in most patients. The current study is a trial to assess the efficacy of serum anti-Toxocaraimmunoglobulin G (IgG) by enzyme-linked immunosorbent assay (ELISA) as a diagnostic tool for ocular toxocariasis (OT) and to detect OT prevalence and the associated ocular manifestations in sera of patients with uveitis. One hundred and twelve patients (62 females and 50 males) with uveitis were diagnosed by ophthalmologists, radiologists and rheumatologists according to ocular manifestations, laboratory and radiological investigations. Serum anti-ToxocaraIgG titers were determined by ELISA in sera of all patients. Our results revealed that OT is highly associated with intermediate and posterior uveitis. Children and young adult females, especially those residing in rural areas, complained mainly of diminution of vision in the left eye, with strabismus and leukocoria. At a cut-off value of 0.258, the sensitivity and specificity of IgG ELISA were 93.3% and 100%, respectively. In conclusion, at a novel cut-off value of 0.258 the serum anti-ToxocaraIgG ELISA is predicted to be a diagnostic tool for OT regarding sensitivity and specificity. Also, it has potential importance in the interpretation and differential diagnosis of OT. Thus, serum anti-ToxocaraIgG ELISA should be a routine test for screening of suspected cases.
Epistaxis and mortality
Authors:   Integrate (The National ENT Trainee Research Network)
Published: November 2018

Background

Epistaxis is a common emergency presentation to ENT. The ‘Epistaxis 2016: national audit of management’ collected prospective data over a 30-day audit window in 113 centres. A 30-day all-cause mortality rate of 3.4 per cent was identified. This study examines in more detail the subgroup of patients who died during the audit period.

Methods

There were 985 eligible patients identified. Of these, 33 patients died within the audit period. World Health Organization bleeding score, Modified Early Warning System score, haemostasis time, source of referral, co-morbidities and cause of death were investigated from the dataset.

Results

Patients who died were more likely to come from a ward environment, have co-existing cardiovascular disease, diabetes or a bleeding diathesis, be on antithrombotic medication, or have received a blood transfusion. Patients did not die from exsanguination.

Conclusion

Epistaxis may be seen as a general marker of poor health and a poor prognostic sign.
States before relations: On misrecognition and the bifurcated regime of sovereignty
Authors: Holm Minda , Sending Ole Jacob
Published: November 2018

The symbolic structure of the international system, organised around sovereignty, is sustained by an institutional infrastructure that shapes how states seek sovereign agency. We investigate how the modern legal category of the state is an institutional expression of the idea of the state as a liberal person, dependent on a one-off recognition in establishing the sovereign state. We then discuss how this institutional rule coexists with the ongoing frustrated search for recognition in terms of sociopolitical registers. While the first set of rules establishes a protective shield against others, regardless of behaviour, the second set of rules specify rules for behaviour of statehood, which produces a distinct form of misrecognition. States are, at one level, already recognised as sovereign and are granted rights akin to individuals in liberal thought, and yet they are continually misrecognised in their quest to actualise the sovereign agency they associate with statehood. We draw on examples from two contemporary phenomena – fragile states, and assertions of non-interference and sovereignty from the populist right and non-Western great powers, to discuss the misrecognition processes embedded in the bifurcated symbolic structure of sovereignty, and its implications for debates about hierarchy and sovereignty in world affairs.
Evaluating anaerobic soil disinfestation and other biological soil management strategies for open-field tomato production in Florida
Authors: Paudel Bodh R. , Di Gioia Francesco , Zhao Xin , Ozores-Hampton Monica , Hong Jason C. , Kokalis-Burelle Nancy , Pisani Cristina , Rosskopf Erin N.
Published: November 2018

