bluuebunny/crossref_metadata_2025 huggingface dataset:
Annotating regulatory elements by heterogeneous network embedding
Authors: Lu Yurun , Feng Zhanying , Zhang Songmao , Wang Yong
Published: March 2022

Motivation

Regulatory elements (REs), such as enhancers and promoters, are known as regulatory sequences functional in a heterogeneous regulatory network to control gene expression by recruiting transcription regulators and carrying genetic variants in a context specific way. Annotating those REs relies on costly and labor-intensive next-generation sequencing and RNA-guided editing technologies in many cellular contexts.

Results

We propose a systematic Gene Ontology Annotation method for Regulatory Elements (RE-GOA) by leveraging the powerful word embedding in natural language processing. We first assemble a heterogeneous network by integrating context specific regulations, protein–protein interactions and gene ontology (GO) terms. Then we perform network embedding and associate regulatory elements with GO terms by assessing their similarity in a low dimensional vector space. With three applications, we show that RE-GOA outperforms existing methods in annotating TFs’ binding sites from ChIP-seq data, in functional enrichment analysis of differentially accessible peaks from ATAC-seq data, and in revealing genetic correlation among phenotypes from their GWAS summary statistics data.

Availability and implementation

The source code and the systematic RE annotation for human and mouse are available at https://github.com/AMSSwanglab/RE-GOA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Effects of Confounding Bias in Coronavirus Disease 2019 (COVID-19) and Influenza Vaccine Effectiveness Test-Negative Designs Due to Correlated Influenza and COVID-19 Vaccination Behaviors
Authors: Doll Margaret K , Pettigrew Stacy M , Ma Julia , Verma Aman
Published: March 2022

Background

The test-negative design is commonly used to estimate influenza and coronavirus disease 2019 (COVID-19) vaccine effectiveness (VE). In these studies, correlated COVID-19 and influenza vaccine behaviors may introduce a confounding bias where controls are included with the other vaccine-preventable acute respiratory illness (ARI). We quantified the impact of this bias on VE estimates in studies where this bias is not addressed.

Methods

We simulated study populations under varying vaccination probabilities, COVID-19 VE, influenza VE, and proportions of controls included with the other vaccine-preventable ARI. Mean bias was calculated as the difference between estimated and true VE. Absolute mean bias in VE estimates was classified as low (<10%), moderate (10% to <20%), and high (≥20%).

Results

Where vaccination probabilities are positively correlated, COVID-19 and influenza VE test-negative studies with influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ARI controls, respectively, underestimate VE. For COVID-19 VE studies, mean bias was low for all scenarios where influenza represented ≤25% of controls. For influenza VE studies, mean bias was low for all scenarios where SARS-CoV-2 represented ≤10% of controls. Although bias was driven by the conditional probability of vaccination, low VE of the vaccine of interest and high VE of the confounding vaccine increase its magnitude.

Conclusions

Where a low percentage of controls is included with the other vaccine-preventable ARI, bias in COVID-19 and influenza VE estimates is low. However, influenza VE estimates are likely more susceptible to bias. Researchers should consider potential bias and its implications in their respective study settings to make informed methodological decisions in test-negative VE studies.
Menopause modulates the circulating metabolome: evidence from a prospective cohort study
Authors: Karppinen Jari E , Törmäkangas Timo , Kujala Urho M , Sipilä Sarianna , Laukkanen Jari , Aukee Pauliina , Kovanen Vuokko , Laakkonen Eija K
Published: March 2022

Aims

We studied the changes in the circulating metabolome and their relation to the menopausal hormonal shift in 17β-oestradiol and follicle-stimulating hormone levels among women transitioning from perimenopause to early postmenopause.

Methods and results

We analysed longitudinal data from 218 Finnish women, 35 of whom started menopausal hormone therapy during the study. The menopausal transition was monitored with menstrual diaries and serum hormone measurements. The median follow-up was 14 months (interquartile range: 8–20). Serum metabolites were quantified with targeted nuclear magnetic resonance metabolomics. The model results were adjusted for age, follow-up duration, education, lifestyle, and multiple comparisons. Menopause was associated with 85 metabolite measures. The concentration of apoB (0.17 standard deviation [SD], 99.5% confidence interval [CI] 0.03–0.31), very-low-density lipoprotein triglycerides (0.25 SD, CI 0.05–0.45) and particles (0.21 SD, CI 0.05–0.36), low-density lipoprotein (LDL) cholesterol (0.17 SD, CI 0.01–0.34) and particles (0.17 SD, CI 0.03–0.31), high-density lipoprotein (HDL) triglycerides (0.24 SD, CI 0.02–0.46), glycerol (0.32 SD, CI 0.07–0.58) and leucine increased (0.25 SD, CI 0.02–0.49). Citrate (−0.36 SD, CI −0.57 to −0.14) and 3-hydroxybutyrate concentrations decreased (−0.46 SD, CI −0.75 to −0.17). Most metabolite changes were associated with the menopausal hormonal shift. This explained 11% and 9% of the LDL cholesterol and particle concentration increase, respectively. Menopausal hormone therapy was associated with increased medium-to-large HDL particle count and decreased small-to-medium LDL particle and glycine concentration.

