Identification and Characterization of Synthetic Nicotine Product Promotion and Sales on Instagram Using Natural Language Processing

INTRODUCTION

There has been a rapid proliferation of synthetic nicotine products in recent years, despite newly established regulatory authority and limited research into its health risks. Previous research has implicated social media platforms as an avenue for nicotine product unregulated sales. Yet, little is known about synthetic nicotine product content on social media. We utilized natural language processing to characterize the sales of synthetic nicotine products on Instagram.

METHODS

We collected Instagram posts by querying Instagram hashtags (eg, "#tobaccofreenicotine) related to synthetic nicotine. Using Bidirectional Encoder Representations from Transformers, collected posts were categorized into thematically related topic clusters. Posts within topic clusters relevant to study aims were then manually annotated for variables related to promotion and selling (eg, cost discussion, contact information for offline sales).

RESULTS

A total of 7425 unique posts were collected with 2219 posts identified as related to promotion and selling of synthetic nicotine products. Nicotine pouches (52.9%, n = 1174), electronic nicotine delivery systems (30.6%, n = 679), and flavored e-liquids (14.1%, n = 313) were most commonly promoted. About 16.1% (n = 345) of posts contained embedded hyperlinks and 5.8% (n = 129) provided contact information for purported offline transactions. Only 17.6% (n = 391) of posts contained synthetic nicotine-specific health warnings.

CONCLUSIONS

In the United States, synthetic nicotine products can only be legally marketed if they have received premarket authorization from the Food and Drug Administration (FDA). Despite these prohibitions, Instagram appears to be a hub for potentially unregulated sales of synthetic and "tobacco-free" products. Efforts are needed by platforms and regulators to enhance content moderation and prevent unregulated online sales of existing and emerging synthetic nicotine products.

IMPLICATIONS

There is limited clinical understanding of synthetic nicotine's unique health risks and how these novel products are changing over time due to regulatory oversight. Despite synthetic nicotine-specific regulatory measures, such as the requirement for premarket authorization and FDA warning letters issued to unauthorized sellers, access to and promotion of synthetic nicotine is widely occurring on Instagram, a platform with over 2 billion users and one that is popular among youth and young adults. Activities include direct-to-consumer sales from questionable sources, inadequate health warning disclosure, and exposure with limited age restrictions, all conditions necessary for the sale of various tobacco products. Notably, the number of these Instagram posts increased in response to the announcement of new FDA regulations. In response, more robust online monitoring, content moderation, and proactive enforcement are needed from platforms who should work collaboratively with regulators to identify, report, and remove content in clear violation of platform policies and federal laws. Regulatory implementation and enforcement should prioritize digital platforms as conduits for unregulated access to synthetic nicotine products and other future novel and emerging tobacco products.

We've been here before: Reactions to the murder of George Floyd and subsequent protests for justice

Although experiences with police vary widely by race in the United States, many Americans expressed negative reactions to the murder of George Floyd by Minneapolis police in May 2020, which led to racially diverse protests for Floyd's justice.

OBJECTIVE

This study assessed differences in Black and White Americans' reactions to the murder of George Floyd and the presence of White Americans at the subsequent protests for justice.

METHOD

Black and White Americans (N = 290) took part in an online study in which they responded to questions regarding their reactions to the murder of George Floyd, the subsequent protests for justice, and critical knowledge (e.g., previous experiences with police and broad knowledge of Black history).

RESULTS

Results of a preregistered study showed that Black (relative to White) Americans were more surprised by the extent of White participation in protests for justice. Also, Black Americans were more alarmed (i.e., emotionally jarred) by Floyd's murder. These differences in reactions were explained by Black (relative to White) Americans having more negative experiences with police brutality, both personally and among close others.

CONCLUSION

This suggests that reactions to police brutality are experientially rooted, joining long-standing calls to center the lived experiences of Black Americans in psychological research. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Strain Solitons in an Epitaxially Strained van der Waals-like Material

Strain solitons are quasi-dislocations that form in van der Waals materials to relieve the energy associated with lattice or rotational mismatch. Novel electronic properties of strain solitons were predicted and observed. To date, strain solitons have been observed only in exfoliated crystals or mechanically strained crystals. The lack of a scalable approach toward the generation of strain solitons poses a significant challenge in the study of and use of their properties. Here, we report the formation of strain solitons with epitaxial growth of bismuth on InSb(111)B by molecular beam epitaxy. The morphology of the strain solitons for films of varying thickness is characterized with scanning tunneling microscopy, and the local strain state is determined from atomic resolution images. Bending in the solitons is attributed to interactions with the interface, and large angle bending is associated with edge dislocations. Our results enable the scalable generation of strain solitons.

Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery

Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

Pollinator and habitat-mediated selection as potential contributors to ecological speciation in two closely related species

In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of 2 species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the 2 parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. A total of 3 vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and 5 floral traits (corolla length and width, anther insertion, petal color, and nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the Ipomopsis tenuituba site, whereas selection favored the reverse condition at the Ipomopsis aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.

Understanding the effects of sub-inhibitory antibiotic concentrations on the development of β-lactamase resistance based on quantile regression analysis

AIMS

Quantile regression is an alternate type of regression analysis that has been shown to have numerous advantages over standard linear regression. Unlike linear regression, which uses the mean to fit a linear model, quantile regression uses a data set's quantiles (or percentiles), which leads to a more comprehensive analysis of the data. However, while relatively common in other scientific fields such as economic and environmental modeling, it is infrequently used to understand biological and microbiological systems.

METHODS AND RESULTS

We analyzed a set of bacterial growth rates using quantile regression analysis to better understand the effects of antibiotics on bacterial fitness. Using a bacterial model system containing 16 variant genotypes of the TEM β-lactamase enzyme, we compared our quantile regression analysis to a previously published study that uses the Tukey's range test, or Tukey honestly significantly difference (HSD) test. We find that trends in the distribution of bacterial growth rate data, as viewed through the lens of quantile regression, can distinguish between novel genotypes and ones that have been clinically isolated from patients. Quantile regression also identified certain combinations of genotypes and antibiotics that resulted in bacterial populations growing faster as the antibiotic concentration increased-the opposite of what was expected. These analyses can provide new insights into the relationships between enzymatic efficacy and antibiotic concentration.

CONCLUSIONS

Quantile regression analysis enhances our understanding of the impacts of sublethal antibiotic concentrations on enzymatic (TEM β-lactamase) efficacy and bacterial fitness. We illustrate that quantile regression analysis can link patterns in growth rates with clinically relevant mutations and provides an understanding of how increasing sub-lethal antibiotic concentrations, like those found in our modern environment, can affect bacterial growth rates, and provide insight into the genetic basis for varied resistance.