In the search for alternative practices to chemical soil fumigation (CSF), anaerobic soil disinfestation (ASD) has proven to be a promising tool for soil-borne pest management and crop production improvement. The ASD treatment with composted poultry litter (CPL) and molasses (M, a labile carbon source) was identified as an effective approach for a biologically based soil disinfestation system in tomato (Solanum lycopersicum L.) production in Florida. However, environmental and food-safety concerns are associated with animal manure-based amendments, which led to the exploration of composted yard waste (CYW) as a potential substitute for CPL in ASD application. In this study, field trials were conducted in Citra and Immokalee, FL to examine the effects of ASD using CYW, CPL and M compared with a commercially available microbial amendment system on root-knot nematodes, weeds, fruit yield and quality of fresh-market tomato. Treatments included (1) ASD with CPL (11 Mg ha−1) and M (6.9 m3 ha−1) (ASD0.5), (2) ASD with CYW (26.9 Mg ha−1) and M (CYW1 + M), (3) ASD with CYW (13.5 Mg ha−1) and M (CYW0.5 + M), (4) Soil Symphony Amendment (SSA), (5) CYW (26.9 Mg ha−1) alone (CYW1) and (6) a combination of CYW1 + SSA, in comparison with (7) untreated control and (8) CSF (Pic-Clor 60 at 224 kg ha−1). Cumulative soil anaerobiosis was greater in ASD0.5 compared with all the other treatments. The root-knot nematode gall index ratings on the tomato crop were significantly lower in CSF, ASD0.5, CYW1 + M and CYW0.5 + M than untreated control in Citra. Although CYW1 and SSA alone had a moderately suppressive effect on weed coverage and root-knot nematodes, their positive impact on crop performance was limited when used alone. ASD0.5, CYW1 + M and CSF had significantly higher marketable and total fruit yields than untreated control in both locations, while all treatments showed promising results in the Immokalee trial in comparison with untreated control. In general, few differences in major fruit quality attributes were found. Although using CYW in ASD was not as effective as CPL in creating soil anaerobic conditions, the enhanced crop performance in CYW1 + M and CYW0.5 + M suggests the potential of using CYW as an alternative source of organic amendment in combination with M to achieve benefits similar to those obtained with CPL-based ASD.
H�nisch Receives 2018 Paleoceanography and Paleoclimatology Willi Dansgaard Award
Authors:   AGU
Published: November 2018

B�rbel H�nisch will receive the 2018 Willi Dansgaard Award at AGU’s Fall Meeting 2018, to be held 10–14 December in Washington, D. C. The award is given in recognition of the awardee’s “research impact, innovative interdisciplinary work, educational accomplishments (mentoring), societal impact, or other relevant contributions and to acknowledge that the awardee shows exceptional promise for continued leadership in paleoceanography or paleoclimatology.”
Impact of Convective Activity on Precipitation δ18O in Isotope‐Enabled General Circulation Models
Authors: Hu Jun , Emile‐Geay Julien , Nusbaumer Jesse , Noone David
Published: November 2018

The δ18O signal preserved in paleoarchives is widely used to reconstruct past climate conditions. In many speleothems, this signal is classically interpreted via the amount effect. However, recent work has shown that precipitation δ18O (
) is greatly influenced by convective processes distinct from precipitation amount, and new observations indicate that
 is negatively correlated with the fraction of stratiform precipitation. Isotope‐enabled climate models have emerged as a key interpretive tool in water isotope systematics, and it is thus important to determine to what extent they can reproduce these relationships. Here seven isotope‐enabled models, including the state‐of‐the‐art model iCAM5, are evaluated to see whether they can simulate the impact of convective activity on
 in observations. The results show that, of these models, only iCAM5 can simulate the observed anticorrelation between stratiform fraction and
. Furthermore, while all models can simulate the observed relationship between outgoing longwave radiation and
, different models achieve this via different mechanisms—some getting the right answer for the wrong reasons. Because iCAM5 appears in various metrics to correctly simulate
 variability, we use it to examine long‐standing interpretations of
 over Asia. We find that the contribution of convective processes is very site dependent, with local processes accounting for a very small amount of variance at the sites of most Chinese cave records (speleothems). The residual is attributed to source and transport effects. Our results imply that state‐of‐the‐art models like iCAM5 can and should be used to guide the interpretation of
‐based proxies.
Compaction and Melt Transport in Ammonia‐Rich Ice Shells: Implications for the Evolution of Triton
Authors: Hammond Noah P. , Parmenteir E. M. , Barr Amy C.
Published: November 2018

