bluuebunny/crossref_metadata_2025 huggingface dataset:
Active PI3K abrogates central tolerance in high-avidity autoreactive B cells
Authors: Greaves Sarah A. , Peterson Jacob N. , Strauch Pamela , Torres Raul M. , Pelanda Roberta
Published: April 2019

Autoreactive B cells that bind self-antigen with high avidity in the bone marrow undergo mechanisms of central tolerance that prevent their entry into the peripheral B cell population. These mechanisms are breached in many autoimmune patients, increasing their risk of B cell–mediated autoimmune diseases. Resolving the molecular pathways that can break central B cell tolerance could therefore provide avenues to diminish autoimmunity. Here, we show that B cell–intrinsic expression of a constitutively active form of PI3K-P110α by high-avidity autoreactive B cells of mice completely abrogates central B cell tolerance and further promotes these cells to escape from the bone marrow, differentiate in peripheral tissue, and undergo activation in response to self-antigen. Upon stimulation with T cell help factors, these B cells secrete antibodies in vitro but remain unable to secrete autoantibodies in vivo. Overall, our data demonstrate that activation of the PI3K pathway leads high-avidity autoreactive B cells to breach central, but not late, stages of peripheral tolerance.
Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma
Authors: Mack Stephen C. , Singh Irtisha , Wang Xiuxing , Hirsch Rachel , Wu Quilian , Villagomez Rosie , Bernatchez Jean A. , Zhu Zhe , Gimple Ryan C. , Kim Leo J.Y. , Morton Andrew , Lai Sisi , Qiu Zhixin , Prager Briana C. , Bertrand Kelsey C. , Mah Clarence , Zhou Wenchao , Lee Christine , Barnett Gene H. , Vogelbaum Michael A. , Sloan Andrew E. , Chavez Lukas , Bao Shideng , Scacheri Peter C. , Siqueira-Neto Jair L. , Lin Charles Y. , Rich Jeremy N.
Published: April 2019

Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogeneity. Here, we mapped active chromatin landscapes with gene expression, whole exomes, copy number profiles, and DNA methylomes across 44 patient-derived glioblastoma stem cells (GSCs), 50 primary tumors, and 10 neural stem cells (NSCs) to identify essential super-enhancer (SE)–associated genes and the core transcription factors that establish SEs and maintain GSC identity. GSCs segregate into two groups dominated by distinct enhancer profiles and unique developmental core transcription factor regulatory programs. Group-specific transcription factors enforce GSC identity; they exhibit higher activity in glioblastomas versus NSCs, are associated with poor clinical outcomes, and are required for glioblastoma growth in vivo. Although transcription factors are commonly considered undruggable, group-specific enhancer regulation of the MAPK/ERK pathway predicts sensitivity to MEK inhibition. These data demonstrate that transcriptional identity can be leveraged to identify novel dependencies and therapeutic approaches.
Effect of laser induced topography with moderate stiffness on human mesenchymal stem cell behavior
Authors: Gao Chenyuan , Tang Lin , Hong Jieyu , Liang Chunyong , Tan Lay Poh , Li Huaqiong
Published: April 2019

Though the effects of scaffold properties such as stiffness and topography on stem cell behavior was well known of, there were multiple theories that explain such behavior and there has been no common consensus thus far. This study deals with using polydimethylsiloxane (PDMS) to mimic a specific microenvironment that favors human mesenchymal stem cells (hMSCs) differentiation into myogenic lineages through the manipulation of specific surface topography and appropriate substrate stiffness. Femtosecond laser was applied to machine microchannels on PDMS substrates in this work. hMSCs were seeded and cultured on lasercut substrates, uncut substrates and controls. Quantitative and qualitative analyses of stem cell behavior were discussed herein with the use of Picogreen Assay for cell proliferation, staining of cytoskeleton for cell orientation, immunostaining of Myosin Heavy Chain for a myogenic biomarker, and quantitative real time polymerase chain reaction for gene expression analysis. It was found that both myogenic differentiation of hMSCs could be achieved by moderate stiffness or microchannels. And differentiation was further boosted by such PDMS substrates with additional microchannels.
Does Season of Reported Dietary Intake Influence Diet Quality? Analysis From the Women’s Health Initiative
Authors: Crane Tracy E , Latif Yasmin Abdel , Wertheim Betsy C , Kohler Lindsay N , Garcia David O , Rhee Jinnie J , Seguin Rebecca , Kazlauskaite Rasa , Shikany James M , Thomson Cynthia A
Published: April 2019