Conclusions

Menopause is associated with proatherogenic circulating metabolome alterations. Female sex hormones levels are connected to the alterations, highlighting their impact on women’s cardiovascular health.
Colletotrichum falcatum modulates the olfactory behavior of the sugarcane borer, favoring pathogen infection
Authors: Franco Flávia P , Túler Amanda C , Gallan Diego Z , Gonçalves Felipe G , Favaris Arodí P , Peñaflor Maria Fernanda G V , Leal Walter S , Moura Daniel S , Bento José Maurício S , Silva-Filho Marcio C
Published: March 2022

Some pathogens can manipulate their host plants and insects to optimize their fitness, increasing the attraction of insects to the infected plant in ways that facilitate pathogen acquisition. In tropical American sugarcane crops, the fungus Colletotrichum falcatum, the red rot causal agent, usually occurs in association with the sugarcane borer Diatraea saccharalis, resulting in large losses of this crop. Considering this association, we aimed to identify the effects of C. falcatum on D. saccharalis host preference and performance as well as the effect of this insect on C. falcatum sugarcane infection. Here, we show that the fungus C. falcatum modulates D. saccharalis behavior to its own benefit. More specifically, C. falcatum-infected sugarcane plants showed a dramatic increase in VOCs, luring D. saccharalis females to lay eggs on these plants. Therefore, sugarcane infection by the fungus C. falcatum increased in cooccurrence with insect herbivory, benefiting the pathogen when associated with D. saccharalis.
Using a theatre-based programme to prevent gender-based violence: evidence from Australia
Authors: Crisp Beth R , Taket Ann
Published: March 2022

Bystander interventions play an important contribution to efforts to prevent violence against women and arts-based interventions have been effective as part of a range of health promotion programmes. You the Man is a theatre-based programme, which contributes to violence prevention efforts in community settings. Requiring a single actor and minimal props, the programme consists of a 30–35 min play about intimate partner violence and sexual assault followed by a moderated post-performance panel discussion including staff from local support agencies. Although it has received positive feedback in a range of settings, the only previously published evaluation involved establishing short and long-term impacts on American high school students. This article examines the short-term impacts from attending You the Man events on a different audience, i.e. Australian adults. Anonymous online surveys conducted prior and 4 weeks after events were completed by 41 participants of whom 29 were female and 12 were male, three-quarters of whom were aged between 18 and 49, and who attended events at university campuses (46.3%), in workplaces (34.1%), at sporting clubs (12.2%) and community centres (7.3%). At follow up, participants regarded the severity of abusive and coercive behaviours as being higher than at baseline, their capacity to intervene as a bystander had increased, as had the number of sources of support they would recommend to someone experiencing gender-based violence. Hence, theatre-based programmes can positively affect attitudes in relation to gender-based violence, increase bystander knowledge about safe ways to intervene and positively affect intended bystander intervention.
Undertaking graphic facilitation to enable participation in health promotion interventions in disadvantaged neighbourhoods in Denmark
Authors: Sandholdt Catharina Thiel , Srivarathan Abirami , Kristiansen Maria , Malling Gritt Marie Hviid , Olesen Kathrine Vingum Møller , Jeppesen Mette , Lund Rikke
Published: March 2022

This study reports on a health promotion intervention (HPI), where graphic facilitation (GF) was used as an innovative method to enable participation in a co-design process in a multi-ethnic and disadvantaged neighbourhood in Denmark. The aim was to enable middle-aged and older residents to participate in the research process of planning and evaluating the HPI, as well as in the activities it constituted. GF was used to document statements and inputs from residents through visual meeting minutes and resident experiences with coronavirus disease 2019 (COVID-19) lockdown were drawn by a graphic facilitator. We use the ladder of participation as a framework to unfold the participation enabled by GF. During the HPI, data were produced through ethnographic field studies in and outside the neighbourhood and in design workshops with residents. The study finds that GF helped in reaching a target group difficult to engage in research and that the engagement of a graphic facilitator shifted the power-balance between the researchers and the residents, redistributing expertise. Carrying out GF in a HPI is a collaborative endeavour and in addition to research competences, it requires the artistic and relational skills of a graphic facilitator. The co-created process of the visual minutes and COVID-19 experiences created a sense of ownership and encouraged the residents to reflect on their interaction with the researchers. The redistribution of expertise was conditioned by the power dynamics present and GF helped unfold these dynamics. This is especially important in an HPI engaging socio-economically vulnerable populations.
Natural and anthropogenic drivers of escaped farmed salmon occurrence and introgression into wild Norwegian Atlantic salmon populations
Authors: Diserud O H , Fiske P , Karlsson S , Glover K A , Næsje T , Aronsen T , Bakke G , Barlaup B T , Erkinaro J , Florø-Larsen B , Foldvik A , Heino M , Kanstad-Hanssen Ø , Lo H , Lund R A , Muladal R , Niemelä E , Økland F , Østborg G M , Otterå H , Skaala Ø , Skoglund H , Solberg I , Solberg M F , Sollien V P , Sægrov H , Urdal K , Wennevik V , Hindar K
Published: March 2022