Ammonia, if present in the ice shells of icy satellites, could lower the temperature for the onset of melting to 176 K and create a large temperature range where partial melt is thermally stable. The evolution of regions of ammonia‐rich partial melt could strongly influence the geological and thermal evolution of icy bodies. For melt to be extracted from partially molten regions, the surrounding solid matrix must deform and compact. Whether ammonia‐rich melts sink to the subsurface ocean or become frozen into the ice shell depends on the compaction rate and thermal evolution. Here we construct a model for the compaction and thermal evolution of a partially molten, ammonia‐rich ice shell in a one‐dimensional geometry. We model the thickening of an initially thin ice shell above an ocean with 10% ammonia. We find that ammonia‐rich melts can freeze into the upper 5 to 10 km of the ice shell, when ice shell thickening is rapid compared to the compaction rate. The trapping of near‐surface volatiles suggests that, upon reheating of the ice shell, eutectic melting events are possible. However, as the ice shell thickening rate decreases, ammonia‐rich melt is efficiently excluded from the ice shell and the bulk of the ice shell is pure water ice. We apply our results to the thermal evolution of Neptune's moon Triton. As Triton's ice shell thickens, the gradual increase of ammonia concentration in Triton's subsurface ocean helps to prevent freezing and increases the predicted final ocean thickness by up to 50 km.
Dynamics of Postfire Aboveground Carbon in a Chronosequence of Chinese Boreal Larch Forests
Authors: Yang Yuan Z. , Cai Wen H. , Yang Jian , White Megan , Lhotka John M.
Published: November 2018

Boreal forests store a large proportion of the global terrestrial carbon (C), while wildfire plays a crucial role in determining their C storage and dynamics. The aboveground C (AC) pool is an important component of forest C stocks. To quantify the turning point (transforming from C source to C sink) and recovery time of postfire AC, and assess how stand density affects the AC, 175 plots from eight stand age classes were surveyed as a chronosequence in the Great Xing'an Mountains of Northeast China. Linear and nonlinear regression analyses were conducted to describe postfire AC recovery patterns. The results showed that (1) postfire AC exhibited a skewed U‐shaped pattern with the turning point at approximately year 30, when the change rate of AC shifted from negative to positive, (2) it took more than 120 years for this forest ecosystem to recover 80% of AC in unburned old‐growth (200 years) stands, and (3) there was an overall positive relationship between AC and stand density over the entire range of stand age classes; and such relationship was stronger during the early‐ and late‐successional stages, but weaker (p > 0.05) during the midsuccessional stage. Although boreal larch forests have been C sinks under historical fire free intervals, predicted increases in fire frequency could potentially shift it to a C source. Understanding postfire AC dynamics in boreal larch forests is central to predicting C cycling response to wildfire and provides a framework for assessing ecosystem resilience to disturbance in this region.
Corneal Confocal Microscopy detects a Reduction in Corneal Endothelial Cells and Nerve Fibres in Patients with Acute Ischemic Stroke
Authors: Khan Adnan , Kamran Saadat , Akhtar Naveed , Ponirakis Georgios , Al-Muhannadi Hamad , Petropoulos Ioannis N. , Al-Fahdawi Shumoos , Qahwaji Rami , Sartaj Faheem , Babu Blessy , Wadiwala Muhammad Faisal , Shuaib Ashfaq , Malik Rayaz A.
Published: November 2018

Endothelial dysfunction and damage underlie cerebrovascular disease and ischemic stroke. We undertook corneal confocal microscopy (CCM) to quantify corneal endothelial cell and nerve morphology in 146 patients with an acute ischemic stroke and 18 age-matched healthy control participants. Corneal endothelial cell density was lower (P < 0.001) and endothelial cell area (P < 0.001) and perimeter (P < 0.001) were higher, whilst corneal nerve fibre density (P < 0.001), corneal nerve branch density (P < 0.001) and corneal nerve fibre length (P = 0.001) were lower in patients with acute ischemic stroke compared to controls. Corneal endothelial cell density, cell area and cell perimeter correlated with corneal nerve fiber density (P = 0.033, P = 0.014, P = 0.011) and length (P = 0.017, P = 0.013, P = 0.008), respectively. Multiple linear regression analysis showed a significant independent association between corneal endothelial cell density, area and perimeter with acute ischemic stroke and triglycerides. CCM is a rapid non-invasive ophthalmic imaging technique, which could be used to identify patients at risk of acute ischemic stroke.
Modulating the Work Function of Graphene by Pulsed Plasma Aided Controlled Chlorination
Authors: Takehira Hiroshi , Karim Mohammad Razaul , Shudo Yuta , Fukuda Masahiro , Mashimo Tsutomu , Hayami Shinya
Published: November 2018

