bluuebunny/crossref_metadata_2025 huggingface dataset:
The US Media, Foreign Policy, and Public Support for War
Authors: Aday Sean
Published: June 2018

This chapter focuses on the relationship between news media and US foreign policy, with an emphasis on war—a subset of the latter—given that this has been a growing area of concern in political communication scholarship. Although interest in this topic goes back arguably to the roots of mass communication research, this chapter focuses on the explosion of research on it in the last quarter century. It highlights current theoretical and empirical approaches with an eye toward delineating what former Defense Secretary Donald Rumsfeld memorably called the “known unknowns.” Unanswered questions are also discussed.
Affect and Political Choice
Authors: Crigler Ann N. , Hevron Parker R.
Published: June 2018

Whether political observers and participants applaud or decry the presence of emotions in political decision-making, scholars have begun to view the relationship between affect and reason as a key component of decision-making. This chapter provides an overview of the research on affect and political choice. The authors argue that emotions undergird acts of political choice, not simply as additional variables to explain preferences or actions but also as integral to the processing of information and decision-making. They briefly define affect, emotion and mood and outline some of the methodologies commonly used to measure each of the four emotion functions that are central to political communication and choice. These four functions of emotion – expressive, perceptual/attentional, appraisal, and behavioral – are discussed in relation to political decision-making.
From Coo to Code
Authors: Parish-Morris Julia
Published: June 2018

Infants begin the process of language acquisition before birth, and their brains appear specially prepared to acquire complex systems of communication. This chapter charts the child’s journey from coo to code, discussing how children find their first words in a cacophony of sound, how they determine what words mean, and what happens when children have variable input or learn more than one language at the same time. The journey is exciting, enlightening, and filled with surprises as we explore the myriad abilities of a child’s developing mind.
Pharmacological Characteristics and Control Efficacy of a Novel SDHI Fungicide Pydiflumetofen Against Sclerotinia sclerotiorum
Authors: Duan Yabing , Xiu Qian , Li Haoran , Li Tao , Wang Jianxin , Zhou Mingguo
Published: June 2018

Pydiflumetofen is a novel succinate dehydrogenase inhibitor fungicide. In the current research, we determined the sensitivity of 166 Sclerotinia sclerotiorum strains to pydiflumetofen using mycelial growth inhibition method. The results suggest that pydiflumetofen exhibited a strong inhibitory activity against S. sclerotiorum and the EC50 values ranged from 0.0058 to 0.0953 μg ml−1, with a mean EC50 value of 0.0250 μg ml−1. However, the baseline sensitivity was not normally distributed because of a high variation factor. After treatment with pydiflumetofen, cell membrane permeability increases, but exopolysaccharide and oxalic acid production decreases, which contributes to reduced virulence of S. sclerotiorum and leads to failure of disease infection. In addition, protective and curative activity was performed on detached oilseed rape leaves by artificial inoculation. Pydiflumetofen exhibited excellent protective and curative effects against S. sclerotiorum on oilseed rape, and the protective effect was better than the curative effect. Further, field trials were conducted to evaluate the potential of pydiflumetofen in controlling Sclerotinia stem rot (SSR) caused by S. sclerotiorum on oilseed rape. Compared with the currently used fungicides, pydiflumetofen not only exhibited excellent control efficacy against SSR, but also dramatically reduced the dosage of fungicides in the field. Thus, this study provides important references for revealing pharmacological mechanism of pydiflumetofen against S. sclerotiorum and managing SSR on oilseed rape caused by benzimidazole- and dicarboximide-resistant populations.
Histopathologic study from a colorectal cancer screening in Chile: results from the first 2 years of an international collaboration between Chile and Japan
Authors: Kobayashi Maki , Kawachi Hiroshi , Pasternak Samara , Delgado Carlos , Pinto Pablo , Ito Takashi , Karelovic Stanko , Carrasco Hernan , Tanaka Koji , Okada Takuya , Odagaki Tomoyuki , Zárate Alejandro J. , Ponce Alejandra , Kronberg Udo , López-Köstner Francisco , Tsubaki Masahiro , Kawano Tatsuyuki , Eishi Yoshinobu
Published: June 2018

A national colorectal cancer (CRC) screening program began in Chile in 2012, which is an international collaboration between Japan and Chile and is based on a standardized protocol supported by Tokyo Medical and Dental University. We describe the results from the first 2 years of screening at one public hospital in Punta Arenas, Chile. Of 4124 asymptomatic individuals aged between 50 and 75 years, 485 participants with immunological fecal occult blood test values of at least 100 ng/ml and/or those with family histories of CRC underwent colonoscopies. Lesions were found in 291 participants, and 642 histologic samples were obtained. Chilean pathologists made the initial histologic diagnoses, and a Japanese pathologist reviewed the histologic slides and analyzed the results. Of the 291 participants with lesions, 60 (20.6%) were diagnosed with adenocarcinomas, of which 50 (83.3%) were early-phase adenocarcinomas (pTis or pT1), and 163 (56.0%) were diagnosed with conventional adenomas, of which 96 (58.9%) were high-risk adenomas. The cancer prevalence within the screened population was 1.5% (60 of 4124). The colonoscopy cancer detection rate was 12.4% (60 of 485). Notably, we detected one flat-depressed (0–IIc) lesion that measured 5 mm and had invaded the submucosa. The findings from this screening program are the first to show the histopathologic distributions of consecutive lesions and the high incidence of CRC in Chile. The high detection rates for high-risk adenomas and cancer support the feasibility of early CRC screening and its potential to reduce the mortality associated with CRC.
The organization of Danish emergency departments
Authors: Moellekaer Anders , Duvald Iben , Obel Borge , Madsen Bo , Eskildsen Jacob , Kirkegaard Hans
Published: June 2018

Introduction

Twenty-one new Danish emergency departments (EDs) were established following a 2007 policy reform that included ED autonomy to self-organize. The aim of this study was to describe the organization of the 21 departments and their organizational challenges.

