bluuebunny/crossref_metadata_2025 huggingface dataset:
Love and Religion
Authors: Cottingham John
Published: April 2017

In the Judeo-Christian tradition that has shaped much of Western thought, we find an insistence on love as a requirement. Many points of philosophical interest arise from this injunction to love, irrespective of whether one is a religious believer. This chapter begins by asking if it makes sense to suppose that love can be commanded, and moves on to examine various “demandingness” objections to the commandment to love one’s neighbor. The chapter then considers, and rejects, the possibility of purely a secularized interpretation of the Christian ethic that dispenses with the religious framework altogether. The concluding section looks at how various religious conceptions of love connect up with certain fundamental assumptions about the nature of the cosmos we inhabit and the meaning of human life.
Pivotal Years: 1948–1965
Authors: Fuchs Lorelei F.
Published: April 2017

The chapter considers key ecumenical developments in the period 1948–65, between the founding of the World Council of Churches (WCC) and the closing of the Second Vatican Council, at which the Catholic Church finally embraced the ecumenical movement. Explaining how that period can be seen as pivotal in the history of the movement, it tracks the developing understanding of the ecumenical challenge reflected in successive assemblies of the WCC and conferences on Faith and Order, both at world level and in North America, and the growing desire for Catholic engagement in the ecumenical movement manifested particularly in the activities of the Catholic Conference for Ecumenical Questions. It then considers the teaching of Vatican II on ecumenism, for example, regarding degrees of communion, and the impact of Catholic participation on the ecumenical movement, notably in the practice of bilateral dialogues.
Hardwiring Privacy
Authors: Bygrave Lee A.
Published: April 2017

This chapter examines regulatory efforts to ensure that due account is taken of privacy and related interests in the development of information systems such that these interests are, in effect, integrated (or ‘hardwired’) into the resulting systems. Such efforts are typically described in terms of ‘Privacy by Design’ and ‘Data Protection by Design’. The basic argument advanced in the chapter is that such efforts are unlikely to gain broad traction, at least in the short term, despite current moves to provide them with increased legal support. This is due to a broad range of factors the most important of which is that any ambitious privacy-hardwiring efforts will clash with powerful business and state interests at the same time as they remain marginal to the concerns of most consumers and engineers. This marginality is exacerbated by poor communication of such efforts’ parameters, methodologies and requirements.
Zooarchaeology of the Scandinavian settlements in Iceland and Greenland
Authors: Smiarowski Konrad , Harrison Ramona , Brewington Seth , Hicks Megan , Feeley Frank J. , Dupont-Hébert Céline , Prehal Brenda , Hambrecht George , Woollett James , McGovern Thomas H.
Published: April 2017

The Scandinavian Viking Age and Medieval settlements of Iceland and Greenland have been subject to zooarchaeological research for over a century, and have come to represent two classic cases of survival and collapse in the literature of long-term human ecodynamics. The work of the past two decades by multiple projects coordinated through the North Atlantic Biocultural Organization (NABO) cooperative and by collaborating scholars has dramatically increased the available zooarchaeological evidence for economic organization of these two communities, their initial adaptation to different natural and social contexts, and their reaction to Late Medieval economic and climate change. This summary paper provides an overview of ongoing comparative research as well as references for data sets and more detailed discussion of archaeofauna from these two island communities.
Life, Death, and Resurrections
Authors: Streib Jessi , Verma SaunJuhi , Welsh Whitney , Burton Linda M.
Published: April 2017

This article examines the culture of poverty thesis, focusing on its many lives, deaths, and reincarnations. It first considers the intellectual history of the culture of poverty thesis before discussing how the argument has been interspersed throughout U.S. history and applied to various groups. It then considers the argument’s scholarly reproduction, noting how it is underlain by a binary whereby segments of the poor, racial minorities, and immigrants are positioned as having a deviant, morally suspect culture that undermines their potential upward mobility, whereas white middle- and upper-class Americans are positioned as having a normal, morally upstanding culture that secures their class position. The article also describes four routine scholarly practices that engender a specter of support for the culture of poverty thesis. Finally, it argues that the culture of poverty should either be put to rest or allowed to live based on its own merits, and suggests ways to end its unintentional resurrection.
The Historical Origins of Poverty in Developing Countries
Authors: Bhattacharyya Sambit
Published: April 2017

This article explores the historical origins of poverty and the root causes of poverty in developing countries. It first considers the theories that explain the root causes (geography, disease, colonial history, slave trade, culture, and technology) of poverty before describing a novel, unified framework that unites these theories. The central thesis is that Western Europe benefited from favorable geography that led to highly productive agriculture, food surpluses, and institutions conducive to development. In contrast, Africa continues to suffer from unfavorable geography and disease. Institutional weaknesses in Latin America and Russia explain their relatively weak long-term economic performance. The article argues that these historical factors matter for contemporary patterns of development across the globe.
People and Places Left Behind
Authors: Lichter Daniel T. , Schafft Kai A.
Published: April 2017