We evaluated the role of seasonality in self-reported diet quality among postmenopausal women participating in the Women’s Health Initiative (WHI). A total of 156,911 women completed a food frequency questionnaire (FFQ) at enrollment (1993–1998). FFQ responses reflected intake over the prior 3-month period, and seasons were defined as spring (March–May), summer (June–August), fall (September–November), and winter (December–February). FFQ data were used to calculate the Alternate Healthy Eating Index (AHEI), a measure of diet quality that has a score range of 2.5–87.5, with higher scores representing better diet quality. In multivariable linear regression models using winter as the reference season, AHEI scores were higher in spring, summer, and fall (all P values < 0.05); although significant, the variance was minimal (mean AHEI score: winter, 41.7 (standard deviation, 11.3); summer, 42.2 (standard deviation, 11.3)). Applying these findings to hypothesis-driven association analysis of diet quality and its relationship with chronic disease risk (cardiovascular disease) showed that controlling for season had no effect on the estimated hazard ratios. Although significant differences in diet quality across seasons can be detected in this population of US postmenopausal women, these differences are not substantial enough to warrant consideration in association studies of diet quality.
The Impact of Human Immunodeficiency Virus Exposure on Respiratory Syncytial Virus–associated Severe Respiratory Illness in South African Infants, 2011–2016
Authors: McMorrow Meredith L , Tempia Stefano , Walaza Sibongile , Treurnicht Florette K , Moyes Jocelyn , Cohen Adam L , Pretorius Marthi , Hellferscee Orienka , Wolter Nicole , von Gottberg Anne , Nguweneza Arthemon , McAnerney Johanna M , Naby Fathima , Mekgoe Omphile , Venter Marietjie , Madhi Shabir A , Cohen Cheryl
Published: April 2019

From 2011 through 2016, we conducted surveillance for severe respiratory illness in infants. Human immunodeficiency virus exposure significantly increased the risk of respiratory syncytial virus (RSV)–associated hospitalization in infants aged <5 months. More than 60% of RSV-associated hospitalizations occurred in the first 4 months of life and may be preventable through maternal vaccination or birth-dose monoclonal antibody.
Aminoglycoside-induced Hearing Loss Among Patients Being Treated for Drug-resistant Tuberculosis in South Africa: A Prediction Model
Authors: Hong Hyejeong , Dowdy David W , Dooley Kelly E , Francis Howard W , Budhathoki Chakra , Han Hae-Ra , Farley Jason E
Published: April 2019

Background

Individuals treated for drug-resistant tuberculosis (DR-TB) with aminoglycosides (AGs) in resource-limited settings often experience permanent hearing loss, yet there is no practical method to identify those at higher risk. We sought to develop a clinical prediction model of AG-induced hearing loss among patients initiating DR-TB treatment in South Africa.

Methods

Using nested, prospective data from a cohort of 379 South African adults being treated for confirmed DR-TB with AG-based regimens we developed the prediction model using multiple logistic regression. Predictors were collected from clinical, audiological, and laboratory evaluations conducted at the initiation of DR-TB treatment. The outcome of AG-induced hearing loss was identified from audiometric and clinical evaluation by a worsened hearing threshold compared with baseline during the 6-month intensive phase.

Results

Sixty-three percent of participants (n = 238) developed any level of hearing loss. The model predicting hearing loss at frequencies from 250 to 8000 Hz included weekly AG dose, human immunodeficiency virus status with CD4 count, age, serum albumin, body mass index, and pre-existing hearing loss. This model demonstrated reasonable discrimination (area under the receiver operating characteristic curve [AUC] = 0.71) and calibration (χ2[8] = 6.10, P = .636). Using a cutoff of 80% predicted probability of hearing loss, the positive predictive value of this model was 83% and negative predictive value was 40%. Model discrimination was similar for ultrahigh-frequency hearing loss (frequencies >9000 Hz; AUC = 0.81) but weaker for clinically determined hearing loss (AUC = 0.60).

Conclusions

This model may identify patients with DR-TB who are at highest risk of developing AG-induced ototoxicity and may help prioritize patients for AG-sparing regimens in clinical settings where access is limited.
Effects of Water, Sanitation, Handwashing, and Nutritional Interventions on Environmental Enteric Dysfunction in Young Children: A Cluster-randomized, Controlled Trial in Rural Bangladesh
Authors: Lin Audrie , Ali Shahjahan , Arnold Benjamin F , Rahman Md Ziaur , Alauddin Mohammad , Grembi Jessica , Mertens Andrew N , Famida Syeda L , Akther Salma , Hossen Md Saheen , Mutsuddi Palash , Shoab Abul K , Hussain Zahir , Rahman Mahbubur , Unicomb Leanne , Ashraf Sania , Naser Abu Mohd , Parvez Sarker M , Ercumen Ayse , Benjamin-Chung Jade , Haque Rashidul , Ahmed Tahmeed , Hossain Md Iqbal , Choudhury Nuzhat , Jannat Kaniz , Alauddin Sarah T , Minchala Sandra G , Cekovic Rabije , Hubbard Alan E , Stewart Christine P , Dewey Kathryn G , Colford John M , Luby Stephen P
Published: April 2019

Background

We hypothesized that drinking water, sanitation, handwashing (WSH), and nutritional interventions would improve environmental enteric dysfunction (EED), a potential contributor to stunting.

Methods

Within a subsample of a cluster-randomized, controlled trial in rural Bangladesh, we enrolled pregnant women in 4 arms: control, WSH, child nutrition counseling plus lipid-based nutrient supplements (N), and nutrition plus WSH (N+WSH). Among the birth cohort, we measured biomarkers of gut inflammation (myeloperoxidase, neopterin), permeability (alpha-1-antitrypsin, lactulose, mannitol), and repair (regenerating gene 1β) at median ages 3, 14, and 28 months. Analysis was intention-to-treat.

