bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha
Authors: Hardin Aaron , Nevonen Kimberly A , Eckalbar Walter L , Carbone Lucia , Ahituv Nadav
Published: August 2019

Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors.
Opposing Pressures of Speed and Efficiency Guide the Evolution of Molecular Machines
Authors: Wagoner Jason A , Dill Ken A
Published: August 2019

Many biomolecular machines need to be both fast and efficient. How has evolution optimized these machines along the tradeoff between speed and efficiency? We explore this question using optimizable dynamical models along coordinates that are plausible evolutionary degrees of freedom. Data on 11 motors and ion pumps are consistent with the hypothesis that evolution seeks an optimal balance of speed and efficiency, where any further small increase in one of these quantities would come at great expense to the other. For FoF1-ATPases in different species, we also find apparent optimization of the number of subunits in the c-ring, which determines the number of protons pumped per ATP synthesized. Interestingly, these ATPases appear to more optimized for efficiency than for speed, which can be rationalized through their key role as energy transducers in biology. The present modeling shows how the dynamical performance properties of biomolecular motors and pumps may have evolved to suit their corresponding biological actions.
Direct Evidence of an Increasing Mutational Load in Humans
Authors: Aris-Brosou Stéphane
Published: August 2019

The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. Although the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes, and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.
CFEA: a cell-free epigenome atlas in human diseases
Authors: Yu Fulong , Li Kai , Li Shuangquan , Liu Jiaqi , Zhang Yan , Zhou Meng , Zhao Hengqiang , Chen Hongyan , Wu Nan , Liu Zhihua , Su Jianzhong
Published: August 2019

Epigenetic alterations, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and nucleosome positioning (NP), in cell-free DNA (cfDNA) have been widely observed in human diseases, and many available cfDNA-based epigenome-wide profiles exhibit high sensitivity and specificity in disease detection and classification. However, due to the lack of efficient collection, standardized quality control, and analysis procedures, efficiently integrating and reusing these data remain considerable challenges. Here, we introduce CFEA (http://www.bio-data.cn/CFEA), a cell-free epigenome database dedicated to three types of widely adopted epigenetic modifications (5mC, 5hmC and NP) involved in 27 human diseases. We developed bioinformatic pipelines for quality control and standard data processing and an easy-to-use web interface to facilitate the query, visualization and download of these cell-free epigenome data. We also manually curated related biological and clinical information for each profile, allowing users to better browse and compare cfDNA epigenomes at a specific stage (such as early- or metastasis-stage) of cancer development. CFEA provides a comprehensive and timely resource to the scientific community and supports the development of liquid biopsy-based biomarkers for various human diseases.
A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures
Authors: Zhang Ning , Shi Shundi , Jia Tony Z , Ziegler Ashley , Yoo Barney , Yuan Xiaohong , Li Wenjia , Zhang Shenglong
Published: August 2019

A complete understanding of the structural and functional potential of RNA requires understanding of chemical modifications and non-canonical bases; this in turn requires advances in current sequencing methods to be able to sequence not only canonical ribonucleotides, but at the same time directly sequence these non-standard moieties. Here, we present the first direct and modification type-independent RNA sequencing method via introduction of a 2-dimensional hydrophobic end-labeling strategy into traditional mass spectrometry-based sequencing (2D HELS MS Seq) to allow de novo sequencing of RNA mixtures and enhance sample usage efficiency. Our method can directly read out the complete sequence, while identifying, locating, and quantifying base modifications accurately in both single and mixed RNA samples containing multiple different modifications at single-base resolution. Our method can also quantify stoichiometry/percentage of modified RNA versus its canonical counterpart RNA, simulating a real biological sample where modifications exist but may not be 100% at a particular site in the RNA. This method is a critical step towards fully sequencing real complex cellular RNA samples of any type and containing any modification type and can also be used in the quality control of modified therapeutic RNAs.
On the association between undocumented immigration and crime in the United States
Authors: Gunadi Christian
Published: August 2019

Approximately 11 million undocumented individuals live in the United States. At the same time, there are concerns that the presence of undocumented immigrants may contribute to an increase in crime rates. In this article, I examine the institutionalization rate of undocumented immigrants and quantify the change in crime rates attributable to undocumented immigration. The analysis yields a few main results. First, despite possessing characteristics usually associated with crime, undocumented immigrants are 33% less likely to be institutionalized compared to US natives. Second, there is no evidence that undocumented immigrants who have spent more time in the USA are more likely to be institutionalized compared to those who have been in the USA for a shorter time. There is evidence, however, that arriving at a younger age is associated with higher institutionalization rate. Finally, overall property and violent crime rates across US states are not statistically significantly increased by undocumented immigration.
Acceptability and Feasibility of a Pharmacist-Led Human Immunodeficiency Virus Pre-Exposure Prophylaxis Program in the Midwestern United States
Authors: Havens Joshua P , Scarsi Kimberly K , Sayles Harlan , Klepser Donald G , Swindells Susan , Bares Sara H
Published: August 2019

Background

Human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) substantially reduces the risk of HIV acquisition, yet significant barriers exist to its prescription and use. Incorporating pharmacists in the PrEP care process may help increase access to PrEP services.