This article examines the unique issues faced by rural people and places in the new century, with the goal of raising the profile of disadvantaged rural populations for both scholarly and policy audiences. It begins with a discussion of the strengths and weaknesses of the U.S. official poverty measure—based on absolute money (rather than in-kind) income—for evaluating material disadvantage in rural areas. It then considers six key features of contemporary rural poverty that distinguish it from big-city or inner-city poverty (or suburban poverty). It also places current poverty patterns in rural America in the international context, providing a comparative assessment of theory, measurement, and policy on rural disadvantage in the United States and countries of the European Union including the UK. Finally, it looks at alternative approaches to the social welfare state, to conceptualizing poverty, and to better understanding the implications for rural people and places.
Urban Poverty, Race, and Space
Authors: Wilson William Julius
Published: April 2017

This article examines the political, economic, and cultural factors that contributed to the emergence and persistence of concentrated poverty in black inner cities. It begins with a discussion of the political forces that adversely affected black inner-city neighborhoods, followed by an analysis of impersonal economic forces that accelerated neighborhood decline in the black inner city and increased disparities in race and income between cities and suburbs. It then considers two types of cultural forces that contribute to racial inequality: belief systems of the broader society that either explicitly or implicitly give rise to racial inequality; and cultural traits that emerge from patterns of intragroup interaction in settings created by racial segregation and discrimination. It also assesses the impact of the recent rise of immigration on areas of concentrated urban poverty before concluding with suggestions for a new agenda for America’s inner city poor.
Material Deprivation and Consumption
Authors: Kus Basak , Nolan Brian , Whelan Christopher T.
Published: April 2017

This article examines material deprivation and consumption in relation to poverty. In a developing country context, manifest material deprivation and inadequate levels of consumption have always been central to the conceptualization of poverty and living standards. Direct measures of failure to meet “basic needs” are widely used alongside income-based measures such as the World Bank’s “dollar a day” standard. In contrast, both research and official poverty monitoring in rich countries tend to rely on household income. This article begins with a review of recent research on material deprivation, seen primarily as a means to go “beyond income” in capturing poverty and exclusion. It then considers the mismatch between low income and measured deprivation, along with the notion of multidimensionality and the measurement issues raised in the implementation of multidimensional approaches. Finally, it analyzes conceptual and empirical issues relating to the contrast between income and consumption.
Feminist Pedagogy in the Undergraduate Music Survey Course
Authors: Wilbourne Emily
Published: April 2017

This article considers the pragmatic difficulties of implementing feminist pedagogy in the undergraduate music history survey course. Drawing on the author’s teaching experience at the Aaron Copland School of Music, the article tackles the question of what counts as feminist pedagogy. It considers the fundamental problem of feminist scholarship and its application to the music history survey and provides pragmatic examples of how the author teaches, bridging the theoretical/practical divide that often fractures musicology in general and pedagogical speculation in particular. It also explains the author’s syllabi and a particular set writing assignments given as part of a music history survey, considering their effectiveness as components of a distinctly feminist pedagogy and how feminist goals might result in pedagogical choices that themselves seem less obviously feminist. Finally, the article reflects on whether the idea of a feminist history survey is a useful, or even feasible, goal.
New British Nature Writing
Authors: Lilley Deborah
Published: April 2017

This chapter explores the emergence of “new British nature writing” in the twenty-first century and identifies new approaches to its subject and form produced in response to the scale of harm registered by the growing awareness of environmental crisis. It interrogates the notion of “new” nature writing and the ways that it has been received, considering its continuities and breaks with the legacies of the tradition in Britain alongside ecocritical arguments concerning the concept and representation of nature and human–nonhuman relations. The chapter examines defining characteristics of the form— interest in urban, suburban, and industrial landscapes; attention to spatial and temporal intersections of people and place; a re-evaluation of ideas such as “natural” and “wild”; and a critical self-consciousness regarding the representation of nature — in key works by writers including Robert Macfarlane, Kathleen Jamie, Helen Macdonald, Roger Deakin, and Paul Farley and Michael Symmons Roberts.
Cerebral Autoregulation-oriented Therapy at the Bedside
Authors: Rivera-Lara Lucia , Zorrilla-Vaca Andres , Geocadin Romergryko G. , Healy Ryan J. , Ziai Wendy , Mirski Marek A.
Published: April 2017

