The coronavirus disease of 2019 (COVID-19) pandemic rapidly spread around the world, resulting in massive medical morbidity and mortality and substantial mental health consequences. Post-traumatic stress disorder (PTSD) is an important psychiatric disorder associated with disasters, and many published scientific articles have reported post-traumatic stress syndromes in populations studied for COVID-19 mental health outcomes. American diagnostic criteria for PTSD have evolved across editions of the manual, and the current definition excludes naturally occurring medical illness  as a qualifying trauma, ruling out this viral pandemic as the basis for a diagnosis of PTSD. This article provides an in-depth nosological consideration of the diagnosis of PTSD and critically examines three essential elements  of this diagnosis, specifically applying these concepts to the mental health outcomes of the COVID-19 pandemic. The current criteria for PTSD are unsatisfying for guiding the response to mental health consequences associated with this pandemic, and suggestions are made for addressing the conceptual diagnostic problems and designing research to resolve diagnostic uncertainties empirically. Options might be to revise the diagnostic criteria or consider categorization of COVID-19-related psychiatric syndromes as non-traumatic stressor-related syndromes or other psychiatric disorders. The coronavirus disease of 2019 (COVID-19) pandemic, involving the novel coronavirus pathogen Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in the Wuhan province in China and spread rapidly around the world in the first few months of 2020. The seriousness of this illness quickly became apparent with the emergence of many cases with serious and catastrophic morbidity and mortality. The human toll climbed to tens of millions infected and more than a million deaths worldwide before the end of the year. General awareness of serious mental health consequences associated with COVID-19 followed, and within just a few months, the academic literature swelled with articles describing mental health outcomes, including 3504 articles from a PubMed search on 27 November 2020 using the terms “COVID-19” and “mental health”. Thus commenced the most deadly pandemic in more than a century, overwhelming efforts to respond effectively by public health authorities and clinical and academic professionals.In disaster typology, pandemics are classified as natural disasters. Natural disasters have a well-known potential to generate pervasive mental health casualties. The “signature” psychiatric diagnosis of trauma is post-traumatic stress disorder (PTSD) ,2. PTSD n = 15) but also Spain (n = 2), Italy (n = 2), USA (n = 2), Greece (n = 1), France (n = 1), South Korea (n = 1), England (n = 1), Ireland (n = 1), Canada (n = 1), and India (n = 1). As summarized in Numerous scientific articles have been published from studies of post-traumatic stress syndromes as mental health outcomes of COVID-19. The research samples in these studies include infected, exposed, unexposed, and mixed exposure groups, including patients hospitalized for COVID-19 illness, front-line healthcare workers caring for patients with COVID-19 illness, and the general population during the pandemic. A specific PubMed search of the terms “COVID-19” and “PTSD” on 27 November 2020 found 22 studies, which were combined with three additional studies located from citations in review articles emerging from the search. This collection of a total of 25 studies (with results published in 26 articles) includes only COVID-19 studies that collected original data from research samples and measured and reported findings on post-traumatic stress syndromes and symptoms. A firm understanding of the nosology of trauma-related psychopathology is important for designing and conducting research on post-traumatic stress-related outcomes of pandemics in broad populations that may be adversely affected in many ways, not only through personal threat of infection but also by secondary stressors accompanying pandemics. The purpose of this article is to clarify the nosology and conceptualization of PTSD for appropriate application of this diagnosis to disaster mental health outcomes, specifically in relation to the recent COVID-19 pandemic, which has unique issues for this diagnosis. Because PTSD is the “signature diagnosis” of trauma and of vital importance to disaster mental health outcomes, a clear understanding of the disorder and its application to disaster incidents is critical to understanding this literature . This arThere are three major concepts that are essential to the general understanding of the definition of PTSD: (1) objective definitions of trauma and other stressors, 2) objective definitions of exposure to trauma, and (3) subjective emotional and psychological responses to trauma  objectiv. The firPTSD is conceptualized and categorized as a trauma-related disorder. It is a conditional diagnosis specifically requiring the experience of trauma as defined in criterion A ,34,35,36Trauma is narrowly defined in criterion A of the DSM-5 diagnosis of PTSD as a threat to life or limb: “actual or threatened death, serious injury, or sexual violence” p. 271) . Example71 . Examhttps://www.merriam-webster.com/dictionary/trauma; https://www.thefreedictionary.com/trauma). This common usage definition of trauma is much broader than the psychiatric definition and could potentially include almost any experience that is very unpleasant, emotionally upsetting, or deeply distressing. Because the word “trauma” takes a far narrower definition in psychiatric nomenclature than in common language, careful reading of the DSM-5 criteria for PTSD is needed to comprehend that the psychiatric definition of trauma itself does not encompass psychological wounds that may arise from it.The DSM-5 definition of trauma is very different from the meaning of the word “trauma” used in common parlance. Standard dictionary definitions of the word trauma do not limit it to the experience of physical injury but also refer to psychological pain and disordered mental states resulting from severe mental or emotional stress or physical injury  but could, nevertheless, have emotional and psychological consequences . It shouThrough the evolution of versions of the criteria for PTSD from DSM-III through to DSM-IV-TR, the definitions of trauma and exposure to it have historically been jumbled together in the criteria without clear separation into the elements that define trauma and those that define exposure to it . In DSM-The distinction between trauma and exposure to it is critically important to the diagnosis of PTSD, which requires not only a traumatic event but also exposure to it. Thus, conceptualization of trauma and exposure independent of one another is needed to ensure that both are present for accurate diagnosis of PTSD ,31. For Psychiatric symptoms and distress arising in the context of a traumatic event are distinct from the event and the exposure to it, but they are, by definition, connected. The symptoms must be anchored in a qualifying exposure to trauma, specifically beginning or worsening after the event to be considered post-traumatic stress symptoms. Such symptoms are referred to as incident symptoms. These are in contrast to all post-disaster prevalence of symptoms, many or most of which may be pre-existing and not representing disaster outcomes.Psychiatric symptoms not anchored in a qualifying exposure to a traumatic event are not considered post-traumatic, such as symptoms developing after exposure to stressors not qualifying as trauma. Additionally, symptoms that were well entrenched before the traumatic event do not qualify. Thus, not all symptoms present after exposure to a traumatic event count as post-traumatic. Finally, psychiatric symptoms not following exposure to any particular event are simply symptoms.The three nosological elements that are essential for understanding trauma-related psychopathology  have unique considerations for COVID-19. Each of these three elements will next be considered separately in the context of COVID-19.COVID-19 is a naturally occurring infectious disease. Despite the extensive human harm and death wreaked by the current pandemic, naturally occurring illness including COVID-19 does not constitute a qualifying trauma for the DSM-5 definition of PTSD, as stated by the text accompanying the criteria: “A life-threatening illness or debilitating medical condition is not necessarily considered a traumatic event” (p. 274) . Thus, nOf historical interest, the accompanying text to the DSM-IV/-TR criteria directly conflicted with the DSM-5 exclusion of naturally occurring illness from categorization as trauma, specifically including “being diagnosed with a life-threatening illness” in the accompanying text only pp. 424, 464) ,42. Thus4, 464 ,4The severity and potential lethality of COVID-19 do not qualify it as trauma by the DSM-5 definition because naturally occurring medical illness does not qualify even if severe and with potential for rapid fatality. It is thus categorized as a severe medical stressor, similar to acute heart attacks and strokes which are not considered traumatic events even if rapidly fatal. Not even the natural disaster classification of the COVID-19 pandemic can confer trauma status to SARS-CoV-2 infection or COVID-19 illness . The COVID-19 pandemic also generated important secondary stressors in the form of economic, social, and recreational losses that included closures of businesses and loss of jobs, curtailed opportunities to socialize with friends and loved ones, and discontinuation of many of life’s usual pleasurable or meaningful activities , furtherBecause viral infection in the COVID-19 pandemic is not technically classifiable as a trauma by current criteria, it is not plausible to contemplate it as a substrate for PTSD, even though the COVID-19 pandemic is considered to be a disaster. The reported findings of COVID-19-related post-traumatic stress  in the published COVID-19 literature are not consistent with the DSM-5 diagnostic convention. Because the COVID-19 studies measuring post-traumatic stress have nosological problems in the conceptualization of trauma, it follows that the post-traumatic stress syndromes and symptom outcomes reported in these articles do not technically conform to DSM-5 criteria for PTSD. Five of the 25 studies summarized in the current article acknowledged methodological limitations in the assessment of post-traumatic stress symptoms using self-report symptom measures that do not provide diagnostic assessment of PTSD ,22,24,44Because SARS-CoV-2 is classifiable as a stressor but not trauma, exposure to this non-traumatic stressor as well as to the secondary stressors arising from the pandemic is pertinent to the categorization of the ensuing emotional and psychological consequences of COVID-19. Estimates of COVID-19 post-traumatic stress reported in the published literature, thus, do not reflect trauma-related symptoms or syndromes but rather stressor-related symptoms or syndromes. COVID-19 studies have the potential to reintroduce the same methodological errors in estimating adverse mental health consequences described earlier in studies of disasters in very large unexposed populations, first by measuring post-traumatic symptoms, which is not technically justified given the non-traumatic stressor status of viral infection, and second by sampling viral-unexposed populations.https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html). Most of the COVID-19 studies of general populations reported far higher proportions with COVID-19-related “post-traumatic stress” in their samples than the proportions with known SARS-CoV-2 exposures, indicating conceptual problems in the research design and reporting. In the COVID-19 studies of healthcare workers, the exposure status of the workers was likely mixed and more complex. For healthcare workers, when