Wasserstein Wormhole: Scalable Optimal Transport Distance with Transformers.

Optimal transport (OT) and the related Wasserstein metric ( W ) are powerful and ubiquitous tools for comparing distributions. However, computing pairwise Wasserstein distances rapidly becomes intractable as cohort size grows. An attractive alternative would be to find an embedding space in which pairwise Euclidean distances map to OT distances, akin to standard multidimensional scaling (MDS). We present Wasserstein Wormhole, a transformer-based autoencoder that embeds empirical distributions into a latent space wherein Euclidean distances approximate OT distances. Extending MDS theory, we show that our objective function implies a bound on the error incurred when embedding non-Euclidean distances. Empirically, distances between Wormhole embeddings closely match Wasserstein distances, enabling linear time computation of OT distances. Along with an encoder that maps distributions to embeddings, Wasserstein Wormhole includes a decoder that maps embeddings back to distributions, allowing for operations in the embedding space to generalize to OT spaces, such as Wasserstein barycenter estimation and OT interpolation. By lending scalability and interpretability to OT approaches, Wasserstein Wormhole unlocks new avenues for data analysis in the fields of computational geometry and single-cell biology. Software is available at http://wassersteinwormhole.readthedocs.io/en/latest/.

Do Crisis Details Differentiate Suicide-Related 911 Call Outcomes?

Background The outcomes of calling 911 for suicide crises remain largely unexplored. Aims To investigate how characteristics of individuals in a suicidal crisis (e.g., age, gender identity, help-seeking source, means, disclosure of historical suicidality, or self-harm) may differentiate outcomes when contacting 911. Method The authors analyzed 1,073 Washington State Police 911 call logs, coding for characteristics and outcome (unknown, monitoring, intervention, adverse outcome). Descriptive and inferential statistics, including multinomial logistic regressions, were used to explore associations. Results When individuals experiencing a suicidal crisis were referred by bystander or associates' observations, there was a greater likelihood of adverse outcome. Self-referral led to a greater likelihood of intervention. Referral from the suicidal individual contacting a known associate led to a greater likelihood of monitoring. Any disclosure of means led to a greater likelihood of intervention or adverse outcomes. Positive disclosure of historical suicidality or self-harm was more likely to result in monitoring. Limitations The dataset was intended for operational use in acute suicidality triage rather than research purposes. Conclusion This study highlights the importance of supporting first responders with research to enhance their triage of people experiencing suicidal crises.

Effects of sexual orientation and NSSI severity on suicide risk.

INTRODUCTION: People who identify as sexual minorities are at increased risk for suicide. Non-suicidal self-injury (NSSI) is also a risk factor for suicide and NSSI severity may contribute to development of capability for lethal self-injury. Further research is needed to understand how NSSI severity increases suicide risk, specifically in high-risk populations like sexual minorities. The current study seeks to examine whether sexual minority adults exhibit greater NSSI severity and suicide risk than heterosexuals, and if NSSI severity moderates the relationship between sexual orientation and suicide risk. METHODS: Undergraduate students (N = 1,994) who reported five or more acts of NSSI in their lifetime completed online self-report questionnaires including sexual orientation, NSSI severity, and suicide risk. RESULTS: A factorial ANOVA demonstrated main effects of sexual orientation and NSSI severity on suicide risk. DISCUSSION: The lack of significant interaction effect indicates NSSI severity does not amplify the effect of on sexual orientation on suicide risk; rather, it predicts the same level of increased risk across orientations. Therefore, suicidality related to both sexual orientation and NSSI severity are equally important treatment targets.

Maltreatment history and reasons for self-injurious behavior among adolescents engaged in non-suicidal self-injury versus adolescents who attempted suicide.

