bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of hydrogen peroxide concentration on the partial oxidation of methane to methanol in an atmospheric dielectric barrier discharge
Authors: Qian Muyang , Li Gui , Kang Jinsong , Liu Sanqiu , Yuan Dingkun , Ren Chunsheng , Zhang Jialiang , Wang Dezhen
Published: December 2018

It was proved that atmospheric non-equilibrium plasma can be deemed as “reaction carrier”, and is an effective method of partial oxidation of methane to methanol and other higher hydrocarbons. In this paper, hydrogen peroxide vapor is selected as oxygen-containing oxidizer and used to activate and convert methane into methanol in an atmospheric dielectric barrier discharge. A detailed axisymmetric 2D fluid model in CH4/H2O/H2O2 gas mixture is developed, with an emphasis on gas-phase plasma chemistry for partial oxidation of methane and methanol formation. Especially, the effect of hydrogen peroxide concentration on the conversion of methane to methanol is studied. The spatial and temporal distributions of various plasma species are shown as a function of hydrogen peroxide concentration. In addition, the main plasma species and reaction pathways governing the production and loss of CH3OH and OH are determined. It is shown that the increasing hydrogen peroxide concentration results in increase of OH and CH3OH production. Hydroxyl appears to play a significant role during the process of methanol synthesis, which is primarily produced by electron-impact dissociation of H2O2 and H2O molecules.
Exact normalized eigenfunctions for general deformed Hulthén potentials
Authors: Hall Richard L. , Saad Nasser , Sen K. D.
Published: December 2018

The exact solutions of Schrödinger’s equation with the deformed Hulthén potential Vq(x) = −μ e−δ x/(1 − q e−δ x), δ, μ, q > 0 are given, along with a closed-form formula for the normalization constants of the eigenfunctions for arbitrary q > 0. The Crum-Darboux transformation is then used to derive the corresponding exact solutions for the extended Hulthén potentials V(x)=−μ e−δ x/(1−q e−δ x)+q j(j+1) e−δ x/(1−q e−δ x)2,j=0,1,2,…. A general formula for the new normalization condition is also provided.
Enhanced performance of a pulsed neutron detector by the plastic scintillator with a photonic crystal
Authors: Ruan Jinlu , Ouyang Xiaoping , Liu Bo , Chen Liang , Xu Mengxuan , Zhu Zhichao , Zhang Zhongbing , He Shiyi
Published: December 2018

A detector based on the plastic scintillator film with large-area photonic crystals has been designed and demonstrated for measuring pulsed neutron flux. Compared with the reference detector, the neutron sensitivity and the gamma sensitivity of the detector using the scintillator film with photonic crystals were enhanced by more than 20%, which is attributed to the improved light extraction efficiency and the controllable angular profile of scintillation light by the photonic crystal. The application of the photonic crystals is beneficial to the improvement of the signal-to-noise ratio of the detector in the calibration experiment, thus expanding the lower limit of the measurable neutron flux without sacrificing the ratio of the neutron sensitivity to the gamma sensitivity. This research indicates that photonic crystals play an important role in the fields where scintillation photons need to be extracted and collected as many as possible.
Fluoropolymer-diluted small molecule organic semiconductors with extreme thermal stability
Authors: Price Jared S. , Wang Baomin , Kim Taehwan , Grede Alex J. , Sandoval Jesse M. , Xie Renxuan , Shen Yufei , Adams Dillon R. , Eller Michael J. , Sokolov Anatoliy , Mukhopadhyay Sukrit , Trefonas Peter , Gomez Enrique D. , Schweikert Emile A. , Giebink Noel C.
Published: December 2018

Thermal stability is important for many thin film organic semiconductor devices but is challenging due to their weakly Van der Waals-bonded nature. Here, we show that diluting common small molecule hole transport materials through co-evaporation with the amorphous fluoropolymer Teflon AF leads to a dramatic improvement in their thermal and morphological stability without sacrificing electrical performance. Blend films with 25 vol. % Teflon decrease the drive voltage of single layer hole-only devices by more than 30% and dramatically increase their operating temperature limit to over 250 °C. The stability improvement appears to result from a nanoscale network of Teflon chains that repolymerize throughout the blend film following evaporation and inhibit gross movement of the organic semiconductor molecules. These results open up a pathway to stabilize the morphology of small molecule organic semiconductors and point to a more general opportunity to exploit semiconductor dilution to systematically vary thermal, optical, and other material properties without compromising electrical transport.
Goodness of fit testing in dynamic single-molecule force spectroscopy
Authors: Bergues-Pupo Ana E. , Goktas Melis , Tunn Isabell , Lopez-Garcia Patricia , Vila Verde Ana , Blank Kerstin G. , Valleriani Angelo
Published: December 2018

Dynamic single-molecule force spectroscopy (SMFS) is a powerful method to characterize the mechanical stability of biomolecules. We address the problem that the standard manner of reporting the extracted energy landscape parameters does not reveal the intrinsic statistical errors associated with them. This problem becomes particularly relevant when SMFS is used to compare two or more different molecular systems. Here, we propose two methods that allow for a straightforward test of statistical significance. We illustrate the power of the methods by applying them to the experimental results obtained for three dimeric coiled coils of different lengths. Both methods are general and may be applied to any problem involving the fit of models with two correlated parameters.
Exact solution to Lippmann-Schwinger equation for a circular billiard
Authors: Maioli A. C. , Schmidt Alexandre G. M.
Published: December 2018