Results

We assessed 1512 children. At age 3 months, compared to controls, neopterin was reduced by nutrition (–0.21 log nmol/L; 95% confidence interval [CI], –.37, –.05) and N+WSH (–0.20 log nmol/L; 95% CI, –.34, –.06) interventions; similar reductions were observed at 14 months. At 3 months, all interventions reduced lactulose and mannitol (–0.60 to –0.69 log mmol/L). At 28 months, myeloperoxidase was elevated in the WSH and nutrition arms (0.23–0.27 log ng/mL) and lactulose was higher in the WSH arm (0.30 log mmol/L; 95% CI, .07, .53).

Conclusions

Reductions in permeability and inflammation at ages 3 and 14 months suggest that the interventions promoted healthy intestinal maturation; however, by 28 months, the WSH and nutrition arms showed elevated EED biomarkers. These results underscore the importance of developing a better understanding of EED pathophysiology and targeting interventions early in childhood, when they are likely to have the largest benefit to intestinal health.

Clinical Trials Registration

NCT01590095.
Rationale for a Neisseria gonorrhoeae Susceptible–only Interpretive Breakpoint for Azithromycin
Authors: Kersh Ellen N , Allen Vanessa , Ransom Eric , Schmerer Matthew , Cyr Sancta , Workowski Kim , Weinstock Hillard , Patel Jean , Ferraro Mary Jane
Published: April 2019

Background

Azithromycin (AZI) is recommended with ceftriaxone (CRO) for treatment of uncomplicated gonococcal urethritis and cervicitis in the United States, and an AZI-susceptibility breakpoint is needed. Neither the Food and Drug Administration (FDA) nor the Clinical and Laboratory Standards Institute (CLSI) has set interpretive breakpoints for AZI susceptibility. As a result, AZI antimicrobial susceptibility testing (AST) cannot be interpreted using recognized standards. This has contributed to increasingly unavailable clinical laboratory AST, although gonorrhea is on the rise with >550 000 US gonorrhea cases reported to the Centers for Disease Control and Prevention in 2017, the highest number of cases since 1991.

Methods

This article summarizes the rationale data reviewed by the CLSI in June 2018.

Results

The CLSI decided to set a susceptible-only interpretive breakpoint at the minimum inhibitory concentration of ≤1 µg/mL. This is also the epidemiological cutoff value (ECV) (ie, the end of the wild-type susceptibility distribution). This breakpoint presumes that AZI (1-g single dose) is used in an approved regimen that includes an additional antimicrobial agent (ie, CRO 250 mg, intramuscular single dose).

Conclusions

Having a breakpoint can improve patient care and surveillance and allow future development and FDA regulatory approval of modernized AST to guide treatment. The breakpoint coincides with a European Committee on AST decision to remove previously established, differing AZI breakpoints and use the ECV as guidance for testing. The CLSI breakpoint is now the recognized standard that defines AZI susceptibility for gonococcal infections.
The importance of endothelial dysfunction in resistance artery remodelling and cardiovascular risk
Authors: Masi Stefano , Georgiopoulos Georgios , Chiriacò Martina , Grassi Guido , Seravalle Gino , Savoia Carmine , Volpe Massimo , Taddei Stefano , Rizzoni Damiano , Virdis Agostino
Published: April 2019

Aims

The relationship between resistance artery remodelling and endothelial function remains unknown. In this study, we assessed (i) the capacity of endothelial function and nitric oxide (NO) availability to provide more information on the severity of resistance artery remodelling than common cardiovascular risk factors in subjects at low or high cardiovascular risk; and (ii) differences between patterns of resistance artery remodelling associated with deficit of NO availability and with exposure to cardiovascular risk factors.

Methods and results

All analyses were conducted on the microvascular data set of the Italian Society for Arterial Hypertension (SIIA) that includes 356 patients with measures of small resistance arteries remodelling acquired with pressure or wire myography. Information on endothelial function and NO availability were also available in 116 patients. The European Heart Score (HS) was used to define the total cardiovascular risk of each patient. Endothelial function was inversely related with the severity of the resistance artery remodelling, and this association remained significant after adjustment for the HS. By contrast, the HS lost its significant association with the media-to-lumen (M/L) ratio and the media cross-sectional area after adjustment for endothelial function. The strength of these associations was similar in subjects at high and low cardiovascular risk. The addition of endothelial function and NO availability to the HS significantly improved the identification of subjects at more and less severe resistance artery remodelling. A severe deficit of NO availability was associated with hypertrophic remodelling, while a higher HS was more clearly associated with eutrophic remodelling.

Conclusion

Resistance artery endothelial function and NO availability might represent important factors involved in resistance artery remodelling, independently from cardiovascular risk factor exposure.
Continuous thermodilution to assess absolute flow and microvascular resistance: validation in humans using [15O]H2O positron emission tomography
Authors: Everaars Henk , de Waard Guus A , Schumacher Stefan P , Zimmermann Frederik M , Bom Michiel J , van de Ven Peter M , Raijmakers Pieter G , Lammertsma Adriaan A , Götte Marco J , van Rossum Albert C , Kurata Akira , Marques Koen M J , Pijls Nico H J , van Royen Niels , Knaapen Paul
Published: April 2019

Aims

Continuous thermodilution is a novel technique to quantify absolute coronary flow and microvascular resistance (MVR). Notably, intracoronary infusion of saline elicits maximal hyperaemia, obviating the need for adenosine. The primary aim of this study was to validate continuous thermodilution in humans by comparing invasive measurements to [15O]H2O positron emission tomography (PET). As a secondary goal, absolute flow and MVR were compared between invasive measurements obtained with and without adenosine.