OBJECTIVE: Self-injurious behavior (SIB) is a significant public health concern in the United States, especially among adolescents with histories of maltreatment. This study compared maltreatment characteristics and reasons for SIB between three homogenous samples of adolescents with either: (1) non-suicidal self-injury (NSSI); (2) suicide attempt/s (SA), and (3) typically developing controls (TDC). METHOD: Participants (N = 124) aged 13-17 years completed questionnaires about their maltreatment and SIB histories. RESULTS: Maltreatment rates were as follows: 90% NSSI group, 76% SA group, and 40% TDC group. Adolescents in the NSSI group reported significantly higher rates of emotional neglect compared to the SA group. Maltreated adolescents in the NSSI and SA groups reported the same top three SIB reasons: (1) get rid of bad feelings, (2) mental state at the time, and (3) problems with family. However, maltreated NSSI participants were significantly more likely to engage in SIB for emotion regulation reasons than maltreated SA participants, who were more likely to engage in SIB for interpersonal reasons. Physical neglect and physical abuse also arose as significant predictors of specific SIB reasons. CONCLUSIONS: Our findings help elucidate the maltreatment profiles and reasons for SIB among adolescents engaged in NSSI or SA. Specific maltreatment experiences may also influence the reasons why adolescents engaged in SIB.

Sex and age moderate the trajectory of guilt among children and adolescents with and without recent suicidal ideation.

We aimed to examine whether the trajectories of ecologically derived guilt differ among a transdiagnostic sample of youth with and without recent suicidal ideation and whether sex and age moderated this association. We assessed guilt 3 times a day over a 2-week period via ecological momentary assessment (EMA) technology in 102 children recruited from the community, outpatient, and inpatient settings. The average age of children was 10.95 y.o. (SD = 2.26, range 8-16) and the majority were male (54.9%) and White (76.5%). We found that the real-world guilt during a two-week EMA period was higher among youth with greater suicidal ideation severity in the past six months. Moreover, there was a significant moderating effect of sex and age on this association, such that the association between suicidal ideation severity and guilt was particularly strong among females compared to males and youth who were 10 years old or older. The findings were maintained when we adjusted for the relevant demographic and clinical characteristics, including age, minority status, parental income, EMA response rate, and current internalising symptoms. These preliminary findings highlight the clinical relevance of assessing and targeting feelings of guilt in the day-to-day lives of youth, particularly for females and older youth.

Relationship between cognitive flexibility and subsequent course of mood symptoms and suicidal ideation in young adults with childhood-onset bipolar disorder.

Neurocognitive deficits, such as cognitive flexibility impairments, are common in bipolar disorder (BD) and predict poor academic, occupational, and functional outcomes. However, the association between neurocognition and illness trajectory is not well understood, especially across developmental transitions. This study examined cognitive flexibility and subsequent mood symptom and suicidal ideation (SI) course in young adults with childhood-onset BD-I (with distinct mood episodes) vs. BD-not otherwise specified (BD-NOS) vs. typically-developing controls (TDCs). Sample included 93 young adults (ages 18-30) with prospectively verified childhood-onset DSM-IV BD-I (n = 34) or BD-NOS (n = 15) and TDCs (n = 44). Participants completed cross-sectional neuropsychological tasks and clinical measures. Then participants with BD completed longitudinal assessments of mood symptoms and SI at 6-month intervals (M = 39.18 ± 16.57 months of follow-up data). Analyses included ANOVAs, independent-samples t tests, chi-square analyses, and multiple linear regressions. Participants with BD-I had significant deficits in cognitive flexibility and executive functioning vs. BD-NOS and TDCs, and impaired spatial working memory vs. TDCs only. Two significant BD subtype-by-cognitive flexibility interactions revealed that cognitive flexibility deficits were associated with subsequent percentage of time depressed and with SI in BD-I but not BD-NOS, regardless of other neurocognitive factors (full-scale IQ, executive functioning, spatial working memory) and clinical factors (current and prior mood and SI symptoms, age of BD onset, global functioning, psychiatric medications, comorbidity). Thus, cognitive flexibility may be an important etiological brain/behavior mechanism, prognostic indicator, and intervention target for childhood-onset BD-I, as this deficit appears to endure into young adulthood and is associated with worse prognosis for subsequent depression and SI.