We present an exact solution to the Lippmann-Schwinger equation for a two-dimensional circular billiard. After diagonalizing an integral operator whose kernel is a zeroth order Hankel function of first kind, we use its eigenfunctions and eigenvalues to obtain in a straightforward way the exact wavefunctions of the referred Lippmann-Schwinger equation.
Electronic spectroscopy of methyl vinyl ketone oxide: A four-carbon unsaturated Criegee intermediate from isoprene ozonolysis
Authors: Vansco Michael F. , Marchetti Barbara , Lester Marsha I.
Published: December 2018

Ozonolysis of isoprene, one of the most abundant volatile organic compounds in the atmosphere, proceeds through methyl vinyl ketone oxide (MVK-oxide), methacrolein oxide, and formaldehyde oxide (CH2OO) Criegee intermediates. The present study focuses on MVK-oxide, a four-carbon unsaturated carbonyl oxide intermediate, using vacuum ultraviolet photoionization at 118 nm and UV-visible induced depletion of the m/z = 86 mass channel to characterize its first π* ← π electronic transition. The electronic spectrum is broad and unstructured with its peak at 388 nm (3.2 eV). The MVK-oxide spectrum is shifted to a significantly longer wavelength than CH2OO and alkyl-substituted Criegee intermediates studied previously due to extended conjugation across the vinyl and carbonyl oxide groups. Electronic excitation results in rapid dissociation at λ ≤ 430 nm to methyl vinyl ketone and O 1D products, the latter detected by 2 + 1 resonance enhanced multiphoton ionization using velocity map imaging. Complementary electronic structure calculations (CASPT2(12,10)/AVDZ) predict two π* ← π transitions with significant oscillator strength for each of the four conformers of MVK-oxide with vertical excitation energies (and corresponding wavelengths) in the 3.1-3.6 eV (350-400 nm) and 4.5-5.5 eV (220-280 nm) regions. The computed electronic absorption profile of MVK-oxide, based on a Wigner distribution of ground state configurations and summed over the four conformers, is predicted to peak at 397 nm. UV-visible spectroscopy on the first π* ← π transition is shown by a combination of experiment and theory to provide a sensitive method for detection of the MVK-oxide Criegee intermediate that will enable further studies of its photochemistry and unimolecular and bimolecular reaction dynamics.
Chemical bonding in initial building blocks of semiconductors: Geometrical structures and optical absorption spectra of isolated CdSe2+ and Cd2Se2+ species
Authors: Jäger Marc , Shayeghi Armin , Klippenstein Viktor , Johnston Roy L. , Schäfer Rolf
Published: December 2018

We present the first experimental optical absorption spectra of isolated CdSe2+ and Cd2Se2+ species in the photon energy range ℏω = 1.9–4.9 eV. We probe the optical response by measuring photodissociation cross sections and combine our results with time-dependent density functional theory and equation-of-motion coupled cluster calculations. Structural candidates for the time-dependent excited state calculations are generated by a density functional theory based genetic algorithm as a global geometry optimization tool. This approach allows us to determine the cluster geometries present in our molecular beams by a comparison of experimental spectra with theoretical predictions for putative global minimum candidates. For CdSe2+, an excellent agreement between the global minimum and the experimental results is presented. We identify the global minimum geometry of Cd2Se2+ as a trapezium, which is built up of a neutral Se2 and a cationic Cd2+ unit, in contrast to what was previously proposed. We find an excellent overall agreement between experimental spectra and excited state calculations. We further study the influence of total and partial charges on the optical and geometric properties of Cd2Se2 and compare our findings to CdSe quantum dots and to bulk CdSe.
Strain-induced changes in AlGaN/GaN two-dimensional electron gas structures with low surface state densities
Authors: Blanton Eric W. , Siegel Gene , Prusnick Timothy A. , Glavin Nicholas R. , Snure Michael
Published: December 2018

We report on the effects of applied external strain on AlGaN/GaN two dimensional electron gas structures exhibiting a negative strain dependence of the sheet carrier density (ns). Flexible AlGaN/GaN heterojunctions, grown on two-dimensional boron nitride (BN)-on-sapphire templates, were released from the substrate via strain-induced separation at the weak BN van der Waals interface and then transferred to flexible substrates. By releasing the AlGaN/GaN layer from the substrate, residual strain was removed which allowed for isolation and study of the effects of the externally applied strain. By bending samples, uniaxial strain up to 0.15% was applied as measured by the shifts in the GaN E2H Raman mode. Hall effect measurements revealed a 2.5% decrease in ns with 0.11% applied tensile strain, which is contrary to the increase expected from the piezoelectric effect. The observed decrease in ns is attributed to a relatively large increase in the AlGaN surface barrier height. This effect, which is rarely reported, is observable due to a low surface state density (2.2 × 1012 cm−2 eV–1) in the samples. Illumination was found to dramatically alter the ns-strain dependence, an effect potentially related to detrapping of electrons in the GaN buffer.
Observational Studies That Seek to Emulate a Randomized Trial of Screening to Reduce the Incidence of Cancer: Do They Address the Question to Which We’d Like to Have an Answer?
Authors: Weiss Noel S
Published: December 2018