Participants and methods

We used a qualitative design based on COREQ guidelines. All 21 EDs participated, and 123 semi-structured interviews with hospital and ED leaders, physicians, nurses, and secretaries were performed between 2013 and 2015. We used the framework matrix method to investigate the ED goals, setting, structure, staff, task coordination, and incentive structure.

Results

We identified three generic models (virtual, hybrid, and independent). All had goals of high quality of care and high efficiency. The virtual model was staffed by junior physicians and tasks were coordinated by other departments. The hybrid model was staffed by junior physicians and senior physicians according to other departments and the ED. The ED coordinated all activities. The independent model was staffed by junior physicians and senior physicians, and activities were coordinated by the ED. Of the EDs, 19 utilized different organizational models at different times during a 24-h period and on weekdays and weekends. The main challenge of the virtual and hybrid models was high dependency on other departments. The main challenge of the independent model was establishing a high level of quality of emergency medicine.

Discussion and conclusion

We identified three organizational ED models (virtual, hybrid, and independent). Nineteen EDs used more than one organizational model depending on the time of day or day of the week.
Diagnostic Algorithm for Cholesteryl Ester Storage Disease
Authors: Lipiński Patryk , Ługowska Agnieszka , Zakharova Ekaterina Y. , Socha Piotr , Tylki‐Szymańska Anna
Published: June 2018

Background:

Lysosomal acid lipase deficiency (LAL‐D) is a rare autosomal recessive lysosomal lipid storage disorder that results in an early‐onset, severe, and lethal phenotype, known as Wolman disease, or a late‐onset, attenuated phenotype, cholesteryl ester storage disease (CESD). The aim of our study was to describe the clinical presentation of CESD, focusing on the first noted abnormalities in patients. A diagnostic algorithm of CESD was also proposed.

Methods:

This is an observational, 1‐center study of 19 Polish patients with late‐onset LAL‐D.

Results:

The mean age at which the first symptoms were reported was 4 years and 6 months. A mild hepatomegaly was the most common initial abnormality observed in all (100%) patients. Seven (37%) patients were noted to have mildly to moderately elevated serum transaminases. At the time of first hospitalization all (100%) patients presented with hepatomegaly, 15 (79%) patients presented with elevated serum transaminases and all (100%) patients had dyslipidemia. The mean age at the time of CESD diagnosis was 7 years and 2 months. Diagnoses were based on a deficient LAL activity in leukocytes (in all patients) and the LIPA gene mutations (in 47% of them). All the patients were carriers for the mutation c.894G>A in the LIPA gene. There was approximately a 3‐year delay from initial symptoms to final diagnosis.

Conclusions:

Hepatomegaly constitutes the most common presenting clinical sign of CESD. Hepatomegaly and dyslipidemia defined as elevated serum total and LDL cholesterol, elevated triglycerides and normal to low HDL cholesterol, comprises the most characteristic findings at CESD diagnosis.
Peripheral Infiltration and Extravasation Injury Methodology
Authors: Odom Brian , Lowe Leah , Yates Charlotte
Published: June 2018

Peripheral infiltration is defined as the inadvertent delivery of nonvesicant fluid or medication into surrounding tissue that has the potential to harm the patient. Vesicant fluid that has leaked into the tissue space is called extravasation. At present, there is no agreement in the literature on the best practice for managing these injuries in pediatric patients. The purpose of this study was to identify occurrences of peripheral infiltration injuries and examine treatment modalities used to treat pediatric patients who suffered such an injury.
Phlebitis Signs and Symptoms With Peripheral Intravenous Catheters
Authors: Mihala Gabor , Ray-Barruel Gillian , Chopra Vineet , Webster Joan , Wallis Marianne , Marsh Nicole , McGrail Matthew , Rickard Claire M.
Published: June 2018

This study was undertaken to calculate the incidence of 8 signs and symptoms used for the diagnosis of phlebitis with peripheral intravenous catheters, or short peripheral catheters, and the level of correlation between them. A total of 22 789 daily observations of 6 signs (swelling, erythema, leakage, palpable venous cord, purulent discharge, and warmth) and 2 symptoms (pain and tenderness) were analyzed of 5907 catheter insertion sites. Most signs and symptoms of phlebitis occurred only occasionally or rarely; the incidence of tenderness was highest (5.7%). Correlations were mostly low; warmth correlated strongly with tenderness, swelling, and erythema.
Criticality of Maternal Complications During Childbirths
Authors: Guglielminotti Jean , Landau Ruth , Wong Cynthia A. , Li Guohua
Published: June 2018

Background

The incidence of severe maternal morbidity is increasing in the United Sates. To improve maternal outcomes, three maternal complications have been selected for priority intervention based on their proportionate mortality and preventability: obstetric hemorrhage, severe hypertension, and venous thromboembolism. This approach excludes complications that are not associated with high mortality but significantly contribute to maternal morbidity. The aim of this study was to provide an alternative ranking of maternal complications requiring interventions using cost-based criticality analysis.

