bluuebunny/crossref_metadata_2025 huggingface dataset:
Accurate calling of homeoallelic genotypes of iSelect markers using inbred structured populations
Authors: Shah Rohan , Keeble-Gagnère Gabriel , Whan Alex
Published: April 2020

Motivation

Genetic map construction is a foundational step in the analysis of structured experimental populations. For markers that hybridize to several genetically similar locations, or where several alleles are present (such as in multiparental populations), current methods often discard the marker or incorrectly call the genotypes. These errors result in information loss, or incorrect genotypes that can corrupt map construction.

Results

We present a new approach for simultaneously performing genetic map construction and marker calling. Our new approach allows the calling of a larger number of markers, a larger number of unique alleles per marker and the correct use of markers which hybridize to multiple genetically similar locations. We demonstrate our new approach using simulations, a biparental wheat population and an eight-parent population of spring bread wheat. Applying our method to the eight-parent population increased the number of mapped markers by 71%. We show that the new genetic map allows the investigation of synteny in ways that were not previously possible in that dataset.

Availability and implementation

The method described in this article has been incorporated into R package mpMap2. It is available from CRAN and also from https://github.com/rohan-shah/mpMap2.

Supplementary information

Supplementary data are available at Bioinformatics online.
Longitudinal neuroimaging biomarkers differ across Alzheimer’s disease phenotypes
Authors: Sintini Irene , Graff-Radford Jonathan , Senjem Matthew L , Schwarz Christopher G , Machulda Mary M , Martin Peter R , Jones David T , Boeve Bradley F , Knopman David S , Kantarci Kejal , Petersen Ronald C , Jack Clifford R , Lowe Val J , Josephs Keith A , Whitwell Jennifer L
Published: April 2020

Alzheimer’s disease can present clinically with either the typical amnestic phenotype or with atypical phenotypes, such as logopenic progressive aphasia and posterior cortical atrophy. We have recently described longitudinal patterns of flortaucipir PET uptake and grey matter atrophy in the atypical phenotypes, demonstrating a longitudinal regional disconnect between flortaucipir accumulation and brain atrophy. However, it is unclear how these longitudinal patterns differ from typical Alzheimer’s disease, to what degree flortaucipir and atrophy mirror clinical phenotype in Alzheimer’s disease, and whether optimal longitudinal neuroimaging biomarkers would also differ across phenotypes. We aimed to address these unknowns using a cohort of 57 participants diagnosed with Alzheimer’s disease (18 with typical amnestic Alzheimer’s disease, 17 with posterior cortical atrophy and 22 with logopenic progressive aphasia) that had undergone baseline and 1-year follow-up MRI and flortaucipir PET. Typical Alzheimer’s disease participants were selected to be over 65 years old at baseline scan, while no age criterion was used for atypical Alzheimer’s disease participants. Region and voxel-level rates of tau accumulation and atrophy were assessed relative to 49 cognitively unimpaired individuals and among phenotypes. Principal component analysis was implemented to describe variability in baseline tau uptake and rates of accumulation and baseline grey matter volumes and rates of atrophy across phenotypes. The capability of the principal components to discriminate between phenotypes was assessed with logistic regression. The topography of longitudinal tau accumulation and atrophy differed across phenotypes, with key regions of tau accumulation in the frontal and temporal lobes for all phenotypes and key regions of atrophy in the occipitotemporal regions for posterior cortical atrophy, left temporal lobe for logopenic progressive aphasia and medial and lateral temporal lobe for typical Alzheimer’s disease. Principal component analysis identified patterns of variation in baseline and longitudinal measures of tau uptake and volume that were significantly different across phenotypes. Baseline tau uptake mapped better onto clinical phenotype than longitudinal tau and MRI measures. Our study suggests that optimal longitudinal neuroimaging biomarkers for future clinical treatment trials in Alzheimer’s disease are different for MRI and tau-PET and may differ across phenotypes, particularly for MRI. Baseline tau tracer retention showed the highest fidelity to clinical phenotype, supporting the important causal role of tau as a driver of clinical dysfunction in Alzheimer’s disease.
Surveillance for Invasive Salmonella Disease in Bamako, Mali, From 2002 to 2018
Authors: Still William L , Tapia Milagritos D , Tennant Sharon M , Sylla Mamadou , Touré Aliou , Badji Henry , Keita Adama Mamby , Sow Samba O , Levine Myron M , Kotloff Karen L
Published: April 2020

Background

Salmonella enterica bloodstream infections are an important cause of childhood morbidity and mortality, including in Mali. We report 17 years of surveillance for nontyphoidal and typhoidal S. enterica infections among inpatients and outpatients at l’Hôpital Gabriel Touré, the main source of pediatric tertiary care in Bamako, Mali.

Methods

Between June 2002 and December 2018, a blood culture was collected from 54 748 children aged ≤15 years with fever and/or suspected invasive bacterial infection who provided consent (38 152 inpatients, 16 596 outpatients). Bacterial pathogens were identified using standard microbiological techniques and serovars of S. enterica were determined by PCR and/or agglutination with antisera.