Methods and results

Twenty-five patients underwent coronary computed tomography angiography (CCTA), [15O]H2O PET, and invasive assessment. Absolute coronary flow and MVR were measured in the left anterior descending and left circumflex artery using a dedicated infusion catheter and a temperature/pressure sensor-tipped guidewire. Invasive measurements were performed with and without adenosine. In order to compare invasive flow measurements with PET perfusion, subtending myocardial mass of the investigated vessels was derived from CCTA using the Voronoi algorithm. Invasive and non-invasive measurements of adenosine-induced hyperaemic flow and MVR showed strong correlation (r = 0.91; P < 0.001 for flow and r = 0.85; P < 0.001 for MVR) and good agreement [intraclass correlation coefficient (ICC) = 0.90; P < 0.001 for flow and ICC = 0.79; P < 0.001 for MVR]. Absolute flow and MVR also correlated well between measurements with and without adenosine (r = 0.97; P < 0.001 for flow and r = 0.98; P < 0.001 for MVR) and showed good agreement (ICC = 0.96; P < 0.001 for flow and ICC = 0.98; P < 0.001 for MVR).

Conclusions

Continuous thermodilution is an accurate method to measure absolute coronary flow and MVR, which is evidenced by strong agreement with [15O]H2O PET derived flow and resistance. Absolute flow and MVR correlate highly between invasive measurements obtained with and without adenosine, which confirms that intracoronary infusion of room temperature saline elicits steady-state maximal hyperaemia.
Implantable cardioverter-defibrillators and survival in advanced heart failure patients with continuous-flow left ventricular assist devices: a systematic review and meta-analysis
Authors: Elkaryoni Ahmed , Badarin Firas Al , Khan Muhammad Shahzeb , Ellakany Karim , Potturi Nikitha , Poonia Jasmin , Kennedy Kevin F , Magalski Anthony , Sperry Brett W , Wimmer Alan P
Published: April 2019

Aims

Implantable cardioverter-defibrillators (ICDs) implantation in heart failure (HF) patients with reduced ejection fraction improves survival by reducing mortality secondary to arrhythmic events. Whether advanced HF patients treated with continuous-flow left ventricular assist devices (CF-LVADs) derive similar benefit is controversial.

Methods and results

We searched PubMed, Cochrane Central Register of Controlled Trials, Embase, and Scopus from inception through November 2018 for studies examining the association between ICD implantation and all-cause mortality in patients with advanced HF and CF-LVADs. Analyses were performed using a random-effects model. Hazard ratios (HRs) were calculated with 95% confidence intervals (CIs). Heterogeneity and publication bias were formally assessed, using I2 and funnel plots, respectively. Eight observational studies with a total of 6416 patients (ICD group = 3450, no ICD group = 2966) met inclusion criteria. The majority of patients (84.6%) came from the two largest observational studies. There was no difference in mortality in the ICD and no ICD groups (HR 0.96, 95% CI 0.73–1.27, P = 0.79, I2 = 42%), and ICD implantation post-CF-LVAD was not associated with an improvement in mortality (HR 0.87, 95% CI 0.48–1.57, P = 0.64, I2 = 0%). Additionally, there was no significant difference in the likelihood of transplantation (HR 1.10, 95% CI 0.93–1.30, P = 0.28, I2 = 26%) or non-mortality adverse events between the two groups.

Conclusion

Implantable cardioverter-defibrillator use was not associated with improved survival in advanced HF patients with CF-LVADs. These findings underscore the need to formally study the efficacy of ICDs in this population in a dedicated randomized controlled study.
Zoster Vaccination in Older Adults: Efficacy and Public Health Implications
Authors: McElhaney Janet E , Verschoor Chris , Pawelec Graham
Published: April 2019

Shingles and its most common disabling complication, post-herpetic neuralgia, represent a serious public health challenge in the older population. The decline in the T-cell-mediated immune response to varicella zoster virus after age 50 is clearly associated with increased risk of viral reactivation, causing an acutely painful zoster rash, which may have a severe prodrome of dermatomal pain and persist as seriously debilitating post-herpetic neuralgia well beyond the resolution of the rash. However, new vaccines and adjuvants are being developed and trialed and are now more effective in preventing shingles and the sequelae of post-herpetic neuralgia. Those vaccines that possess the ability to enhance antigen presentation and reverse memory T-cell exhaustion, as well as diminish the immune suppressive effects of regulatory T cells, are most likely to be effective in older adults.
A general theory of age-length keys: combining the forward and inverse keys to estimate age composition from incomplete data
Authors: Ailloud Lisa E , Hoenig John M
Published: April 2019