Methods

Discharge records indicating delivery hospitalizations, and 17 maternal complications were identified using International Classification of Diseases, Ninth Revision, Clinical Modification codes in the 2012 National Inpatient Sample, a 20% national representative sample of hospital discharge records from community hospitals. For each complication, criticality was calculated as the product of its incidence and severity. Severity was estimated using excess cost, the difference between the mean costs of discharges with and without the complication. Costs were calculated as the product of hospital charges and a cost-to-charge ratio and adjusted with a linear regression model. Complications were ranked based on criticality.

Results

The study sample included 734,865 delivery hospitalizations. At least one complication was recorded in 80,657 discharges (11.0%, 95% confidence interval = 10.9–11.1). The four highest-ranked critical complications were pre-eclampsia/eclampsia (criticality: $93), postpartum hemorrhage ($47), gestational hypertension ($34), and anesthesia-related complications ($5).

Conclusions

In addition to postpartum hemorrhage and severe hypertension, anesthesia-related complications and gestational hypertension may be new priority targets for interventions during delivery hospitalizations. Criticality analysis seems to be an alternative or complimentary approach for planning healthcare quality improvement programs.
Racial and Ethnic Differences in Viral Suppression Among HIV-Positive Women in Care
Authors: Nwangwu-Ike Ndidi , Frazier Emma L. , Crepaz Nicole , Tie Yunfeng , Sutton Madeline Y.
Published: June 2018

Background:

Women with HIV diagnoses are less likely to be virally suppressed than men. Women of different racial/ethnic groups may be differentially affected by sociodemographic factors. We examined differences in viral suppression among women by race/ethnicity and associated variables to inform prevention interventions.

Methods:

We used data from the 2010–2014 cycles of the Medical Monitoring Project, a cross-sectional survey of HIV-positive adults in care. We limited analyses to black, Hispanic, and white women. We calculated weighted prevalences of recent viral suppression (undetectable or <200 copies/mL) and sustained viral suppression (consistent viral suppression during the past 12 months) among women by race/ethnicity. We computed adjusted prevalence differences (aPDs) and 95% confidence intervals (CIs) for viral suppression by racial/ethnic group, controlling for selected variables, including available social determinants of health variables.

Results:

Among women, 62.9% were black, 19.8% Hispanic, and 17.3% white. Overall, 74.3% had recent viral suppression, and 62.3% had sustained viral suppression. Compared with white women (79.7%, CI: 77.2 to 82.2), black (72.5%, CI: 70.3 to 74.7; PD: 7.2) and Hispanic (75.4%, CI: 72.6 to 78.3; PD: 4.3) women were less likely to have recent viral suppression. In multivariable analyses, after adjusting for antiretroviral therapy adherence, HIV disease stage, age, homelessness, and education, black–white aPDs remained significant for recent (aPD: 4.8, CI: 1.6 to 8.1) and sustained (aPD: 5.0, CI: 1.1 to 9.0) viral suppression.

Conclusion:

Viral suppression was suboptimal for all women, but more for black and Hispanic women. Differences between black, Hispanic, and white women may be partially due to antiretroviral therapy adherence, HIV disease stage, and social determinants of health factors.
Brief Report: Safety and Tolerability of Inguinal Lymph Node Biopsy in Individuals With Acute HIV Infection in Thailand
Authors: Chintanaphol Michelle , Sacdalan Carlo , Chottanapund Suthat , Pinyakorn Suteeraporn , Buranapraditkun Supranee , Crowell Trevor A. , Kroon Eugene , Manasnayakorn Sopark , Chipman Jeffrey G. , Schacker Timothy W. , Michael Nelson , Phanuphak Nittaya , Spudich Serena S. , Colby Donn J. , Ananworanich Jintanat ,   on behalf of the RV254/SEARCH010 study groups
Published: June 2018

Introduction:

Latent HIV reservoirs are rapidly established in lymphoid tissues during acute HIV infection (AHI). Sampling these tissues provides important information about HIV pathogenesis. This period is associated with viral replication and immune activation that may affect procedure-related adverse events (AEs). We examined the safety and tolerability of inguinal lymph node (LN) biopsy in research participants with AHI in Bangkok, Thailand.

Methods:

Between 2013 and 2016, 67 AHI participants in the RV254/SEARCH010 study underwent at least one optional inguinal LN biopsy during AHI at the baseline visit and/or after antiretroviral therapy (median 48 weeks after antiretroviral therapy). Biopsy-related AEs were graded according to NIH Division of AIDS guidelines. Poisson regression was used to calculate incidence rate ratios and 95% confidence intervals to evaluate associations of demographic and HIV characteristics, procedure timing, and repetition with AE incidence.

Results:

Of the 67 participants, 97% were male with a median age of 26. Among 78 LN biopsies (39 at baseline and 39 at follow-up), 10 (12.8%) AEs were reported: 6 (7.7%) grade 1 and 4 (5.1%) grade 2. The AEs were biopsy-site discomfort (n = 8, 10.2%) and hematoma (n = 2, 2.6%). No factors were significantly associated with AE incidence. All biopsy-related AEs were transient and self-limited.