Chlorine on graphene (G) matrices was doped by pulsed plasma stimulation on graphite electrode submerged in organochlorine solvents (CH2Cl2, CHCl3, CCl4). The study of work function by Kelvin probe force microscopy (KPFM) measurement clearly indicates that Cl-doped G behave like semiconductor and GG@CHCl3 exhibits the lowest value for the work function. We propose that this report not only represents a new route for tuning the semiconductivity of G but also indicates that doping level of halogen on G based carbon framework can be controlled by pulsed plasma treatment of carbon materials on various organohalogen derivatives.
Minimising oxygen contamination through a liquid copper-aided group IV metal production process
Authors: Yoo Bung Uk , Lee Young Jun , Ri Vladislav , Lee Seong Hun , Nersisyan Hayk , Kim Hyun You , Lee Jong Hyeon , Earner Nicholas , MacDonald Alister
Published: November 2018

This paper demonstrates for the first time the fabrication of Zr-Cu alloy ingots from a Hf- free ZrO2 precursor in a molten CaCl2 medium to recover nuclear-grade Zr. The reduction of ZrO2 in the presence of CaO was accelerated by the formation of Ca metal in the intermediate stage of the process. Tests conducted with various amounts of ZrO2 indicate that the ZrO2 was reduced to the metallic form at low potentials applied at the cathode, and the main part of the zirconium was converted to a CuZr alloy with a different composition. The maximum oxygen content values in the CuZr alloy and Zr samples upon using liquid Cu were less than 300 and 891 ppm, respectively. However, Al contamination was observed in the CuZr during the electroreduction process. In order to solve the Al contamination problem, the fabrication process of CuZr was performed using the metallothermic reduction process, and the produced CuZr was used for electrorefining. The CuZr alloy was further purified by a molten salt electrorefining process to recover pure nuclear-grade Zr in a LiF-Ba2ZrF8-based molten salt, the latter of which was fabricated from a waste pickling acid of a Zr clad tube. After the electrorefining process, the recovered Zr metal was fabricated into nuclear-grade Zr buttons through arc melting following a salt distillation process. The results suggest that the removal of oxygen from the reduction product is a key reason for the use of a liquid CaCu reduction agent.
Genomic Analysis of Colombian Leishmania panamensis strains with different level of virulence
Authors: Urrea Daniel Alfonso , Duitama Jorge , Imamura Hideo , Álzate Juan F. , Gil Juanita , Muñoz Natalia , Villa Janny Alexander , Dujardin Jean-Claude , Ramirez-Pineda José R. , Triana-Chavez Omar
Published: November 2018

The establishment of Leishmania infection in mammalian hosts and the subsequent manifestation of clinical symptoms require internalization into macrophages, immune evasion and parasite survival and replication. Although many of the genes involved in these processes have been described, the genetic and genomic variability associated to differences in virulence is largely unknown. Here we present the genomic variation of fourLeishmania (Viannia) panamensisstrains exhibiting different levels of virulence in BALB/c mice and its application to predict novel genes related to virulence.De novoDNA sequencing and assembly of the most virulent strain allowed comparative genomics analysis with sequencedL. (Viannia) panamensisandL. (Viannia) braziliensisstrains, and showed important variations at intra and interspecific levels. Moreover, the mutation detection and a CNV search revealed both base and structural genomic variation within the species. Interestingly, we found differences in the copy number and protein diversity of some genes previously related to virulence. Several machine-learning approaches were applied to combine previous knowledge with features derived from genomic variation and predict a curated set of 66 novel genes related to virulence. These genes can be prioritized for validation experiments and could potentially become promising drug and immune targets for the development of novel prophylactic and therapeutic interventions.
Ternary crystal structure of human RORγ ligand-binding-domain, an inhibitor and corepressor peptide provides a new insight into corepressor interaction
Authors: Noguchi Masato , Nomura Akihiro , Doi Satoki , Yamaguchi Keishi , Hirata Kazuyuki , Shiozaki Makoto , Maeda Katsuya , Hirashima Shintaro , Kotoku Masayuki , Yamaguchi Takayuki , Katsuda Yoshiaki , Crowe Paul , Tao Haiyan , Thacher Scott , Adachi Tsuyoshi
Published: November 2018

