Predicting state level suicide fatalities in the united states with realtime data and machine learning.

Digital trace data and machine learning techniques are increasingly being adopted to predict suicide-related outcomes at the individual level; however, there is also considerable public health need for timely data about suicide trends at the population level. Although significant geographic variation in suicide rates exist by state within the United States, national systems for reporting state suicide trends typically lag by one or more years. We developed and validated a deep learning based approach to utilize real-time, state-level online (Mental Health America web-based depression screenings; Google and YouTube Search Trends), social media (Twitter), and health administrative data (National Syndromic Surveillance Program emergency department visits) to estimate weekly suicide counts in four participating states. Specifically, per state, we built a long short-term memory (LSTM) neural network model to combine signals from the real-time data sources and compared predicted values of suicide deaths from our model to observed values in the same state. Our LSTM model produced accurate estimates of state-specific suicide rates in all four states (percentage error in suicide rate of -2.768% for Utah, -2.823% for Louisiana, -3.449% for New York, and -5.323% for Colorado). Furthermore, our deep learning based approach outperformed current gold-standard baseline autoregressive models that use historical death data alone. We demonstrate an approach to incorporate signals from multiple proxy real-time data sources that can potentially provide more timely estimates of suicide trends at the state level. Timely suicide data at the state level has the potential to improve suicide prevention planning and response tailored to the needs of specific geographic communities.

WITHDRAWN: Oncogenic KRAS G12D extrinsically induces an immunosuppressive microenvironment in lung adenocarcinoma.

This manuscript has been withdrawn by the authors due to a dispute over co-first authorship that is currently being arbitrated by the medical school at our institution. Therefore, the authors do not wish this work to be cited as reference for the project. Upon completion of the arbitration process, we will take steps to revert the current withdrawn status. If you have any questions, please contact the corresponding author.

Modeling Molecular Pathogenesis of Idiopathic Pulmonary Fibrosis-Associated Lung Cancer in Mice.

Idiopathic pulmonary fibrosis (IPF) is characterized by progressive, often fatal loss of lung function due to overactive collagen production and tissue scarring. Patients with IPF have a sevenfold-increased risk of developing lung cancer. The COVID-19 pandemic has increased the number of patients with lung diseases, and infection can worsen prognoses for those with chronic lung diseases and disease-associated cancer. Understanding the molecular pathogenesis of IPF-associated lung cancer is imperative for identifying diagnostic biomarkers and targeted therapies that will facilitate prevention of IPF and progression to lung cancer. To understand how IPF-associated fibroblast activation, matrix remodeling, epithelial-to-mesenchymal transition (EMT), and immune modulation influences lung cancer predisposition, we developed a mouse model to recapitulate the molecular pathogenesis of pulmonary fibrosis-associated lung cancer using the bleomycin and Lewis lung carcinoma models. We demonstrate that development of pulmonary fibrosis-associated lung cancer is likely linked to increased abundance of tumor-associated macrophages and a unique gene signature that supports an immune-suppressive microenvironment through secreted factors. Not surprisingly, preexisting fibrosis provides a pre-metastatic niche and results in augmented tumor growth, and tumors associated with bleomycin-induced fibrosis are characterized by a dramatic loss of cytokeratin expression, indicative of EMT. IMPLICATIONS: This characterization of tumors associated with lung diseases provides new therapeutic targets that may aid in the development of treatment paradigms for lung cancer patients with preexisting pulmonary diseases.

Combination therapy with simultaneous delivery of spinal cord stimulation modalities: COMBO randomized controlled trial.

Aim: The Combining Mechanisms for Better Outcomes randomized controlled trial assessed the effectiveness of various spinal cord stimulation (SCS) modalities for chronic pain. Specifically, combination therapy (simultaneous use of customized sub-perception field and paresthesia-based SCS) versus monotherapy (paresthesia-based SCS) was evaluated. Methods: Participants were prospectively enrolled (key inclusion criterion: chronic pain for ≥6 months). Primary end point was the proportion with ≥50% pain reduction without increased opioids at the 3 month follow-up. Patients were followed for 2 years. Results: The primary end point was met (n = 89; p < 0.0001) in 88% of patients in the combination-therapy arm (n = 36/41) and 71% in the monotherapy arm (n = 34/48). Responder rates at 1 and 2 years (with available SCS modalities) were 84% and 85%, respectively. Sustained functional outcomes improvement was observed out to 2 years. Conclusion: SCS-based combination therapy can improve outcomes in patients with chronic pain. Clinical Trial Registration: NCT03689920 (ClinicalTrials.gov), Combining Mechanisms for Better Outcomes (COMBO).