Neurophysiological trajectories in Alzheimer's disease progression

Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β and misfolded tau proteins causing synaptic dysfunction, and progressive neurodegeneration and cognitive decline. Altered neural oscillations have been consistently demonstrated in AD. However, the trajectories of abnormal neural oscillations in AD progression and their relationship to neurodegeneration and cognitive decline are unknown. Here, we deployed robust event-based sequencing models (EBMs) to investigate the trajectories of long-range and local neural synchrony across AD stages, estimated from resting-state magnetoencephalography. The increases in neural synchrony in the delta-theta band and the decreases in the alpha and beta bands showed progressive changes throughout the stages of the EBM. Decreases in alpha and beta band synchrony preceded both neurodegeneration and cognitive decline, indicating that frequency-specific neuronal synchrony abnormalities are early manifestations of AD pathophysiology. The long-range synchrony effects were greater than the local synchrony, indicating a greater sensitivity of connectivity metrics involving multiple regions of the brain. These results demonstrate the evolution of functional neuronal deficits along the sequence of AD progression.

A cucumber protein, Phloem Phosphate Stress-Repressed 1, rapidly degrades in response to a phosphate stress condition

Under depleted external phosphate (Pi), many plant species adapt to this stress by initiating downstream signaling cascades. In plants, the vascular system delivers nutrients and signaling agents to control physiological and developmental processes. Currently, limited information is available regarding the direct role of phloem-borne long-distance signals in plant growth and development under Pi stress conditions. Here, we report on the identification and characterization of a cucumber protein, Cucumis sativus Phloem Phosphate Stress-Repressed 1 (CsPPSR1), whose level in the phloem translocation stream rapidly responds to imposed Pi-limiting conditions. CsPPSR1 degradation is mediated by the 26S proteasome; under Pi-sufficient conditions, CsPPSR1 is stabilized by its phosphorylation within the sieve tube system through the action of CsPPSR1 kinase. Further, we discovered that CsPPSR1 kinase was susceptible to Pi starvation-induced degradation in the sieve tube system. Our findings offer insight into a molecular mechanism underlying the response of phloem-borne proteins to Pi-limited stress conditions.

Examining the Peer-Reviewed Literature on Tobacco-Related Social Media Data: Scoping Review

INTRODUCTION

Tobacco researchers have used social media data to examine tobacco industry marketing practices (eg, influencers), and to document user experience with tobacco products. This study summarized the literature that analyzed tobacco-related social media data, including domain, social media platform, tobacco product type, and themes of findings, among other variables.

AIMS AND METHODS

PubMed, PsycINFO, Web of Science, and Communication Source were searched between 2004 and 2022. Peer-reviewed articles were included if they were written in English, included at least one tobacco-related term, and one social media-related term, and analyzed a social media post. Two coders screened all-titles and abstracts. The final sample consisted of (n = 255) articles. Studies were coded for domain, social media platform, tobacco product type, data source, type of data, coding and analytic method, and presence of validation procedure, among other variables.

RESULTS

A total of 10 504 820 581 tobacco-related social media posts were assessed across 255 studies. User experience (54.1%) and promotion (23.1%) were the most researched domains. Researchers used data from Twitter the most (42.7%). Text (43.1%) was the most common type of data analyzed. Thematic analysis (80.8%) was the most common analytic technique. Themes of findings from content analyses often pertained to the health effects of tobacco use (61.0%) and promotion (44.2%).

CONCLUSIONS

Researchers have analyzed billions of tobacco-related social media posts to describe user experience with, and promotions related to, tobacco products like e-cigarettes on platforms like Twitter. Future research may examine tobacco-related social media data from newer platforms like TikTok.

IMPLICATIONS

Real-time surveillance of tobacco-related content on social media can keep the tobacco control community abreast of tobacco industry promotional strategies, user experience with tobacco products, and perceived health effects of tobacco use. A framework may be developed to establish best-practices for social media data collection and analysis, including strategies to identify posts from bot accounts and validate methodological approaches used in thematic analysis.

Examining Tobacco-Related Social Media Research in Government Policy Documents: Systematic Review

BACKGROUND

Social media data have been used to describe tobacco industry marketing practices, user experiences with tobacco, and youth-oriented protobacco content.

OBJECTIVE

Examine the extent to which tobacco-related social media research is cited in government policy documents.

SEARCH METHODS

Peer-reviewed tobacco-related social media studies were searched for on Web of Science, PubMed, and other databases from 2004 to 2022. The DOI number for each identified article was then used to search the Overton database to find policy documents citing such research. A secondary, manual search of national and international governmental agency websites was also conducted.

SELECTION CRITERIA

Documents were included in this study if they were tobacco-related, written in English, cited social media research in the document text and reference section, and were published by a governmental office or agency.

DATA COLLECTION AND ANALYSIS

The analytic sample consisted of (n = 38) government policy documents, and were coded for content themes, agency type, document type, and subsequent citations.

MAIN RESULTS

When this research was utilized, it was often in the context of highlighting tobacco industry marketing practices, bringing attention to an issue (eg, youth e-cigarette use), and/or describing how social media platforms can be used as a data source to understand tobacco-related attitudes and behaviors. Agencies that often cited this research were the WHO, FDA, and CDC. The document types included research reports, policy recommendations, industry guidance, legal complaints, and practice-based recommendations.

CONCLUSIONS

Tobacco-related social media research has been utilized by government agencies in the last decade to guide the policy process.

IMPLICATIONS

Tobacco-related social media research has been used in government policy documents to detail tobacco industry marketing and bring attention to youth exposure to protobacco content online. Continued surveillance of social media may be necessary to track the changing tobacco landscape.

Blood oxygen transport and depletion in diving emperor penguins

Oxygen store management underlies dive performance and is dependent on the slow heart rate and peripheral vasoconstriction of the dive response to control tissue blood flow and oxygen uptake. Prior research has revealed two major patterns of muscle myoglobin saturation profiles during dives of emperor penguins. In Type A profiles, myoglobin desaturated rapidly, consistent with minimal muscle blood flow and low tissue oxygen uptake. Type B profiles, with fluctuating and slower declines in myoglobin saturation, were consistent with variable tissue blood flow patterns and tissue oxygen uptake during dives. We examined arterial and venous blood oxygen profiles to evaluate blood oxygen extraction and found two primary patterns of venous hemoglobin desaturation that complemented corresponding myoglobin saturation profiles. Type A venous profiles had a hemoglobin saturation that (a) increased/plateaued for most of a dive's duration, (b) only declined during the latter stages of ascent, and (c) often became arterialized [arterio-venous (a-v) shunting]. In Type B venous profiles, variable but progressive hemoglobin desaturation profiles were interrupted by inflections in the profile that were consistent with fluctuating tissue blood flow and oxygen uptake. End-of-dive saturation of arterial and Type A venous hemoglobin saturation profiles were not significantly different, but did differ from those of Type B venous profiles. These findings provide further support that the dive response of emperor penguins is a spectrum of cardiac and vascular components (including a-v shunting) that are dependent on the nature and demands of a given dive and even of a given segment of a dive.

Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa

The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.

Preventing zoonotic and zooanthroponotic disease transmission at wild great ape sites: Recommendations from qualitative research at Bwindi Impenetrable National Park

Employees at wild great ape sites are at high risk of transmitting infectious diseases to endangered great apes. Because of the significant amount of time employees spend near great apes, they are a priority population for the prevention and treatment of zoonotic and zooanthroponotic spillover and need adequate preventive and curative healthcare. Qualitative, semi-structured interviews with 46 staff (rangers and porters) at Bwindi Impenetrable National Park, Uganda (BINP) and key informants from five other wild great ape sites around the world were performed. The objectives of the study were to 1) evaluate health-seeking behavior and health resources used by staff in contact with great apes at Bwindi Impenetrable National Park; 2) evaluate existing occupational health programs for employees working with great apes in other parts of the world; and 3) make recommendations for improvement of occupational health at BINP. Results show that BINP employees do not frequently access preventive healthcare measures, nor do they have easy access to diagnostic testing for infectious diseases of spillover concern. Recommendations include assigning a dedicated healthcare provider for great ape site staff, providing free annual physical exams, and stocking rapid malaria tests and deworming medication in first aid kits at each site.

Automated Detection of Pediatric Foreign Body Aspiration from Chest X-rays Using Machine Learning

OBJECTIVE/HYPOTHESIS

Standard chest radiographs are a poor diagnostic tool for pediatric foreign body aspiration. Machine learning may improve upon the diagnostic capabilities of chest radiographs. The objective is to develop a machine learning algorithm that improves the diagnostic capabilities of chest radiographs in pediatric foreign body aspiration.

METHOD

This retrospective, diagnostic study included a retrospective chart review of patients with a potential diagnosis of FBA from 2010 to 2020. Frontal view chest radiographs were extracted, processed, and uploaded to Google AutoML Vision. The developed algorithm was then evaluated against a pediatric radiologist.

RESULTS

The study selected 566 patients who were presented with a suspected diagnosis of foreign body aspiration. One thousand six hundred and eighty eight chest radiograph images were collected. The sensitivity and specificity of the radiologist interpretation were 50.6% (43.1-58.0) and 88.7% (85.3-91.5), respectively. The sensitivity and specificity of the algorithm were 66.7% (43.0-85.4) and 95.3% (90.6-98.1), respectively. The precision and recall of the algorithm were both 91.8% with an AuPRC of 98.3%.

CONCLUSION

Chest radiograph analysis augmented with machine learning can diagnose foreign body aspiration in pediatric patients at a level similar to a read performed by a pediatric radiologist despite only using single-view, fixed images. Overall, this study highlights the potential and capabilities of machine learning in diagnosing conditions with a wide range of clinical presentations.

LEVEL OF EVIDENCE

3 Laryngoscope, 2024.

Navigating a climate of administrative burden: the perspectives of young adult undocumented immigrants in applying for COVID-19 disaster relief assistance for immigrants in California

Undocumented immigrants experienced high levels of economic insecurity during the COVID-19 pandemic while being excluded from government-based relief and unemployment benefits. In April 2020, California became the first state to offer financial aid to undocumented immigrants through the innovative Disaster Relief Assistance for Immigrants (DRAI) program in collaboration with several community-based organizations (CBOs). However, the process of applying for aid was marked by many implementation challenges, such as intake and language access; however, little data exists on the direct experiences of the undocumented community. This qualitative study examines the experiences of undocumented Asian and Latinx young adults living in California in applying for DRAI through framework of administrative burden. Themes distilled from participant experiences highlight how administrative burden via learning, psychological, and compliance costs shape the ways in which undocumented immigrants navigate policies and programs, such as DRAI. These experiences highlight the need for policymakers to address structural and programmatic administrative burdens in policy development; failure to do so result in detrimental impacts that outweigh financial benefits or cause communities to forgo needed resources.

Historical Redlining Is Associated with Disparities in Environmental Quality across California

Historical policies have been shown to underpin environmental quality. In the 1930s, the federal Home Owners' Loan Corporation (HOLC) developed the most comprehensive archive of neighborhoods that would have been redlined by local lenders and the Federal Housing Administration, often applying racist criteria. Our study explored how redlining is associated with environmental quality across eight California cities. We integrated HOLC's graded maps [grades A (i.e., "best" and "greenlined"), B, C, and D (i.e., "hazardous" and "redlined")] with 10 environmental hazards using data from 2018 to 2021 to quantify the spatial overlap among redlined neighborhoods and environmental hazards. We found that formerly redlined neighborhoods have poorer environmental quality relative to those of other HOLC grades via higher pollution, more noise, less vegetation, and elevated temperatures. Additionally, we found that intraurban disparities were consistently worse for formerly redlined neighborhoods across environmental hazards, with redlined neighborhoods having higher pollution burdens (77% of redlined neighborhoods vs 18% of greenlined neighborhoods), more noise (72% vs 18%), less vegetation (86% vs 12%), and elevated temperature (72% vs 20%), than their respective city's average. Our findings highlight that redlining, a policy abolished in 1968, remains an environmental justice concern by shaping the environmental quality of Californian urban neighborhoods.

Autoimmune disease and the risk of anal cancer in the US population aged 66 years and over

BACKGROUND

In the United States, anal squamous cell carcinoma rates have increased rapidly, particularly among women 50 or older than 66 years of age. As immunosuppression is associated with increased risk, autoimmune conditions may be associated with greater risk of anal squamous cell carcinoma.

METHODS

We conducted a population-based, case-control study using Surveillance, Epidemiology, and End Results-Medicare data (2000-2017). Anal squamous cell carcinoma cases (n = 4505) were matched to 200 000 cancer-free controls. Using multivariable logistic regression, we calculated odds ratios (ORs) and 95% confidence intervals (CIs) for associations between 47 autoimmune conditions diagnosed before selection, identified using Medicare claims, and anal squamous cell carcinoma. The Bonferroni threshold was used to correct for multiple comparisons. Population attributable fractions were calculated for conditions nominally associated with anal squamous cell carcinoma.

