bluuebunny/crossref_metadata_2025 huggingface dataset:
Shared social mechanisms underlying the risk of nine cancers: A life course study
Authors: Nicolau Belinda , Madathil Sreenath Arekunnath , Castonguay Genevieve , Rousseau Marie‐Claude , Parent Marie‐Elise , Siemiatycki Jack
Published: July 2018

Identifying life periods during which social conditions have the highest impact on risk of common cancers in a population may help to reveal their underlying shared social mechanisms. We used the life course framework to estimate the extent to which life course SEP is associated with risk of nine cancers. In addition, we tested whether these associations conform to a critical period or cumulative life course model. Data were from a population‐based case–control study of occupational exposures and cancer conducted in Montreal, Canada. Participants were males aged 35–70 years (n = 2,547) residing in the Montreal metropolitan area with primary, histologically confirmed cancers diagnosed between 1979 and 1985. Population controls (n = 512) were sampled from electoral lists. SEP was measured at three different periods of life based on respondent's report: during childhood, young adulthood and mid‐life. We used a structured modeling approach using a series of unconditional logistic regressions to test which models best fit the data. Life course SEP increased the risk of all cancers. SEP in childhood was identified as a critical period for prostate and all gastrointestinal tract cancers except for esophagus cancer. In addition, the accumulation model best explained the data for melanoma and lung squamous cell carcinoma. Our findings suggest that childhood social circumstances are a common risk factor for several cancers among men; our results provide insights into the mechanisms involved in the etiology of nine cancers.
Survival from childhood cancers in Eastern Africa: A population‐based registry study
Authors: Joko‐Fru W. Yvonne , Parkin D. Maxwell , Borok Margaret , Chokunonga Eric , Korir Anne , Nambooze Sarah , Wabinga Henry , Liu Biying , Stefan Cristina
Published: July 2018

Cancers occurring in children in Africa are often underdiagnosed, or at best diagnosed late. As a result, survival is poor, even for cancers considered ‘curable’. With limited population‐level data, understanding the actual burden and survival from childhood cancers in Africa is difficult. In this study, we aimed at providing survival estimates for the most common types of cancers affecting children aged 0–14 years, in three population‐based Eastern African registries; Harare, Zimbabwe (Kaposi sarcoma, Wilms tumour (WT), non‐Hodgkin lymphoma (NHL), retinoblastoma, and acute lymphocytic leukaemia (ALL)), Kampala, Uganda (Burkitt lymphoma, Kaposi sarcoma, WT, and retinoblastoma), and Nairobi, Kenya (ALL, retinoblastoma, WT, Burkitt lymphoma, and Hodgkin lymphoma). We included cases diagnosed within the years 1998–2009 and followed up till the end of 2011. We estimated the observed and relative survival at 1, 3, and 5 years after diagnosis. We studied 627 individual patient records. Median follow‐up ranged from 2.2 months for children with Kaposi sarcoma in Harare to 30.2 months for children with ALL in Nairobi. The proportion of children lost to follow‐up was highest in the first year after diagnosis. In Harare and Kampala, the 5‐year relative survival was <46% for all cancer types. The 5‐year relative survival was best for children in Nairobi, though with wider confidence intervals. Survival from childhood cancers in Africa is still poor, even for cancers with good prognosis and potential for cure. Supporting cancer detection, treatment, and registration activities could help improve survival chances for children with cancers in Africa.
Dual TGF‐β and PD‐1 blockade synergistically enhances MAGE‐A3‐specific CD8+ T cell response in esophageal squamous cell carcinoma
Authors: Chen Xinfeng , Wang Liping , Li Pupu , Song Mengjia , Qin Guohui , Gao Qun , Zhang Zhen , Yue Dongli , Wang Dan , Nan Shufeng , Qi Yu , Li Feng , Yang Li , Huang Lan , Zhang Mingzhi , Zhang Bin , Gao Yanfeng , Zhang Yi
Published: July 2018

PD‐1 is highly expressed on tumor‐infiltrated antigen‐specific T cells and limit the antitumor function. Blocking of PD‐1/PD‐L1 signaling has shown unprecedented curative efficacies in patients with advanced cancer. However, only a limited population of patients benefited from such therapies. Our study aimed to explore biological properties, functional regulation and reversal of MAGE‐A3‐specific CD8+ T cells in patients with esophageal squamous cell carcinoma (ESCC). The underlying principle of deficiency and restoring MAGE‐A3‐specific CD8+ T cells function in tumor microenvironment (TME) was evaluated. MAGE‐A3‐specific CD8+ T cells could lyse HLA‐A2+/MAGE‐A3+ tumor cells. Tetramer+ T cell frequency was higher in elder patients, but lower in patients with lymph node metastasis and late tumor stage (p < 0.05). CD107ahigh expression on functional T cells was an independent prognostic factor in Cox regression analysis. PD‐1 was highly expressed on dysfunctional antigen‐specific CD8+ T cells and tumor infiltrating T lymphocytes (p < 0.05). Myeloid‐derived suppressor cells (MDSCs) derived‐TGF‐β mediated PD‐1high expression on CD8+ T cells, which led to be resistance to PD‐1/PD‐L1 blockade in TME. Dual PD‐1/PD‐L1 and TGF‐β signaling pathway blockades synergistically restored the function and antitumor ability of antigen‐specific CD8+ T cells in vitro/vivo assay. The presence of functional MAGE‐A3‐specific CD8+ T cells had an independent prognostic impact on survival of patients with ESCC. Furthermore, MDSCs‐derived TGF‐β increased PD‐1 expression on T cells and decreased the sensitivity to PD‐1/PD‐L1 blockade. Combining T cell‐based therapy with dual PD‐1/PD‐L1 and TGF‐β signaling pathway blockade could be considered a promising strategy for cancer treatment.
Modification of α2,6‐sialylation mediates the invasiveness and tumorigenicity of non‐small cell lung cancer cells in vitro and in vivo via Notch1/Hes1/MMPs pathway
Authors: Yuan Qingmin , Chen Xixi , Han Yang , Lei Ting , Wu Qiang , Yu Xiao , Wang Liping , Fan Zhe , Wang Shujing
Published: July 2018