Spinal cord stimulation (SCS) is a device-based therapy for chronic pain that delivers electrical impulses to the spinal cord, disrupting pain signals to the brain. Pain relief can be achieved using different SCS techniques that use or do not use paresthesia (stimulation that produces a tingling sensation). These approaches affect patients in different ways, suggesting that different biological processes are involved in enabling pain relief. Research also suggests that better long-term results occur when patients can choose the therapy that is best for their own needs. This clinical study compared pain relief and other functional activities in those receiving combination therapy (simultaneous use of SCS that does and does not produce tingling sensation) against those receiving monotherapy (only SCS therapy producing tingling sensation) for 3 months. In the study, 88% of those receiving combination therapy and 71% with monotherapy alone reported a 50% (or greater) decrease in overall pain (the 'responder rate') without an increased dose of opioid drugs at 3 months after the start of therapy. This responder rate was found to be 84% at 1 year and 85% at 2 years (with all SCS therapy options available). Analysis of functional activities or disability showed that patients improved from 'severely disabled' at study start to 'moderately disabled' after 2 years, indicating that effective long-term (2 year) improvement can be achieved using SCS-based combination therapy for chronic pain.

Clinical Features and Outcomes of Patients with Pancreaticobiliary Malignancies in Los Angeles County and Their Association with CA 19-9 Levels.

Although CA 19-9 is a commonly used tumor marker in the management of PBMs, the literature describing outcomes in patients with PBMs who have undetectable or low (hereinafter "low") CA 19-9 levels remains scarce. In this study, we sought to compare clinical features and outcomes in patients with PBMs and low CA 19-9 levels to those with normal and elevated CA 19-9 levels. METHODS: We retrospectively collected data on patients with biopsy-confirmed PBMs and stratified patients into categories based on their CA 19-9 level at diagnosis. Survival curves were estimated for patients in each of the three aforementioned CA 19-9 groups using the Kaplan-Meier method and compared using a Cox proportional hazards regression model. RESULTS: Of the 283 patients identified, 23 (8.1%) had low, 70 (24.7%) had normal, and 190 (67.1%) had elevated CA 19-9 levels. After controlling for sex, age, BMI, the presence of metastases at the time of diagnosis, and treatment with curative intent, the hazard ratio for death in the elevated CA 19-9 group compared to the low CA 19-9 group was 1.993 (95% CI 1.089-3.648; p = 0.025). CONCLUSION: The elevated CA 19-9 level compared to the low CA 19-9 level and the presence of metastases were associated with an increased hazard of death, while treatment with curative intent was associated with a decreased hazard of death.

Applying Lean Kaizen to Improve Timely Computed Tomography Scan Appointments for Oncology Patients in a Safety Net Hospital.

PURPOSE: Timely radiographic studies are essential to oncology care. At our institution, a safety net hospital in a large metropolitan area, baseline assessment determined that the overwhelming majority of outpatient computed tomographic (CT) scans for oncology patients were overdue and not scheduled within 2 weeks of their first requested date. METHODS: We conducted a series of structured, interdisciplinary meetings including staff from radiology, oncology, scheduling, and administration to critically review the scheduling process utilizing Lean Kaizen quality improvement methods. A new workflow was developed in which clinic staff scheduled CT scans before clinic discharge. Three months after our initial meeting, the new workflow was launched. We set a target of decreasing the percentage of overdue scans to below 20%. RESULTS: At baseline, 87% (65 of 75) of CT scans awaiting scheduling were overdue. Data were gathered at 5 and 10 weeks after implementation of our workflow. The percentage of CT scans overdue for scheduling was 17% (9 of 53) at 5 weeks and 0.97% (1 of 103) at 10 weeks after implementation. Clinic visit durations were not affected. CONCLUSION: The Lean Kaizen QI model was successful in decreasing the rate of oncology patients overdue for CT scan scheduling with minimal effects on clinic visit durations. This study demonstrated the importance of interdepartmental collaboration and continuous monitoring for improvement. Given the success of this project, this workflow will be expanded to other outpatient clinics within our institution.