Some forms of cancer screening have the potential to reduce cancer incidence, if the screening modality can identify not only a malignancy but a treatable premalignant condition (such as a colon polyp) as well. Cohort studies of the efficacy of these forms of screening in reducing the incidence of cancer face many challenges, notably the difficulty in distinguishing whether a test performed in a given individual was screening or diagnostic in nature. Downward bias in the estimated efficacy of screening resulting from misclassification of test indication is a particular problem in cohort studies that seek to gauge cancer incidence beginning at the time of screening (and a corresponding point in time among unscreened persons). The downward bias is accentuated in those cohort studies that have sought to mimic the “intention-to-treat” analytical approach used in randomized trials, in which initially unscreened persons are retained in this category even if later they themselves undergo screening.
Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps
Authors: Carron L , Morlot J B , Matthys V , Lesne A , Mozziconacci J
Published: December 2018

Motivation

Genome-wide chromosomal contact maps are widely used to uncover the 3D organization of genomes. They rely on collecting millions of contacting pairs of genomic loci. Contacts at short range are usually well measured in experiments, while there is a lot of missing information about long-range contacts.

Results

We propose to use the sparse information contained in raw contact maps to infer high-confidence contact counts between all pairs of loci. Our algorithmic procedure, Boost-HiC, enables the detection of Hi-C patterns such as chromosomal compartments at a resolution that would be otherwise only attainable by sequencing a hundred times deeper the experimental Hi-C library. Boost-HiC can also be used to compare contact maps at an improved resolution.

Availability and implementation

Boost-HiC is available at https://github.com/LeopoldC/Boost-HiC.

Supplementary information

Supplementary data are available at Bioinformatics online.
Human Immunodeficiency Virus (HIV) Viral Suppression After Transition From Having No Healthcare Coverage and Relying on Ryan White HIV/AIDS Program Support to Medicaid or Private Health Insurance
Authors: Raifman Julia , Althoff Keri , Rebeiro Peter F , Mathews W Christopher , Cheever Laura W , Hauck Heather , Aberg Judith A , Gebo Kelly A , Moore Richard , Berry Stephen A ,   The HIV Research Network
Published: December 2018

Among 1942 persons with human immunodeficiency virus (HIV) without healthcare coverage in 2012–2015, transitioning to Medicaid (adjusted prevalence ratio, 0.95 [0.87, 1.04]) or to private health insurance (1.04 [0.95, 1.13]) was not associated with a change in consistent HIV viral suppression compared to continued reliance on the Ryan White HIV/AIDS Program.
A Web Browser Fingerprinting Method Based on the Web Audio API
Authors: Queiroz Jordan S , Feitosa Eduardo L
Published: December 2018

Web Browser Fingerprinting is a process in which the users are, with high likelihood, uniquely identified by the extracted features from their devices, generating an identifier key (fingerprint). Although it can be used for malicious purposes, especially regarding privacy invasion, Web Browser Fingerprinting can also be used to enhance security (e.g. as a factor in two-factor authentication). This paper investigates the use of Web Audio API as a Web Browser Fingerprinting method capable of identifying the devices. The idea is to prove or not if audio can provide features capable to identify users and devices. Our initial results show that the proposed method is capable of identifying the device’s class, based on features like device’s type, web browser’s version and rendering engine.
Results of surgical management of infective endocarditis associated with Staphylococcus aureus
Authors: Suzuki Kota , Yoshioka Daisuke , Toda Koichi , Yokoyama Jun-Ya , Samura Takaaki , Miyagawa Shigeru , Yoshikawa Yasushi , Hata Hiroki , Takano Hiroshi , Matsumiya Goro , Sakaguchi Taichi , Fukuda Hirotsugu ,   Osaka Cardiovascular Research (OSCAR) Study Group, Sawa Yoshiki
Published: December 2018

OBJECTIVES

Staphylococcus aureus (SA) is a leading cause of infective endocarditis (IE), and such cases are on the rise. Our objective was to evaluate the clinical outcomes of surgical intervention in patients with SA-associated IE and to identify the factors associated with outcomes.

METHODS

Between 2009 and 2017, 585 patients underwent valve surgery for definitive left-sided IE at 14 affiliated hospitals. Their medical records were retrospectively reviewed, and the preoperative variables and clinical results of patients with (n = 117) or without SA infection (n = 468) were compared.

RESULTS

The SA group had a more critical preoperative condition with higher rates of chronic haemodialysis, preoperative embolic events and preoperative inflammation levels, as well as worse renal function. In-hospital mortality was 20% and 7% in the patients with or without SA infection, respectively. The overall survival rate at 1 year and 5 years was 72% and 62% in the SA group, and 88% and 81% in the non-SA group, respectively (P < 0.001). The Cox hazard analysis revealed that methicillin-resistant SA infection was an independent risk factor for overall mortality in the SA group. The rate of freedom from recurrence of endocarditis at 1 year and 5 years was 95% and 90% in the SA group and 96% and 92% in the non-SA group, respectively (P = 0.43).