Marine aquaculture of Atlantic salmon (Salmo salar) is a relatively new industry where breeding programs have led to rapid genetic change in the captive populations that were built up alongside conspecific wild individuals. Throughout its 50-years history, marine aquaculture of Atlantic salmon has been associated with escapes, and studies have shown that escapees may enter rivers, spawn successfully, and this may lead to farmed-to-wild genetic introgression and maladaptation in wild populations. Yet, an open question is what factors can best explain the variability in the proportion of farmed escapees in wild populations, and when present, which additional factors lead to introgression. Here, we combine two large-scale data sets from monitoring escaped farmed salmon and introgression in Norwegian rivers between 2006 and 2018 to model how anthropogenic, environmental, and population factors influence proportion of escapees and level of introgression. We found that increasing farming intensity and river discharge increase the expected proportions of escaped farmed salmon in rivers, whereas a larger wild salmon population size reduces the expected proportion of escapees despite increasing the expected absolute numbers of escaped farmed salmon. On a large scale, introgression is primarily a function of proportions of escaped farmed salmon, and only to a minor extent a function of local environmental factors or salmon population characteristics. This suggests that as long as salmon aquaculture is based on technologies where non-sterile fish can escape, all anadromous wild Atlantic salmon populations are at risk. Large marine protected areas without salmon aquaculture may slow down the rate of intrusion and introgression by increasing the distance between intensive aquaculture and wild populations.
Constructing Equality in EU Asylum Law
Authors: Salomon Stefan
Published: March 2022

The view that subsidiary protection status is a lesser form of protection than refugee status is widespread among European Union (EU) Member States’ asylum authorities and courts. This view is based on the assumption that the protection needs of beneficiaries of subsidiary protection are of shorter duration than those of refugees. Based on this assumption, several EU Member States have curtailed the rights of beneficiaries of subsidiary protection and national courts have upheld these restrictions. This article argues that the assumption of a shorter duration of subsidiary protection, and therefore lesser protection needs, is empirically unfounded and normatively untenable. The assumption is based on the premise that the principal circumstances justifying subsidiary protection – poor security situations or armed conflicts – are temporary in nature. Contrary to tendencies in EU Member States, it is argued that the development of EU asylum law points towards the creation of a uniform status of protection that entails the same rights for refugees and beneficiaries of subsidiary protection. Why, then, does the assumption of the temporary nature of subsidiary protection persist? This article posits that the persistence of the assumption of the temporary nature of subsidiary protection derives from a more profound perception in international legal thought of wartime as exceptional and of short duration.
ICLAS LAQ Network for the Promotion of Animal Quality in Research
Authors: Vergara Patri , Ballard Gregory , Besch-Williford Cynthia , Hayashimoto Nobuhito , Pekow Cynthia , Perez Ana , Schmidt Katja , Shek William , Toft Martin , Yoshiki Atsushi
Published: March 2022

ICLAS Laboratory Animal Quality Network (LAQN) programs currently consist of the Performance Evaluation Program (PEP), which focuses on microbial monitoring by and for laboratory animal diagnostic laboratories, and the Genetic Reference Monitoring Program (GENRef), which provides assay-ready reference DNA for genetic testing of mouse strains. Since 2008, PEP has grown to become a truly international program with participating laboratories in 5 continents. Launched in 2016, GENRef currently distributes DNA from 12 common inbred mouse strains for use in genetic monitoring of locally inbred colonies as well as for genetic testing of stocks, particularly genetically engineered stocks, of uncertain origins. GENRef has the capacity to include additional strains as well as additional species. PEP and GENRef provide the reagents at cost, as a resource to the international scientific community, in the interest of improving research quality in an environment of growing concern for research quality, rigor, and reproducibility.
Comparing medical history data derived from electronic health records and survey answers in the All of Us Research Program
Authors: Sulieman Lina , Cronin Robert M , Carroll Robert J , Natarajan Karthik , Marginean Kayla , Mapes Brandy , Roden Dan , Harris Paul , Ramirez Andrea
Published: March 2022

Objective

A participant’s medical history is important in clinical research and can be captured from electronic health records (EHRs) and self-reported surveys. Both can be incomplete, EHR due to documentation gaps or lack of interoperability and surveys due to recall bias or limited health literacy. This analysis compares medical history collected in the All of Us Research Program through both surveys and EHRs.

Materials and Methods

The All of Us medical history survey includes self-report questionnaire that asks about diagnoses to over 150 medical conditions organized into 12 disease categories. In each category, we identified the 3 most and least frequent self-reported diagnoses and retrieved their analogues from EHRs. We calculated agreement scores and extracted participant demographic characteristics for each comparison set.

Results

The 4th All of Us dataset release includes data from 314 994 participants; 28.3% of whom completed medical history surveys, and 65.5% of whom had EHR data. Hearing and vision category within the survey had the highest number of responses, but the second lowest positive agreement with the EHR (0.21). The Infectious disease category had the lowest positive agreement (0.12). Cancer conditions had the highest positive agreement (0.45) between the 2 data sources.