Spinal Cord Stimulation in Special Populations: Best Practices from the American Society of Pain and Neuroscience to Improve Safety and Efficacy.

Chronic bleeding disorders, allergy to implants, and chronic infections are all complicating factors when considering neuromodulation therapies. The American Society of Pain and Neuroscience (ASPN) determined a need for clinical guidance in these special patient populations that have increased risk of complications, in order to ensure patient safety and optimal outcomes with device implantation. The purpose of this publication was to review the published literature and explore the unique clinical challenges encountered among several special patient populations with relation to spinal cord stimulation. The executive board of the ASPN appointed a diverse group of well-established physicians to develop best practice guidelines regarding spinal cord stimulation implantation in these special populations. The physicians used the United States Preventive Services Task Force (USPSTF) structured guidelines for grading and level of certainty to make evidence-based recommendations about clinical practice. Where sufficient evidence was lacking to justify a USPSTF ranking, the physicians queried experts in neuromodulation and achieved consensus. These best practices and interventional guideline found the evidence for the use of neuromodulation in specialized patient populations to be relatively modest.

User Engagement and Assessment of Treatment Effectiveness in Patients Using a Novel Digital mHealth App During Spinal Cord Stimulation Screening Trials.

BACKGROUND: Patient outcomes and experience during a Spinal Cord Stimulation (SCS) screening trial can have a significant effect on whether to proceed with long-term, permanent implantation of an SCS device for the treatment of chronic pain. Enhancing the ability to track and assess patients during this initial trial evaluation offers the potential for improved understanding regarding the suitability of permanent device implantation as well as identification of the SCS-based neurostimulative modalities and parameters that may provide substantial analgesia in a patient-specific manner. OBJECTIVE: In this report, we aimed to describe a preliminary, real-world assessment of a new, real time tracking, smart, device-based digital app used by patients with chronic pain undergoing trial screening for SCS therapy. METHODS: This is a real-world, retrospective evaluation of 13,331 patients diagnosed with chronic pain who used the new "mySCS" mobile app during an SCS screening trial. The app design is health insurance portability and accountability act (HIPAA)-compliant and compatible with most commercially available smartphones (eg, Apple, iPhone, and Android). The app enables tracking of user-inputted health-related responses (ie, pain relief, activity level, and sleep quality) in addition to personal trial goals and a summary of overall experience during the SCS trial. A deidentified, aggregate analysis of user engagement, user-submitted responses, and overall trial success was conducted. RESULTS: When provided the opportunity, the percentage of users who engaged with the tracking app for ≥50% of the time during their trial was found to be 64.43% (n=8589). Among the 13,331 patients who used the app, 58.24% (n=7764) entered a trial goal. Most patients underwent SCS screening with a trial duration of at least 7 days (n=7739, 58.05%). Of those patients who undertook a 7-day SCS trial, 62.30% (n=3456) engaged the app for 4 days or more. In addition, among all who submitted descriptive responses using the app, health-related improvements were reported by 77.84% (n=10,377) of patients who reached day 3 of the screening phase assessment and by 83.04% (n=11,070) of those who reached trial completion. A trial success rate of 91% was determined for those who used the app (versus 85% success rate for nonusers). CONCLUSIONS: Data from this initial, real-world examination of a mobile, digital-health-based tracking app ("mySCS"), as used during the SCS screening phase, demonstrate that substantial patient engagement can be achieved while also providing for the acquisition of more real time patient-outcome measures that may help facilitate improved SCS trial success.

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification.

Maximizing the personal, public, research, and clinical value of genomic information will require the reliable exchange of genetic variation data. We report here the Variation Representation Specification (VRS, pronounced "verse"), an extensible framework for the computable representation of variation that complements contemporary human-readable and flat file standards for genomic variation representation. VRS provides semantically precise representations of variation and leverages this design to enable federated identification of biomolecular variation with globally consistent and unique computed identifiers. The VRS framework includes a terminology and information model, machine-readable schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. VRS was developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH).

