bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutational signature learning with supervised negative binomial non-negative matrix factorization
Authors: Lyu Xinrui , Garret Jean , Rätsch Gunnar , Lehmann Kjong-Van
Published: May 2020

Motivation

Understanding the underlying mutational processes of cancer patients has been a long-standing goal in the community and promises to provide new insights that could improve cancer diagnoses and treatments. Mutational signatures are summaries of the mutational processes, and improving the derivation of mutational signatures can yield new discoveries previously obscured by technical and biological confounders. Results from existing mutational signature extraction methods depend on the size of available patient cohort and solely focus on the analysis of mutation count data without considering the exploitation of metadata.

Results

Here we present a supervised method that utilizes cancer type as metadata to extract more distinctive signatures. More specifically, we use a negative binomial non-negative matrix factorization and add a support vector machine loss. We show that mutational signatures extracted by our proposed method have a lower reconstruction error and are designed to be more predictive of cancer type than those generated by unsupervised methods. This design reduces the need for elaborate post-processing strategies in order to recover most of the known signatures unlike the existing unsupervised signature extraction methods. Signatures extracted by a supervised model used in conjunction with cancer-type labels are also more robust, especially when using small and potentially cancer-type limited patient cohorts. Finally, we adapted our model such that molecular features can be utilized to derive an according mutational signature. We used APOBEC expression and MUTYH mutation status to demonstrate the possibilities that arise from this ability. We conclude that our method, which exploits available metadata, improves the quality of mutational signatures as well as helps derive more interpretable representations.

Availability and implementation

https://github.com/ratschlab/SNBNMF-mutsig-public.

Supplementary information

Supplementary data are available at Bioinformatics online.
Minimum Status, Matching and Domination of Graphs
Authors: Liang Caixia , Zhou Bo , Guo Haiyan
Published: May 2020

Given a graph, the status of a vertex is the sum of the distances between the vertex and all other vertices. The minimum status of a graph is the minimum of statuses of all vertices of this graph. We give a sharp upper bound for the minimum status of a connected graph with fixed order and matching number (domination number, respectively) and characterize the unique trees achieving the bound. We also determine the unique tree such that its minimum status is as small as possible when order and matching number (domination number, respectively) are fixed.
Shared decision-making in atrial fibrillation: patient-reported involvement in treatment decisions
Authors: Ali-Ahmed Fatima , Pieper Karen , North Rebecca , Allen Larry A , Chan Paul S , Ezekowitz Michael D , Fonarow Gregg C , Freeman James V , Go Alan S , Gersh Bernard J , Kowey Peter R , Mahaffey Kenneth W , Naccarelli Gerald V , Pokorney Sean D , Reiffel James A , Singer Daniel E , Steinberg Benjamin A , Peterson Eric D , Piccini Jonathan P , O’Brien Emily C
Published: May 2020

Aims 

To determine the extent of shared decision-making (SDM), during selection of oral anticoagulant (OAC) and rhythm control treatments, in patients with newly diagnosed atrial fibrillation (AF).

Methods and results 

We evaluated survey data from 1006 patients with new-onset AF enrolled at 56 US sites participating in the SATELLITE substudy of the Outcomes Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT II). Patients completed surveys at enrolment and at 6-month follow-up. Patients were asked about who made their AF treatment decisions. Shared decision-making was classified as one that the patient felt was an autonomous decision or a shared decision with their healthcare provider (HCP). Approximately half of patients reported that their OAC treatment decisions were made entirely by their HCP. Compared with those reporting no SDM, patients reporting SDM for OAC were more often female (47.2% vs. 38.4%), while patients reporting SDM for rhythm control were more often male (62.2% vs. 57.6%). The most important factors cited by patients during decision-making for OAC were reducing stroke and bleeding risk, and their HCP’s recommendations. After adjustment, patients with self-reported understanding of OAC, and rhythm control options, had higher odds of having participated in SDM [odds ratio (OR) 2.54, confidence interval (CI): 1.75–3.68 and OR 2.36, CI: 1.50–3.71, both P ≤ 0.001, respectively].

Conclusion 

Shared decision-making is not widely implemented in contemporary AF practice. Patient understanding about available therapeutic options is associated with a more than a two-fold higher likelihood of SDM, and may be a potential target for future interventions.
Percutaneous vs. surgical revascularization for patients with unprotected left main stenosis: a meta-analysis of 5-year follow-up randomized controlled trials
Authors: D’Ascenzo Fabrizio , De Filippo Ovidio , Elia Edoardo , Doronzo Mattia Paolo , Omedè Pierluigi , Montefusco Antonio , Pennone Mauro , Salizzoni Stefano , Conrotto Federico , Gallone Guglielmo , Angelini Filippo , Franchin Luca , Bruno Francesco , Boffini Massimo , Gaudino Mario , Rinaldi Mauro , De Ferrari Gaetano Maria
Published: May 2020

Aims

A 5-year survival of patients with unprotected left main (ULM) stenosis according to the choice of revascularization (percutaneous vs. surgical) remains to be defined.