Discussion and Conclusion

Our study quantified the agreement of medical history between 2 sources—EHRs and self-reported surveys. Conditions that are usually undocumented in EHRs had low agreement scores, demonstrating that survey data can supplement EHR data. Disagreement between EHR and survey can help identify possible missing records and guide researchers to adjust for biases.
PCM1-JAK2Fusion Tyrosine Kinase Gene-Related Neoplasia: A Systematic Review of the Clinical Literature
Authors: Kaplan Henry G , Jin Ruyun , Bifulco Carlo B , Scanlan James M , Corwin David R
Published: March 2022

Background

This review summarizes the case studies of PCM1-JAK2 fusion tyrosine kinase gene-related neoplasia. Recommended treatment includes JAK2 inhibitors and hematologic stem cell transplantation (HSCT), although the small number of patients has limited study of their efficacy. Herein, we present all available cases in the current searchable literature with their demographics, diagnoses, treatments, and outcomes.

Methods

PubMed, ScienceDirect, Publons, the Cochrane Library, and Google were searched with the following terms: PCM1-JAK2, ruxolitinib and myeloid/lymphoid.

Results

Sixty-six patients (mean age = 50, 77% male) had an initial diagnosis of myeloproliferative neoplasm (MPN) in 40, acute leukemia in 21 and T-cell cutaneous lymphoma in 5. Thirty-five patients (53%) had completed 5-year follow-up. The 5-year survival for the MPN, acute myelogenous leukemia (AML), acute lymphocytic leukemia, and lymphoma groups are 62.7, 14.9%, 40.0%, and 100%, respectively. Too few patients have been treated with ruxolitinib to draw conclusions regarding its effect on survival while the 5-year survival for MPN patients with or without HSCT was 80.2% (40.3%-94.8%) versus 51.5% (22.3%-74.6%), respectively. The T-cell cutaneous lymphoma patients have all survived at least 7 years.

Conclusion

This rare condition may be increasingly detected with wider use of genomics. Ruxolitinib can yield hematologic and molecular remissions. However, HSCT is, at this time, the only potentially curative treatment. Useful prognostic markers are needed to determine appropriate timing for HSCT in patients with MPN. Patients presenting with acute leukemia have a poor prognosis.
Missing the Target
Authors: Roe Mark J.
Published: March 2022

Stock-market-driven short-termism is crippling the US economy, according to legal, judicial, and media thinking. Firms forgo the R&D they need, cut capital spending, and buy back their own stock so feverishly that they starve themselves of cash. The stock market is the primary cause: directors and managers cannot manage for the long-term when their shareholders furiously trade their companies’ stocks, they cannot invest enough when stockholders demand rising quarterly profits, they must slash R&D when investors demand that precious cash be used to buy back stock, and they cannot even strategize about the long-term when shareholder activists demand immediate results. The stock market’s short-termism is also blamed for environmental degradation, for contributing to global warming, and for employee mistreatment. This book shows, however, that the purported ills emanating from stock-market short-termism are either not shown, likely to minor, demonstrably false, or due to other pernicious economic causes. The social costs attributed to corporate short-termsim—environmental degradation, mistreatment of stakeholders, riaking climate catastrophe—emanate more from selfishness than from distorted time horizons, as we shall see. Moreover, public and policymaker obsession with stock-market short-termism as upsetting the economy and settled arrangements is explained more by dissatisfaction with the rapidity of technological change, the increasing uncertainty and instability of the workplace, and a dissatisfaction with overall economic arrangements. Lawmakers and pundits can readily miss more likely causes of the underlying issues—like how best to push forward US R&D—by mistakenly aiming at stock-market short-termism. After considering what the evidence tells us, we consider what political and social reasons could explain the issue’s prominence.
They Eat Our Sweat
Authors: Agbiboa Daniel E.
Published: March 2022

Most accounts of corruption in Africa and the Global South are generally overly simplistic and macro-oriented, and commonly disconnect everyday (petty) corruption from political (grand) corruption. Contrary to standard approaches, Daniel Agbiboa offers a fresh and engaging look at the corruption complex in Africa through a micro analysis of its informal transport sector, where collusion between state and nonstate actors is most rife. Focusing on Lagos, Nigeria’s commercial capital and Africa’s largest city, They Eat Our Sweat investigates the workaday world of road transport operators as refracted through the extortion racket and violence of transport unions in complicity with the state. Steeped in an embodied knowledge of Lagos and backed by two years of thorough ethnographic fieldwork, including working as an informal bus conductor, Agbiboa provides an emic perspective on precarious labor, popular agency, and the daily pursuit of survival under the shadow of the modern world system. Corruption, Agbiboa argues, is not rooted in Nigerian “culture” but is shaped by the struggle to get by and get ahead on the fast and slow lanes of Lagos. The pursuit of economic survival compels transport operators to participate in the reproduction of the very transgressive system they denounce. They Eat Our Sweat is not just a book about corruption but also about transportation, politics, and governance in urban Africa.
Generation of Arc-Like and OIB-Like Magmas Triggered by Slab Detachment in the Eastern Mexican Alkaline Province: Petrological Evidence from the Cenozoic Sierra de San Carlos-Cruillas Complex, Tamaulipas
Authors: Elizondo-Pacheco Luis Alejandro , Ramírez-Fernández Juan Alonso , De Ignacio Cristina , González-Guzmán Reneé , Rodríguez-Saavedra Pedro , Leal-Cuellar Víctor Alejandro , Velasco-Tapia Fernando , Montalvo-Arrieta Juan Carlos
Published: March 2022