CONCLUSIONS

The short- and mid-term outcomes after valve surgery for active IE in patients with SA are still challenging. Methicillin-resistant SA infection is an independent predictor of mid-term mortality.
Open descending aortic replacement after Thoraflex™ hybrid graft implantation
Authors: Fujikawa Takuya , Ho Jacky Y K , Wong Henry M K , Wong Randolph H L
Published: December 2018

The Thoraflex™ device is a composite 4-branched graft with a distal endovascular stent that allows either a one-stage treatment or an endovascular second-stage treatment of multisegment aortic pathologies. Reports on open second-stage treatment after the Thoraflex™ device implantation are sparse especially regarding the technical aspects. We described our surgical procedure of open second-stage descending thoracic aortic replacement after Thoraflex™ implantation with a special focus on the anastomosis technique to a stent graft. We found excellent haemostasis and a good postoperative outcome using our approach of the stent graft to graft anastomosis.
Occupational Physical Activity and Coronary Heart Disease in Women’s Health Initiative Observational Study
Authors: Wang Conglong , De Roos Anneclaire J , Fujishiro Kaori , Allison Matthew A , Wallace Robert , Seguin Rebecca A , Nassir Rami , Michael Yvonne L
Published: December 2018

Background

Women comprise nearly half of the labor force in our society, but the impact of the occupational psychical activity on women’s heart health in later life was unclear. We conducted a case-cohort study to assess the association of occupational physical activity (OPA), alone and jointly with leisure-time physical activity (LTPA) and risk of coronary heart disease (CHD).

Methods

We included women enrolled in Women’s Health Initiative Observational Study who provided an occupational history at baseline and were followed until 2013 for the first occurrence of myocardial infarction or death from CHD (mean age ± SD = 63.4 ± 7.2). A total of 5,243 women free of CHD at baseline were randomly selected into a subcohort and 3,421 CHD events were adjudicated during follow-up. Through linkage of Standard Occupational Classification codes to the Occupational Information Network, we assessed cumulative and most recent exposure of OPA. LTPA was assessed through Women’s Health Initiative’s physical activity questionnaire. Weighted Cox proportional hazard models were used to evaluate CHD risk.

Results

After adjustment for demographic and socioeconomic factors, levels of OPA were not associated with CHD risk. Compared with women with low OPA and high LTPA, women with moderate to high cumulative OPA and low LTPA had relative high CHD risk (hazard ratio [HR]: 1.54, 95% confidence interval [CI]: 1.26, 1.88 for moderate OPA and HR: 1.46. 95% CI: 1.20, 1.78 for high OPA).

Discussion

Results from this study suggest no overall association between lifetime OPA and CHD risk in women, but the impact of OPA varies by LTPA levels.
Universal Influenza Virus Vaccines That Target the Conserved Hemagglutinin Stalk and Conserved Sites in the Head Domain
Authors: Krammer Florian , Palese Peter
Published: December 2018

Due to limitations of current influenza virus vaccines, new vaccines that mediate broad protection and show high efficacy against seasonal and pandemic viruses are urgently needed. The conserved stalk of the viral hemagglutinin has been identified as potential target antigen for this new generation of vaccines. A vaccination strategy based on chimeric hemagglutinin (cHA), which refocuses the immune response toward the stalk domain and the conserved neuraminidase, is currently being tested in clinical trials. Here we discuss how to improve the cHA antigens to generate vaccine candidates that both induce a broad antistalk response and target conserved immunosubdominant epitopes in the head domain of the hemagglutinin. These novel constructs, termed mosaic hemagglutinins, should provide enhanced protection and should be tested in clinical trials to assess their improved potential as universal influenza virus vaccine candidates.
Gastroscopy Should Come Before Colonoscopy Using CO2 Insufflation in Same Day Bidirectional Endoscopies: A Randomized Controlled Trial
Authors: Jowhari Fahd , Hookey Lawrence
Published: December 2018

Background and Aims

Same day bidirectional endoscopies (esophagogastroduodenoscopies [EGD]s and colonoscopies) are routinely performed. However, the best sequence of procedures is unknown, as is whether the use of carbon dioxide (CO2) affects the preferred sequence of procedures. This study aims to determine the preferred sequence of procedures and choice of insufflation gas (air or CO2) in patients undergoing same day bidirectional endoscopies.

Methods

Two hundred adults with a clinical indication for same day bidirectional endoscopies were randomized equally into four groups: A1 (EGD first, CO2 as insufflator); A2 (EGD first, air as insufflator); B1 (colonoscopy first, CO2 as insufflator); and B2 (colonoscopy first, air as insufflator). All procedures were performed with conscious sedation (Midazolam/Fentanyl). The primary outcome was patients’ overall comfort/satisfaction with the procedures and sedation received, as assessed by questionnaires and validated scoring scales (Nurse-Assessed Patient Comfort Score [NAPCOMS], La Crosse [WI]) collected during the procedures, before discharge, and on day 7 postprocedure.

