Zika virus (ZIKV) emerged at a global level when it spread to the Americas and began causing congenital malformations and microcephaly in 2015. A rapid response by academia, government, public health infrastructure, and industry has enabled the expedited development and testing of a suite of vaccine platforms aiming to control and eliminate ZIKV-induced disease. Analysis of key immunization and pathogenesis studies in multiple animal models, including during pregnancy, has begun to define immune correlates of protection. Nonetheless, the deployment of ZIKV vaccines, along with the confirmation of their safety and efficacy, still has major challenges, one of which is related to the waning of the epidemic. In this review, we discuss the measures that enabled rapid progress and highlight the path forward for successful deployment of ZIKV vaccines. Expected final online publication date for the Annual Review of Medicine Volume 70 is January 27, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The American Diabetes Association (ADA) "Standards of Medical Care in Diabetes" includes the ADA's current clinical practice recommendations and is intended to provide the components of diabetes care, general treatment goals and guidelines, and tools to evaluate quality of care. Members of the ADA Professional Practice Committee, a multidisciplinary expert committee (https://doi.org/10.2337/dc20-SPPC), are responsible for updating the Standards of Care annually, or more frequently as warranted. For a detailed description of ADA standards, statements, and reports, as well as the evidence-grading system for ADA's clinical practice recommendations, please refer to the Standards of Care Introduction (https://doi.org/10.2337/dc20-SINT). Readers who wish to comment on the Standards of Care are invited to do so at professional.diabetes.org/SOC.

Pulmonary arterial hypertension (PAH) is a pulmonary vasculopathy that causes right ventricular dysfunction and exercise limitation and progresses to death. New findings from translational studies have suggested alternative pathways for treatment. These avenues include sex hormones, genetic abnormalities and DNA damage, elastase inhibition, metabolic dysfunction, cellular therapies, and anti-inflammatory approaches. Both novel and repurposed compounds with rationale from preclinical experimental models and human cells are now in clinical trials in patients with PAH. Findings from these studies will elucidate the pathobiology of PAH and may result in clinically important improvements in outcome. Expected final online publication date for the Annual Review of Medicine Volume 70 is January 27, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The American Diabetes Association (ADA) "Standards of Medical Care in Diabetes" includes the ADA's current clinical practice recommendations and is intended to provide the components of diabetes care, general treatment goals and guidelines, and tools to evaluate quality of care. Members of the ADA Professional Practice Committee, a multidisciplinary expert committee (https://doi.org/10.2337/dc21-SPPC), are responsible for updating the Standards of Care annually, or more frequently as warranted. For a detailed description of ADA standards, statements, and reports, as well as the evidence-grading system for ADA's clinical practice recommendations, please refer to the Standards of Care Introduction (https://doi.org/10.2337/dc21-SINT). Readers who wish to comment on the Standards of Care are invited to do so at professional.diabetes.org/SOC.

Every person on Earth has been affected in some way by the coronavirus disease (COVID-19) pandemic. However, there is a marked inequity in the impact and threat of the disease for the 370 million Indigenous Peoples worldwide. While honouring diversity in peoples and cultures, this editorial (written by a collaborative of Indigenous nurses from Australia, Aotearoa (New Zealand), Canada, the United States of America and Central America), explores contemporary issues raised for Indigenous communities by this latest public health emergency. Please note, while we may describe a situation about a specific Indigenous group, readers can be assured that the issues we raise are endemic across colonised Indigenous communities globally.

Viruses constitute the largest group of emerging pathogens, and geminiviruses (plant viruses with circular, single-stranded DNA genomes) are the major group of emerging plant viruses. With their high potential for genetic variation due to mutation and recombination, their efficient spread by vectors, and their wide host range as a group, including both wild and cultivated hosts, geminiviruses are attractive models for the study of the evolutionary and ecological factors driving virus emergence. The epidemiological features of geminivirus diseases have traditionally focused primarily on crop plants. Nevertheless, knowledge of geminivirus infection in wild plants, and especially at the interface between wild and cultivated plants, is necessary to provide a complete view of their ecology, evolution, and emergence. In this review, we address the most relevant aspects of geminivirus variability and evolution in wild and crop plants and geminiviruses' potential to emerge in crops. Expected final online publication date for the Annual Review of Virology Volume 6 is September 30, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