Methods and results

Randomized controlled trials (RCTs) comparing percutaneous coronary intervention (PCI) vs. coronary artery bypass graft (CABG) with a follow-up of at least 5 years were included. All-cause death was the primary endpoint. MACCE [a composite endpoint of all-cause mortality, myocardial infarction (MI), stroke, and repeat revascularization] along with its single components and cardiovascular (CV) death were the secondary ones. Analyses were stratified according to the use of first- vs. last-generation coronary stents. Subgroup comparisons were performed according to SYNTAX score (below or above 33) and to age (using cut-offs of each trial’s subgroup analysis). Four RCTs with 4394 patients were identified: 2197 were treated with CABG, 657 with first generation, and 1540 with last-generation stents. At 5-year rates of all-cause death did not differ [odds ratio (OR) 0.93, 95% confidence interval (CI) 0.71–1.21], as those of CV death and stroke. Coronary artery bypass graft reduced rates of MACCE (OR 0.69, 95% CI 0.60–0.79), mainly driven by MI (OR 0.48, 95% CI 0.36–0.65) and revascularization (OR 0.53, 95% CI 0.45–0.64). Benefit of CABG for MACCE was consistent, although with different extent, across values of SYNTAX score (OR 0.76, 95% CI 0.59–0.97 for values < 32 and OR 0.63, 95% CI 0.47–0.84 for values ≥ 33) while was not evident for ‘younger’ patients (OR 0.83, 95% CI 0.65–1.07 vs. OR 0.65, 95% CI 0.51–0.84 for ‘older’ patients).

Conclusion

For patients with ULM disease followed-up for 5 years, no significant difference was observed in all-cause and cardiovascular death between PCI and CABG. Coronary artery bypass graft reduced risk of MI, revascularization, and MACCE especially in older patients and in those with complex coronary disease and a high SYNTAX score.
Exploring Online Discussions Through an Academic Literacies Approach
Authors: Roose Tamara Mae , Newell George E
Published: May 2020

This preliminary study explores how international students bring their cultural knowledge and experiences into relationship with other writers’ ideas as they engage in an online discussion in response to a news text. This article focuses on a language excerpt from an online discussion group, including the assignment prompt, reading text, student responses, and comments to one another within a university ESL composition course. An intertextual analysis suggests that students’ engagement with multiple texts in this dialogic space and the integration of their own cultural resources led to socially constructed learning, relationship building, and a deepened understanding of the source text. This study extends the conversation in Academic Literacies research by illustrating how the construct can be used as a design frame for teaching an academic practice (writing about text) while also deliberately incorporating ways for students to draw upon their cultural identities and resources.
Advancing knowledge on social capital for young people’s mental health
Authors: Morgan Antony , Svedberg Petra , Nyholm Maria , Nygren Jens
Published: May 2020

Inequalities in young people’s mental health have been documented according to social class but less is known about determinants that can buffer or mediate the relationship. Social capital has the potential to contribute to alleviating observed health inequalities. However, clarity about how it can be understood and measured in relation to mental health among younger populations remains inconsistent. This scoping review examined published literature to investigate how social capital has been researched for young people’s mental health. An established framework was used to guide the methodology. Studies were included: on age (10–19 years); publication year (since 2000); language (English). Only studies using social capital as a central theme were included. No restriction was placed on mental health outcomes. Nine bibliographic databases were interrogated. Articles (1541) were screened, 793 retained for analysis and 73 articles were included. Most studies were conducted in North America and Europe. Twenty per cent provided insights into how social capital should be described in relation to young people. A majority of the studies provided links between varying social capital indicators and a range of mental health outcomes (70%), however such evidence was associational. Only few studies inferred the causal direction between social capital and health (10%) and there were no dedicated studies on measurement. Findings suggest that literature on social capital and young people’s mental health has grown but continues to be variously described and measured. It requires better utilization of existing knowledge and new research to improve its application in practice.
Self-management strategies to consider to combat endometriosis symptoms during the COVID-19 pandemic
Authors: Leonardi Mathew , Horne Andrew W , Vincent Katy , Sinclair Justin , Sherman Kerry A , Ciccia Donna , Condous George , Johnson Neil P , Armour Mike
Published: May 2020

