bluuebunny/crossref_metadata_2025 huggingface dataset:
Dermatologic care of sexual and gender minority/LGBTQIA youth, Part 2: Recognition and management of the unique dermatologic needs of SGM adolescents
Authors: Kosche Cory , Mansh Matthew , Luskus Mark , Nguyen Andy , Martinez‐Diaz Gabriel , Inwards‐Breland David , Yeung Howa , Boos Markus D.
Published: July 2019

Sexual and gender minority (SGM) individuals, including lesbian, gay, bisexual, transgender/gender diverse, questioning/queer, intersex, and asexual (LGBTQIA) persons, represent a historically underserved population within the field of medicine, though their unique health needs are increasingly recognized. Part 2 of this two‐part review will address unique concerns regarding acne, tanning behavior, sexually transmitted infections, and other health disparities among SGM adolescents. A more comprehensive understanding of the dermatologic needs of SGM youth will better allow pediatric dermatologists to actively and compassionately care for this health disparity population.
Cardiac transplantation in children with Noonan syndrome
Authors: McCallen Leslie M. , Ameduri Rebecca K. , Denfield Susan W. , Dodd Debra A. , Everitt Melanie D. , Johnson Jonathan N. , Lee Teresa M. , Lin Angela E. , Lohr Jamie L. , May Lindsay J. , Pierpont Mary Ella , Stevenson David A. , Chatfield Kathryn C.
Published: July 2019

NS and related RAS/MAPK pathway (RASopathy) disorders are the leading genetic cause of HCM presenting in infancy. HCM is a major cause of morbidity and mortality in children with Noonan spectrum disorders, especially in the first year of life. Previously, there have been only isolated reports of heart transplantation as a treatment for heart failure in NS. We report on 18 patients with NS disorders who underwent heart transplantation at seven US pediatric heart transplant centers. All patients carried a NS diagnosis: 15 were diagnosed with NS and three with NSML. Sixteen of eighteen patients had comprehensive molecular genetic testing for RAS pathway mutations, with 15 having confirmed pathogenic mutations in PTPN11, RAF1, and RIT1 genes. Medical aspects of transplantation are reported as well as NS‐specific medical issues. Twelve of eighteen patients described in this series were surviving at the time of data collection. Three patients died following transplantation prior to discharge from the hospital, and another three died post‐discharge. Heart transplantation in NS may be a more frequent occurrence than is evident from the literature or registry data. A mortality rate of 33% is consistent with previous reports of patients with HCM transplanted in infancy and early childhood. Specific considerations may be important in evaluation of this population for heart transplant, including a potentially increased risk for malignancies as well as lymphatic, bleeding, and coagulopathy complications.
Efficiency of insect‐proof net tunnels in reducing virus‐related seed degeneration in sweet potato
Authors: Ogero K. O. , Kreuze J. F. , McEwan M. A. , Luambano N. D. , Bachwenkizi H. , Garrett K. A. , Andersen K. F. , Thomas‐Sharma S. , van der Vlugt R. A. A.
Published: July 2019

Virus‐related degeneration constrains production of quality sweet potato seed, especially under open field conditions. Once in the open, virus‐indexed seed is prone to virus infection leading to decline in performance. Insect‐proof net tunnels have been proven to reduce virus infection under researcher management. However, their effectiveness under farmer‐multiplier management is not known. This study investigated the ability of net tunnels to reduce degeneration in sweet potato under farmer‐multiplier management. Infection and degeneration were assessed for two cultivars, Kabode and Polista, grown in net tunnels and open fields at two sites with varying virus pressures. There was zero virus incidence at both sites during the first five generations. Sweet potato feathery mottle virus and sweet potato chlorotic stunt virus were present in the last three generations, occurring singly or in combination to form sweet potato virus disease. Virus infection increased successively, with higher incidences recorded at the high virus pressure site. Seed degeneration modelling illustrated that for both varieties, degeneration was reduced by the maintenance of vines under net tunnel conditions. The time series of likely degeneration based on a generic model of yield loss suggested that, under the conditions experienced during the experimental period, infection and losses within the net tunnels would be limited. By comparison, in the open field most of the yield could be lost after a small number of generations without the input of seed with lower disease incidence. Adopting the technology at the farmer‐multiplier level can increase availability of clean seed, particularly in high virus pressure areas.
Testing Predictors of Mutual Efficacy
Authors: Gearhart Michael C.
Published: July 2019

Objectives

Collective efficacy has developed concurrently in both sociology and psychology. In sociology, collective efficacy is the process by which social cohesion is activated as informal social control. In psychology, collective efficacy is a construct that focuses on a group's belief in its ability to achieve shared goals. Mutual efficacy reflects group members' beliefs that collective action can be successful at achieving group goals. Mutual efficacy was developed as a bridge between the sociological and psychological conceptualizations of collective efficacy. Prior research supports mutual efficacy as a mediator of the relationship between social cohesion and informal social control. However, little is known about the individual and neighborhood‐level characteristics that predict mutual efficacy.