Conclusions:

Inguinal LN biopsies were safe and well tolerated in mostly Thai men with AHI. As LN biopsies become an integral part of HIV research, this study provides information to participants, researchers, and institutional review boards that these samples can be safely obtained.
Cotransmission of Malaria and HIV to Infants of Mothers Coinfected With Malaria and HIV in the HAART Era in Benin City, Nigeria
Authors: Sadoh Ayebo , Eki-Udoko Fidelis E.
Published: June 2018

Introduction:

Malaria and HIV are vertically transmitted to infants. In an era where specific interventions are available to reduce the burden of malaria in pregnancy and vertical transmission of HIV, we examined the transmission and cotransmission of HIV and malaria to infants of mothers coinfected with malaria and HIV.

Methods:

A cross-sectional analytic study performed on 101 HIV/malaria–coinfected mothers and their infants for whom DNA polymerase chain reaction results were available. Blood film for malaria parasites was performed on cord blood and peripheral blood on days 1, 3, and 7 in the newborns. Maternal peripheral blood film for malaria parasite was performed at delivery, and placental tissue was obtained for confirmation of placental malaria by histology. All infants received DNA polymerase chain reaction testing for HIV at 6–8 weeks of life.

Results:

Cotransmission of malaria and HIV occurred in 2 (1.98%) infants. Vertical transmission of HIV occurred in 7 (7%) babies, whereas congenital malaria was present in 32 (31.7%) babies. The transmission of HIV and presence of congenital malaria were not significantly associated with each otherP= 1.000. Of the 88 babies of mothers who commenced highly active antiretroviral treatment (HAART) before pregnancy, 5 (5.7^) had HIV, which was significantly less than 2 (40%) of 5 babies of mothers who commenced HAART during pregnancyP= 0.04.

Conclusions:

Among mothers coinfected with malaria and HIV, vertical transmission of malaria and HIV was not associated with each other. HAART reduces vertical transmission of HIV especially if started before pregnancy.
Diagnostic Value of Diffusion-Weighted Imaging and Apparent Diffusion Coefficient in Assessment of the Activity of Crohn Disease: 1.5 or 3 T
Authors: Abd-El Khalek Abd-ALRazek Ahmed , Fahmy Dalia Monir
Published: June 2018

Objective

The objective of this study is to evaluate the role of diffusion-weighted imaging (DWI) in assessment of the activity of Crohn disease (CD) and to explore differences between DWI in 3 T and 1.5 T.

Methods

Postcontrast magnetic resonance enterography with DWI of 72 patients with pathological proof of CD was retrospectively evaluated for restricted diffusion qualitatively and quantitavely in 3 T (n = 40) and 1.5 T (n = 32). Magnetic resonance activity score of 7 or higher was used as reference of activity.

Results

Fifty-five patients had active lesions. Diffusion-weighted imaging hyperintensity showed sensitivity (100%, 100%) and specificity (88.89%, 100%) in 1.5/3 T for activity assessment. Mean ± SD apparent diffusion coefficient for active lesions was 1.21 ± 0.42 and 1.28 ± 0.59 × 10−3 mm2/s in 1.5 and 3 T, respectively. The proposed cutoff values of 1.35 and 1.38 × 10−3 mm2/s in 1.5 and 3 T, respectively, had sensitivity (80%, 93%), specificity (100%, 90%), accuracy (88%, 93%), and no significant difference in accuracy between 1.5/3 T (P = 0.48).

Conclusions

Diffusion-weighted imaging hypersensitivity and apparent diffusion coefficient values accurately assessed the activity of CD. No significant statistical difference in diagnostic accuracy was detected between 1.5 and 3 T.
Single-Shot Coronary Quiescent-Interval Slice-Selective Magnetic Resonance Angiography Using Compressed Sensing: A Feasibility Study in Patients With Congenital Heart Disease
Authors: Shen Daming , Edelman Robert R. , Robinson Joshua D. , Haji-Valizadeh Hassan , Messina Marci , Giri Shivraman , Koktzoglou Ioannis , Rigsby Cynthia K. , Kim Daniel
Published: June 2018

Objective

The aim of this study was to determine whether it is feasible to visualize the coronary origins in patients with congenital heart disease (CHD) using single-shot coronary quiescent-interval slice-selective (QISS) magnetic resonance angiography (MRA) with compressed sensing (CS).

Methods

This retrospective study leveraged a parent study, which aimed to compare breath-hold, 2.1-fold accelerated, 2-shot coronary QISS MRA and clinical standard contrast-enhanced (CE) MRA in 14 patients with CHD (mean age, 17.0 ± 8.6 years, 6 females and 8 males). We evaluated the feasibility of single-shot coronary QISS MRA by retrospectively undersampling the 2-shot data set by an additional factor of 2, performing CS reconstruction, and comparing the retrospectively derived single-shot QISS MRA to 2-shot coronary QISS MRA and clinical standard CE MRA. For quantitative analysis, structural similarity index and normalized root mean square error were calculated. For qualitative analysis, 2 experienced readers scored the conspicuity of coronary origins on a 5-point Likert scale (1 = nondiagnostic, 2 = poor, 3 = clinically acceptable, 4 = good, 5 = excellent).

