Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Analysis of Phylogenetic Tree Space

Abstract Phylogenetic analyses often produce large numbers of trees. Mapping trees’ distribution in “tree space” can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences between different data sources or phylogenetic methods—but the high-dimensional spaces defined by metric distances are necessarily distorted when represented in fewer dimensions. Here, I explore the consequences of this transformation in phylogenetic search results from 128 morphological data sets, using stratigraphic congruence—a complementary aspect of tree similarity—to evaluate the utility of low-dimensional mappings. I find that phylogenetic similarities between cladograms are most accurately depicted in tree spaces derived from information-theoretic tree distances or the quartet distance. Robinson–Foulds tree spaces exhibit prominent distortions and often fail to group trees according to phylogenetic similarity, whereas the strong influence of tree shape on the Kendall–Colijn distance makes its tree space unsuitable for many purposes. Distances mapped into two or even three dimensions often display little correspondence with true distances, which can lead to profound misrepresentation of clustering structure. Without explicit testing, one cannot be confident that a tree space mapping faithfully represents the true distribution of trees, nor that visually evident structure is valid. My recommendations for tree space validation and visualization are implemented in a new graphical user interface in the “TreeDist” R package. [Multidimensional scaling; phylogenetic software; tree distance metrics; treespace projections. ]
Corticosteroids in the prevention and treatment of infants with bronchopulmonary dysplasia: Part I. systemic corticosteroids

Bronchopulmonary dysplasia (BPD) is the most significant respiratory complication of prematurity, and its consequences last from birth into adulthood. Unfortunately, the dramatic improvements in the management of premature infants have not led to a decreased incidence of BPD, or to breakthroughs in treatments offered for this long‐lasting chronic respiratory disorder. Over recent decades the pathological picture of BPD has changed from inflammation, interstitial fibrosis and emphysema attributed to volu‐, barotrauma and oxygen toxicity to larger, simplified alveoli and dysmorphic vessels related to arrested alveolarization and vasculogenesis with inflammation maintaining a central role. Corticosteroids (CSs) play a key role in the development of respiratory epithelial cells and lung maturation. These potent anti‐inflammatory agents have long been used for the prevention and treatment of BPD; however, the risk/benefit ratio of their use remains unresolved. CSs administered antenatally have contributed to reduce mortality and respiratory distress syndrome, no such effect on BPD reduction has been observed. Postnatal systemic CSs reduced the rate and severity of BPD, yet their long‐term neurodevelopmental and respiratory consequences markedly limit routine administration. This is the first in a two‐part State‐of‐the‐Art series that reviews the latest relevant clinical trials investigating the short‐term and long‐term effects of CSs in the prevention and treatment of BPD.
Sustainability in Transformation of Maternal Mortality by Interaction Based Approach in Dairi, Indonesia

Background Health and mortality problems are closely related to the maternal mortality rate (MMR). Efforts to reduce MMR have been carried out by many countries, including the Indonesian government. Design and Methods This research was conducted using two approaches, namely quantitative and qualitative or mixed methods and 149 respondents and 26 informants, to reduce MMR in Dairi Regency. This study was also carried out to determine the dominant variable that affects mother's behavior in an effort to reduce MMR in accordance with the existing theory. Result Mother's intention to contribute to the reduction of MMR in this study was influenced by the good factor directly or indirectly. This is indicated by the score p<0.005. The study also shows that it is very important for the health workers to be able to communicate well with individuals and communities. Conclusion The present study will help to reduce maternal fatalities, and will help to build systems and processes that will allow control the behaviour of the pregnant women and determine the cause of death as well as its contributing factors.
Persons With Histories of Traumatic Brain Injury and Problematic Sexual Behavior: An Exploratory Analysis