Methods

This study tests predictors of mutual efficacy using regression while accounting for clustering at the neighborhood level through the use of Huber–White sandwich estimators.

Results

Findings show that multiple factors influence mutual efficacy including social cohesion, resident mobility, income, and education.

Conclusion

Findings highlight the importance of building mutual efficacy through facilitating interactions among neighbors, increasing access to education, and fostering economic stability.
Media Consumption and Fear of Crime in a Large Chinese City
Authors: Wu Yuning , Li Feng , Triplett Ruth A. , Sun Ivan Y.
Published: July 2019

Objective

While empirical research on Chinese people's perceptions of crime has developed encouragingly during the past decade, an important issue regarding correlates of such fear – the media effect, frequently found by the Western literature as a critical source of fear – has largely eluded scholarly attention. This study investigates the effects of consumption of different media types on Chinese fear of crime, while taking a wide range of other theoretically relevant and empirically validated factors into consideration.

Methods

Relying on data collected from a sample of residents in a large Chinese city, this study uses ordinary least squares regression to investigate the correlates of fear of crime.

Results

Consumption of newspapers and radio reports of news is associated with lower levels of fear, and consumption of political and social news from television and the Internet is connected to higher levels of fear of crime. The vulnerability model, crime and justice model, and community model have also received some support in these data.

Conclusion

This study provides robust support for the importance of the media in shaping public fear of crime, and indicates that the cultural context in which the media reports on crime is critical to understanding its role and impact.
Plasticity in Triticeae centromere DNA sequences: a wheat × tall wheatgrass (decaploid) model
Authors: Zhao Jing , Hao Weiwei , Tang Caiguo , Yao Han , Li Baochun , Zheng Qi , Li Zhensheng , Zhang Xueyong
Published: July 2019

Centromeres mediate chromosome attachment to microtubules and maintain the integrity of chromosomes for proper segregation of the sister chromatids during cell division. Advances in the assembly of Triticeae genome sequences combined with the capacity to recover hybrid species derived from very distantly related species provides potential experimental systems for linking retrotransposon amplification and repositioning of centromeres via non‐mendelian inheritance in partial amphiploid breeds. The decaploid tall wheatgrass (Thinopyrum ponticum) is one of the most successfully used perennial species in wheat breeding for generating translocation lines with valuable agronomic traits. We found that wheat centromere retrotransposons CRW and Quinta widely occur within the tall wheatgrass genome. In addition, one of the genome donors to Th. ponticum, Pseudoroegneria stipifolia (StSt), has been shown to have Abigail and a satellite repeat, CentSt. We also found two other centromeric retrotransposons, Abia and CL135 in Th. ponticum by ChIP‐seq. Examination of partial amphiploid lines that were generated in the 1970s demonstrated extensive modification in centromere sequences using CentSt, Abigail and Abia as probes. We also detected that St‐genome chromosomes were more enriched with Abigail and CentSt, whereas E‐genome chromosomes were enriched with CRW and Quinta in tall wheatgrass and its closer relatives. It can be concluded that bursts of transposition of retrotransposons and repositioning of centromeres via non‐mendelian segregation are common in partial amphiploids derived from interspecific hybrids. Practically speaking, our study reveals that the existence of homologous centromere functional sequences in both a donor and its receptor can substantially contribute to the successful transfer of alien genes into crop species.

Open Research Badges

This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/sra/SRR9089557; https://www.ncbi.nlm.nih.gov/sra/SRR9089558; https://www.ncbi.nlm.nih.gov/sra/SRR9089559; https://www.ncbi.nlm.nih.gov/sra/SRR9089560; https://www.ncbi.nlm.nih.gov/sra/SRR9089561; https://www.ncbi.nlm.nih.gov/sra/SRR9089562; https://www.ncbi.nlm.nih.gov/sra/SRR9089563; https://www.ncbi.nlm.nih.gov/sra/SRR9089564; https://www.ncbi.nlm.nih.gov/nuccore/MK999394; https://www.ncbi.nlm.nih.gov/nuccore/MK999395; https://www.ncbi.nlm.nih.gov/nuccore/MK999396
The volatility of world trade in the 21st century: Whose fault is it anyway?
Authors: Bennett Federico , Lederman Daniel , Pienknagura Samuel , Rojas Diego
Published: July 2019

This paper explores the drivers of the volatility of international trade. It decomposes trade growth into six components that have gained attention in the literature and studies their contribution to overall volatility. It yields three main findings. First, trade volatility in the 1990–2015 period is mostly explained by a common factor, changes in the gravity‐related characteristics of a country's trading partners and country‐specific factors. Product composition and the identity of trading partners appear to be less important in explaining volatility. Second, the pre‐2009 decline in volatility and the post‐2009 increase in volatility appear to be driven by different factors. The former is mostly explained by a decline in the variance of country‐specific factors; the latter appears to be driven by an increase in the volatility of common factors. Third, diversification is a likely force behind the steady decline in the volatility stemming from country‐specific factors, especially in developing countries.
Interactions Between Structural Remodeling and Hypertrophy in the Right Ventricle in Response to Pulmonary Arterial Hypertension
Authors: Avazmohammadi Reza , Mendiola Emilio A. , Li David S. , Vanderslice Peter , Dixon Richard A. F. , Sacks Michael S.
Published: July 2019