Results

Compared with 2-shot QISS, single-shot QISS produced normalized root mean square error of 5.8% ± 0.8% and structural similarity index of 95.4% ± 1.6%, suggesting high data fidelity by CS reconstruction. Compared with the mean conspicuity scores for clinical CE MRA (4.2 ± 0.5 and 4.1 ± 0.6 for right and left coronary origins, respectively), the mean conspicuity scores were not significantly different (P > 0.3) for 2-shot QISS (4.4 ± 0.9 and 4.2 ± 1.1, respectively) and single-shot QISS with CS (4.3 ± 1.1 and 3.8 ± 1.3, respectively) and deemed clinically acceptable to good (scores ≥3.0).

Conclusions

This study shows that it is feasible to visualize the coronary origins in patients with CHD with clinically acceptable to good image quality using single-shot coronary QISS MRA with CS.
A novel regulatory factor affecting the transcription of methionine biosynthesis genes in Escherichia coli experiencing sustained nitrogen starvation
Authors: Switzer Amy , Evangelopoulos Dimitrios , Figueira Rita , de Carvalho Luiz Pedro S. , Brown Daniel R. , Wigneshweraraj Sivaramesh
Published: June 2018

The initial adaptive transcriptional response to nitrogen (N) starvation in Escherichia coli involves large-scale alterations to the transcriptome mediated by the transcriptional activator, NtrC. One of these NtrC-activated genes is yeaG, which encodes a conserved bacterial kinase. Although it is known that YeaG is required for optimal survival under sustained N starvation, the molecular basis by which YeaG benefits N starved E. coli remains elusive. By combining transcriptomics with targeted metabolomics analyses, we demonstrate that the methionine biosynthesis pathway becomes transcriptionally dysregulated in ΔyeaG bacteria experiencing sustained N starvation. It appears the ability of MetJ, the master transcriptional repressor of methionine biosynthesis genes, to effectively repress transcription of genes under its control is compromised in ΔyeaG bacteria under sustained N starvation, resulting in transcriptional derepression of MetJ-regulated genes. Although the aberrant biosynthesis does not appear to be a contributing factor for the compromised viability of ΔyeaG bacteria experiencing sustained N starvation, this study identifies YeaG as a novel regulatory factor in E. coli affecting the transcription of methionine biosynthesis genes under sustained N starvation.
Genesis of theαβT-cell receptor
Authors: Dupic Thomas , Marcou Quentin , Walczak Aleksandra M. , Mora Thierry
Published: June 2018

The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, calledαandβ, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human TCR repertoires, we quantitively characterize theαβgeneration process. We estimate the probabilities of a rescue recombination of theβchain on the second chromosome upon failure or success on the first chromosome. Unlikeβchains,αchains recombine simultaneously on both chromosomes, resulting in correlated statistics of the two genes which we predict using a mechanistic model. We find that∼28% of cells express bothαchains. Altogether, our statistical analysis gives a complete quantitative mechanistic picture that results in the observed correlations in the generative process. We learn that the probability to generate any TCRαβis lower than 10–12and estimate the generation diversity and sharing properties of theαβTCR repertoire.
Distinct isoforms of Nrf1 diversely regulate different subsets of its cognate target genes
Authors: Wang Meng , Qiu Lu , Ru Xufang , Song Yijiang , Zhang Yiguo
Published: June 2018

The single Nrf1 gene has capability to be differentially transcripted alongside with alternative mRNA-splicing and subsequent translation through different initiation signals so as to yield distinct lengths of polypeptide isoforms. Amongst them, three of the most representatives are Nrf1α, Nrf1β and Nrf1γ, but the putative specific contribution of each isoform to regulating ARE-driven target genes remains unknown. To address this, we have here established three cell lines on the base of the Flp-In™ T-REx™ system, which are allowed for tetracycline-inducibly stable expression of Nrf1α, Nrf1β and Nrf1γ. The RNA-Sequencing results have demonstrated that a vast majority of differentially expressed genes (i.e. >90% DEGs detected) were dominantly up-regulated by Nrf1α and/or Nrf1β following induction by tetracycline. By contrast, other DEGs regulated by Nrf1γ were far less than those regulated by Nrf1α/β (i.e. ~11% of Nrf1α and 7% of Nrf1β). Further transcriptomic analysis revealed that tetracycline-induced expression of Nrf1γ significantly increased the percentage of down-regulated genes in total DEGs. These statistical data were further validated by quantitative real-time PCR. The experimental results indicate that distinct Nrf1 isoforms make diverse and even opposing contributions to regulating different subsets of target genes, such as those encoding 26S proteasomal subunits and others involved in various biological processes and functions. Collectively, Nrf1γ acts as a major dominant-negative competitor against Nrf1α/β activity, such that a number of DEGs regulated by Nrf1α/β are counteracted by Nrf1γ.
Demand elasticity predicts addiction endophenotypes and the therapeutic efficacy of an orexin/hypocretin-1 receptor antagonist in rats
Authors: James Morgan H , Bowrey Hannah E , Stopper Colin M , Aston-Jones Gary
Published: June 2018