RESULTS

In total, 18% of anal squamous cell carcinoma cases and 15% of cancer-free controls had a diagnosed autoimmune condition. Any autoimmune condition was associated with an increased risk of anal squamous cell carcinoma (OR = 1.11, 95% CI = 1.02 to 1.21; population attributable fraction = 1.8%). Anal squamous cell carcinoma was associated with systemic lupus erythematosus (OR = 1.79, 95% CI = 1.32 to 2.42; population attributable fraction = 0.4%) and nominally associated (P < .05) with sarcoidosis (OR = 2.09, 95% CI = 1.30 to 3.37; population-attributable fraction = 0.2%) and psoriasis (OR = 1.28, 95% CI = 1.06 to 1.56; population attributable fraction = 0.5%). Stratified by sex, only women showed statistically significant associations for systemic lupus erythematosus (OR = 1.97, 95% CI = 1.46 to 2.68). Statistically significant interaction was observed by sex for psoriasis (men vs women: OR = 1.68 [95% CI = 1.03 to 4.28] vs OR = 1.12 [95% CI = 0.88 to 1.43]) and polymyalgia rheumatica (OR = 0.33 [95% CI = 0.12 to 0.89] vs OR = 0.99 [95% CI = 0.75 to 1.30]).

CONCLUSION

Systemic lupus erythematosus, sarcoidosis, and psoriasis were associated with a moderately increased risk of anal squamous cell carcinoma. Given these conditions' rarity and moderate associations with anal squamous cell carcinoma, autoimmune diseases cannot explain the rising trend in this disease.

Association between a network-based physician linchpin score and cancer patient mortality: a SEER-Medicare analysis

BACKGROUND

Patients with cancer frequently require multidisciplinary teams for optimal cancer outcomes. Network analysis can capture relationships among cancer specialists, and we developed a novel physician linchpin score to characterize "linchpin" physicians whose peers have fewer ties to other physicians of the same oncologic specialty. Our study examined whether being treated by a linchpin physician was associated with worse survival.

METHODS

In this cross-sectional study, we analyzed Surveillance, Epidemiology, and End Results-Medicare data for patients diagnosed with stage I to III non-small cell lung cancer or colorectal cancer (CRC) in 2016-2017. We assembled patient-sharing networks and calculated linchpin scores for medical oncologists, radiation oncologists, and surgeons. Physicians were considered linchpins if their linchpin score was within the top 15% for their specialty. We used Cox proportional hazards models to examine associations between being treated by a linchpin physician and survival, with a 2-year follow-up period.

RESULTS

The study cohort included 10 081 patients with non-small cell lung cancer and 9036 patients with CRC. Patients with lung cancer treated by a linchpin radiation oncologist had a 17% (95% confidence interval = 1.04 to 1.32) greater hazard of mortality, and similar trends were observed for linchpin medical oncologists. Patients with CRC treated by a linchpin surgeon had a 22% (95% confidence interval = 1.03 to 1.43) greater hazard of mortality.

CONCLUSIONS

In an analysis of Medicare beneficiaries with nonmetastatic lung cancer or CRC, those treated by linchpin physicians often experienced worse survival. Efforts to improve outcomes can use network analysis to identify areas with reduced access to multidisciplinary specialists.

Neural basis of speech and grammar symptoms in non-fluent variant primary progressive aphasia spectrum

The non-fluent/agrammatic variant of primary progressive aphasia (nfvPPA) is a neurodegenerative syndrome primarily defined by the presence of apraxia of speech (AoS) and/or expressive agrammatism. In addition, many patients exhibit dysarthria and/or receptive agrammatism. This leads to substantial phenotypic variation within the speech-language domain across individuals and time, in terms of both the specific combination of symptoms as well as their severity. How to resolve such phenotypic heterogeneity in nfvPPA is a matter of debate. 'Splitting' views propose separate clinical entities: 'primary progressive apraxia of speech' when AoS occurs in the absence of expressive agrammatism, 'progressive agrammatic aphasia' (PAA) in the opposite case, and 'AOS + PAA' when mixed motor speech and language symptoms are clearly present. While therapeutic interventions typically vary depending on the predominant symptom (e.g. AoS versus expressive agrammatism), the existence of behavioural, anatomical and pathological overlap across these phenotypes argues against drawing such clear-cut boundaries. In the current study, we contribute to this debate by mapping behaviour to brain in a large, prospective cohort of well characterized patients with nfvPPA (n = 104). We sought to advance scientific understanding of nfvPPA and the neural basis of speech-language by uncovering where in the brain the degree of MRI-based atrophy is associated with inter-patient variability in the presence and severity of AoS, dysarthria, expressive agrammatism or receptive agrammatism. Our cross-sectional examination of brain-behaviour relationships revealed three main observations. First, we found that the neural correlates of AoS and expressive agrammatism in nfvPPA lie side by side in the left posterior inferior frontal lobe, explaining their behavioural dissociation/association in previous reports. Second, we identified a 'left-right' and 'ventral-dorsal' neuroanatomical distinction between AoS versus dysarthria, highlighting (i) that dysarthria, but not AoS, is significantly influenced by tissue loss in right-hemisphere motor-speech regions; and (ii) that, within the left hemisphere, dysarthria and AoS map onto dorsally versus ventrally located motor-speech regions, respectively. Third, we confirmed that, within the large-scale grammar network, left frontal tissue loss is preferentially involved in expressive agrammatism and left temporal tissue loss in receptive agrammatism. Our findings thus contribute to define the function and location of the epicentres within the large-scale neural networks vulnerable to neurodegenerative changes in nfvPPA. We propose that nfvPPA be redefined as an umbrella term subsuming a spectrum of speech and/or language phenotypes that are closely linked by the underlying neuroanatomy and neuropathology.

Association between love breakup and suicidal ideation in Peruvian medical students: a cross-sectional study during the COVID-19 pandemic

Objective

We aimed to determine the association between a major romantic breakup and suicidal ideation in medical students from three universities in Peru.

Methods

A cross-sectional study was conducted during the first pandemic wave in 2021 on medical students from three universities in northern Peru. The outcome was suicidal ideation, measured with question nine of the Patient Health Questionnaire-9 (PHQ-9). Generalized Anxiety Disorder Scale-7 (GAD-7) and Insomnia Severity Index (ISI) were also used to assess mental health symptoms. The exposure was the experience of a major love breakup during the pandemic. In addition, its association with other covariates (age, sex, family members infected with COVID-19, deceased family members with COVID-19, insomnia, and anxiety, among others) was examined.

Results and discussions

Out of 370 students, 19.5% reported a major love breakup during the pandemic (95%CI: 15.5-23.8), and 34.3% had suicidal ideation (95%CI: 29.4-39.4). Having a major love breakup was associated with a higher prevalence of suicidal ideation (PR: 1.49, 95%CI: 1.32-1.67, p < 0.001). Moderate insomnia (PR: 2.56, 95%CI: 1.70-3.87, p < 0.001) and anxiety symptoms (PR: 1.94, 1.10-3.44, p = 0.023) were also associated with suicidal ideation.

Conclusion

Our study provides evidence of a significant association between a major love breakup and suicidal ideation. This finding emphasizes the need for further research to better understand this association and inform the development of effective suicide prevention policies in medical education.