personal protective equipment (PPE) is used and it functions properly, the worker wearing it is not bodily exposed to the virus, which stops, as intended, outside the PPE. Only when the PPE is not used, is not used properly, or fails is the worker physically exposed to the virus. Because the virus is imperceptible, healthcare workers may not be able to discern personal exposure to the virus unless they test positive for it or develop COVID-19 illness symptoms. The proportions of healthcare workers who were personally exposed to SARS-CoV-2 in caring for patients with COVID-19 illness in these studies are unknown and may have been diminutive, creating further validity problems.In the published COVID-19 research literature, the different exposure characteristics of the three populations sampled  and potential variability in individual exposure within these populations makes it difficult to compare findings across studies and to understand what the widely differing rates reported actually reflect. Samples of patients hospitalized for COVID-19 illness were all clearly exposed to COVID-19. In the general population studies, very few individuals likely had SARS-CoV-2 exposure or infection, an assumption based on the small fractions of general populations worldwide known to have been exposed or infected . More severe exposure may be experienced in higher levels respectively among individuals testing positive for infection with the virus but not becoming symptomatic. Among those individuals who do develop COVID-19 illness, the medical illness itself constitutes yet another dimension of exposure severity. Among those who become medically ill, in turn, different levels of medical effects ensue, including illness requiring medical care and more severe illness requiring intensive care and even ventilator assistance. These considerations suggest that not only does exposure to the virus have dose-related direct effects on both medical complications of the viral illness and mental health, but the severity of the medical illness may serve to further drive more severe emotional and psychological consequences. Besides direct personal exposure, other types of exposure to the virus may prove stressful, including witnessing the course of severe COVID-19 illness in previously healthy patients, learning about severe COVID-19 illness in a close family member or a close friend, or even having personally exposed or infected a close family member or close friend.Potential for exposure is a major source of worry, fear, and anxiety that has been extensively articulated by medical professionals and members of general populations during the COVID-19 pandemic. The DSM-5 criteria for PTSD do not include risk of exposure to trauma as a qualifying exposure type . Risk ofRegardless, fears of exposure create emotional burdens for both healthcare workers and general populations. People affected by concerns about risk for exposure constitute the largest segment of the population and could include almost everyone not exposed to the virus but who, nevertheless, find the pandemic to be stressful, anxiety-provoking, and fear-inducing. . These widespread concerns about risk of exposure are of potentially limitless dimensions and might even be at least as distressing as the specific and contained awareness of an actual and identifiable virus exposure, as in a popular saying, “Fear of the unknown is the greatest fear of all” . Particularly in the initial phases of the pandemic when less was understood about the virus and its transmission, realistic assessment of the level of risk from daily activities for potential exposure to the virus, infection, and medical illness and complications was particularly difficult. Initial research on the psychological effects of the COVID-19 pandemic conflated actual exposures with concerns about risk for exposure in various samples, consequently mixing mental health consequences of actual exposures to the virus with concerns about potential exposure.Examination of published COVID-19 research can illustrate the importance of addressing the objective elements of trauma and exposure to it separately from, and in relation to, the subjective emotional/psychological responses. Because COVID-19 illness does not qualify as trauma according to DSM-5 criteria, mental health problems related to SARS-CoV-2 exposure cannot be considered to represent trauma-related syndromes, and PTSD—a post-traumatic syndrome—cannot be diagnosed with these criteria in these studies. Instead, COVID-19-related symptoms can more appropriately be characterized as representing stressor-related symptoms or syndromes.Because psychological symptoms reported by people not exposed to SARS-CoV-2 cannot be attributed to trauma exposure according to the DSM-5 criterion A for PTSD, the reported post-traumatic stress syndromes in the published COVID-19 literature are technically not valid by these criteria. Because people without exposure to the virus cannot be considered to meet the DSM-5 criterion A for PTSD related to the pandemic, measurement of post-traumatic symptoms in trauma-unexposed individuals departs from the DSM-5 definition of post-traumatic stress syndromes by not satisfying both of the two required elements of criterion A: trauma and exposure to it. The self-report symptom tools used to collect data in the published studies either did not anchor the symptoms to COVID-19 exposure or inappropriately ascribed symptoms related to SARS-CoV-2 exposure as trauma-related, not fulfilling the requirement in DSM-5 criteria that the symptoms must be anchored in exposure to a qualifying traumatic event to be considered post-traumatic stress symptoms. Non-diagnostic self-report symptom measures are well known to have these inherent problems and contribute to overestimation of diagnostic prevalence. Therefore, these instruments cannot be used for diagnosis or estimation of population prevalence of post-traumatic stress arising from the COVID-19 pandemic ,40,45,46Even though the mental health outcomes of COVID-19 in these studies did not have adequate methodological designs to identify post-traumatic stress as envisioned, importantly, they seem to have identified many symptomatic individuals. This growing body of research collectively points to substantive psychological and emotional reactions to the COVID-19 pandemic that may be not only distressing but also possibly including pathological outcomes. Inability to classify the mental health consequences as trauma-related psychopathology does not automatically render the mental health outcomes trivial or unimportant. Many more people experience distress than disaster-related psychopathology, representing more opportunities for distress intervention than for formal treatment of trauma-related psychopathology.Because naturally occurring medical illness such as viral infection does not represent a source of PTSD according to DSM-5 criteria, a pertinent question emerges. Among those directly exposed to or infected with SARS-CoV-2, if the reported psychiatric symptoms are not manifestations of PTSD, what do they represent? There are several possibilities for addressing this dilemma in the diagnostic nomenclature.First, if the criterion A definition of trauma could be rewritten to allow naturally occurring serious medical illness  as a qualifying trauma, then COVID-19 illness could lead to a diagnosis of PTSD. However, inclusion of a broad collection of medical illnesses in the definition of trauma could widen its definition so far as to make it meaningless. It might create difficulties with decisions of which illnesses to include, such as COVID-19, influenza,  cancer, or even diabetes mellitus, all of which significantly increase an individual’s risk of fatality. Additionally, no one survives life without eventual fatality, and thus, even birth itself could be conceptually construed as meeting criteria for trauma by this logic. None of these medical conditions conform to the stated rule that they must not only be potentially life-threatening but also sudden and catastrophic. Including these medical illnesses in the PTSD definition of trauma might introduce syndromes that are very different from the PTSD defined by the DSM-5 criteria.Alternatively, it is possible that the psychiatric symptom response to SARS-CoV-2 exposure or COVID-19 illness represents a yet-undefined stress-related syndrome similar to PTSD based on exposure to a stressor not considered a trauma. This possibility could lead to a new diagnostic entity for psychological syndromes associated with acute life-threatening medical illnesses that is not currently available in the DSM-5 criteria. This could potentially avoid the proverbial dubious attempts to fit a square peg into a round hole by inserting a diagnostic entity into the PTSD definition that is fundamentally not the same disorder. Potential solutions involving new diagnostic entities, however, are not without potential problems. First, the longitudinal trend in successive versions of the diagnostic manuals has been to greatly expand the numbers of established psychiatric diagnoses , yieldinAnother possibility might be that the psychological syndrome related to SARS-CoV-2 exposure or infection or COVID-19 illness might actually be part of another well-established psychiatric illness such as anxiety or depressive disorders, which have been well documented . Such diYet another possibility is that the psychological syndrome related to SARS-CoV-2 exposure or infection or COVID-19 illness could represent emotional distress not rising to the level of diagnosable psychopathology. Such distress is well documented by research to be nearly universally reported after exposures to severe trauma such as disasters ,49,50,51Much of the focus of the discussion of COVID-19-related concerns in this article has been on post-traumatic stress-related outcomes of known or confirmed exposure to the virus. If the DSM-5 criteria for PTSD were rewritten to include risk of exposure as a qualifying trauma exposure, then simply having potential for exposure could lead to a diagnosis of PTSD. This solution would have the same issue with naturally occurring medical illness not meeting the criteria for categorization as trauma in addition to the lack of actual exposure. Expansion of PTSD criteria to include fear of exposure as a qualifying trauma exposure could be expected to render the criteria meaninglessly broad. For example, just as concerns about risk for trauma exposure in general could be extended beyond reason to include simply driving on a highway, concerns about risk for COVID-19 could be extended beyond reason to include simply taking a breath of fresh outside air from an open window. Nevertheless, the substantial proportion of general populations and healthcare workers reporting psychiatric symptoms related to concerns about potential viral exposure in published COVID-19 research studies supports the concept of concern about risk for viral exposure as an important stressor with potential for mental health consequences. Research might find the mental health outcomes related to fear of exposure to also represent stressor-related disorders, other psychiatric illness such as depressive and anxiety disorders, and non-pathological distress, with all the same potential issues for diagnostic categorization discussed above for categorization of viral exposure.This article’s review of disaster-related PTSD has addressed nosological issues of this diagnosis specific to the current COVID-19 pandemic. The issues rising from the DSM-5 diagnostic criteria for PTSD are unsatisfying for guiding the response to this disaster because the constraint of its definition of trauma, which excludes natural illness such as viral infection, has not been fully investigated. The international criteria do not include this constraint, and supporting evidence for this new change in the American diagnostic criteria is needed. To determine whether exposure to the SARS-CoV-2 virus represents a qualifying traumatic event or a non-traumatic stressor will require empirical data. Research must be designed to compare SARS-CoV-2 exposure to exposure to qualifying traumatic events according to DSM-5 criteria to determine whether the symptomatic response to both types of events is similar or distinct.A time-honored approach to differentiation of disorders from one another has been to invoke the five-phase validation procedure applied to psychiatric diagnoses by Robins and Guze . Using tJust as the case has been convincingly made for the need for diagnosis in medical and psychiatric practice, it also applies to the categorization of psychiatric syndromes related to the COVID-19 pandemic. Accurate diagnosis is central to all of medical practice; it guides the clinician to select the most appropriate and effective treatment, helps determine a likely prognosis, allows communication with professional colleagues, facilitates education of clinicians and researchers, and organizes scientific research . All of