The care of patients with endometriosis has been complicated by the coronavirus disease 2019 (COVID-19) pandemic. Medical and allied healthcare appointments and surgeries are being temporarily postponed. Mandatory self-isolation has created new obstacles for individuals with endometriosis seeking pain relief and improvement in their quality of life. Anxieties may be heightened by concerns over whether endometriosis may be an underlying condition that could predispose to severe COVID-19 infection and what constitutes an appropriate indication for presentation for urgent treatment in the epidemic. Furthermore, the restrictions imposed due to COVID-19 can impose negative psychological effects, which patients with endometriosis may be more prone to already. In combination with medical therapies, or as an alternative, we encourage patients to consider self-management strategies to combat endometriosis symptoms during the COVID-19 pandemic. These self-management strategies are divided into problem-focused and emotion-focused strategies, with the former aiming to change the environment to alleviate pain, and the latter address the psychology of living with endometriosis. We put forward this guidance, which is based on evidence and expert opinion, for healthcare providers to utilize during their consultations with patients via telephone or video. Patients may also independently use this article as an educational resource. The strategies discussed are not exclusively restricted to consideration during the COVID-19 pandemic. Most have been researched before this period of time and all will continue to be a part of the biopsychological approach to endometriosis long after COVID-19 restrictions are lifted.
Clinical Characteristics of Patients With Coronavirus Disease 2019 in Japan: A Single-Center Case Series
Authors: Kobayashi Ken-ichiro , Kaki Takahiro , Mizuno Shinsuke , Kubo Kenji , Komiya Nobuhiro , Otsu Satoko
Published: May 2020

We report a case series of 6 patients with confirmed coronavirus disease 2019 (COVID-19) in Wakayama prefecture, Japan. All 6 of the patients tested positive via pharyngeal swab polymerase chain reaction (PCR) tests, and 2 of the 6 were still positive at 3 weeks after onset. All of the patients exhibited bilateral ground glass opacities on computed tomography (CT). This article also reports narrative information on the spectrum of symptoms collected directly from the patients. It would be difficult to triage patients with COVID-19 based on the typical symptoms of fever and/or cough, although PCR and CT are definitive in diagnosis.
Self-perceived competence and training needs analysis on antimicrobial stewardship among government ward pharmacists in Malaysia
Authors: Teoh Cherh Yun , Mhd. Ali Adliah , Mohamed Shah Noraida , Hassan Rohana , Lau Chee Lan
Published: May 2020

Background

There is a paucity of data on pharmacists’ competency and learning needs in antimicrobial stewardship (AMS).

Objectives

To identify and prioritize learning needs based on self-perceived competence of ward pharmacists in AMS, to identify predictors of self-perceived competence, learning methods in AMS and perceived barriers to learning.

Methods

A cross-sectional survey involving ward pharmacists from Hospital Canselor Tuanku Muhriz (HCTM) and hospitals under the Ministry of Health was conducted from May to July 2018.

Results

A total of 553 ward pharmacists from 67 hospitals responded to this survey (71.3% response rate). Knowledge of infections, antimicrobials and AMS systems, confidence to advise on various issues relating to antimicrobial therapy and participation in clinical audit and evaluation were among the learning needs identified (median score 3.00). Meanwhile, knowledge on the epidemiology of infections, off-label use of antimicrobials and pharmacoeconomics relating to antimicrobials had lower median scores (2.00) and were thus prioritized as high learning needs. Significant predictors of self-perceived competence in AMS were: gender (P < 0.001); prior specific training in infections and AMS (P < 0.001); postgraduate degree (P < 0.001); practising in the area of infectious disease (P < 0.05); and years of working experience as a ward pharmacist (P < 0.005). Continuing medical education, seminars, courses and workshops were the most common (78.1%) and preferred (84.6%) learning methods in AMS. Lack of appropriate training (67.8%), time (44.5%) and funding (42.5%) topped the list of barriers to learning in AMS.

Conclusions

Findings in this study suggest the need to establish and intensify standardized training in AMS among government ward pharmacists.
Predicting the thickness of sand strata in a sand-shale interbed reservoir based on seismic facies analysis
Authors: Li Huilin , Gao Rui , Wang Yanghua
Published: May 2020

Seismic facies analysis is of great significance for the detection of residual oil in a sand-shale interbed reservoir. In this study, we propose to predict spatial distribution of sand thickness over a reservoir, based on seismic facies analysis. The target reservoir is a thin sand-shale interbed layer, and the layer thickness varies between 2 and 10 m. The thickness of sand strata within the reservoir layer appears to have a fragmentary distribution in lateral space. Thin thickness and fragmentary distribution are two factors that cause difficulty in sand thickness prediction. To tackle this problem, this study adopted a three-stage strategy. First, the reservoir over the entire study area was classified into five different lithofacies, following sedimentary microfacies analysis against the characteristics of gamma-ray logging data, and the corresponding seismic responses were meticulously depicted. Then, exploiting these seismic responses, or seismic facies, the spatial distribution of the gamma-ray values was evaluated within the thin sand-shale interbed reservoir. Finally, the spatial distribution of the sand thickness was predicted according to the spatial distribution of the gamma-ray values. The prediction was conducted independently for each seismic facies, rather than in a non-discriminatory manner. Comparing the prediction to the actual evaluation derived from well-logging data demonstrated that the thickness distribution resulting from seismic data has a high accuracy, because of the facies-based analysis.
Rebels and the Regime: The Politics of Civilian Victimization
Authors: Curtice Travis B
Published: May 2020