This comprehensive review summarizes the evidence regarding use of cerebral autoregulation-directed therapy at the bedside and provides an evaluation of its impact on optimizing cerebral perfusion and associated functional outcomes. Multiple studies in adults and several in children have shown the feasibility of individualizing mean arterial blood pressure and cerebral perfusion pressure goals by using cerebral autoregulation monitoring to calculate optimal levels. Nine of these studies examined the association between cerebral perfusion pressure or mean arterial blood pressure being above or below their optimal levels and functional outcomes. Six of these nine studies (66%) showed that patients for whom median cerebral perfusion pressure or mean arterial blood pressure differed significantly from the optimum, defined by cerebral autoregulation monitoring, were more likely to have an unfavorable outcome. The evidence indicates that monitoring of continuous cerebral autoregulation at the bedside is feasible and has the potential to be used to direct blood pressure management in acutely ill patients.
Successful Continuation of Pregnancy After Treatment of Group A Streptococci Sepsis
Authors: Alhousseini Ali , Layne Mia E. , Gonik Bernard , Bryant David , Patwardhan Sanjay , Patwardhan Manasi
Published: April 2017

BACKGROUND:

Invasive group A streptococci infections in pregnancy have historically led to severe maternal and neonatal morbidity and mortality. We are reporting a rare and novel case of successful treatment of third-trimester group A streptococci infection with early, aggressive intervention and maintenance of the pregnancy to term.

CASE:

A 35 year old woman initially presented with fever, flu-like symptoms, and preterm contractions at 34 weeks of gestation. She demonstrated signs of early stages of septic shock, ultimately attributed to group A streptococci bacteremia. Early, aggressive intervention allowed the pregnancy to continue until 38 weeks of gestation with normal maternal and neonatal outcomes.

CONCLUSION:

Early and aggressive treatment of invasive group A streptococci infection during pregnancy can potentially avoid severe maternal and perinatal morbidity and mortality with a successful continuation of pregnancy.
Maternal Cardiovascular Mortality in Illinois, 2002–2011
Authors: Briller Joan , Koch Abigail R. , Geller Stacie E. ,   for the Illinois Department of Public Health Maternal Mortality Review Committee Working Group
Published: April 2017

OBJECTIVE:

To describe the demographic characteristics of women in Illinois who died from cardiovascular disease during pregnancy or up until 1 year postpartum, addressing specific etiologies, timing of death, proportion of potentially preventable mortality, and factors associated with preventability.

METHODS:

This is a retrospective analysis from the Illinois Department of Public Health Maternal Mortality Review process using International Classification of Diseases, 9th Revision codes that attributed cardiovascular disease as the immediate or underlying cause of maternal death in Illinois from 2002 to 2011. We categorized the etiology of cardiovascular mortality, analyzed demographic factors associated with cardiovascular mortality in comparison with noncardiovascular causes, defined the relationship to pregnancy, and identified factors associated with preventability.

RESULTS:

There were 636 deaths in Illinois from 2002 to 2011 of pregnant women or within 1 year postpartum. One hundred forty women (22.2%) died of cardiovascular causes, for a cardiovascular mortality rate of 8.2 (95% confidence interval 6.9–9.6) per 100,000 live births. Women with cardiovascular mortality were likely to be older and die postpartum. The most common etiologies were related to acquired cardiovascular disease (97.1%) as compared with congenital heart disease (2.9%). Cardiomyopathy was the most common etiology (n=39 [27.9%]), followed by stroke (n=32 [22.9%]), hypertensive disorders (n=18 [12.9%]), arrhythmias (n=15 [10.7%]), and coronary disease (n=13 [9.3%]). Nearly 75% of cardiac deaths were related to pregnancy as compared with 35.3% of noncardiac deaths. More than one fourth of cardiac deaths (28.1%) were potentially preventable, attributable primarily to health care provider and patient factors.

CONCLUSION:

From 2002 to 2011, more than one fifth of maternal deaths in Illinois were attributed to cardiovascular disease such as cardiomyopathy. More than one fourth of these deaths were potentially preventable. Health care provider and patient factors were identified, which may be modifiable through education and intensive postpartum monitoring, which may diminish mortality. State maternal mortality reviews can identify opportunities for reducing maternal deaths.
Accommodating Immigrant Women's Preferences for Female Health Care Providers
Authors: Aubrey Christa , Mumtaz Zubia , Patterson Patrick B. , Chari Radha , Mitchell B. F. (Peter)
Published: April 2017

OBJECTIVE:

To investigate obstetricians' perspectives of the importance, effect, and challenges of providing intrapartum care to immigrant women who request a female obstetrician.