Immune Thrombocytopenic Purpura (ITP) as an Uncommon Extraintestinal Complication of Crohn's Disease: Case Vignette and Systematic Literature Review.

While the association of immune thrombocytopenic purpura (ITP) and inflammatory bowel disease (IBD) has been described in a few case reports, management of ITP as an extraintestinal manifestation of Crohn's disease (CD) is less studied. There are approximately a dozen cases describing the management of patients dually diagnosed with CD/ITP. Previous reports postulated that the mechanism of ITP in CD was through the presence of circulating immune complexes in the serum and antigenic mimicry due to increased mucosal permeability in active colitis, versus increased mucosal production of TH1-type proinflammatory cytokines during CD flares, which may account for remission of ITP with surgery for CD. We present a case of a 27-year-old man who presented with medically refractory CD and ITP who responded to surgical management with colectomy and splenectomy, along with a systematic review of the literature. These cases suggest that colectomy should be considered in the treatment of medically refractory ITP among patients with concomitant CD.

A Directed Route to Colloidal Nanoparticle Synthesis of the Copper Selenophosphate Cu3 PSe4.

The first colloidal nanoparticle synthesis of the copper selenophosphate Cu3 PSe4 , a promising new material for photovoltaics, is reported. Because the formation of binary copper selenide impurities seemed to form more readily, two approaches were developed to install phosphorus bonds directly: 1) the synthesis of molecular P4 Se3 and subsequent reaction with a copper precursor, (P-Se)+Cu, and 2) the synthesis of copper phosphide, Cu3 P, nanoparticles and subsequent reaction with a selenium precursor, (Cu-P)+Se. The isolation and purification of Cu3 P nanoparticles and subsequent selenization yielded phase-pure Cu3 PSe4 . Solvent effects and Se precursor reactivities were elucidated and were key to understanding the final reaction conditions.

ClinVar: improving access to variant interpretations and supporting evidence.

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.

Symmetry recognition by pigeons: Generalized or not?

This note looks into the reasons why earlier reports may have arrived at differing conclusions about pigeons' capacity to categorize bilaterally symmetric and asymmetric visual patterns. Attention is drawn to pigeons' comparatively superior visual flicker resolution and superior visual linear acuity by reporting results of two ad-hoc experiments. This circumstance turns out to constrain conclusions drawn by earlier symmetry-asymmetry studies that used computer-generated patterns displayed on cathode ray tube monitors as these suffered from pictorial distortions. Additionally one of the studies involved patterns of inconsistent symmetry at global and local levels. A smaller-scale experiment using slide-projected unequivocal symmetric and asymmetric patterns yielded results compatible with the supposition that pigeons are capable of a symmetry-asymmetry categorization. The possibility that an artfactual cue may have inadvertently accentuated this capability in an earlier own experiment is considered.

Using ClinVar as a Resource to Support Variant Interpretation.

ClinVar is a freely accessible, public archive of reports of the relationships among genomic variants and phenotypes. To facilitate evaluation of the clinical significance of each variant, ClinVar aggregates submissions of the same variant, displays supporting data from each submission, and determines if the submitted clinical interpretations are conflicting or concordant. The unit describes how to (1) identify sequence and structural variants of interest in ClinVar by multiple searching approaches, including Variation Viewer and (2) understand the display of submissions to ClinVar and the evidence supporting each interpretation. By following this protocol, ClinVar users will be able to learn how to incorporate the wealth of resources and knowledge in ClinVar into variant curation and interpretation.

ClinVar: public archive of interpretations of clinically relevant variants.