The alterations of sialylation on cell surface N‐glycans due to overexpression of different sialyltransferases play a vital role in tumorigenesis and tumor progression. The β‐galactoside α2–6‐sialyltransferase 1 (ST6Gal‐I) has been reported to be highly expressed in several cancers, including breast cancer, hepatocellular cancer and colon carcinoma. However, the roles and underlying mechanisms of ST6Gal‐I in non‐small cell lung cancer (NSCLC) still need to be elucidated. In this study, we determined that mRNA levels of ST3GAL1, ST6GALNAC3 and ST8SIA6 were remarkably reduced in lung cancer tissues and cells, whereas ST6GAL1 level significantly increased. The mRNA, protein and glycan levels of ST6Gal‐I were higher in lung cancer tissues and cells. Moreover, down‐regulation of ST6Gal‐I decreased protein levels of Jagged1, DLL‐1, Notch1, Hes1, Hey1, matrix‐metalloproteinases (MMPs) and VEGF, and suppressed proliferation, migration and invasion capabilities of A549 and H1299 cells in vitro. In vivo, ST6Gal‐I silencing suppressed tumorigenicity of NSCLC cells in athymic nude mice via the Notch1/Hes1/MMPs pathway. In addition, overexpression of Notch1 rescued the reduced growth and metastasis of A549 and H1299 cells resulted by ST6Gal‐I silencing. Modification of α2,6‐sialylation positively associates with lung cancer progression, thereby indicating that ST6Gal‐I may mediate the invasiveness and tumorigenicity of NSCLC cells via the Notch1/Hes1/MMPs pathway both in vitro and in vivo. Thus, our results provide a novel therapeutic approach for blocking metastasis in lung cancer patients.
Seroprevalence of hepatitis C virus among the newcomer students, Kafrelsheikh University, Egypt
Authors: El Batae Hassan , Amer Ibrahim , Kobtan Abdelrahman , Saied Shimaa M. , Ghazy Amany , Elkalla Ferial , El Sharawy Shimaa
Published: July 2018

Background

Hepatitis C virus (HCV) constitutes a global public health problem in Egypt, as it has the highest worldwide prevalence. This study aimed at determining the seroprevalence of HCV among the newcomer students of Kafrelsheikh University, Egypt.

Methods

A cross‐sectional serosurvey was conducted including 9049 students. Medical examination, ultrasonography, and laboratory investigations were done. Liver function tests and HCV antibody testing were carried out for all students who gave an informed consent; HCV‐RNA polymerase chain reaction was performed for students with positive HCV antibody testing.

Results

The mean age of screened students were 18.6 ± 0.39 years. In total, 4233 (46.8%) were males and 4816 (53.2%) were females. Using HCV antibody testing, only 25 students (0.0028%) had positive antibodies; among them, 24 students (0.0026%) had HCV RNA positive; the study showed none statistically significant higher percentage of HCV infection among males (13 out of 24, 54.2%) than females (11 out of 24, 48.5%), P > 0.05. The results of liver function tests were not significantly different between the HCV‐positive and HCV‐negative students. However, the liver transaminase enzymes were significantly higher (
P < 0.0001) in HCV positive students compared to the negative ones, despite its mean values did not exceed the upper normal level. HCV infection among young Egyptian generations showed a marked decline.

Conclusion

Prevalence of HCV infection among young Egyptian generations had markedly decline, indicating the start of successful control of HCV infection.
Molecular epidemiology of coxsackievirus A6 derived from hand, foot, and mouth disease in Fukuoka between 2013 and 2017
Authors: Yoshitomi Hideaki , Ashizuka Yuki , Ichihara Sachiko , Nakamura Tomofumi , Nakamura Asako , Kobayashi Takayuki , Kajiwara Junboku
Published: July 2018