METHODS:

A focused ethnography was conducted at a large teaching hospital, which serves a high proportion of immigrant clientele (predominantly North or East African, Middle Eastern, and South Asian) in Edmonton, Alberta, Canada. Data collection comprised single, semistructured interviews with a purposive sample of 20 obstetric health care providers (10 resident and 10 staff obstetricians). Interviews were audio-recorded and transcribed verbatim. Data were managed with Quirkos and analyzed using thematic analysis.

RESULTS:

A total of 13 female and seven male physicians were interviewed. Physicians recognized the validity of immigrant women's preference and requests for female health care providers and expressed sympathy for them. However, they were also resistant and expressed several concerns about accommodating these requests, including fear of perpetuating and exacerbating gender inequalities in medicine, the extent to which patient decision-making was coercion-free, the ability of the health system to meet the demands, and implications for training and quality of care.

CONCLUSION:

Although physicians were sympathetic to immigrant women's requests for female obstetricians, they placed greater value on maintaining gender equity both within the medical profession and in wider society and resisted accommodating gender-of-health-care-provider requests. Our qualitative study suggests a need for greater research to inform policy that meets the professional and personal values of both physicians and patients.
Comparison of Vaginal Hysterectomy Techniques and Interventions for Benign Indications
Authors: Jeppson Peter C. , Balgobin Sunil , Rahn David D. , Matteson Kristen A. , Dieter Alexis A. , Ellington David R. , Aschkenazi Sarit O. , Grimes Cara , Mamik Mamta M. , Balk Ethan M. , Murphy Miles ,   for the Society of Gynecologic Surgeons Systematic Review Group
Published: April 2017

OBJECTIVE:

To create evidence-based clinical practice guidelines based on a systematic review of published literature regarding the risks and benefits of available preoperative, intraoperative, and postoperative technical steps and interventions at the time of vaginal hysterectomy for benign indications.

DATA SOURCES:

We systematically searched the literature to identify studies that compared technical steps or interventions during the preoperative, intraoperative, and postoperative periods surrounding vaginal hysterectomy. We searched MEDLINE, Cochrane Central Register of Controlled Trials, Health Technology Assessments, and ClinicalTrials.gov from their inception until April 10, 2016, using the MeSH term “Hysterectomy, Vaginal” and associated text words. We included comparative studies, single-group studies, and systematic reviews published in English.

METHODS OF STUDY SELECTION:

We double-screened 4,250 abstracts, identifying 60 eligible studies. Discrepancies were adjudicated by a third reviewer. We followed standard systematic review methodology and the Grades for Recommendation, Assessment, Development and Evaluation approach to evaluate the evidence and generate guideline recommendations.

TABULATION, INTEGRATION, AND RESULTS:

Because of limited literature, only 16 perioperative risks, technical steps, and interventions were identified: obesity, large uteri, prior surgery, gonadotropin-releasing hormone agonists, vaginal antisepsis, bilateral salpingo-oophorectomy, morcellation, apical closure, uterine sealers, hemostatic injectants, hot cone, retractor, cystoscopy, vaginal packing, bladder management, and accustimulation. We organized and reported these as four domains: patient selection, preoperative, intraoperative, and postoperative. We did not identify any patient characteristics precluding a vaginal approach; chlorhexidine or povidone is appropriate for vaginal antisepsis; vasopressin decreases blood loss by 130 cc; tissue-sealing devices decrease blood loss by 44 cc and operative time by 15 minutes with uncertain complication implications; vertical cuff closure results in 1-cm increased vaginal length; either peritoneum or epithelium can be used for colpotomy closure; and routine vaginal packing is not advised.

CONCLUSION:

Minimal data exist to guide surgeons with respect to planning and performing a vaginal hysterectomy. This study identifies available information and future areas for investigation.
What Is New in Amniotic Fluid Embolism?
Authors: Benson Michael D.
Published: April 2017

This month, we focus on current research in amniotic fluid embolism. Dr. Benson discusses four recent publications, and each is concluded with a “bottom line” that is the take-home message. The complete reference for each can be found in Box 1 on this page, along with direct links to the abstracts.
Does Sex Influence Publication Productivity Among Colorectal Surgeons Participating in Fellowship Training Programs?
Authors: Geltzeiler Cristina B. , Kelley Katherine A. , Srikanth Priya , Deveney Karen E. , Diamond Sarah , Thomas Charles R. , Enestvedt Brintha K. , Tsikitis Vassiliki L.
Published: April 2017

BACKGROUND:

Underrepresentation of highly ranked women in academic surgery is recognized.

OBJECTIVE:

Our objective was to examine whether sex differences exist in faculty representation, academic rank, and publication productivity among colorectal faculty in fellowship programs.