There are two approaches to estimating age composition from a large number of length observations and a limited number of age determinations: the forward and the inverse age-length keys. The forward key looks at the distribution of age within each length bin while the inverse key looks at the distribution of length at each age. The former is more precise but has stringent requirements for the way data are collected. The latter approach is more widely applicable. We review the theory of the two keys with particular attention to necessary assumptions and the restrictions on when the methods are applicable. We show it is possible to combine the two approaches into a combined forward-inverse age-length key. This approach can be used to estimate age composition in several years simultaneously. It takes advantage of the efficiency of the forward key in years when that is appropriate, applies the inverse key to years with no age data, and uses a blending of the two approaches for years with moderate amounts of age data.
Systematic Evaluation of Patient-Reported Outcome Protocol Content and Reporting in Cancer Trials
Authors: Kyte Derek , Retzer Ameeta , Ahmed Khaled , Keeley Thomas , Armes Jo , Brown Julia M , Calman Lynn , Gavin Anna , Glaser Adam W , Greenfield Diana M , Lanceley Anne , Taylor Rachel M , Velikova Galina , Brundage Michael , Efficace Fabio , Mercieca-Bebber Rebecca , King Madeleine T , Turner Grace , Calvert Melanie
Published: April 2019

Background

Patient-reported outcomes (PROs) are captured within cancer trials to help future patients and their clinicians make more informed treatment decisions. However, variability in standards of PRO trial design and reporting threaten the validity of these endpoints for application in clinical practice.

Methods

We systematically investigated a cohort of randomized controlled cancer trials that included a primary or secondary PRO. For each trial, an evaluation of protocol and reporting quality was undertaken using standard checklists. General patterns of reporting where also explored.

Results

Protocols (101 sourced, 44.3%) included a mean (SD) of 10 (4) of 33 (range = 2–19) PRO protocol checklist items. Recommended items frequently omitted included the rationale and objectives underpinning PRO collection and approaches to minimize/address missing PRO data. Of 160 trials with published results, 61 (38.1%, 95% confidence interval = 30.6% to 45.7%) failed to include their PRO findings in any publication (mean 6.43-year follow-up); these trials included 49 568 participants. Although two-thirds of included trials published PRO findings, reporting standards were often inadequate according to international guidelines (mean [SD] inclusion of 3 [3] of 14 [range = 0–11]) CONSORT PRO Extension checklist items). More than one-half of trials publishing PRO results in a secondary publication (12 of 22, 54.5%) took 4 or more years to do so following trial closure, with eight (36.4%) taking 5–8 years and one trial publishing after 14 years.

Conclusions

PRO protocol content is frequently inadequate, and nonreporting of PRO findings is widespread, meaning patient-important information may not be available to benefit patients, clinicians, and regulators. Even where PRO data are published, there is often considerable delay and reporting quality is suboptimal. This study presents key recommendations to enhance the likelihood of successful delivery of PROs in the future.
CRISPRai for simultaneous gene activation and inhibition to promote stem cell chondrogenesis and calvarial bone regeneration
Authors: Truong Vu Anh , Hsu Mu-Nung , Kieu Nguyen Nuong Thi , Lin Mei-Wei , Shen Chih-Che , Lin Chin-Yu , Hu Yu-Chen
Published: April 2019

Calvarial bone healing remains difficult but may be improved by stimulating chondrogenesis of implanted stem cells. To simultaneously promote chondrogenesis and repress adipogenesis of stem cells, we built a CRISPRai system that comprised inactive Cas9 (dCas9), two fusion proteins as activation/repression complexes and two single guide RNA (sgRNA) as scaffolds for recruiting activator (sgRNAa) or inhibitor (sgRNAi). By plasmid transfection and co-expression in CHO cells, we validated that dCas9 coordinated with sgRNAa to recruit the activator for mCherry activation and also orchestrated with sgRNAi to recruit the repressor for d2EGFP inhibition, without cross interference. After changing the sgRNA sequence to target endogenous Sox9/PPAR-γ, we packaged the entire CRISPRai system into an all-in-one baculovirus for efficient delivery into rat bone marrow-derived mesenchymal stem cells (rBMSC) and verified simultaneous Sox9 activation and PPAR-γ repression. The activation/inhibition effects were further enhanced/prolonged by using the Cre/loxP-based hybrid baculovirus. The CRISPRai system delivered by the hybrid baculovirus stimulated chondrogenesis and repressed adipogenesis of rBMSC in 2D culture and promoted the formation of engineered cartilage in 3D culture. Importantly, implantation of the rBMSC engineered by the CRISPRai improved calvarial bone healing. This study paves a new avenue to translate the CRISPRai technology to regenerative medicine.
Interplay between small RNA pathways shapes chromatin landscapes in C. elegans
Authors: Gushchanskaia Ekaterina S , Esse Ruben , Ma Qicheng , Lau Nelson C , Grishok Alla
Published: April 2019

The nematode Caenorhabditis elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both ‘silencing’ siRNAs bound by Worm-specific Argonautes (WAGO) and ‘activating’ siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here, we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partially rescued null mutant strain (WM193), this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements and an increased number of small RNAs that match enhancers in both drh-3 and csr-1 mutants. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to sites with increased silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.
Early Modern Voices
Authors: Varwig Bettina
Published: April 2019