Recent scholarship contends that during civil conflict rebels victimize civilians more when fighting democracies than authoritarian states. Yet to understand why rebels victimize civilians, it is important to consider when rebels target civilians and the severity of violence they use against civilians. Considering this distinction is critical to understanding the strategic calculus that rebels face while fighting states with varying regime types. By doing so, I argue that although civilian victimization by rebel groups is more likely in democracies, the count of civilians killed by rebels is higher when rebels fight autocracies. Employing a dataset of armed conflicts from 1989 to 2009 and a series of hurdle models, this study finds that rebel organizations fighting in authoritarian regimes are less likely to engage in civilian victimization; however, if they do use violence against civilians, the count of civilians targeted is higher.
Closed traumatic avulsion of both ring finger flexors with successful primary repair more than 4 weeks after injury and a review of the literature†
Authors: Johnson Miguel A , Colville James
Published: May 2020

Closed flexor digitorum profundus (FDP) tendon avulsions are a recognized injury in hand surgery. However, closed tendon avulsion of both flexor tendons in the same digit is rare, with the few cases reported in the literature and presented here. Management includes primary repair ideally within the first 2 weeks to achieve optimal outcome. While beyond 4 weeks a two-stage repair is the dictum, we present a case where both tendons were avulsed but primary repair of the FDP was possible more than 4 weeks after the injury, with a good outcome. This case highlights that primary tendon repair at 32 days, the longest noted in the literature in this group of patients, can result in a good outcome even if the injury is more than 4 weeks old. However, good intraoperative decision-making is key and the skillset must be present for conversion to a two-stage repair if necessary.
Urban coyotes are genetically distinct from coyotes in natural habitats
Authors: Adducci Anthony , Jasperse Jeremy , Riley Seth , Brown Justin , Honeycutt Rodney , Monzón Javier
Published: May 2020

Urbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically related to distant coyotes in similar natural habitats and less related to coyotes in urban areas due to natal habitat-biased dispersal. We also hypothesized that increasing urbanization would result in decreased genetic diversity due to habitat fragmentation, dispersal barriers and genetic drift. We analyzed 10 microsatellite genetic markers from 125 individual coyotes sampled across a spectrum of highly urban to highly natural areas in southern California. Most coyotes clustered into four distinct genetic populations, whereas others appeared to have admixed ancestry. Three genetic populations were associated primarily with urban habitats in Los Angeles and Orange Counties. In contrast, the remaining population was associated with more naturally vegetated land near the surrounding mountains. Coyotes living in natural areas formed a genetically distinct cluster despite long geographic distances separating them. Genetic diversity was negatively associated with urban/suburban land cover and local road density, and positively associated with the relative amount of natural vegetation. These results indicate that genetic differentiation and loss of genetic diversity coincided with the extremely rapid expansion of Greater Los Angeles throughout the 1900s. Thus, urbanization reduces gene flow and erodes genetic diversity even in a habitat generalist thought to be minimally impacted by land development.
Culture, Identity, and Psycho-social Development
Authors: Rothe Eugenio M. , Pumariega Andres J.
Published: May 2020

The chapter on culture and identity defines the current use of these terms and discusses how culture influences identity formation from a developmental perspective, starting in early childhood and throughout the life span. It also introduces new neurobiological findings related to theory of mind, neural mapping, object representation, and emotional reactivity and how these exert an influence on culture and identity formation. It covers a historical perspective that includes the contributions of pioneers such as Freud, Vigotsky, Montessori, Bandura, Mead, and Erikson. It also discusses ethnicity and race and the social and biological origins of prejudice and explains the meaning of ethnic-racial socialization messages, the dynamics of biracial identities, the importance of language in the development of the American identity and the role of culture and identity in psycho-social functioning and resiliency, including such variables as religion and spirituality. It also describes the influences of globalization and the diminishing importance of national boundaries on cultural identity for both minority and majority group members. Some of the concepts are illustrated and explained with clinical cases.
Immigration Trends in the United States
Authors: Rothe Eugenio M. , Pumariega Andres J.
Published: May 2020

The chapter on immigration trends describes the current legal and illegal paths of immigration to the United States; a historical perspective of the reasons for migration; the past and current numbers of immigrants who have arrived in the United States and their demographic profile; which countries contribute immigrants and which states receive them; the changing race and ethnicity of the immigrants throughout the country’s history; the immigrants’ levels of education, skill sets, and financial attainment at the time of arrival and after the second generation. A demographic profile of the illegal immigrants, their vulnerability for exploitation, and their financial importance to the country’s economy is presented. The composition of immigrant families, some of the psychological effects of geographical separations and deportations on the family, factors that facilitate or impede assimilation and adaptation, the intergroup relations, values, and political orientation of the different immigrant groups, and the immigrants’ financial contributions to the United States are discussed.
Acculturation
Authors: Rothe Eugenio M. , Pumariega Andres J.
Published: May 2020