DESIGN:

American Society of Colon and Rectal Surgeons fellowship program faculty were identified. Bibliometric data were obtained for each faculty member, including Hirsch index, the Hirsch index divided by research career duration, and number of publications. Linear mixed-effect regression models were constructed to determine the association between the Hirsch index and the Hirsch index divided by research career duration and sex, when controlling for institutional measures. A subset analysis of academic faculty examined the association between academic rank, sex, and Hirsch index and the Hirsch index divided by research career duration.

SETTINGS:

Colorectal fellowship programs, defined as academic, satellite-academic, and nonacademic, were evaluated.

RESULTS:

Three hundred fifty-eight faculty members were examined across 55 training programs; 22% (n = 77) were women and 78% (n = 281) were men. Sixty-one percent (n = 220) practiced in an academic setting, 23% (n = 84) in a satellite-academic setting, and 15% (n = 54) in a nonacademic setting. There was no difference in median number of publications between sexes (15 vs 10, p = 0.33); men, however, had longer careers (18 vs 11 years, p < 0.001). When controlling for confounders, there was no difference in the Hirsch index (p = 0.42) or the Hirsch index divided by research career duration (p = 0.73) between sexes. Academic rank was significantly associated with Hirsch index and the Hirsch index divided by research career duration (p < 0.001) after controlling for sex.

LIMITATIONS:

Our assessment of association between publication productivity and academic rank was only possible in the subset of academic faculty. In addition, this study is limited by its retrospective nature.

CONCLUSIONS:

We found no difference in median number of publications between men and women. When controlling for possible confounders, sex was not a significant predictor of a faculty member’s publication productivity, as measured by the Hirsch index or the Hirsch index divided by research career duration; academic rank, however, was.
Use of Anal Acoustic Reflectometry in the Evaluation of Men With Passive Fecal Leakage
Authors: Hornung Benjamin R. , Telford Karen J. , Carlson Gordon L. , Mitchell Peter J. , Klarskov Niels , Kiff Edward S.
Published: April 2017

BACKGROUND:

Men with passive fecal leakage represent a distinct clinical entity in which the pathophysiology remains unclear. Standard anorectal investigations fail to demonstrate consistent abnormalities in this group. Anal acoustic reflectometry is a new test of anal sphincter function with greater sensitivity and discriminatory ability than conventional anal manometry.

OBJECTIVE:

The aim of this study was to determine whether men with fecal leakage have an abnormality in anal sphincter function that is detectable by anal acoustic reflectometry.

DESIGN:

This was an age-matched study of continent and incontinent men.

SETTINGS:

The study was conducted at a university teaching hospital.

PATIENTS:

Male patients with isolated symptoms of fecal leakage were recruited. Anal acoustic reflectometry, followed by conventional anal manometry, was performed. Results were then compared with those from an age-matched group of men with no symptoms of anal incontinence or anorectal pathology.

MAIN OUTCOME MEASURES:

Variables measured with anal acoustic reflectometry and anal manometry in the incontinent and continent men were compared.

RESULTS:

Thirty subjects were recruited, of whom 15 were men with fecal leakage and 15 were continent men. There was a significantly higher incidence of previous anorectal surgery in the men with leakage. The anal acoustic reflectometry variables of opening and closing pressure were significantly lower in leakers compared with continent subjects (p = 0.003 and p = 0.001). Hysteresis was significantly greater in the male leaker group (p = 0.026). No difference was seen in anal manometry.

LIMITATIONS:

With a larger sample size, the effect of previous anorectal surgery and the presence of an anal sphincter defect could be clarified.

CONCLUSIONS:

Anal acoustic reflectometry is a sensitive test of anal sphincter function and, unlike anal manometry, can discriminate male leakers from continent subjects. An identifiable abnormality has been detected using anal acoustic reflectometry, which may further our understanding of the pathogenesis in this group.
Mock Institutional Review Board: Promoting Analytical and Reasoning Skills in Research Ethics
Authors: Dols Jean Dowling , Hoke Mary M. , Rauschhuber Maureen L.
Published: April 2017

Although it is critical that nurses possess ethical reasoning skills for research, there is limited information on effective strategies to develop these skills in graduate health care students. A research study analyzing educational interventions including the effect of online human subjects training followed by a mock institutional review board simulation demonstrated that knowledge acquisition is not enough to acquire the ethical reasoning skills needed to implement health care research. Situational context is also needed to envision the application of ethical principles.
Improving Triage Accuracy
Authors: Brosinski Carmen M. , Riddell Autumn J. , Valdez Sherwin
Published: April 2017

Purpose:

The purpose of the process improvement initiative was to improve the percentage of undertriaged patients to less than 10% (benchmark) using the Emergency Severity Index tool. Undertriaged patients have an increased potential for poor outcomes due to a lengthier waiting room stay, which results in delay of care.