Coxsackievirus (CV)‐A6 has been the primary causative agent of hand, foot, and mouth disease (HFMD) in Japan since 2011. In Fukuoka, CV‐A6‐associated HFMD caused epidemics in 2013, 2015, and 2017. This paper reports the genetic characteristics of the CV‐A6 entire viral protein 1 (VP1) derived from patients with HFMD in Fukuoka between 2013 and 2017. CV‐A6 was detected in 105 of 280 clinical specimens, and the entire VP1 sequences could be analyzed for 90 of the 105 specimens. Phylogenetic analysis revealed that the CV‐A6 strains were classified into clade A and subgrouped into subclade A3 or subclade A4. Each subclade strain carried amino acid substitutions in the presumed DE and GH loops of the VP1, and no amino acid substitutions were identified as deleterious to the protein function. No significant difference was found in the clinical symptoms between the genetic subclades using statistical analyses. In conclusion, this study clarified the genetic diversity of CV‐A6 in Fukuoka from 2013 to 2017. The emergence of the CV‐A6 strains was classified into derived new subclades based on phylogenetic analysis of the VP1 gene that may cause CV‐A6‐associated HFMD epidemics approximately every 2 years.
Prevalence of C‐C chemokine receptor type 5 tropism among human immunodeficiency virus 1–infected patients in South Korea
Authors: Song Je Eun , Ahn Mi Young , Kim Woo Joo , Kim Shin‐Woo , Lee Jin Soo , Ku Nam Su , Kim Joon Hyung , Kim Ki‐Hyon , Ann Heawon , Choi Jun Yong
Published: July 2018

Objective

The discovery of two main coreceptors for human immunodeficiency virus (HIV), C‐C chemokine receptor type 5 (CCR5), and C‐X‐C chemokine receptor type 4 has led to a better understanding of the interaction between HIV envelope and host cells, and development of new therapeutic approaches. The purpose of this study was to estimate the prevalence of CCR5 tropism among HIV‐1–infected Koreans and identify the predictors for CCR5 tropism.

Methods

We enrolled 250 HIV‐1–infected subjects from four medical centers of three different cities in South Korea between April 2013 and May 2014. Genotypic assay for identifying coreceptor tropism of HIV‐1 was performed with HIV RNA or HIV DNA. Nested polymerase chain reaction and population‐based sequencing for the V3 region (HXB2 position 6225‐7758) of the envelope were performed with HIV RNA or proviral DNA. Proviral DNA was used if the viral load of the subject was below 2000 copies/mL. Genotypic tropism was determined by a web‐based bioinformatics tool (http://coreceptor.bioinf.mpi‐inf.mpg.de/).

Results

Among 250 individuals enrolled, only 143 subjects could be analyzed for genotypic tropism assay with HIV RNA or proviral DNA. The prevalence of CCR5 tropism was 69.2% (N = 99). We could not identify any significant clinical or epidemiological predictors for CCR5 tropism among enrolled subjects.

Conclusions

The prevalence of CCR5 tropism in HIV‐1–infected Korean individuals was 69.2%. Since we cannot predict coreceptor tropism by clinical factors, tropism assay should be performed before treatment with the CCR5 antagonist.
The Role of Stress in the Social Support–Mental Health Relationship
Authors: Watkins Kaitlin , Hill Erin M.
Published: July 2018

This study examined the mediating effect of psychological stress in the relationship between social support and mental health symptomatology in undergraduate students. Participants (n = 368) completed measures of social support, psychological stress, and mental health symptomatology. Bootstrapping estimates of indirect effects indicated a significant influence of psychological stress in the relationship between social support and both anxiety and depression symptomatology. Implications for mental health promotion and treatment on college campuses are discussed.
Trauma and Dissociation: Predictors of Loneliness in Students at an Urban University
Authors: Kearney Moriah A. , Zeligman Melissa , Brack Jane L. , Payne Ellyce
Published: July 2018

Loneliness is often seen in college students as they leave established support networks and family. Loneliness is also associated with negative mental health outcomes, including depression and decreased life satisfaction. The authors explored relationships between trauma, dissociation, and loneliness, and assessed the predictive ability of trauma and dissociation on feelings of loneliness. Hierarchical regression analyses indicated that trauma experience and dissociation significantly predicted loneliness in the current sample (n = 429). Implications for counseling are discussed.
Impact of expiratory strength training in amyotrophic lateral sclerosis: Results of a randomized, sham‐controlled trial
Authors: Plowman Emily K. , Tabor‐Gray Lauren , Rosado K. Michelle , Vasilopoulos Terrie , Robison Raele , Chapin Jennifer L. , Gaziano Joy , Vu Tuan , Gooch Clifton
Published: July 2018

Introduction

The purpose of this study was to determine the impact of an in‐home expiratory muscle strength training (EMST) program on pulmonary, swallow, and cough function in individuals with amyotrophic lateral sclerosis (ALS).

Methods

EMST was tested in a prospective, single‐center, double‐blind, randomized, controlled trial of 48 ALS individuals who completed 8 weeks of either active EMST (n = 24) or sham EMST (n = 24). The primary outcome to assess treatment efficacy was change in maximum expiratory pressure (MEP). Secondary outcomes included: cough spirometry; swallowing; forced vital capacity; and scoring on the ALS Functional Rating Scale—Revised.

Results

Treatment was well tolerated with 96% of patients completing the protocol. Significant differences in group change scores were noted for MEP and Dynamic Imaging Grade of Swallowing Toxicity scores (P < 0.02). No differences were noted for other secondary measures.

