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Power and sample-size estimation in human microbiome research

Zhou, Qianyi; Lu, Yingzhou; Wang, Luman; Zhou, Wei; Oba, Haley; Zhou, Yanjiao; Shen, Minjie; Qu, Xiaodong; De Souza, Cristabelle; Rayner, Andre; Chen, Yanfei; Cheng, Tess Y; Ling, Zongxin; Li, Lanjuan; Liu, Chang; Voigt, Anita Y; Xiong, Ruoyun; Oh, Julia; Spakowicz, Daniel; Dravillas, Caroline; Tian, Amy Wen; Nicolls, Mark R; Huynh, Amber-Thy; Chen, Xin; Hu, Jiyuan; He, Mingguang; He, Fuchu; Snyder, Michael P; Yang, Jing; Zhou, Xin
Human microbiome research has become pivotal in advancing our understanding of complex diseases such as diabetes, inflammatory bowel disease, and cancer. Much of this work relies on comparing microbial communities across health and disease states, or case-control cohorts, using high-throughput metagenomic sequencing. Yet the very nature of sequencing-derived microbiome data makes robust cohort design and power-based sample-size estimation unusually difficult. Unlike other omics, microbiome profiles are compositional, sparse, and often zero inflated, properties that complicate statistical modeling and inflate sample-size requirements. These challenges are further compounded by the diversity of analytical frameworks-ranging from diversity indices to causal inference-each built on different statistical assumptions and optimized for a distinct research hypothesis. This review synthesizes current approaches around the study design and sample-size estimation in microbiome research, aiming to provide clinicians and researchers with practical guidance for navigating the statistical complexities unique to this field.
PMID: 42302785
ISSN: 2666-6340
CID: 6049662

Corrigendum to "Long-Term outcomes of induction chemotherapy-guided reduced-dose chemoradiotherapy in poor-risk HPV-Positive oropharyngeal Cancer: Results from the sequential quarterback trials" [Oral Oncol. 174 (2026) 107858]

Lovett, J T; Wotman, M T; Westra, W H; Ahn, S; Gupta, V; Bakst, R L; Roof, Scott; Miles, B A; Genden, E; Misiukiewicz, K; Worona, L; Ramos, E; Botzler, J; Chen, T; Posner, M
PMID: 42309926
ISSN: 1879-0593
CID: 6050032

Clinical Implementation of Opportunistic Screening for Osteoporosis

Dogra, Siddhant; Bussey, Olivia; Dane, Bari; Bredella, Miriam A; Recht, Michael P; Gyftopoulos, Soterios
Opportunistic screening leverages existing imaging examinations performed for unrelated routine clinical indications to systematically extract quantitative biomarkers. Artificial intelligence tools have made deployment at scale increasingly feasible. However, the pathway from a validated algorithm to a functioning clinical program remains poorly defined, and prospective implementation at scale is uncommon. Successful deployment requires coordinated engagement from radiologists, information technology and operational teams, and clinical care teams, each facing distinct decisions that determine whether a program functions reliably and delivers patient benefit. This article presents a practical framework for opportunistic screening implementation organized around these three stakeholder groups. We apply this framework to opportunistic CT osteoporosis screening, drawing on our experience developing such a program at a large academic medical center. The framework presented is intended to be broadly applicable across opportunistic screening applications as the field moves from algorithmic validation toward clinical translation.
PMID: 42308093
ISSN: 1546-3141
CID: 6049902

Detection of MEN1 resistance mutations in cell-free DNA from acute leukemia patients treated with menin inhibitors [Letter]

Shukla, Neerav; Charalambous, Karmelina; Li, Shanita; Ko, Kaitlyn H; Casanova, Hilary; Buehler, Eric; Cobbs, Cassidy; Patel, Ruchi; Brannon, Angela Rose; Ewalt, Mark D; Sulis, Maria Luisa; Carroll, William L; Arcila, Maria E; Mohibullah, Neeman; Berger, Michael; Levine, Ross L; Stein, Eytan M; Shah, Ronak; Cai, Sheng F
PMCID:13272672
PMID: 42303978
ISSN: 2044-5385
CID: 6049752

Gestational Exposure to 10 Classes of Priority Chemicals and Birth Outcomes in the ECHO Cohort