Understanding the Barriers to Pooled SARS-CoV-2 Testing in the United States.

Pooled testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is instrumental for increasing test capacity while decreasing test cost. Pooled testing programs permit sustainable, long-term surveillance measures, which are essential for the early detection of virus resurgence in communities or the emergence of variants of concern. While numerous pooled approaches have been proposed to increase test capacity, uptake by laboratories has been limited. On 9 December 2020, we invited 362 U.S. laboratories that inquired about the Yale School of Public Health SalivaDirect test to participate in a survey to evaluate testing constraints and pooling strategies for SARS-CoV-2 testing. The survey was distributed using Qualtrics, and three reminders were sent. The survey closed on 21 January 2021. Of 93 responses received (25.7% response rate), 90 were from Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories conducting SARS-CoV-2 testing. The remaining three were excluded from the analyses. Responses indicated that the major barriers to the uptake of pooled testing in the United States may not simply be the number of tests a laboratory can process per day, but rather the lack of clear protocols and adequate resources; laboratories are working with fixed physical and human capital constraints. Importantly, laboratories across the country are heterogeneous in infrastructure and workflow. The need for SARS-CoV-2 testing will remain for years to come. Testing programs can be maintained through pooled PCR testing strategies, and while statisticians, operations researchers, and others with expertise in sampling design have important value to add, laboratories require support on how to transition from traditional diagnostic testing to pooled surveillance. IMPORTANCE While numerous pooled SARS-CoV-2 testing approaches have been described in an effort to increase testing capacity and decrease test prices, uptake by laboratories has been limited. Responses to our survey of United States-based laboratories highlight the importance of consulting end-users-those that solutions are being designed for-so challenges can be addressed in a manner tailored to meet the specific needs out in the field. It may be surprising to those designing pooled testing strategies to learn that laboratories view pooling as more time-consuming than testing samples individually, and therefore that it is thought to create delays in test reporting.

This Is Your Brain on Irritability: A Clinician's Guide to Understanding How We Know What We Know Now, and What We Need to Know in the Future, About Irritability in Children and Adolescents.

Irritability is a common reason why children and adolescents are brought for psychiatric care. Although research is advancing what is known about the underlying brain and behavior mechanisms of irritability, clinicians often are shut out of that research. This article explains some of these research methods, providing brief summaries of what is known about brain/behavior mechanisms in disorders involving irritability, including bipolar disorder, disruptive mood dysregulation disorder, attention-deficit/hyperactivity disorder, and autism spectrum disorder. Greater access to these methods may help clinicians now and in the future, with such mechanisms translated into improved care, as occurs in the treatment of childhood leukemia.

Facial emotion recognition and mood symptom course in young adults with childhood-onset bipolar disorder.

Facial emotion recognition deficits are common in bipolar disorder (BD) and associated with impairment. However, the relationship between facial emotion recognition and mood course is not well understood. This study examined facial emotion recognition and subsequent mood symptoms in young adults with childhood-onset BD versus typically developing controls (TDCs). The sample included 116 young adults (ages 18-30, 58% male, 78% White) with prospectively verified childhood-onset BD (n = 52) and TDCs (n = 64). At baseline, participants completed a facial emotion recognition task (Diagnostic Analysis of Non-Verbal Accuracy-2) and clinical measures. Then, participants with BD completed mood symptom assessments every 6 months (M = 8.7 ± 5.2 months) over two years. Analyses included independent-samples t tests and mixed-effects regression models. Participants with BD made significantly more recognition errors for child expressions than TDCs. There were no significant between-group differences for recognition errors for adult expressions, or errors for specific child or adult emotional expressions. Participants had moderate baseline mood symptoms. Significant time-by-facial emotion recognition interactions revealed more recognition errors for child emotional expressions predicted lower baseline mania and stable/consistent trajectory; fewer recognition errors for child expressions predicted higher baseline mania and decreasing trajectory. In addition, more recognition errors for adult sad expressions predicted stable/consistent depression trajectory and decreasing mania; fewer recognition errors for adult sad expressions predicted decreasing depression trajectory and stable/consistent mania. Effects remained when controlling for baseline demographics and clinical variables. Facial emotion recognition may be an important brain/behavior mechanism, prognostic indicator, and intervention target for childhood-onset BD, which endures into young adulthood and is associated with mood trajectory.