Methods

Our pharmacist-led PrEP program (P-PrEP) included pharmacists from a university-based HIV clinic, a community pharmacy, and 2 community-based clinics. Through a collaborative practice agreement, pharmacists conducted PrEP visits with potential candidates for PrEP, according to the recommended Centers for Disease Control and Prevention guidelines, and authorized emtricitabine-tenofovir disoproxil fumarate prescriptions. Demographics and retention in care over 12 months were summarized, and participant satisfaction and pharmacist acceptability with the P-PrEP program were assessed by Likert-scale questionnaires.

Results

Sixty patients enrolled in the P-PrEP program between January and June 2017 completing 139 visits. The mean age was 34 years (range, 20–61 years), and 88% identified as men who have sex with men, 91.7% were men, 83.3% were white, 80% were commercially insured, and 89.8% had completed some college education or higher. Participant retention at 3, 6, 9, and 12 months was 73%, 58%, 43%, and 28%, respectively. To date, no participant has seroconverted. One hundred percent of the participants who completed the patient satisfaction questionnaire would recommend the P-PrEP program. Pharmacists reported feeling comfortable performing point-of-care testing and rarely reported feeling uncomfortable during PrEP visits (3 occasions, 2.2%) or experiencing workflow disruption (1 occasion, 0.7%).

Conclusions

Implementation of a pharmacist-led PrEP program is feasible and associated with high rates of patient satisfaction and pharmacist acceptability.
Crime and networks: ten policy lessons
Authors: Lindquist Matthew J , Zenou Yves
Published: August 2019

Social network analysis can help us understand the root causes of delinquent behaviour and crime and provide practical guidance for the design of crime prevention policies. To illustrate these points, we first present a selective review of several key network studies and findings from the criminology and police studies literature. We then turn to a presentation of recent contributions made by network economists. We highlight ten policy lessons and provide a discussion of recent developments in the use of big data and computer technology.
Lotus japonicus Triterpenoid Profile and Characterization of the CYP716A51 and LjCYP93E1 Genes Involved in Their Biosynthesis In Planta
Authors: Suzuki Hayato , Fukushima Ery Odette , Shimizu Yuko , Seki Hikaru , Fujisawa Yukiko , Ishimoto Masao , Osakabe Keishi , Osakabe Yuriko , Muranaka Toshiya
Published: August 2019

Lotus japonicus is an important model legume plant in several fields of research, such as secondary (specialized) metabolism and symbiotic nodulation. This plant accumulates triterpenoids; however, less information regarding its composition, content and biosynthesis is available compared with Medicago truncatula and Glycine max. In this study, we analyzed the triterpenoid content and composition of L. japonicus. Lotus japonicus accumulated C-28-oxidized triterpenoids (ursolic, betulinic and oleanolic acids) and soyasapogenols (soyasapogenol B, A and E) in a tissue-dependent manner. We identified an oxidosqualene cyclase (OSC) and two cytochrome P450 enzymes (P450s) involved in triterpenoid biosynthesis using a yeast heterologous expression system. OSC9 was the first enzyme derived from L. japonicus that showed α-amyrin (a precursor of ursolic acid)-producing activity. CYP716A51 showed triterpenoid C-28 oxidation activity. LjCYP93E1 converted β-amyrin into 24-hydroxy-β-amyrin, a metabolic intermediate of soyasapogenols. The involvement of the identified genes in triterpenoid biosynthesis in L. japonicus plants was evaluated by quantitative real-time PCR analysis. Furthermore, gene loss-of-function analysis of CYP716A51 and LjCYP93E1 was conducted. The cyp716a51-mutant L. japonicus hairy roots generated by the genome-editing technique produced no C-28 oxidized triterpenoids. Likewise, the complete abolition of soyasapogenols and soyasaponin I was observed in mutant plants harboring Lotus retrotransposon 1 (LORE1) in LjCYP93E1. These results indicate that the activities of these P450 enzymes are essential for triterpenoid biosynthesis in L. japonicus. This study increases our understanding of triterpenoid biosynthesis in leguminous plants and provides information that will facilitate further studies of the physiological functions of triterpenoids using L. japonicus.
Arabidopsis SCO Proteins Oppositely Influence Cytochrome c Oxidase Levels and Gene Expression during Salinity Stress
Authors: Mansilla Natanael , Welchen Elina , Gonzalez Daniel H
Published: August 2019

