and Apraxia of speech involves lesions of dorsal arcuate fasciculus and insula in patients with aphasia By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 Objective To determine the contributions of apraxia of speech (AOS) and anomia to conversational dysfluency. Methods In this observational study of 52 patients with chronic aphasia, 47 with concomitant AOS, fluency was quantified using correct information units per minute (CIUs/min) from propositional speech tasks. Videos of patients performing conversational, how-to and picture-description tasks, word and sentence repetition, and diadochokinetic tasks were used to diagnose AOS using the Apraxia of Speech Rating Scale (ASRS). Anomia was quantified by patients' scores on the 30 even-numbered items from the Boston Naming Test (BNT). Results Together, ASRS and BNT scores accounted for 51.4% of the total variance in CIUs/min; the ASRS score accounted for the majority of that variance. The BNT score was associated with lesions in the left superior temporal gyrus, left inferior frontal gyrus, and large parts of the insula. The global ASRS score was associated with lesions in the left dorsal arcuate fasciculus (AF), pre- and post-central gyri, and both banks of the central sulcus of the insula. The ASRS score for the primary distinguishing features of AOS (no overlap with features of aphasia) was associated with less AF and more insular involvement. Only ~27% of this apraxia-specific lesion overlapped with lesions associated with the BNT score. Lesions associated with AOS had minimal overlap with the frontal aslant tract (FAT) (<1%) or the extreme capsule fiber tract (1.4%). Finally, ASRS scores correlated significantly with damage to the insula but not to the AF, extreme capsule, or FAT. Conclusions Results are consistent with previous findings identifying lesions of the insula and AF in patients with AOS, damage to both of which may create dysfluency in patients with aphasia. Full Article
and Levodopa-induced dyskinesia in dementia with Lewy bodies and Parkinson disease with dementia By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 Objective To investigate the frequency of levodopa-induced dyskinesia in dementia with Lewy bodies (DLBs) and Parkinson disease with dementia (PDD) and compare these frequencies with patients with incident Parkinson disease (PD) through a population-based cohort study. Methods We identified all patients with DLB, PDD, and PD without dementia in a 1991–2010 population-based parkinsonism-incident cohort, in Olmsted County, Minnesota. We abstracted information about levodopa-induced dyskinesia. We compared patients with DLB and PDD with dyskinesia with patients with PD from the same cohort. Results Levodopa use and dyskinesia data were available for 141/143 (98.6%) patients with a diagnosis of either DLB or PDD; 87 (61.7%), treated with levodopa. Dyskinesia was documented in 12.6% (8 DLB and 3 PDD) of levodopa-treated patients. Among these patients, median parkinsonism diagnosis age was 74 years (range: 64–80 years); 63.6%, male. The median interval from levodopa initiation to dyskinesia onset was 2 years (range: 3 months–4 years); the median daily levodopa dosage was 600 mg (range: 50–1,600 mg). Dyskinesia severity led to levodopa adjustments in 5 patients, and all improved. Patients with dyskinesia were diagnosed with parkinsonism at a significantly younger age compared with patients without dyskinesia (p < 0.001). Levodopa dosage was unrelated to increased risk of dyskinesias among DLB and PDD. In contrast, 30.1% of levodopa-treated patients with PD developed dyskinesia. In age-, sex-, and levodopa dosage–adjusted models, Patients with DLB and PDD each had lower odds of developing dyskinesia than patients with PD (odds ratio = 0.42, 95% CI 0.21–0.88; p = 0.02). Conclusions The dyskinesia risk for levodopa-treated patients with DLB or PDD was substantially less than for levodopa-treated patients with PD. Full Article
and Cerebral venous thrombosis: Associations between disease severity and cardiac markers By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 Background Plasma cardiac troponin (cTn) elevation occurs in acute ischemic stroke and intracranial hemorrhage and can suggest a poor prognosis. Because acute cerebral venous thrombosis (CVT) might lead to venous stasis, which could result in cardiac stress, it is important to evaluate whether cTn elevation occurs in patients with CVT. Methods Inpatients at Johns Hopkins Hospital from 2005 to 2015 meeting the following criteria were included: CVT (ICD-9 codes with radiologic confirmation) and available admission electrocardiogram (ECG) and cTn level. In regression models, presence of ECG abnormalities and cTn elevation (>0.06 ng/mL) were evaluated as dependent variables in separate models, with location and severity of CVT involvement as independent variables, adjusted for age, sex, and hypertension. Results Of 81 patients with CVST, 53 (66%) met the inclusion criteria. Participants were, on average, aged 42 years, white (71%), and female (66%). The left transverse sinus was most commonly thrombosed (47%), with 66% having >2 veins thrombosed. Twenty-two (41%) had cTn elevation. Odds of cTn elevation increased per each additional vein thrombosed (adjusted OR 2.79, 95% CI [1.08–7.23]). Of those with deep venous involvement, 37.5% had cTn elevation compared with 4.4% without deep clots (p = 0.02). Venous infarction (n = 15) was associated with a higher mean cTn (0.14 vs 0.02 ng/mL, p = 0.009) and was predictive of a higher cTn in adjusted models (β = 0.15, 95% CI [0.06–0.25]). Conclusions In this single-center cohort study, markers of CVT severity were associated with increased odds of cTn elevation; further investigation is needed to elucidate causality and significance. Full Article
and Neurology and baseball: Who wants to win? By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 Teams fail when they cannot achieve a common goal. They also fail when they do not have one. In baseball, different goals between players and staff are unusual. Everyone wants to win. In neurology, where teams may be loosely defined and comprise people from many disciplines, goals differ. A win for you may not be a win for me. Full Article
and Author response: Functional neurologic disorders: Bringing the informal and hidden curriculum to light By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 Dr. Sethi raises an excellent point about the term functional neurologic disorder (FND) in his comment on the editorial.1 It seems clear that reticence to use the term functional creates the ambiguity he mentions. Medically unexplained symptoms, categorized in the international classification of diseases as undifferentiated somatoform disorders, are a diagnosis that many providers are loathed to give. Whether that is because of concern about missing a diagnosis is not clear. Having evaluated and treated more than 400 of these individuals in the FND clinic at the University of Colorado, I can attest to the fact that patients arrive confused about their diagnosis. Multiple incorrect diagnoses, as Dr. Sethi points out, pack the medical histories of patients with FND, leading doctors and patients astray. I believe that the commentary by Perez et al.2 gives us the best chance for a way forward, by teaching a new generation of residents and fellows how to approach patients in a nonjudgmental and open-minded fashion. It took 30 years to add Functional Neurologic Disorder to the Diagnostic and Statistical Manual, and it is still parenthetical to the term Conversion.3 Stripping the diagnosis of FND of its stigma and empowering care providers to rule in functional disorders is an actionable step which should be taken. Full Article