Buckley, Jessie P; Pacyga, Diana C; Xun, Xiaoshuang; Barr, Dana Boyd; Barrett, Emily S; Bastain, Theresa; Bennett, Deborah H; Braun, Joseph M; Breton, Carrie V; Carignan, Courtney; Croen, Lisa A; Dunlop, Anne L; Farzan, Shohreh F; Ferrara, Assiamira; Gilliland, Frank D; Herbstman, Julie B; Karagas, Margaret R; Karr, Catherine J; Kuiper, Jordan R; Meeker, John D; Miller, Rachel L; Morello-Frosch, Rachel; O'Connor, Thomas G; Oh, Jiwon; Perera, Frederica P; Porucznik, Christina A; Romano, Megan E; Sathyanarayana, Sheela; Schantz, Susan L; Schmidt, Rebecca J; Sherris, Allison R; Trasande, Leonardo; Volk, Heather; Watkins, Deborah J; Zhao, Qi; Zhu, Yeyi; Li, Zhongmin; Pellizzari, Edo; Kannan, Kurunthachalam; Woodruff, Tracey J; ,
IMPORTANCE/UNASSIGNED:Gestational environmental chemical exposures are widespread. Some chemicals are known to adversely affect birth outcomes, but many remain understudied. OBJECTIVE/UNASSIGNED:To evaluate associations of gestational exposure to a priori identified chemicals in 10 classes with birth outcomes in a large, diverse US cohort. DESIGN, SETTING, AND PARTICIPANTS/UNASSIGNED:In the prospective Environmental influences on Child Health Outcomes Cohort study, 5318 mother-child pairs were enrolled from January 1, 2000, to December 31, 2021, with data on gestational urinary chemical concentrations, gestational age at birth, and birth weight. Statistical analysis was performed from January 2024 to February 2026. EXPOSURES/UNASSIGNED:In single, midgestation (median, 25 weeks [IQR, 21-30 weeks]) urine samples, concentrations of 113 analytes (chemicals or their metabolites) from 10 chemical classes were simultaneously measured: fungicides and herbicides (n = 11), insecticides (n = 20), halogenated phenols (n = 5), organophosphate esters (n = 10), benzophenones (n = 6), bisphenols (n = 14), parabens (n = 6), antimicrobials (n = 2), phthalates or alternative plasticizers (n = 32), and polycyclic aromatic hydrocarbons (PAHs) (n = 7). MAIN OUTCOMES AND MEASURES/UNASSIGNED:Linear mixed-effects regression models with a random effect for site were used to estimate covariate-adjusted differences in gestational age at birth (days) and birth weight-for-gestational age (BW-GA) z scores per IQR increase in urinary analyte concentrations. In secondary analyses, odds ratios (ORs) for preterm birth and small for gestational age (SGA) were estimated. RESULTS/UNASSIGNED:In the sample of 5318 mother-child pairs, most infants (2667 female [50%]; median gestational age at birth, 39.0 weeks [IQR, 38.0-40.0 weeks]) were born to college-educated (67% [3218 of 4785]), parous (56% [2815 of 5007]) mothers (median age at delivery, 30.7 years [IQR, 26.1-34.3 years]). A total of 43 of 113 analytes (38%) were detected in 50% or more of samples. Multiple phthalates or alternative plasticizers were associated with younger gestational age at birth or lower BW-GA z scores; for example, summed diisononyl phthalate metabolites were associated with a 0.6-day (95% CI, -1.0 to -0.1 days) younger gestational age (preterm birth OR, 1.16 [95% CI, 1.01-1.34]), and summed phthalate or alternative plasticizers were associated with a 0.06 (95% CI, -0.11 to -0.02) lower BW-GA z score (SGA OR, 1.09 [95% CI, 0.93-1.27]). Two halogenated phenols, benzophenone 8, bisphenol F, and several PAHs were associated with lower BW-GA z scores; for example, 1- and 9-hydroxphenanthrene were associated with a 0.04 (95% CI, -0.08 to -0.01) lower BW-GA z score (SGA OR, 1.13 [95% CI, 1.01-1.27]). CONCLUSIONS AND RELEVANCE/UNASSIGNED:This large cohort study of diverse US pregnancies found widespread exposure to 10 classes of environmental chemicals, many of which were associated with differences in gestational age at birth or lower BW-GA z scores. These findings indicate that reducing gestational exposure to chemicals, particularly phthalates or alternative plasticizers and PAHs, could promote healthy deliveries and better child outcomes.
PMCID:13276631
PMID: 42307947
ISSN: 2574-3805
CID: 6049882

Sleep Disturbances Among Yazidi Survivors of the ISIS Genocide: Epidemiology, Neuropsychology, and Culturally Sensitive Interventions

Kizilhan, Jan Ilhan; Ag, Zelal; Ahmed, Qanta A; Avidan, Alon Y
The Yazidi community endured an unprecedented genocide by the Islamic State (ISIS) in August 2014, resulting in mass killings, kinocide, abductions, ongoing disappearances, and sexual enslavement. The intense trauma led to high prevalence rates of posttraumatic stress disorder (PTSD), depression, anxiety, and profound sleep disturbances. This comprehensive article integrates epidemiological data, neurobiological mechanisms, and clinical case reports to elucidate sleep disorders among Yazidi survivors. We detail the historical context, transgenerational trauma, specific sleep-related pathologies (insomnia, nightmares, parasomnias, and disrupted circadian rhythms), neurobiological underpinnings, cultural factors, and evidence-based interventions (e.g., Narrative Exposure Therapy (NET); Cognitive Behavioral Therapy for Insomnia (CBT-I)). Furthermore, we discuss the establishment and role of the Institute for Psychotherapy and Psychotraumatology (IPP) at the University of Duhok, outline barriers to care, and propose future research directions and policy recommendations.
PMCID:13272635
PMID: 42304608
ISSN: 2162-3279
CID: 6049782