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) at the National Center for Biotechnology Information (NCBI) is a freely available archive for interpretations of clinical significance of variants for reported conditions. The database includes germline and somatic variants of any size, type or genomic location. Interpretations are submitted by clinical testing laboratories, research laboratories, locus-specific databases, OMIM®, GeneReviews™, UniProt, expert panels and practice guidelines. In NCBI's Variation submission portal, submitters upload batch submissions or use the Submission Wizard for single submissions. Each submitted interpretation is assigned an accession number prefixed with SCV. ClinVar staff review validation reports with data types such as HGVS (Human Genome Variation Society) expressions; however, clinical significance is reported directly from submitters. Interpretations are aggregated by variant-condition combination and assigned an accession number prefixed with RCV. Clinical significance is calculated for the aggregate record, indicating consensus or conflict in the submitted interpretations. ClinVar uses data standards, such as HGVS nomenclature for variants and MedGen identifiers for conditions. The data are available on the web as variant-specific views; the entire data set can be downloaded via ftp. Programmatic access for ClinVar records is available through NCBI's E-utilities. Future development includes providing a variant-centric XML archive and a web page for details of SCV submissions.

Chemical Control over Cellular Uptake of Organic Nanoparticles by Fine Tuning Surface Functional Groups.

The functional groups displayed on the surface of nanoparticles (NP) are known to play an important role in NP cellular uptake. However, only a few systematic studies have been reported to address their role, in large part because of the difficulty in regularly varying the number and structure of the functional groups on the NP surface. We employ a bottom-up strategy for the synthesis of water-soluble organic nanoparticles (ONPs) with different sizes and functional groups, using readily available monomers. Utilizing flow cytometry, we measured the HeLa cell uptake efficiency of ONPs that contain side-chains with a different (a) length, (b) number of hydroxyl groups, and (c) number of methyl groups. We have also investigated ONPs with the same functional groups but different sizes. The potential formation and influence of protein corona was examined using the same approach but in the presence of serum. The results demonstrate that under both serum and serum-free conditions the surface-exposed functional groups determine the efficiency of cellular uptake of the particles, and that the trend can be partially predicted by the lipophilicity of the polymeric ONP's repeating units. Also, by using a "masking" strategy, these particles' cellular uptake behavior could be altered conveniently.

ClinVar: public archive of relationships among sequence variation and human phenotype.

ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) provides a freely available archive of reports of relationships among medically important variants and phenotypes. ClinVar accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation. The database is tightly coupled with dbSNP and dbVar, which maintain information about the location of variation on human assemblies. ClinVar is also based on the phenotypic descriptions maintained in MedGen (http://www.ncbi.nlm.nih.gov/medgen). Each ClinVar record represents the submitter, the variation and the phenotype, i.e. the unit that is assigned an accession of the format SCV000000000.0. The submitter can update the submission at any time, in which case a new version is assigned. To facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, assigns a distinct accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations. Data in ClinVar are available in multiple formats, including html, download as XML, VCF or tab-delimited subsets. Data from ClinVar are provided as annotation tracks on genomic RefSeqs and are used in tools such as Variation Reporter (http://www.ncbi.nlm.nih.gov/variation/tools/reporter), which reports what is known about variation based on user-supplied locations.

The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae).

A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.

The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency.

The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information's databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html).

Circadian regulation of cortisol release in behaviorally split golden hamsters.

The master circadian clock located within the hypothalamic suprachiasmatic nucleus (SCN) is necessary for the circadian rhythm of glucocorticoid (GC) release. The pathways by which the SCN sustains rhythmic GC release remain unclear. We studied the circadian regulation of cortisol release in the behaviorally split golden hamster, in which the single bout of circadian locomotor activity splits into two bouts approximately 12 h apart after exposing the animals to constant light conditions. We show that unsplit control hamsters present a single peak of cortisol release that is concomitant with a single peak of ACTH release. In contrast, split hamsters show two peaks of cortisol release that are approximately 12 h appart and are appropriately phased to each locomotor activity bout but surprisingly do not rely on rhythmic release of ACTH. Our results are consistent with a model in which the circadian pacemaker within the SCN regulates the circadian release of GC via input to the hypothalamo-pituitary-adrenal axis and via a second regulatory pathway, which likely involves sympathetic innervation of the adrenal and can operate even in the absence of ACTH circadian rhythmic release. Furthermore, we show that although the overall 24-h cortisol output in split hamsters is lower than in unsplit controls, split hamsters release constant low levels of ACTH. This result suggests that the timing, rather than the absolute amount, of cortisol release is more critical for the induction of negative feedback effects that regulate the hypothalamo-pituitary-adrenal axis.