Persons with traumatic brain injuries (TBI) who have engaged in problematic or illegal sexual behavior present with complex assessment and intervention needs yet remain understudied within the empirical literature. In the current exploratory analysis, important differences in adaptive and clinical functioning, adverse childhood experiences, and criminal offense history are examined in 25 persons with previous brain injury, 118 persons with intellectual disability but no known TBI, and 103 persons with no history of brain injury or intellectual disability, all of whom have engaged in problematic sexual behavior and who were residing in secure forensic inpatient care. Group differences were examined using comparisons of means and chi-squares. Results highlight important differences in education and employment experiences, diagnostic presentation, exposure to childhood maltreatment, and justice system involvement and characteristics of their sexual offense victims. Associations with prior literature and future research directions are discussed.
Human Endogenous Retroviruses as Gene Expression Regulators: Insights from Animal Models into Human Diseases

The human genome contains many retroviral elements called human endogenous retroviruses (HERVs), resulting from the integration of retroviruses throughout evolution. HERVs once were considered inactive junk because they are not replication-competent, primarily localized in the heterochromatin, and silenced by methylation. But HERVs are now clearly shown to actively regulate gene expression in various physiological and pathological conditions such as developmental processes, immune regulation, cancers, autoimmune diseases, and neurological disorders. Recent studies report that HERVs are activated in patients suffering from coronavirus disease 2019 (COVID-19), the current pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection. In this review, we describe internal and external factors that influence HERV activities. We also present evidence showing the gene regulatory activity of HERV LTRs (long terminal repeats) in model organisms such as mice, rats, zebrafish, and invertebrate models of worms and flies. Finally, we discuss several molecular and cellular pathways involving various transcription factors and receptors, through which HERVs affect downstream cellular and physiological events such as epigenetic modifications, calcium influx, protein phosphorylation, and cytokine release. Understanding how HERVs participate in various physiological and pathological processes will help develop a strategy to generate effective therapeutic approaches targeting HERVs.
Experimental investigation on the seismic response of a steel liquid storage tank equipped with floating roof by shaking table tests

In this paper, the effectiveness of the base isolation on steel storage tanks has been investigated through numerical models and then checked by shaking table tests on a reduced scale (1:14) model of a real steel tank, typically used in petrochemical plants. In the experimental campaign the floating roof has also been taken into account. The tests have been performed on the physical model both in fixed and isolated base configurations; in particular two alternative base isolation systems have been used: high‐damping rubber bearings devices and sliding isolators with elasto‐plastic dampers. Finally, a comparison between experimental and numerical results has also been performed. Copyright © 2009 John Wiley & Sons, Ltd.
Corticosteroids in the prevention and treatment of infants with bronchopulmonary dysplasia: Part II. Inhaled corticosteroids alone or in combination with surfactants

This paper is the second in a two‐part State‐of‐the‐Art series that reviews the latest relevant clinical trials investigating the short‐term and long‐term effects of corticosteroids in the prevention and treatment of bronchopulmonary dysplasia (BPD). Inhaled postnatal corticosteroids demonstrate low systemic bioavailability and rapid systemic clearance with high pulmonary deposition and were expected to reduce the incidence of BPD with reduced adverse effects, however, increased rate of mortality in the neonatal period and at the 18–24 months follow‐up was observed. In a milestone study, intratracheal instillation of corticosteroids combined with surfactant decreased the incidence of BPD without increasing the mortality or the long‐term neurodevelopmental adverse outcomes. However, subsequent trials using different types of surfactants, different surfactant to budesonide ratio, different time of the drug administration for infants with different severity of respiratory distress syndrome could not reproduce all the beneficial effects. Future perspectives for the identification of premature infants at high risk of BPD and the prevention or treatment of established BPD are discussed.
DWDN: Deep Wiener Deconvolution Network for Non-Blind Image Deblurring