The chapter on acculturation describes the possible reactions of the immigrant to the encounter with the new host culture and describes the history and meaning of the term acculturation, the strategies used by immigrants in order to adapt to the new host culture, the styles and models of acculturation, and the distance or proximity in which they place themselves with respect to the new culture that surrounds them. It explains the concepts of acculturation stress—the risk factors and protective factors and other variables that facilitate or slow down acculturation—and the concept of acculturative family distancing, which occurs when different members of the family acculturate at different rates and the conflicts that are generated by this phenomenon. The chapter also explains the role of the acquisition of a new language and how acculturation is measured, the epidemiological findings brought by acculturation on the different generations of the immigrant family, and how individual, family, and community factors influence acculturation. It also explains the role of acculturation in nonimmigrant historical minorities who have resided in the country but do not partake of the mainstream culture. Treatment interventions are discussed, and the chapter is further illustrated with case studies.
The Immigrant Narrative
Authors: Rothe Eugenio M. , Pumariega Andres J.
Published: May 2020

The chapter on the immigrant narrative explains the role of human narratives in identity development and explains the origins, meanings, and importance of the quintessential American narrative, which is known as the narrative of the redemptive self. It explains how understanding the dynamics of this particular narrative facilitates the understanding of the American cultural experience and how many aspects of this narrative parallel the immigrant experience. It discusses the concepts of historical truth and narrative truth. It explains how the use of narratives can serve as a useful therapeutic tool to help the immigrant work through the traumas and losses associated with migration and to negotiate the different stages of transformation of the immigrant’s identity. This chapter also explains the neurobiology of memory formation and the distortions of memory and narrative that may result from psychological trauma. It discusses how psychotherapy involves the creation of new, more adaptive narratives that can provide healing and personal growth and its relevance in the immigrant experience. It also discusses immigrant narratives in contemporary literature and how these can be used as a therapeutic tool with the younger generations of immigrants. The chapter is illustrated with various clinical cases.
Treatment Interventions for Immigrants, Refugees, and Their Families
Authors: Rothe Eugenio M. , Pumariega Andres J.
Published: May 2020

The chapter on treatment interventions for immigrants, refugees, and their families describes the importance for clinicians to familiarize themselves with how to treat these populations given the changing demographics in the United States. It explains the cultural competence model, the cultural sensibility model, and the community systems of care model, as well as other variations of treatment that take into account cultural nuances. The chapter outlines specific recommendations to treat child, adolescent, and adult immigrants and refugees based on the Practice Parameter on Child and Adolescent Psychiatric Culturally Competent Care by the American Academy of Child and Adolescent Psychiatry and other sources. These include how to overcome barriers to mental health treatment, the role of language barriers and how to overcome them, the generational challenges in treating the family, awareness of cultural biases and how to address them, understanding cultural idioms of distress in diagnosis and formulation, the need to assess and treat immigration-related losses and traumas and to evaluate acculturation-related family conflicts, identification of key family members in the treatment, and the need to design treatment interventions that are consonant with the cultural values and beliefs of the immigrant family. The need to provide evidence-based pharmacological treatments and to consider ethnopharmacological factors is addressed. Other evidence-based treatments such as cognitive behavioral therapy for post-traumatic stress disorder, testimonial psychotherapy, narrative exposure therapy, eye movement desensitization and reprocessing, and others are discussed.
Cinema, MD
Authors: Wijdicks Eelco F.M.
Published: May 2020

Cinema, MD argues that within cinema there is a history of medicine—one version in the many different histories of medicine. How did filmmakers write a history of medicine? This book discusses how cinema depicts medicine, in all its glory and all its failures, and what can we learn from it. It offers an account of all the major films with medical themes. The book asks a number of critical questions, such as why scriptwriters and directors chose the subjects, the plots, the cast, and the images that they did. Films have covered a wide range of medical topics, depicting not only physicians, nurses, and other health-care personnel working in hospitals, clinics, and asylums but also epidemics, diseases and disabilities, mental illness, and addictions. Films have portrayed medical feats such as vaccinations and organ transplantations. Filmmakers also have tackled subjects such as death and dying, medical experimentation, and rare diseases, as well as documenting criticism of the medical status quo.
Addicted
Authors: Wijdicks Eelco F.M.
Published: May 2020

Cinema has a terrible reputation in its portrayal of drug use, alcohol consumption, and smoking. Early to mid-20th-century films frequently glamorized smoking and drinking. Drunkenness could also be milked for humor. Organizations that provide ratings for films have been continuously challenged by advocates of moderation. For responsible screenwriters, portraying the abuse of these substances creates great “morality plays.” They can show the downward trajectory and consequently poor quality of life of people with addictions. This chapter discusses how cinema has depicted drug use and smoking but also places it into the history of addiction throughout the decades of the 20th century. Filmmakers have used addiction to great effect. In the dreamed-up world of medicine in cinema, the physician is often blamed for prescribing therapeutic drugs that the patient goes on to abuse.
Grotesques
Authors: Wijdicks Eelco F.M.
Published: May 2020