The disconnect between researcher ambitions and reality in achieving impact in the Earth & Environmental Sciences - author survey.

Background: There is an increasing desire for research to provide solutions to the grand challenges facing our global society, such as those expressed in the UN SDGs ("real-world impact"). Herein, we undertook an author survey to understand how this desire influenced the choice of research topic, choice of journal, and preferred type of impact. Methods: We conducted a survey of authors who had published in >100 of our Earth & Environmental Science journals. The survey was sent to just under 60,000 authors and we received 2,695 responses (4% response rate).   Results: Respondents indicated that the majority of their research (74%) is currently concerned with addressing urgent global needs, whilst 90% of respondents indicated that their work either currently contributed to meeting real-world problems or that it would be a priority for them in the future; however, the impetus for this research focus seems to be altruistic researcher desire, rather than incentives or support from publishers, funders, or their institutions. Indeed, when contextualised within existing reward and incentive structures, respondents indicated that citations or downloads were more important to them than contributing to tackling real-world problems. Conclusions: At present, it seems that the laudable and necessary ambition of researchers in the Earth & Environmental Sciences to contribute to the tackling of real-world problems, such as those included in the UN SDGs, is seemingly being lost amidst the realities of being a researcher, owing to the prioritisation of other forms of impact, such as citations and downloads.

Maladaptive personality traits and the course of suicidal ideation in young adults with bipolar disorder: Cross-sectional and prospective approaches.

BACKGROUND: Childhood-onset bipolar disorder (BD) has considerable morbidity and mortality, including suicide. Many risk factors have been identified for suicidality, but the potential role of personality traits as assessed by a computer-assisted self-report measure remains unclear. AIMS: To address this gap in knowledge, we tested relations between pathological-range personality traits and suicidal ideation among young adults whose childhood-onset BD was prospectively confirmed by enrollment in the Course and Outcome of Bipolar Youth study (COBY) as children (n = 45) and a newly enrolled group of typically developing controls (TDCs; n = 52) both cross-sectionally and longitudinally after 1.5 years of follow up. MATERIALS & METHODS: Personality traits were assessed with the computerized Schedule for Nonadaptive and Adaptive Personality-2 (SNAP-2). RESULTS: Cross-sectionally, we found that participants with BD had elevated Suicide Proneness and Low Self-esteem versus TDCs at baseline. Furthermore, longitudinal analyses in the BD participants for whom we had 1.5 years of prospectively collected illness-course data showed that greater Suicide Proneness and Low Self-esteem prospectively predicted greater levels, shorter time until occurrence, and greater frequency of suicidal ideation during the follow-up. CONCLUSION: Our findings suggest the role of specific personality-related vulnerabilities in the course of BD that, pending replication, could contribute to development of interventions focused on personality traits among individuals with BD.

Acknowledging and Addressing Allostatic Load in Pregnancy Care.

The USA is one of the few countries in the world in which maternal and infant morbidity and mortality continue to increase, with the greatest disparities observed among non-Hispanic Black women and their infants. Traditional explanations for disparate outcomes, such as personal health behaviors, socioeconomic status, health literacy, and access to healthcare, do not sufficiently explain why non-Hispanic Black women continue to die at three to four times the rate of White women during pregnancy, childbirth, or postpartum. One theory gaining prominence to explain the magnitude of this disparity is allostatic load or the cumulative physiological effects of stress over the life course. People of color disproportionally experience social, structural, and environmental stressors that are frequently the product of historic and present-day racism. In this essay, we present the growing body of evidence implicating the role of elevated allostatic load in adverse pregnancy outcomes among women of color. We argue that there is a moral imperative to assign additional resources to reduce the effects of elevated allostatic load before, during, and after pregnancy to improve the health of women and their children.