The origin of the Eastern Mexican Alkaline Province has been explained by landward arc migration and subsequent asthenospheric upwelling after slab roll-back of the Farallon Plate. In this work, we present new petrographic, mineral chemical, geochemical, and geochronological data of the Sierra de San Carlos-Cruillas (SSCC), one of the most important complexes in the province. This information, together with published data, helped us to reinterpret the tectonic processes operating during the generation of this province, as well as the mantle sources involved in the partial melting process. Detailed geochemical analysis suggests the participation of two types of metasomatized mantle regions: a lithospheric source modified by past subduction processes and an asthenospheric source slightly affected by carbonatite-related metasomatism. Variations in the partial melting degrees controlled the extent of magma enrichment in the latter. Major and trace element geochemistry, together with geochronological data and field relations, evinced an older post-orogenic setting related to the arc-like rocks (Eocene) and a younger intraplate extensional environment associated with all enriched igneous rocks (Oligocene-Miocene). Bivariate diagrams of SiO2-trace element ratios and multi-element patterns indicate that magmas from the SSCC complex dominantly evolved through fractional crystallization with a limited crustal contribution. Petrographic and mineral chemistry features suggest that some of these magmas experienced open-system processes (e.g. recharge events) in a complex and dynamic magmatic feeding system. In contrast to the traditional petrotectonic model, we propound that the passage and subsequent foundering of the Hess conjugate under northeastern Mexico resulted in its eclogitization and triggered slab tearing and succeeding detachment. This latter process occasioned mantle upwelling and the partial melting of the two recognized metasomatized mantle sources, thus generating the San Carlos-Cruillas magmatism.
Distinct neural couplings to shared goal and action coordination in joint action: evidence based on fNIRS hyperscanning
Authors: Cheng Xiaojun , Guo Bing , Hu Yinying
Published: March 2022

Joint action is central to human nature, enabling individuals to coordinate in time and space to achieve a joint outcome. Such interaction typically involves two key elements: shared goal and action coordination. Yet, the substrates entrained to these two components in joint action remained unclear. In the current study, dyads performed two tasks involving both sharing goal and action coordination, i.e. complementary joint action and imitative joint action, a task only involving shared goal and a task only involving action coordination, while their brain activities were recorded by the functional near-infrared spectroscopy hyperscanning technique. The results showed that both complementary and imitative joint action (i.e. involving shared goal and action coordination) elicited better behavioral performance than the task only involving shared goal/action coordination. We observed that the interbrain synchronization (IBS) at the right inferior frontal cortex (IFC) entrained more to shared goal, while left-IFC IBS entrained more to action coordination. We also observed that the right-IFC IBS was greater during completing a complementary action than an imitative action. Our results suggest that IFC plays an important role in joint action, with distinct lateralization for the sub-components of joint action.
Women Who Break the Glass Ceiling Get a “Paper Cut”: Gender, Fame, and Media Sentiment
Authors: Shor Eran , van de Rijt Arnout , Kulkarni Vivek
Published: March 2022

Past quantitative studies have shown that most media coverage is of men. Here we ask if the scarce coverage that women get is qualitatively different from that of men. We use computer-coded sentiment scores for 14 million person names covered in 1,323 newspapers to investigate the three-way relationship between gender, fame, and sentiment. Additional large-scale data on occupational categories allow us to compare women and men within the same profession and rank. We propose that as women’s fame increases their media coverage becomes negative more quickly when compared to men (a “paper cut”), because their violation of gender hierarchies and social expectations about typical feminine behavior evokes disproportionate scrutiny. We find that while overall media coverage is much more positive for women than for men, this difference disappears and even reverses at higher levels of fame. In encyclopedic sentiment data we find no biographic basis for women’s disproportionate decline in media coverage sentiment at high fame, consistent with the conjectured double standard in media discourse.
Development and Implementation of a Novel Case-Based Gun Violence Prevention Training Program for First-Year Residents
Authors: Rickert Charles G. , Felopulos Gretchen , Shoults Benjamin , Hathi Sejal , Scott-Vernaglia Shannon E. , Currier Paul , Masiakos Peter T. , Sacks Chana A.
Published: March 2022

Problem

Gun violence results in approximately 40,000 deaths in the United States each year, yet physicians rarely discuss gun access and firearm safety with patients. Lack of education about how to have these conversations is an important barrier, particularly among trainees.

Approach

A 2-part training curriculum was developed for first-year residents. It included (1) a didactic presentation outlining a framework to understand types of firearm-related violence, describing institutional resources, and reviewing strategies for approaching discussions about firearms with patients, and (2) interactive case scenarios, adjusted for clinical disciplines, with standardized patients. Before and after the training, participants completed surveys on the training’s relevance, efficacy, and benefit. Standardized patients provided real-time feedback to participants and completed assessments based on prespecified learning objectives.

Outcomes

In June–August 2019, 148 first-year residents in internal medicine (n = 74), general surgery (n = 12), emergency medicine (n = 15), pediatrics (n = 22), psychiatry (n = 16), and OB/GYN (n = 9) completed the training. Most (70%, n = 104) reported having no prior exposure to gun violence prevention education. Knowledge about available resources increased among participants from 3% (n = 5) pretraining to 97% (n = 143) post-training. Awareness about relevant laws, such as Extreme Risk Protection Orders, and their appropriate use increased from 3% (n = 4) pretraining to 98% (n = 145) post-training. Comfort discussing access to guns and gun safety with patients increased from a median of 5 pretraining to 8 post-training (on a scale of 1–10, with higher scores indicating more comfort).