SCO (synthesis of cytochrome c oxidase) proteins are involved in the insertion of copper during the assembly of cytochrome c oxidase (COX), the final enzyme of the mitochondrial respiratory chain. Two SCO proteins, namely, homolog of copper chaperone 1 and 2 (HCC1 and HCC2) are present in seed plants, but HCC2 lacks the residues involved in copper binding, leading to uncertainties about its function. In this study, we performed a transcriptomic and phenotypic analysis of Arabidopsis thaliana plants with reduced expression of HCC1 or HCC2. We observed that a deficiency in HCC1 causes a decrease in the expression of several stress-responsive genes, both under basal growth conditions and after applying a short-term high salinity treatment. In addition, HCC1 deficient plants show a faster decrease in chlorophyll content, photosystem II quantum efficiency and COX levels after salinity stress, as well as a faster increase in alternative oxidase capacity. Notably, HCC2 deficiency causes opposite changes in most of these parameters. Bimolecular fluorescence complementation analysis indicated that both proteins are able to interact. We postulate that HCC1 is a limiting factor for COX assembly during high salinity conditions and that HCC2 probably acts as a negative modulator of HCC1 activity through protein–protein interactions. In addition, a direct or indirect role of HCC1 and HCC2 in the gene expression response to stress is proposed.
Association of health-risk behaviors and depressive symptoms and anxiety symptoms: a school-based sample of Chinese adolescents
Authors: Luo Xiaomin , Zhou Yu , Zheng Ruimin , Li Xin , Dai Yue , Narayan Anuradha , Huang Xiaona , Tian Xiaobo , Jin Xi , Mei Lili , Xie Xinyan , Gu Huaiting , Hou Fang , Liu Lingfei , Luo Xiu , Meng Heng , Zhang Jiajia , Song Ranran
Published: August 2019

Background Depressive symptoms and anxiety symptoms of adolescents not only affect youth but also have wide-ranging impacts on the health of adults. The study was carried out to determine the epidemiological characteristics of depressive symptoms and anxiety symptoms and the associations between the two and health-risk behaviors in Chinese adolescents.

Methods Participants were recruited from the junior and senior high schools in China. Data were collected by self-designed questionnaires. The questionnaires included questions about demographic characteristics, depressive symptom scales, anxiety symptom scales and nine categories of health-risk behaviors. Descriptive analysis and binary logistic regression were performed by SPSS 21.0 software.

Results There were 4.4% of the participants with depressive symptoms. Approximately 32.0% of the participants had anxiety symptoms. Girls and general senior school students were risk factors for depressive symptoms and anxiety symptoms. Multiple health-risk behaviors were associated with depressive symptoms and anxiety symptoms in Chinese adolescents.

Conclusion Depressive symptoms and anxiety symptoms were prevalent in Chinese adolescents. Their distribution was affected by certain health-risk behaviors. Multiple health-risk behaviors were associated with depressive symptoms and anxiety symptoms in Chinese adolescents.
Analysis and forecast of the HIV/AIDS epidemic in Mainland China, 1985–2016
Authors: Guo Zuiyuan , Xiao Dan , Xu Shuang , He Kevin
Published: August 2019

Background

We aimed to forecast the number of unidentified and newly acquired HIV-infected individuals each year and to estimate the effectiveness of government prevention and control programs in China.

Methods

Dynamic and stochastic models were established based on officially published data regarding the four main modes of transmission: male homosexual sexual behavior, heterosexual sexual behavior, injection drug use (IDU) and plasma donation. Finally, we performed sensitivity analyses on model parameters.

Results

Nationally, by December 2016, approximately 280 790 individuals were estimated to have an unidentified HIV infection, with transmission via male homosexual sexual behavior (n = 100 710), heterosexual sexual behavior (n = 174 310), IDU (n = 5 620) and plasma donation (n = 150). Moreover, 196 970 newly acquired HIV-infected individuals were expected in 2016, via male homosexual sexual behavior (n = 78 610), heterosexual sexual behavior (n = 116,540), IDU (n = 1820), and plasma donation (n < 2).

Conclusions

Our results show that HIV transmission via IDU and plasma donation has been effectively controlled; transmission via heterosexual sexual contact is being somewhat controlled; however, transmission via male homosexual sexual contact is not controlled. Hence, China should strengthen efforts aimed at control of unsafe sexual behaviors.
Non-medical use of loperamide in the UK and the USA
Authors: Webb N E , Wood D M , Black J C , Amioka E , Dart R C , Dargan P I
Published: August 2019

Background

Loperamide is a mu-opioid receptor agonist that is available as an over-the-counter anti-motility agent in the US and UK; recommended maximum doses of 12-16 mg/day. Anecdotal reports of non-medical use (NMU) have increased over the past decade with supra-therapeutic doses (70-800 mg/day) associated with cardiotoxicity. Little data exists on the prevalence of loperamide NMU.

Aim

The aim of this study was to determine the prevalence of loperamide NMU in the UK and US and to describe characteristics of non-medical loperamide users.

Design

The Researched, Abuse, Diversion and Addiction Related Surveillance (RADARS® ) Survey of Nonmedical Use of Prescription Drugs (NMURx) was utilized to study NMU of loperamide among the adult population in the UK and US in 2017. The RADARS® NMURx is anonymous and self-administered online.

Methods

A total of 40,029 completed surveys were included (10,019 from the UK and 30,010 from the US). Respondents were asked questions about medical and NMU of loperamide, frequency of and reasons for NMU, route of use problematic drug use markers, and demographics.

Results

Prevalence of lifetime loperamide use (95% CI) and lifetime NMU of loperamide were: UK 28.5% (27.67-29.4), and 0.66% (0.5-0.8), respectively; US 33.7% (33.1-34.2), and 5.19% (4.9-5.5), respectively. Problematic drug use markers were elevated in those who reported NMU of loperamide in both the UK and US, however high-risk use was more prevalent in the UK than in the US.