Retinoic acid-related orphan receptor gamma (RORγ) plays pivotal roles in autoimmune diseases by controlling the lineage of interleukin 17 (IL-17)-producing CD4+ T cells (Th17 cells). Structure-based drug design has proven fruitful in the development of inhibitors targeting the ligand binding domain (LBD) of RORγ. Here, we present the crystal structure of a novel RORγ inhibitor co-complex, in the presence of a corepressor (CoR) peptide. This ternary complex with compound T reveals the structural basis for an inhibitory mechanism different from the previously reported inverse agonist. Compared to the inverse agonist, compound T induces about 2 Å shift of helix 5 (H5) backbone and side-chain conformational changes of Met365 on H5. These conformational changes correlate to reduced CoR peptide binding to RORγ-LBD in the presence of compound T, which suggests that the shift of H5 is responsible. This crystal structure analysis will provide useful information for the development of novel and efficacious drugs for autoimmune disorders.
Systematic Analysis and Biomarker Study for Alzheimer’s Disease
Authors: Li Xinzhong , Wang Haiyan , Long Jintao , Pan Genhua , He Taigang , Anichtchik Oleg , Belshaw Robert , Albani Diego , Edison Paul , Green Elaine K , Scott James
Published: November 2018

Revealing the relationship between dysfunctional genes in blood and brain tissues from patients with Alzheimer’s Disease (AD) will help us to understand the pathology of this disease. In this study, we conducted the first such large systematic analysis to identify differentially expressed genes (DEGs) in blood samples from 245 AD cases, 143 mild cognitive impairment (MCI) cases, and 182 healthy control subjects, and then compare these with DEGs in brain samples. We evaluated our findings using two independent AD blood datasets and performed a gene-based genome-wide association study to identify potential novel risk genes. We identified 789 and 998 DEGs common to both blood and brain of AD and MCI subjects respectively, over 77% of which had the same regulation directions across tissues and disease status, including the known ABCA7, and the novel TYK2 and TCIRG1. A machine learning classification model containing NDUFA1, MRPL51, and RPL36AL, implicating mitochondrial and ribosomal function, was discovered which discriminated between AD patients and controls with 85.9% of area under the curve and 78.1% accuracy (sensitivity = 77.6%, specificity = 78.9%). Moreover, our findings strongly suggest that mitochondrial dysfunction, NF-κB signalling and iNOS signalling are important dysregulated pathways in AD pathogenesis.
Uncovering the mechanism of Maxing Ganshi Decoction on asthma from a systematic perspective: A network pharmacology study
Authors: Song Wenjie , Ni Shenglou , Fu Yanling , Wang Yun
Published: November 2018

Maxing GanshiDecoction (MXGSD) is used widely for asthma over thousands of years, but its underlying pharmacological mechanisms remain unclear. In this study, systematic and comprehensive network pharmacology was utilized for the first time to reveal the potential pharmacological mechanisms of MXGSD on asthma. Specifically, we collected 141 bioactive components from the 600 components in MXGSD, which shared 52 targets common to asthma-related ones. In-depth network analysis of these 52 common targets indicated that asthma might be a manifestation of systemic neuro-immuno-inflammatory dysfunction in the respiratory system, and MXGSD could treat asthma through relieving airway inflammation, improving airway remodeling, and increasing drug responsiveness. After further cluster and enrichment analysis of the protein-protein interaction network of MXGSD bioactive component targets and asthma-related targets, we found that the neurotrophin signaling pathway, estrogen signaling pathway, PI3K-Akt signaling pathway, and ErbB signaling pathway might serve as the key points and principal pathways of MXGSD gene therapy for asthma from a systemic and holistic perspective, and also provides a novel idea for the development of new drugs for asthma.
Using mimicry of body movements by a virtual agent to increase synchronization behavior and rapport in individuals with schizophrenia
Authors: Raffard Stéphane , Salesse Robin N. , Bortolon Catherine , Bardy Benoit G. , Henriques José , Marin Ludovic , Stricker Didier , Capdevielle Delphine
Published: November 2018