In pigs, the major histocompatibility complex (MHC), or swine leukocyte antigen (SLA) complex, maps to Sus scrofa chromosome 7. It consists of three regions, the class I and class III regions mapping to 7p1.1 and the class II region mapping to 7q1.1. The swine MHC is divided by the centromere, which is unique among mammals studied to date. The SLA complex spans between 2.4 and 2.7 Mb, depending on haplotype, and encodes approximately 150 loci, with at least 120 genes predicted to be functional. Here we update the whole SLA complex based on the Sscrofa11.1 build and annotate the organization for all recognized SLA genes and their allelic sequences. We present SLA nomenclature and typing methods and discuss the expression of SLA proteins, as well as their role in antigen presentation and immune, disease, and vaccine responses. Finally, we explore the role of SLA genes in transplantation and xenotransplantation and their importance in swine biomedical models. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 8 is February 15, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Chronic vertebral osteomyelitis is a disease of substantial morbidity. Although uncommon to most spinal surgeons, the incidence of pyogenic and granulomatous spondylitis worldwide is on the rise. Although antibiotic therapy remains the initial treatment for most patients, surgical debridement with or without stabilization may be required for effective eradication of the disease. Indications for surgery in pyogenic and granulomatous osteomyelitis include the need to obtain a bacteriologic diagnosis when other methods have failed, the presence of a clinically significant abscess, an infection refractory to prolonged nonoperative treatment, cord compression with considerable neurologic deficit, and substantial deformity or spinal instability. Currently, controversy remains regarding the timing of surgery, the approach used, and the use of instrumentation. We reviewed the contemporary literature available through the Medline database, focusing on larger case series and, when existing, prospective randomized trials. The rationale for surgical treatment of the most common pathogens (eg, Mycobacterium tuberculae and Staphylococcus aureus) is reviewed. Commonly, anterior debridement with or without posterior instrumentation is used for cases of advanced disease, but more limited approaches may have a role in less severe cases or patients unable to tolerate extensive surgery.

METHODS

Therapeutic study, level III (systematic review of level III studies). Please see the Guidelines for Authors for a complete description of levels of evidence.

Research into the prevalence and impact of low-value medical practices has evolved substantially over the past two decades. However, despite international efforts, many challenges still remain with regards to progress in this field, including limits in the capacity to identify and prioritize low-value care practices and to systematically appraise clinical and policy attempts at redressing low-value care. A recent article by Niven et al. in BMC Medicine consolidates the current literature and terminology on the de-adoption of clinical practices, advocating the use of de-adoption as an appropriate term to label low-value care and proposes a new synthesis model to facilitate efforts to reverse ineffective and harmful medical practices. We hope that this work will facilitate advances in low-value care research and policy, and shift focus towards establishing evidence for de-adopting low-value interventions, which is crucial since attempts to reduce low-value care interventions have shown mixed results. Please see related article: http://www.biomedcentral.com/1741-7015/13/255.

Despite continued high HIV risk among Hispanic men who have sex with men (HMSM), culturally tailored, theoretically based interventions have yet to be developed and tested. As a first step toward intervention development, we collected quantitative and qualitative data on sociocultural and psychological factors associated with drug use and risky sex among 566 HMSM recruited from community and Internet venues. Participants reported high rates of drug use (43%), unprotected anal sex (45%), and multiple sex partners (median 4) in the past 6 months. In multivariate analyses, use of drugs was associated with HIV seropositivity, less orientation to the Hispanic community, stronger attachment to the gay community, lower levels of homophobia, higher numbers of sex partners and more unprotected anal sex. The need for acceptance and desire to please partners emerged as core drivers of HIV risk in the qualitative data. Findings were used to guide development of Proyecto SOL, a theoretically grounded intervention that targets core determinants of HIV risk, builds on protective cultural influences, and strengthens positive social connections.