Methamphetamine (meth) use among men who have sex with men (MSM) is associated with increased HIV prevalence and transmission and substandard advancement along the HIV prevention and care continuum. Given the growth of mobile health  technologies, it is no longer necessary to limit meth treatment options to physical, brick-and-mortar sites, and administration using generic, nontailored content.In a 2-arm randomized controlled trial , we aim to evaluate the use of an mHealth intervention (Getting Off) to assess the impact and noninferiority of a cross-platform app  to help MSM reduce meth use and HIV sexual risk behaviors and improve their advancement along the HIV prevention and care continuum .Participants will be randomized into 2 arms: arm A, with immediate access to the app (immediate delivery: n=150), or arm B, with delayed access to the app after a 30-day period (delayed delivery: n=150). Participants in both arms will use the same Getting Off app and will have 30 days to complete the 24 sessions. Participants will be assessed at the 1-, 2- (delayed delivery arm only), 3-, 6-, and 9-month timepoints to determine observed treatment effects and will be compared with a historical matched sample of participants (n=~600) who received the brick-and-mortar group-based Getting Off intervention.Recruitment began in January 2019 for phase 1, the formative phase. In January and February 2019, 4 focus groups (N=36) were formed to provide input on the adaptation of the group-based manual intervention to a mobile app. Data collection for phase 2, the RCT, is expected to be completed in January 2023. The final results are anticipated in April 2023.By creating a culturally responsive mobile app, Getting Off aims to reduce meth use and improve sexual health outcomes among meth-using MSM. The Getting Off app could have significant public health impact by greatly expanding access to effective, affordable, private, culturally competent, and highly scalable meth treatment for MSM.Clinicaltrials.gov NCT03884946; https://clinicaltrials.gov/ct2/show/NCT03884946DERR1-10.2196/22572 Men who have sex with men (MSM) have elevated rates of methamphetamine (meth) use relative to non-MSM -3, as meHIV prevalence is significantly higher among MSM who use meth ,25-29 anMSM use smartphones for sexual partner selection, sexual health information, and sexual identity expression at a higher rate than non-MSM -41, and Providing theory-driven, MSM-specific meth treatment, which integrates HIV risk reduction programming, reminders about HIV testing, PrEP, PEP, and information about HIV care (including ART reminders), will address a range of HIV-related health deficits and address key priorities set by the National Institutes of Health HIV/AIDS research priorities and the National HIV/AIDS Strategy. Furthermore, the overall public health benefits could be tremendous, as meth use has also been associated with major physical harm , dental Given the growth of mobile technology, it is no longer reasonable or necessary to limit meth treatment to physical, brick-and-mortar sites. Only 1% of app-using MSM express a preference to participate in programs delivered in person, whereas 70% prefer content delivered via smartphones . The GetMobile apps are available for download and use 24 hours a day, 7 days a week, making it easier to attempt treatment and access information in a contextualized and need-based manner; such immediacy cannot be achieved at a brick-and-mortar facility. In addition, the adaptation of a group-based intervention to a self-directed and individualized format provides the opportunity for novel delivery modalities such as gamifying formerly group-based intervention activities; insights and information will be conveyed to participants through activities such as sorting, matching, and interactive board games.The overall goal of this research study is to (1) adapt the Getting Off meth treatment intervention from a physical, brick-and-mortar facility to computerized delivery; a counselor-delivered intervention to self-directed; and a group-based to an individualized format and (2) assess the impact and noninferiority of the Getting Off app. The final Getting Off app will provide meth-using MSM and service providers with a culturally competent, free-to-own, cross-platform mobile health  smartphone app that can be broadly disseminated.Getting Off: A Behavioral Treatment Intervention for Gay and Bisexual Male Methamphetamine Users, and the highly promising findings from our successful stage 1 proof-of-concept study to complete translation of Getting Off into a cross-platform (iOS and Android) mHealth smartphone app and to assess the app’s efficacy and noninferiority in a scientifically rigorous randomized trial. The stage 2 development of the cross-platform Getting Off app will be based on user feedback from the feasibility pilot test, current literature on app preferences among MSM, and state-of-the-art technology. The app will be an interactive presentation of the Getting Off manual. Health content, behavioral self-assessments, homework assignments, and multimedia content will be integrated in a walk-through  manner, where the consumer will be presented dynamic content, all under the guidance of a culturally competent, user-friendly, and attractive interface. The app could broadly disseminate culturally competent meth use and HIV risk reduction content to large numbers of demographically and geographically diverse users who otherwise could not access such services, particularly racial or ethnic minority MSM and MSM living in rural areas [The project builds upon the established efficacy of our manualized meth treatment intervention, al areas ,47,59.The aims of the research include the following:Primary aim 1: Refine and enhance the first 8 sessions of the Getting Off meth-use treatment intervention developed in stage 1 based on feasibility pilot test user feedback.Approach: Integrate findings from stage 1, and refine or enhance the first 8 sessions with the technology team and input from our community advisory board.Primary aim 2: Conduct formative research to develop the remaining 16 sessions of the Getting Off meth-use treatment intervention into a cross-platform computerized mobile app targeted to reduce meth use and HIV sexual risk behaviors and increase advancement along the HIV prevention or care continuum.Approach: Design and develop the complete app by guiding technology team revisions using focus group and community advisory board feedback; conduct a usability pilot study to assess the feasibility, acceptability, and preliminary effects of the Getting Off app; and refine app iterations through community input.Primary aim 3: Conduct a randomized controlled trial (RCT) to evaluate reductions in meth use and HIV sexual risk behaviors  and increase advancement along the HIV prevention  or care continuum .Approach 3a: A 2-arm RCT to determine intervention effects through comparison of the immediate delivery  and delayed delivery  armsAim 3a hypothesis: Exposure to the Getting Off app will produce significant reductions in meth use and HIV sexual risk behaviors as well as increased odds of advancement along the HIV prevention or care continuum.Approach 3b: An observed treatment effects analysis powered for prospective subgroup contrasts to compare longitudinal pre- or postdata from the pooled ID and DD arms (N=300)Aim 3b hypothesis: Exposure to the Getting Off app will be associated with significant reductions in meth use and HIV sexual risk behaviors as well as increased odds of advancement along the HIV prevention or care continuum.Approach 3c: A 2-arm historical matched comparison design to evaluate the outcomes of the Getting Off app  relative to a matched sample of participants who previously attended the brick-and-mortar group-based Getting Off intervention .Aim 3c hypothesis: Reductions in meth use and HIV sexual risk behaviors as well as increased advancement along the HIV prevention or care continuum will be statistically noninferior to those observed in the brick-and-mortar group-based Getting Off intervention.Secondary aim 1: Determine the impact of structural-  and individual-level  factors as moderators of intervention outcomes.All study procedures were approved by the Western Institutional Review Board . The study was registered as a clinical trial . All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.App refinement of the first 8 sessions addressed the areas identified through the feasibility pilot test. The research and app development teams designed and developed a cross-platform mobile app using a cross-platform framework  that will permit downloading the app on both the iOS and Android platforms. The cross-platform framework approach promotes extensive code reusability between the 2 platforms and ensures a consistent user experience. The app will be for the latest versions of iOS and Android operating systems and will include backward compatibility for one operating system version of each.The research team conducted formative research to translate the remaining 16 sessions from the group-based manual-driven intervention to a computerized app, conducted alpha-phase postdevelopment bug testing, conducted beta-phase usability pilot testing, and refined the app according to alpha- and beta-phase testing.Four focus groups (N=36) provided input on the development of the Getting Off app: (1) out-of-treatment, meth-using MSM (n=10); (2) meth-using MSM who are currently in outpatient treatment in the Getting Off program (n=10); (3) prior meth-using MSM with a minimum of 1 year recovery who have completed a minimum of 18 out of 24 sessions (75%) of the brick-and-mortar Getting Off program (n=6); and (4) prior meth-using MSM with a minimum of 1 year of recovery who have had no previous experience or knowledge of the Getting Off intervention (n=10). The focus groups were structured to provide guidance on translating Getting Off into an app that is responsive to culture  and meth treatment needs. Additional input was obtained through the ongoing community advisory board and usability pilot testing.Following app development, alpha-phase testing has uncovered and removed unwanted bugs. Beta-phase usability pilot testing will be conducted with members of the target population (N=30) to test the feasibility and acceptability of the Getting Off app. Furthermore, pilot testing will be used to ensure the functionality of the app . Inclusion criteria for the pilot test were as follows: (1) self-identified MSM, (2) prior meth user but no meth use in the past 365 days, (3) aged between 18 and 65 years, and (4) able and willing to provide informed consent. The behavioral assessments will be consistent with those of the RCT. Although the group-based Getting Off intervention is delivered over 8 weeks (24 sessions at 3 groups per week), it is expected that it will take far less time to