Next Steps

Delivery of a case-based gun violence prevention training program was effective and feasible in a single institution. Next steps include expanding the training to other learners (across undergraduate and graduate medical education) and institutions and assessing how the program changes practice over time.
A New Technique for Anterior Pelvic Ring Fixation Using a Minimally Invasive Approach
Authors: Qoreishy Mohamad , Alamian Aliasghar , Movahedinia Mohammad , Keyhani Sohrab
Published: March 2022

Introduction:

Percutaneous screw fixation have been introduced as a minimally invasive method in anterior pelvic ring fractures. The aim of the study is to present the outcomes of a new minimally invasive technique for fixation of anterior pelvic ring fractures medial to the pubic tubercle.

Materials and Methods:

Sixty-two patients were referred to our center during 5 years for the fixation of the anterior pelvic ring fracture under the new procedure. The fracture site was bridged using a 3-hole 3.5 mm reconstruction plate when 1 or 2 long retrograde screw was passed through the plate in the superior ramus.

Results:

A case of device failure was observed in the patient treated with the new method, which did not lead to loss of reduction and did not limit the patient’s activity. Apart from this, we did not have any abnormalities in the follow-up radiographs of the patients and no complications were reported.

Conclusion:

The results of this study showed the potential of our new method for fixation of various types of anterior pelvic ring injuries.

Level of Evidence:

Level IV.
Exercise Progression Protocol for Lung Transplant GO: A Multicomponent Telerehab Exercise Intervention for Patients After Lung Transplantation
Authors: Hergenroeder Andrea L. , Willey Bryan M. , Vendetti Melissa L. , DeVito Dabbs Annette
Published: March 2022

Lung transplantation is one of the fastest growing solid organ transplant procedures in the United States. After transplantation, lung function typically returns to near normal levels; however, reduced physical function and an inactive lifestyle compromise this benefit. To promote rehabilitation goals, lung transplant recipients (LTRs) are advised to participate in pulmonary rehab, but participation is low due to barriers related to scheduling, travel requirements, lack of insurance coverage, and the concern about exposure to infection. Telerehabilitation offers a flexible alternative with the potential to promote self-management of exercise in LTRs. The purpose of this report was to describe the exercise progression protocol for the Lung Transplant GO multicomponent telerehab exercise intervention for patients after lung transplantation. The progression protocol is an evidence-informed exercise protocol designed to improve physical function and physical activity in LTRs safely and effectively in a remote environment. The protocol standardizes the prescription of exercise while permitting adaptation of the program to meet the needs of the individual. Using this model, the decisions about program progression are systematic, transparent, and replicable to other LTRs.
Tissue Expander–associated T Cells: Relevance to Breast Implant–associated Anaplastic Large-cell Lymphoma
Authors: Shiokawa Ichiro , Sato Takuya , Ogawa Youichi , Nagasaka Yuka , Ishikawa Aoha , Shimada Shinji , Kawamura Tatsuyoshi , Momosawa Akira
Published: March 2022

Background:

The generation of breast implant–associated anaplastic large-cell lymphoma (BIA-ALCL) is closely associated with textured implants. The phenotype of BIA-ALCL cells is well examined, but its cell of origin remains unknown. Here we investigate what types of T cells are recruited and differentiated in the surrounding capsules and tissues as a consequence of continuous contact with a textured surface.

Methods:

Capsule and pericapsule tissues were recovered from patients who had textured or smooth tissue expanders (TEs). These samples were enzymatically digested, and T cells in the samples were analyzed using flow cytometry. Peripheral blood mononuclear cells from the same donors were utilized as a control.

Results:

Effector memory CD4+ T cells predominantly infiltrated capsules and tissues without apparent differences between textured and smooth TEs. In these effector memory CD4+ T cells, CD4+ resident memory T cells were generated by smooth TEs but not by textured TEs. However, TNFRSF8/CD30 mRNA expression is higher in the CD69− effector memory CD4+ T cells than in the CD69+ ones.

Conclusion:

Textured and smooth TEs differentially recruit and/or differentiate T cells in situ.
Challenges in Interpreting Obstetrics and Gynecology Literature
Authors: Bruno Ann M. , Blue Nathan R.
Published: March 2022

The field of obstetrics and gynecology is constantly replenished with the newest research findings. In an era of rapidly available study publications, there are a number of challenges to interpreting the obstetrics and gynecology literature. Common pitfalls include the over reliance on the dichotomized P-value, lack of transparency, bias in study reporting, limitations of resources, absence of standardized practices and outcomes in study design, and the rare concerns for data integrity. We review these predominant challenges and their potential solutions, in interpreting the obstetrics and gynecology literature.
LONG-TERM EFFICACY OF FLUOCINOLONE IN EYES WITH IRIS–LENS DIAPHRAGM DISRUPTION AND PCME WITH MEDICATION FIXED IN THE SCLERA (MEFISTO)
Authors: Herold Tina R. , Vounotrypidis Efstathios , Liegl Raffael , Koenig Susanna F. , Priglinger Siegfried G. , Wolf Armin
Published: March 2022

Purpose:

The aim of our prospective off-label, interventional clinical trial was to evaluate the efficacy and safety of the fluocinolone-loop-anchoring technique over two years in eyes with iris–lens diaphragm disruption and pseudophakic cystoid macular edema.