Conclusion

NMU of loperamide is common. In the current international environment of opioid addiction involving both therapeutic and illicit opioids, awareness of the NMU of loperamide is important.
Comparing Cross-Section and Time-Series Factor Models
Authors: Fama Eugene F , French Kenneth R
Published: August 2019

We use the cross-section regression approach of Fama and MacBeth (1973) to construct cross-section factors corresponding to the time-series factors of Fama and French (2015). Time-series models that use only cross-section factors provide better descriptions of average returns than time-series models that use time-series factors. This is true when we impose constant factor loadings and when we use time-varying loadings that are natural for time-series factors and time-varying loadings that are natural for cross-section factors.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Bubbles and Financial Professionals
Authors: Weitzel Utz , Huber Christoph , Huber Jürgen , Kirchler Michael , Lindner Florian , Rose Julia
Published: August 2019

The efficiency of financial markets and their potential to produce bubbles are central topics in academic and professional debates. Yet, little is known about the contribution of financial professionals to price efficiency. We run 116 experimental markets with 412 professionals and 502 students. We find that professional markets with bubble drivers – capital inflows or high initial capital supply – are susceptible to bubbles, although they are more efficient than student markets. In mixed markets with students, bubbles also occur, but professionals act as price stabilizers. We show that heterogeneous price beliefs drive overpricing, especially in bubble-prone market environments.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Risk of progression of interstitial pneumonia with autoimmune features to a systemic autoimmune rheumatic disease
Authors: Alevizos Michail K , Giles Jon T , Patel Nina M , Bernstein Elana J
Published: August 2019

Objective

The aim of this study was to determine the risk of developing a systemic autoimmune rheumatic disease (ARD) after an initial diagnosis of interstitial pneumonia with autoimmune features (IPAF).

Methods

We performed a retrospective cohort study of patients with interstitial lung disease (ILD) who were evaluated at Columbia University Irving Medical Center from 2009 to 2017. We divided patients with idiopathic ILD into two groups: those who met IPAF criteria and those who did not meet IPAF criteria at initial ILD diagnosis. We examined the association between IPAF and diagnosis of ARD during the follow-up period using a multivariable-adjusted logistic regression model.

Results

Of the 697 patients with ILD who were screened, 174 met inclusion criteria (50 met IPAF criteria and 124 did not). During a median follow-up period of 5.2 years, 16% (8/50) of subjects with IPAF were diagnosed with an ARD compared with 1.6% (2/124) of subjects without IPAF (P = 0.001). Adjusting for age, sex, smoking status and use of immunosuppressive therapy, the odds of progressing to an ARD were 14 times higher in subjects with IPAF than in those without IPAF (odds ratio 14.18, 95% CI 1.44–138.95, P = 0.02).

Conclusion

The presence of IPAF confers an increased risk of developing an ARD. Patients with IPAF should therefore be followed closely for the development of an ARD.
Comorbidities in familial Mediterranean fever: analysis of 2000 genetically confirmed patients
Authors: Balcı-Peynircioğlu Banu , Kaya-Akça Ümmüşen , Arıcı Zehra Serap , Avcı Edibe , Akkaya-Ulum Z Yeliz , Karadağ Ömer , Kalyoncu Umut , Bilginer Yelda , Yılmaz Engin , Özen Seza
Published: August 2019

Objectives

FMF is the most common periodic fever syndrome, characterized by recurrent episodes of fever and serosal inflammation accompanied with high acute phase reactants. The analysis of possible comorbidities is important to understand the impact of these conditions on clinical care and whether they share a common aetiological pathway. In this study, we aimed to evaluate the comorbidities associated with FMF patients in a large genetically diagnosed cohort.

Methods

We retrospectively evaluated the medical and genetic records of FMF patients who were followed up by rheumatologists in Hacettepe University for 15 years. The FMF patients who had homozygous or compound heterozygous mutations were included in the study. Comorbidities associated with FMF were divided into three groups: (i) comorbidities directly related to FMF, (ii) comorbidities due to increased innate inflammation, and (iii) comorbidities that were regarded as being incidental.

Results

A total of 2000 patients with a diagnosis of FMF were enrolled in the study. Among them 636 were children (31.8%) and M694V was the most common mutation in patients with associated inflammatory conditions. The frequency of AS, Iga Vasculitis (Henoch–Schönlein purpura), juvenile idiopathic arthritis, polyarteritis nodosa, multiple sclerosis and Behçet’s disease were increased in patients with FMF when compared with those in the literature.