Synchronization of behavior such as gestures or postures is assumed to serve crucial functions in social interaction but has been poorly studied to date in schizophrenia. Using a virtual collaborative environment (VCS), we tested 1) whether synchronization of behavior, i.e., the spontaneous initiation of gestures that are congruent with those of an interaction partner, was impaired in individuals with schizophrenia compared with healthy participants; 2) whether mimicry of the patients’ body movements by the virtual interaction partner was associated with increased behavioral synchronization and rapport. 19 patients and 19 matched controls interacted with a virtual agent who either mimicked their head and torso movements with a delay varying randomly between 0.5 s and 4 s or did not mimic, and rated feelings of rapport toward the virtual agent after each condition. Both groups exhibited a higher and similar synchronization behavior of the virtual agent forearm movements when they were in the Mimicry condition rather than in the No-mimicry condition. In addition, both groups felt more comfortable with a mimicking virtual agent rather than a virtual agent not mimicking them suggesting that mimicry is able to increase rapport in individuals with schizophrenia. Our results suggest that schizophrenia cannot be considered anymore as a disorder of imitation, particularly as regards behavioral synchronization processes in social interaction contexts.
Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae
Authors: Kundu Shantanu , Kumar Vikas , Tyagi Kaomud , Chakraborty Rajasree , Singha Devkant , Rahaman Iftikar , Pakrashi Avas , Chandra Kailash
Published: November 2018

The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle,Nilssonia nigricanswas sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency inN. nigricans,N. formosa, andR. swinhoei. InN. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except fortrnS1(GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except fortrnE(TTC),trnQ(TTG), andtrnM(CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome ofN. nigricansalso revealed two unique tandem repeats (ATTAT)8,and (TATTA)20in the CR. Further, the conserved motif 5′-GACATA-3′ and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering ofN. nigricanswithN. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.
A comparison of the Macintosh laryngoscope, McGrath video laryngoscope, and Pentax Airway Scope in paediatric nasotracheal intubation
Authors: Yoo Ji Young , Chae Yun Jeong , Lee Young Bok , Kim Sujin , Lee Jaemoon , Kim Dae Hee
Published: November 2018

We evaluated the performance of the McGrath video laryngoscope and Pentax Airway Scope in comparison with the Macintosh laryngoscope for nasotracheal intubation in paediatric patients. For this, 108 patients were enrolled in an open-label, randomized controlled trial. Patients were randomly allocated to one of three groups based on use of the Macintosh laryngoscope, McGrath video laryngoscope, or Pentax Airway Scope. Time to intubation, the intubation difficulty, and the quality of navigation were compared among groups. The median nasotracheal intubation time [interquartile range] in the Macintosh group (33.5 [28.3–39.8] s) was significantly shorter than those of the McGrath (39.0 [32.0–43.0] s) and Pentax groups (43.0 [35.0–52.0] s). The difficulty of nasotracheal intubation was similar among all groups. When navigating and aligning the tube from the oropharynx into the glottic inlet, the cuff inflation method was required in significantly fewer patients for the Macintosh group (11.1%) than for the McGrath (48.6%) and Pentax (51.4%) groups. Thus, compared to the McGrath video laryngoscope and Pentax Airway Scope, the Macintosh laryngoscope allowed shorter nasotracheal intubation times and better facilitated tracheal navigation, requiring less use of the cuff inflation method to navigate the tracheal tube into the glottic inlet.
Variations in the immune and metabolic response of proactive and reactive Sparus aurata under stimulation with Vibrio anguillarum vaccine
Authors: Vargas R. , Balasch J. C. , Brandts I. , Reyes-López F. , Tort L. , Teles M.
Published: November 2018