The portrayal of dysmorphologies, monsters, and other grotesques entered the horror category early, and the films were filled with exploitation, gruesomeness, and degeneracy. Physicians must be intrigued by the underlying nature of the major anomalies depicted on the screen. This chapter examines several extraordinary works that explore the disabled protagonist’s isolation and mistreatment. Many films in the horror genre have sparked important discussions of bioethics. Films about those who look different or are disabled due to congenital defects or disease have proliferated. Filmmakers used disability to evoke the audience’s pity in the early years, but this later changed to themes of acceptance and compassion. Cinema can play a critical role in highlighting abuse, isolation, and tribulations among persons with disabilities and in encouraging acceptance.
Epilogue
Authors: Wijdicks Eelco F.M.
Published: May 2020

This epilogue summarizes how medicine has been depicted in cinema through the ages, providing another way to look at the many different histories of medicine. Cinema has used fictional and factual situations, and sometimes just single moments, to show the unpredictability of illness—all is well but then it is not—causing story twists and consternation. Filmmakers may glamorize, exaggerate, misrepresent, or even falsify the practice of medicine, distorting its complexity. Cinema of medicine does not approximate the practice of medicine, nor do practitioners live similarly to their celluloid counterparts. However, medicine as practiced onscreen is plausible with all its cinematic flourishes, and, on balance, salutary. We can learn from it and teach others.
Fetal and Neonatal Care
Authors: Enciso Josephine M. , Nguyen Margaret P.
Published: May 2020

The chapter on neonatology provides a set of questions, answers with explanations, and references that provide a useful review of the content outlined in the Fetus and Newborn section of the General Pediatrics board exam as specified by the American Board of Pediatrics. Topics covered include medical conditions associated with prematurity and fetal growth restriction; neurological disorders; neonatal respiratory disorders; newborn hemodynamics; congenital and acquired surgical conditions in neonates; effects of maternal medical conditions, medications, and drug use on the fetus and newborn; neonatal hematologic abnormalities; bilirubin disorders; neonatal fluid and nutrition management; congenital and acquired infections in the fetus and newborn; delivery room assessment and management of the newborn; neonatal resuscitation; and the fundamentals of newborn care.
Infectious Diseases
Authors: Deville Jaime G. , Baker Amira N. , Arrieta Antonio C.
Published: May 2020

This chapter on pediatric infectious diseases first presents patient scenarios, followed by a question-and-answer format to provide active learning to emphasize key points regarding clinically relevant topics, which are also covered in the American Board of Pediatrics Content Outline for certification exams. The topics addressed in this chapter range from common infectious processes encountered by pediatricians to more unusual, but important, conditions. Specific topics include infections in immunocompromised hosts, sepsis, central nervous system infections, respiratory infections, gastrointestinal infections, hepatitis, bone and joint infections, regional mycoses, parasites, sexually transmitted infections, infections in neonates, management of antimicrobial agents, pediatric HIV-1, and immunizations.
Endocrinology
Authors: Capodanno Gina , Srinivasan Shylaja , Ferrara-Cook Christine T.
Published: May 2020

Disruptions of growth and puberty are typically the first signs of an endocrine disorder. Using vignettes and a question-and-answer format, this chapter discusses common and uncommon cases of hormone dysfunction presenting from infancy through adolescence. Topics in the chapter include short stature, delayed puberty, obesity, diabetes, hypoglycemia, conditions of endocrine hormone deficiencies and excess and associated genetic syndromes. Challenges in distinguishing normal versus abnormal growth are also reviewed.
Dermatology
Authors: Yoo Ki-Young , Hogeling Marcia , Sandhu Sophia K. , Lee Delphine J.
Published: May 2020

This chapter on dermatologic disorders presents patient scenarios in a series of vignettes. Each vignette is followed by a question-and-answer format to provide active learning that emphasizes key points regarding clinically relevant topics. These topics are also covered in the American Board of Pediatrics Content Outline for certification exams. The topics addressed in this chapter range from common dermatologic conditions encountered by pediatricians to important more rare conditions that may be part of pediatric practice. Specific topics include skin problems in neonates, atopic dermatitis, infections and infestations, hair loss, neurocutaneous syndromes, pigmented lesions, acne, inflammatory skin conditions, and inherited rare skin conditions.
Ethics
Authors: Hynds James A. , Raho Joseph A.
Published: May 2020