progress through the self-directed app, and because of the interactive features, participants may choose to replay treatment modules multiple times in the 30-day period. Behavioral assessments will be conducted at baseline and at the 1-month follow-up. In addition, at the 1-month follow-up visit, an open-ended, in-person, qualitative user experience exit interview will be collected to collect feedback on the app, including the perceived benefits, concerns, and suggestions for improvements. Qualitative interviews will be digitally recorded and analyzed using the same methodology as the focus groups.intent-to-treat design; participants will be assessed regardless of participation or retention.Following screening, informed consent, and baseline assessments, participants will be randomized into 1 of 2 arms: arm A, immediate access to the Getting Off app (ID), or arm B, participants will have access to the Getting Off app after a delayed 30-day period (DD). Participants in both arms will receive the same Getting Off app and will be given 30 days to complete the 24 sessions. The randomized 2-arm repeated measures design will assess participants at 1, 2- (DD arm only), 3-, 6-, and 9-months after randomization to determine longitudinal intervention effects, observed treatment effects, and a historical comparison with a matched sample of participants who attended the brick-and-mortar group-based Getting Off intervention  and 2. TTo ensure comparability of outcomes with those of the group-based Getting Off intervention manual, inclusion criteria must mirror that of the brick-and-mortar treatment site: (1) self-identified MSM, (2) any meth use in the past 365 days, (3) aged between 18 and 65 years, and (4) able and willing to provide informed consent. Both HIV-positive and HIV-negative participants will be eligible.To ensure a steady stream of diverse participants, 4 recruitment strategies will be used: (1) online recruitment: banner ads or digital flyers will be placed on gay websites, apps, and social media sites that specifically target MSM, such as Scruff, Adelante, Craigslist, Adam4Adam, Jack’d, and Grindr; established relationships with web-based venues that cater to MSM will enable a successful and robust internet-based recruitment strategy. (2) Street- and venue-based outreach: a semistructured time-space sampling methodology will be used to conduct street- and venue-based outreach identified through the community advisory board and ongoing community mapping as locations where meth-using MSM congregate. (3) Poster advertisement: posters that introduce the study will be posted to inform potential participants who to contact for further information regarding the research study. (4) Long-chain referral sampling: the participants of this study will be asked to recruit potential new participants. The participants of this study participants will receive US $2 when they bring a potential participant to the site and US $18 if an eligible participant is enrolled. Potential participants who inquire about the study will be scheduled for intake within 24-48 hours. These strategies have previously been used to recruit similar samples in prior studies.Following informed consent and completion of the baseline assessment, participants will be randomized to either the ID or DD arm through a computerized variable-balanced procedure. Recent work with substance-dependent (predominantly meth) MSM revealed treatment outcomes to be associated with participant substance use histories and sociodemographics . A variaThe study intervention will be delivered via the identical cross-platform Getting Off mobile app for participants in both arms. Postrandomization participants will download the app onto their phone or tablets. Those randomized into the ID arm will immediately be given a unique user passcode to access the intervention content, whereas those randomized into the DD arm receive their unique user passcode 30 days after randomization .action stage by the time they seek treatment at a brick-and-mortar facility. In contrast, due to the privacy and availability of a computerized intervention, the Getting Off app would be of interest and value to any meth-using MSM who has moved beyond the precontemplation stage, allowing for broader dissemination, earlier interruption of meth use and HIV sexual risk behaviors, and increased opportunities for advancement through the HIV prevention or care continuum, maximizing potential public health impacts.The SOC model -67 conceThe computerized Getting Off app, like the group-based intervention before it, will be guided by CBT and will use a broad set of psychological and educational techniques to provide meth-using MSM with critical knowledge about their meth use, teaching skills to initiate abstinence and to return to abstinence should relapse occur . The theDiagnostic Mental Health and Substance Use Disorder; Stages of Change; Sociodemographics, Familiar, Legal, and Health Status; Substance Use; Meth Use and Sexual Risks; and Biological Markers) describe the measures used to address the study’s specific aims.All data will be collected on an Audio Computer-Assisted Self-Interview administered via the Qualtrics system. All materials will be stored in Qualtrics’ Health Insurance Portability and Accountability Act-compliant (secure and encrypted) cloud-based databases. Data from historical comparators will be sampled from participants enrolled in the brick-and-mortar Getting Off intervention beginning in 2012, as research indicates that 2012 is when up to 95% of meth-using MSM in Friends Community Center reported owning their own cellphone . The folDiagnostic and Statistical Manual of Mental Disorders (DSM-5) Methamphetamine Use Disorder contains the DSM-5 diagnostic items necessary to determine mild, moderate, or severe meth use disorder. This information will determine the app’s utility for consumers at various levels of meth use. It will be administered only at baseline.The University of Rhode Island Change Assessment (URICA) is a brief, self-administered inventory used to assess the participant’s current position regarding readiness for change  . In nontAdmission or follow-up form collects demographic information, housing status, food security, educational attainment, alcohol and other drug use history, family and social history, legal status, HIV status, location on the HIV prevention or care continuum, experiences with stigma and/or discrimination, and general and mental health status. The full form will be administered at baseline, and an abbreviated version  will be administered at all follow-up time points.Substance use frequency is a brief assessment, developed by the principal investigator that assesses substance use, injection drug use, and injection protocols in the past 30 days. It will be administered at all time points.Behavioral Questionnaire-Amphetamine (BQA)-abbreviated version gathers information on HIV-related drug and sexual risk behaviors, assesses self-efficacy for sexual behavior change, collects detailed information on discrete sexual behaviors (with primary or nonprimary partners and whether or not the behavior occurred under the influence of meth and/or other substances), and collects episodic data about participants’ most recent sexual encounters ,78. AlthUrine drug screen: urine samples will be collected, monitored, and analyzed using a 5-panel Food and Drug Administration–approved urine test cup . The tesRapid HIV antibody test: HIV-negative and status unknown participants will receive a rapid point-of-care fingerstick HIV-antibody blood test  at 3-monNeisseria gonorrhoeae (N. gonorrhea) and Chlamydia in the urethra via urine sample. Pharyngeal and rectal swabs will be taken for N. gonorrhea and Chlamydia, and syphilis will be tested by serum red plasma reagin and confirmed by fluorescent treponemal antibody absorption testing. Positive STI results will be reported per state guidelines and will be immediately referred to care. Prior studies found high rates of undiagnosed STIs among out-of-treatment, meth-using MSM [Sexually transmitted infection (STI) testing: participants will be tested for sing MSM ,83, whicVirologic control for HIV-positive participants: as indicated by an undetectable HIV-1 level on the COBAS AmpliPrep/COBAS TaqMan HIV test kit , which hDried blood spot (DBS) for HIV-negative participants who report PrEP uptake: a blood sample will be collected and a DBS analysis for intraerythrocytic tenofovir-diphosphate will be performed. It will be conducted at each 3-month assessment.Health study locator form: the locator form asks participants to give consent for follow-up and to provide names; addresses; email and internet site profiles, particularly social network sites; and phone numbers of 3 relatives or friends who can reach the participant. Information is also collected on where  and with whom the participant associates . This will be administered at baseline, each follow-up time point, and on the off months of each follow-up time point, that is, on the months when a follow-up assessment is not being conducted.All primary outcomes are operationalized and assessed in at least two discrete ways, increasing accuracy of measurements, reducing concerns of fully missing data, and allowing for posthoc comparisons of concurrent validity across assessment modalities , psychosocial , barriers and facilitators , and/or sociodemographic variables will be tested for significant association with study outcomes , with specific tests of association chosen based on the distributional properties of the outcome variables in question. All variables demonstrating significant statistical association with one or more of the study outcomes will be included as statistical covariates in all multivariate outcome analyses associated with primary aims 3a, 3b, and 3c and will additionally be included in exploratory subgroup analyses to test for moderating effects on treatment response and/or contingent effects among subsets of participants. Primary outcome analyses for primary aims 3a, 3b, and 3c will be carried out using mixed effects generalized linear model (GLM) equations.Advancement through the HIV prevention or care continuum will be assessed at all time points throughout the study and will be operationalized dichotomously  and as a counted variable . Power calculations related to advancement through either continuum will assume a 30% probability of achievement of at least one of the steps on either the HIV prevention or care continuum . Meth use outcomes will be assessed repeatedly  and will be operationalized dichotomously  as a counted variable  and as a continuous variable  as a counted variable  and as a continuous variable . Power calculations for engagement in HIV sexual risk behaviors assume a 65% probability of engagement during the preintervention period for participants in the DD arm .Multivariable inferential analyses of dichotomous outcomes will take the form of GLMs employing the Bernoulli family and logit link function; counted outcomes will be analyzed with GLMs employing the Poisson-log or negative binomial link functions, as distributional patterns dictate . Continuous outcomes will be analyzed using GLMs employing the identity link and Gaussian family functions and assume a single covariate unless otherwise stated . Mixed effects GLM models are considered the best linear unbiased estimators for repeated measures data employing nonparametric and/or limited dependent variables. All power calculations are premised on tests of association across 2 time points , providing the most conservative estimate of minimum detectable effect size estimations. All power calculations assume α≤.05 (2-tailed) and 1−β=.80.Recruitment began in January 2019 for phase 1, the formative phase. In January and February 2019, 4 separate focus groups (N=36) were conducted to provide input on the adaptation of the Getting Off group-based manual intervention to a cross-platform, computerized