This chapter explores early modern conceptions of voice and vocal timbre, focusing on French and German philosophical and musical writings of the long seventeenth century. It argues that a Cartesian paradigm of representation, which has tended to underpin most present-day interpretations of the music of this period, falls short of recognizing the capacity of the early modern (musical) voice to bridge the realms of the material and immaterial, of body and soul. Such a historically situated consideration of timbre – configured here as a quality arising at the intersection of the physiological and spiritual processes that constituted the human voice – thereby offers a way towards recuperating certain off-Cartesian modes of thinking, feeling and listening.
Ion Channel Permeation and Selectivity
Authors: Nogueira Juan J. , Corry Ben
Published: April 2019

Many biological processes essential for life rely on the transport of specific ions at specific times across cell membranes. Such exquisite control of ionic currents, which is regulated by protein ion channels, is fundamental for the proper functioning of the cells. It is not surprising, therefore, that the mechanism of ion permeation and selectivity in ion channels has been extensively investigated by means of experimental and theoretical approaches. These studies have provided great mechanistic insight but have also raised new questions that are still unresolved. This chapter first summarizes the main techniques that have provided significant knowledge about ion permeation and selectivity. It then discusses the physical mechanisms leading to ion permeation and the explanations that have been proposed for ion selectivity in voltage-gated potassium, sodium, and calcium channels.
Political Economy, Sexuality, and Intimacy
Authors: Adam Barry
Published: April 2019

This chapter explores how political economy shapes the social organization of sexuality and intimacy, in particular, modern formations of LGBT people. Political economy affects sexuality at three broad levels: (1) through the articulation of kinship and gender with the division of labor, it creates both openings and limits to same-sex relationships; (2) through demands imposed on contemporary workers, citizens, and consumers by neoliberalism, markets influence norms of conduct and success strategies even in personal relationships; (3) political economy generates hierarchies of entitlement and exclusion which impact LGBT peoples and the social constituencies around them who construct them as symbols of progress or decline. Reviewing both historical and anthropological evidence and the growing international divide between LGBT-affirming and repressing countries, the chapter contextualizes current contentions about the rise of homonationalism in a larger geopolitics of north and south.
Management’s Gurus
Authors: Collins David
Published: April 2019

This chapter offers a critical examination of management’s gurus. It argues that there is a need to take these actors seriously because their preferred representations of the world of work have served to alter quite fundamentally how we think about, talk about, and practise the work of management. Noting difficulties associated with attempts to personify—or to name and acclaim—the gurus, the author offers an analysis of the deeper structure of ‘guru theory’ which, he suggests, persists even as individual gurus come and go. The author then proceeds to offer an analysis of the ‘guru industry’ which has grown up to provide critical reflections on the ways and means of the gurus. The chapter concludes with an account of more recent analytical developments which, in an attempt to consider the full cycle of ‘guru theory’, have examined ‘guru speak’.
Disruption of the Gene trx-m1 Impedes the Growth of Anabaena sp. PCC 7120 under Nitrogen Starvation
Authors: Deschoenmaeker Frï¿½dï¿½ric , Mihara Shoko , Niwa Tatsuya , Taguchi Hideki , Nomata Jiro , Wakabayashi Ken-Ichi , Hisabori Toru
Published: April 2019

Cyanobacteria possess a sophisticated photosynthesis-based metabolism with admirable plasticity. This plasticity is possible via the deep regulation network, the thiol-redox regulations operated by thioredoxin (hereafter, Trx). In this context, we characterized the Trx-m1-deficient mutant strain of Anabaena sp., PCC 7120 (shortly named A.7120), cultivated under nitrogen limitation. Trx-m1 appears to coordinate the nitrogen response and its absence induces large changes in the proteome. Our data clearly indicate that Trx-m1 is crucial for the diazotrophic growth of A.7120. The lack of Trx-m1 resulted in a large differentiation of heterocysts (>20% of total cells), which were barely functional probably due to a weak expression of nitrogenase. In addition, heterocysts of the mutant strain did not display the usual cellular structure of nitrogen-fixative cells. This unveiled why the mutant strain was not able to grow under nitrogen starvation.
PRELIMINARY TECHNICAL DISCUSSION ON A NEW RADON AND ITS PROGENY CONTINUOUS MONITOR USING TWO-FILTER METHOD
Authors: Igarashi Yu , Nozaki Takahiro , Mizuno Hiroyuki , Kuroki Tomohiro , Uchida Yuki , Janik Miroslaw , Iimoto Takeshi
Published: April 2019

Focusing on the scalability of Two-Filter Method, we started to develop a monitor for the concentration of radon and its progeny. In this study, we investigated the influence of a high-humidity environment on measuring radon concentration, and the influence of the decay chamber of the monitor on the measurement. In the high-humidity test, the conversion factor of (Bqm−3)/(cpm) tends to raise with increasing humidity. On the measurement of radon progeny, existence of the decay chamber of the monitor makes measurement sensitivity lower under environments of little aerosols. Radon concentration measurement by the developed monitor could be influenced by environmental humidity, and that counting loss could occur due to deposition of radon progeny inside of the decay chamber. Correction relating these would be needed based on the data of calibration tests.
Mycorrhizas enhance drought tolerance of citrus by altering root fatty acid compositions and their saturation levels
Authors: Wu Qiang-Sheng , He Jia-Dong , Srivastava A K , Zou Ying-Ning , Kuča Kamil
Published: April 2019