Discussion

This respiratory training program was well‐tolerated and led to improvements in respiratory and bulbar function in ALS. Muscle Nerve 59:40–46, 2019
Muscle morphology of the lower leg in ambulant children with spastic cerebral palsy
Authors: Pitcher Christian A. , Elliott Catherine M. , Valentine Jane P. , Stannage Katherine , Williams Sian A. , Shipman Peter J. , Reid Siobhán L.
Published: July 2018

Introduction: In this study we aimed to determine the lower limb morphological characteristics of skeletal muscle of ambulant children with spastic cerebral palsy (CP) and typically developing (TD) children. Methods: Seventeen children with spastic diplegic CP (10 boys and 7 girls, 5–12 years of age, Gross Motor Function Classification System [GMFCS] level I or II) and 19 TD children (8 boys and 11 girls, 5–11 years of age) underwent lower limb T1‐weighted MRI. Morphological characteristics of the triceps surae, including muscle volume, anatomical cross‐sectional area, muscle length, and subcutaneous adipose tissue, were digitally quantified, and the proportional distribution calculated. Results: Children with GMFCS II had significantly reduced muscle volume, cross‐sectional area, and muscle length, and increased subcutaneous fat compared with TD children. Children classified as GMFCS II consistently exhibited the greatest deficits in all morphology variables. Discussion: Morphological variables were significantly different between the groups. These alterations have the potential to influence the functional capabilities of the triceps surae muscle group. Muscle Nerve 58:818–823, 2018
A prognostic model for the patient‐reported outcome of surgical treatment of carpal tunnel syndrome
Authors: Bowman Angela , Rudolfer Stephan , Weller Peter , Bland Jeremy D. P.
Published: July 2018

Introduction: Many prognostic factors have been studied in carpal tunnel decompression, but most studies consider only a subset of variables. Methods: Three thousand three hundred thirty‐two operations were used to develop prognostic models, and 885 operations were used for validation. Outcome recorded on a Likert scale was dichotomized into success or failure. Modeling was performed with both logistic regression and artificial neural networks using 87 candidate variables. Results: Both approaches produced predictive multivariate models for outcome with areas under a receiver operating characteristic curve of 0.7 in the validation data set. Patients with moderately severe nerve conduction abnormalities, night waking, a family history of carpal tunnel syndrome, a good response to corticosteroid injection, and women have better outcomes. Greater functional impairment, diabetes, hypertension, and surgery on the dominant hand are associated with poorer outcomes. Discussion: A multivariate model partially predicts the outcome of carpal tunnel surgery, aids decision making, and helps to manage patient expectations. Muscle Nerve 58:784–789, 2018
Frequency of mental disorders among chronic pain patients with or without fibromyalgia in Japan
Authors: Miki Kenji , Nakae Aya , Shi Kenrin , Yasuda Yuka , Yamamori Hidenaga , Fujimoto Michiko , Ikeda Manabu , Shibata Masahiko , Yukioka Masao , Hashimoto Ryota
Published: July 2018

Aim

To explore the characteristics of psychiatric morbidity in chronic pain patients who present with or without fibromyalgia.

Methods

Patients are referred to our chronic pain clinic from primary medical institutions, as we are a secondary medical institution. Although some patients have chronic pain, they have no clear organic disorder such as rheumatoid arthritis to account for the pain. Among the 367 new patients seen during the period from March 2009 to August 2012, 347 patients underwent psychiatric evaluation in face‐to‐face interviews with mental health specialists before a physical examination.

Results

Of the 347 patients examined, at least one psychiatric diagnosis was made for 94.6%. The average number of DSM‐IV‐TR diagnoses was 1.46 in the 330 chronic pain patients who had at least one psychiatric diagnosis. The breakdown of the number of psychodiagnoses was one in 60.8%, two in 27.1%, three in 4.9%, and more than three in 2.3% chronic pain patients with or without fibromyalgia. In fibromyalgia patients, the highest relative frequencies were found for somatoform disorders (76%), followed by dysthymic disorder (17%) and major depressive disorder (15%). In patients without fibromyalgia, the highest relative frequencies were found for somatoform disorders (64%), followed by major depressive disorder (15%) and dysthymic disorder (14%). Psychiatric disorders were found in 96.9% of fibromyalgia patients, and in 93.5% of chronic pain patients without fibromyalgia in Japan (no significant difference using chi‐square test).

Conclusion

Results show that chronic pain patients with or without fibromyalgia are extremely likely to be diagnosed with a psychiatric disorder.
Comments on the SN orbifold CFT in the large N-limit
Authors: Roumpedakis Konstantinos
Published: July 2018

Abstract

We elaborate on various aspects of the conformal field theory of the symmetric orbifold. We collect various results that have appeared in the literature, and we present a coherent picture of the operator content of this CFT, relying on the orbifold extension of the Virasoro algebra. We then focus on the largeN-limit of this theory, discuss the OPE of two twist operators, and find various selection rules. We review how to calculate four-point functions of twist operators, and we write down the most general four-point function in the covering space for largeN.We show that it depends on some functions that obey a set of algebraic equations, that resemble the scattering equations. Finally, we provide a recipe on how to calculate correlation functions with insertions of the orbifold Virasoro generators.
Entanglement, quantum randomness, and complexity beyond scrambling
Authors: Liu Zi-Wen , Lloyd Seth , Zhu Elton , Zhu Huangjun
Published: July 2018