Results

Two hundred patients were randomized, with data available for 186. Mean Midazolam dose between groups was significantly less in the EGD first groups (P=0.01). During the procedures, no differences were found in patients’ comfort as per the nurse reported NAPCOMS scores (P=0.19) or the Lacrosse (WI) endoscopy scores (P=0.05). On postprocedure days 0 and 7, no differences were found in the patients’ reported Lacrosse (WI) scores, nausea, sore throat, dizziness, satisfaction with sedation or overall level of procedural satisfaction (P>0.05 for each). However, bloating and discomfort were significantly lower in the CO2 arms (P<0.001).

Conclusions

This randomized controlled trial using validated patient comfort scoring assessments for same day bidirectional endoscopies demonstrated that the sequence of procedures affects the sedation used but does not affect overall patient comfort or satisfaction. Lesser sedation is needed in the EGD first group, and less postprocedural abdominal pain/discomfort and bloating is seen with CO2 insufflation.
Targeting IDH1-Mutated Malignancies with NRF2 Blockade
Authors: Liu Yang , Lu Yanxin , Celiku Orieta , Li Aiguo , Wu Qixin , Zhou Yiqiang , Yang Chunzhang
Published: December 2018

Background

Neomorphic IDH1 mutations disrupt the redox balance by promoting reactive oxygen species (ROS) production. However, the mechanism by which IDH1-mutant cells maintain ROS homeostasis remains elusive. It is also not known whether reprogrammed ROS homeostasis establishes targetable vulnerability in IDH1-mutated cancers.

Methods

We investigated ROS homeostasis in wild-type (GSC827, GSC923, GSC627, and GSC711) and IDH1-mutated cells (IDH1R132C- and IDH1R132H-transduced U87, U251; MGG152, and TS603 cells). We analyzed the stability and transcriptional activity of NRF2 in IDH1-mutated cells. The oxidative DNA damage was analyzed using NRF2-targeting small interfering RNA. Moreover, we evaluated the effect of the NRF2 inhibitor brusatol in an IDH1-mutated subcutaneous xenograft nude mouse model (control group, n = 5; brusatol-treated group, n = 6). All statistical tests were two-sided.

Results

We showed that IDH1-mutated cells develop a dependency on the NRF2 antioxidative pathway. Genetic or pharmacologic blockade of NRF2 not only disrupted ROS homeostasis (mean [SD] ROS levels increased by 317 [42.1]%, P = .001, in IDH1R132C and by 286. 5 [48.7]%, P = .003, in IDH1R132H cells) but also enhanced oxidative DNA damage and decreased proliferation of IDH1-mutated cells. Brusatol selectively suppressed IDH1-mutated cancer progression in vivo (mean [SD] final tumor volume was 761.6 [391.6] mm3 in the control and 246.2 [215] mm3 in the brusatol-treated group, P = .02).

Conclusions

IDH1 mutation reprograms ROS homeostasis in cancer cells, which leads to dependency on the NRF2 antioxidant pathway for ROS scavenging. NRF2 blockade might be a novel therapeutic approach to treat malignancies with IDH1 mutation.
Personalized Risk-Stratified Cancer Follow-Up Care: Its Potential for Healthier Survivors, Happier Clinicians, and Lower Costs
Authors: Mayer Deborah K , Alfano Catherine M
Published: December 2018

The growth in the number of cancer survivors in the face of projected health-care workforce shortages will challenge the US health-care system in delivering follow-up care. New methods of delivering follow-up care are needed that address the ongoing needs of survivors without overwhelming already overflowing oncology clinics or shuttling all follow-up patients to primary care providers. One potential solution, proposed for over a decade, lies in adopting a personalized approach to care in which survivors are triaged or risk-stratified to distinct care pathways based on the complexity of their needs and the types of providers their care requires. Although other approaches may emerge, we advocate for development, testing, and implementation of a risk-stratified approach as a means to address this problem. This commentary reviews what is needed to shift to a risk-stratified approach in delivering survivorship care in the United States.
Markers of Immune Activation and Inflammation, and Non-Hodgkin Lymphoma: A Meta-Analysis of Prospective Studies
Authors: Makgoeng Solomon B , Bolanos Rachel S , Jeon Christie Y , Weiss Robert E , Arah Onyebuchi A , Breen Elizabeth C , Martínez-Maza Otoniel , Hussain Shehnaz K
Published: December 2018

Background

Chronic inflammation and immune activation are reported to play a key role in the etiology of non-Hodgkin lymphoma (NHL). We conducted a meta-analysis on the associations between prediagnosis circulating levels of immune stimulatory markers, interleukin 6 (IL-6), IL-10, tumor necrosis factor α (TNF-α), CXCL13, soluble CD23 (sCD23), sCD27, sCD30, and the risk of NHL.

Methods

Relevant studies were identified from PubMed, EMBASE, and Web of Science up to January 1, 2017. We calculated summary odds ratio (OR) estimates for the association between one natural log increase in concentration of each biomarker and NHL using random-effects models for NHL as a composite outcome and for several histological subtypes of NHL.