Results

Nontyphoidal Salmonella (NTS) was identified in 671 enrolled inpatients (1.8% of all enrolled inpatients, 13.8% of enrolled inpatients with a positive culture). S. Enteritidis, the most common NTS serovar, accounted for 38.5% of all NTS isolates (n = 258), followed by S. Typhimurium (31.7%, n = 213). The median (SD) age of children with a culture positive for NTS was 1.8 (3) years. Overall case fatality was 20.9%. An additional 138 inpatients (0.4%) had a positive culture for typhoidal Salmonella. NTS was identified in 11 outpatients (0.07%), while typhoidal Salmonella was found in 49 outpatients (0.3%). The annual incidence of invasive NTS disease decreased over the study period, but case fatality remained high.

Conclusions

Although incidence decreased, NTS remained a major cause of invasive bacterial infection and mortality among hospitalized children in Bamako, while typhoidal Salmonella was uncommon. Because 87% of NTS belonged to only 4 serovars, a multivalent vaccine may be an effective strategy to reduce the burden and mortality of invasive NTS.
Structural Racism in Schools: A View through the Lens of the National School Social Work Practice Model
Authors: Crutchfield Jandel , Phillippo Kate L , Frey Andy
Published: April 2020

Structural racism—implicitly discriminatory practices and policies that have negative consequences for individuals and groups of color—is a powerful force in contemporary American society, including in our public education system. This article explores the potential for school social workers (SSWers) to address structural racism through the use of the national school social work (SSW) practice model as a tool to guide systemic, ecologically oriented intervention within schools and educational policy spaces. In this article, the authors review data on racial disparities in educational attainment, placement, opportunity, and discipline practices that have led to increased attention to structural racism in schools. They then discuss and describe the national SSW practice model and its suitability for the structural interventions in response to structural racism in schools. Finally, they provide recommendations for how SSWers can respond effectively to this pressing social problem. These recommendations include a list of resources for addressing structural racism.
Optimization of FAME composition for improved engine performance and emissions reduction
Authors: Awogbemi Omojola , Inambao Freddie , Onuh Emmanuel I
Published: April 2020

Continuous application of biodiesel as an alternative fuel for compression ignition (CI) engines has necessitated the need to unearth an optimal mix to enhance engine performance and mitigated emissions. This particular work employed a numerical approach to solve linear equations generated for biodiesel properties using fatty acid (FA) composition for the determination of an optimal fatty acid methyl ester (FAME) candidate. Transesterification of waste vegetable oil employed to experimentally produce the FAME candidate generated through numerical intervention. The gas chromatography-mass spectrometer analysis of the resulting FAME revealed that the type of used vegetable oil, the food the oil was used to fry and catalyst particle size influenced the FA composition of the FAME. Numerical evaluation of the objective function and the constraints yielded a FAME candidate with palmitic and oleic acids at 36.4% and 59.8%, respectively. The outcome of this research indicates that two FA compositions are enough to describe optimized FAME candidate for better engine performance and reduced emissions of an unmodified CI engine.
Considerations for Empiric Antimicrobial Therapy in Sepsis and Septic Shock in an Era of Antimicrobial Resistance
Authors: Strich Jeffrey R , Heil Emily L , Masur Henry
Published: April 2020

Patients with sepsis present across a spectrum of infection sites and severity of illnesses requiring complex decision making at the bedside as to when prompt antibiotics are indicated and which regimen is warranted. Many hemodynamically stable patients with sepsis and low acuity of illness may benefit from further work up before initiating therapy, whereas patients with septic shock warrant emergent broad-spectrum antibiotics. The precise empiric regimen is determined by assessing patient and epidemiological risk factors, likely source of infection based on presenting signs and symptoms, and severity of illness. Hospitals should implement quality improvement measures to aid in the rapid and accurate diagnosis of septic patients and to ensure antibiotics are given to patients in an expedited fashion after antibiotic order.
Cultural Competence and Humility in Infectious Diseases Clinical Practice and Research
Authors: Hussen Sophia A , Kuppalli Krutika , Castillo-Mancilla José , Bedimo Roger , Fadul Nada , Ofotokun Ighovwerha
Published: April 2020

Infectious diseases as a specialty is tilted toward social justice, and practitioners are frequently on the front lines of the battle against health inequity in practices that are diverse and sometimes cross international borders. Whether caring for patients living with the human immunodeficiency virus, tuberculosis, or Ebola, infectious diseases practitioners often interact with those at the margins of societies (eg, racial/ethnic/sexual/gender minorities), who disproportionately bear the brunt of these conditions. Therefore, cultural barriers between providers and patients are often salient in the infectious diseases context. In this article, we discuss cultural competence broadly, to include not only the knowledge and the skills needed at both the organizational and the individual levels to provide culturally appropriate care, but also to include “cultural humility”—a lifelong process of learning, self-reflection, and self-critique. To enhance the quality and the impact of our practices, we must prioritize cultural competence and humility and be mindful of the role of culture in the patient-provider-system interactions, in our larger healthcare systems, and in our research agendas and workforce development.
On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat
Authors: Büdel Thomas , Kuenzli Esther , Campos-Madueno Edgar I , Mohammed Ali Haji , Hassan Nadir Khatib , Zinsstag Jakob , Hatz Christoph , Endimiani Andrea
Published: April 2020

Objectives

Intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacterales (Ent) can be driven by contact with colonized animals and/or contamination of the food chain. We studied the ESC-R-Ent and COL-R-Ent colonizing poultry as well as contaminating chicken meat in Zanzibar (Tanzania). Results were compared with recently published data obtained from rectal swabs of people in the community.