We present a simple and effective approach for non-blind image deblurring, combining classical techniques and deep learning. In contrast to existing methods that deblur the image directly in the standard image space, we propose to perform an explicit deconvolution process in a feature space by integrating a classical Wiener deconvolution framework with learned deep features. A multi-scale cascaded feature refinement module then predicts the deblurred image from the deconvolved deep features, progressively recovering detail and small-scale structures. The proposed model is trained in an end-to-end manner and evaluated on scenarios with simulated Gaussian noise, saturated pixels, or JPEG compression artifacts as well as real-world images. Moreover, we present detailed analyses of the benefit of the feature-based Wiener deconvolution and of the multi-scale cascaded feature refinement as well as the robustness of the proposed approach. Our extensive experimental results show that the proposed deep Wiener deconvolution network facilitates deblurred results with visibly fewer artifacts and quantitatively outperforms state-of-the-art non-blind image deblurring methods by a wide margin.
Methods and Barriers to Communication Between Pharmacists During Transitions of Care

Background: Effective communication between pharmacists across healthcare settings is essential to facilitate transitions of care (TOC) and improve patient outcomes. Objective: To explore pharmacists’ communication methods and preferences and identify barriers to communication during TOC. Methods: A survey was distributed to a convenience sample of pharmacists in California, Connecticut, Illinois, Massachusetts, New Jersey, and Texas. The survey collected information on pharmacists’ demographics, practice settings, and clinical services, and their methods, preferences, and barriers to communication during TOC. Results: A total of 308 responses were included in the analysis. The majority of pharmacists practiced in inpatient pharmacy (39.3%) followed by outpatient community pharmacy (23.4%). About 57.8% of pharmacists reported involvement in TOC services. Among respondents, most reported electronic health record (EHR) as their primary method of communication to receive (66.2%) and send (55.5%) information to perform TOC services. Additionally, EHR was reported as the preferred method of communication to receive (75.4%) and send (75.5%) information during TOC. The primary reasons pharmacists reported not utilizing patient health information were lack of information (38.4%), incorrect information (36.7%), delay in receiving information (36.7%), and lack of time (34.5%). Barriers to providing TOC services included poor communication during handoffs (44.2%) and difficulty obtaining needed patient medical information (43.9%). Conclusion: This study identified methods and barriers to communication between pharmacists during TOC across healthcare settings. This provides an opportunity for future research to develop interventions to improve communication between pharmacists at different practice settings.
AP2M1 mediates autophagy-induced CLDN2 (claudin 2) degradation through endocytosis and interaction with LC3 and reduces intestinal epithelial tight junction permeability