and Reader response: Functional neurologic disorders: Bringing the informal and hidden curriculum to light By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 I read with interest the editorial by Strom1 about functional neurologic disorders (FNDs). As a treating physician, I have struggled with the multiple diagnostic labels attached to these patients by physicians of different medical specialties during the course of their clinical disease presentation. A neurologist may assign a patient who presents with chronic fatigue the diagnostic labels of narcolepsy, idiopathic hypersomnia, or chronic Lyme disease. A rheumatologist may assign the label of collagen vascular disease, and a psychiatrist may diagnose depression. This diagnostic ambiguity is troublesome for patients and clinicians alike. I contend that even the term FND needs to be revisited. A patient should be broadly labeled as having a functional disorder and only after characterization sublabeled and referred to an appropriate specialty physician. Full Article
and Progressive supranuclear palsy and pawpaw By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 Consider consumption of annonacin-containing plant products, including pawpaw, as a possible environmental risk factor for atypical parkinsonism. Full Article
and Unusual and important cause of acute neck pain: Longus colli calcific tendinitis By cp.neurology.org Published On :: 2020-04-06T12:45:20-07:00 Early recognition of longus colli calcific tendinitis can prevent unnecessary interventions including antibiotics and surgical procedures. Full Article
and Shellhaas RA, Burns JW, Barks JDE, Fauziya Hassan F, Chervin RD. Maternal Voice and Infant Sleep in the Neonatal Intensive Care Unit. Pediatrics. 2019;144(3):e30190288 By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
and Nickel Allergic Contact Dermatitis: Identification, Treatment, and Prevention By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Nickel is a ubiquitous metal added to jewelry and metallic substances for its hardening properties and because it is inexpensive. Estimates suggest that at least 1.1 million children in the United States are sensitized to nickel. Nickel allergic contact dermatitis (Ni-ACD) is the most common cutaneous delayed-type hypersensitivity reaction worldwide. The incidence among children tested has almost quadrupled over the past 3 decades. The associated morbidities include itch, discomfort, school absence, and reduced quality of life. In adulthood, individuals with Ni-ACD may have severe disabling hand eczema. The increasing rate of Ni-ACD in children has been postulated to result from early and frequent exposure to metals with high amounts of nickel release (eg, as occurs with ear piercing or with products used daily in childhood such as toys, belt buckles, and electronics). To reduce exposure to metal sources with high nickel release by prolonged and direct contact with human skin, Denmark and the European Union legislated a directive several decades ago with the goal of reducing high nickel release and the incidence of Ni-ACD. Since then, there has been a global reduction in incidence of Ni-ACD in population-based studies of adults and studies of children and young adults being tested for allergic contact dermatitis. These data point to nickel exposure as a trigger for elicitation of Ni-ACD and, further, provide evidence that legislation can have a favorable effect on the economic and medical health of a population. This policy statement reviews the epidemiology, history, and appearances of Ni-ACD. Examples of sources of high nickel release are discussed to highlight how difficult it is to avoid this metal in modern daily lives. Treatments are outlined, and avoidance strategies are presented. Long-term epidemiological interventions are addressed. Advocacy for smarter nickel use is reviewed. The American Academy of Pediatrics supports US legislation that advances safety standards (as modeled by the European Union) that protect children from early and prolonged skin exposure to high–nickel-releasing items. Our final aim for this article is to aid the pediatric community in developing nickel-avoidance strategies on both individual and global levels. Full Article
and Emerging Issues in Male Adolescent Sexual and Reproductive Health Care By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Pediatricians are encouraged to address male adolescent sexual and reproductive health on a regular basis, including taking a sexual history, discussing healthy sexuality, performing an appropriate physical examination, providing patient-centered and age-appropriate anticipatory guidance, and administering appropriate vaccinations. These services can be provided to male adolescent patients in a confidential and culturally appropriate manner, can promote healthy sexual relationships and responsibility, can and involve parents in age-appropriate discussions about sexual health. Full Article
and Children With Intellectual and Developmental Disabilities as Organ Transplantation Recipients By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 The demand for transplantable solid organs far exceeds the supply of deceased donor organs. Patient selection criteria are determined by individual transplant programs; given the scarcity of solid organs for transplant, allocation to those most likely to benefit takes into consideration both medical and psychosocial factors. Children with intellectual and developmental disabilities have historically been excluded as potential recipients of organ transplants. When a transplant is likely to provide significant health benefits, denying a transplant to otherwise eligible children with disabilities may constitute illegal and unjustified discrimination. Children with intellectual and developmental disabilities should not be excluded from the potential pool of recipients and should be referred for evaluation as recipients of solid organ transplants. Full Article
and Ames SG, Davis BS, Marin JR, L. Fink EL, Olson LM, Gausche-Hill M, Kahn JM. Emergency Department Pediatric Readiness and Mortality in Critically Ill Children. Pediatrics. 2019;144(3):e20190568 By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
and Early and Often: The Need for Comprehensive Discussion of Treatment-Induced Cancer Late Effects By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
and The Time Is Now: Standardized Sedation Training for Pediatric Hospitalists By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