Methods

During June and July 2018, we collected poultry faecal material (n = 62) and retail chicken meat (n = 37) samples. ESC-R and CST-R strains were isolated implementing selective approaches and characterized with different molecular methods, including WGS coupled with core-genome analyses.

Results

The prevalence of ESC-R-Ent and CST-R-Ent, respectively, were: 88.7% and 48.4% in poultry; and 43.2% and 18.9% in chicken meat. Overall, the following strains and main resistance mechanisms were found in the two settings: 69 ESC-R Escherichia coli (CTX-M-15 subgroup, 75%), 34 ESC-R Klebsiella pneumoniae (CTX-M-9 group, 54.5%), 24 non-ESC-R but CST-R E. coli (mcr-1, 95.8%) and 17 non-ESC-R but CST-R K. pneumoniae (D150G substitution in PhoQ). Several clones (differing by only 0–13 single nucleotide variants) were concomitantly and frequently found in human and non-human settings: mcr-1-carrying E. coli ST46; CTX-M-15-producing E. coli ST361; CTX-M-14-producing K. pneumoniae ST17; and CTX-M-15-producing K. pneumoniae ST1741.

Conclusions

This is one of the few studies that have assessed the occurrence of identical MDR Enterobacterales in human and non-human settings. The frequent human gut colonization observed in the community might be favoured by the spread of ESC-R-Ent and CST-R-Ent in poultry and chicken meat. Further studies with a One Health approach should be carried out to better investigate this phenomenon.
Plant and animal chromatin three-dimensional organization: similar structures but different functions
Authors: Dong Pengfei , Tu Xiaoyu , Liang Zizheng , Kang Byung-Ho , Zhong Silin
Published: April 2020

Chromatin is the main carrier of genetic information and is non-randomly distributed within the nucleus. Next-generation sequence-based chromatin conformation capture technologies have enabled us to directly examine its three-dimensional organization at an unprecedented scale and resolution. In the best-studied mammalian models, chromatin folding can be broken down into three hierarchical levels, compartment, domains, and loops, which play important roles in transcriptional regulation. Although similar structures have now been identified in plants, they might not possess exactly the same functions as the mammalian ones. Here, we review recent Hi-C studies in plants, compare plant chromatin structures with their mammalian counterparts, and discuss the differences between plants with different genome sizes.
Reduction of Intraocular Pressure and Glaucoma Progression
Authors: Penman Alan D. , Crowder Kimberly W. , Watkins William M.
Published: April 2020

The Early Manifest Glaucoma Trial (EMGT) was a randomized, placebo-controlled clinical trial in patients with newly detected, previously untreated, primary open-angle glaucoma (POAG) to determine whether immediate institution of intraocular pressure (IOP)–lowering therapy reduces the risk of progression compared to delayed treatment or observation. The study showed that IOP-lowering therapy offered a definitive benefit in patients with early glaucoma by delaying progression of glaucomatous optic neuropathy, especially in eyes with higher IOPs (>21 mm Hg) at baseline. Even modest reduction in IOP decreased the risk of progression. However, a large percentage of treated eyes still showed progression during follow-up. The progression of glaucomatous optic neuropathy was highly variable and difficult to predict for an individual patient.
Intraocular Injections of Ranibizumab in Patients with Macular Edema Following Branch Retinal Vein Occlusion
Authors: Penman Alan D. , Crowder Kimberly W. , Watkins William M.
Published: April 2020

The Ranibizumab for Macular Edema following Branch Retinal Vein Occlusion (BRAVO) study was a 6-month, phase III, randomized, injection-controlled trial, with an additional 6 months of follow-up (total 12 months), to evaluate the safety and efficacy of intraocular injections of 0.3 mg and 0.5 mg ranibizumab (an anti–vascular endothelial growth factor [VEGF] agent) in patients with macular edema following branch retinal vein occlusion (BRVO). The study showed that intraocular injections of 0.3 mg or 0.5 mg ranibizumab provided rapid, effective treatment for macular edema following BRVO with low rates of ocular and nonocular adverse events. This study led to a paradigm shift toward anti-VEGF agents as the first-line treatment for macular edema secondary to BRVO.
Grid Pattern Photocoagulation for Macular Edema in Central Vein Occlusion
Authors: Penman Alan D. , Crowder Kimberly W. , Watkins William M.
Published: April 2020