A rank-based marker selection method for high throughput scRNA-seq data.

BACKGROUND: High throughput microfluidic protocols in single cell RNA sequencing (scRNA-seq) collect mRNA counts from up to one million individual cells in a single experiment; this enables high resolution studies of rare cell types and cell development pathways. Determining small sets of genetic markers that can identify specific cell populations is thus one of the major objectives of computational analysis of mRNA counts data. Many tools have been developed for marker selection on single cell data; most of them, however, are based on complex statistical models and handle the multi-class case in an ad-hoc manner. RESULTS: We introduce RANKCORR, a fast method with strong mathematical underpinnings that performs multi-class marker selection in an informed manner. RANKCORR proceeds by ranking the mRNA counts data before linearly separating the ranked data using a small number of genes. The step of ranking is intuitively natural for scRNA-seq data and provides a non-parametric method for analyzing count data. In addition, we present several performance measures for evaluating the quality of a set of markers when there is no known ground truth. Using these metrics, we compare the performance of RANKCORR to a variety of other marker selection methods on an assortment of experimental and synthetic data sets that range in size from several thousand to one million cells. CONCLUSIONS: According to the metrics introduced in this work, RANKCORR is consistently one of most optimal marker selection methods on scRNA-seq data. Most methods show similar overall performance, however; thus, the speed of the algorithm is the most important consideration for large data sets (and comparing the markers selected by several methods can be fruitful). RANKCORR is fast enough to easily handle the largest data sets and, as such, it is a useful tool to add into computational pipelines when dealing with high throughput scRNA-seq data. RANKCORR software is available for download at https://github.com/ahsv/RankCorr with extensive documentation.

White matter correlates of cognitive flexibility in youth with bipolar disorder and typically developing children and adolescents.

Prior studies using behavioral tasks and neuroimaging have shown that children and adolescents with bipolar disorder (BD) have deficits in cognitive flexibility (CF)-defined as adaptation to changing rewards and punishments. However, no study, to our knowledge, has examined the white matter microstructural correlates of CF in youth with BD. To address this gap, we examined the relationship between CF assessed with the Cambridge Neuropsychological Testing Automated Battery (CANTAB)'s Intra-Extra Dimensional Set Shift task (ID/ED) and diffusion tensor imaging analyzed with FSL's preprocessing tools and Tract-Based Spatial Statistics (TBSS). We found a significantly different relationship between microstructural integrity of multiple white matter regions and CF performance in BD (n=28) and age-matched typically developing control (TDC) youths (n=26). Evaluation of the slopes of linear regressions in BD vs. TDC (ID/ED Simple Reversal error rate vs. fractional anisotropy) revealed significantly different slopes across the groups, indicating an aberrant relationship between CF and underlying white matter microstructure in youth with BD. These results underscore the importance of examining specific CF-neuroimaging relationships in BD youth. Future longitudinal studies could seek to define the white matter microstructural trajectories in BD vs. TDC, and relative to CF deficits and BD illness course.

Do styles of emotion dysregulation differentiate adolescents engaging in non-suicidal self-injury from those attempting suicide?

Emotion dysregulation is implicated in both suicide attempts (SA) and non-suicidal self-injury (NSSI). However, little is known about how emotion dysregulation may differ between adolescents who have made an SA from those engaged in NSSI. We sought to address this gap by comparing emotion dysregulation profiles across three homogenous groups of adolescents (1) SA-only (2) NSSI-only (3) and typically developing controls (TDCs). Mean comparisons suggest that adolescents with a history of NSSI reported significantly lower distress tolerance and higher emotional reactivity when compared to adolescents who made an SA. After controlling for shared variance across emotion dysregulation measures, parent report of affective lability was the only scale to uniquely distinguish between NSSI and SA groups. Accurately distinguishing emotion dysregulation patterns across self-injurious groups has practical implications towards assessment, treatment, course of illness, and prevention.

