Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-related stigma and optimism as predictors of anxiety and depression among HIV-positive men who have sex with men in the United Kingdom and Ireland

ABSTRACT This study investigated the associations between forms of HIV-related optimism, HIV-related stigma, and anxiety and depression among HIV-positive men who have sex with men (MSM) in the United Kingdom and Ireland. HIV health optimism (HHO) and HIV transmission optimism (HTO) were hypothesised to be protective factors for anxiety and depression, while the components of HIV-related stigma (enacted stigma, disclosure concerns, concern with public attitudes, and internalised stigma) were hypothesised to be risk factors. Data were collected from 278 HIV-positive MSM using an online questionnaire. The prevalence of psychological distress was high, with close to half (48.9%) of all participants reporting symptoms of anxiety, and more than half (57.9%) reporting symptoms of depression. Multiple linear regressions revealed that both anxiety and depression were positively predicted by internalised stigma and enacted stigma, and negatively predicted by HHO. For both anxiety and depression, internalised stigma was the strongest and most significant predictor. The results highlight the continued psychological burden associated with HIV infection among MSM, even as community support services are being defunded across the United Kingdom and Ireland. The results point to the need for clinicians and policy makers to implement stigma reduction interventions among this population.
Lidar ratios of stratospheric volcanic ash and sulfate aerosols retrieved from CALIOP measurements

Abstract. We apply a two-way transmittance constraint to nighttime CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) observations of volcanic aerosol layers to retrieve estimates of the particulate lidar ratio (Sp) at 532 nm. This technique is applied to three volcanic eruption case studies that were found to have injected aerosols directly into the stratosphere. Numerous lidar observations permitted characterization of the optical and geometric properties of the volcanic aerosol layers over a time period of 1–2 weeks. For the volcanic ash-rich layers produced by the Puyehue-Cordon Caulle eruption (June 2011), we obtain mean and median particulate lidar ratios of 69 ± 13 sr and 67 sr, respectively. For the sulfate-rich aerosol layers produced by Kasatochi (August 2008) and Sarychev Peak (June 2009), the means of the retrieved lidar ratios were 66 ± 19 sr (median 60 sr) and 63 ± 14 sr (median 59 sr), respectively. The 532 nm layer-integrated particulate depolarization ratios (δp) observed for the Puyehue layers (δp = 0.33 ± 0.03) were much larger than those found for the volcanic aerosol layers produced by the Kasatochi (δp = 0.09 ± 0.03) and Sarychev (δp = 0.05 ± 0.04) eruptions. However, for the Sarychev layers we observe an exponential decay (e-folding time of 3.6 days) in δp with time from 0.27 to 0.03. Similar decreases in the layer-integrated attenuated colour ratios with time were observed for the Sarychev case. In general, the Puyehue layers exhibited larger colour ratios (χ′ = 0.53 ± 0.07) than what was observed for the Kasatochi (χ′ = 0.35 ± 0.07) and Sarychev (χ′ = 0.32 ± 0.07) layers, indicating that the Puyehue layers were generally composed of larger particles. These observations are particularly relevant to the new stratospheric aerosol subtyping classification scheme, which has been incorporated into version 4 of the level 2 CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation) data products.
70-kDa Heat Shock Protein Downregulates Dynamin in Experimental Stroke: A New Therapeutic Target?

Background and Purpose— The 70-kDa heat shock protein (Hsp70) protects brain cells in models of cerebral ischemia. Proteomic screening of mice subjected to middle cerebral artery occlusion identified dynamin as a major downregulated protein in Hsp70-overexpressing mice (Hsp70 transgenic mice). Dynamin-1 is expressed in neurons and participates in neurotransmission, but also transports the death receptor Fas to the cell surface, where it can be bound by its ligand and lead to apoptosis. Methods— Mice were subjected to distal middle cerebral artery occlusion. Neuro-2a cells were subjected to oxygen glucose deprivation. Hsp70 transgenic and Hsp70-deficient (Hsp70 knockout) mice were compared with wild-type mice for histological and behavioral outcomes. Some mice and neuro-2a cell cultures were given dynasore, a dynamin inhibitor. Results— Hsp70 transgenic mice had better outcomes, whereas Hsp70 knockout mice had worse outcomes compared with wild-type mice. This correlated with decreased and increased dynamin expression, respectively. Dynamin colocalized to neurons and Fas, with higher Fas levels and increased caspase-8 expression. Hsp70 induction in neuro-2a cells was protected from oxygen glucose deprivation, while downregulating dynamin and Fas expression. Further, dynamin inhibition was found to be neuroprotective. Conclusions— Dynamin may facilitate Fas-mediated apoptotic death in the brain, and Hsp70 may protect by preventing this trafficking. Dynamin should be explored as a new therapeutic target for neuroprotection.
Optimization of inhomogeneous magnetization transfer (ihMT) MRI contrast for preclinical studies using dipolar relaxation time (T1D) filtering