Pulmonary arterial hypertension (PAH) exerts substantial pressure overload on the right ventricle (RV), inducing RV remodeling and myocardial tissue adaptation often leading to right heart failure. The associated RV free wall (RVFW) adaptation involves myocardial hypertrophy, augmented intrinsic contractility, collagen fibrosis, and structural remodeling in an attempt to cope with pressure overload. If RVFW adaptation cannot maintain the RV stroke volume (SV), RV dilation will prevail as an exit mechanism, which usually decompensates RV function, leading to RV failure. Our knowledge of the factors determining the transition from the upper limit of RVFW adaptation to RV decompensation and the role of fiber remodeling events such as extracellular fibrosis and fiber reorientation in this transition remains very limited. Computational heart models that connect the growth and remodeling (G&R) events at the fiber and tissue levels with alterations in the organ-level function are essential to predict the temporal order and the compensatory level of the underlying mechanisms. In this work, building upon our recently developed rodent heart models (RHM) of PAH, we integrated mathematical models that describe volumetric growth of the RV and structural remodeling of the RVFW. The time-evolution of RV remodeling from control and post-PAH time points was simulated. The results suggest that the augmentation of the intrinsic contractility of myofibers, accompanied by an increase in passive stiffness of RVFW, is among the first remodeling events through which the RV strives to maintain the cardiac output. Interestingly, we found that the observed reorientation of the myofibers toward the longitudinal (apex-to-base) direction was a maladaptive mechanism that impaired the RVFW contractile pattern and advanced along with RV dilation at later stages of PAH. In fact, although individual fibers were more contractile post-PAH, the disruption in the optimal transmural fiber architecture compromised the effective contractile function of the RVFW, contributing to the depressed ejection fraction (EF) of the RV. Our findings clearly demonstrate the critical need for developing multiscale approaches that can model and delineate relationships between pathological alterations in cardiac function and underlying remodeling events across fiber, cellular, and molecular levels.
Self-perceived stressors of Bachelor of Oral Health students and implications for student support
Authors: Olson Hanna , Beckett Deanna M , Adam Lee A , Tawse-Smith Andrew , Moffat Susan M
Published: July 2019

Introduction: Despite a greater recent interest in students’ stressors in the dentistry learning environment, there is little research on oral health therapy students’ stressors. This study aimed to identify self-perceived stressors of Bachelor of Oral Health (BOH) students in order to determine whether the learning support provided to them at the University of Otago, Faculty of Dentistry is meeting their needs and to make recommendations for future support strategies.Methods: All Bachelor of Oral Health students (n = 135) were invited to complete an online modified version of the Dental Environmental Stress Survey in 2016. The questionnaire included 31 items on potential sources of stress, which students were asked to rate on a 5-point Likert-type scale ranging from 1 “not at all stressful” to 5 “extremely stressful”.Results: About half of the respondents were first-year students, with the remainder equally distributed between second- and third-year students. The items “fear of being unable to catch up if behind” and “examinations and assessments” scored the highest, indicating that the students perceived these to be their greatest stressors. Although there were some individual high-scoring self-perceived personal stressors for students, overall, academic requirements were the highest scoring stressors, regardless of year group. Clinical environment stressors were rated highest for students in the second year, corresponding to when students start seeing patients.Conclusion: This study identified several self-perceived stressors for BOH students. The findings suggest that students require extra support at different stages of the program, for example, when they begin to treat patients. Future research should be directed at investigating what types of support programs would be of most benefit to students.
Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature
Authors: Wu Ling , Han Cheng , Zhu Guangwei , Zhong Wenhui
Published: July 2019

Both archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.
A Vibrating Mesh Nebulizer as an Alternative to the Collison Three-Jet Nebulizer for Infectious Disease Aerobiology
Authors: Bowling Jennifer D. , O’Malley Katherine J. , Klimstra William B. , Hartman Amy L. , Reed Douglas S.
Published: July 2019

Respiratory infection by pathogens via aerosol remains a major concern for both natural disease transmission as well as intentional release of biological weapons. Critical to understanding the disease course and pathogenesis of inhaled pathogens are studies in animal models conducted under tightly controlled experimental settings, including the inhaled dose. The route of administration, particle size, and dose can affect disease progression and outcome. Damage to or loss of pathogens during aerosolization could increase the dose required to cause disease and could stimulate innate immune responses, altering outcome. Aerosol generators that reduce pathogen loss would be ideal. This study compares two aerosol generators to determine which is superior for animal studies. Aerosol research methods and equipment need to be well characterized to optimize the development of animal models for respiratory pathogens, including bioterrorism agents. This information will be critical for pivotal efficacy studies in animals to evaluate potential vaccines or treatments against these agents.
Accumulation and Release of Rare Earth Ions by Spores of
Bacillus
Species and the Location of These Ions in Spores
Authors: Dong Wei , Li Siyu , Camilleri Emily , Korza George , Yankova Maya , King Stephen M. , Setlow Peter
Published: July 2019