Behavioral economics is a powerful, translational approach for measuring drug demand in both humans and animals. Here, we asked if demand for cocaine in rats with limited drug experience could be used to identify individuals most at risk of expressing an addiction phenotype following either long (LgA) or intermittent (IntA) access self-administration schedules, both of which model the transition to uncontrolled drug seeking. Moreover, because the orexin-1 receptor antagonist SB-334867 (SB) is particularly effective at reducing drug-seeking in highly motivated individuals, we asked whether demand measured after prolonged drug experience could predict SB efficacy. Demand elasticity (α) measured immediately following acquisition of cocaine self-administration (‘baseline α’) was positively correlated with α assessed after 2w of LgA or IntA. Baseline α also predicted the magnitude of compulsive responding for cocaine, drug seeking in initial abstinence, and cued reinstatement following LgA, IntA or standard short access (ShA). When demand was measured after LgA, IntA or ShA, α predicted the same addiction endophenotypes predicted by baseline α, as well as primed reinstatement and the emergence of negative emotional mood behavior following abstinence. Post-LgA/IntA/ShA α also predicted the efficacy of SB, such that high demand rats showed greater reductions in motivation for cocaine following SB (10 and 30mg/kg) compared to low demand rats. Together, these findings indicate that α might serve as a behavioral biomarker to predict individuals most likely to progress from controlled to uncontrolled drug use, and to identify individuals most likely to benefit from orexin-based therapies for the treatment of addiction.
Genome analysis of the unicellular eukaryoteEuplotes vannusreveals molecular basis for sex determination and tolerance to environmental stresses
Authors: Chen Xiao , Jiang Yaohan , Gao Feng , Zheng Weibo , Krock Timothy J. , Stover Naomi A. , Lu Chao , Katz Laura A. , Song Weibo
Published: June 2018

As a model organism in studies of cell and environmental biology, the free-living and cosmopolitan ciliated protistEuplotes vannushas more than ten mating types (sexes) and shows strong resistance to environmental stresses. However, the molecular basis of its sex determination mechanism and how the cell responds to stress remain largely unknown. Here we report a combined analysis ofde novoassembled high-quality macronucleus (MAC; i.e. somatic) genome and partial micronucleus (MIC; i.e. germline) genome ofEuplotes vannus. Furthermore, MAC genomic and transcriptomic data from several mating types ofE. vannuswere investigated and gene expression levels were profiled under different environmental stresses, including nutrient scarcity, extreme temperature, salinity and the presence of free ammonia. We found thatE. vannus, which possesses gene-sized nanochromosomes in its MAC, shares a similar pattern on frameshifting and stop codon usage asEuplotes octocarinatusand may be undergoing incipient sympatric speciation withEuplotes crassus. Somatic pheromone loci ofE. vannusare generated from programmed DNA rearrangements of multiple germline macronuclear destined sequences (MDS) and the mating types ofE. vannusare distinguished by the different combinations of pheromone loci instead of possessing mating type-specific genes. Lastly, we linked the resilience to environmental temperature change to the evolved loss of temperature stress-sensitive regulatory regions of HSP70 gene inE. vannus. Together, the genome resources generated in this study, which are available online atEuplotes vannusDB (http://evan.ciliate.org), provide new evidence for sex determination mechanism in eukaryotes and common pheromone-mediated cell-cell signaling and cross-mating.
3’ Branch Ligation: A Novel Method to Ligate Non-Complementary DNA to Recessed or Internal 3’OH Ends in DNA or RNA
Authors: Wang Lin , Xi Yang , Zhang Wenwei , Wang Weimao , Shen Hanjie , Wang Xiaojue , Zhao Xia , Alexeev Andrei , Peters Brock A. , Albert Alayna , Xu Xu , Ren Han , Wang Ou , Kirkconnell Killeen , Perazich Helena , Clark Sonya , Hurowitz Evan , Chen Ao , Xu Xun , Drmanac Radoje , Jiang Yuan
Published: June 2018

Nucleic acid ligases are crucial enzymes that repair breaks in DNA or RNA during synthesis, repair and recombination. Various molecular tools have been developed using the diverse activities of DNA/RNA ligases. Herein, we demonstrate a non-conventional ability of T4 DNA ligase to join 5’ phosphorylated blunt-end double-stranded DNA to DNA breaks at 3’ recessive ends, gaps, or nicks to form a 3’ branch structure. Therefore, this base pairing-independent ligation is termed 3’ branch ligation (3’BL). In an extensive study of optimal ligation conditions, similar to blunt-end ligation, the presence of 10% PEG-8000 in the ligation buffer significantly increased ligation efficiency. A low level of nucleotide preference was observed at the junction sites using different synthetic DNAs. Furthermore, we discovered that T4 DNA ligase efficiently ligated DNA to the 3’ recessed end of RNA, not to that of DNA, in a DNA/RNA hybrid, whereas RNA ligases are less efficient in this reaction. These novel properties of T4 DNA ligase can be utilized as a broad molecular technique in many important applications. We performed a proof-of-concept study of a new directional tagmentation protocol for next generation sequencing (NGS) library construction that eliminates inverted adapters and allows sample barcode insertion adjacent to genomic DNA. 3’BL after single transposon tagmentation can theoretically achieve 100% usable template, and our empirical data demonstrate that the new approach produced higher yield compared with traditional double transposon or Y transposon tagmentation. We further explore the potential use of 3’BL for preparing targeted RNA NGS libraries with mitigated structure-based bias and adapter dimer problems.
CRISPRi-Seq for the Identification and Characterisation of Essential Mycobacterial Genes and Transcriptional Units
Authors: de Wet Timothy J. , Gobe Irene , Mhlanga Musa M. , Warner Digby F.
Published: June 2018