Methods:

In 10 eyes, scleral fixation of fluocinolone implant was performed. Main outcome measures were the development of best-corrected visual acuity (BCVA), central retinal thickness over 24 months, and general safety of the procedure.

Results:

A significant improvement to 0.57 ± 0.38 log MAR (Snellen 20/80) (range 0–1.30) was observed (P = 0.003) at 1 month. Further improvement to 0.45 ± 036 log MAR (Snellen 20/60) was observed until month 18 (P = 0.081). Mean central retinal thickness decreased by 22% from 601.6 ± 235.5 µm to 449.1 ± 128.9 µm at 1 month. In one patient, the implant has to be removed at Month 7 because of elevated intraocular pressure and one patient after globe rupture had a retinal redetachment at Month 4.

Conclusion:

In this study, we showed that the treatment of recalcitrant pseudophakic cystoid macular edema with scleral fixated fluocinolone implant in eyes with disruption of the iris–lens diaphragm provides good anatomical and functional results with a reasonable safety profile over 24 months in eyes where pseudophakic cystoid macular edema is otherwise difficult to treat and often left untreated.
OCT-Angiography Face Mask–Associated Artifacts During the COVID-19 Pandemic
Authors: El-Nimri Nevin W. , Micheletti Eleonora , Mohammadzadeh Vahid , Nishida Takashi , Kamalipour Alireza , Zangwill Linda M. , Bowd Christopher , Moghimi Sasan , Weinreb Robert N.
Published: March 2022

Précis:

Face mask wearing has no significant effects on artifacts or vessel density measurements in optic nerve head (ONH) and macular optical coherence tomography-angiography (OCT-A) scans.

Purpose:

The aim was to assess the difference in area of artifacts observed in optical OCT-A scans with and without face mask wear and to verify if mask wear interferes with OCT-A vessel density measurements.

Subjects and Controls:

A total of 64 eyes of 10 healthy subjects, 4 ocular hypertensive, 8 glaucoma suspects, and 17 glaucoma patients were included.

Materials and Methods:

High-density ONH and macula OCT-A scans were obtained in patients with and without surgical masks. Seven different artifacts (motion, decentration, defocus, shadow, segmentation failure, blink, and Z-offset) were quantitatively evaluated by 2 trained graders. The changes in the area (% of scan area) of artifacts, without and with mask wearing, and differences of vessel density were evaluated.

Results:

Trends of increasing motion artifact area for the ONH scans [4.23 (−0.52, 8.98) %, P=0.08] and defocus artifact area for the macular scans [1.06 (−0.14, 2.26) %, P=0.08] were found with face mask wear. However, there were no significant differences in the mean % area of any artifacts (P>0.05 for all). Further, the estimated mean difference in vessel density in images acquired without and with masks was not significant for any type of artifact.

Conclusion:

Face mask wearing had no significant effect on area of artifacts or vessel density measurements. OCT-A vessel density measurements can be acquired reliably with face mask wear during the pandemic.
SARS-CoV-2 IgG Seroprevalence Detected by Chemiluminescence Immunoassay Among Healthcare Personnel and Patients in a Province With a Low Incidence Rate of COVID-19 During the First Wave of COVID-19 in Thailand
Authors: Patamatamkul Samadhi , Rawangban Pratya , Prommongkol Bhurapol , Potongcamphan Maythinee
Published: March 2022

Background

There is limited evidence regarding seroprevalence during the first wave of COVID-19 in Thailand. The limited capacity of molecular laboratories in distant provinces may have resulted in fewer confirmed COVID-19 cases and possible undetected ongoing transmission, as suggested by a previously published seroprevalence study.

Objectives

This study aimed to assess the SARS-CoV-2 IgG and IgM seroprevalence among healthcare personnel and patients in Suddhavej Hospital and cross-reactivity of SARS-CoV-2 antibody assays with infectious and autoimmune diseases.

Methods

We conducted a cross-sectional study to determine seroprevalence among healthcare personnel and patients in Suddhavej Hospital, a secondary care hospital in Mahasarakham Province (population of 974,534 as of 2015). A chemiluminescence assay was used to test for IgG and/or IgM SARS-CoV-2 antibodies.

Results

The study included 112 healthcare personnel and 78 patients with a median age of 29 years (interquartile range, 25–40 years); 35.8% were male. The study found an IgG seroprevalence of 3 of 190 (1.6%; 95% confidence interval, 0.3%–4.5%). The 3 IgG-positive cases recalled possible exposure risk to COVID-19 infection outside the province. One case had a persistent elevated IgG level after 10 months of follow-up. No cross-reactivity was found among patients with a variety of infectious or immunologic diseases.