Biosorption of rare earth ions by growing cells of
Bacillus
species has been well studied and has attracted attention for possible hydrometallurgy applications. However, the interaction of spores from
Bacillus
species with rare earth ions has not been well studied. We investigated here the adsorption and/or desorption of two rare earth ions, Tb
3+
and Dy
3+
, by
Bacillus
spores, the location of the adsorbed ions, and the spore properties after ion accumulation. The significant adsorption of rare earth ions on the surfaces of
Bacillus
spores and the ions’ rapid release by a chelator could allow the development of these spores as a biosorbent to recover rare earth ions from the environment.
Heat and Chemical Treatments Affect the Viability, Morphology, and Physiology of
Staphylococcus aureus
and Its Subsequent Antibody Labeling for Flow Cytometric Analysis
Authors: Kennedy Deirdre , Cronin Ultan P. , Piterina Anna , Wilkinson Martin G.
Published: July 2019

FCM data indicated that cells conventionally considered to be dead and which would not give rise to CFU in a plate count assay, e.g., cells heated to 80°C, were labeled by antibody staining. This finding suggests that without the inclusion of a live/dead discriminating dye, these cells would be erroneously detected as viable within an FCM assay. Reductions in antibody staining due to physicochemical treatment were strain related, reflecting the complexity of the phenomenon under study and illustrating that substantial validation of any new antibody detection-based method, including physiological staining and cell sorting, should be undertaken. Researchers should be aware of physicochemical treatments causing false-negative results: in this study, freeze-thawing severely reduced antibody binding without affecting the viability of a substantial percentage of cells. Scanning electron microscopy carried out on treated cells revealed a range of morphological changes resulting from physicochemical treatments which may have hindered antibody binding.
Vibrio parahaemolyticus in the Chesapeake Bay: OperationalIn SituPrediction and Forecast Models Can Benefit from Inclusion of Lagged Water Quality Measurements
Authors: Davis Benjamin J. K. , Jacobs John M. , Zaitchik Benjamin , DePaola Angelo , Curriero Frank C.
Published: July 2019

Vibrio parahaemolyticusis one of the leading causes of seafood-borne illness in the United States and across the globe. Exposure often occurs from the consumption of raw shellfish. Despite public health concerns, there have been only sporadic efforts to develop environmental prediction and forecast models for the bacterium preharvest. This analysis used commonly sampled water quality measurements of temperature, salinity, dissolved oxygen, and clarity to develop models forV. parahaemolyticusin surface water. Predictors also included measurements taken months before water was tested for the bacterium. Results revealed that the use of multiple water quality measurements is necessary for satisfactory prediction performance, challenging current efforts to manage the risk of infection based upon water temperature alone. The results also highlight the potential advantage of including historical water quality measurements. This analysis shows promise and lays the groundwork for future operational prediction and forecast models.
Antibiotic-Induced Shifts in Fecal Microbiota Density and Composition during Hematopoietic Stem Cell Transplantation
Authors: Morjaria Sejal , Schluter Jonas , Taylor Bradford P. , Littmann Eric R. , Carter Rebecca A. , Fontana Emily , Peled Jonathan U. , van den Brink Marcel R. M. , Xavier Joao B. , Taur Ying
Published: July 2019

Dramatic microbiota changes and loss of commensal anaerobic bacteria are associated with adverse outcomes in hematopoietic cell transplantation (HCT) recipients. In this study, we demonstrate these dynamic changes at high resolution through daily stool sampling and assess the impact of individual antibiotics on those changes.
Multicenter Clinical Validation of the Molecular BD Max Enteric Viral Panel for Detection of Enteric Pathogens
Authors: Stokes William , Simner Patricia J. , Mortensen Joel , Oethinger Margret , Stellrecht Kathleen , Lockamy Elizabeth , Lay Tricia , Bouchy Peggy , Pillai Dylan R.
Published: July 2019

The conventional methodology for gastrointestinal pathogen detection remains time-consuming, expensive, and of limited sensitivity. The objective of this study was to evaluate the performance of the BD Max enteric viral panel (Max EVP) assay for identification of viral pathogens in stool specimens from individuals with symptoms of acute gastroenteritis, enteritis, or colitis.
Crosstalk of Cellulose and Mannan Perception Pathways Leads to Inhibition of Cellulase Production in Several Filamentous Fungi
Authors: Hassan Lara , Lin Liangcai , Sorek Hagit , Sperl Laura E. , Goudoulas Thomas , Hagn Franz , Germann Natalie , Tian Chaoguang , Benz J. Philipp
Published: July 2019