Results

Seventeen nested case control studies were included. Elevated levels of several biomarkers were more strongly associated with increased odds of NHL: TNF-α, OR = 1.18 (95% confidence interval [CI] = 1.04 to 1.34); CXCL13, OR = 1.47 (95% CI = 1.03 to 2.08); sCD23, OR = 1.57 (95% CI = 1.21 to 2.05); sCD27, OR = 2.18 (95% CI = 1.20 to 3.98); sCD30, OR = 1.65 (95% CI = 1.22 to 2.22). In stratified analyses, IL-6, TNF-α, sCD27, and sCD30 were more strongly associated with NHL in HIV-infected individuals compared to HIV-uninfected individuals. Between-study heterogeneity was observed across multiple biomarkers for overall NHL and by subtypes.

Conclusion

This meta-analysis provides evidence that elevated circulating levels of TNF-α, CXCL13, sCD23, sCD27, and sCD30 are consistently associated with an increased risk of NHL, suggesting the potential utility of these biomarkers in population risk stratification and prediction.
Turnover and transferable skills in a professional service firm
Authors: Olsen Karen M , Egeland Therese , Kalleberg Arne L
Published: December 2018

Retaining the most valuable employees is a core priority of professional service firms (PSFs). Our study addresses turnover (quit) among employees in a PSF that hires lawyers, auditors, and management consultants. We examine the extent to which the decision to quit varies by professions, skills, and job satisfaction in a PSF in Norway. The analyses are based on a survey of employees conducted in 2013 (N = 455) combined with information on those who quit after 28 months. We find that the sub-group of non-certified auditors quit more often than all other professional groups. In addition, we find that client-contact and transferability of skills are positively related to quits, when controlling for job satisfaction, suggesting that these skills provide employees with alternative job opportunities and greater bargaining power. These measures of skills are also positively related to job satisfaction. Our study contributes to the literature on turnover and professions by emphasizing the interplay between the skills of professional workers and job satisfaction in employees’ decision to quit. In addition, we add to our understanding of the concepts of general- and firm-specific skills in a multi-profession context.
On the Possibility of Hallucinations
Authors: Masrour Farid
Published: December 2018

Many take the possibility of hallucinations to imply that a relationalist account, according to which perceptual experiences are constituted by direct relations to ordinary mind-independent objects, is false. The common reaction among relationalists is to adopt a disjunctivist view that denies that hallucinations have the same nature as perceptual experiences. This paper proposes a non-disjunctivist response to the argument from hallucination by arguing that the alleged empirical and a priori evidence in support of the possibility of hallucinations is inconclusive. A corollary upshot of the article is that whether hallucinations are possible or not is still an open empirical question.
Professionals and populists: the making of a free market for medicine in the United States, 1787–1860
Authors: Habinek Jacob , Haveman Heather A
Published: December 2018

In the early decades of the 19th century, physicians in the USA enjoyed unquestioned authority in medicine and increasing state recognition. But by mid-century, their monopoly had given way to a raucous free market for medical care. To explain the causes and consequences of this dismantling of a professional monopoly, we draw on political sociology. We argue that to maintain a monopoly, a dominant profession must defend its cultural authority against rival claims and preserve its institutional support from the state. A dominant profession can lose its monopoly if rival occupations mobilize to challenge its cultural authority and if populist political coalitions mobilize to repeal laws upholding professional monopolies. Our analysis, which covers all states in the Union by 1860, reveals that the dynamics of contention, both within the system of professions and in the wider political arena, can erode the foundations of professional monopolies.
Effect of maternal diet on select fecal bacteria of foals
Authors: Pyles Morgan B , Fowler Ashley L , Bill Veronica T , Harlow Brittany E , Crum Andrea D , Hayes Susan H , Flythe Michael D , Lawrence Laurie M
Published: December 2018

Adult horses depend on the microbial community in the hindgut to digest fiber and produce short-chain fatty acids that are use for energy. Colonization of the foal gastrointestinal tract is essential to develop this symbiosis. However, factors affecting colonization are not well understood. The objectives of this study were to evaluate the age-related changes and effects of maternal diet on select fecal bacterial groups in foals from 1 to 28 d of age. Thoroughbred foals (n = 18) were from dams fed forage and one of two concentrates: an oat-based (OB) or corn and wheat middlings-based (CWB) pelleted concentrate. The mares had access to assigned concentrates, along with a mixed hay and cool-season grass pasture, 28 d before and 28 d after parturition. Fecal samples were collected from foals at 1 d (14 to 36 h), 4, 14, and 28 d after birth. Fecal samples were serially diluted with phosphate-buffered saline before inoculation of enriched, selective media to enumerate Lactobacillus spp., amylolytic bacteria, and cellulolytic bacteria. Enumeration data were log-transformed then analyzed with mixed model analysis of variance with repeated measures (SAS 9.3) to test the main effects of maternal diet (OB or CWB), time of sample, and interaction between maternal diet and time. Cellulolytic bacteria first appeared in foal feces between 4 and 14 d of age and increased with age (P < 0.05). Amylolytic bacteria and lactobacilli were abundant at 1 d and then increased with age (P < 0.05). There was an interaction between maternal diet and time for Lactobacillus spp. with OB foals having more lactobacilli than CWB foals at 1 and 4 d (P < 0.05); however, there were no differences observed at 14 d (P > 0.05). Maternal diet did not influence amylolytic or cellulolytic bacteria (P > 0.05). These results indicate that colonization of the hindgut is a sequential process beginning early in the foal’s life and that maternal diet may influence some bacteria in the gastrointestinal tract of foals.
Genetics of fasting indices of glucose homeostasis using GWIS unravels tight relationships with inflammatory markers
Authors: Fedko Iryna O. , Nivard Michel G. , Hottenga Jouke-Jan , Zudina Liudmila ,   Cross Consortia Pleiotropy (XC-Pleiotropy) Group, CHARGE Inflammation working group, Balkhiyarova Zhanna , Chasman Daniel I. , Ganesh Santhi , Huang Jie , Nalls Mike A. , O’Donnell Christopher J. , Paré Guillaume , Ridker Paul M. ,   Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) Investigators, Mägi Reedik , Kaakinen Marika , Prokopenko Inga , Boomsma Dorret I.
Published: December 2018