Conclusion

This study represents the largest genetically confirmed cohort and compares the frequencies with existing national and international figures for each disease. The increased innate immune system inflammation seen in FMF may be considered as a susceptibility factor since it predisposes to certain inflammatory conditions.
COMPARISON OF THE RADIATION SENSITIVITY OF THE BREAST CANCER CELL LINE MCF7 AND HUMAN ADIPOSE-DERIVED STEM CELLS
Authors: Michaelidesová Anna , Vachelová Jana , Cupal Lukáš , Konířová Jana , Brabcová Kateřina Pachnerová , Bačáková Lucie , Vandrovcová Marta , Davídková Marie
Published: August 2019

A comparison between breast cancer cell line MCF7 and human adipose-derived stem cells (ADSC) after irradiation by the same doses of megavoltage X-rays was performed. The cell growth, the induction of apoptosis and the expression of selected genes were analyzed. Irradiated MCF7 related to its control sample grows slower than ADSC and it undergoes apoptosis in much higher levels than ADSC. This was confirmed by real-time polymerase chain reaction as well, where the expression of apoptotic genes was found to be considerably higher for MCF7 than for ADSC. From the results of this project, it could be stated that MCF7 is more radiosensitive than ADSC.
RADIATION-INDUCED PLASMID DNA DAMAGE: EFFECT OF CONCENTRATION AND LENGTH
Authors: Brabcová Kateřina Pachnerová , Jamborová Zuzana , Michaelidesová Anna , Davídková Marie , Kodaira Satoshi , Šefl Martin , Štěpán Václav
Published: August 2019

Plasmid DNA is commonly used as a simpler substitute for a cell in studies of early effects of ionizing radiation because it allows to determine yields of primary DNA lesions. Experimental studies often employ plasmids of different lengths, in different concentrations in the aqueous solution. Influence of these parameters on the heavy-ion induced yields of primary DNA damage has been studied, using plasmids pUC19 (2686 bp), pBR322 (4361 bp) and pKLAC2 (9107 bp) in 10 and 50 ng/μl concentration. Results demonstrate the impact of plasmid length, while no significant difference was observed between the two concentrations. The uncertainty of the results is discussed.
ETHANOL AS A MODIFIER OF RADIATION SENSITIVITY OF LIVING CELLS AGAINST UV-C RADIATION
Authors: Neužilová Barbora , Ondrák Lukáš , Čuba Václav , Múčka Viliam
Published: August 2019

The protection of Escherichia coli bacteria and the yeast Saccharomyces cerevisiae against UV-C radiation by ethanol was studied. It was found that the fraction of surviving cells increases with increasing ethanol concentration. The specific protection depends on the dose rate, concentration range of ethanol, and it is higher for yeast compared to the bacteria.
RESPONSE OF THE CZECH RMN NETWORK TO THUNDERSTORM ACTIVITY
Authors: Šlegl J , Minářová J , Kuča P , Kolmašová I , Santolík O , Sokol Z , Reitz G , Ambrožová I , Ploc O
Published: August 2019

Thunderstorm ground enhancement (TGE) is a phenomenon that enhances radiation background on the ground related to thunderstorm activity and charge structure of the thundercloud. On the other hand, the rise of gamma background is connected with precipitation by the washout of radon progeny from the atmosphere. In our analysis, we examined known enhancements of gamma background, previously attributed solely to radon progeny, using data from the Czech Radiation Monitoring Network (RMN) to investigate the enhancements with respect to thunderstorms and TGE phenomena. We also used radar precipitation data and data from the lightning location network to analyze their influences on the radiation background enhancement during three thunderstorm events that occurred in summer 2016 over the Czech Republic (Central Europe). We state that the RMN might have detected TGE over the Czech Republic.
COMPARISON OF MCNP AND VISIPLAN DOSE-FIELD CALCULATIONS FOR MULTILAYER SHIELDING
Authors: Bednár Dávid , Lištjak Martin , Slimák Andrej , Nečas Vladimír
Published: August 2019

An important factor in calculation of quantities describing the radiation situation is the selection of a calculation code. In this article, the radiation situation for selected geometries with multilayer shields was judged. Calculations were carried out using deterministic code VISIPLAN and stochastic code MCNP5. Inter-comparison of calculations with experiment was done. The aim was to compare and evaluate the results achieved by the measurements and calculations, to analyze the methods of individual calculation codes and to discuss deviations in the results. Comparison of MCNP calculations and FH40G measurements shows that the relative deviations were ±20% for each shielding configuration. The results obtained by VISIPLAN code are strongly dependent on the selected buildup factor (BUF). However, in almost all cases, it appears that using Broder’s formula to calculate BUF for multilayer shields is a good approach to refine the calculation.
ESTE—DECISION SUPPORT SYSTEM FOR NUCLEAR AND RADIOLOGICAL ACCIDENTS
Authors: Fojcíková Eva , Lipták Ľudovít , Krpelanová Monika , Chylý Miroslav , Čarný Peter
Published: August 2019

Described are functions, models and approaches of software tool Emergency Source Term code (ESTE), which is decision support system for crisis staff in case of nuclear or radiological accidents. The first task of ESTE in emergency situation at nuclear facility is to evaluate state of reactor core or state of fuel in spent fuel pool, on the base of state of barriers which should prevent the release of radionuclides to the environment. The main task is to prepare outputs, which can be utilised for recommendation of protective measures. Measures include sheltering, iodine prophylaxis and evacuation inside the emergency planning zone and potentially beyond the zone. The paper summarizes approaches of ESTE, including dispersion models and reverse modeling approach applied for estimation of real release to the atmosphere of the environment. Compared are intervention levels implemented in ESTE for urgent measures in Slovakia, Czech Republic, Bulgaria, Iran and Austria.
THE USE OF THE EXRADIN W1 PLASTIC SCINTILLATOR FOR MEASUREMENTS IN EXTERNAL RADIOTHERAPY
Authors: Koniarová Irena , Konček Ondřej
Published: August 2019