High-throughput essentiality screens have enabled genome-wide assessments of the genetic requirements for growth and survival of a variety of bacteria in different experimental models. The reliance in many of these studies on transposon (Tn)-based gene inactivation has, however, limited the ability to probe essential gene function or design targeted screens. We interrogated the potential of targeted, large-scale, pooled CRISPR interference (CRISPRi)-based screens to extend conventional Tn approaches in mycobacteria through the capacity for positionally regulable gene repression. Here, we report the utility of the “CRISPRi-Seq” method for targeted, pooled essentiality screening, confirming strong overlap with Tn-Seq datasets. In addition, we exploit this high-throughput approach to provide insight into CRISPRi functionality. By interrogating polar effects and combining image-based phenotyping with CRISPRi-mediated depletion of selected essential genes, we demonstrate that CRISPRi-Seq can functionally validate Transcriptional Units within operons. Together, these observations suggest the utility of CRISPRi-Seq to provide insights into (myco)bacterial gene regulation and expression on a genome-wide scale.
Identification and characterisation of serotonin signalling in the potato cyst nematodeGlobodera pallidareveals new targets for crop protection
Authors: Crisford Anna , Calahorro Fernando , Ludlow Elizabeth , Marvin Jessica M.C. , Hibbard Jennifer K. , Lilley Catherine J. , Kearn James , Keefe Francesca , Harmer Rachael , Urwin Peter E. , O’Connor Vincent , Holden-Dye Lindy
Published: June 2018

Plant parasitic nematodes are microscopic pests that invade plant roots and cause extensive damage to crops worldwide. To investigate mechanisms underpinning their parasitic behaviour we used a chemical biology approach: We discovered that reserpine, a plant alkaloid known for its antagonism of the mammalian vesicular monoamine transporter VMAT and ability to impart a global depletion of synaptic biogenic amines in the nervous system, potently impairs the ability of the potato cyst nematodeGlobodera pallidato enter the host plant root. We show that this effect of reserpine is mediated by an inhibition of serotonergic signalling that is essential for activation of the stylet, a lance-like organ that protrudes from the mouth of the worm and which is used to pierce the host root to gain access. Prompted by this we identified core molecular components ofG. pallidaserotonin signalling encompassing the target of reserpine, VMAT; the synthetic enzyme for serotonin, tryptophan hydroxylase; the G protein coupled receptor SER-7 and the serotonin-gated chloride channel MOD-1. We found that inhibitors of tryptophan hydroxylase, SER-7 and MOD-1 phenocopy the plant protecting action of reserpine. Thus targeting the serotonin signalling pathway presents a promising new route to control plant parasitic nematodes.

Indian snakeroot, an herbal medicine prepared from the roots of the shrubRauwolfia serpentina, has been used for centuries for its calming action. The major active constituent is reserpine which works by depleting a specific class of mood regulating chemical in the brain, the biogenic amines. We have discovered a remarkable effect of reserpine on a pest of global concern, the plant parasitic nematodes. These microscopic worms invade the roots of crops presenting a severe threat to food production. We show that reserpine disables serotonin signalling in the worm’s ‘brain’ that regulates the rhythmic thrusting of the stylet: a lance-like structure that protrudes from its mouth to pierce the plant root and which is essential to its parasitic lifecycle. Thus, reserpine joins nicotine as another intriguing example of Nature evolving its own protection against pests. We have identified key components of the serotonin signalling pathway in the potato cyst nematodeGlobodera pallidaand show that chemicals that target these sites inhibit the ability of the nematode to invade its host plant. We conclude that biogenic amine transmitters are intimately involved in the worm’s parasitic behaviour and provide a new discrete route to crop protection.
Machine Learning in Multi-Omics Data to Assess Longitudinal Predictors of Glycaemic Health
Authors: Prélot Laurie , Draisma Harmen , Anasanti Mila D. , Balkhiyarova Zhanna , Wielscher Matthias , Yengo Loic , Balkau Beverley , Roussel Ronan , Sebert Sylvain , Ala-Korpela Mika , Froguel Philippe , Jarvelin Marjo-Riitta , Kaakinen Marika , Prokopenko Inga
Published: June 2018

Type 2 diabetes (T2D) is a global health burden that will benefit from personalised risk prediction and targeted prevention programmes. Omics data have enabled more detailed risk prediction; however, most studies have focussed on directly on the ability of DNA variants predicting T2D onset with less attention given to epigenetic regulation and glycaemic trait variability. By applying machine learning to the longitudinal Northern Finland Birth Cohort 1966 (NFBC 1966) at 31 (T1) and 46 (T2) years old, we predicted fasting glucose (FG) and insulin (FI), glycated haemoglobin (HbA1c) and 2-hour glucose and insulin from oral glucose tolerance test (2hGlu, 2hIns) at T2 in 513 individuals from 1,001 variables at T1 and T2, including anthropometric, metabolic, metabolomic and epigenetic variables. We further tested whether the information obtained by the machine learning models in NFBC could be used to predict glycaemic traits in the independent French study with 48 matching predictors (DESIR, N=769, age range 30-65 years at recruitment, interval between data collections: 9 years). In this study, FG and FI were best predicted, with average R2 values of 0.38 and 0.53. Sex, branched-chain and aromatic amino acids, HDL-cholesterol, glycerol, ketone bodies, blood pressure at T2 and measurements of adiposity at T1, as well as multiple methylation marks at both time points were amongst the top predictors. In the validation analysis, we reached R2 values of 0.41/0.55 for FG/FI when trained and tested in NFBC1966 and 0.17/0.30 when trained in NFBC1966 and tested in DESIR. We identified clinically relevant sets of predictors from a large multi-omics dataset and highlighted the potential of methylation markers and longitudinal changes in prediction.
A multi-model Framework for the Arabidopsis life cycle
Authors: Zardilis Argyris , Hume Alastair , Millar Andrew J.
Published: June 2018