Using a chat-based informed consent tool in large-scale genomic research

OBJECTIVE

We implemented a chatbot consent tool to shift the time burden from study staff in support of a national genomics research study.

MATERIALS AND METHODS

We created an Institutional Review Board-approved script for automated chat-based consent. We compared data from prospective participants who used the tool or had traditional consent conversations with study staff.

RESULTS

Chat-based consent, completed on a user's schedule, was shorter than the traditional conversation. This did not lead to a significant change in affirmative consents. Within affirmative consents and declines, more prospective participants completed the chat-based process. A quiz to assess chat-based consent user understanding had a high pass rate with no reported negative experiences.

CONCLUSION

Our report shows that a structured script can convey important information while realizing the benefits of automation and burden shifting. Analysis suggests that it may be advantageous to use chatbots to scale this rate-limiting step in large research projects.

The Varroa paradox: infestation levels and hygienic behavior in feral scutellata-hybrid and managed Apis mellifera ligustica honey bees

The Varroa destructor mite is a parasitic threat to managed and feral honey bee colonies around the world. Beekeepers use miticides to eliminate Varroa in commercial hives, but these chemicals can diminish bee health and increase miticide resistance. In contrast, feral honey bees have developed multiple ways to counteract mites without chemical treatment. We compared mite levels, grooming habits, and mite-biting behavior between feral Africanized honey bees (genomically verified Apis mellifera scutellata hybrids) and managed Italian honey bees (A. mellifera ligustica). Surprisingly, there was no difference in mite infestation levels between scutellata-hybrids and managed bees over one year despite the regular use of miticides in managed colonies. We also found no differences in the social immunity responses of the two groups, as measured by their hygienic habits (through worker brood pin-kill assays), self-grooming, and mite-biting behavior. However, we provide the first report that both scutellata-hybrids and managed honey bees bite off mite chemosensory forelegs, which the mites use to locate brood cells for reproduction, to a significantly greater degree than other legs (a twofold greater reduction in foreleg length relative to the most anterior legs). Such biting may impair mite reproduction.

Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change

Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the "translation-compensation hypothesis" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N:P.

Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts

Most vertebrate species undergo tooth replacement throughout adult life. This process is marked by the shedding of existing teeth and the regeneration of tooth organs. However, little is known about the genetic circuitry regulating tooth replacement. Here, we tested whether fish orthologs of genes known to regulate mammalian hair regeneration have effects on tooth replacement. Using two fish species that demonstrate distinct modes of tooth regeneration, threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), we found that transgenic overexpression of four different genes changed tooth replacement rates in the direction predicted by a hair regeneration model: Wnt10a and Grem2a increased tooth replacement rate, whereas Bmp6 and Dkk2 strongly inhibited tooth formation. Thus, similar to known roles in hair regeneration, Wnt and BMP signals promote and inhibit regeneration, respectively. Regulation of total tooth number was separable from regulation of replacement rates. RNA sequencing of stickleback dental tissue showed that Bmp6 overexpression resulted in an upregulation of Wnt inhibitors. Together, these data support a model in which different epithelial organs, such as teeth and hair, share genetic circuitry driving organ regeneration.

COVID-19-related stressors exacerbate food insecurity and depressive symptoms among graduate students receiving campus basic needs services: Cross-sectional findings from seven California public universities

Prior to the COVID-19 pandemic, food insecurity and depression were growing public health concerns among graduate students. Yet, little is known about how COVID-19-related stressors exacerbated these health outcomes among graduate students. To address this research gap, this study examined two types of COVID-19-related stressors, anticipated concerns about remote learning and challenges interfering with academic and research responsibilities, in relation to food insecurity and depressive symptoms among public university graduate students. Between August and October 2020, 631 graduate students who utilised basic needs services from seven University of California campuses completed an online survey assessing the effects of COVID-19 on their academic experiences, mental health, and basic needs security. Regression analyses examined associations of COVID-19-related concerns and COVID-19-related challenges with food insecurity as well as COVID-19-related concerns and COVID-19-related challenges in relation to depressive symptoms. All four models were adjusted for age, sex, race and ethnicity, campus affiliation, and living with a partner. Models examining food security status as the dependent variable were adjusted for depressive symptoms and vice versa. Graduate students concerned about delayed graduation, post-graduate employment, isolation from faculty and not having access to healthcare reported higher counts of depressive symptoms. Challenges associated with higher counts of depressive symptoms included caring for family more than usual, spending more time on errands and not paying for utilities in full. Students concerned about accessing healthcare had higher odds of experiencing food insecurity. Challenges associated with food insecurity included spending more time on errands, being unable to afford housing and sending money to family members during the pandemic. Our findings illuminate the pandemic's deleterious consequences on graduate students' mental health and food security, underscoring the need for strong academic and basic needs programs and policies.

The reference genome assembly of the bright cobblestone lichen, Acarospora socialis

Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.

A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta

The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 109 scaffolds spanning 443 mega base (Mb) pairs, with a contig N50 of 14.6 Mb, a scaffold N50 of 15.2 Mb, and BUSCO complete score of 98.9%. In combination with the forthcoming A. californica reference genome, the B. philenor hirsuta genome will be a powerful tool for documenting landscape genomic diversity and plant-insect co-evolution in a rapidly changing California landscape.

Targeted Reversible Covalent Modification of a Noncatalytic Lysine of the Krev Interaction Trapped 1 Protein Enables Site-Directed Screening for Protein-Protein Interaction Inhibitors

The covalent reversible modification of proteins is a validated strategy for the development of probes and candidate therapeutics. However, the covalent reversible targeting of noncatalytic lysines is particularly challenging. Herein, we characterize the 2-hydroxy-1-naphthaldehyde (HNA) fragment as a targeted covalent reversible ligand of a noncatalytic lysine (Lys720) of the Krev interaction trapped 1 (KRIT1) protein. We show that the interaction of HNA with KRIT1 is highly specific, results in prolonged residence time of >8 h, and inhibits the Heart of glass 1 (HEG1)-KRIT1 protein-protein interaction (PPI). Screening of HNA derivatives identified analogs exhibiting similar binding modes as the parent fragment but faster target engagement and stronger inhibition activity. These results demonstrate that HNA is an efficient site-directing fragment with promise in developing HEG1-KRIT1 PPI inhibitors. Further, the aldimine chemistry, when coupled with templating effects that promote proximity, can produce a long-lasting reversible covalent modification of noncatalytic lysines.