The Exradin W1 plastic scintillator (Standard Imaging) was examined for measurement suitability in high-energy photon beams, high-energy electron beams and tomotherapy in terms of dose to water for reference fields. For photon beams, pulse repetition rate dependence, calibration stability, noise from the photodiode enclosure, detector motion during treatment, output factors, off-axis doses and percentage depth doses were tested. For electron and tomotherapy beams, energy non-dependence was verified. All features make the detector suitable in small and non-standards fields, and for electron beams.
CONTINUOUS RADON-IN-WATER MONITORING—COMPARISON OF METHODS UNDER LABORATORY CONDITIONS AND RESULTS OF IN SITU MEASUREMENTS
Authors: Vyletělová Petra , Froňka Aleš
Published: August 2019

The extraction of dissolved radon from water to gas is the most common way to measure radon concentration in water continuously. The response delay of continuous radon-in-water detection system (continuous monitor + equilibrator) is influenced by the response time of the continuous monitor and a rate of an establishment of equilibrium in the equilibrator (exchanger unit). Two types of equilibrators were used in performed experiments to compare the response time of various detection systems—RAD AQUA that uses water spraying and equilibrator with ACCUREL® PP membrane that enables radon diffusion. Each of these was connected to the continuous monitor RAD7 or RM-3. The response delay after turning on the water flow through the equilibrator was determined. The fastest detection system was RAD7 + RAD AQUA that was subsequently tested during the insitu measurement of thermal water in the healing spa and water sources near Cheb and České Budějovice.
Blindness, Psychosis, and the Visual Construction of the World
Authors: Pollak Thomas A , Corlett Philip R
Published: August 2019

The relationship between visual loss and psychosis is complex: congenital visual loss appears to be protective against the development of a psychotic disorder, particularly schizophrenia. In later life, however, visual deprivation or visual loss can give rise to hallucinosis, disorders of visual insight such as blindsight or Anton syndrome, or, in the context of neurodegenerative disorders, more complex psychotic presentations. We draw on a computational psychiatric approach to consider the foundational role of vision in the construction of representations of the world and the effects of visual loss at different developmental stages. Using a Bayesian prediction error minimization model, we describe how congenital visual loss may be protective against the development of the kind of computational deficits postulated to underlie schizophrenia, by increasing the precision (and consequent stability) of higher-level (including supramodal) priors, focusing on visual loss-induced changes in NMDA receptor structure and function as a possible mechanistic substrate. In simple terms, we argue that when people cannot see from birth, they rely more heavily on the context they extract from the other senses, and the resulting model of the world is more impervious to the false inferences, made in the face of inevitably noisy perceptual input, that characterize schizophrenia. We show how a Bayesian prediction error minimization framework can also explain the relationship between later visual loss and other psychotic symptoms, as well as the effects of visual deprivation and hallucinogenic drugs, and outline experimentally testable hypotheses generated by this approach.
Dapsone Hydroxylamine, an Active Metabolite of Dapsone, Can Promote the Procoagulant Activity of Red Blood Cells and Thrombosis
Authors: Bian Yiying , Kim Keunyoung , An Gwang-Jin , Ngo Thien , Bae Ok-Nam , Lim Kyung-Min , Chung Jin-Ho
Published: August 2019

Dapsone hydroxylamine (DDS-NHOH), N-hydroxylated metabolite of a sulfonamide antibiotic, dapsone, is responsible for various adverse effects of dapsone that include methemoglobinemia, hemolytic anemia, and thrombosis. However, the mechanism underlying DDS-NHOH-induced thrombosis remains unclear. Here, we demonstrated that DDS-NHOH, but not dapsone, could increase prothrombotic risks through inducing the procoagulant activity of red blood cells (RBCs). In freshly isolated human RBCs in vitro, sub-hemolytic concentrations of DDS-NHOH (10–50 μM) increased phosphatidylserine (PS) exposure and augmented the formation of PS-bearing microvesicles (MV). Reactive oxygen species (ROS) generation and the subsequent dysregulation of enzymes maintaining membrane phospholipid asymmetry were found to induce the procoagulant activity of DDS-NHOH. Dapsone hydroxylamine also accelerated thrombin generation and enhanced RBC self-aggregation and adherence of RBCs to endothelial cells in vitro. Most importantly, both the single dose of 50 or 100 mg/kg (i.p.) DDS-NHOH and repeated doses of 10 mg/kg per day (i.p.) for 4 days increased thrombus formation in rats (six rats per dose) in vivo, substantiating a potential prothrombotic risk of DDS-NHOH. Collectively, these results demonstrated the central role of RBC procoagulant activity induced by DDS-NHOH in the thrombotic risk of dapsone.
Posterior Reversible Encephalopathy (PRES) in a Child with Severe Dengue
Authors: Sawant Yogini , Birajdar Suresh , Doshi Hiren , Soni Pooja , Patkar Deepak , Joshi Narayan C
Published: August 2019