and Adolescent Sexual Health Interventions: Innovation, Efficacy, Cost, and the Urgent Need to Scale By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
and Optimizing Human Papillomavirus Immunization: The Role of Centralized Reminder and Recall Systems By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
and Parental Considerations Regarding Cure and Late Effects for Children With Cancer By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: More than 80% of children with cancer become long-term survivors, yet most survivors experience late effects of treatment. Little is known about how parents and physicians consider late-effects risks against a potential survival benefit when making treatment decisions. METHODS: We used a discrete choice experiment to assess the importance of late effects on treatment decision-making and acceptable trade-offs between late-effects risks and survival benefit. We surveyed 95 parents of children with cancer and 41 physicians at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center to assess preferences for 5 late effects of treatment: neurocognitive impairment, infertility, cardiac toxicity, second malignancies, and impaired growth and development. RESULTS: Each late effect had a statistically significant association with treatment choice, as did survival benefit (P < .001). Avoidance of severe cognitive impairment was the most important treatment consideration to parents and physicians. Parents also valued cure and decreased risk of second malignancies; physician decision-making was driven by avoidance of second malignancies and infertility. Both parents and physicians accepted a high risk of infertility (parents, a 137% increased risk; physicians, an 80% increased risk) in exchange for a 10% greater chance of cure. CONCLUSIONS: Avoidance of severe neurocognitive impairment was the predominant driver of parent and physician treatment preferences, even over an increased chance of cure. This highlights the importance of exploring parental late-effects priorities when discussing treatment options. Full Article
and Racial and Ethnic Differences in Emergency Department Pain Management of Children With Fractures By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: To test the hypotheses that minority children with long-bone fractures are less likely to (1) receive analgesics, (2) receive opioid analgesics, and (3) achieve pain reduction. METHODS: We performed a 3-year retrospective cross-sectional study of children <18 years old with long-bone fractures using the Pediatric Emergency Care Applied Research Network Registry (7 emergency departments). We performed bivariable and multivariable logistic regression to measure the association between patient race and ethnicity and (1) any analgesic, (2) opioid analgesic, (3) ≥2-point pain score reduction, and (4) optimal pain reduction (ie, to mild or no pain). RESULTS: In 21 069 visits with moderate-to-severe pain, 86.1% received an analgesic and 45.4% received opioids. Of 8533 patients with reassessment of pain, 89.2% experienced ≥2-point reduction in pain score and 62.2% experienced optimal pain reduction. In multivariable analyses, minority children, compared with non-Hispanic (NH) white children, were more likely to receive any analgesics (NH African American: adjusted odds ratio [aOR] 1.72 [95% confidence interval 1.51–1.95]; Hispanic: 1.32 [1.16–1.51]) and achieve ≥2-point reduction in pain (NH African American: 1.42 [1.14–1.76]; Hispanic: 1.38 [1.04–1.83]) but were less likely to receive opioids (NH African American: aOR 0.86 [0.77–0.95]; Hispanic: aOR 0.86 [0.76–0.96]) or achieve optimal pain reduction (NH African American: aOR 0.78 [0.67–0.90]; Hispanic: aOR 0.80 [0.67–0.95]). CONCLUSIONS: There are differences in process and outcome measures by race and ethnicity in the emergency department management of pain among children with long-bone fractures. Although minority children are more likely to receive analgesics and achieve ≥2-point reduction in pain, they are less likely to receive opioids and achieve optimal pain reduction. Full Article
and Asking for Identification and Retail Tobacco Sales to Minors By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND AND OBJECTIVES: A previous single-county study found that retail stores usually asked young-looking tobacco customers to show proof-of-age identification, but a large proportion of illegal tobacco sales to minors occurred after the customers had shown identification proving they were too young to purchase tobacco. We sought to investigate these findings on a larger scale. METHODS: We obtained state reports for federal fiscal years 2017 and 2018 from a federal agency that tracks tobacco sales to supervised minors conducting compliance checks in retail stores. We used descriptive and multivariable logistic regression methods to determine (1) how often stores in 17 states requested identifications, (2) what proportion of violations occurred after identification requests, and (3) if violation rates differed when minors were required versus forbidden to carry identification. RESULTS: Stores asked minors for identification in 79.6% (95% confidence interval: 79.3%–80.8%) of compliance checks (N = 17 276). Violations after identification requests constituted 22.8% (95% confidence interval: 20.0%–25.6%; interstate range, 1.7%–66.2%) of all violations and were nearly 3 times as likely when minors were required to carry identification in compliance checks. Violations were 42% more likely when minors asked for a vaping product versus cigarettes. CONCLUSIONS: Stores that sell tobacco to underage customers are more likely to be detected and penalized when youth inspectors carry identification during undercover tobacco sales compliance checks. The new age-21 tobacco sales requirement presents an opportunity to require identifications be carried and address other long-standing weaknesses in compliance-check protocols to help combat the current adolescent vaping epidemic. Full Article
and ACA Medicaid Expansion and Insurance Coverage Among New Mothers Living in Poverty By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: Medicaid plays a critical role during the perinatal period, but pregnancy-related Medicaid eligibility only extends for 60 days post partum. In 2014, the Affordable Care Act’s (ACA’s) Medicaid expansions increased adult Medicaid eligibility to 138% of the federal poverty level in participating states, allowing eligible new mothers to remain covered after pregnancy-related coverage expires. We investigate the impact of ACA Medicaid expansions on insurance coverage among new mothers living in poverty. METHODS: We define new mothers living in poverty as women ages 19 to 44 with incomes below the federal poverty level who report giving birth in the past 12 months. We use 2010–2017 American Community Survey data and a difference-in-differences approach using parental Medicaid-eligibility thresholds to estimate the effect of ACA Medicaid expansions on insurance coverage among poor new mothers. RESULTS: A 100-percentage-point increase in parental Medicaid-eligibility is associated with an 8.8-percentage-point decrease (P < .001) in uninsurance, a 13.2-percentage-point increase (P < .001) in Medicaid coverage, and a 4.4-percentage-point decrease in private or other coverage (P = .001) among poor new mothers. The average increase in Medicaid eligibility is associated with a 28% decrease in uninsurance, a 13% increase in Medicaid coverage, and an 18% decline in private or other insurance among poor new mothers in expansion states. However, in 2017, there were ~142 000 remaining uninsured, poor new mothers. CONCLUSIONS: ACA Medicaid expansions are associated with increased Medicaid coverage and reduced uninsurance among poor new mothers. Opportunities remain for expansion and nonexpansion states to increase insurance coverage among new mothers living in poverty. Full Article