mobile app–based intervention. The data collection for phase 2, the RCT, is expected to be completed in January 2023. The final results are anticipated in April 2023.The Getting Off app is designed to expand access to effective, affordable, private, culturally competent, and highly scalable meth treatment for MSM. MSM experience higher rates of meth use relative to non-MSM, as meth use is deeply integrated into the sexual identities and sexual behaviors among MSM. Use of meth by this population, before or during sex, is associated with decreased behavioral inhibition and increased engagement in HIV risk behaviors. Given the growth of mobile technology, it is no longer reasonable to limit meth treatment options to physical sites, clustered in urban areas and administered using generic, nontailored content. A cross-platform mHealth smartphone app is well suited for engaging MSM because apps are easily accessible, widely used, private, portable, and inexpensive.There are limitations to the Getting Off study. Given that the study procedures are entirely virtual and that the intervention is app based, enrollment is limited to those that can afford a modern smartphone with an active monthly data plan, as the study does not provide smartphones to participants. However, given that smartphone use is ubiquitous among this population, it is expected that this will not be a major impediment to enrollment. In addition, the study will be conducted in a west coast metropolitan city, and therefore, findings may not be representative of meth-using MSM in other regions of the United States or globally. Finally, the sample may be biased toward MSM who are more likely to enroll in a research study; thus, it may not reflect meth-using MSM that do not self-select to participate in a clinical trial.The Getting Off app aims to reduce meth use and improve HIV prevention and care continuum outcomes among MSM by providing a culturally competent, user-friendly, and attractive interface that promotes reduced drug use and engagement in high-risk sexual behaviors. The Getting Off mobile app is highly scalable, and if successful, it can be made publicly accessible through the Apple App Store for iOS platforms or Google Play Store for Android platforms for widespread distribution. Given that meth use has also been associated with negative physical and mental health consequences ,45,50-53


Although machine learning methods were widely used in computationally identifying PAS, the need for tremendous amounts of annotation data hinder applications of existing methods in species without experimental data on PAS. Therefore, cross-species PAS identification, which enables the possibility to predict PAS from untrained species, naturally becomes a promising direction. In our works, we propose a novel deep learning method named Poly(A)-DG for cross-species PAS identification. Poly(A)-DG consists of a Convolution Neural Network-Multilayer Perceptron (CNN-MLP) network and a domain generalization technique. It learns PAS patterns from the training species and identifies PAS in target species without re-training. To test our method, we use four species and build cross-species training sets with two of them and evaluate the performance of the remaining ones. Moreover, we test our method against insufficient data and imbalanced data issues and demonstrate that Poly(A)-DG not only outperforms state-of-the-art methods but also maintains relatively high accuracy when it comes to a smaller or imbalanced training set.In eukaryotes, polyadenylation (poly(A)) is an essential process during mRNA maturation. Identifying the  cis-determinants of PAS on the DNA sequence. PAS leads to correct identification of Poly(A) sites which play an essential role in understanding human diseases. While many researchers have employed deep learning methods to improve the performance of PAS identification, an underlying problem is the expensive and time-consuming nature of PAS data collection, which makes the application of deep learning models for identifying PAS from a broad range of species a tough task. We attempt to use domain generalization methods, inspired by its thrive in the field of computer vision, to overcome the insufficient annotation data challenge in PAS data. Here, empirical results suggest that our proposed model Poly(A)-DG can extract species-invariant features from multiple training species and be directly applied to the target species without fine-tuning. Furthermore, Poly(A)-DG is a promising practical tool for PAS identification with its stable performance on insufficient or species-imbalanced training data. We share the implementation of our proposed model on the GitHub. (https://github.com/Szym29/PolyADG).The key to understanding the mechanism of translation regulation and mRNA metabolism is to identify the  PLOS Computational Biology Methods paper.This is a cis-regulatory elements are needed for polyadenylation: i) a highly conserved AAUAAA hexamer (or a close variant) located at 10-40 nucleotides (nt) upstream of the poly(A) site, which is usually referred to as the polyadenylation signal (PAS) [Most eukaryotic mRNA, after being transcribed from its coding DNA, typically undergoes post-transcriptional modification, such as 5’ capping, splicing, and polyadenylation, before it is translocated to the cytoplasm and translated into proteins . Polyadeal (PAS) , 7 ii) aal (PAS) , 9.TP53 expression and has been associated with the progression of thyroid tumors. [The location of the poly(A) site determines the length of the 3’ untranslated regions (3’-UTR), which further modulates the expression and of the gene , 11. Rec tumors. , 19 Ther tumors. , 20 and  tumors. , 3P-seq  tumors. , SAPAS [ tumors. , 3’READ  tumors. , and RNA tumors.  have beeComputational methods enable efficient PASs identification by learning the contexts of PASs motif and discriminating true PASs related DNA sequences from sequences which don’t contain PAS. Ji et al.  modifiedArabidopsis thaliana coding DNA. In 2019, Xia et al. [Deep learning methods have been proposed to automatically learn features of DNA sequences and predict unknown sequences based on learned knowledge. With the increasing popularity of Convolution Neural Network (CNN), DeepPolyA  first apa et al.  proposeda et al.  built Dea et al.  developea et al.  extendedDeeReCT-PolyA  first prThe main contributions of this paper are organized as follows:We propose a neural network CNN-MLP to extract both motif features and species information about PAS related DNA sequences.We first introduce a domain generalization technique, HEX, in PAS recognition to force the model to learn invariant features so that the model can generalize to different species.We evaluate Poly(A)-DG by learning from a cross-species dataset and predicting PAS of new species directly.We investigate the performance of Poly(A)-DG when there are limited amount of training data or they are imbalanced.We explore the performance of Poly(A)-DG in imbalanced ratio of positive and negative PAS DNA samples.We visualize the motif patterns captured by convolution filters, and the contribution of regions of DNA sequence.We evaluate the performance of Poly(A)-DG by predicting whole genome in chromosome 1 of rat.We explore the homology effect of Poly(A)-DG in cross-species PAS identification.We also investigate how the Poly(A)-DG performs on single PAS genes and multiple PAS genes.The main challenge of identifying PAS of new species is the limitation of annotated data , 36, espj, denotes as < Xj, Yj > where Xj is a DNA sequence and Yj is the annotation. The length of each DNA sequences is 206-nt and PAS locates in the middle of sequences where its upstream and downstream are both 100-nt. DNA sequences need to be one-hot encoded into four-channel data sequences and each channel represents a type of nucleobase. The annotation of each DNA sequence is {0, 1}, denoting whether the sequence contains PAS or not.The data sample, We propose a neural network aiming to automatically extract both general features and motif features of DNA sequences from different species.FG , Wi is a vector of weights that hidden nodes used to connect with nodes in the input layer and bi is a set of bias.Multilayer Perceptron (MLP) has a good reputation for portraying the whole distribution owing to each node in the hidden layers connected with a certain weight to every node in previous layers. Each node in the hidden layer can be considered as a sequence descriptor that scans through all nucleotides of inputs DNA sequences and obtain a score to describe the sequence. In the training session, MLP tends to fit the training data and try to find proper weights vectors to describe the training set accurately. Given a DNA sequence dataset consists of different species, the MLP would learn to describe the general information among species instead of learning to fit specific features. Therefore, we try to employ the MLP to extract general information about different species. Previous work  showed tFG  where X Different species share the same PAS patterns and flanking motifs may relate to PAS regulations. For using MLP to extract features that can describe species instead of PAS related motifs, we use shuffled-DNA as the inputs of MLP. Therefore, the representations, namely confounding species-specific factors, extracted by MLP intend to describe the specific species and become impossible to identify PAS. The comparison of performance of feeding shuffled DNA sequences and non-shuffled DNA sequences to MLP is shown in section 2 of Then we construct another neural network aiming to identify PAS in single species and use domain generalization techniques to enable cross-species PAS identification by neutralizing the influence of species-specific features extracted by MLP. We feed non-shuffled DNA sequences into a Convolution Neural Network (CNN), which is famous for extracting motif features from DNA sequences. As shown by previous works , 32, CNNWi to each hidden node. The inputs are directly fed to CNN and 16 convolution kernels are used to capture motif features. The architecture of feature extraction is detailed section in 1.1 & 1.2 in FA is directly used in predicting whether the sequence contains PASs or not. The outputs of CNN sub-network and MLP sub-network are concatenated and then fed into HEX. Now we need to force the model to learn species-invariant features. With FA and FG used in FA so that it is least explainable by FG. Directly adopting subtraction maybe problematic because the FA − FG can still be correlated with FG. Wang et al. [FG out of FA. Since both FA and FG are in the same space and the only operation left in the network is the argmax operation, which is linear, we can safely use linear operations.As the variance of the distributions may not be simply coded in some available labels, invariance-driven methods such as DANN  and otheg et al.  proposedk of FA, denoted by β is the coefficient vector of linear regression in i.e. when the number of rows of FG is greater than number of columns of FG), and the closed form solution is:To form a standard linear regression problem, we first consider the column kth column of FA, what cannot be explained by FG is  as the cost function to calculate the loss of every training epoch. Adam optimizer  is used Inspired by the cross-validation strategy, we employ a new cross-species training strategy in our work. We randomly divide every training species into five folds and define three of them as training fold and the other two folds as optimization fold. The training fold is used in model training and the optimization fold is used in searching optimal models. The accuracy of cross-species training is obtained by testing models on all sequences from the target species.The random sampling strategy is applied to search a relative better hyper-parameter for the different training sets. We evaluate those hyper-parameter sets in optimization folds and