Description of the Project:

An evidence-based project designed for staff development was conducted for a 7-month period. Project procedures consisted of triage chart reviews for a 3-month period during pre– and post–Emergency Severity Index training. Emergency Severity Index refresher training for nurses triaging in the emergency department was conducted for a 1-month period.

Outcome:

Chart reviews revealed that 102 of 388 patients (26.3%) were undertriaged before Emergency Severity Index training. After Emergency Severity Index training, chart reviews depicted that 41 of 440 patients (9.3%) were undertriaged. This difference was statically significant (P < .001), when tested using a 1-sided t test at the 95% confidence level and achieving at least 80% power.

Implications:

Regardless of previous training or years of emergency department nursing experience, triage refresher training has been shown to increase accuracy of triage categorization, thus leading to a decreased risk of poor patient outcomes.
Improving Culture, One Quality Improvement Project at a Time
Authors: Vander Schaaf Emily B. , Cornett Amanda C. , Randolph Greg D.
Published: April 2017

Context:

A culture of quality improvement (QI) values collaboration, transparency, and staff empowerment. Organizations exhibiting a culture of QI are more likely to engage in QI.

Objective:

We examined whether local health departments' (LHDs') participation in a longitudinal, experiential QI training program changes QI culture.

Design:

Prior to and following participation in a QI training program, all employees of participating LHDs were asked to complete an 8-item survey assessing components of QI culture on a 5-point scale.

Intervention:

From 2010 to 2015, multidisciplinary teams from North Carolina LHDs participated in sequential cohorts of a 6-month QI training program, during which the teams completed a QI project.

Main Outcome Measure:

We dichotomized culture survey responses, with 4 or 5 being “Supportive.” We compared adjusted proportions, using linear regression, clustering at LHD, and controlling for cohort.

Results:

Data from 42 LHDs were included. At baseline, 7.8% responded that their LHD had a supportive culture for all 8 components, compared with 12% at follow-up (P < .001), adjusted for cohort and clustering by LHD. At follow-up, the percentage of employees responding that their LHDs had supportive cultures increased for all components of culture including communication by 4.1% (95% CI: 2.0%-6.2%), problem solving by 2.9% (95% CI: 1.6%-5.5%), team work by 5.2% (95% CI: 2.5%-7.8%), vision by 4.3% (95% CI: 1.1%-7.5%), performance measures by 5.6% (95% CI: 1.6%-9.6%), recognition by 4.7% (95% CI: 1.4%-8.0%), for conflict by 5.5% (95% CI: 1.7%-9.4%), and alignment by 5.8% (95% CI: 2.3%-9.2%).

Conclusions:

Engagement with structured QI training programs—and perhaps simply completing QI projects—can cause small, but important changes in organizations' cultures, thus increasing engagement in future QI and improving overall care and services. The article demonstrates that when LHDs participate in a longitudinal, experiential QI training program, their cultures of QI improve. Local health departments participating in similar training programs might experience similar improvements in culture, increasing subsequent participation in QI projects and improving related health outcomes.
Effects of California Assembly Bill 2109 in Low Vaccination Rate Counties: Are We Looking at the Right Variables?
Authors: Rosentrater Cody , Finlayson Tracy L. , Peddecord K. Michael
Published: April 2017

Objectives:

California Assembly Bill 2109 (AB2109) was passed in 2012 and restricted the obtainment of personal belief exemptions (PBEs) for vaccination requirements for school-aged children. This study examined changes in up-to-date (UTD) vaccination rates, PBEs, and conditionally accepted students (CASs) at 3 time points. The study also examined the association of PBEs and CASs on county and school immunization rates.

Design:

This study utilized 6 academic years of immunization data from all kindergartens in California from 2010-2011 to 2015-2016. The years were selected to include data 2 years prior to the introduction of the bill, 2 years prior to implementation, and 2 years after the new legislation went into effect in 2014. Data were analyzed for changes in variables over time at the state, county, and school levels. A Pearson correlation was performed to assess the association between CAS, PBE, and not-UTD rates in low- and high-UTD counties.

Results:

Counties with the highest percentage of unimmunized students have significantly higher mean CAS rates than PBE rates (P < .01 for all years). CASs were found to be more highly correlated with students not-UTD with immunizations than PBEs in all years studied (P < .01 for all years) and with far greater effect size in low-UTD counties (<90% UTD rate). There was a small rise in PBEs and a small reduction in UTD rates after AB2109 was signed but a fall in PBE and CAS rates and a rise in UTD rates postimplementation.