The practice of medicine is an intrinsically ethical endeavor because its fundamental goal is health, a good necessary for and integral to human flourishing. This goal also helps define and identify what counts as ethical behavior in the practice of medicine. Fundamentally, actions that promote the possibility of health are generally to be accounted as ethically good actions. Conversely, those that tend to frustrate or destroy the possibility of health are to be accounted as ethically bad. In addition to having an identity-defining goal, clinical medicine also has a nature or structure proper to it. That structure is relational. The authentic and effective practice of medicine requires a relationship of deep mutual trust between the physician and the physician’s patient and the patient’s family. Therefore, a commitment to and an ability to create and sustain such a relationship is a legitimate moral expectation of a physician and is the source of many of the physician’s ethical responsibilities. In the eleven case studies that follow, common ethical challenges that pediatricians might reasonably expect to encounter in their practice are explored. In each case, it is recommended that the pediatrician adopt the course of action that is most consistent with the nature and goal of medicine understood as a healing profession rooted in and requiring a relationship of mutual trust.
Research Methods, Statistics, Patient Safety, and Quality Improvement
Authors: Lerner Carlos
Published: May 2020

The chapter on research methods, statistics, patient safety, and quality improvement (QI) uses a question-and-answer format to make concepts in these areas relevant and accessible to general pediatricians. Research topics covered include study design and study types, validity, sources of bias, types of errors, sensitivity and specificity, positive and negative predictive values, likelihood ratios, incidence and prevalence, p values and confidence intervals. The patient safety questions focus on medical errors and adverse events, including their categorization, detection, prevention, and disclosure. Finally, the QI questions address key QI principles and methods, including tools to understand systems (e.g. fishbone diagrams and Pareto charts), analysis of variation, and the Langley Model for Improvement.
Structure Defines Function
Authors: Guilliams Thomas G.
Published: May 2020

This chapter will outline the basic features that define the interface functions of the gastrointestinal (GI) tract, emphasizing its barrier, digestive, elimination, and sensing functions. Since the GI tract is the largest biological interface with the external environment, understanding how it functions and remains healthy is vital for all medical practitioners. Through a description of the different architectural features and cell types that progressively change from the stomach to the distal colon, this chapter will show that the distinctive functions of the GI tract are geographically defined by these structures. Failure in one important function of the GI tract inevitably increases the burden on others; culminating in an increased burden on the immune system, which inevitably triggers a compensatory innate inflammatory response and leads to a wide range of GI and non-GI signs and symptoms.
The Brain-Gut-Microbiome Axis Communication
Authors: Sanmiguel Claudia , Mayer Emeran A.
Published: May 2020

The chapter on brain-gut-microbiome (BGM) axis communication analyzes the interactions between the gut microbiome, the regulatory processes within the gut (including the enteric nervous system [ENS], enteroendocrine cells [EECs], and immune system), and the central nervous system (CNS) (including the brain, hypothalamic-pituitary axis [HPA], and autonomic nervous system), both in brain development and in health, such as modulation of emotional states and ingestive behaviors, and in disease, such as autism spectrum disorder (ASD), irritable bowel syndrome (IBS), Parkinson’s disease, and obesity. Special emphasis is placed on new developments in our understanding of the role that the gut microbiome plays within the BGM axis.
Energy Medicine and Gastrointestinal Disorders
Authors: Chiasson Ann Marie
Published: May 2020

Energy medicine (EM) consists of a range of modalities and techniques that work with the underlying energy field of the body. Techniques range from hands-on healing to using vibration, movement or sound. There is moderate evidence that energy medicine significantly decreases many types of chronic pain and is most utilized in patients with chronic pain syndromes. Energy medicine prevalence of use and evidence, specifically in GI disorders, has been less investigated. There are a few small studies demonstrating evidence for decreasing symptoms in inflammatory bowel disease and colorectal cancer. Despite the lack of specific data for GI disorders, due to its role in increasing relaxation and decreasing pain, it can be a useful adjunct therapy. Most energy medicine modalities have specific techniques for GI disorders. Finding a skilled practitioner, as well as learning how to use self-healing techniques, can be valuable additions to a patient’s plan of care.
An Integrative Approach to Abdominal Pain
Authors: Alois Marika , Selfe Terry Kit , Estores Irene M.
Published: May 2020

This chapter discusses abdominal pain in the context of functional gastrointestinal disease (FGID) and some chronic inflammatory bowel diseases, recognizing the huge burden it places on the health care system and emotional costs to patients and health care professionals. It presents a review of several modalities that include mind–body medicine practices, natural products, botanicals, manual and movement-based therapies, and pharmaceuticals that can be used as part of an integrative health plan for patients presenting with FGID and abdominal pain. It describes an integrative approach that weaves in concepts of patient-centered care, effective communication, empathic listening, mindfulness, and evidence-informed practice.
Upper Gastrointestinal Disorders
Authors: Slater III Robert T. , Mathis Samuel , Sierpina Victor
Published: May 2020