Abstract

Scrambling is a process by which the state of a quantum system is effectively randomized due to the global entanglement that “hides” initially localized quantum information. Closely related notions include quantum chaos and thermalization. Such phenomena play key roles in the study of quantum gravity, many-body physics, quantum statistical mechanics, quantum information etc. Scrambling can exhibit different complexities depending on the degree of randomness it produces. For example, notice that the complete randomization implies scrambling, but the converse does not hold; in fact, there is a significant complexity gap between them. In this work, we lay the mathematical foundations of studying randomness complexities beyond scrambling by entanglement properties. We do so by analyzing the generalized (in particular Rényi) entanglement entropies of designs, i.e. ensembles of unitary channels or pure states that mimic the uniformly random distribution (given by the Haar measure) up to certain moments. A main collective conclusion is that the Rényi entanglement entropies averaged over designs of the same order are almost maximal. This links the orders of entropy and design, and therefore suggests Rényi entanglement entropies as diagnostics of the randomness complexity of corresponding designs. Such complexities form a hierarchy between information scrambling and Haar randomness. As a strong separation result, we prove the existence of (state) 2-designs such that the Rényi entanglement entropies of higher orders can be bounded away from the maximum. However, we also show that the min entanglement entropy is maximized by designs of order only logarithmic in the dimension of the system. In other words, logarithmic-designs already achieve the complexity of Haar in terms of entanglement, which we also call max-scrambling. This result leads to a generalization of the fast scrambling conjecture, that max-scrambling can be achieved by physical dynamics in time roughly linear in the number of degrees of freedom. This paper is an extended version of Phys. Rev. Lett.
120 (2018) 130502 [1].
Dynamically-coupled partial-waves in ρπ isospin-2 scattering from lattice QCD
Authors: Woss Antoni J. , Thomas Christopher E. , Dudek Jozef J. , Edwards Robert G. , Wilson David J. ,   for the Hadron Spectrum collaboration
Published: July 2018

Abstract

We present the first determination of ρπ scattering, incorporating dynamically-coupled partial-waves, using lattice QCD, a first-principles numerical approach to QCD. Considering the case of isospin-2 ρπ, we calculate partial-wave amplitudes with J ≤ 3 and determine the degree of dynamical mixing between the coupled S and D-wave channels with J

P
= 1+. The analysis makes use of the relationship between scattering amplitudes and the discrete spectrum of states in the finite volume lattice. Constraints on the scattering amplitudes are provided by over one hundred energy levels computed on two lattice volumes at various overall momenta and in several irreducible representations of the relevant symmetry groups. The spectra follow from variational analyses of matrices of correlations functions computed with large bases of meson-meson operators. Calculations are performed with degenerate light and strange quarks tuned to the physical strange quark mass so that m

π
∼ 700 MeV, ensuring that the ρ is stable against strong decay. This work demonstrates the successful application of techniques, opening the door to calculations of scattering processes that incorporate the effects of dynamically-coupled partial-waves, including those involving resonances or bound states.
Minimal models for dark matter and the muon g − 2 anomaly
Authors: Calibbi Lorenzo , Ziegler Robert , Zupan Jure
Published: July 2018

Abstract

We construct models with minimal field content that can simultaneously explain the muon g − 2 anomaly and give the correct dark matter relic abundance. These models fall into two general classes, whether or not the new fields couple to the Higgs. For the general structure of models without new Higgs couplings, we provide analytical expressions that only depend on the SU(2)
L
representation. These results allow to demonstrate that only few models in this class can simultaneously explain (g − 2)
μ
and account for the relic abundance. The experimental constraints and perturbativity considerations exclude all such models, apart from a few fine-tuned regions in the parameter space, with new states in the few 100 GeV range. In the models with new Higgs couplings, the new states can be parametrically heavier by a factor

$$ \sqrt{1/{y}_{\mu }} $$

1
/

y
μ

, with y

μ
the muon Yukawa coupling, resulting in masses for the new states in the TeV regime. At present these models are not well constrained experimentally, which we illustrate on two representative examples.
The Condition of Eruption Column Collapse: 1. A Reference Model Based on Analytical Solutions
Authors: Koyaguchi Takehiro , Suzuki Yujiro J.
Published: July 2018

The critical condition at which an eruption column collapses to generate a pyroclastic flow (the column collapse condition) generally depends on magmatic properties, crater shape (radius, depth, and opening angle), and the magma supply rate through the volcanic conduit. Here we propose a reference model for the column collapse condition based on analytical solutions of a one‐dimensional (1‐D) eruption column model and a quasi‐1‐D conduit flow model, which considers the effects of the crater. In the reference model, the column collapse condition is expressed by a single surface in a dimensionless parameter space related to magma discharge rate, magma supply rate (per unit area) at the crater base, and the ratio of the cross‐sectional areas at the top and base of the crater. The dependence of the column collapse condition on magmatic properties is included in the normalization factors of these dimensionless parameters. Previous criteria for the column collapse condition, which were based on the relationship between water content and magma discharge rate and that between magma discharge rate and crater radius, are regarded as part of, or a projection of, the present reference model. The reference model provides a framework for a comprehensive analysis of the diverse scenarios resulting in column collapse during explosive eruptions.
A Test of the Tropical 200‐ to 300‐hPa Warming Rate in Climate Models
Authors: McKitrick Ross , Christy John
Published: July 2018

Overall climate sensitivity to CO2 doubling in a general circulation model results from a complex system of parameterizations in combination with the underlying model structure. We refer to this as the model's major hypothesis, and we assume it to be testable. We explain four criteria that a valid test should meet: measurability, specificity, independence, and uniqueness. We argue that temperature change in the tropical 200‐ to 300‐hPa layer meets these criteria. Comparing modeled to observed trends over the past 60 years using a persistence‐robust variance estimator shows that all models warm more rapidly than observations and in the majority of individual cases the discrepancy is statistically significant. We argue that this provides informative evidence against the major hypothesis in most current climate models.
Space Weather in the Machine Learning Era
Authors: Camporeale Enrico , Wing Simon , Johnson Jay
Published: July 2018