Conclusion:

Many California counties have high levels of CASs at the time of kindergarten entry. The extent to which schools require CASs to complete required vaccinations is not known, which could contribute to the pool of undervaccinated students in California. Public health officials should be vigilant to ensure that schools follow up and enforce the completion of vaccines for conditionally admitted students. This study has policy implications due to the fact that it has been revealed that there is a large undervaccinated population remaining relatively unaccounted for in California despite recent efforts.
MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures
Authors: Bradley Anthony R. , Rose Alexander S. , Pavelka Antonín , Valasatava Yana , Duarte Jose M. , Prlić Andreas , Rose Peter W.
Published: April 2017

Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data are updated on a weekly basis.
Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions
Authors: Brinegar Amy E. , Xia Zheng , Loehr James A. , Li Wei , Rodney George G. , Cooper Thomas A.
Published: April 2017

Postnatal development of skeletal muscle is a highly dynamic period of tissue remodeling. Here we used RNA-seq to identify transcriptome changes from late embryonic to adult mouse muscle and demonstrate that alternative splicing developmental transitions impact muscle physiology. The first two weeks after birth are particularly dynamic for differential gene expression and AS transitions, and calciumhandling functions are significantly enriched among genes that undergo alternative splicing. We focused on the postnatal splicing transitions of three calcineurin A genes, calcium-dependent phosphatases that regulate multiple aspects of muscle biology. Redirected splicing of calcineurin A to the fetal isoforms in adult muscle and in differentiated C2C12 slows the timing of muscle relaxation, promotes nuclear localization of calcineurin targets Nfatc3 and Nfatc2, and affects expression of Nfatc transcription targets. The results demonstrate a previously unknown specificity of calcineurin isoforms as well as the broader impact of AS during muscle postnatal development.
Modeling the consequences of heterogeneity in microbial population dynamics
Authors: Herrmann Helena , Lawless Conor
Published: April 2017

Chapter 1

The rate at which unicellular micro-organisms progress through the cell cycle is a major component of their evolutionary fitness. Measuring fitness phenotypes in a given environment or genetic background forms the basis of most quantitative assays of drug sensitivity or genetic interaction, including genome-wide assays. Growth rate is typically measured in bulk cell populations, inoculated with anything from hundreds to millions of cells sampled from purified, isogenic colonies. High-throughput microscopy reveals that striking levels of growth rate heterogeneity arise between isogenic cell lineages (Levyet al., 2012). Using publishedSaccharomyces cerevisiaedata, I examine the implications for interpreting bulk, population scale growth rate observations, given observed levels of growth rate heterogeneity at the lineage level. I demonstrate that selection between cell lineages with a range of growth rates can give rise to an apparent lag phase at the population level, even in the absence of evidence for a lag phase at the lineage level. My simulations further predict that, given observed levels of heterogeneity, final populations should be dominated by one or a few lineages.

Chapter 2

In order to validate and further explore the conclusions from Chapter 1, I re-analyzed high-throughput microscopy experiments carried out on Quantitative Fitness Analysis (QFA)S. cerevisiaecultures (Addinallet al., 2011), an approach referred to asμQFA. To allow for precise observation of purely clonal lineages including very fast-growing lineages and non-dividing cells, I re-designed an existing image analysis tool forμQFA, now available as an open source Python package. Fast-growing outliers in particular influence the extent of the lag phase apparent at the population level, making the precision of growth rate estimation a key ingredient for successfully simulating population observations.μQFA data include population observations which I used to validate the population simulations generated from individual lineage data. I explored various options for modeling lineage growth curves and for carrying out growth rate parameter inference, and included the full workflow in an open source R package.

Contact

helena.herrmann@postgrad.manchester.ac.uk
The DDR at telomeres lacking intact shelterin does not require substantial chromatin decompaction
Authors: Timashev Leonid A. , Babcock Hazen , Zhuang Xiaowei , de Lange Titia
Published: April 2017