Multimodality Imaging of Two Unique Etiologies of Supravalvular Aortic Stenosis [Case Report]

Chen, Kevin; Loulmet, Didier; Williams, Mathew; Saric, Muhamed; Vainrib, Alan
• The authors present supravalvular stenosis from congenital and iatrogenic etiologies. • Multimodality imaging is essential for diagnosing supravalvular stenosis. • Echocardiography assesses severity, while CCT provides diagnostic clarity.
PMCID:13270935
PMID: 42312010
ISSN: 2468-6441
CID: 6050112

Prophylactic versus therapeutic sucralfate in patients at high risk for radiation esophagitis: randomized controlled trial

Shin, Jacob Y; Assel, Melissa; Wu, Abraham J; Gelblum, Daphna Y; Guttmann, David M; Shepherd, Annemarie F; Reyngold, Marsha; Gewanter, Richard; Rimner, Andreas; Mueller, Boris A; Iyengar, Puneeth; Chaunzwa, Tafadzwa; Ma, Jennifer; Billing, David; McMillan, Matthew T; Mankuzhy, Nikhil P; Austria, Mia D; Simone, Charles B; Shaverdian, Narek; Vickers, Andrew J; Gomez, Daniel R
INTRODUCTION/BACKGROUND:We hypothesized that, in patients at high risk for RE, giving sucralfate prophylactically would reduce the need for opioid pain medication. METHODS AND MATERIALS/METHODS:Patients were enrolled from January 2023 to April 2025 at a single tertiary care center. Patients were randomized to receive 1 gram twice a day within the first five fractions of radiotherapy (RT), with frequency increased during RT at clinician discretion, or standard supportive care. The proportion of patients who took any opioids over the previous 24 hours at the end of the treatment course was compared between groups using logistic regression with the stratification variables and concurrent chemotherapy status as covariates. RESULTS:The trial was closed early due to lack of differences between arms with 117 patients randomized (n=56 in the experimental arm). Rates of opioid use were 30% in both groups (absolute adjusted decrease in the prophylactic sucralfate arm -0.4%; 95% CI -14%, 13%, p>0.9). Rates of grade 2 - 3 RE were non-significantly lower in the prophylactic sucralfate arm (59% vs 69%, absolute adjusted risk decrease 11%; 95% CI -7.2%, 28%; p=0.2). In patients receiving very high esophageal dose (V60 Gy ≥15%), all controls (n=4) experienced grade 2-3 RE compared to only half of those in the experimental arm (6 of 12) (Fisher's exact test p=0.2). CONCLUSIONS:We did not find evidence to support early use of sucralfate in patients at high risk of radiation esophagitis. Limited medical options for the management of RE warrant the continued need to explore further avenues to combat this painful condition.
PMID: 42303122
ISSN: 1879-8519
CID: 6049692

Allergic Contact Dermatitis to Personal Care Products: A Focus on Established and Emerging Allergens

Smale, Natalie E; Karagounis, Theodora K; Milam, Emily C; Cohen, David E; Flamm, Alexandra
Allergic contact dermatitis (ACD) to personal care products (PCPs) represents a significant and growing clinical challenge, with increasing use of diverse PCPs and their expanding range of ingredients. Common allergenic components include fragrances, botanicals, preservatives, surfactants, emollients, emulsifiers, vitamins, and ultraviolet (UV) filters. Patch testing remains the gold standard for diagnosing ACD and identifying causative allergens, but traditional panels often fail to capture emerging PCP-related allergens. This review highlights key established and emerging PCP allergens, such as limonene and linalool hydroperoxides, sodium benzoate, octocrylene, and benzophenone-4. Strategies are discussed to optimize diagnostic accuracy through targeted series and repeated open application tests. Patient education about PCP labeling is paramount when assisting patients with allergen avoidance. Clinicians must balance precise allergen identification with practical management knowledge to improve outcomes in PCP-related ACD.
PMID: 42309282
ISSN: 1097-6787
CID: 6049992

Approaches to Approximating National Public Health Data [Editorial]

Spoer, Ben R; Thorpe, Lorna E; Gourevitch, Marc N
PMCID:13277480
PMID: 42308444
ISSN: 1541-0048
CID: 6049922