In fungi, the production of enzymes for polysaccharide degradation is controlled by complex signaling networks. Previously, these networks were studied in response to simple sugars or single polysaccharides. Here, we tackled for the first time the molecular interplay between two seemingly unrelated perception pathways: those for cellulose and the hemicellulose (gluco)mannan. We identified a so far unknown competitive inhibition between the respective degradation products acting as signaling molecules. Competition was detected both at the level of the uptake and intracellularly, upstream of the main transcriptional regulator CLR-2. Our findings provide novel insights into the molecular communication between perception pathways. Also, they present possible targets for the improvement of industrial strains for higher cellulase production through the engineering of mannan insensitivity.
New Insights into the Intrinsic and Extrinsic Factors That Shape the Human Skin Microbiome
Authors: Dimitriu Pedro A. , Iker Brandon , Malik Kausar , Leung Hilary , Mohn W. W. , Hillebrand Greg G.
Published: July 2019

Many studies have highlighted the importance of body site and individuality in shaping the composition of the human skin microbiome, but we still have a poor understanding of how extrinsic (e.g., lifestyle) and intrinsic (e.g., age) factors influence its composition. We characterized the bacterial microbiomes of North American volunteers at four skin sites and the mouth. We also collected extensive subject metadata and measured several host physiological parameters. Integration of host and microbial features showed that the skin microbiome was predominantly associated with demographic, lifestyle, and physiological factors. Furthermore, we uncovered reproducible associations between chronological age, skin aging, and members of the genus
Corynebacterium
. Our work provides new understanding of the role of host selection and lifestyle in shaping skin microbiome composition. It also contributes to a more comprehensive appreciation of the factors that drive interindividual skin microbiome variation.
In Situ
Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States
Authors: Yang Wen , Cassidy C. Keith , Ames Peter , Diebolder Christoph A. , Schulten Klaus , Luthey-Schulten Zaida , Parkinson John S. , Briegel Ariane
Published: July 2019

In
Escherichia coli
, membrane-bound chemoreceptors, the histidine kinase CheA, and coupling protein CheW form highly ordered chemosensory arrays. In core signaling complexes, chemoreceptor trimers of dimers undergo conformational changes, induced by ligand binding and sensory adaptation, which regulate kinase activation. Here, we characterize by cryo-electron tomography the kinase-ON and kinase-OFF conformations of the
E. coli
serine receptor in its native array context. We found distinctive structural differences between the members of a receptor trimer, which contact different partners in the signaling unit, and structural differences between the ON and OFF signaling complexes. Our results provide new insights into the signaling mechanism of chemoreceptor arrays and suggest an important functional role for a previously postulated flexible region and glycine hinge in the receptor molecule.
Identification of Host Biomarkers of Epstein-Barr Virus Latency IIb and Latency III
Authors: Messinger Joshua E. , Dai Joanne , Stanland Lyla J. , Price Alexander M. , Luftig Micah A.
Published: July 2019

EBV is a ubiquitous pathogen, with >95% of adults harboring a life-long latent infection in memory B cells. In immunocompromised individuals, latent EBV infection can result in lymphoma. The established expression profile of these lymphomas is latency III, which includes expression of all latency genes. However, single-cell analysis of EBV latent gene expression in these lymphomas suggests heterogeneity where most cells express the transcription factor, EBNA2, and only a fraction of the cells express membrane protein LMP1. Our work describes an early phase after infection where the EBNAs are expressed without LMP1, called latency IIb. However, LMP1 levels within latency III vary widely, making these states hard to discriminate. This may have important implications for therapeutic responses. It is crucial to distinguish these states to understand the molecular pathogenesis of these lymphomas. Ultimately, better tools to understand the heterogeneity of these cancers will support more-efficacious therapies in the future.
RadD Contributes to R-Loop Avoidance in Sub-MIC Tobramycin
Authors: Negro Veronica , Krin Evelyne , Aguilar Pierlé Sebastian , Chaze Thibault , Giai Gianetto Quentin , Kennedy Sean P. , Matondo Mariette , Mazel Didier , Baharoglu Zeynep
Published: July 2019

Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using
E. coli
, the Gram-negative bacterial paradigm, and
V. cholerae
, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage.
The Stringent Response Inhibits DNA Replication Initiation in E. coli by Modulating Supercoiling of
oriC
Authors: Kraemer James A. , Sanderlin Allen G. , Laub Michael T.
Published: July 2019

To survive bouts of starvation, cells must inhibit DNA replication. In bacteria, starvation triggers production of a signaling molecule called ppGpp (guanosine tetraphosphate) that helps reprogram cellular physiology, including inhibiting new rounds of DNA replication. While ppGpp has been known to block replication initiation in
Escherichia coli
for decades, the mechanism responsible was unknown. Early work suggested that ppGpp drives a decrease in levels of the replication initiator protein DnaA. However, we found that this decrease is not necessary to block replication initiation. Instead, we demonstrate that ppGpp leads to a change in DNA topology that prevents initiation. ppGpp is known to inhibit bulk transcription, which normally introduces negative supercoils into the chromosome, and negative supercoils near the origin of replication help drive its unwinding, leading to replication initiation. Thus, the accumulation of ppGpp prevents replication initiation by blocking the introduction of initiation-promoting negative supercoils. This mechanism is likely conserved throughout proteobacteria.
Allergic Airway Disease Prevents Lethal Synergy of Influenza A Virus-Streptococcus pneumoniae Coinfection
Authors: Roberts Sean , Salmon Sharon L. , Steiner Donald J. , Williams Clare M. , Metzger Dennis W. , Furuya Yoichi
Published: July 2019