Environmental insults, such as exposure to pathogens, modulate the behavioural coping style of animals to stressors, and repeated exposure to stressful environments may lead to species-specific infection phenotypes. To analyse the influence of stress behavioural phenotypes on immune and metabolic performance, gilthead sea bream (Sparus aurata L.) were first screened for proactive and reactive coping styles. Once characterized, both behavioural phenotypes fish groups were bath vaccinated with bacterin from Vibrio anguillarum, an opportunistic widespread pathogen of fish. Gills and liver were sampled at 0 (control group), 1, 3 and 7 days post-vaccination. Immune-, oxidative stress- and metabolic-related transcripts (il1β, tnfα, igm, gpx1, sod, cat, lpl, ghr1 and ghr2), metabolic endpoints (glucose, cholesterol and triglycerides), hepatic health indicators (aspartate aminotransferase, alanine transaminase and alkaline phosphatase), oxidative stress status (esterase activity, total antioxidant capacity and total oxidative status) and stress biomarkers (cortisol) were determined. Present results indicate that screening for coping styles in the gilthead sea bream segregated the two distinct phenotypes as expected: proactive and reactive. Results also indicate that under bath vaccination proactive fish show high immune response and lower metabolism, whereas reactive fish show low immune and higher metabolic responses.
Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Authors: Du Zhonghua , Jia Lin , Wang Yichen , Wang Cong , Wen Xue , Chen Jingcheng , Zhu Yanbo , Yu Dehai , Zhou Lei , Chen Naifei , Zhang Shilin , Celik Ilkay , Ay Ferhat , Gao Sujun , Zhang Songling , Li Wei , Hoffman Andrew R. , Cui Jiuwei , Hu Ji-Fan
Published: November 2018

Pluripotent stem cells hold great investigative potential for developmental biology and regenerative medicine. Recent studies suggest that long noncoding RNAs (lncRNAs) may function as key regulators of the maintenance and the lineage differentiation of stem cells. However, the underlying mechanisms by which lncRNAs affect the reprogramming process of somatic cells into pluripotent cells remain largely unknown. Using fibroblasts and induced pluripotent stem cells (iPSCs) at different stages of reprogramming, we performed RNA transcriptome sequencing (RNA-Seq) to identify lncRNAs that are differentially-expressed in association with pluripotency. An RNA reverse transcription-associated trap sequencing (RAT-seq) approach was then utilized to generate a database to map the regulatory element network for lncRNA candidates. Integration of these datasets can facilitate the identification of functional lncRNAs that are associated with reprogramming. Identification of lncRNAs that regulate pluripotency may lead to new strategies for enhancing iPSC induction in regenerative medicine.
Anthropomorphic breast model repository for research and development of microwave breast imaging technologies
Authors: Omer Muhammad , Fear Elise
Published: November 2018

A repository of anthropomorphic numerical breast models is made available for the scientific community to support research and development of microwave imaging technologies for diagnostic and therapeutic applications. These models are constructed from magnetic resonance imaging (MRI) scans acquired at our university hospital. Our 3D breast modelling method is used to translate the MRI scans into 3D models representing the geometry and microwave-frequency properties of tissues in the breast. The reconstructed models demonstrate anatomical realism, reconfigurable complexity, and flexibility to adapt to simulations of various microwave imaging techniques and prototype systems. With these models, realistic and rigorous test scenarios can be defined in simulations to support feasibility analysis, performance verification and design improvements of developing microwave imaging techniques, prior to testing on experimental systems. A repository of breast models is created which includes breasts of varying classification – fatty, scattered, heterogeneous, and dense. In addition, the models include brief documentation to facilitate researchers in selecting a model by matching its features with their requirements.
Generation and quality control of lipidomics data for the alzheimer’s disease neuroimaging initiative cohort
Authors: Barupal Dinesh Kumar , Fan Sili , Wancewicz Benjamin , Cajka Tomas , Sa Michael , Showalter Megan R. , Baillie Rebecca , Tenenbaum Jessica D. , Louie Gregory ,   Alzheimer’s Disease Neuroimaging Initiative,   Alzheimer’s Disease Metabolomics Consortium, Kaddurah-Daouk Rima , Fiehn Oliver
Published: November 2018

Alzheimer’s disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository athttp://adni.loni.usc.edu/
Tunable band offsets in the BP/P4O10 van der Waals heterostructure: first-principles calculations
Authors: Dou Wenzhen , Huang Anping , Shi Hongliang , Zhang Xinjiang , Zheng Xiaohu , Wang Mei , Xiao Zhisong , Liu Liming , Chu Paul K.
Published: November 2018

The separation of photoexcited electron–hole pairs in the BP/P4O10 vdW heterostructure.
Solar-driven biocatalytic C-hydroxylation through direct transfer of photoinduced electrons
Authors: Le Thien-Kim , Park Jong Hyun , Choi Da Som , Lee Ga-Young , Choi Woo Sung , Jeong Ki Jun , Park Chan Beum , Yun Chul-Ho
Published: November 2018