The key idea behind the Clinical Frailty Scale (CFS) is that, as people age, they are more likely to have things wrong with them. Those things they have wrong (health deficits) can, as they accumulate, erode their ability to do the high order functions which define their overall health. These high order functions include being able to: think and do as they please; look after themselves; interact with other people; and move about without falling. The Clinical Frailty Scale brings that information together in one place. This paper is a guide for people new to the Clinical Frailty Scale. It also introduces an updated version (CFS version 2.0), with revised level names (e.g., "vulnerable" becomes "living with very mild frailty") and minor edits to level descriptions. The key points discussed are that the Clinical Frailty Scale assays the baseline state, it is not widely validated in younger people or those with stable single-system disabilities, and it requires clinical judgement. The Clinical Frailty Scale is now commonly used as a triage tool to make important clinical decisions such as allocating scarce health care resources for COVID-19 management; therefore, it is important that the scale is used appropriately.

Keywords: Clinical Frailty Scale; ageing; frailty.

Our present day understanding of nervous system development is an amalgam of insights gained from studying different aspects and stages of nervous system development in a variety of invertebrate and vertebrate model systems, with each model system making its own distinctive set of contributions. One aspect of nervous system development that has been among the most extensively studied in the nematode Caenorhabditis elegans is the nature of the gene regulatory programs that specify hardwired, terminal cellular identities. I first summarize a number of maps (anatomical, functional, and molecular) that describe the terminal identity of individual neurons in the C. elegans nervous system. I then provide a comprehensive summary of regulatory factors that specify terminal identities in the nervous system, synthesizing these past studies into a regulatory map of cellular identities in the C. elegans nervous system. This map shows that for three quarters of all neurons in the C. elegans nervous system, regulatory factors that control terminal identity features are known. In-depth studies of specific neuron types have revealed that regulatory factors rarely act alone, but rather act cooperatively in neuron-type specific combinations. In most cases examined so far, distinct, biochemically unlinked terminal identity features are coregulated via cooperatively acting transcription factors, termed terminal selectors, but there are also cases in which distinct identity features are controlled in a piecemeal fashion by independent regulatory inputs. The regulatory map also illustrates that identity-defining transcription factors are reemployed in distinct combinations in different neuron types. However, the same transcription factor can drive terminal differentiation in neurons that are unrelated by lineage, unrelated by function, connectivity and neurotransmitter deployment. Lastly, the regulatory map illustrates the preponderance of homeodomain transcription factors in the control of terminal identities, suggesting that these factors have ancient, phylogenetically conserved roles in controlling terminal neuronal differentiation in the nervous system. WIREs Dev Biol 2016, 5:474-498. doi: 10.1002/wdev.233 For further resources related to this article, please visit the WIREs website.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Corresponding Author, Yoshihiro Sato, and the co-authors have been informed. Dr. Sato wishes to retract this article on the grounds that it contains fabricated clinical trial data, which he was responsible for producing. In addition, Dr. Sato claims he listed all of the named co-authors without their consent. The co-authors were therefore unaware of the presence of fabricated data in this publication and their participation in the publication. This retraction was initiated by Dr. Sato, and the Editor-in-Chief of Bone was informed by the author directly.

Twenty-five years into the HIV/AIDS epidemic, condom use among married/stable couples remains low and under-researched in developing countries, even countries with high HIV prevalence. Introducing condoms into a long-standing relationship, in spite of HIV risk, is likely to be awkward. We conducted a qualitative study in Kampala, Uganda, with 39 couples reporting 100% condom use in the previous three months. The women were recruited from among women in a clinical trial who were using condoms and whose partners also agreed to participate. Twenty-two of the women and six of the men reported having taken the initiative to suggest condom use; the remaining couples disagreed who raised the subject first. Women used insistence, refusal to have sex, persuasion, and condoms for family planning or to protect children, which helped to deflect distrust and get their partner to agree. Some men resisted initially but their reactions were often more positive than expected. Men's reasons for accepting condoms were to please their partner, protect her from HIV, protect their children, protect themselves and, in some cases, continue having other partners. Although condom use is a couple behaviour, an encouraging environment and condom availability are all crucial to increasing condom use by couples in settings like Uganda.