The Central Vein Occlusion Study (CVOS) was a randomized, controlled, clinical trial to determine whether treatment with macular grid photocoagulation improved or preserved visual acuity in eyes with macular edema involving the fovea secondary to nonischemic central retinal vein occlusion (CRVO) and best corrected visual acuity of 20/50 or worse. The study found that, overall, visual acuity results were not different for treated and control eyes. Based on this, the standard of care at that time continued to be observation. (Treatment with intravitreal anti–vascular endothelial growth factor [VEGF] agents is now the standard of care.)
A Clinical Activity Score That Discriminates Between Inflammatory and Noninflammatory Graves’ Ophthalmopathy
Authors: Penman Alan D. , Crowder Kimberly W. , Watkins William M.
Published: April 2020

In this chapter the results of a retrospective analysis of pooled data from a randomized, double blind, clinical trial comparing oral prednisone to radiotherapy in patients with both inflammatory and noninflammatory Graves’ disease are described. The aim of the analysis was to determine whether a previously developed index (the Clinical Activity Score, CAS) could discriminate between inflammatory and noninflammatory Graves’ ophthalmopathy. The analysis showed that the CAS had a high predictive value for the outcome of immunosuppressive treatment in Graves’ ophthalmopathy. A high CAS helped to select patients who benefited from immunosuppressive treatment; a low CAS, however, did not exclude favorable therapeutic results. Disease activity (measured by the CAS), and not disease duration, is the prime determinant of therapeutic outcome in Graves’ ophthalmopathy.
Can You Go Change the Family’s Mind?
Authors: Ajayi Toluwalase
Published: April 2020

Parents and legal guardians of seriously ill children are often faced with challenging decisions regarding code status and cardiopulmonary resuscitation. There is commonly a certain amount of discomfort and negative emotions surrounding these conversations. Unfortunately, because of this, when clinicians do initiate these conversations, it is often too late in the course of disease, and opportunities for the children and their families to have their preferred end-of-life wishes may be missed. This chapter reviews the common myths and misconceptions surrounding the code status conversation by addressing the emotions associated with it. In addition, the chapter provides a step-by-step guideline on how to approach this topic.
How Do We Go Back to Work Now?
Authors: Ragsdale Lindsay B.
Published: April 2020

Patient care can have a significant impact on health care professionals both professionally and personally. Understanding and responding to these emotionally charged situations can help providers work through their emotions and build resiliency over time. Many institutions use debriefings to help providers unpack these situations and learn how to cope together. Debriefing after a significant patient event can help provide a time for medical staff to discuss the event, talk about their emotions, enhance teamwork, and improve the feeling of being supported by peers. Creating a space for these difficult conversations can help providers recover and get back to patient care.
The Lack of Movement
Authors: Winegard Billie
Published: April 2020

Constipation is a common and often overlooked symptom for pediatric palliative care patients. In this chapter, constipation for children receiving palliative care is defined as the passage of small, hard feces infrequently and with difficulty. Patients with constipation may present with a variety of gastrointestinal or urinary symptoms requiring a thorough history and exam. Some patients may have a treatable underlying etiology, but it is very common that the underlying cause may not be reversible or cannot be identified. These cases will require laxatives to treat and prevent constipation. Cases of opioid-induced constipation may benefit from opioid antagonists. This chapter presents a review of etiologies of constipation in children receiving palliative care as well as a review of laxatives that may be used in these patients.
Is My Baby Feeling Hungry?
Authors: Ragsdale Lindsay B.
Published: April 2020

The decision to withhold or withdraw artificial nutrition and hydration (ANH) can be highly emotional and challenge caregivers’ duty to their child. Medical providers should explore the burdens and benefits of ANH and use a shared decision-making model to build a care plan. Time-limited trials of ANH can be used to meet the family’s goals and values with close monitoring for distressing symptoms. ANH can have spiritual and cultural implications for families, and spiritual leaders and chaplains should be engaged in these discussions if the family desires. The American Academy of Pediatrics has guidelines regarding the withholding or withdrawing of ANH in pediatric patients.
A Winding Path
Authors: Marsac Meghan L.
Published: April 2020

Anticipatory grief and bereavement include a range of emotional reactions leading up to and following the loss of a child. Grief often involves reactions related to both the loss of life and other losses, such as expectations, hopes, and dreams that the child and their family had. Individual family members express grief in different ways. Medical teams have the opportunity to help prepare families and guide them through the grief process. Medical teams may be particularly helpful in guiding parents about what reactions to expect in themselves, how to support their dying child, and how to support surviving siblings. Medical teams also have the opportunity to identify individuals who are exhibiting more extreme, impairing, persistent reactions and refer these individuals for additional services.
Mayo Clinic General Surgery
Authors: Abdelsattar Jad M. , El Khatib Moustafa M. , Pandian T. K. , Allen Samuel J. , Farley David R.
Published: April 2020

This book presents the core concepts of general surgery instruction at Mayo Clinic. It was created to provide succinct and accurate information in a written, imaging, and audiovisual format that allows efficient access to surgical learners—especially those with just a few minutes to spare. Its purpose is to better prepare students, residents, and fellows for their surgical experiences , leading to better understanding with long-term retention. Contents include surgery by organ system and a chapter devoted to trauma cases. Each chapter contains information on the organ system (including embryology), anatomy, physiology, clinical presentation, imaging techniques, common operations, and potential complications.
Breast
Authors: Abdelsattar Jad M. , El Khatib Moustafa M. , Pandian T. K. , Allen Samuel J. , Farley David R.
Published: April 2020