ABSTRACT The intestinal epithelial tight junctions (TJs) provide barrier against paracellular permeation of lumenal antigens. Defects in TJ barrier such as increased levels of pore-forming TJ protein CLDN2 (claudin-2) is associated with inflammatory bowel disease. We have previously reported that starvation-induced macroautophagy/autophagy enhances the TJ barrier by degrading pore-forming CLDN2. In this study, we examined the molecular mechanism underlying autophagy-induced CLDN2 degradation. CLDN2 degradation was persistent in multiple modes of autophagy induction. Immunolocalization, membrane fractionation, and pharmacological inhibition studies showed increased clathrin-mediated CLDN2 endocytosis upon starvation. Inhibition of clathrin-mediated endocytosis negated autophagy-induced CLDN2 degradation and enhancement of the TJ barrier. The co-immunoprecipitation studies showed increased association of CLDN2 with clathrin and adaptor protein AP2 (AP2A1 and AP2M1 subunits) as well as LC3 and lysosomes upon starvation, signifying the role of clathrin-mediated endocytosis in autophagy-induced CLDN2 degradation. The expression and phosphorylation of AP2M1 was increased upon starvation. In-vitro, in-vivo (mouse colon), and ex-vivo (human colon) inhibition of AP2M1 activation prevented CLDN2 degradation. AP2M1 knockout prevented autophagy-induced CLDN2 degradation via reduced CLDN2-LC3 interaction. Site-directed mutagenesis revealed that AP2M1 binds to CLDN2 tyrosine motifs (YXXФ) (67–70 and 148–151). Increased baseline expression of CLDN2 and TJ permeability along with reduced CLDN2-AP2M1-LC3 interactions in ATG7 knockout cells validated the role of autophagy in modulation of CLDN2 levels. Acute deletion of Atg7 in mice increased CLDN2 levels and the susceptibility to experimental colitis. The autophagy-regulated molecular mechanisms linking CLDN2, AP2M1, and LC3 may provide therapeutic tools against intestinal inflammation. Abbreviations: Amil: amiloride; AP2: adaptor protein complex 2; AP2A1: adaptor related protein complex 2 subunit alpha 1; AP2M1: adaptor related protein complex 2 subunit mu 1; ATG7: autophagy related 7; CAL: calcitriol; Cas9: CRISPR-associated protein 9; Con: control; CPZ: chlorpromazine; DSS: dextran sodium sulfate; EBSS: Earle’s balanced salt solution; IBD: inflammatory bowel disease; TER: trans-epithelial resistance; KD: knockdown; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MβCD: Methyl-β-cyclodextrin; MET: metformin; MG132: carbobenzoxy-Leu-Leu-leucinal; MTOR: mechanistic target of rapamycin kinase; NT: non target; RAPA: rapamycin; RES: resveratrol; SMER: small-molecule enhancer 28; SQSTM1: sequestosome 1; ST: starvation; ULK1: unc-51 like autophagy activating kinase 1; WT: wild type.
First-in-Human Experience and Acute Procedural Outcomes Using a Novel Pulsed Field Ablation System: The PULSED AF Pilot Trial

Supplemental Digital Content is available in the text. Background: Pulsed field ablation (PFA) is a novel form of ablation using electrical fields to ablate cardiac tissue. There are only limited data assessing the feasibility and safety of this type of ablation in humans. Methods: PULSED AF (Pulsed Field Ablation to Irreversibly Electroporate Tissue and Treat AF; https://www.clinicaltrials.gov; unique identifier: NCT04198701) is a nonrandomized, prospective, multicenter, global, premarket clinical study. The first-in-human pilot phase evaluated the feasibility and efficacy of pulmonary vein isolation using a novel PFA system delivering bipolar, biphasic electrical fields through a circular multielectrode array catheter (PulseSelect; Medtronic, Inc). Thirty-eight patients with paroxysmal or persistent atrial fibrillation were treated in 6 centers in Australia, Canada, the United States, and the Netherlands. The primary outcomes were ability to achieve acute pulmonary vein isolation intraprocedurally and safety at 30 days. Results: Acute electrical isolation was achieved in 100% of pulmonary veins (n=152) in the 38 patients. Skin-to-skin procedure time was 160±91 minutes, left atrial dwell time was 82±35 minutes, and fluoroscopy time was 28±9 minutes. No serious adverse events related to the PFA system occurred in the 30-day follow-up including phrenic nerve injury, esophageal injury, stroke, or death. Conclusions: In this first-in-human clinical study, 100% pulmonary vein isolation was achieved using only PFA with no PFA system–related serious adverse events. Graphic Abstract: A graphic abstract is available for this article.
Role of the Telemental Health Services During the COVID-19 Pandemic: A Systematic Review.