Space Weather: A Multi-disciplinary Approach; Leiden, Netherlands, 25–29 September 2017
Alternating Trench Advance and Retreat: Insights From Paleozoic Magmatism in the Eastern Tianshan, Central Asian Orogenic Belt
Authors: Zhang Yunying , Sun Min , Yuan Chao , Long Xiaoping , Jiang Yingde , Li Pengfei , Huang Zongying , Du Long
Published: July 2018

Accretionary orogens generally involve trench advance and retreat, recognition of which is critical to understand the thermal evolution and geodynamics of the lithosphere. A systematic study has been conducted on the Silurian to Carboniferous volcanic rocks from the Dananhu‐Harlik arc in the Chinese eastern Tianshan. Three distinct episodes of volcanism have been recognized: Late Silurian normal andesite, high Sr/Y andesite and sanukitoid, Late Devonian bimodal high‐alumina basalt and dacite, and Early Carboniferous high‐alumina basalt. These magmatism experienced variable degrees of interaction between a depleted mantle wedge and subducting slab‐/sediment‐derived fluid/melt. Combining with previous geological data, we propose that the Dananhu‐Harlik arc was formed by the northward subduction of the North Tianshan Ocean (NTO), different from the traditional southward subduction of the Junggar Ocean, which was likely subducted northward to account for the East Junggar arc system. Temporal changes in Ce/Y of basalts and Ho/Yb of felsic rocks in the Dananhu‐Harlik arc imply that the arc crust underwent episodic thickening and thinning, which probably reflect the trench advance/retreat processes. The high Ce/Y and Ho/Yb ratios in the Late Ordovician to Devonian and Late Carboniferous correspond to two phases of trench advance. Conversely, the low Ce/Y and Ho/Yb ratios in the Early Carboniferous record a period of trench retreat, which caused the splitting of the Dananhu‐Harlik arc and formation of the Bogda back‐arc basin. Meanwhile, a southward subduction initiated along the south margin of the NTO, producing the Yamansu arc. Late Carboniferous bipolar subduction of the NTO led to its final closure.
Integrate‐and‐fire spiking neuron circuit exhibiting spike‐triggered adaptation through input current modulation with back gate effect
Authors: Kim T. , Oh M.H. , Kwon M.W. , Park B.‐G.
Published: July 2018

The authors present a spike‐triggered adaptive neuron circuit with input current modulation. Unlike adaptive neuron circuits where adaptation is realised by leakage modulation, the circuit presented in this Letter modulates the input current to membrane capacitor. Therefore, it is possible to reduce extra power consumption originating from increased leakage. Threshold voltage modulation of silicon on insulator (SOI) MOSFET by back gate effect is used to change the amount of injected current for the same input voltage. Through this method, the circuit in this work consumed 25.9% less power than the one modulating leakage.
Digital linear GFSK demodulator for IoT devices
Authors: Aldana‐Lopez Rodrigo , Valencia‐Velasco Jose , Longoria‐Gandara Omar , Pizano‐Escalante Luis
Published: July 2018

Companies and developers of emerging Internet‐of‐Things (IoT) technologies consider Bluetooth low‐energy (BLE) standard as a strong candidate to be the backbone of wireless IoT devices and support their low‐power requirements. Likewise, the BLE has adopted Gaussian frequency shift‐keying (GFSK) signalling due to its power and spectral efficiencies, which are the most fundamental performance criteria for modulation schemes. For this reason, it is worthwhile to research and develop transceivers that maintain these advantages and achieve a low‐complexity implementation for the digital modulator and demodulator. Different techniques have been proposed for this purpose, such as hardware usage optimisation, efficient pulse shaping and decomposition of the signal. This study presents a novel linear GFSK demodulator which has the following attractive advantages: low complexity, near‐optimal performance in the additive white Gaussian noise channel and the possibility of operating with different GFSK modulators (with a nominal modulation index of 0.5) so it could be applied in BLE devices. In addition, the theoretical error probability is obtained and compared with simulation results.
Non‐coherent transmission for two‐way relaying systems with relay having large‐scale antennas
Authors: Li Guo , Gong Feng‐Kui , Zhang Hang , Chen Xiang
Published: July 2018

Without channel state information at the users and relay node, a non‐coherent transmission scheme for the two‐way relaying systems is investigated in this study. At the relay node, the authors first detect the uplink data with non‐coherent maximum likelihood receiver by fully utilising the large receiving freedom of relay's large‐scale antennas. Channel estimations can also be obtained by treating the detected uplink data as pilot symbols. Then, the relay node forwards the detected data by using beamforming. To assure the reliable detection of the users' transmitted symbols non‐coherently, the authors propose a transmitting constellation design with the idea of searching an optimal angle for rotating one user's constellation. Specially, for M‐PSK constellations, they derive the optimal rotation angle, which is highly consistent with the exhaustive searching results. In addition, they also analyse the lower bound of channel estimations in terms of normalised mean square error (NMSE). From simulation results, the proposed non‐coherent transmission scheme achieves considerable error performance, and the NMSE lower bounds of channel estimations are also tight when the number of relay's antennas approaches to be large.
End‐to‐end visual grounding via region proposal networks and bilinear pooling
Authors: Xiang Chenchao , Yu Zhou , Zhu Suguo , Yu Jun , Yang Xiaokang
Published: July 2018