Breast tissue develops from ectoderm, the primary mammary buds being noted during the fifth week of gestation. Glandular epithelium, stroma, and fat receive blood from the internal mammary and posterior intercostal arteries. In females, estrogen mediates ductal development. In males, androgen leads to destruction of the epithelial component of the breast bud. Most breast complaints are due to a mass, nipple discharge, or pain. Ultrasonography is useful in young women and as an adjunct to mammography. Wide local excision, mastectomy, sentinel lymph node biopsy, and axillary dissection can be useful in men and women undergoing breast surgery. Lymphedema may occur after axillary lymph node dissection or radiation therapy.
My Journey as an Advocate for People with Epilepsy
Authors: MacLeish Mary
Published: April 2020

Furthering the missions of epilepsy organizations, by either volunteering for, starting, or running an organization that serves people with epilepsy have been the goals of the advocates who have dedicated their lives to organizational advocacy.
Making Changes in the World
Authors: Malone Kevin
Published: April 2020

Furthering the missions of epilepsy organizations, by either volunteering for, starting, or running an organization that serves people with epilepsy have been the goals of the advocates who have dedicated their lives to organizational advocacy.
Together There Is Hope
Authors: Soeby Lisa Dunn
Published: April 2020

In this section, people’s experiences with rare forms of epilepsy have given rise to many forms of advocacy for people with epilepsy. From forming an organization to tracking seizures, there is no act of advocacy too large or small.
Hope for Better Options—
Authors: Wohlberg Seth
Published: April 2020

In this section, people’s experiences with rare forms of epilepsy have given rise to many forms of advocacy for people with epilepsy. From forming an organization to tracking seizures, there is no act of advocacy too large or small.
Rattled by the Shakes?
Authors: Tang Richard , Foster David
Published: April 2020

The neonatal age group is at highest risk for seizures when compared with other age groups. Neonatal seizures may be subtle and an early timely diagnosis is critical. With a broad differential diagnosis, timely recognition of metabolic abnormalities, such as hypoglycemia, are an important etiology that requires rapid, aggressive management. As with the management of any other sick infant, the clinician should adhere to the ABCs of resuscitation, ensuring adequate airway and cardiovascular support. An algorithmic approach to status epilepticus facilitates termination of seizure activity. Acute treatment of neonatal seizures should be continued until all seizures, both clinical and EEG, are controlled.
My Broken Heart
Authors: Bonaventura Bridget , Bubolz Beth
Published: April 2020

This is a case of a 3-month-old male presenting with a 2-week history of crying and pallor during feeds. Common etiologies for a crying infant need to be considered and include corneal abrasions, incarcerated hernias, testicular torsion, hair tourniquets and others. It is critical to not neglect consideration of the life threatening causes of crying in an infant including neurologic, gastrointestinal, and, of course, cardiac diagnoses. Symptoms that worsen with feeding may be likened to cardiac symptoms in adults that worsen with exercise. The best treatment in this child is to screen for hypoglycemia, avoid feeding and get an EKG and chest x-ray.
Sneezing, Wheezing, Having Trouble Breathing
Authors: Quarrie Renee
Published: April 2020

This chapter deals with one of the most common chronic diseases of childhood—asthma. It reviews the diagnosis of this disease and the acute emergency management of a pediatric patient who presents to the emergency department in respiratory distress from asthma. The current treatment modalities and indications for their use are discussed. Key points include that asthma diagnosis in the pediatric patient is largely clinical; early recognition and intervention are critical for successful management of asthma exacerbations; early administration of corticosteroids is important as it has been shown to reduce the rate of hospitalization; and routine chest radiographs do not play a part in the management of asthma.
Introduction: A ‘fourth age’ of psychiatric epidemiology?
Authors: Das-Munshi Jayati , Ford Tamsin , Hotopf Matthew , Prince Martin , Stewart Robert
Published: April 2020

This is the introduction to the second edition of ‘Practical Psychiatric Epidemiology’ published by Oxford University Press. In this introduction the Editors reflect on developments since the first edition. Themes touched upon include the ongoing need for high quality descriptive data, the contribution of wearable devices and technologies to generating data for psychiatric epidemiological studies, developments relating to the availability of large-scale data resources or so-called ‘big data’ in psychiatric epidemiology, ongoing issues relating to accurate measurement in psychiatric epidemiology and the contribution of complex interventions to effective healthcare service delivery, and in particular, the way in which these are effectively implemented. The chapter concludes with a reflection on the continued importance of psychiatric epidemiology to the field of mental health.
Culture and psychiatric epidemiology
Authors: Kohrt Brandon A. , Patel Vikram
Published: April 2020