Asthma has become one of the most common chronic diseases and has been identified as a risk factor for developing influenza. However, the impact of asthma on postinfluenza secondary bacterial infection is currently not known. Here, we developed a novel triple-challenge model of allergic airway disease, primary influenza infection, and secondary
Streptococcus pneumoniae
infection to investigate the impact of asthma on susceptibility to viral-bacterial coinfections. We report for the first time that mice recovering from acute allergic airway disease are highly resistant to influenza-pneumococcal coinfection and that this resistance is due to inhibition of influenza virus-mediated impairment of bacterial clearance. Further characterization of allergic airway disease-associated resistance against postinfluenza secondary bacterial infection may aid in the development of prophylactic and/or therapeutic treatment against coinfection.
From paper maps to digital maps: enhancing routine immunisation microplanning in Northern Nigeria
Authors: Dougherty Leanne , Abdulkarim Masduq , Mikailu Fiyidi , Tijani Usman , Owolabi Kazeem , Gilroy Kate , Naiya Ahmed , Abdullahi Adamu , Bodinga Hadiza , Olayinka Folake , Moise Imelda
Published: July 2019

Geographical information systems (GIS) can be effective decision-support tools. In this paper, we detail a GIS approach implemented by the Bauchi and Sokoto state primary healthcare development agencies in Nigeria to generate and convert routine immunisation (RI) paper maps to digital maps for microplanning. The process involved three stages: primary and secondary data collection and reconciliation, geospatial data processing and analysis, and production and validation of maps. The data collection and reconciliation stage identified a number of challenges with secondary data sources, including the need to standardise and reconcile health facility and settlement names. The study team was unable to apply population estimates generated from the Global Polio Eradication Initiative to RI planning because operational boundaries for polio activities are defined differently from RI activities. Application of open-source GIS software enabled the combination of multiple datasets and analysis of geospatial data to calculate catchment areas for primary health centres (PHCs) and assign vaccination strategies to communities. The activity resulted in the development of PHC catchment area digital maps, and captured next steps and lessons learnt for RI microplanning in the two states. While the digital maps provided input into the microplanning process, more work is needed to build capacity, standardise processes and ensure the quality of data used to generate the maps. RI service providers and communities must be engaged in the process to validate, understand the data, the contextual factors that influence decisions about which vaccination strategies RI microplans include and how resources are allocated.
Machine learning for prediction of sudden cardiac death in heart failure patients with low left ventricular ejection fraction: study protocol for a retroprospective multicentre registry in China
Authors: Meng Fanqi , Zhang Zhihua , Hou Xiaofeng , Qian Zhiyong , Wang Yao , Chen Yanhong , Wang Yilian , Zhou Ye , Chen Zhen , Zhang Xiwen , Yang Jing , Zhang Jinlong , Guo Jianghong , Li Kebei , Chen Lu , Zhuang Ruijuan , Jiang Hai , Zhou Weihua , Tang Shaowen , Wei Yongyue , Zou Jiangang
Published: July 2019

Introduction

Left ventricular ejection fraction (LVEF) ≤35%, as current significant implantable cardioverter-defibrillator (ICD) indication for primary prevention of sudden cardiac death (SCD) in heart failure (HF) patients, has been widely recognised to be inefficient. Improvement of patient selection for low LVEF (≤35%) is needed to optimise deployment of ICD. Most of the existing prediction models are not appropriate to identify ICD candidates at high risk of SCD in HF patients with low LVEF. Compared with traditional statistical analysis, machine learning (ML) can employ computer algorithms to identify patterns in large datasets, analyse rules automatically and build both linear and non-linear models in order to make data-driven predictions. This study is aimed to develop and validate new models using ML to improve the prediction of SCD in HF patients with low LVEF.

Methods and analysis

We will conduct a retroprospective, multicentre, observational registry of Chinese HF patients with low LVEF. The HF patients with LVEF ≤35% after optimised medication at least 3 months will be enrolled in this study. The primary endpoints are all-cause death and SCD. The secondary endpoints are malignant arrhythmia, sudden cardiac arrest, cardiopulmonary resuscitation and rehospitalisation due to HF. The baseline demographic, clinical, biological, electrophysiological, social and psychological variables will be collected. Both ML and traditional multivariable Cox proportional hazards regression models will be developed and compared in the prediction of SCD. Moreover, the ML model will be validated in a prospective study.

Ethics and dissemination

The study protocol has been approved by the Ethics Committee of the First Affiliated Hospital of Nanjing Medical University (2017-SR-06). All results of this study will be published in international peer-reviewed journals and presented at relevant conferences.