Photoactivation of flavins is coupled productively with the direct transfer of photoinduced electrons to P450s to achieve photobiocatalytic C-hydroxylation reactions in the absence of nicotinamide cofactors.
The synergistic effect of oxygen-containing functional groups on CO2 adsorption by the glucose–potassium citrate-derived activated carbon
Authors: Liu Baogen , Li Haoyang , Ma Xianchen , Chen Ruofei , Wang Shaobin , Li Liqing
Published: November 2018

A high surface area activated carbon which was prepared by an innovative approach using glucose as a carbon source and neutral potassium citrate as an activator was compared with the porous carbon using corrosive potassium hydroxide as activator.
Anion–cation co-operative catalysis by artificial sweetener saccharine-based ionic liquid for sustainable synthesis of 3,4-dihydropyrano[c]chromenes, 4,5-dihydropyrano[4,3-b]pyran and tetrahydrobenzo[b]pyrans in aqueous medium
Authors: Sharma Himani , Srivastava Suman
Published: November 2018

Artificial sweetener saccharine based ionic for sustainable synthesis of 3,4-dihydropyrano[c]chromenes, 4,5-dihydropyrano[4,3-b]pyran and tetrahydrobenzo[b]pyrans in aqueous medium scaffolds through Domino Knoevenagel–Michael reaction.
Modification of dry/wet hybrid fabrication method for preparing a perovskite absorption layer on a PCBM electron transport layer
Authors: Kagae Junta , Yamanaka Takaaki , Takahashi Shun , Yamashita Kenichi
Published: November 2018

A dry/wet hybrid method was modified and improved for fabricating a high quality perovskite absorption layer on a PCBM electron transport layer.
Fabrication of graphene oxide/montmorillonite nanocomposite flexible thin films with improved gas-barrier properties
Authors: Kim Se Jung , Kim Tan young , Kang Byung Hyun , Lee Gun-Hwan , Ju Byeong-Kwon
Published: November 2018

Nanocomposites are potential substitutes for inorganic materials in fabricating flexible gas-barrier thin films.
Hierarchically porous metal–organic frameworks: rapid synthesis and enhanced gas storage
Authors: Duan Chongxiong , Zhang Hang , Li Feier , Xiao Jing , Luo Shaojuan , Xi Hongxia
Published: November 2018

A simple, rapid and versatile method was developed to increase the pore sizes and pore volumes of microporous MOFs (HKUST-1, ZIF-8, ZIF-67, and ZIF-90) by employing organic amine as the template. The resultant hierarchically porous HKUST-1 exhibited significantly enhanced adsorption capacities and faster diffusion rates for CH4 and CO2 gas storage.
Macroscopic supramolecular assembly of rigid hydrogels assisted by a flexible spacing coating
Authors: Ju Guannan , Zhang Qian , Guo Fengli , Xie Peichen , Cheng Mengjiao , Shi Feng
Published: November 2018

A flexible spacing coating is introduced to a rigid hydrogel surface to improve the surface compliance for efficient macroscopic supramolecular assembly.
In situ growth of Au nanoparticles on natural melanin as biocompatible and multifunctional nanoagent for efficient tumor theranostics
Authors: Wang Zhaojie , Yu Nuo , Yu Wanjian , Xu Hao , Li Xuan , Li Maoquan , Peng Chen , Wang Qian , Zhu Meifang , Chen Zhigang
Published: November 2018

The in situ growth of Au nanoparticles on melanin was realized, and the Au-decorated melanin (Au–M) nanocomposite can be used as a novel and multifunctional theranostic nanoagent for simultaneous tumor CT/PA/thermal imaging and PTT.
Suppressed hysteresis and enhanced performance of triple cation perovskite solar cell with chlorine incorporation
Authors: Li Lingfeng , Zhou Peng , Li Jing , Mo Yanping , Huang Wenchao , Xiao Junyan , Li Wei , Ku Zhiliang , Zhong Jie , Peng Yong , Cheng Yi-Bing , Huang Fuzhi
Published: November 2018

Cl-Incorporated triple-cation perovskite, as a novel absorber, has been developed to suppress hysteresis and enhance photoelectric performance.