Telomeres are protected by shelterin, a six-subunit protein complex that represses the DNA damage response (DDR) at chromosome ends. Extensive data suggest that TRF2 in shelterin remodels telomeres into the t-loop structure, thereby hiding telomere ends from double-stranded break repair and ATM signaling, whereas POT1 represses ATR signaling by excluding RPA. An alternative protection mechanism was suggested recently by which shelterin subunits TRF1, TRF2, and TIN2 mediate telomeric chromatin compaction, which was proposed to minimize access of DDR factors. We performed superresolution imaging of telomeres in mouse cells after conditional deletion of TRF1, TRF2, or both, the latter of which results in the complete loss of shelterin. Upon removal of TRF1 or TRF2, we observed only minor changes in the telomere volume in most of our experiments. Upon codeletion of TRF1 and TRF2, the telomere volume increased by varying amounts, but even those samples exhibiting small changes in telomere volume showed DDR at nearly all telomeres. Upon shelterin removal, telomeres underwent 53BP1-dependent clustering, potentially explaining at least in part the apparent increase in telomere volume. Furthermore, chromatin accessibility, as determined by ATAC-seq (assay for transposase-accessible chromatin [ATAC] with high-throughput sequencing), was not substantially altered by shelterin removal. These results suggest that the DDR induced by shelterin removal does not require substantial telomere decompaction.
The making of a lymphocyte: the choice among disparate cell fates and the IKAROS enigma
Authors: Georgopoulos Katia
Published: April 2017

Lymphocyte differentiation is set to produce myriad immune effector cells with the ability to respond to multitudinous foreign substances. The uniqueness of this developmental system lies in not only the great diversity of cellular functions that it can generate but also the ability of its differentiation intermediates and mature effector cells to expand upon demand, thereby providing lifelong immunity. Surprisingly, the goals of this developmental system are met by a relatively small group of DNA-binding transcription factors that work in concert to control the timing and magnitude of gene expression and fulfill the demands for cellular specialization, expansion, and maintenance. The cellular and molecular mechanisms through which these lineage-promoting transcription factors operate have been a focus of basic research in immunology. The mechanisms of development discerned in this effort are guiding clinical research on disorders with an immune cell base. Here, I focus on IKAROS, one of the earliest regulators of lymphoid lineage identity and a guardian of lymphocyte homeostasis.
The developmental proteome of Drosophila melanogaster
Authors: Casas-Vila Nuria , Bluhm Alina , Sayols Sergi , Dinges Nadja , Dejung Mario , Altenhein Tina , Kappei Dennis , Altenhein Benjamin , Roignant Jean-Yves , Butter Falk
Published: April 2017

Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila’s life cycle, resulting in 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9f3Ψ as a protein-coding gene, and to obtain evidence of 268 small proteins. Moreover, the comparison with available transcriptomic data uncovered examples of poor correlation between mRNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes provide a powerful resource and can be explored in detail in our interactive web interface.
Direct determination of diploid genome sequences
Authors: Weisenfeld Neil I. , Kumar Vijay , Shah Preyas , Church Deanna M. , Jaffe David B.
Published: April 2017

Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses, and in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed free of reference bias, but nearly all were constructed by merging homologous loci into single “consensus” sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing, and one using thousands of clone pools. Here, we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ∼1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new “pushbutton” algorithm, Supernova. Each computation took 2 d on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.
Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
Authors: Despic Vladimir , Dejung Mario , Gu Mengting , Krishnan Jayanth , Zhang Jing , Herzel Lydia , Straube Korinna , Gerstein Mark B. , Butter Falk , Neugebauer Karla M.
Published: April 2017

During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNA-bound proteome. This protein constellation consists of many conserved RBPs, some of which are potential stage-specific mRNA interactors that likely reflect the dynamics of RNA–protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of these RBPs in embryogenesis, we focused on Hnrnpa1. iCLIP and subsequent mRNA reporter assays revealed a function for Hnrnpa1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3′ UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that Hnrnpa1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-mir-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of Hnrnpa1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA–protein interactions during vertebrate MZT and shows that Hnrnpa1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.
Changes in the geography of Brazilian diet diversity
Authors: Mores Giana de Vargas , Talamini Edson , Dewes Homero
Published: April 2017

Purpose

The purpose of this paper is to present the evolution of Brazilian food patterns, based on the 2002-2003 and 2008-2009 Brazilian Household Budget Surveys (POFs), and to evaluate similarities in food acquisition among the Brazilian states, in search for the main drivers of the changes.

Design/methodology/approach

Using the data gathered from the 17 food groups within the POFs and multidimensional scaling, the Brazilian states were divided into groups and analysed according to their similarities in terms of annual per capita household food acquisition.

Findings

The study’s results point to five groups with similarities in terms of food acquisition among the Brazilian states. Additionally, the issues that reflect Brazil’s diversity were discussed, highlighting possible factors that caused the movement of some states between groups during the analysis period. The heterogeneity observed in food acquisition in Brazil emphasises Brazilian agribusiness development and underscores the influence of the food supply chains on the regional food patterns.

Originality/value

This research presents the geographic changes in the Brazilian agribusiness, and how these changes are reflected in the population food patterns and in the heterogeneity in food acquisition among the Brazilian states. Concerning this work, supply chains of agri-industrial products focussed on the domestic market can be analysed in depth, offering guidelines for future research in logistics and agri-industrial economy.