OBJECTIVE The COVID-19 pandemic has directed the use of telemedicine and digital mental health services to meet the needs of people in order to maintain physical distancing by preventing person to person contact. The aim of this review is to highlight the role of telemental health services during the COVID-19 pandemic. METHOD An electronic search was carried out between January 01, 2020 and October 31, 2020 to explore the utilization of telehealth services for mental health problems among adults during the COVID-19 pandemic. The primary source of literature was the structured search of major electronic databases from the MEDLINE (PubMed), CINAHL Plus, Science Direct and the Web of Science. We included nine published studies meeting the the eligibility criteria. RESULTS The role of telehealth identified in this review mainly focused on the applicability of this modality for assessing and managing various mental health problems in these unprecedented times. It also pointed out that the provision of telemental health support reduced the burden of mental health diseases and promoted the wellbeing of the individual. Further, it was witnessed that patients preferred remote consultation as compared to face-to-face visits in order to avoid contracting the virus and found online mental health interventions and psychological counseling very helpful to cope up with the current crisis. CONCLUSION The current COVID-19 lockdown has changed the management of the mental health problems of patients. The use of this innovative modality prevents transmission of infection and provides timely treatment to the community members most in need.
2AB protein of Senecavirus A antagonizes selective autophagy and type I interferon production by degrading LC3 and MARCHF8

ABSTRACT Senecavirus A (SVA), an important emerging porcine virus, has outbreaks in different regions and countries each year, becoming a virus with global prevalence. SVA infection has been reported to induce macroautophagy/autophagy; however, the molecular mechanisms of autophagy induction and the effect of SVA on autophagy remain unknown. This study showed that SVA infection induced the autophagy process in the early stage of SVA infection, and the rapamycin-induced autophagy inhibited SVA replication by degrading virus 3 C protein. To counteract this, SVA utilized 2AB protein inhibiting the autophagy process from promoting viral replication in the late stage of SVA infection. Further study showed that SVA 2AB protein interacted with MARCHF8/MARCH8 and LC3 to degrade the latter and inhibit the autophagy process. In addition, we found that MARCHF8 was a positive regulator of type I IFN (IFN-I) signaling. During the autophagy process, the SVA 2AB protein targeted MARCHF8 and MAVS forming a large complex for degradation to deactivate IFN-I signaling. Together, our study reveals the molecular mechanisms of selective autophagy in the host against viruses and reveals potential viral strategies to evade the autophagic process and IFN-I signaling for successful pathogenesis. Abbreviations: Baf A1: bafilomycin A1; Co-IP: co-immunoprecipitation; CQ: chloroquine; DAPI: 4′,6-diamidino-2-phenylindole; hpi: hours post-infection; IFN: interferon; ISG: IFN-stimulated gene; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MARCHF8/MARCH8: membrane associated ring-CH-type finger 8; MAVS: mitochondrial antiviral signaling protein; MOI: multiplicity of infection; Rapa: rapamycin; RT: room temperature; siRNA: small interfering RNA; SVA: Senecavirus A; TCID50: 50% tissue culture infectious doses.
Evaluating the Benefits of a SNAP-Ed-Funded Community Garden Intervention Using Ripple Effect Mapping

In North Carolina, rural communities experience high rates of chronic illness due to health inequities exacerbated by the decline of major industries. Community gardens increase access to fresh produce and opportunities for physical activity and may offer additional benefits. These benefits can be difficult to measure as they are often unplanned or unintended. This article describes how we utilized Ripple Effect Mapping (REM), a participatory approach for evaluating complex interventions, to understand the impact of a SNAP-Ed-funded program. We purposively selected six community gardens to participate in 2-hour, facilitated REM sessions. On average, 15 people participated in each session. Participants developed a map of benefits using Appreciative Inquiry, mind mapping, and consensus-building methods. The map organized benefits across three levels: first ripple (individual), second ripple (interpersonal), and third ripple (community). In addition, participants coded benefits using the Community Capitals Framework. After the sessions, the research team extracted identified impacts into a matrix, aligned them with the SNAP-Ed Evaluation Framework, and developed digitized maps. These data corroborated findings from previous evaluations and offered insight into community-identified benefits not previously documented, including other types of capital generated by community gardens in rural communities. In addition, REM was an effective approach to measure and report several SNAP-Ed evaluation indicators, including LT11: Unexpected Benefits. Ultimately, the research team found REM to be an effective community-engaged method for understanding a complex intervention’s benefits while centering participant community voices and transferring ownership of the data to community partners, a key principle in equitable evaluation.