Phrase‐based visual grounding aims to localise the object in the image referred by a textual query phrase. Most existing approaches adopt a two‐stage mechanism to address this problem: first, an off‐the‐shelf proposal generation model is adopted to extract region‐based visual features, and then a deep model is designed to score the proposals based on the query phrase and extracted visual features. In contrast to that, the authors design an end‐to‐end approach to tackle the visual grounding problem in this study. They use a region proposal network to generate object proposals and the corresponding visual features simultaneously, and multi‐modal factorised bilinear pooling model to fuse the multi‐modal features effectively. After that, two novel losses are posed on top of the multi‐modal features to rank and refine the proposals, respectively. To verify the effectiveness of the proposed approach, the authors conduct experiments on three real‐world visual grounding datasets, namely Flickr‐30k Entities, ReferItGame and RefCOCO. The experimental results demonstrate the significant superiority of the proposed method over the existing state‐of‐the‐arts.
Regularised transfer learning for hyperspectral image classification
Authors: Shi Qian , Zhang Yipeng , Liu Xiaoping , Zhao Kefei
Published: July 2018

This study presents a transfer learning method for addressing the insufficient sample problem in hyperspectral image classification. In order to find common feature representation for both the source domain and target domain, we introduce a regularisation based on Bregman divergence into the objective function of the subspace learning algorithm, which can minimise the Bregman divergence between the distribution of training samples in the source domain and the test samples in the target domain. Hyperspectral image with biased sampling is used to evaluate the effectiveness of the proposed method. The results show that the proposed method can achieve a higher classification accuracy than traditional subspace learning methods under the condition of biased sampling.
Toward online multi‐period power dispatch with AC constraints and renewable energy
Authors: Bie Pei , Chiang Hsiao‐Dong , Zhang Buhan , Zhou Ning
Published: July 2018

In this study, a comprehensive online multi‐period power dispatch formulation that takes AC constraints, renewable energy, and ramping constraints into account is proposed. The AC power flow equations, voltage limits, and thermal limits are respected to ensure the obtained solution causes no static violation while guaranteeing transfer capability. A four‐stage solution methodology is proposed to solve the non‐linear constrained optimisation problem in which the thermal limit constraints are equivalently represented by active‐set‐based constraints in the third stage, and an adaptive homotopy‐enhanced primal‐dual interior point method (PDIPM) in solving power dispatch problem is presented in the fourth stage to reliably and efficiently obtain the solution. This solution methodology enhances both the robustness and speed of the PDIPM. The proposed four‐stage solution methodology has been evaluated on several testing systems, ranging from a 30‐bus system to a 3012‐bus system with four time periods, with promising results.
Control design for stable connected cruise control systems to enhance safety and traffic efficiency
Authors: Qin Yanyan , Wang Hao , Ran Bin
Published: July 2018

To enhance safety and traffic efficiency, stability of a mixed human and connected cruise control (CCC) system is studied. The authors consider individual vehicle platoons, in which the tail CCC vehicle receives feedback from multiple human‐driven vehicles ahead via vehicle‐to‐vehicle communications, with the objective of stability analysis and feedback control design. To deal with this, the transfer function theory is used. Simulations are also performed to evaluate impacts of the mixed human and CCC system on safety and traffic efficiency. Results show that the output bounds of the CCC feedback coefficients can be appropriately designed to keep local individual vehicle platoons stable for all possible vehicle speeds. The feedback coefficient has a larger design range and the required lower bound value decreases as the feedback length increases. Additionally, the system design would improve traffic safety and efficiency even at lower CCC vehicle penetration rates.
HVDC transmission for access to off‐shore renewable energy: a review of technology and fault detection techniques
Authors: Mitra Bhaskar , Chowdhury Badrul , Manjrekar Madhav
Published: July 2018

The ever‐increasing demand for electric power has partially been met with access to offshore renewable energy, such as wind and tidal energy. With the development in power electronics, high‐voltage direct current (HVDC) transmission is taking over as the primary choice for connecting off‐shore generation to on‐shore grids. Voltage source converter (VSC)‐based HVDC is set to become the backbone of the multi‐terminal DC grids replacing the conventional line commutated converter networks. VSC‐HVDC networks offer the flexibility for HVDC grids to be connected as conventional AC grids in a meshed network. Advancement of technology has led to the development of the modular multilevel converter which has higher efficiency compared to the two‐level VSC configurations. They are gradually becoming a popular choice. Although VSC‐based grids offer a varied range of advantages, it is highly vulnerable to DC faults. Many designs of breakers have been patented over the years and various means have been proposed for their control. This study aims to review the available designs of HVDC terminals, the available protection devices and the protection and control methods for HVDC breakers. By comparing the state‐of‐the‐art technologies that are currently available, this study aims to address the research issues and the additional research and development work that needs to be done.
Conditional generative adversarial network for gene expression inference
Authors: Wang Xiaoqian , Ghasedi Dizaji Kamran , Huang Heng
Published: July 2018

Motivation

The rapid progress of gene expression profiling has facilitated the prosperity of recent biological studies in various fields, where gene expression data characterizes various cell conditions and regulatory mechanisms under different experimental circumstances. Despite the widespread application of gene expression profiling and advances in high-throughput technologies, profiling in genome-wide level is still expensive and difficult. Previous studies found that high correlation exists in the expression pattern of different genes, such that a small subset of genes can be informative to approximately describe the entire transcriptome. In the Library of Integrated Network-based Cell-Signature program, a set of ∼1000 landmark genes have been identified that contain ∼80% information of the whole genome and can be used to predict the expression of remaining genes. For a cost-effective profiling strategy, traditional methods measure the profiles of landmark genes and then infer the expression of other target genes via linear models. However, linear models do not have the capacity to capture the non-linear associations in gene regulatory networks.