Imaging from the inside out: inverse scattering with photoactivated internal sources.

We propose a method to reconstruct the optical properties of a scattering medium with subwavelength resolution. The method is based on the solution to the inverse scattering problem with internal sources. Applications to photoactivated localization microscopy are described.

Training differentially regulates elastin level and proteolysis in skeletal and heart muscles and aorta in healthy rats.

Exercise induces changes in muscle fibers and the extracellular matrix that may depend on elastin content and the activity of proteolytic enzymes. We investigated the influence of endurance training on the gene expression and protein content and/or activity of elastin, elastase, cathepsin K, and plasmin in skeletal and heart muscles and in the aorta. Healthy rats were randomly divided into untrained (n=10) and trained (n=10; 6 weeks of endurance training with increasing load) groups. Gene expression was evaluated via qRT-PCR. Elastin content was measured via enzyme-linked immunosorbent assay and enzyme activity was measured fluorometrically. Elastin content was significantly higher in skeletal (P=0.0014) and heart muscle (P=0.000022) from trained rats versus untrained rats, but not in the aorta. Although mRNA levels in skeletal muscle did not differ between groups, the activities of elastase (P=0.0434), cathepsin K (P=0.0343) and plasmin (P=0.000046) were higher in trained rats. The levels of cathepsin K (P=0.0288) and plasminogen (P=0.0005) mRNA were higher in heart muscle from trained rats, but enzyme activity was not. Enzyme activity in the aorta did not differ between groups. Increased elastin content in muscles may result in better adaption to exercise, as may remodeling of the extracellular matrix in skeletal muscle.

Activity of Cathepsin B in Serum of Patients after Kidney Transplantation Depends on Glucocorticosteroids Treatment.

BACKGROUND: Kidney diseases are characterized by deterioration of the function of this organ, often leading to irreversible failure, where transplantation is the only alternative to permanent dialysis. Proteolytic enzymes, including cathepsins B, cleave the peptide bond by hydrolysis reaction. They are also involved in pathological processes such as carcinogenesis and inflammatory processes. The aim of this study was to determine the activity of cathepsin B in the serum of patients after kidney transplantation and to assess the correlation with glucocorticosteroids treatment. MATERIAL AND METHODS: In the study, blood samples of 100 renal transplant recipients were used. The subjects were divided into groups according to the time elapsed since transplantation and the use of steroids in the current and primary treatment. Enzyme activity was measured by spectrofluorometric technique. RESULTS: The study showed significant correlations of cathepsin B with the time since renal transplantation (p<0.05) and steroid used in the primary and current treatment. Steroid treatment is associated with a decrease of the activity of cathepsin B in serum. CONCLUSIONS: The obtained results show decreasing activity of cathepsin B with longer time elapsed since transplantation. We have shown that steroids decrease activity of cathepsin B after renal transplantation. A significant increase in cathepsin B activity is observed mainly in cancer and atherosclerosis. Decreased activity of cathepsin B is probably due to the stabilizing action of steroids on the lysosomal membrane. The impact of steroid therapy for patients with these diseases appears to be significant.

[Physical activity in prevention and treatment of colon cancer]. / Wysilek fizyczny w prewencji i leczeniu raka jelita grubego.

Colon cancer is currently the third most common cancer disease in men and second in women. Physical exercise of sufficient intensity and duration reduces the risk of colon cancer by as much as 30-50%. Despite many studies the mechanism of this phenomenon remains unclear. However it is known, to be caused by coexistence of various factors. The control of energy balance, body weight and insulin resistance seems to be most important. Myokines also play a very important role. Among them: SPARC that causes inhibition of proliferation and apoptosis and anti-inflammatory cytokines. In addition, physical activity exerts local anti-inflammatory effect by decreased expression of COX-2 and iNOS in the colon mucosa. Physical exercise also improves survival rates after treatment of colon cancer. But it seems that better prognosis is only observed in selected group of patients diagnosed with specific biomarkers of cancer cells. Despite beneficial effects of physical activity, awareness of this fact is very low.