Trial registration number

ChiCTR-POC-17011842; Pre-results.
Impact of audit and feedback with action implementation toolbox on improving ICU pain management: cluster-randomised controlled trial
Authors: Roos-Blom Marie-José , Gude Wouter T , de Jonge Evert , Spijkstra Jan Jaap , van der Veer Sabine N , Peek Niels , Dongelmans Dave A , de Keizer Nicolette F
Published: July 2019

Background

Audit and feedback (A&F) enjoys widespread use, but often achieves only marginal improvements in care. Providing recipients of A&F with suggested actions to overcome barriers (action implementation toolbox) may increase effectiveness.

Objective

To assess the impact of adding an action implementation toolbox to an electronic A&F intervention targeting quality of pain management in intensive care units (ICUs).

Trial design

Two-armed cluster-randomised controlled trial. Randomisation was computer generated, with allocation concealment by a researcher, unaffiliated with the study. Investigators were not blinded to the group assignment of an ICU.

Participants

Twenty-one Dutch ICUs and patients eligible for pain measurement.

Interventions

Feedback-only versus feedback with action implementation toolbox.

Outcome

Proportion of patient-shift observations where pain management was adequate; composed by two process (measuring pain at least once per patient in each shift; re-measuring unacceptable pain scores within 1 hour) and two outcome indicators (acceptable pain scores; unacceptable pain scores normalised within 1 hour).

Results

21 ICUs (feedback-onlyn=11;feedback-with-toolboxn=10) with a total of 253 530 patient-shift observations were analysed. We found absolute improvement on adequate pain management in thefeedback-with-toolboxgroup (14.8%; 95% CI 14.0% to 15.5%) and thefeedback-onlygroup (4.8%; 95% CI 4.2% to 5.5%). Improvement was limited to the two process indicators. Thefeedback-with-toolboxgroup achieved larger effects than thefeedback-onlygroup both on the composite adequate pain management (p<0.05) and on measuring pain each shift (p<0.001). No important adverse effects have occurred.

Conclusion

Feedback with toolbox improved the number of shifts where patients received adequate pain management compared with feedback alone, but only in process and not outcome indicators.

Trial registration number

NCT02922101.
Bott–Taubes–Vassiliev cohomology classes by cut-and-paste topology
Authors: Koytcheff Robin
Published: July 2019

Bott and Taubes used integrals over configuration spaces to produce finite-type a.k.a. Vassiliev knot invariants. Cattaneo, Cotta-Ramusino and Longoni then used these methods together with graph cohomology to construct “Vassiliev classes” in the real cohomology of spaces of knots in higher-dimensional Euclidean spaces, as first promised by Kontsevich. Here we construct integer-valued cohomology classes in spaces of knots and links in [Formula: see text] for [Formula: see text]. We construct such a class for any integer-valued graph cocycle, by the method of gluing compactified configuration spaces. Our classes form the integer lattice among the previously discovered real cohomology classes. Thus we obtain nontrivial classes from trivalent graph cocycles. Our methods generalize to yield mod-[Formula: see text] classes out of mod-[Formula: see text] graph cocycles, which need not be reductions of classes over the integers.
Admissible Perturbations of the Lorenz-84 Climate Model
Authors: Musafirov Eduard V.
Published: July 2019

The set of admissible perturbations have been obtained for the Lorenz-84 climate model. Reflecting functions of the set of admissible perturbed systems and the Lorenz-84 system coincide. This allows for investigating the admissible perturbed systems using outcomes of researches of the well-known Lorenz-84 climate model and the theory of reflecting function.
Nonlinear Complexity and Chaotic Behaviors on Finite-Range Stochastic Epidemic Financial Dynamics
Authors: Wang Guochao , Zheng Shenzhou , Wang Jun
Published: July 2019

In this paper, a novel stochastic financial price model, based on the theory of finite-range stochastic interacting epidemic system, is proposed to reproduce the nonlinear dynamic mechanism of price fluctuations in financial markets. To better understand the complexity behavior of the proposed model, we develop a new entropy-based approach called index fluctuation fuzzy entropy (IFFE) and construct four measure criteria. The effectiveness of this approach is experimentally validated by logistic map time series, white noise time series, [Formula: see text] noise time series and six financial time series. Moreover, the largest Lyapunov exponents and Kolmogorov–Sinai entropy method are applied to analyze the chaotic property of the proposed model. To verify the rationality of the proposed model, the same analyses for the real market data are comparatively investigated with the simulation ones. The empirical results reveal that the novel financial price model is able to reproduce some important features of the financial markets.
Tricomplex Distance Estimation for Filled-In Julia Sets and Multibrot Sets
Authors: Brouillette Guillaume , Parisé Pierre-Olivier , Rochon Dominic
Published: July 2019

In this article, we present a distance estimation formula that can be used to ray trace 3D slices of the filled-in Julia sets and the Multibrot sets generated by the tricomplex polynomials of the form [Formula: see text] where [Formula: see text] is any integer greater than [Formula: see text].
Extreme Multistability with Hidden Attractors in a Simplest Memristor-Based Circuit
Authors: Chang Hui , Li Yuxia , Yuan Fang , Chen Guanrong
Published: July 2019