Results

As a flexible model with high representative power, deep learning models provide an alternate to interpret the complex relation among genes. In this paper, we propose a deep learning architecture for the inference of target gene expression profiles. We construct a novel conditional generative adversarial network by incorporating both the adversarial and ℓ1-norm loss terms in our model. Unlike the smooth and blurry predictions resulted by mean squared error objective, the coupled adversarial and ℓ1-norm loss function leads to more accurate and sharp predictions. We validate our method under two different settings and find consistent and significant improvements over all the comparing methods.
Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks
Authors: Kobayashi Naohiro , Hattori Yoshikazu , Nagata Takashi , Shinya Shoko , Güntert Peter , Kojima Chojiro , Fujiwara Toshimichi
Published: July 2018

Motivation

Multi-dimensional NMR spectra are generally used for NMR signal assignment and structure analysis. There are several programs that can achieve highly automated NMR signal assignments and structure analysis. On the other hand, NMR spectra tend to have a large number of noise peaks even for data acquired with good sample and machine conditions, and it is still difficult to eliminate these noise peaks.

Results

We have developed a method to eliminate noise peaks using convolutional neural networks, implemented in the program package Filt_Robot. The filtering accuracy of Filt_Robot was around 90–95% when applied to 2D and 3D NMR spectra, and the numbers of resulting non-noise peaks were close to those in corresponding manually prepared peaks lists. The filtering can strongly enhance automated NMR spectra analysis.

Availability and implementation

The full package of the program, documents and example data are available from http://bmrbdep.pdbj.org/en/nmr_tool_box/Filt_Robot.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fast characterization of segmental duplications in genome assemblies
Authors: Numanagić Ibrahim , Gökkaya Alim S , Zhang Lillian , Berger Bonnie , Alkan Can , Hach Faraz
Published: July 2018

Motivation

Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common cause of genomic structural variation and several are associated with diseases of genomic origin including schizophrenia and autism. Despite their functional importance, SDs present one of the major hurdles for de novo genome assembly due to the ambiguity they cause in building and traversing both state-of-the-art overlap-layout-consensus and de Bruijn graphs. This causes SD regions to be misassembled, collapsed into a unique representation, or completely missing from assembled reference genomes for various organisms. In turn, this missing or incorrect information limits our ability to fully understand the evolution and the architecture of the genomes. Despite the essential need to accurately characterize SDs in assemblies, there has been only one tool that was developed for this purpose, called Whole-Genome Assembly Comparison (WGAC); its primary goal is SD detection. WGAC is comprised of several steps that employ different tools and custom scripts, which makes this strategy difficult and time consuming to use. Thus there is still a need for algorithms to characterize within-assembly SDs quickly, accurately, and in a user friendly manner.

Results

Here we introduce SEgmental Duplication Evaluation Framework (SEDEF) to rapidly detect SDs through sophisticated filtering strategies based on Jaccard similarity and local chaining. We show that SEDEF accurately detects SDs while maintaining substantial speed up over WGAC that translates into practical run times of minutes instead of weeks. Notably, our algorithm captures up to 25% ‘pairwise error’ between segments, whereas previous studies focused on only 10%, allowing us to more deeply track the evolutionary history of the genome.

Availability and implementation

SEDEF is available at https://github.com/vpc-ccg/sedef.
Towards an accurate and efficient heuristic for species/gene tree co-estimation
Authors: Wang Yaxuan , Nakhleh Luay
Published: July 2018

Motivation

Species and gene trees represent how species and individual loci within their genomes evolve from their most recent common ancestors. These trees are central to addressing several questions in biology relating to, among other issues, species conservation, trait evolution and gene function. Consequently, their accurate inference from genomic data is a major endeavor. One approach to their inference is to co-estimate species and gene trees from genome-wide data. Indeed, Bayesian methods based on this approach already exist. However, these methods are very slow, limiting their applicability to datasets with small numbers of taxa. The more commonly used approach is to first infer gene trees individually, and then use gene tree estimates to infer the species tree. Methods in this category rely significantly on the accuracy of the gene trees which is often not high when the dataset includes closely related species.

Results

In this work, we introduce a simple, yet effective, iterative method for co-estimating gene and species trees from sequence data of multiple, unlinked loci. In every iteration, the method estimates a species tree, uses it as a generative process to simulate a collection of gene trees, and then selects gene trees for the individual loci from among the simulated gene trees by making use of the sequence data. We demonstrate the accuracy and efficiency of our method on simulated as well as biological data, and compare them to those of existing competing methods.

Availability and implementation

The method has been implemented in PhyloNet, which is publicly available at http://bioinfocs.rice.edu/phylonet.