and A Triadic Intervention for Adolescent Sexual Health: A Randomized Clinical Trial By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: In this study, we evaluate the efficacy of Families Talking Together (FTT), a triadic intervention to reduce adolescent sexual risk behavior. METHODS: Adolescents aged 11 to 14 and their female caregivers were recruited from a pediatric clinic; 900 families were enrolled; 84 declined. Families were randomly assigned to FTT or 1 of 2 control conditions. The FTT triadic intervention consisted of a 45-minute face-to-face session for mothers, health care provider endorsement of intervention content, printed materials for families, and a booster call for mothers. The primary outcomes were ever having had vaginal intercourse, sexual debut within the past 12 months, and condom use at last sexual intercourse. Assessments occurred at baseline, 3 months post baseline, and 12 months post baseline. RESULTS: Of enrolled families, 73.4% identified as Hispanic, 20.4% as African American, and 6.2% as mixed race. Mean maternal age was 38.8 years, and mean adolescent grade was seventh grade. At the 12-month follow-up, 5.2% of adolescents in the experimental group reported having had sexual intercourse, compared with 18% of adolescents in the control groups (P < .05). In the experimental group, 4.7% of adolescents reported sexual debut within the past 12 months, compared with 14.7% of adolescents in the control group (P < .05). In the experimental group, 74.2% of sexually active adolescents indicated using a condom at last sexual intercourse, compared with 49.1% of adolescents in the control group (P < .05). CONCLUSIONS: This research suggests that the FTT triadic intervention is efficacious in delaying sexual debut and reducing sexual risk behavior among adolescents. Full Article
and Bereaved Parents, Hope, and Realism By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
and All for One and One Delivery Room Approach for All? By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Multiple births are increasing in frequency related to advanced maternal age and fertility treatments, and they have an increased risk for congenital anomalies compared to singleton births. However, twins have the same congenital anomalies <15% of the time. Thus, having multiple births with discordant anomalies is a growing challenge for neonatologists. Although external anomalies can often be spotted quickly at delivery or sex differences between multiples can rapidly identify those with internal anomalies described on prenatal ultrasound, we present a case of male multiples, who would optimally receive different initial resuscitation strategies on the basis of the presence or absence of an internal anomaly. The similar size of 4 extremely preterm quadruplets raises concern for whether accurate, immediate identification of 1 neonate with a congenital diaphragmatic hernia will be reliable in the delivery room. Clinicians discuss the ethical considerations of an "all for one" approach to this resuscitation. Full Article
and Rates and Stability of Mental Health Disorders in Children Born Very Preterm at 7 and 13 Years By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: Children born very preterm (VPT) are at an increased risk of developing mental health (MH) disorders. Our aim for this study was to assess rates of MH disorders in children born VPT and term at 13 years of age and stability of MH disorders between ages 7 and 13 years by using a diagnostic measure. METHODS: Participants were from the Victorian Infant Brain Study longitudinal cohort and included 125 children born VPT (<30 weeks’ gestational age and/or <1250 g) and 49 children born term (≥37 weeks’ gestational age) and their families. Participants were followed-up at both 7 and 13 years, and the Development and Well-Being Assessment was administered to assess for MH disorders. RESULTS: Compared with term peers, 13-year-olds born VPT were more likely to meet criteria for any MH disorder (odds ratio 5.9; 95% confidence interval 1.71–20.03). Anxiety was the most common disorder in both groups (VPT = 14%; term = 4%), whereas attention-deficit/hyperactivity disorder carried the greatest differential elevated risk (odds ratio 5.6; 95% confidence interval 0.71–43.80). Overall rates of MH disorders remained stable between 7 and 13 years, although at an individual level, many participants shifted in or out of diagnostic categories over time. CONCLUSIONS: Children born VPT show higher rates of MH disorders than their term peers, with changing trajectories over time. Findings highlight the importance of early identification and ongoing assessment to support those with MH disorders in this population. Full Article
and Effect of State Immunization Information System Centralized Reminder and Recall on HPV Vaccination Rates By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: Although autodialer centralized reminder and recall (C-R/R) from state immunization information systems (IISs) has been shown to raise childhood vaccination rates, its impact on human papillomavirus (HPV) vaccination rates is unclear. METHODS: In a 4-arm pragmatic randomized controlled trial across 2 states, we randomly selected practices representative of the specialty (pediatrics, family medicine, and health center) where children received care. Within each practice, patients 11 to 17.9 years old who had not completed their HPV vaccine series (NY: N = 30 616 in 123 practices; CO: N = 31 502 in 80 practices) were randomly assigned to receive 0, 1, 2, or 3 IIS C-R/R autodialer messages per vaccine dose. We assessed HPV vaccine receipt via the IIS, calculated intervention costs, and compared HPV vaccine series initiation and completion rates across study arms. RESULTS: In New York, HPV vaccine initiation rates ranged from 37.0% to 37.4%, and completion rates were between 29.1% and 30.1%, with no significant differences across study arms. In Colorado, HPV vaccine initiation rates ranged from 31.2% to 33.5% and were slightly higher for 1 reminder compared with none, but vaccine completion rates, ranging from 27.0% to 27.8%, were similar. On adjusted analyses in Colorado, vaccine initiation rates were slightly higher for 1 and 3 C-R/R messages (adjusted risk ratios 1.07 and 1.04, respectively); completion rates were slightly higher for 1 and 3 C-R/R messages (adjusted risk ratios 1.02 and 1.03, respectively). CONCLUSIONS: IIS-based C-R/R for HPV vaccination did not improve HPV vaccination rates in New York and increased vaccination rates slightly in Colorado. Full Article