A simplest memristor-based circuit as a quasi-Hamiltonian system with extreme multistability is proposed and analyzed. There is no equilibrium in the system, but chaotic, quasi-periodic and periodic hidden attractors are present. The coexisting bifurcation diagrams associated with the coexisting singular attractors are observed by varying the system parameters. Of particular interest is that the coexistence of an infinite number of hidden attractors for a set of system parameters is discovered. Finally, two routes to chaos, intermittent chaotic and transient chaotic routes, are analyzed systematically, which reveal the mechanisms of chaos generation in the new circuit system.
Youth Engaging Almustafa: Cross-Generational Interactions in “Science, Technology, and Society” Education
Authors: Dyson Freeman J. , Neuenschwander Dwight E.
Published: July 2019

Both nature and the human species are constantly evolving. Neither could survive without the creative force of evolution to overcome disasters and replace worn-out parts — Freeman Dyson.
Ising Model and Its Application to Modeling Learning Environment
Authors: Tan Jyh Harng , Ang Han Wei , Bae Soo Kyung , Sim Jonathan Yeow Huat , Chong Kenneth Bao Shen , Fann Melissa Hui Jing , Ho Lucas Wei-Jie , Cai Nicholas Xianhui , Seow Yvette Yuwei , Li Daryl Zhizhang , Rifaaie Fathima Raiza Ahmed , Koh Hui Li , Zhang Will Chen , Chong Anne Suet Lin , Kuah Ting Ting , Seah Kar Heng , Leong Hon Wai , Chan Kok Hoe , Tan Yan Han , Chng Huang Hoon , Holbo John Christian , Chan Aik Hui
Published: July 2019

A modified Teaching-Learning in Classroom (TLC) theoretical model is presented in this paper. It describes the general learning process of undergraduates in NUS in the context of the GEQ1000 module offered by the Office of Provost. The results of the simulations are within the range of expectations, such that in general, the students’ knowledge level increases over the course of a 13 weeks module. GEQ1000 is a compulsory module taken by all NUS first year students ([Formula: see text]2800 per semester).
Flow diagnostics for naturally fractured reservoirs
Authors: Spooner Victoria , Geiger Sebastian , Arnold Dan
Published: July 2019

Reliable production forecasting for fractured carbonate reservoirs is a challenge. Natural fractures, adverse wettability and complex matrix heterogeneity are all uncertain and can all negatively impact upon recovery. Ideally, we should consider different reservoir concepts encapsulated in a large ensemble of reservoir models to quantify the impact of these and other geological uncertainties on reservoir performance. However, the computational cost of considering many scenarios can be significant, especially for dual porosity/permeability models, rendering robust uncertainty quantification impractical for most asset teams.

Flow diagnostics provide a complement to full-physics simulations for comparing models. Flow diagnostics approximate the dynamic response of the reservoir in seconds. In this paper we describe the extension of flow diagnostics to dual porosity models for naturally fractured reservoirs. Our new diagnostic tools link the advective time of flight in the fractures to the transfer from the matrix, identifying regions where transfer and flux are not in balance leading to poor matrix oil sweep and early breakthrough. Our new diagnostics tools have been applied to a real field case and are shown to compare well with full-physics simulation results.

Thematic collection:
This article is part of the Naturally Fractured Reservoirs collection available at:
https://www.lyellcollection.org/cc/naturally-fractured-reservoirs
Functional Skin Grafts: Where Biomaterials Meet Stem Cells
Authors: Kaur Amtoj , Midha Swati , Giri Shibashish , Mohanty Sujata
Published: July 2019

Skin tissue engineering has attained several clinical milestones making remarkable progress over the past decades. Skin is inhabited by a plethora of cells spatiotemporally arranged in a 3-dimensional (3D) matrix, creating a complex microenvironment of cell-matrix interactions. This complexity makes it difficult to mimic the native skin structure using conventional tissue engineering approaches. With the advent of newer fabrication strategies, the field is evolving rapidly. However, there is still a long way before an artificial skin substitute can fully mimic the functions and anatomical hierarchy of native human skin. The current focus of skin tissue engineers is primarily to develop a 3D construct that maintains the functionality of cultured cells in a guided manner over a period of time. While several natural and synthetic biopolymers have been translated, only partial clinical success is attained so far. Key challenges include the hierarchical complexity of skin anatomy; compositional mismatch in terms of material properties (stiffness, roughness, wettability) and degradation rate; biological complications like varied cell numbers, cell types, matrix gradients in each layer, varied immune responses, and varied methods of fabrication. In addition, with newer biomaterials being adopted for fabricating patient-specific skin substitutes, issues related to escalating processing costs, scalability, and stability of the constructs under in vivo conditions have raised some concerns. This review provides an overview of the field of skin regenerative medicine, existing clinical therapies, and limitations of the current techniques. We have further elaborated on the upcoming tissue engineering strategies that may serve as promising alternatives for generating functional skin substitutes, the pros and cons associated with each technique, and scope of their translational potential in the treatment of chronic skin ailments.