Arbuscular mycorrhizas (AMs) have the ability to enhance drought tolerance of citrus, but the underlying mechanisms have not been clearly elucidated. Considering the strong association of cell membrane fatty acid (FA) unsaturation with plant drought tolerance, the present study hypothesized that AM fungi (AMF) modulated the composition and unsaturation of FAs to enhance drought tolerance of host plants. Drought-sensitive citrus rootstocks, trifoliate orange (Poncirus trifoliata) seedlings, were inoculated with AMF (Funneliformis mosseae) for 3 months and were subsequently exposed to drought stress (DS) for 8 weeks. Mycorrhizal seedlings exhibited better plant growth performance, higher leaf water potential and lower root abscisic acid concentrations under both well-watered (WW) and DS conditions. Arbuscular mycorrhiza fungus inoculation considerably increased root methyl oleate (C18:1), methyl linoleate (C18:2) and methyl linolenate (C18:3N3) concentrations under both WW and DS conditions, and root methyl palmitoleate (C16:1) concentrations under WW, while it decreased root methyl stearate (C18:0) levels under both WW and DS. These changes in the composition of FAs of mycorrhized roots resulted in higher unsaturation index of root FAs, which later aided in reducing the oxidative damage on account of lower concentration of malondialdehyde and superoxide radicals. The changes of these FAs were a result of AMF-up-regulating root FA desaturase 2 (PtFAD2), FA desaturase 6 (PtFAD6) and Δ9 FA desaturase (PtΔ9) genes under WW and PtFAD2, PtFAD6 and Δ15 FA desaturase (PtΔ15) genes under DS conditions. Our results confirmed that mycorrhization brought significant changes in root FA compositions, in addition to regulation of gene expression responsible for increasing the unsaturation level of FAs, a predisposing physiological event for better drought tolerance of citrus.
Elicitation of superinfection exclusion by p28 of turnip crinkle virus is separable from its replication function with mutations at specific amino acid residues
Authors: Guo Qin , Zhang Shaoyan , Sun Rong , Yao Xiaolong , Zhang Xiao-Feng , Tatineni Satyanarayana , Meulia Tea , Qu Feng
Published: April 2019

We recently reported that the p28 auxiliary replication protein encoded by turnip crinkle virus (TCV) is also responsible for eliciting superinfection exclusion (SIE) against superinfecting TCV. However, it remains unresolved whether the replication function of p28 could be separated from its ability to elicit SIE. Here we report the identification of two single amino acid (aa) mutations that decouple these two functions. Using an Agrobacterium infiltration-based delivery system, we transiently expressed a series of p28 deletion and point mutants, and tested their ability to elicit SIE against a co-introduced TCV replicon. We found that substituting alanine (A) for valine (V) and phenylalanine (F) at p28 positions 181 and 182, respectively, modestly compromised SIE in transiently expressed p28 derivatives. Upon incorporation into TCV replicons, V181A and F182A decoupled TCV replication and SIE diametrically. While V181A impaired SIE without detectably compromising replication, F182A abolished TCV replication but had no effect on SIE once the replication of the defective replicon was restored through complementation. Both mutations diminished accumulation of p28 protein, suggesting that p28 must reach a concentration threshold in order to elicit a strong SIE. Importantly, the severe reduction of F182A protein levels correlated with a dramatic loss in the number of intracellular p28 foci formed by p28-p28 interactions. Together these findings not only decouples the replication and SIE functions of p28, but also unveils a concentration dependence for p28 coalescence and SIE elicitation. These data further highlight the role of p28 multimerization in driving the exclusion of secondary TCV infections.

IMPORTANCE

Superinfection exclusion (SIE) insulates virus-infected cells from subsequent invasion by the same or closely related viruses. SIE has been observed in both animal and plant virus-infected cells. Therefore, a thorough understanding of how SIE is achieved at the molecular level is expected to inspire novel strategies for combating virus infections in humans, animals, and plants. Our group has been using turnip crinkle virus (TCV) to elucidate the molecular interactions critical for SIE elicitation. The current study builds on the previous observation that TCV SIE is elicited by one single TCV-encoded protein (p28), and further identifies key regions and amino acids that are needed for SIE. We unravel key amino acid changes that decouple the replication and SIE functions of p28, and provides novel mechanistic insights of SIE.
A roadmap to mammalian oral microbiome evolution with dental calculus
Authors: Brealey Jaelle C. , Leitão Henrique G. , van der Valk Tom , Xu Wenbo , Bougiouri Katia , Dalén Love , Guschanski Katerina
Published: April 2019

Animals and their associated microbiomes share a long evolutionary history, influenced by a complex interplay between extrinsic environmental and intrinsic host factors. However, we know little about microbiome responses to long-lasting environmental and host-centred processes, which require studying microbiome changes through time. Here, we apply a temporal metagenomics approach to dental calculus, the calcified oral microbial biofilm. We establish dental calculus as a valuable tool for the study of host microbiome evolution by characterising the taxonomic and functional composition of the oral microbiome in a variety of wild mammals. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterise antibiotic resistance genes even before the advent of industrial antibiotic production, reconstruct components of the host diet and recover host genetic profiles. Our work demonstrates how dental calculus can be used in the future to study the evolution of oral microbiomes and pathogens, and the impact of anthropogenic changes on wildlife and the environment.
A new massively-parallel transposon mutagenesis approach comparing multiple datasets identifies novel mechanisms of action and resistance to triclosan
Authors: Yasir Muhammad , Turner A. Keith , Bastkowski Sarah , Page Andrew J. , Telatin Andrea , Phan Minh-Duy , Monahan Leigh G. , Darling Aaron E. , Webber Mark A. , Charles Ian G.
Published: April 2019