and Teenager With Abdominal Pain and Decreased Appetite By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 A 16-year-old girl presented to her primary care physician with a one-month history of decreased appetite and abdominal pain. She had normal bowel movements and no vomiting, but her periumbilical pain limited her ability to finish most meals. She had gradual weight loss over the previous 2 years, and during the previous 4 years, she intermittently received counseling for depression after the loss of her mother. Her initial physical examination and laboratory evaluation were unremarkable. She was referred to a nutritionist, adolescent medicine, and pediatric gastroenterology. Her presentation evolved over time, which ultimately led to a definitive diagnosis. Full Article
and Breastfeeding and Mortality Under 2 Years of Age in Sub-Saharan Africa By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: Several studies have investigated the association of breastfeeding status with offspring mortality in Africa, but most studies were from one center only or had limited statistical power to draw robust conclusions. METHODS: Data came from 75 nationally representative cross-sectional Demographic and Health Surveys in 35 countries in sub-Saharan Africa conducted between 2000 and 2016. Our study relied on 217 112 individuals aged 4 days to 23 months for breastfeeding pattern analysis, 161 322 individuals aged 6 to 23 months for breastfeeding history analysis, and 104 427 individuals aged 12 to 23 months for breastfeeding duration analysis. RESULTS: Compared with children aged 4 days to 23 months exclusively breastfed in the first 3 days of life, those not breastfed had a high risk of mortality at <2 years of age (odds ratio [OR] = 13.45; 95% confidence interval [CI] = 11.43–15.83). Young children who were predominantly breastfed or partially breastfed had moderately increased risk of mortality at <2 years of age (OR = 1.11, 95% CI = 1.03–1.21 for predominant pattern; OR = 1.12, 95% CI = 0.99–1.27 for partial pattern). Compared with children aged 6 to 23 months who were breastfed within the first 6 months of life, those not breastfed had a high risk of mortality (OR = 5.65; 95% CI = 4.27–7.47). Compared with children aged 12 to 23 months who were breastfed for ≥6 months, those who were breastfed for shorter periods had a higher risk of mortality (OR = 2.78, 95% CI = 1.45–5.32 for duration of <3 months; OR = 5.28, 95% CI = 3.24–8.61 for those who were not breastfed). CONCLUSIONS: Our findings support exclusive breastfeeding during the first 6 months of life and continued breastfeeding up to 2 years of age recommended by the World Health Organization for reducing mortality of children <2 years old in sub-Saharan Africa. Full Article
and Peanut Allergy: New Advances and Ongoing Controversies By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Peanut allergy is one of the most common food allergies in children, with increasing prevalence over time. The dual-allergen exposure hypothesis now supports transcutaneous sensitization to peanut as a likely pathophysiologic mechanism for peanut allergy development. As a result, there is emerging evidence that early peanut introduction has a role in peanut allergy prevention. Current first-line diagnostic tests for peanut allergy have limited specificity, which may be enhanced with emerging tools such as component-resolved diagnostics. Although management of peanut allergy includes avoidance and carrying an epinephrine autoinjector, risk of fatal anaphylaxis is extremely low, and there is minimal risk related to cutaneous or inhalational exposure. Quality of life in children with peanut allergy requires significant focus. Moving forward, oral and epicutaneous immunotherapy are emerging and exciting tools that may have a role to play in desensitization to peanut. Full Article
and Use of Standing Orders for Vaccination Among Pediatricians By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: Standing orders are an effective way to increase vaccination rates, yet little is known about how pediatricians use this strategy for childhood immunizations. We assessed current use of, barriers to using, and factors associated with use of standing orders for vaccination among pediatricians. METHODS: Internet and mail survey from June 2017 to September 2017 among a nationally representative sample of pediatricians. In the principal component analysis of barrier items, we identified 2 factors: physician responsibility and concerns about office processes. A multivariable analysis that included barrier scales and physician and/or practice characteristics was used to identify factors associated with use of standing orders. RESULTS: The response rate was 79% (372 of 471); 59% of respondents reported using standing orders. The most commonly identified barriers among nonusers were concern that patients may mistakenly receive the wrong vaccine (68%), concern that patients prefer to speak with the physician about a vaccine before receiving it (62%), and belief that it is important for the physician to be the person who recommends a vaccine to patients (57%). These 3 items also made up the physician responsibility barrier factor. Respondents with higher physician responsibility scores were less likely to use standing orders (risk ratio: 0.59 [95% confidence interval: 0.53–0.66] per point increase). System-level decision-making about vaccines, suburban or rural location, and lower concerns about office processes scores were each associated with use of standing orders in the bivariate, but not the multivariable, analysis. CONCLUSIONS: Among pediatricians, use of standing orders for vaccination is far from universal. Interventions to increase use of standing orders should address physicians’ attitudinal barriers as well as organizational factors. Full Article
and E-cigarette Product Characteristics and Subsequent Frequency of Cigarette Smoking By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: There is a dearth of evidence regarding the association of use of electronic cigarettes (e-cigarettes) with certain product characteristics and adolescent and young adult risk of unhealthy tobacco use patterns (eg, frequency of combustible cigarette smoking), which is needed to inform the regulation of e-cigarettes. METHODS: Data were collected via an online survey of participants in the Southern California Children’s Health Study from 2015 to 2016 (baseline) and 2016 to 2017 (follow-up) (N = 1312). We evaluated the association of binary categories of 3 nonmutually exclusive characteristics of the e-cigarette used most frequently with the number of cigarettes smoked in the past 30 days at 1-year follow-up. Product characteristics included device (vape pen and/or modifiable electronic cigarette [mod]), use of nicotine in electronic liquid (e-liquid; yes or no), and use for dripping (directly dripping e-liquid onto the device; yes or no). RESULTS: Relative to never e-cigarette users, past-30-day e-cigarette use was associated with greater frequency of past-30-day cigarette smoking at follow-up. Among baseline past-30-day e-cigarette users, participants who used mods (versus vape pens) smoked >6 times as many cigarettes at follow-up (mean: 20.8 vs 1.3 cigarettes; rate ratio = 6.33; 95% confidence interval: 1.64–24.5) after adjustment for sociodemographic characteristics, baseline frequency of cigarette smoking, and number of days of e-cigarette use. After adjustment for device, neither nicotine e-liquid nor dripping were associated with frequency of cigarette smoking. CONCLUSIONS: Baseline mod users (versus vape pen users) smoked more cigarettes in the past 30 days at follow-up. Regulation of e-cigarette device type warrants consideration as a strategy to reduce cigarette smoking among adolescents and young adults who vape. Full Article