Among neurological complications associated with dengue, posterior reversible encephalopathy syndrome (PRES) has not been reported in pediatric population. We report a 10-year-old girl with severe dengue who developed PRES. The patient presented with hemorrhagic shock that required fluid resuscitation and inotropic support. She developed seizures with encephalopathy 2 days after recovering from the shock. Cerebrospinal fluid (CSF) examination was negative for dengue (no white blood cells in CSF with negative polymerase chain reaction for dengue). Her clinical features and magnetic resonance imaging (MRI) findings showed typical changes associated with posterior encephalopathy that reverted after resolution of hypertension. Repeat MRI after a month was normal. PRES should be considered as a possible differential diagnoses of dengue associated encephalopathy, especially in cases with normal CSF examination and characteristic MRI changes.
Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations
Authors: Müller Nicola F , Dudas Gytis , Stadler Tanja
Published: August 2019

Population dynamics can be inferred from genetic sequence data by using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume migration rates and effective population sizes to be constant through time in structured populations. When considering rates to vary through time in structured populations, the number of parameters to infer increases rapidly and the available data might not be sufficient to inform these. Additionally, it is often of interest to know what predicts these parameters rather than knowing the parameters themselves. Here, we introduce a method to  infer the predictors for time-varying migration rates and effective population sizes by using a generalized linear model (GLM) approach under the marginal approximation of the structured coalescent. Using simulations, we show that our approach is able to reliably infer the model parameters and its predictors from phylogenetic trees. Furthermore, when simulating trees under the structured coalescent, we show that our new approach outperforms the discrete trait GLM model. We then apply our framework to a previously described Ebola virus dataset, where we infer the parameters and its predictors from genome sequences while accounting for phylogenetic uncertainty. We infer weekly cases to be the strongest predictor for effective population size and geographic distance the strongest predictor for migration. This approach is implemented as part of the BEAST2 package MASCOT, which allows us to jointly infer population dynamics, i.e. the parameters and predictors, within structured populations, the phylogenetic tree, and evolutionary parameters.
What to do when ontogenetic tracking is unavailable: a morphometric method to classify instars in Milnesium (Tardigrada)
Authors: Surmacz Bartłomiej , Morek Witold , Michalczyk Łukasz
Published: August 2019

Identification of tardigrade species is still reliant mostly on morphological and morphometric traits. Given that the number of taxonomically significant traits available in the genus Milnesium is exceptionally low, ontogenetic variability may provide additional methods for species delineation. However, it is notoriously difficult to establish whether both immature and sexually mature instars are present in examined populations. Here, we developed a simple analytical morphometric method that helps in testing whether both immature and mature life stages are present in a given set of individuals. In order to achieve this, we analysed 21 populations representing 11 Milnesium species, with developmental tracking data available for four species. Using cluster analysis, individuals were assigned accurately to three groups of instars: hatchlings, juveniles and adults (third instar onwards). Our analyses revealed that the most useful character in life-stage classification is buccal tube length. The method of classification of instars presented herein could be used as a simple tool for identification of the number of life stages present in a population. Finally, using our algorithm, we analysed morphometric datasets underlying the descriptions and redescriptions of all known Milnesium species to date and concluded that the majority of them did not include all three life-stage groups.
hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean
Authors: McCoy Austin G. , Noel Zachary , Sparks Adam H. , Chilvers Martin
Published: August 2019

Phytophthora sojae is a significant pathogen of soybean worldwide. Pathotype surveys for Phytophthora sojae are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for P. sojae or other gene-for-gene pathosystem studies.
Regulation of mitochondrial metabolism in murine skeletal muscle by the medium‐chain fatty acid receptor Gpr84
Authors: Montgomery Magdalene K. , Osborne Brenna , Brandon Amanda E. , O'Reilly Liam , Fiveash Corrine E. , Brown Simon H. J. , Wilkins Brendan P. , Samsudeen Azrah , Yu Josephine , Devanapalli Beena , Hertzog Ashley , Tolun Adviye A. , Kavanagh Tomas , Cooper Antony A. , Mitchell Todd W. , Biden Trevor J. , Smith Nicola J. , Cooney Gregory J. , Turner Nigel
Published: August 2019

Fatty acid receptors have been recognized as important players in glycaemic control. This study is the first to describe a role for the medium‐chain fatty acid (MCFA) receptor G‐protein‐coupled receptor (Gpr) 84 in skeletal muscle mitochondrial function and insulin secretion. We are able to show that Gpr84 is highly expressed in skeletal muscle and adipose tissue. Mice with global deletion of Gpr84 [Gpr84 knockout (KO)] exhibit a mild impairment in glucose tolerance when fed a MCFA‐enriched diet. Studies in mice and pancreatic islets suggest that glucose intolerance is accompanied by a defect in insulin secretion. MCFA‐fed KO mice also exhibit a significant impairment in the intrinsic respiratory capacity of their skeletal muscle mitochondria, but at the same time also exhibit a substantial increase in mitochondrial content. Changes in canonical pathways of mitochondrial biogenesis and turnover are unable to explain these mitochondrial differences. Our results show that Gpr84 plays a crucial role in regulating mitochondrial function and quality control.—Montgomery, M. K., Osborne, B., Brandon, A. E., O'Reilly, L., Fiveash, C. E., Brown, S. H. J., Wilkins, B. P., Samsudeen, A., Yu, J., Devanapalli, B., Hertzog, A., Tolun, A. A., Kavanagh, T., Cooper, A. A., Mitchell, T. W., Biden, T. J., Smith, N. J., Cooney, G. J., Turner, N. Regulation of mitochondrial metabolism in murine skeletal muscle by the medium‐chain fatty acid receptor Gpr84. FASEB J. 33, 12264‐12276 (2019). www.fasebj.org
A Schwann cell–enriched circular RNA circ‐Ankib1 regulates Schwann cell proliferation following peripheral nerve injury
Authors: Mao Susu , Zhang Shanshan , Zhou Shuoshuo , Huang Tao , Feng Wei , Gu Xiaosong , Yu Bin
Published: August 2019