The mechanisms by which antimicrobials exert inhibitory effects against bacterial cells and by which bacteria display resistance vary under different conditions. Our understanding of the full complement of genes which can influence sensitivity to many antimicrobials is limited and often informed by experiments completed in a small set of exposure conditions. Capturing a broader suite of genes which contribute to survival under antimicrobial stress will improve our understanding of how antimicrobials work and how resistance can evolve. Here, we apply a new version of ‘TraDIS’ (Transposon Directed Insert Sequencing); a massively parallel transposon mutagenesis approach to identify different responses to the common biocide triclosan across a 125-fold range of concentrations. We have developed a new bioinformatic tool ‘AlbaTraDIS’ allowing both predictions of the impacts of individual transposon inserts on gene function to be made and comparisons across multiple TraDIS data sets. This new TraDIS approach allows essential genes as well as non-essential genes to be assayed for their contribution to bacterial survival and growth by modulating their expression. Our results demonstrate that different sets of genes are involved in survival following exposure to triclosan under a wide range of concentrations spanning bacteriostatic to bactericidal. The identified genes include those previously reported to have a role in triclosan resistance as well as a new set of genes not previously implicated in triclosan sensitivity. Amongst these novel genes are those involved in barrier function, small molecule uptake and integrity of transcription and translation. These data provide new insights into potential routes of triclosan entry and bactericidal mechanisms of action. Our data also helps to put recent work which has demonstrated the ubiquitous nature of triclosan in people and the built environment into context in terms of how different triclosan exposures may influence evolution of bacteria. We anticipate the approach we show here that allows comparisons across multiple experimental conditions of TraDIS data will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.
Influenza Classification from Short Reads with VAPOR Facilitates Robust Mapping Pipelines and Zoonotic Strain Detection for Routine Surveillance Applications
Authors: Southgate J. A. , Bull M. J. , Brown C. M. , Watkins J. , Corden S. , Southgate B. , Moore C. , Connor T. R.
Published: April 2019

Background

Influenza viruses are associated with a significant global public health burden. The segmented RNA genome of influenza changes continually due to mutation, and the accumulation of these changes within the antigenic recognition sites of haemagglutinin (HA) and neuraminidase (NA) in turn leads to annual epidemics. Influenza A is also zoonotic, allowing for exchange of segments between human and non-human viruses, resulting in new strains with pandemic potential. These processes necessitate a global surveillance system for influenza monitoring. To this end, whole-genome sequencing (WGS) has begun to emerge as a useful tool. However, due to the diversity and mutability of the influenza genome, and noise in short-read data, bioinformatics processing can present challenges.

Results

Conventional mapping approaches can be insufficient when a sub-optimal reference strain is chosen. For short-read datasets simulated from influenza H1N1 HA sequences, read recovery after single-reference mapping was routinely as low as 90% for human-origin influenza sequences, and often lower than 10% for those from avian hosts. To this end, we developed adeBruijn Graph (DBG)-based classifier of influenza WGS datasets: VAPOR. In real data benchmarking using 257 WGS read sets with correspondingde novoassemblies, VAPOR provided classifications for all samples with a mean of >99.8% identity to assembled contigs. This resulted in an increase in the number of mapped reads by 6.8% on average, up to a maximum of 13.3%. Additionally, using simulations, we demonstrate that classification from reads may be applied to detection of reassorted strains.

Conclusions

VAPOR has potential to simplify bioinformatics pipelines for surveillance, providing a novel method for detection of influenza strains of human and non-human origin directly from reads, minimization of potential data loss and bias associated with conventional mapping, and allowing visualization of alignments that would otherwise require slowde novoassembly. Whilst with expertise and time these pitfalls can largely be avoided, with pre-classification they are remedied in a single step. Furthermore, our algorithm could be adapted in future to surveillance of other RNA viruses. VAPOR is available athttps://github.com/connor-lab/vapor.
Computational design of a protein family that adopts two well-defined and structurally divergent de novo folds
Authors: Wei Kathy Y. , Moschidi Danai , Bick Matthew J. , Nerli Santrupti , McShan Andrew C. , Carter Lauren P. , Huang Po-Ssu , Fletcher Daniel A. , Sgourakis Nikolaos G. , Boyken Scott E. , Baker David
Published: April 2019

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used to de novo design proteins that fold to a single state with a deep free energy minima (Huang et al., 2016), and to reengineer natural proteins to alter their dynamics (Davey et al., 2017) or fold (Alexander et al., 2009), the de novo design of closely related sequences which adopt well-defined, but structurally divergent structures remains an outstanding challenge. Here, we design closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations -- one short (∼66 Å height) and the other long (∼100 Å height) -- reminiscent of the conformational transition of viral fusion proteins (Ivanovic et al., 2013; Podbilewicz, 2014; Skehel and Wiley, 2000). Crystallographic and NMR spectroscopic characterization show that both the short and long state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large scale conformational switches between structurally divergent forms.