and In Utero Antidepressants and Neurodevelopmental Outcomes in Kindergarteners By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: To determine if in utero selective serotonin reuptake inhibitor (SSRI) or selective serotonin norepinephrine inhibitor (SNRI) exposure is associated with developmental vulnerability in kindergarten among children whose mothers were diagnosed with prenatal mood or anxiety disorder. METHODS: Linkable administrative data were used to create a population-based cohort of 266 479 mother-child dyads of children born in Manitoba, Canada, between 1996 and 2014, with follow-up through 2015. The sample was restricted to mothers who had a mood or anxiety disorder diagnosis between 90 days before conception (N = 13 818). Exposed women had ≥2 SSRI or SNRI dispensations during pregnancy (n = 2055); unexposed mothers did not have a dispensation of an SSRI or SNRI during pregnancy (n = 10 017). The Early Development Instrument (EDI) was used to assess developmental health in kindergarten children. The EDI is a 104-component kindergarten teacher-administered questionnaire, encompassing 5 developmental domains. RESULTS: Of the 3048 children included in the study who met inclusion criteria and had an EDI, 21.43% of children in the exposed group were assessed as vulnerable on 2 or more domains versus 16.16% of children in the unexposed group (adjusted odds ratio = 1.43; 95% confidence interval 1.08–1.90). Children in the exposed group also had a significant risk of being vulnerable in language and/or cognition (adjusted odds ratio = 1.40; 95% confidence interval 1.03–1.90). CONCLUSIONS: Exposure to SSRIs or SNRIs during pregnancy was associated with an increased risk of developmental vulnerability and an increased risk of deficits in language and/or cognition. Replication of results is necessary before clinical implications can be reached. Full Article
and The Genetics of Mating Song Evolution Underlying Rapid Speciation: Linking Quantitative Variation to Candidate Genes for Behavioral Isolation [Corrigendum] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Full Article
and A Novel Variation in the FRIZZLE PANICLE (FZP) Gene Promoter Improves Grain Number and Yield in Rice [Genetics of Complex Traits] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Secondary branch number per panicle plays a crucial role in regulating grain number and yield in rice. Here, we report the positional cloning and functional characterization for SECONDARY BRANCH NUMBER7 (qSBN7), a quantitative trait locus affecting secondary branch per panicle and grain number. Our research revealed that the causative variants of qSBN7 are located in the distal promoter region of FRIZZLE PANICLE (FZP), a gene previously associated with the repression of axillary meristem development in rice spikelets. qSBN7 is a novel allele of FZP that causes an ~56% decrease in its transcriptional level, leading to increased secondary branch and grain number, and reduced grain length. Field evaluations showed that qSBN7 increased grain yield by 10.9% in a temperate japonica variety, TN13, likely due to its positive effect on sink capacity. Our findings suggest that incorporation of qSBN7 can increase yield potential and improve the breeding of elite rice varieties. Full Article
and Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize [Genomic Prediction] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize. Full Article
and Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data [Population and Evolutionary Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here, we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies (GWAS). We find that most common summary statistics have distributions that differ substantially from those seen in well-mixed populations, especially when Wright’s neighborhood size is < 100 and sampling is spatially clustered. "Stepping-stone" models reproduce some of these effects, but discretizing the landscape introduces artifacts that in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations revealed surprisingly little systematic bias. We also show that the combination of spatially autocorrelated environments and limited dispersal causes GWAS to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms. Full Article
and Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection [Population and Evolutionary Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The question of the relative evolutionary roles of adaptive and nonadaptive processes has been a central debate in population genetics for nearly a century. While advances have been made in the theoretical development of the underlying models, and statistical methods for estimating their parameters from large-scale genomic data, a framework for an appropriate null model remains elusive. A model incorporating evolutionary processes known to be in constant operation, genetic drift (as modulated by the demographic history of the population) and purifying selection, is lacking. Without such a null model, the role of adaptive processes in shaping within- and between-population variation may not be accurately assessed. Here, we investigate how population size changes and the strength of purifying selection affect patterns of variation at "neutral" sites near functional genomic components. We propose a novel statistical framework for jointly inferring the contribution of the relevant selective and demographic parameters. By means of extensive performance analyses, we quantify the utility of the approach, identify the most important statistics for parameter estimation, and compare the results with existing methods. Finally, we reanalyze genome-wide population-level data from a Zambian population of Drosophila melanogaster, and find that it has experienced a much slower rate of population growth than was inferred when the effects of purifying selection were neglected. Our approach represents an appropriate null model, against which the effects of positive selection can be assessed. Full Article
and Identifying and Classifying Shared Selective Sweeps from Multilocus Data [Population and Evolutionary Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term and to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses. Full Article