Linking our understanding of biological processes at different scales is a major conceptual challenge in biology, which is aggravated by differences in research methods. Modelling can be a useful approach to consolidating our understanding across traditional research domains. The laboratory model speciesArabidopsis thalianais very widely used to study plant growth processes and has also been tested more recently in eco-physiology and population genetics. However, approaches from crop modelling that might link these domains are rarely applied to Arabidopsis. Here, we combine plant growth models with phenology models from eco-physiology, using the agent-based modelling language Chromar. We introduce a simpler Framework Model of vegetative growth for Arabidopsis,FM-lite.By extending this model to include inflorescence and fruit growth and seed dormancy, we present a whole-life-cycle, multi-modelFM-life,which allows us to simulate at the population level in various genotype x environment scenarios. Environmental effects on plant growth distinguish between the simulated life history strategies that were compatible with previously-described Arabidopsis phenology. Our results simulate reproductive success that is founded on the broad range of physiological processes familiar from crop models and suggest an approach to simulate evolution directly in future.

Highlight

A whole-life-cycle multi-model forArabidopsis thalianacombines phenology and physical growth models to explain reproductive success in different genotype x environment scenarios.
The functional genomic circuitry of human glioblastoma stem cells
Authors: MacLeod Graham , Bozek Danielle A. , Rajakulendran Nishani , Monteiro Vernon , Ahmadi Moloud , Steinhart Zachary , Kushida Michelle M. , Yu Helen , Coutinho Fiona J. , Restall Ian , Hao Xiaoguang , Hart Traver , Luchman H. Artee , Weiss Samuel , Dirks Peter B. , Angers Stephane
Published: June 2018

Successful glioblastoma (GBM) therapies have remained elusive due to limitations in understanding mechanisms of growth and survival of the tumorigenic population. Using CRISPR-Cas9 approaches in patient-derived GBM stem cells to interrogate function of the coding genome, we identify diverse actionable pathways responsible for growth that reveal the gene-essential circuitry of GBM stemness. In particular, we describe the Sox developmental transcription factor family; H3K79 methylation by DOT1L; and ufmylation stress responsiveness programs as essential for GBM stemness. Additionally, we find mechanisms of temozolomide resistance and sensitivity that could lead to combination strategies with this standard of care treatment. By reaching beyond static genome analysis of bulk tumors, with a genome wide functional approach, we dive deep into a broad range of biological processes to provide new understanding of GBM growth and treatment resistance.

Significance

Glioblastoma (GBM) remains an incurable disease despite an increasingly thorough depth of knowledge of the genomic and epigenomic alterations of bulk tumors. Evidence from multiple approaches support that GBM reflects an aberrant developmental hierarchy, with GBM stem cells (GSCs), fueling tumor growth and invasion. The properties of this tumor subpopulation may also in part explain treatment resistance and disease recurrence. Unfortunately, we still have a limited knowledge of the molecular circuitry of these cells and progress has been slow as we have not been able, until recently, to interrogate function at the genome-wide scale. Here, using parallel genome-wide CRISPR-Cas9 screens, we identify the essential genes for GSC growth. Further, by screening in the presence of low and high dose temozolomide, we identify mechanisms of drug resistance and sensitivity. These functional screens in patient derived cells reveal new aspects of GBM biology and identify a diversity of actionable targets such as genes governing stem cell traits, epigenome regulation and the response to stress stimuli.
Modeling the growth of organisms validates a general relation between metabolic costs and natural selection
Authors: Ilker Efe , Hinczewski Michael
Published: June 2018

Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to date unproven, hypothesis is that this disadvantage is equal to the fractional cost relative to the total resting metabolic expenditure. This hypothesis has found a recent resurgence as a powerful tool for quantitatively understanding the strength of selection among different classes of organisms. Our work explores the validity of the hypothesis from first principles through a generalized metabolic growth model, versions of which have been successful in describing organismal growth from single cells to higher animals. We build a mathematical framework to calculate how perturbations in maintenance and synthesis costs translate into contributions to the selection coefficient, a measure of relative fitness. This allows us to show that the hypothesis is an approximation to the actual baseline selection coefficient. Moreover we can directly derive the correct prefactor in its functional form, as well as analytical bounds on the accuracy of the hypothesis for any given realization of the model. We illustrate our general framework using a special case of the growth model, which we show provides a quantitative description of overall metabolic synthesis and maintenance expenditures in data collected from a wide array of unicellular organisms (both prokaryotes and eukaryotes). In all these cases we demonstrate that the hypothesis is an excellent approximation, allowing estimates of baseline selection coefficients to within 15% of their actual values. Even in a broader biological parameter range, covering growth data from multicellular organisms, the hypothesis continues to work well, always within an order of magnitude of the correct result. Our work thus justifies its use as a versatile tool, setting the stage for its wider deployment.