Advanced glycation endproducts (AGEs) are present in the vasculature and are associated with vascular disease. We determined levels of AGEs in eight distinct adult vascular tissues using tissue microarray (TMA) technology and associated these levels with clinical characteristics. Medium-to-large caliber blood vessels were harvested from 100 adult autopsies to create 17 TMAs. AGE levels were evaluated by IHC using a polyclonal anti-AGE antibody on over 700 unique blood vessels. Slides were digitally scanned, and quantitative analysis was performed using a color deconvolution image analysis technique. Medial AGE staining was strongly correlated between all eight blood vessels. In the media, AGE staining levels were significantly higher at older ages (p=0.009), in white subjects (p<0.001) and with longer postmortem interval (PMI; p<0.0001). These associations remained significant after simultaneous adjustment for age, race/ethnicity, PMI, and diabetes status. Diabetes was associated with elevated AGE levels but only after adjustment for confounding by clinical variables including race/ethnicity, hypertension, and kidney function. This extensive vascular study shows that AGE accumulation in the macrovasculature is a global process affecting atherosclerosis-prone and -resistant vessels. It also suggests ethnicity has a previously undescribed role in vascular tissue AGE levels. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.

BACKGROUND

Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools. Due to the heterogeneity of bioinformatics tools in usage and data requirements, scientists spend much effort on technical issues including data format, storage and management of input and output, and memorization of numerous parameters and multi-step analysis procedures.

RESULTS

In this paper, we present the design and implementation of AnaBench, an interactive, Web-based bioinformatics Analysis workBench allowing streamlined data analysis. Our philosophy was to minimize the technical effort not only for the scientist who uses this environment to analyze data, but also for the administrator who manages and maintains the workbench. With new bioinformatics tools published daily, AnaBench permits easy incorporation of additional tools. This flexibility is achieved by employing a three-tier distributed architecture and recent technologies including CORBA middleware, Java, JDBC, and JSP. A CORBA server permits transparent access to a workbench management database, which stores information about the users, their data, as well as the description of all bioinformatics applications that can be launched from the workbench.

CONCLUSIONS

AnaBench is an efficient and intuitive interactive bioinformatics environment, which offers scientists application-driven, data-driven and protocol-driven analysis approaches. The prototype of AnaBench, managed by a team at the Université de Montréal, is accessible on-line at: http://malawimonas.bcm.umontreal.ca:8091/anabench. Please contact the authors for details about setting up a local-network AnaBench site elsewhere.

BACKGROUND

To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components.

RESULTS

This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects.

BACKGROUND

Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms.

BACKGROUND

imagene home page: http://wwwabi.snv.jussieu.fr/imagene

Since 1986, antiretroviral therapy (ART) has been available free of charge to individuals living with HIV in British Columbia (BC), Canada, through the BC Centre of Excellence in HIV/AIDS (BC-CfE) Drug Treatment Program (DTP). The Highly Active Antiretroviral Therapy (HAART) Observational Medical Evaluation and Research (HOMER) cohort was established in 1996 to maintain a prospective record of clinical measurements and medication profiles of a subset of DTP participants initiating HAART in BC. This unique cohort provides a comprehensive data source to investigate mortality, prognostic factors and treatment response among people living with HIV in BC from the inception of HAART. Currently over 5000 individuals are enrolled in the HOMER cohort. Data captured include socio-demographic characteristics (e.g. sex, age, ethnicity, health authority), clinical variables (e.g. CD4 cell count, plasma HIV viral load, AIDS-defining illness, hepatitis C co-infection, mortality) and treatment variables (e.g. HAART regimens, date of treatment initiation, treatment interruptions, adherence data, resistance testing). Research findings from the HOMER cohort have featured in numerous high-impact peer-reviewed journals. The HOMER cohort collaborates with other HIV cohorts on both national and international scales to answer complex HIV-specific research questions, and welcomes input from external investigators regarding potential research proposals or future collaborations. For further information please contact the principal investigator, Dr Robert Hogg (robert_hogg@sfu.ca).

BACKGROUND

Cesarean delivery is the most common inpatient surgery in the United States, where 1.3 million cesarean sections occur annually, and rates vary widely by hospital. Identifying sources of variation in cesarean use is crucial to improving the consistency and quality of obstetric care. We used hospital discharge records to examine the extent to which variability in the likelihood of cesarean section across US hospitals was attributable to individual women's clinical diagnoses.