select the one with the best performance as the parameter of the final model. In our experiments, this method helps us choose hyper-parameters such as learning rate and keep probability. Details can be found in section 1.4 in We use PAS datasets from four species, Mouse, Rat, bovine, and Human, in our experiments. The Omni Human Poly(A) dataset is recently established by Magana-Mora et al.  which coPAS patterns have various variants, we have thirteen PAS motif variants from mouse and twelve from human and Rat poly(A) dataset. However, in this paper, we only focus on identifying the same PAS variants among different species; thus we select the eleven PAS motif variants that Omni human, Rat, bovine and BL mouse shared. Therefore, we use remained 37,230 sequences from Omni human Poly(A), 42,428 for BL mouse, 42,008 for rat and 22,782 for bovine in our experiments. Human, bovine and Mouse PAS datasets can be found in We compare Poly(A)-DG with our feature extraction module, MLP-CNN, to evaluate whether HEX can force the model to learn invariant features among different species or not, DeeReCT-PolyA (DeeReCT),  which isOwing to different distributions of DNA sequences among different species, people can hardly use a well-trained model to identify PAS of a new species. Therefore, we want to evaluate whether Poly(A)-DG is promising to learn invariant PASs related features from a cross-species dataset to overcome domain shifts or not.First, we build six cross-species training sets, including Human-Mouse, Human-Rat, Mouse-Rat, Rat-bovine, Mouse-bovine, and Human-bovine, by mixing any two datasets discussed in Section Datasets and define the remaining species as the target species. Following the cross-species training method in Section Cross-species training and hyper-parameter search, we split each species in cross-species training sets into the training fold and the optimization fold. Then we train models on training folds and report the average accuracy over the target species. In experiments, we observe that the best learning rate and dropout rate vary when the models train on different cross-species datasets. Therefore, we run every methods a few times to obtain their best performance on different source domains. Experimental results are shown in Tables Generally speaking, Poly(A)-DG outperforms remaining methods. Compared with CNN-MLP, Poly(A)-DG achieves higher accuracy in all experiments in this section by employing HEX module. For example, in Compared with DeeReCT, we notice that Poly(A)-DG does not need to find out the most suitable pre-train and fine-tune order to obtain the highest testing accuracy. We conjecture that Poly(A)-DG can simultaneously learn the features from all species in the source domain and reduce the superficial species-specific information automatically. Due to problems in the order of pre-train and fine-tune of DeeReCT and reliability of SanPolyA, Poly(A)-DG is more promising in resolving practical tasks.In addition, we want to investigate the effectiveness of Poly(A)-DG given different amounts of data, especially when the amount of data is limited. Therefore, we define the training fold used in the Section Standard experiments as the standard training fold and further uniformly split each standard training fold into ten sub-folds. The size of a new training fold ranges from 10% to 100% of the standard training fold by increasing sub-folds. We show eight groups of experiments in this section and other four groups of experiments can be found in the section 4 in In general, the accuracy of Poly(A)-DG has an increasing tendency when the amounts of sequences are increasing. Impressively, in Our experiments demonstrate that Poly(A)-DG can be applied in addressing the insufficient data problems.We intend to investigate the performance of our method dealing with variations of sample abundance of the species, because the amount of available data for different species may differ, training sets are usually imbalanced to take advantage of the abundance of the data sets. However, insufficient species may become noise in training due to distribution differences and even confuse the model so that it produces undesirable predictions. , 48 WhilIn some situations, the performance of DeeReCT performs close or even better than Poly(A)-DG, but when it comes to another species in target domains or takes other order of pre-train and fine-tune, the performance will be undesirable.In contrast, experimental results show that Poly(A)-DG can adapt to different cross-species datasets and it works stably when the size of insufficient species are various. We also find that CNN-MLP does not work as effectively as Poly(A)-DG. We conjecture that, confused by the imbalanced training set, CNN-MLP could mistakenly learn species-specific motif information from cross-species datasets.The result of experiments shows that Poly(A)-DG can be promising in addressing imbalanced dataset problems.In experiments conducted above, we assume that the ratio of the number of positive and negative PAS is equal. However, in real conditions, the number of pseudo PAS sequences could be higher than true PAS sequences and the ratio of positive and negative samples may vary among species. In this section, we train Poly(A)-DG in new training sets in different ratios of positive and negative PAS, including 1:5, 1:3 and 1:2 and predict PAS from new species with equal number of false and true PAS sequences. We set the Poly(A)-DG models training on standard training sets as control groups. Experimental results are shown in Some genes have more than one PAS while others have only one PAS. In this section, we build two new Rat PAS datasets, single PAS Rat datasets and multiple PAS Rat datasets, to investigate the performance of Poly(A)-DG on them. PolyA DB v3.2  providesPoly(A)-DG directly processes DNA sequences and automatically extracts features instead of processing hand-crafted features. As discussed in the section CNN-MLP for feature extraction, convolution neural network in Poly(A)-DG is responsible for extracting motif features. In this section, we visualize the motif features that the convolution filters most likely to capture. Each convolution kernel in convolution layer has a sliding window with a width of 10 nucleotides to scan every 10-mer sub-sequences of input sequences. We utilize the values calculated by convolution kernels to visualize the learned motif features. For each convolution kernels, we search the 10-nt sub-sequence that kernels give the largest activation value for each DNA sequences sample. For all input DNA sequences, we construct position weight matrices and use WebLogo 3  to visuaDifferent positions in PAS DNA sequences may contribute differently in PAS identification. To find out the part with the biggest difference between true and pseudo PAS sequences, we propose to visualize the contribution of every position in PAS recognition. As we mentioned in the previous subsection, Visualization of captured features in convolution filters, a filter in convolution layers of Poly(A)-DG scans every 10-mer sub-sequences with a stride of one nucleotide and it calculates a score to each scanned sub-sequence at every position. For 16 filters in convolution layers, we average the scores assigned by them at every position and obtain scores for every position when sequences are sent to Poly(A)-DG. For every two-species source domain, we first feed positive PAS sequences to the Poly(A)-DG to get positive position scores and then send negative PAS sequences to obtain negative scores. We plot positive and negative position values in To further investigate the availability of Poly(A)-DG, we examine the performance of Poly(A)-DG on the whole genome of chromosome 1 of rat. PolyA-DB v3.2 provides 5,755 annotated PAS for chromosome 1 of rat. We first extract the whole genome of chromosome 1 in rat from genome database, and divided them into 206 nucleotides subsequences with a stride of 50 nucleotides. Owing to the PAS is a 6-nt motif, the same PAS contained by several consecutive 206-nt subsequences, though the position of PAS varies. In practical usage, the position of PAS within the DNA segments is unknown if we don’t have any annotation. Therefore, we label the sequences contain the entire PAS motif as positive samples and the remaining sequences as negative. Owing to the different strands of PAS, we reverse the chromosome 1 of rat and repeat the process mentioned above to extract positive and negative PAS sequences. The final established rat chromosome 1 PAS datasets contains 11,541,504 negative PAS sequences and 17,920 DNA sequences that contains PAS. We predict the rat chromosome 1 PAS datasets by Poly(A)-DG trained on three cross-species source domains. We report the false positive rate (FPR), false negative rate (FNR), and accuracy in We sought to examine whether the homology sequence among four PAS datasets affect the PAS identification. According to previous works , 51, we In our work, we propose a neural-network-based domain generalization model which can be trained on cross-species PAS datasets and directly applied to identify PAS from a new species. In our experiments, we mix each two of four datasets, Omni Human, BL Mouse, Rat, and bovine to build cross-species training sets and evaluate our method on rest species. According to the experimental results, Poly(A)-DG achieves relatively high accuracy over balanced cross-species datasets. Moreover, we investigate the performance of Poly(A)-DG on insufficient and imbalanced cross-species training sets. We observe that the performance of Poly(A)-DG would not decline drastically when the available training data significantly decreases. On imbalanced cross-species training sets, Poly(A)-DG works relatively stably when the size of one species varies. on imbalanced PAS positive-negative ratio cross-species datasets, the Poly(A)-DG can still work and detect the PAS even the number of negative samples is five times larger than the positive ones in the training domains. We conjecture that Poly(A)-DG outperforms existing methods may owe to its ability to learn invariant distributions between different species. Experimental results show that Poly(A)-DG, which is well adaptable to different species, provides us a promising way to address practical PAS identification problems. We investigate the homology effect of PAS datasets and empirical results indicate that Poly(A)-DG is slightly affected by the homology DNA sequences. We examine the performance of Poly(A)-DG in identifying the PAS from genes with single poly(A) site and multiple poly(A) site, and find that our model works better on gene with only one poly(A) site. We try to apply Poly(A)-DG on the whole genome from chromosome 1 of rat to evaluate the availability of Poly(A)-DG on practical usage and the relatively low false positive rate means that Poly(A)-DG may be a tool to help researchers to exclude DNA sequences that don’t contain PAS. We visualize the convolution filters and find most captured motifs are A-rich, T-rich and GT-rich DNA subsequences. We also visualize the position impact of PAS identification and find the 20-40 nt downstream of PAS contribute most in distinguishing true PAS from pseudo ones. We understand the RNA binding proteins (RBPs) are essential in polyadenylation regulation, while the current version of Poly(A)-DG doesn’t support the RBPs motif matching and the RBPs variants discovering among species. We will further work on this issue and hope to facilitate it in future works.S1 Supporting Information(PDF)Click here for additional data file.S1 FileThese three datasets are produced by previous researchers and we use them in our experiments.(ZIP)Click here for additional data file.S2 FileWe extract labeled Poly(A) signals sequences following the PolyA DB v3.2 dataset .(TXT)Click here for additional data file.S3 FileThe pseudo Poly(A) signal datasets used in experiments.(ZIP)Click here for additional data file.