Culture refers to values, beliefs, knowledge, norms, and practices and the notion that these are shared among a specific set of people. Culture shapes the meaning and social experience of mental illness; influences the types of exposures to factors that cause mental illness; and moderates the relationship between risks and mental health outcomes. Cultural differences in models of causality and labelling of mental illnesses contribute to degree of family support, use of religious and traditional healing, and engagement with biomedical care systems. Cultural variations in describing, disclosing, and categorizing suffering are also sources of potential bias in epidemiological research. Instruments developed in one culture may be used in others, but greater emphasis must be placed on their adaptation to ensure equivalence. Use of cultural frameworks is crucial to optimize utilization and outcomes of culturally adapted psychological treatments and other mental health interventions.
Introduction to epidemiological study designs
Authors: Ford Tamsin , Das-Munshi Jayati , Prince Martin
Published: April 2020

This chapter provides a brief overview for each of the main types of study design commonly used in psychiatric epidemiology. The chapter begins with a discussion of the importance of study design. This is followed by a section on classifying study design, including descriptive studies, ecological studies, cross-sectional surveys, cohort studies, case–control studies, intervention studies, and qualitative and mixed methods studies. The chapter concludes with a description of the basic steps which should be observed in the conduct of studies employing quantitative methodologies (including cross-sectional, cohort, and case–control studies), as well as discussing interviews/assessments, and data collection and processing.
Randomized controlled trials
Authors: Banerjee Sube , Taylor Rod S. , Hellier Jennifer
Published: April 2020

This chapter on randomized controlled trials (RCTs) considers some of the key factors in the design, conduct, analysis, and interpretation of RCTs. The chapter provides an overview of what constitutes an RCT and why they are needed. The chapter also provides an overview of the major practical elements of the design and conduct of RCTs, including undertaking a background review of literature, the need for formulation of a clear primary hypothesis and objective, selection and definition of the study population, collecting outcomes at baseline and follow-up, and appropriate methods of statistical analysis and inference. The chapter concludes with a consideration of the need for clinical trial units, complex interventions, and alternative RCT designs.
Evidence-based mental health policy
Authors: Iemmi Valentina , Votruba Nicole , Thornicroft Graham
Published: April 2020

This chapter describes evidence-based mental health policy with the help of illustrative examples. After briefly setting the use of research evidence to inform mental health policy within the broader historical context, the second section of the chapter provides a brief description of evidence-based mental health policy and its rationale. The third section illustrates how mental health research may help inform mental health policy, with a description of the research cycle, the policy cycle, their relationship, and the use of epidemiological studies for policymaking. The fourth section provides examples of the use of research evidence in mental health policy at different organizational levels, from the clinical level (micro-level), through the service provision/healthcare facility level (meso-level) and the whole health system level (macro-level), to the global level (mega-level). Finally, the chapter concludes by reflecting on some of the opportunities and challenges that influence evidence-based mental health policy.
Rheumatology
Authors: Frise Charlotte , Collins Sally
Published: April 2020

This chapter covers rheumatic diseases in the pregnant patient. It gives background, clinical features, and management in the pregnant patient for rheumatoid arthritis, Sjögren’s syndrome, psoriatic arthritis, systemic lupus erythematosus, antiphospholipid syndrome, and ankylosing spondylitis among others. It also covers systemic sclerosis, osteoporosis, and other musculoskeletal problems. Medications and the use of biologics in pregnancy are also discussed, with reference to breastfeeding.
Venous thromboembolism
Authors: Frise Charlotte , Collins Sally
Published: April 2020

Venous thromboembolism is a major cause of maternal mortality and morbidity. This chapter discusses thromboprophylaxis (including low-molecular-weight heparin and doses by patient weight), risk factors, deep vein thrombosis, pulmonary embolism, associated investigations, and management. Anticoagulants and bleeding while anticoagulated are both covered. Finally, superficial vein thrombosis in the first month postpartum is described.
Anatomy and physiology
Authors: Jefferis Helen , Price Natalia
Published: April 2020

This chapter provides the anatomy of the urinary tract and pelvic floor. It covers the ureter, bladder, and urethra. It also describes the pelvic floor muscles (role and levels of vaginal support), and the control of micturition.
Basic symptoms in deficit states and their relation to negative symptoms
Authors: Schultze-Lutter Frauke
Published: April 2020

Basic symptoms are subtle, subjectively experienced disturbances in mental processes including thinking, speech, attention, perception, drive, stress tolerance, and affect, originally described by Gerd Huber. Basic symptoms are present in prodromal, psychotic, and residual/deficit states of schizophrenia and have been conceptualized as the most immediate psychopathological expression of the neurobiological abnormalities underlying the development and persistence of psychosis. Basic symptoms are currently mostly recognized for their potential to detect psychosis prior to the first psychotic episode and, thus, for their ability to herald persistent positive symptoms. Although initially described to facilitate understanding of deficit states in schizophrenia, their contribution to negative symptoms has less been studied, although the evaluation of basic symptoms helps in improving understanding of the psychopathology—including differentiation of primary and secondary negative symptoms—and course of schizophrenia and in planning better treatment.
Oxford Case Histories in Infectious Diseases and Microbiology
Authors: Humphreys Hilary , Irving William , Atkins Bridget , Woodhouse Andrew
Published: April 2020