RESULTS

Using data from the 2009 and 2010 Nationwide Inpatient Sample from the Healthcare Cost and Utilization Project--a 20% sample of US hospitals--we analyzed data for 1,475,457 births in 1,373 hospitals. We fitted multilevel logistic regression models (patients nested in hospitals). The outcome was cesarean (versus vaginal) delivery. Covariates included diagnosis of diabetes in pregnancy, hypertension in pregnancy, hemorrhage during pregnancy or placental complications, fetal distress, and fetal disproportion or obstructed labor; maternal age, race/ethnicity, and insurance status; and hospital size and location/teaching status. The cesarean section prevalence was 22.0% (95% confidence interval 22.0% to 22.1%) among women with no prior cesareans. In unadjusted models, the between-hospital variation in the individual risk of primary cesarean section was 0.14 (95% credible interval 0.12 to 0.15). The difference in the probability of having a cesarean delivery between hospitals was 25 percentage points. Hospital variability did not decrease after adjusting for patient diagnoses, socio-demographics, and hospital characteristics (0.16 [95% credible interval 0.14 to 0.18]). A limitation is that these data, while nationally representative, did not contain information on parity or gestational age.

CONCLUSIONS

Variability across hospitals in the individual risk of cesarean section is not decreased by accounting for differences in maternal diagnoses. These findings highlight the need for more comprehensive or linked data including parity and gestational age as well as examination of other factors-such as hospital policies, practices, and culture--in determining cesarean section use. Please see later in the article for the Editors' Summary.

A large number of criteria have been proposed for determining when a behavior has become automatic. Almost all of these were developed before the widespread acceptance of multiple memory systems. Consequently, popular frameworks for studying automaticity often neglect qualitative differences in how different memory systems guide initial learning. Unfortunately, evidence suggests that automaticity criteria derived from these frameworks consistently misclassify certain sets of initial behaviors as automatic. Specifically, criteria derived from cognitive science mislabel much behavior still under the control of procedural memory as automatic, and criteria derived from animal learning mislabel some behaviors under the control of declarative memory as automatic. Even so, neither set of criteria make the opposite error-that is, both sets correctly identify any automatic behavior as automatic. In fact, evidence suggests that although there are multiple memory systems and therefore multiple routes to automaticity, there might nevertheless be only one common representation for automatic behaviors. A number of possible cognitive and cognitive neuroscience models of this single automaticity system are reviewed. WIREs Cogn Sci 2012, 3:363-376. doi: 10.1002/wcs.1172 For further resources related to this article, please visit the WIREs website.

Lynne Mofenson and Heather Watts discuss the context and implications of the study by J. Sibuide and colleagues, which provides a detailed analysis of birth defects in infants with in utero antiretroviral drug exposure in the French Perinatal Cohort. Please see later in the article for the Editors' Summary.

This article begins with a description of space- and object-based guidance of attentional selection. It goes on to discuss the most influential, two-rectangle, paradigm for demonstrating the existence of space- and object-based attentional effects. The article then considers two different mechanisms, attentional spreading and attentional prioritization, that can potentially explain how object representations come to guide attentional selection. Finally, it discusses several empirical findings that have emerged in support of the two different mechanisms. It concludes by putting forth a new framework for investigating object-based effects. WIREs Cogn Sci 2012, 3:163-169. doi: 10.1002/wcs.1162 For further resources related to this article, please visit the WIREs website.

Cognitive enhancement refers to the improvement of cognitive ability in normal healthy individuals. In this article, we focus on the use of pharmaceutical agents and brain stimulation for cognitive enhancement, reviewing the most common methods of pharmacologic and electronic cognitive enhancement, and the mechanisms by which they are believed to work, the effectiveness of these methods and their prevalence. We note the many gaps in our knowledge of these matters, including open questions about the size, reliability and nature of the enhancing effects, and we conclude with recommendations for further research. WIREs Cogn Sci 2014, 5:95-103. doi: 10.1002/wcs.1250 CONFLICT OF INTEREST: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.