and Development of the Proximal-Anterior Skeletal Elements in the Mouse Hindlimb Is Regulated by a Transcriptional and Signaling Network Controlled by Sall4 [Developmental and Behavioral Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The vertebrate limb serves as an experimental paradigm to study mechanisms that regulate development of the stereotypical skeletal elements. In this study, we simultaneously inactivated Sall4 using Hoxb6Cre and Plzf in mouse embryos, and found that their combined function regulates development of the proximal-anterior skeletal elements in hindlimbs. The Sall4; Plzf double knockout exhibits severe defects in the femur, tibia, and anterior digits, distinct defects compared to other allelic series of Sall4; Plzf. We found that Sall4 regulates Plzf expression prior to hindlimb outgrowth. Further expression analysis indicated that Hox10 genes and GLI3 are severely downregulated in the Sall4; Plzf double knockout hindlimb bud. In contrast, PLZF expression is reduced but detectable in Sall4; Gli3 double knockout limb buds, and SALL4 is expressed in the Plzf; Gli3 double knockout limb buds. These results indicate that Plzf, Gli3, and Hox10 genes downstream of Sall4, regulate femur and tibia development. In the autopod, we show that Sall4 negatively regulates Hedgehog signaling, which allows for development of the most anterior digit. Collectively, our study illustrates genetic systems that regulate development of the proximal-anterior skeletal elements in hindlimbs. Full Article
and Pits and CtBP Control Tissue Growth in Drosophila melanogaster with the Hippo Pathway Transcription Repressor Tgi [Developmental and Behavioral Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The Hippo pathway is an evolutionarily conserved signaling network that regulates organ size, cell fate, and tumorigenesis. In the context of organ size control, the pathway incorporates a large variety of cellular cues, such as cell polarity and adhesion, into an integrated transcriptional response. The central Hippo signaling effector is the transcriptional coactivator Yorkie, which controls gene expression in partnership with different transcription factors, most notably Scalloped. When it is not activated by Yorkie, Scalloped can act as a repressor of transcription, at least in part due to its interaction with the corepressor protein Tgi. The mechanism by which Tgi represses transcription is incompletely understood, and therefore we sought to identify proteins that potentially operate together with Tgi. Using an affinity purification and mass-spectrometry approach we identified Pits and CtBP as Tgi-interacting proteins, both of which have been linked to transcriptional repression. Both Pits and CtBP were required for Tgi to suppress the growth of the Drosophila melanogaster eye and CtBP loss suppressed the undergrowth of yorkie mutant eye tissue. Furthermore, as reported previously for Tgi, overexpression of Pits repressed transcription of Hippo pathway target genes. These findings suggest that Tgi might operate together with Pits and CtBP to repress transcription of genes that normally promote tissue growth. The human orthologs of Tgi, CtBP, and Pits (VGLL4, CTBP2, and IRF2BP2) have previously been shown to physically and functionally interact to control transcription, implying that the mechanism by which these proteins control transcriptional repression is conserved throughout evolution. Full Article
and Alcohol Causes Lasting Differential Transcription in Drosophila Mushroom Body Neurons [Developmental and Behavioral Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Repeated alcohol experiences can produce long-lasting memories for sensory cues associated with intoxication. These memories can problematically trigger relapse in individuals recovering from alcohol use disorder (AUD). The molecular mechanisms by which ethanol changes memories to become long-lasting and inflexible remain unclear. New methods to analyze gene expression within precise neuronal cell types can provide further insight toward AUD prevention and treatment. Here, we used genetic tools in Drosophila melanogaster to investigate the lasting consequences of ethanol on transcription in memory-encoding neurons. Drosophila rely on mushroom body (MB) neurons to make associative memories, including memories of ethanol-associated sensory cues. Differential expression analyses revealed that distinct transcripts, but not genes, in the MB were associated with experiencing ethanol alone compared to forming a memory of an odor cue associated with ethanol. Adult MB-specific knockdown of spliceosome-associated proteins demonstrated the necessity of RNA-processing in ethanol memory formation. These findings highlight the dynamic, context-specific regulation of transcription in cue-encoding neurons, and the lasting effect of ethanol on transcript usage during memory formation. Full Article
and Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila [Gene Expression] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 BEAF (Boundary Element-Associated Factor) was originally identified as a Drosophila melanogaster chromatin domain insulator-binding protein, suggesting a role in gene regulation through chromatin organization and dynamics. Genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, suggesting a role in promoter function. This would be a nontraditional role for an insulator-binding protein. To gain insight into molecular mechanisms of BEAF function, we identified interacting proteins using yeast two-hybrid assays. Here, we focus on the transcription factor Serendipity (Sry-). Interactions were confirmed in pull-down experiments using bacterially expressed proteins, by bimolecular fluorescence complementation, and in a genetic assay in transgenic flies. Sry- interacted with promoter-proximal BEAF both when bound to DNA adjacent to BEAF or > 2-kb upstream to activate a reporter gene in transient transfection experiments. The interaction between BEAF and Sry- was detected using both a minimal developmental promoter (y) and a housekeeping promoter (RpS12), while BEAF alone strongly activated the housekeeping promoter. These two functions for BEAF implicate it in playing a direct role in gene regulation at hundreds of BEAF-associated promoters. Full Article
and Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif [Genome Integrity and Transmission] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs. Full Article