Upper gastrointestinal disorders are common conditions that have afflicted humans since antiquity. They can be categorized by primary location (esophagus or stomach) and by the presence of identifiable pathological changes. Symptoms range in severity and may not correlate with severity of underlying disease. This chapter explores the pathophysiology, symptoms, and diagnoses of gastroesophageal reflux disease, gastritis, peptic ulcer disease, and functional dyspepsia. Modifiable risk factors and potential benefits and harms of conventional treatments are examined. Specific recommendations for comprehensive lifestyle modifications for these conditions are described, including proper nutrition, physical activity, stress management, sleep, toxin reduction, and other external factors. Integrative approaches are then explained, with a focus on botanicals and supplements, followed by a review of homeopathy, psychological therapy, and acupuncture. Finally, lifestyle changes and integrative treatments are summarized.
Colorectal Cancer
Authors: John George Kunnackal , Razvi Mohammed
Published: May 2020

Colorectal cancer (CRC) is a leading cause of cancer-related mortality globally. However, the adoption of a healthier lifestyle, including modifications in diet, physical activity, and regular screening can drastically reduce the risk for CRC. Major risk factors for CRC include lack of a balanced diet, high red meat intake, physical inactivity, alcohol, and smoking. There is widespread geographic variation in the rates of CRC across the world, reflecting differences in exposure to these risk factors and the influence of protective factors in these regions. In this chapter, we summarize the epidemiology, pathogenesis, and risk factors, and focus on the prevention of CRC through an integrative approach.
Conventional Assessment of Gastrointestinal Disorders
Authors: Mullin Gerard E.
Published: May 2020

The gastrointestinal tract is a highly complex and dynamic organ system having a multitude of physiological functions. The choice of laboratory tests should be personalized and not performed in a shotgun manner, which can lead to false positive results and imparts financial stress to patients. The assessment of digestive health conditions requires giving astute attention to the patient’s history and a methodical utilization of laboratory tests to define root causation of illness and opportunities for intervention. This chapter segregates the most common tests and procedures to evaluating gastrointestinal condition into conventional tests that are usually covered by medical insurance and functional medicine and genomic testing that by-in-large have larger out-of-pocket expenses. Strategic utilization of these tests are essential to the proper evaluation of gastrointestinal illness.
Personalized and Functional Medicine Testing for Digestive Dysfunction
Authors: Messier Helen
Published: May 2020

Appropriate laboratory testing can provide insights into both the cause and possible interventions for digestive dysfunction. This chapter describes certain functional medicine laboratory testing that has been available for a number of years, as well as some of the recently available testing that is based on new scientific discoveries, and the development of next-generation high-throughput sequencing and mass spectrometry technologies. As with all laboratory testing, the results of these tests must be taken in the context of the overall clinical picture. A knowledge of the methodologies used will provide an understanding of the pros and cons of each test, and will enable the appropriate use of testing that is likely to be an out-of-pocket expense.
Conclusions
Authors: Singh Marvin M. , Parian Alyssa , Mullin Gerard , Clarke John
Published: May 2020

Integrative gastroenterology is an important field of medicine whereby the practitioner has the opportunity to not only improve troubling gastrointestinal symptoms but also to attain this goal from a multifaceted approach, using principles and modalities that involve the mind, body, gut microbiome, nutrition, stress management, and lifestyle modifications in order to address the entire patient while modulating gene expression, epigenetics, and the gut microbiome. This chapter presents conclusions regarding the future of integrative gastroenterology and its implementation.
Principles of Animal Research Ethics
Authors: Beauchamp Tom L. , DeGrazia David
Published: May 2020

This book is the first to present a framework of general principles for animal research ethics together with an analysis of the principles’ meaning and moral requirements. This new framework of six moral principles constitutes a more suitable set of moral guidelines than any currently available, including the influential framework presented in the Principles of Humane Experimental Technique published in 1959 by zoologist and psychologist William M. S. Russell and microbiologist Rex L. Burch. Their “principles”—commonly referred to as the Three Rs—are better described as specific directives than as general moral principles, and they are insufficient as a moral framework of basic values in the context of contemporary biomedical and behavioral research. The framework presented in Principles of Animal Research Ethics is more comprehensive in addressing ethical requirements pertaining to societal benefit (the most important consideration in justifying the harming of animals in research) and features a more thorough, ethically defensible program of animal welfare (the area on which Russell and Burch focus). The present framework is also more likely than the Three Rs to foster extensive agreement between the biomedical and animal protection communities—an agreement deeply needed at the present time. The book features commentaries on the framework of principles written by eminent figures in animal research ethics representing an array of relevant disciplines: veterinary medicine, biomedical research, biology, zoology, comparative psychology, primatology, law, and bioethics. The seven commentators on the authors’ Principles are Larry Carbone, Frans B. M. de Waal, Rebecca Dresser, Joseph P. Garner, Brian Hare, Margaret S. Landi, and Julian Savulescu.