To assess the impact of the lockdown due to coronavirus disease 2019 (COVID-19) on key quality indicators for the treatment of ST-segment elevation myocardial infarction (STEMI) patients.Data were obtained from 41 hospitals participating in the prospective Feedback Intervention and Treatment Times in ST-Elevation Myocardial Infarction (FITT-STEMI) study, including 15,800 patients treated for acute STEMI from January 2017 to the end of March 2020.p = 0.017) with a particular decline in intra-hospital infarctions and transfer patients from other hospitals, while the proportion of patients transported by emergency medical service (EMS) remained stable. In EMS-transported patients, predefined quality indicators, such as percentages of pre-hospital ECGs , direct transports from the scene to the catheterization laboratory bypassing the emergency department , and contact-to-balloon-times of less than or equal to 90 min  were not significantly altered during the COVID-19 crisis, as was in-hospital mortality .There was a 12.6% decrease in the total number of STEMI patients treated at the peak of the pandemic in March 2020 as compared to the mean number treated in the March months of the preceding years. This was accompanied by a significant difference among the modes of admission to hospitals  contains supplementary material, which is available to authorized users. According to a well-established recommendation in the current guidelines, patients presenting with ST-segment elevation myocardial infarction (STEMI) require instant revascularization by percutaneous coronary intervention (PCI), since any time delay in treatment is associated with increased cardiac damage and elevated mortality . Given tThe FITT-STEMI trial, which currently recruits more than 10% of all STEMI cases in Germany , was iniThe participating 41 PCI hospitals are all tertiary care centres included seven university clinics. All centres collected detailed clinical information for each consecutive STEMI patient on treatment times, including time intervals from symptom onset to arrival of the emergency medical service (EMS) on the scene, the duration of out-of-hospital treatment and the transport time to the nearest PCI centre as well as intra-hospital times for the transfer to the catheterization laboratory and the time to balloon inflation. In addition, comorbid diagnoses, medical history, Thrombolysis in Myocardial Infarction (TIMI) risk score for STEMI , medicalt test between the two groups of patients treated in March 2020 versus the three March months in the preceding years 2017–2019. Categorical variables from these two groups were analyzed using chi-square tests. For some of the analyses, the study cohort was classified along the guideline-recommended threshold for a contact-to-balloon time equal or less than 90 min. A series of linear regression models were computed with intervals of treatment times as dependent variable and study recruitment in March 2020 during the corona virus outbreak versus the March months in the three preceding years as independent variable. These models were adjusted for gender, age, TIMI risk score, infarct localization, and thrombolytic therapy. Logistic regression models for key quality markers in STEMI care as independent, dichotomous variables were created using the same set of covariables. In addition, a subgroup analysis was performed for all FITT-STEMI clinics in the Lower Rhine area around Heinsberg located close to Aachen, because this region in North Rhine-Westphalia was most heavily affected by the SARS-CoV-2 outbreak. As shown in the catchment area maps in Fig. p values are two-sided, and p values < 0.05 were considered statistically significant. No formal adjustment for multiple testing was carried out.For this post hoc study of the influence of the COVID-19-induced lockdown on German regional STEMI care networks, raw data from January 2017 to inclusively March 2020 were analyzed. Descriptive statistics were calculated as means with standard errors of the mean for continuous variables and frequencies with percentages for categorical variables. Continuous data were compared using Student´s n = 12,070, 76.4%) were transported directly from the field to the PCI hospital by EMS . During the total study period starting from January 2017, the average number of patients treated monthly who had a documented myocardial infarction experienced during hospital stay was ten patients (2.5%). Among all STEMI patients treated, 122 patients had pre-PCI fibrinolysis (0.8%) and 14,186 patients received primary PCI (89.8%). A detailed description of the total study population, including the comparison between the two groups of STEMI patients treated in March 2020 and the preceding three March months in the years 2017–2019, is given in Table In total, 15,800 consecutive STEMI patients presenting within 24 h of symptom onset were treated from January 1, 2017, to March 31, 2020 in all participating centres of the FITT-STEMI study group. Of those, the majority of patients (p = 0.017)  (Table p = 0.846). Similarly, the number of direct transfers to PCI treatment bypassing the emergency department remained at the same high level, as n = 179 (66.3%) patients reached the catheterization laboratory without a time-consuming delay before the reperfusion therapy. In the three preceding March months, the percentage of patients arriving at the catheterization laboratory without a stop at the emergency department was not significantly changed . In addition, there was no significant difference in the proportion of STEMI patients with treatment times from first medial contact to balloon inflation of equal or less than 90 min . Except for longer transport times from the field to the hospital (p = 0.003), the seven university clinics did not differ from other tertiary hospitals with respect to treatment times and quality indicators for STEMI care during the lockdown.The total number of EMS-transported patients treated within 360 min after first medical contact was reduced when compared to the mean of monthly cases in the preceding three March months (p = 0.433). For all STEMI patients transported by EMS and treated within 360 min after first medical contact, the mean contact-to-door time in the March months from 2017–2019 was 39.9 ± 0.5 min (Table p = 0.629). Likewise, the mean door-to-balloon time was similar in the last March month to the three preceding ones  . Regression models adjusted for gender, age, TIMI risk score, infarct localization, and thrombolytic therapy confirmed these results . However, in univariate analysis, there was a small but significant difference in the mean times from arrival at the catheterization laboratory to vessel puncture between patients treated before or during the COVID-19 outbreak .We found no evidence that symptomatic STEMI patient waited longer to seek medical help during the virus outbreak for fear of an hospital-acquired infection, as the mean time interval from symptom onset to first medical contact was not prolonged  (Table p = 0.739) . Similarly, neither was the number of direct transports to the catheterization laboratory bypassing the emergency department  nor the proportion of contact-to-balloon times within 90 min  reduced significantly at the peak of the coronavirus outbreak. Likewise, the proportion of pre-announcement by telephone before the ambulance arrived at the hospital did not differ between the groups . Except for a shorter EMS transport time by 3 min during the lockdown , all other measured time intervals did not differ when compared for the months with and without infections . Secondly, this decrease included STEMI patients with self-referral, transfer patients from non-PCI hospitals, and patients suffering myocardial infarction during hospital stay, whereas the number of EMS-transported STEMI cases remained stable. Thirdly, except for a significantly prolonged time from arrival at the catheterization laboratory to vessel puncture, there were no significant changes in parameters of STEMI care and time lines of the treatment chain in the group of STEMI patients directly brought by EMS to the PCI-hospitals. Fourthly, even in the hot spot of SARS-CoV-2 infections during March 2020 in the heavily affected Lower Rhine area, which was completely covered by hospitals involved in the FITT-STEMI programme, we found no impairment in the established quality indicators for STEMI care.In Germany, STEMI patients transported by EMS from the scene constitute the vast majority of acute PCI-treated STEMI cases and this number did not decline during the virus outbreak. Although the case numbers of patients with self-referral or inter-facility transports were remarkably reduced, there was only a moderate decrease in total STEMI numbers at the peak of the infections. This finding is in contrast to three recent reports on decreasing numbers of STEMI treatment published from cardiac catheterization laboratories in the United States and Spanish PCI centres , 20, 21.Notably, in our cohort, there were neither significant delays in the contact-to-door nor the door-to-balloon time related to the outbreak of the virus. However, owing to safety precautions in preparation for the PCI procedure, the time interval from arrival at the catheterization laboratory to vessel puncture was significantly prolonged. This observation indicates that the interventional cardiologists took concerns seriously having been raised about the risk of peri-procedural transmission of SARS-CoV-2 between STEMI patients and medical staff as well as a further dissemination of the disease , 21, 22.Other process-relevant and clinically important indicators of STEMI care performance were also not impaired, such as the proportion of pre-hospital ECG recordings, direct transports to the catheterization laboratory bypassing the emergency department and the achievement of the guideline-recommended contact-to-balloon time of less than 90 min. These data from Germany are not in line with a recent report from a small sample of seven STEMI patients treated in Hong Kong during the COVID-19 pandemic, which showed dramatic changes in treatment times . A reporIn the FITT-STEMI programme, feedback mechanisms had been successfully implemented to shorten treatment times and improve prognosis in STEMI patients in previous years , 18, 24.Even clinics confronted with high case numbers of SARS-CoV-2-infected patients, such as the hospitals in the Lower Rhine area, were capable of maintaining high process standards in their routine STEMI management. Our measurements were sensitive enough to detect small changes in treatment times, as there was a significant 3-min shortening during the virus outbreak from the scene to the hospital, which probably reflects the slowdown of traffic at that time, thereby promoting road-based transportation. Despite their fight against the spread of the virus, the hot-spot hospitals in the Heinsberg area preserved their obligations for protocol-based STEMI care using predefined quality markers for timely reperfusion. Therefore, concerns about a limited number of interventional cardiologists and expert medical personnel available in the catheterization laboratory during the outbreak period proved to be unfounded.When faced by the challenge of SARS-CoV-2-positive patients or subjects with an unknown viral status, some authors reconsidered intravenous thrombolysis as an alternative, albeit less effective strategy for coronary revascularization , 25, 26.Several issues merit consideration in the interpretation of the present results from the observational FITT-STEMI study. Firstly, the registry-based, cross-sectional nature of the FITT-STEMI trial may be susceptible to unmeasured confounding and selection bias, such as non-system reasons for treatment delays independent of the coronavirus crisis. Secondly, other German PCI hospitals, which are not members in the FITT-STEMI consortium, may be less privileged in their treatment pathways for STEMI patients, because they do not receive regular site-specific data assessments on treatment times and in-hospital mortality using interactive feedback sessions. Therefore, it is formally not possible to extrapolate our findings to all German PCI centres. Thirdly, we assessed only short-term outcome, as data on long-term follow-up are currently not available and the SARS-CoV-2 outbreak is still not under control. Fourthly, the findings from our study conducted in Germany are not applicable to STEMI management care systems in other countries, in which exclusively paramedics are part of the EMS transportation teams and not physicians experienced in emergency medicine. Thus, our results cannot be generalized to STEMI care systems in other countries using different pathways for treating their patients.In summary, during the COVID-19 crisis, we observed no impairment in the quality of STEMI care in the German FITT-STEMI hospitals. Our data suggest that a pre-established, robust organisational structure for STEMI care is an important requirement for timely treatment of STEMI patients and ensures the stability of outcome-relevant performance parameters, even when confronted with the burden of the global, ongoing pandemic.Supplementary file1 (DOCX 34 kb)Below is the link to the electronic supplementary material.