Purpose

Homeostasis Model Assessment of β-cell function and Insulin Resistance (HOMA-B/-IR) indices are informative about the pathophysiological processes underlying type 2 diabetes (T2D). Data on both fasting glucose and insulin levels are required to calculate HOMA-B/-IR, leading to underpowered Genome-Wide Association studies (GWAS) of these traits.

Methods

We overcame such power loss issues by implementing Genome-Wide Inferred Statistics (GWIS) approach and subsequent dense genome-wide imputation of HOMA-B/-IR summary statistics with SS-imp to 1000 Genomes project variant density, reaching an analytical sample size of 75,240 European individuals without diabetes. We dissected mechanistic heterogeneity of glycaemic trait/T2D loci effects on HOMA-B/-IR and their relationships with 36 inflammatory and cardiometabolic phenotypes.

Results

We identified one/three novel HOMA-B (FOXA2)/HOMA-IR (LYPLAL1, PER4,PPP1R3B) loci. We detected novel strong genetic correlations between HOMA-IR/-B and Plasminogen Activator Inhibitor 1 (PAI-1, rg=0.92/0.78, P=2.13×10-4/2.54×10-3). HOMA-IR/-B were also correlated with C-Reactive Protein (rg=0.33/0.28, P=4.67×10-3/3.65×10-3). HOMA-IR was additionally correlated with T2D (rg=0.56, P=2.31×10-9), glycated haemoglobin (rg=0.28, P=0.024) and adiponectin (rg=-0.30, P=0.012).

Conclusion

Using innovative GWIS approach for composite phenotypes we report novel evidence for genetic relationships between fasting indices of insulin resistance/beta-cell function and inflammatory markers, providing further support for the role of inflammation in T2D pathogenesis.
Namdinator - Automatic Molecular Dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
Authors: Kidmose Rune Thomas , Juhl Jonathan , Nissen Poul , Boesen Thomas , Karlsen Jesper Lykkegaard , Pedersen Bjørn Panyella
Published: December 2018

Model building into experimental maps is a key element of structural biology, but can be both time consuming and error-prone. Here we present Namdinator, an easy-to-use tool that enables the user to run a Molecular Dynamics Flexible Fitting (MDFF) simulation in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited models and maps from cryo-EM and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large scale conformational changes compared to the starting model. Namdinator is a fast and easy way to create suitable initial models for both cryo-EM and crystallography. It can fix model errors in the final steps of model building, and is usable for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or can be run locally as a command-line tool.

Synopsis

A pipeline tool called Namdinator is presented that enables the user to run a Molecular Dynamics Flexible Fitting (MDFF) simulation in a fully automated manner, both online and locally. This provides a fast and easy way to create suitable initial models for both cryo-EM and crystallography and help fix errors in the final steps of model building.
Sex-dependent dominance maintains migration supergene in rainbow trout
Authors: Pearse Devon E. , Barson Nicola J. , Nome Torfinn , Gao Guangtu , Campbell Matthew A. , Abadía-Cardoso Alicia , Anderson Eric C. , Rundio David E. , Williams Thomas H. , Naish Kerry A. , Moen Thomas , Liu Sixin , Kent Matthew , Minkley David R. , Rondeau Eric B. , Brieuc Marine S. O. , Rød Sandve Simen , Miller Michael R. , Cedillo Lucydalila , Baruch Kobi , Hernandez Alvaro G. , Ben-Zvi Gil , Shem-Tov Doron , Barad Omer , Kuzishchin Kirill , Garza John Carlos , Lindley Steven T. , Koop Ben F. , Thorgaard Gary H. , Palti Yniv , Lien Sigbjørn
Published: December 2018

Traits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.
Structural basis of eIF2B-catalyzed GDP exchange and phosphoregulation by the integrated stress response
Authors: Anand Aditya A , Kenner Lillian R , Nguyen Henry C , Myasnikov Alexander G , Klose Carolin J , McGeever Lea A , Tsai Jordan C , Miller-Vedam Lakshmi E , Walter Peter , Frost Adam
Published: December 2018