and Topoisomerases Modulate the Timing of Meiotic DNA Breakage and Chromosome Morphogenesis in Saccharomyces cerevisiae [Genome Integrity and Transmission] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 During meiotic prophase, concurrent transcription, recombination, and chromosome synapsis place substantial topological strain on chromosomal DNA, but the role of topoisomerases in this context remains poorly defined. Here, we analyzed the roles of topoisomerases I and II (Top1 and Top2) during meiotic prophase in Saccharomyces cerevisiae. We show that both topoisomerases accumulate primarily in promoter-containing intergenic regions of actively transcribing genes, including many meiotic double-strand break (DSB) hotspots. Despite the comparable binding patterns, top1 and top2 mutations have different effects on meiotic recombination. TOP1 disruption delays DSB induction and shortens the window of DSB accumulation by an unknown mechanism. By contrast, temperature-sensitive top2-1 mutants exhibit a marked delay in meiotic chromosome remodeling and elevated DSB signals on synapsed chromosomes. The problems in chromosome remodeling were linked to altered Top2 binding patterns rather than a loss of Top2 catalytic activity, and stemmed from a defect in recruiting the chromosome remodeler Pch2/TRIP13 to synapsed chromosomes. No chromosomal defects were observed in the absence of TOP1. Our results imply independent roles for Top1 and Top2 in modulating meiotic chromosome structure and recombination. Full Article
and Fast Algorithms for Conducting Large-Scale GWAS of Age-at-Onset Traits Using Cox Mixed-Effects Models [Statistical Genetics and Genomics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Age-at-onset is one of the critical traits in cohort studies of age-related diseases. Large-scale genome-wide association studies (GWAS) of age-at-onset traits can provide more insights into genetic effects on disease progression and transitions between stages. Moreover, proportional hazards (or Cox) regression models can achieve higher statistical power in a cohort study than a case-control trait using logistic regression. Although mixed-effects models are widely used in GWAS to correct for sample dependence, application of Cox mixed-effects models (CMEMs) to large-scale GWAS is so far hindered by intractable computational cost. In this work, we propose COXMEG, an efficient R package for conducting GWAS of age-at-onset traits using CMEMs. COXMEG introduces fast estimation algorithms for general sparse relatedness matrices including, but not limited to, block-diagonal pedigree-based matrices. COXMEG also introduces a fast and powerful score test for dense relatedness matrices, accounting for both population stratification and family structure. In addition, COXMEG generalizes existing algorithms to support positive semidefinite relatedness matrices, which are common in twin and family studies. Our simulation studies suggest that COXMEG, depending on the structure of the relatedness matrix, is orders of magnitude computationally more efficient than coxme and coxph with frailty for GWAS. We found that using sparse approximation of relatedness matrices yielded highly comparable results in controlling false-positive rate and retaining statistical power for an ethnically homogeneous family-based sample. By applying COXMEG to a study of Alzheimer’s disease (AD) with a Late-Onset Alzheimer’s Disease Family Study from the National Institute on Aging sample comprising 3456 non-Hispanic whites and 287 African Americans, we identified the APOE 4 variant with strong statistical power (P = 1e–101), far more significant than that reported in a previous study using a transformed variable and a marginal Cox model. Furthermore, we identified novel SNP rs36051450 (P = 2e–9) near GRAMD1B, the minor allele of which significantly reduced the hazards of AD in both genders. These results demonstrated that COXMEG greatly facilitates the application of CMEMs in GWAS of age-at-onset traits. Full Article
and Fear and Foxes: An Educational Primer for Use with "Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes" [Primer] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The way genes contribute to behavior is complicated. Although there are some single genes with large contributions, most behavioral differences are due to small effects from many interacting genes. This makes it hard to identify the genes that cause behavioral differences. Mutagenesis screens in model organisms, selective breeding experiments in animals, comparisons between related populations with different behaviors, and genome-wide association studies in humans are promising and complementary approaches to understanding the heritable aspects of complex behaviors. To connect genes to behaviors requires measuring behavioral differences, locating correlated genetic changes, determining when, where, and how these candidate genes act, and designing causative confirmatory experiments. This area of research has implications from basic discovery science to human mental health. Full Article
and Phenotypic Plasticity: From Theory and Genetics to Current and Future Challenges [Perspectives] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Phenotypic plasticity is defined as the property of organisms to produce distinct phenotypes in response to environmental variation. While for more than a century, biologists have proposed this organismal feature to play an important role in evolution and the origin of novelty, the idea has remained contentious. Plasticity is found in all domains of life, but only recently has there been an increase in empirical studies. This contribution is intended as a fresh view and will discuss current and future challenges of plasticity research, and the need to identify associated molecular mechanisms. After a brief summary of conceptual, theoretical, and historical aspects, some of which were responsible for confusion and contention, I will formulate three major research directions and predictions for the role of plasticity as a facilitator of novelty. These predictions result in a four-step model that, when properly filled with molecular mechanisms, will reveal plasticity as a major factor of evolution. Such mechanistic insight must be complemented with comparative investigations to show that plasticity has indeed created novelty and innovation. Together, such studies will help develop a true developmental evolutionary biology. Full Article
and Phosphoflow Protocol for Signaling Studies in Human and Murine B Cell Subpopulations [NOVEL IMMUNOLOGICAL METHODS] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points Method for highly sensitive detection of phosphorylation in B cell subpopulations. B cell subpopulations show different phosphorylation levels upon BCR stimulation. Full Article
and Localized Immunomodulation with PD-L1 Results in Sustained Survival and Function of Allogeneic Islets without Chronic Immunosuppression [TRANSPLANTATION] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points Islets are engineered with SA-PDL1 protein without impacting viability/function. SA-PDL1–engineered islets show indefinite survival in allogeneic hosts. Survival is associated with elevated intragraft Th2, Treg, and M2 transcripts. Full Article
and Role of V-ATPase a3-Subunit in Mouse CTL Function [MOLECULAR AND STRUCTURAL IMMUNOLOGY] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points The a3-subunit of V-ATPase acidifies cytotoxic granules in mouse CD8+ T lymphocytes. Neutralization of luminal pH leads to altered morphology of cytotoxic granules. Knockdown of a3-subunit disturbs trafficking of cytotoxic granules. Full Article