This work presents a formation method of mechanically-induced long-period fiber gratings using laminated plates. The mechanically-induced long-period fiber grating is temporarily inscribed by compressing the optical fiber between a flat plate and the proposed laminated plate. In turn, the new laminated plate consists of a parallel assembling of single-edged utility blades. We present the experimental characterization of mechanically-induced long-period fiber gratings while employing three laminated plates with a period of 480 ± 20 µm and low duty cycles. These mechanically-induced long-period fiber gratings display a leading rejection band (>15 dB) with a couple of shallow rejection bands (<2 dB) in the range of 1100–1700 nm. This spectral behavior is due to the new mechanical fabrication process that is based on laminated plates that we have proposed, which consists of piling multiple blades with trapezoidal edges that are polished with different levels to obtain different duty-cycles. With the proposed method, we can obtain values of duty-cycles around 10%, much lower than those obtained using traditional methods. Additionally, with this new method, the required mechanical pressure to form the grating is remarkably reduced, which minimizes the probability of the optical fiber failure in the mechanically-induced long-period fiber gratings (MI-LPFGs). Moreover, the proposed mechanically-induced long-period fiber gratings with a single rejection band open the feasibility to implement coarse wavelength division multiplexing systems that are based on long-period fiber gratings. The transversal refractive index modulation induced in the optical fiber when it is subjected to a uniaxial pressure has been studied while using different methods ,32. In tOn the other hand, according to the mechanical axial profile of the laminated plate and assuming a very weak cross-sensitivity between transversal and longitudinal strain for small applied perturbation over the fiber . The lonThe aforementioned Three laminated plates: L10, L20, and L30 with lengths of 10, 20, and 30 mm were prepared following the methodology that was described in the previous section. In the same way, L30 presents a leading rejection band at 1276 nm with two lateral lobes in the right and two shallow rejection bands at 1480 nm and 1690 nm; see A new laminated plate (NL20) was prepared following the grinding and polished process before described in order to understand the impact of the ADC on the spectrum transmission in the MI-LPFGs. By this process the ADC was varied from 10 to 50% in steps of around 10%. Subsequently, the uniaxial pressure on the optical fiber over the laminated plate was controlled by the static weight applied. As is well-known, the spectrum transmission of conventional MI-LPFGs is characterized by multiple rejection bands with deeper attenuation bands for high order couplings. In contrast, the proposed laminated plates allow for MI-LPFGs with only a stable leading rejection band and lower secondary shallow attenuations bands for high order couplings. Where, the attenuation depth of the secondary attenuation bands are more than one order lower with respect to the attenuation depth of the leading rejection bands, as can be observed in The leading rejection bands present other attractive optical and mechanical characteristics with respect to rejection bands in conventional MI-LPFGs. The leading rejection bands are located below 1300 nm with a contrast >15 dB for a 480 µm period, see The spectrum transmission of MI-LPFGs depends on the laminated plate quality. This, in turn, depends on the precision of the blade sizes and cutting-edge variation. In this case, the cutting-edge diameter of the blades varies from 25–35 µm. Additionally, the cutting-edge of the blades do not maintain their vertical symmetry, and the cutting-edge angle varies ±3°. On the other hand, the quality of the laminated plate also depends on the fabrication process. The manual cutting of the rectangular blades and the hand assembling process produced a significant scattering of the period and the In this work, a new method for implementing MI-LPFGs using laminated plates is presented. According to the experimental results, the proposed MI-LPFGs exhibit a spectrum transmission with a leading rejection band, and secondary shallow attenuation bands one order smaller. The leading rejection bands stand out for their high attenuation depth and low average background losses. To our best knowledge, this is the first time that MI-LPFGS with a single rejection band has been reported. Additionally, we experimentally analyze the influence of the ADC on the leading rejection band in the MI-LPFGs. In this respect, we report a MI-LPFG with an ADC of 20%, 10 mm of length, and 1700 g of static weight applied to obtain a leading rejection band with 20 dB of attenuation depth. As far as we know, the proposed laminated plates with low ADC require the lowest uniaxial pressure being reported on MI-LPFGs. Furthermore, the concept of LPFGs with a leading rejection band can be extended to other inscription methods, like UV or the fs-lasers. Finally, the proposed MI-LPFGs show the potential implementation of wavelength division multiplexing of sensors or devices based on MI-LPFGs at 1300 nm and 1500 nm bands for the first time.


The global spread of COVID-19 remains unabated in the past few months with a rise in the number of available literature on the novel virus. There are very few paediatric studies and are mainly from developed countries with a paucity of information on the clinical manifestation of COVID-19 disease in African children, including Nigeria.We described the clinical presentation, laboratory findings, treatment and outcome in a group of five Nigerian children managed at a COVID-19 isolation and treatment centre in Nigeria.We managed a total of five children with an age range of 3 months to 8 years in the last four weeks (16th April to 15th May 2020). Three of the five children were males. All the children had close contact with family members that tested positive for COVID-19. Out of the five children, one had moderate disease, three had mild symptomatic disease, and one was asymptomatic. Two out of the five children had lymphocytosis. Out of the four children who had chest radiograph, two had features of pneumonia.COVID-19 is not uncommon in Nigerian children, and all had a confirmed family member with COVID-19. Besides, contrary to leucopaenia with lymphopaenia observed in the adult’s population, we found lymphocytosis in this cohort and about 50.0% had pneumonic changes on chest radiograph. The coronavirus disease 2019 (COVID-19) is a ravaging global pandemic that affects both the children and adults . Since tThis study was a retrospective review of a series of five cases, with an age range of 3 months to 8 years. They were brought to the designated COVID-19 treatment centre, in Katsina-Nigeria, between 16th April to 15th May 2020, because they had a positive real-time Polymerase chain reaction (RT-PCR) test for COVID-19. We carried out the COVID-19 confirmatory tests on oropharyngeal and nasopharyngeal swabs at the National Reference Laboratory in Abuja through the real-time polymerase chain reaction. The hospital ethic review committee approved this study, and we obtained informed consent from the parents of the children. We examined demographic variables, clinical presentations, laboratory findings, treatment and outcome in a group of five Nigeria children managed at the centre. The laboratory tests included full blood count and its differentials and chest radiograph. We carried out descriptive analysis using Microsoft Excel version 2016.Cases 1, 2 and 3 were siblings from the same parents and aged two years, four years and eight years, respectively. Their father had earlier tested positive for SARS-CoV-2. The two-year-old male child presented with a mild cough and nasal discharge. The examinations findings were unremarkable. The total full blood count was within a normal limit . HoweverCase four was an asymptomatic seven-year-old girl whose older siblings (aged 19 and 21) and mother tested positive for SARS-CoV-2. The full blood count was normal . She recThe age range of this study showed that children are vulnerable to COVID-19 across all age categories. This age range also falls within reported ages of children who had COVID-19 in china , Iran 66 and othThe main laboratory finding in our study is lymphocytosis (two out of five), which contrast with the observation of leucopaenia with lymphopaenia reported among the adult’s population . The ingThis study showed that the COVID-19 is not uncommon in Nigerian children and infected family members are potential sources of infection of children with COVID-19. Besides, contrary to leucopaenia with lymphopaenia observed in the adult’s population, we found lymphocytosis in this cohort, and 50.0% had pneumonic changes on chest radiograph..The author declares no competing interests.