Schwann cells (SCs) play an essential role in nerve injury repair. A striking feature of the cellular response to peripheral nerve injury is the proliferation of SCs. Circular (circ)RNAs are enriched in the nervous system and are involved in physiologic and pathologic processes. However, the potential role of circRNAs in SC proliferation post nerve injury remains largely unknown. Using a sciatic nerve crush model, we obtained an expression profiling of circRNAs in injured sciatic nerves in rats by RNA sequencing and bioinformatics analysis, and we further identified a circRNA [circ–ankyrin repeat and in‐between Ring finger (IBR) domain containing 1 (Ankib1)] involved in SC proliferation by the transfection of specific small interfering RNAs. Overexpression of circ‐Ankib1, which was specifically and highly enriched in SCs, impaired SC proliferation and axon regeneration following sciatic nerve injury. Mechanistically, increased expression of DEx/H‐box helicase 9 (DHX9) postinjury might contribute to the down‐regulation of circ‐Ankib1, which further suppressed cytochrome P450, family 26, subfamily B, polypeptide 1 expression by sponging miR‐423‐5p, miR‐485‐5p, and miR‐666‐3p, leading to the induction of SC proliferation and nerve regeneration. Taken together, our results reveal a crucial role for circRNAs in regulating proliferation of SCs involved in sciatic nerve regeneration; as such, circRNAs may serve as a potential therapeutic avenue for nerve injury repair.—Mao, S., Zhang, S., Zhou, S., Huang, T., Feng, W., Gu, X., Yu, B. A Schwann cell‐enriched circular RNA circ‐Ankib1 regulates Schwann cell proliferation following peripheral nerve injury. FASEB J. 33, 12409–12424 (2019). www.fasebj.org
Comparison of Stand-alone Lateral Lumbar Interbody Fusion Versus Open Laminectomy and Posterolateral Instrumented Fusion in the Treatment of Adjacent Segment Disease Following Previous Lumbar Fusion Surgery
Authors: Louie Philip K. , Haws Brittany E. , Khan Jannat M. , Markowitz Jonathan , Movassaghi Kamran , Ferguson Joseph , Lopez Gregory D. , An Howard S. , Phillips Frank M.
Published: August 2019

Study Design.

Retrospective cohort study.

Objective.

The aim of this study was to compare clinical and radiographic outcomes of patients who underwent stand-alone lateral lumbar interbody fusion (LLIF) to those who underwent posterolateral fusion (PLF) for symptomatic adjacent segment disease (ASD).

Summary of Background Data.

Recent studies have suggested that LLIF can successfully treat ASD; however, there are no studies to date that compare LLIF with the traditional open PLF in this cohort.

Methods.

A total of 47 consecutive patients who underwent LLIF or PLF for symptomatic ASD between January 2007 and August 2016 after failure of conservative management were reviewed for this study. Patient-reported outcomes (PROs) were collected on all patients at preoperative, postoperative, and most recent post-operative visit using the Oswestry Disability Index, Visual Analog Scale (VAS)–Back, and VAS–Leg surveys. Preoperative, immediate postoperative, and most recent postoperative radiographs were assessed for pelvic incidence, fusion, intervertebral disc height, segmental and overall lumbar lordosis (LL). Symptomatic ASD was diagnosed if back pain, neurogenic claudication, or lower extremity radiculopathy presented following a previous lumbar fusion. Preoperative plain radiographs were evaluated for evidence of adjacent segment degeneration.

Results.

A total of 47 patients (23 LLIF, 24 PLF) met inclusion criteria. Operative times (P < 0.001) and intraoperative blood loss (P < 0.001) were significantly higher in the PLF group. Patients who underwent PLF were discharged approximately 3 days after the LLIF patients (P < 0.001). PROs in the PLF and LLIF cohorts showed significant and equivalent improvement, with equivalent radiographic fusion rates. LLIF significantly improve segmental lordosis (P < 0.001), total LL (P = 0.003), and disc height (P < 0.001) from preoperative to immediate postoperative and final follow-up (P = 0.004, P = 0.019, P ≤ 0.001, respectively).

Conclusion.

Although LLIF may provide less perioperative morbidity and shorter length of hospitalization, both techniques are safe and effective approaches to restore radiographic alignment and provide successful clinical outcomes in patients with adjacent segment degeneration following previous lumbar fusion surgery.

Level of Evidence: 3