The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a GTPase, that becomes activated by eIF2B, a large two-fold symmetric and heterodecameric complex that functions as eIF2's dedicated nucleotide exchange factor. Phosphorylation converts eIF2 from substrate into an inhibitor of eIF2B. We report cryoEM structures of eIF2 bound to eIF2B in the dephosphorylated state. The structures reveal that the eIF2B decamer is a static platform upon which one or two flexible eIF2 trimers bind and align with eIF2B's catalytic centers to catalyze guanine nucleotide exchange. Phosphorylation refolds eIF2, allowing it to contact eIF2B at a different interface and, we surmise, thereby sequesters it into a non-productive complex.
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
Authors: Lee Isac , Razaghi Roham , Gilpatrick Timothy , Molnar Michael , Sadowski Norah , Simpson Jared T. , Sedlazeck Fritz J. , Timp Winston
Published: December 2018

Understanding how the genome and the epigenome work together to control gene transcription has applications in our understanding of diseases such as human cancer. In this study, we combine the ability of NOMe-seq to simultaneously evaluate CpG methylation and chromatin accessibility, with long-read nanopore sequencing technology, a method we call nanoNOMe. We generated >60Gb whole-genome nanopore sequencing data for each of four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231) including repetitive regions inaccessible by short read sequencing. Using the long reads, we find that we can observe phased methylation and chromatin accessibility, large scale pattern changes, and genetic changes such as structural variations from a single assay.
Calcium-Induced Differentiation in Normal Human Colonoid Cultures
Authors: Attili Durga , McClintock Shannon D. , Rizvi Areeba H. , Pandya Shailja , Rehman Humza , Nadeem Daniyal M , Richter Aliah , Thomas Dafydd , Dame Michael K. , Turgeon D. Kim , Varani James , Aslam Muhammad Nadeem
Published: December 2018

Colonoid cultures were established from histologically-normal human colon tissue and maintained in a low-calcium (0.25 mM) medium or in medium supplemented with an amount of calcium (1.5 - 3.0 mM) that was shown in a previous study to induce differentiation in colonoids derived from large adenomas. Calcium alone was compared to Aquamin, a multi-mineral natural product that contains magnesium and detectable levels of 72 additional trace elements in addition to calcium. Unlike the previously-studied tumor-derived colonoids (which remained un-differentiated in the absence of calcium-supplementation), normal tissue colonoids underwent differentiation as indicated by gross and microscopic appearance, a low proliferative index and high-level expression of cytokeratin 20 (CK20) in the absence of intervention. Only modest additional changes were seen in these parameters with either calcium alone or Aquamin (providing up to 3.0 mM calcium). In spite of this, proteomic analysis and immunohistochemistry revealed that both interventions induced strong up-regulation of proteins that promote cell-cell and cell-matrix adhesive functions, barrier formation and tissue integrity. Transmission electron microscopy revealed an increase in desmosomes in response to intervention. These findings demonstrate that histologically normal human colonoids can undergo differentiation in the presence of a low ambient calcium concentration. However, higher calcium levels can induce elaboration of proteins that promote cell-cell and cell-matrix adhesion. These changes could lead to improved barrier function and improved colon tissue health.
Quantum energy levels of glutamate modulate neural biophotonic signals
Authors: Han Zhengrong , Chai Weitai , Wang Zhuo , Xiao Fangyan , Dai Jiapei
Published: December 2018

Glutamate is the most abundant excitatory neurotransmitter in the brain, and it plays an essential and important role in neural functions. Hypofunction of the glutamatergic pathway and the changes in the glutamate-glutamine cycle function are important neuropathological mechanisms of severe mental disorders including schizophrenia and depression. Current studies have shown that glutamate can induce neural biophotonic activity and transmission, which may involve the mechanism of photon quantum brain; however, it is unclear whether such a mechanism follows the principle of quantum mechanics. Here we show that the action of glutamate on its receptors leads to a decrease in its quantum energy levels, and glutamate then partially or completely loses its function to further induce the biophotonic activity in mouse brain slices. The reduced quantum energy levels of glutamate can be restored by direct-current electrical discharges and the use of energy transfer of chloroplast photosynthesis; hence, the quantum energy recovered glutamate can again induce significant biophotonic activity. Furthermore, the changes in quantum energy levels of glutamate are related to the exchange and transfer of electron energy on its active hydrogen atom. These findings suggest that the glutamate-induced neural biophotonic signals may be involved in the transfer of the quantum energy levels of glutamate, which implies a quantum mechanism of neurotransmitter action. The process of glutamate recycling that is related to the synergism of neurons and glial cells and certain key enzymes may be necessary for the recovery of quantum energy levels of glutamate after completion of the neural signal transmission. These findings may also provide a new idea to develop quantum drugs.
DeepCell Kiosk: Scaling deep learning-enabled cellular image analysis with Kubernetes
Authors: Bannon Dylan , Moen Erick , Schwartz Morgan , Borba Enrico , Kudo Takamasa , Greenwald Noah , Vijayakumar Vibha , Chang Brian , Pao Edward , Osterman Erik , Graf William , Van Valen David
Published: December 2018

Deep learning is transforming the analysis of biological images but applying these models to large datasets remains challenging. Here we describe the DeepCell Kiosk, cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets. To demonstrate the scalability and affordability of this software, we identified cell nuclei in 106 1-megapixel images in ~5.5 h for ~$250, with a sub-$100 cost achievable depending on cluster configuration. The DeepCell Kiosk can be downloaded at https://github.com/vanvalenlab/kiosk-console; a persistent deployment is available at https://deepcell.org.