The case format highlights key issues in presenting features, diagnosis, management, and prevention, and lends itself well to cases of infection. Those chosen reflect both common and important pathogens/infections, and less frequent but important conditions in terms of the outcome or the risk of onward spread. The cases are divided according to the main organ systems, such as respiratory and gastrointestinal, with a section for systemic infections and miscellaneous for those cases that do not neatly fit into any category. The book focuses on ensuring that the reader is aware of how to confirm a diagnosis rapidly, with references throughout to evolving laboratory techniques, provides advice on therapy, discusses recent epidemiological features, and addresses areas where there is some controversy. A combination of clinical photographs, imaging, laboratory illustrations, tables, and figures are included to highlight key points or features. Further reading provides information on aspects where there are ongoing developments. For the trainee in clinical microbiology and infection, it is not possible to cover all aspects of any curriculum in this format, and they are recommended to consult other sources. However, the cases presented will assist both them and their trainers in keeping abreast of recent developments and reminding them of key principles.
Case 3
Authors: Woodhouse Andrew
Published: April 2020

Chickenpox is caused by varicella-zoster virus and is predominantly a self-limiting disease of childhood. Chickenpox in adults is more likely to be associated with complications such as varicella pneumonia. Treatment with antivirals is helpful in adults if given early after the onset of rash in uncomplicated disease. In complicated disease such as pneumonia, intravenous treatment is essential to optimize drug levels although an evidence base for this is lacking. Exposure to varicella during pregnancy is a particular concern for non-immune women and passive immunization with varicella immune globulin is indicated.
Case 4
Authors: Humphreys Hilary
Published: April 2020

Measles is an important cause of an exanthem (i.e. fever and a rash in a child). However, there are other viral causes depending on the nature of the rash such as chickenpox if the rash is vesicular, and chikungunya virus if there has been travel abroad. Laboratory confirmation of measles is through the detection of immunoglobulin M (IgM) antibodies in serum or measles RNA in an oral swab. Individual patient management is largely symptomatic but as it is very infectious, patients should be isolated. Pneumonia, otitis media, and encephalitis are the commonest complications. Encephalitis may arise shortly after the onset of the acute illness or many years later. In some resource-rich countries there has been an increase in the incidence of measles recently because some children have not received the second dose of the measles vaccine. Globally, measles remains one of the leading causes of death in children less than five years old.
Case 27
Authors: Humphreys Hilary
Published: April 2020

The presence of fever, altered behaviour, and seizures are strongly suggestive of encephalitis. Herpes simplex is the commonest cause in the United Kingdom, rabies is common globally, but no aetiology is identified in about half of all cases. Other causes include varicella-zoster, enteroviruses, arboviruses, human herpes virus-6, cytomegalovirus, and Epstein–Barr virus. Monoplex, PCR, and multiplex assays are used to confirm a diagnosis but metagenomics are identifying new causes. Included in the differential diagnosis are auto-immune forms of encephalitis which are diagnosed by excluding infection and detecting specific antibodies. High-dose aciclovir is required for herpes encephalitis but for many other causes—for example, West Nile virus—there is no specific treatment. Patients presenting with a coma, seizures, and a cranial nerve deficit have a poorer prognosis. However, with early diagnosis and aggressive antiviral treatment, the mortality from herpes simplex encephalitis may be just 10%.
Case 35
Authors: Woodhouse Andrew
Published: April 2020

Malaria is among the most common imported infection brought into the United Kingdom . Recognition of malaria is crucial given the potential severe consequences including death, particularly from Plasmodium falciparum infection. Prompt diagnosis and correct treatment improves outcome and malaria must be considered in the differential diagnosis of fever in all travellers with an appropriate exposure history.
Case 43
Authors: Barrett Lucinda , Atkins Bridget
Published: April 2020

The number of joint replacements performed in resource-rich countries has increased significantly in the last few decades and has allowed a significant improvement in the quality of life for many patients. Despite preventative measures, a small fraction (around 1% for hip replacements) will become infected. These can present as acute or chronic infections. They can also occur at any time after the primary procedure. Late acute infections are usually via the haematogenous route and often present to the acute medical take or via infection services. A prompt, appropriate medical and surgical management strategy is important.
Case 44
Authors: Irving Will
Published: April 2020

Healthcare workers can transmit blood-borne virus (BBV) infections to their patients during the course of performing exposure prone procedures. To reduce the risk of this happening, healthcare workers entering the National Health Service who wish to perform EPPs in the UK must be tested for BBV infection. Hepatitis B- infected healthcare workers may perform EPPs providing they are HBE antigen negative and have a viral load below 200 IU/ml, subject to annual viral load checks. If their viral load is >200 but < 20,000 IU/ml, then they may suppress HBV replication using nucleos(t)ide analogue antiviral therapy, subject to 3-monthly viral load measurement. Healthcare workers known to be currently infected with hepatitis C virus are not allowed to perform EPPs but may do so if they are clear of HCV RNA 12 weeks after antiviral therapy. HIV-infected healthcare workers may perform EPPs if their viral load is suppressed to < 200 copies/ml whilst on combination antiretroviral therapy, subject to 3-monthly monitoring.
The impact of filamentary accretion of subhaloes on the shape and orientation of haloes
Authors: Morinaga Yu , Ishiyama Tomoaki
Published: April 2020