Ocular Surface Regeneration by Limbal Stem Cells Therapies: State of the Art, Challenges, and Perspectives

Limbal stem cells (LSCs) are adult stem cells located at the limbus ensuring the continuous renewal of the corneal epithelium, critical to maintain an optimal visual function. Damages to the LSCs or their niche microenvironment lead to limbal stem cell deficiency (LSCD), a potentially blinding disease. Transplantation of LSCs as a treatment for severe to total LSCD has gained popularity since 1980s, owing to the clinical success of the first direct limbal autograft transplantation. Recent advances in the understanding of the LSCs' molecular identity and regulation have enabled preclinical and clinical advancements of promising LSCs therapies. However, lack of standardization of the diagnostic methods, staging of the disease severity, manufacturing process, and clinical outcome measures have hindered the advancement of the therapy. To move these therapies to the clinic, optimization and standardization of the diagnostic strategy, cell product manufacturing, and assessment of clinical efficacy with potency assays are key points to the development of customized therapies. Recent findings suggest that residual LSCs exist in eyes presenting with clinical signs of total LSCD, which opens new therapeutic strategies for eyes with partial LSCD. Prospective, randomized, multicentric controlled clinical trials are necessary to determine the efficacy of different LSCs therapies for different stages of LSCD using a set of standardized outcome measures.

Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations

Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 data sets do not fit this mold. There are currently over 14 million sequenced SARS-CoV-2 genomes in online databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an "online" approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between likelihood and parsimony approaches to phylogenetic inference. Maximum likelihood (ML) and pseudo-ML methods may be more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare because each internal branch is expected to be extremely short. Therefore, it may be that approaches based on maximum parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger data sets. Here, we evaluate the performance of de novo and online phylogenetic approaches, as well as ML, pseudo-ML, and MP frameworks for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimization with UShER and matOptimize produces equivalent SARS-CoV-2 phylogenies to some of the most popular ML and pseudo-ML inference tools. MP optimization with UShER and matOptimize is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo inference. Our results therefore suggest that parsimony-based methods like UShER and matOptimize represent an accurate and more practical alternative to established ML implementations for large SARS-CoV-2 phylogenies and could be successfully applied to other similar data sets with particularly dense sampling and short branch lengths.

The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth

The maize ligule is an epidermis-derived structure that arises from the preligule band (PLB) at a boundary between the blade and sheath. A hinge-like auricle also develops immediately distal to the ligule and contributes to blade angle. Here, we characterize the stages of PLB and early ligule development in terms of topography, cell area, division orientation, cell wall rigidity and auxin response dynamics. Differential thickening of epidermal cells and localized periclinal divisions contributed to the formation of a ridge within the PLB, which ultimately produces the ligule fringe. Patterns in cell wall rigidity were consistent with the subdivision of the PLB into two regions along a distinct line positioned at the nascent ridge. The proximal region produces the ligule, while the distal region contributes to one epidermal face of the auricles. Although the auxin transporter PIN1 accumulated in the PLB, observed differential auxin transcriptional response did not underlie the partitioning of the PLB. Our data demonstrate that two zones with contrasting cellular properties, the preligule and preauricle, are specified within the ligular region before ligule outgrowth.

Consequences and Control of Multiscale Order/Disorder in Chiral Magnetic Textures

Transition metal intercalated transition metal dichalcogenides (TMDs) are promising platforms for next-generation spintronic devices based on their wide range of electronic and magnetic phases, which can be tuned by varying the host lattice or intercalant's identity, stoichiometry, or spatial order. Some of these compounds host a chiral magnetic phase in which the helical winding of magnetic moments propagates along a high-symmetry crystalline axis. Previous studies have demonstrated that variation in intercalant concentrations can have a dramatic effect on the formation of chiral domains and ensemble magnetic properties. However, a systematic and comprehensive study of how atomic-scale order and disorder impact these chiral magnetic textures is so far lacking. Here, we leverage a combination of imaging modes in the (scanning) transmission electron microscope (S/TEM) to directly probe (dis)order across multiple length scales and show how subtle changes in the atomic lattice can tune the mesoscale spin textures and bulk magnetic response in Cr1/3NbS2, with direct implications for the fundamental understanding and technological implementation of such compounds.

Development and Validation of a Prediction Model for Incident Hypothyroidism in a National Chronic Kidney Disease Cohort

CONTEXT

Hypothyroidism is a common yet under-recognized condition in patients with chronic kidney disease (CKD), which may lead to end-organ complications if left untreated.

OBJECTIVE

We developed a prediction tool to identify CKD patients at risk for incident hypothyroidism.

METHODS

Among 15 642 patients with stages 4 to 5 CKD without evidence of pre-existing thyroid disease, we developed and validated a risk prediction tool for the development of incident hypothyroidism (defined as thyrotropin [TSH] > 5.0 mIU/L) using the Optum Labs Data Warehouse, which contains de-identified administrative claims, including medical and pharmacy claims and enrollment records for commercial and Medicare Advantage enrollees as well as electronic health record data. Patients were divided into a two-thirds development set and a one-third validation set. Prediction models were developed using Cox models to estimate probability of incident hypothyroidism.

RESULTS

There were 1650 (11%) cases of incident hypothyroidism during a median follow-up of 3.4 years. Characteristics associated with hypothyroidism included older age, White race, higher body mass index, low serum albumin, higher baseline TSH, hypertension, congestive heart failure, exposure to iodinated contrast via angiogram or computed tomography scan, and amiodarone use. Model discrimination was good with similar C-statistics in the development and validation datasets: 0.77 (95% CI 0.75-0.78) and 0.76 (95% CI 0.74-0.78), respectively. Model goodness-of-fit tests showed adequate fit in the overall cohort (P = .47) as well as in a subcohort of patients with stage 5 CKD (P = .33).

CONCLUSION

In a national cohort of CKD patients, we developed a clinical prediction tool identifying those at risk for incident hypothyroidism to inform prioritized screening, monitoring, and treatment in this population.

Demystification and feasibility of CRISPR technology and gene editing in African laboratories

Clustered regularly interspaced short palindromic repeats, or CRISPR, is a powerful molecular biology tool that is enabling high-quality genetic research and engineering. However, for practical reasons, but more specifically because of the lack of training and the rapid development of gene-editing technology, the technique is still not well established in African laboratories. For this reason, a consortium formed by the Institut Pasteur of Tunis and Learn and Win decided to organise an international conference and workshop on CRISPR technology in particular and gene editing in general, focusing on the low-budget model more appropriate to the African context. From 12 to 17 June 2023, more than 200 interdisciplinary researchers and students from the life sciences and more than 20 international speakers and trainers gathered at the Institut Pasteur in Tunis, Tunisia, for the First African Conference and Workshop on CRISPR to discuss the latest gene editing technologies and discoveries. This Meeting Review describes the scientific event and highlights the main outcomes of both the conferences and the practical sessions. The symposium was a real success and thrives to educate, train and network international and young scientists in the field of gene editing and gene engineering.