Conclusions

Our study suggests that there is a low seroprevalence among high-risk exposure groups. This evidence supports that the preventive measures used during the first wave of COVID-19 were effective in preventing asymptomatic transmission in a remote province with a low COVID-19 incidence rate.
Drug–drug–gene interaction risk among opioid users in the U.S. Department of Veterans Affairs
Authors: Chanfreau-Coffinier Catherine , Tuteja Sony , Hull Leland E. , MacDonald Sally , Efimova Olga , Bates Jill , Voora Deepak , Oslin David W. , DuVall Scott L. , Lynch Julie A.
Published: March 2022

Response to analgesic therapy is influenced by several factors including genetics and drug–drug interactions. Pharmacogenetic (PGx) variants in the CYP2D6 gene modify response to opioids by altering drug metabolism. We sought to determine the potential impact of PGx testing on the care of Veterans with noncancer pain prescribed opioids metabolized by CYP2D6 (codeine, hydrocodone, or tramadol). A retrospective analysis was performed within the Veterans Health Administration evaluating prescription records for pain medications metabolized by CYP2D6 and interacting drugs from 2012 to 2017. Among 2,436,654 Veterans Health Administration pharmacy users with at least 1 opioid prescription, 34% met the definition of chronic use (longer than 90 days with more than 10 prescriptions or 120 days-supply). Opioids were commonly coprescribed with antidepressants interacting with CYP2D6 (28%). An estimated 21.6% (n = 526,905) of these patients are at an elevated risk of an undesirable response to their opioid medication based on predicted phenotypes and drug–drug interactions: 3.5% are predicted CYP2D6 ultrarapid metabolizers and at increased risk for toxicity, 5.4% are poor metabolizers at higher risk for nonresponse, and 12.8% are normal or intermediate metabolizers coprescribed a CYP2D6 inhibitor leading to phenoconversion into poor metabolizer. Despite the high rate of coprescription of opioids and interacting drugs, CYP2D6 testing was infrequent in the sample (0.02%), and chart review suggests that test results were used to optimize antidepressant treatments rather than pain medications. Using PGx testing combined with consideration of phenoconversion may allow for an enhanced precision medicine approach to pain management in Veterans.
Stent Evaluation for Expiratory Central Airway Collapse
Authors: Majid Adnan , Ospina-Delgado Daniel , Ayala Alvaro , Gangadharan Sidhu P. , Alape Daniel , Buitrago Daniel , Parikh Mihir S. , Wilson Jennifer L. , Chee Alex C. , Fernandez-Bussy Sebastian , Herth Felix J.F. , Kheir Fayez
Published: March 2022

Background:

Careful selection of patients with expiratory central airway collapse (ECAC) that may benefit from tracheobronchoplasty (TBP) can be aided by a short-term airway stent evaluation. This can be performed with either silicone Y-stents (SYSs) or uncovered self-expanding metallic airway-stents (USEMAS). No direct comparison has been made between these 2 stent types.

Methods:

This was a small retrospective review of consecutive patients that underwent a stent evaluation. A propensity score was used to match patients in the USEMAS and SYS groups. Outcomes included complications, changes in the health-related quality-of-life (HR-QoL), and changes in exercise capacity. Baseline measurements were compared with those obtained during stent evaluation and after TBP.

Results:

Forty-two patients with severe ECAC underwent USEMAS placement, while 18 patients had an SYS placed. Propensity score matching resulted in 13 matched SYS and USEMAS pairs. The SYS group had an increased rate of mucus plugging (38.5% vs. 0%, P<0.047). Although not statically significant, a clinical improvement was observed in HR-QoL and exercise capacity in the USEMAS group during stent placement. In patients who underwent TBP, both USEMAS and SYS groups had a statistically significant change in the Modified Medical Research Council Dyspnea Scale during stent evaluation and after TBP.

Conclusion:

In patients with severe ECAC, short-term evaluation with airway stents appears to be safe and improves respiratory symptoms, HR-QoL, and exercise capacity. The use of USEMAS led to a lower complication rate, a greater improvement in HR-QoL and exercise capacity, and appeared to better predict how the patients would respond to TBP.
Novel Left Atrial Cannulation Technique for Attachment of a Pumpless Artificial Lung
Authors: Prater Aaron R. , Fallon Brian P. , Hirschl Ronald B. , Drake Daniel H. , Rojas-Pena Alvaro
Published: March 2022

A pumpless artificial lung has the potential to provide a bridge to recovery or transplantation in children with respiratory failure. Pulmonary artery inflow and left atrial outflow are necessary for low-gradient, pumpless systems; however, long-term cannulation of the fragile left atrium remains problematic. In this technique, the left atrium and pulmonary artery were exposed through a left anterior thoracotomy. Inflow to the artificial lung was created using an end-to-side anastomosis with the pulmonary artery. Device outflow was established through the left atrium. A single-stage venous cannula was passed through a free PTFE graft. Using polypropylene with pledgets, two concentric purse-string sutures were placed in the dome of the left atrium. The venous cannula was inserted. The graft was slid down the cannula and circumferentially secured to the adjacent left atrial tissue and pledgets. The other end of the graft was secured to the cannula with silk ties. The procedure was successful in 10 sheep. Initial device blood flow was 969 ± 222 ml/min, which remained stable for up to 7 days with no anastomotic complications. This is an effective method of achieving secure, long-term left atrial cannulation without cardiopulmonary bypass for use in a low-resistance, pumpless artificial lung. And, most importantly, improves the ease and safety of cannula replacement and final decannulation when AL support is no longer required.