Dark matter haloes are formed through hierarchical mergers of smaller haloes in large-scale cosmic environments, and thus anisotropic subhalo accretion through cosmic filaments has some impacts on halo structures. Recent studies using cosmological simulations have shown that the orientations of haloes correlate with the direction of cosmic filaments, and these correlations significantly depend on the halo mass. Using high-resolution cosmological N-body simulations, we quantified the strength of filamentary subhalo accretion for galaxy- and group-sized host haloes (Mhost = 5 × 1011–13 M⊙) by regarding the entry points of subhaloes as filaments and present statistical studies on how the shape and orientation of host haloes at redshift zero correlate with the strength of filamentary subhalo accretion. We confirm previous studies that found the host halo mass dependence of the alignment between orientations of haloes and filaments. We also show that, for the first time, the shape and orientation of haloes weakly correlate with the strength of filamentary subhalo accretion even if the host halo masses are the same. Minor-to-major axial ratios of haloes tend to decrease as their filamentary accretion gets stronger. Haloes with highly anisotropic accretion become more spherical or oblate, while haloes with isotropic accretion become more prolate or triaxial. For haloes with strong filamentary accretion, their major axes are preferentially aligned with the filaments, while their angular momentum vectors tend to be slightly more misaligned.
Infrared interferometry to spatially and spectrally resolve jets in X-ray binaries
Authors: Markoff Sera , Russell David M , Dexter Jason , Pfuhl Oliver , Eisenhauer Frank , Abuter Roberto , Miller-Jones James C A , Russell Thomas D
Published: April 2020

Infrared interferometry is a new frontier for precision ground-based observing, with new instrumentation achieving milliarcsecond (mas) spatial resolutions for faint sources, along with astrometry on the order of 10 microarcseconds (μas). This technique has already led to breakthroughs in the observations of the supermassive black hole at the Galactic centre and its orbiting stars, active galactic nucleus, and exo-planets, and can be employed for studying X-ray binaries (XRBs), microquasars in particular. Beyond constraining the orbital parameters of the system using the centroid wobble and spatially resolving jet discrete ejections on mas scales, we also propose a novel method to discern between the various components contributing to the infrared bands: accretion disc, jets, and companion star. We demonstrate that the GRAVITY instrument on the Very Large Telescope Interferometer should be able to detect a centroid shift in a number of sources, opening a new avenue of exploration for the myriad of transients expected to be discovered in the coming decade of radio all-sky surveys. We also present the first proof-of-concept GRAVITY observation of a low-mass XRB transient, MAXI J1820+070, to search for extended jets on mas scales. We place the tightest constraints yet via direct imaging on the size of the infrared emitting region of the compact jet in a hard state XRB.
specphot: a comparison of spectroscopic and photometric exoplanet follow-up methods
Authors: Cooke Benjamin F , Pollacco Don
Published: April 2020

We set out a simulation to explore the follow-up of exoplanet candidates. We look at comparing photometric (transit method) and spectroscopic (Doppler shift method) techniques using three instruments: Next-Generation Transit Survey, High-Accuracy Radial-velocity Planetary Search, and CORALIE. We take into account the precision of follow-up and required observing time in attempt to rank each method for a given set of planetary system parameters. The methods are assessed on two criteria: signal-to-noise ratio (S/N) of the detection and follow-up time before characterization. We find that different follow-up techniques are preferred for different regions of parameter space. For S/N, we find that the ratio of spectroscopic to photometric S/N for a given system goes like $R_{\rm p}/P^{{1}/{3}}$. For follow-up time, we find that photometry is favoured for the shortest period systems (<10 d) as well as systems with small planet radii. Spectroscopy is then preferred for systems with larger radius, and thus more massive planets (given our assumed mass–radius relationship). Finally, we attempt to account for the availability of telescopes and weight the two methods accordingly.
Probingintermediate-mass black holes in M87 through multiwavelength gravitational wave observations
Authors: Emami Razieh , Loeb Abraham
Published: April 2020

We analyse triple systems composed of the supermassive black hole (SMBH) near the centre of M87 and a pair of black holes (BHs) with masses in the range of $10{-}10^3\, {\rm M}_{\odot }$. We consider the post Newtonian precession as well as the Kozai–Lidov interactions at the quadruple and octupole levels in modelling the evolution of binary black hole (BBH) under the influence of the SMBH. Kozai–Lidov oscillations enhance the gravitational wave (GW) signal in some portions of the parameter space. We identify frequency peaks and examine the detectability of GWs with LISA as well as future observatories such as μAres and DECIGO. We show examples in which GW signal can be observed with a few or all of these detectors. Multiwavelength GW spectroscopy holds the potential to discover stellar to intermediate mass BHs near the centre of M87. We estimate the rate, Γ, of collisions between the BBHs and fly-by stars at the centre of M87. Our calculation suggest $\Gamma \lt 10\, \rm {Gyr}^{-1}$ for a wide range of the mass and semimajor axes of the inner binary.