Metabolite Stability in Archived Neonatal Dried Blood Spots Used for Epidemiologic Research

Epidemiologic studies of low-frequency exposures or outcomes using metabolomics analyses of neonatal dried blood spots (DBS) often require assembly of samples with substantial differences in duration of storage. Independent assessment of stability of metabolites in archived DBS will enable improved design and interpretation of epidemiologic research utilizing DBS. Neonatal DBS routinely collected and stored as part of the California Genetic Disease Screening Program between 1983 and 2011 were used. The study population included 899 children without cancer before age 6 years, born in California. High-resolution metabolomics with liquid-chromatography mass spectrometry was performed, and the relative ion intensities of common metabolites and selected xenobiotic metabolites of nicotine (cotinine and hydroxycotinine) were evaluated. In total, we detected 26,235 mass spectral features across 2 separate chromatography methods (C18 hydrophobic reversed-phase chromatography and hydrophilic-interaction liquid chromatography). For most of the 39 metabolites related to nutrition and health status, we found no statistically significant annual trends across the years of storage. Nicotine metabolites were captured in the DBS with relatively stable intensities. This study supports the usefulness of DBS stored long-term for epidemiologic studies of the metabolome. -Omics-based information gained from DBS may also provide a valuable tool for assessing prenatal environmental exposures in child health research.

Actin and CDC-42 contribute to nuclear migration through constricted spaces in C. elegans

Successful nuclear migration through constricted spaces between cells or in the extracellular matrix relies on the ability of the nucleus to deform. Little is known about how this takes place in vivo. We have studied confined nuclear migration in Caenorhabditis elegans larval P cells, which is mediated by the LINC complex to pull nuclei towards the minus ends of microtubules. Null mutations of the LINC component unc-84 lead to a temperature-dependent phenotype, suggesting a parallel pathway for P-cell nuclear migration. A forward genetic screen for enhancers of unc-84 identified cgef-1 (CDC-42 guanine nucleotide exchange factor). Knockdown of CDC-42 in the absence of the LINC complex led to a P-cell nuclear migration defect. Expression of constitutively active CDC-42 partially rescued nuclear migration in cgef-1; unc-84 double mutants, suggesting that CDC-42 functions downstream of CGEF-1. The Arp2/3 complex and non-muscle myosin II (NMY-2) were also found to function parallel to the LINC pathway. In our model, CGEF-1 activates CDC-42, which induces actin polymerization through the Arp2/3 complex to deform the nucleus during nuclear migration, and NMY-2 helps to push the nucleus through confined spaces.

Impact of SARS-CoV-2 Infection on the Association Between Laboratory Tests and Severe Outcomes Among Hospitalized Children

Background

To assist clinicians with identifying children at risk of severe outcomes, we assessed the association between laboratory findings and severe outcomes among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected children and determined if SARS-CoV-2 test result status modified the associations.

Methods

We conducted a cross-sectional analysis of participants tested for SARS-CoV-2 infection in 41 pediatric emergency departments in 10 countries. Participants were hospitalized, had laboratory testing performed, and completed 14-day follow-up. The primary objective was to assess the associations between laboratory findings and severe outcomes. The secondary objective was to determine if the SARS-CoV-2 test result modified the associations.

Results

We included 1817 participants; 522 (28.7%) SARS-CoV-2 test-positive and 1295 (71.3%) test-negative. Seventy-five (14.4%) test-positive and 174 (13.4%) test-negative children experienced severe outcomes. In regression analysis, we found that among SARS-CoV-2-positive children, procalcitonin ≥0.5 ng/mL (adjusted odds ratio [aOR], 9.14; 95% CI, 2.90-28.80), ferritin >500 ng/mL (aOR, 7.95; 95% CI, 1.89-33.44), D-dimer ≥1500 ng/mL (aOR, 4.57; 95% CI, 1.12-18.68), serum glucose ≥120 mg/dL (aOR, 2.01; 95% CI, 1.06-3.81), lymphocyte count <1.0 × 109/L (aOR, 3.21; 95% CI, 1.34-7.69), and platelet count <150 × 109/L (aOR, 2.82; 95% CI, 1.31-6.07) were associated with severe outcomes. Evaluation of the interaction term revealed that a positive SARS-CoV-2 result increased the associations with severe outcomes for elevated procalcitonin, C-reactive protein (CRP), D-dimer, and for reduced lymphocyte and platelet counts.

Conclusions

Specific laboratory parameters are associated with severe outcomes in SARS-CoV-2-infected children, and elevated serum procalcitonin, CRP, and D-dimer and low absolute lymphocyte and platelet counts were more strongly associated with severe outcomes in children testing positive compared with those testing negative.

The determination of optimum segmentation parameters using genetic algorithms: Application to different segmentation algorithms and transmission electron microscopy tomography reconstructed volumes

A method for optimizing an automatic selection of values for parameters that feed segmentation algorithms is proposed. Evolutionary optimization techniques in combination with a fitness function based on a mutual information parameter have been used to find the optimal parameter values of region growing, fuzzy c-means and graph cut segmentation algorithms. To validate the method, the segmentation of two transmission electron microscopy tomography reconstructed volumes of a carbon black-reinforced rubber and a polylactic acid and clay nanocomposite is carried out (i) using evolutionary optimization techniques and (ii) manually by experts. The results confirm that the use of evolutionary optimization techniques, such as genetic algorithms, reduces the computational operation cost needed for a total grid search of segmentation parameters, reducing the probability of reaching a false optimum, and improving the segmentation quality. HIGHLIGHTS: A new approach to optimize 3D segmentation algorithms. Methodology to optimize segmentation parameters and improve segmentation quality. Improvement on the results when using region growing, fuzzy c-means and graph cuts algorithms.

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.

A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri)

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.

Mechanical force regulates Sox9 expression at the developing enthesis

Entheses transmit force from tendons and ligaments to the skeleton. Regional organization of enthesis extracellular matrix (ECM) generates differences in stiffness required for force transmission. Two key transcription factors co-expressed in entheseal tenocytes, scleraxis (Scx) and Sox9, directly control production of enthesis ECM components. Formation of embryonic craniofacial entheses in zebrafish coincides with onset of jaw movements, possibly in response to the force of muscle contraction. We show dynamic changes in scxa and sox9a mRNA levels in subsets of entheseal tenocytes that correlate with their roles in force transmission. We also show that transcription of a direct target of Scxa, Col1a, in enthesis ECM is regulated by the ratio of scxa to sox9a expression. Eliminating muscle contraction by paralyzing embryos during early stages of musculoskeletal differentiation alters relative levels of scxa and sox9a in entheses, primarily owing to increased sox9a expression. Force-dependent TGF-β (TGFβ) signaling is required to maintain this balance of scxa and sox9a expression. Thus, force from muscle contraction helps establish a balance of transcription factor expression that controls specialized ECM organization at the tendon enthesis and its ability to transmit force.

Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae

Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.

In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment

Individuals with cystic fibrosis (CF) are susceptible to chronic lung infections that lead to inflammation and irreversible lung damage. While most respiratory infections that occur in CF are caused by bacteria, some are dominated by fungi such as the slow-growing black yeast Exophiala dermatitidis. Here, we analyze isolates of E. dermatitidis cultured from two samples, collected from a single subject 2 years apart. One isolate genome was sequenced using long-read Nanopore technology as an in-population reference to use in comparative single nucleotide polymorphism and insertion-deletion variant analyses of 23 isolates. We then used population genomics and phylo-genomics to compare the isolates to each other as well as the reference genome strain E. dermatitidis NIH/UT8656. Within the CF lung population, three E. dermatitidis clades were detected, each with varying mutation rates. Overall, the isolates were highly similar suggesting that they were recently diverged. All isolates were MAT 1-1, which was consistent with their high relatedness and the absence of evidence for mating or recombination between isolates. Phylogenetic analysis grouped sets of isolates into clades that contained isolates from both early and late time points indicating there are multiple persistent lineages. Functional assessment of variants unique to each clade identified alleles in genes that encode transporters, cytochrome P450 oxidoreductases, iron acquisition, and DNA repair processes. Consistent with the genomic heterogeneity, isolates showed some stable phenotype heterogeneity in melanin production, subtle differences in antifungal minimum inhibitory concentrations, and growth on different substrates. The persistent population heterogeneity identified in lung-derived isolates is an important factor to consider in the study of chronic fungal infections, and the analysis of changes in fungal pathogens over time may provide important insights into the physiology of black yeasts and other slow-growing fungi in vivo.

Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation

The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].

Biomechanical Phenotyping of Chronic Low Back Pain: Protocol for BACPAC

OBJECTIVE

Biomechanics represents the common final output through which all biopsychosocial constructs of back pain must pass, making it a rich target for phenotyping. To exploit this feature, several sites within the NIH Back Pain Consortium (BACPAC) have developed biomechanics measurement and phenotyping tools. The overall aims of this article were to: 1) provide a narrative review of biomechanics as a phenotyping tool; 2) describe the diverse array of tools and outcome measures that exist within BACPAC; and 3) highlight how leveraging these technologies with the other data collected within BACPAC could elucidate the relationship between biomechanics and other metrics used to characterize low back pain (LBP).

METHODS

The narrative review highlights how biomechanical outcomes can discriminate between those with and without LBP, as well as among levels of severity of LBP. It also addresses how biomechanical outcomes track with functional improvements in LBP. Additionally, we present the clinical use case for biomechanical outcome measures that can be met via emerging technologies.

RESULTS

To answer the need for measuring biomechanical performance, our "Results" section describes the spectrum of technologies that have been developed and are being used within BACPAC.

CONCLUSION AND FUTURE DIRECTIONS

The outcome measures collected by these technologies will be an integral part of longitudinal and cross-sectional studies conducted in BACPAC. Linking these measures with other biopsychosocial data collected within BACPAC increases our potential to use biomechanics as a tool for understanding the mechanisms of LBP, phenotyping unique LBP subgroups, and matching these individuals with an appropriate treatment paradigm.

Deformation Rate-Adaptive Conducting Polymers and Composites

Materials are more easily damaged during accidents that involve rapid deformation. Here, a design strategy is described for electronic materials comprised of conducting polymers that defies this orthodox property, making their extensibility and toughness dynamically adaptive to deformation rates. This counterintuitive property is achieved through a morphology of interconnected nanoscopic core-shell micelles, where the chemical interactions are stronger within the shells than the cores. As a result, the interlinked shells retain material integrity under strain, while the rate of dissociation of the cores controls the extent of micelle elongation, which is a process that adapts to deformation rates. A prototype based on polyaniline shows a 7.5-fold increase in ultimate elongation and a 163-fold increase in toughness when deformed at increasing rates from 2.5 to 10 000% min-1 . This concept can be generalized to other conducting polymers and highly conductive composites to create "self-protective" soft electronic materials with enhanced durability under dynamic movement or deformation.

Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA

Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.

Optogenetic control of Wnt signaling models cell-intrinsic embryogenic patterning using 2D human pluripotent stem cell culture

In embryonic stem cell (ESC) models for early development, spatially and temporally varying patterns of signaling and cell types emerge spontaneously. However, mechanistic insight into this dynamic self-organization is limited by a lack of methods for spatiotemporal control of signaling, and the relevance of signal dynamics and cell-to-cell variability to pattern emergence remains unknown. Here, we combine optogenetic stimulation, imaging and transcriptomic approaches to study self-organization of human ESCs (hESC) in two-dimensional (2D) culture. Morphogen dynamics were controlled via optogenetic activation of canonical Wnt/β-catenin signaling (optoWnt), which drove broad transcriptional changes and mesendoderm differentiation at high efficiency (>99% cells). When activated within cell subpopulations, optoWnt induced cell self-organization into distinct epithelial and mesenchymal domains, mediated by changes in cell migration, an epithelial to mesenchymal-like transition and TGFβ signaling. Furthermore, we demonstrate that such optogenetic control of cell subpopulations can be used to uncover signaling feedback mechanisms between neighboring cell types. These findings reveal that cell-to-cell variability in Wnt signaling is sufficient to generate tissue-scale patterning and establish a hESC model system for investigating feedback mechanisms relevant to early human embryogenesis.

Saccharomyces cerevisiae DNA polymerase IV overcomes Rad51 inhibition of DNA polymerase δ in Rad52-mediated direct-repeat recombination

Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat recombination. Our results reveal that the requirement for Pol4 in repeat recombination was suppressed by the absence of Rad51, suggesting that Pol4 counteracts the Rad51 inhibition of Rad52-mediated repeat recombination events. Using purified proteins and model substrates, we reconstituted in vitro reactions emulating DNA synthesis during direct-repeat recombination and show that Rad51 directly inhibits Polδ DNA synthesis. Interestingly, although Pol4 was not capable of performing extensive DNA synthesis by itself, it aided Polδ in overcoming the DNA synthesis inhibition by Rad51. In addition, Pol4 dependency and stimulation of Polδ DNA synthesis in the presence of Rad51 occurred in reactions containing Rad52 and RPA where DNA strand-annealing was necessary. Mechanistically, yeast Pol4 displaces Rad51 from ssDNA independent of DNA synthesis. Together our in vitro and in vivo data suggest that Rad51 suppresses Rad52-dependent/Rad51-independent direct-repeat recombination by binding to the primer-template and that Rad51 removal by Pol4 is critical for strand-annealing dependent DNA synthesis.