A pulsed inhomogeneous magnetization transfer (ihMT)‐prepared fast imaging sequence was implemented at 11.75 T for preclinical studies on mouse central nervous system. A strategy based on filtering the ihMT signal originating from short dipolar relaxation time (T1D) components is proposed. It involves increasing the repetition time of consecutive radiofrequency (RF) pulses of the dual saturation and allows improved signal specificity for long T1D myelinated structures. Furthermore, frequency offset, power and timing saturation parameters were adjusted to optimize the ihMT sensitivity. The optimization of the ihMT sensitivity, whilst preserving the strong specificity for the long T1D component of myelinated tissues, allowed measurements of ihMT ratios on the order of 4–5% in white matter (WM), 2.5% in gray matter (GM) and 1–1.3% in muscle. This led to high relative ihMT contrasts between myelinated tissues and others (~3–4 between WM and muscle, and ≥2 between GM and muscle). Conversely, higher ihMT ratios (~6–7% in WM) could be obtained using minimal T1D filtering achieved with short saturation pulse repetition time or cosine‐modulated pulses for the dual‐frequency saturation. This study represents a first stage in the process of validating ihMT as a myelin biomarker by providing optimized ihMT preclinical sequences, directly transposable and applicable to other preclinical magnetic fields and scanners. Finally, ihMT ratios measured in various central nervous system areas are provided for future reference.
Operative methods for delayed paralysis after osteoporotic vertebral fracture

Purpose: How to select operative methods for delayed paralysis after osteoporotic vertebral fracture remains a matter of debate. It is unclear which procedure provides better neurological and functional recovery. This study aimed to compare the various operative methods and investigate postoperative outcomes. Methods: The study included 42 delayed paralysis patients (mean age 73.7 years). The operative methods were posterior spinal shortening osteotomy with direct decompression and short or long fusion and posterior laminectomy and short fusion with vertebroplasty. All patients in the vertebroplasty group were fitted with hooks to prevent correction loss. We investigated postoperative complications, surgery time, intraoperative blood loss, and changes in walking ability and local kyphotic angle (LKA). Patients were divided into three groups: shortening with a peripheral fusion range of one intervertebral level (the SS group, n = 18), the same procedure with a peripheral fusion range of ≥2 intervertebral levels (the SL group, n = 12), and posterior laminectomy and short fusion with vertebroplasty (the VP group, n = 12). Results: Postoperative complications were observed in five patients, all of whom were in the SS and SL group. There were no significant differences between the SS and SL groups. The VP group experienced significantly shorter mean surgery times, significantly lower mean intraoperative blood loss, and an improvement in paralysis, walking ability, LKA, and correction loss. Overall, the VP group had significantly better outcomes. Conclusion: Posterior laminectomy and short fusion with vertebroplasty with the addition of hooks is useful in cases of delayed paralysis in elderly patients.
Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

Abstract. The advent of next‐generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next‐generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target “probe” region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep‐level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea + Gelechioidea + Thyridoidea) + (Papilionoidea + Pyraloidea + Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.
Treatment preferences and advance care planning at end of life: The role of ethnicity and spiritual coping in cancer patients

Background:Although studies have reported ethnic differences in approaches to end of life, the role of spiritual beliefs is less well understood.Purpose: This study investigated differences between African American and White patients with cancer in their use of spirituality to cope with their cancer and examined the role of spiritual coping in preferences at end-of-life.Methods: The authors analyzed data from interviews with 68 African American and White patients with an advanced stage of lung or colon cancer between December 1999 and June 2001.Results: Similar high percentages of African American and White patients reported being “moderately to very spiritual” and “moderately to very religious. ” African American patients were more likely to report using spirituality to cope with their cancer as compared to their White counterparts (p = .002). Patients who reported belief in divine intervention were less likely to have a living will (p = .007). Belief in divine intervention, turning to higher power for strength, support and guidance, and using spirituality to cope with cancer were associated with preference for cardiopulmonary resuscitation, mechanical ventilation, and hospitalization in a near-death scenario.Conclusions: It was found that patients with cancer who used spiritual coping to a greater extent were less likely to have a living will and more likely to desire life-sustaining measures. If efforts aimed at improving end-of-life care are to be successful, they must take into account the complex interplay of ethnicity and spirituality as they shape patients’ views and preferences around end of life.
Feature selection methodology for longitudinal cone-beam CT radiomics

Abstract Background: Cone-beam CT (CBCT) scans are typically acquired daily for positioning verification of non-small cell lung cancer (NSCLC) patients. Quantitative information, derived using radiomics, can potentially contribute to (early) treatment adaptation. The aims of this study were to (1) describe and investigate a methodology for feature selection of a longitudinal radiomics approach (2) investigate which time-point during treatment is potentially useful for early treatment response assessment. Material and methods: For 90 NSCLC patients CBCT scans of the first two fractions of treatment (considered as ‘test-retest’ scans) were analyzed, as well as weekly CBCT images. One hundred and sixteen radiomic features were extracted from the GTV of all scans and subsequently absolute and relative differences were calculated between weekly CBCT images and the CBCT of the first fraction. Test-retest scans were used to determine the smallest detectable change (C = 1.96 * SD) allowing for feature selection by choosing a minimum number of patients for which a feature should change more than ‘C’ to be considered as relevant. Analysis of which features change at which moment during treatment was used to investigate which time-point is potentially relevant to extract longitudinal radiomics information for early treatment response assessment. Results: A total of six absolute delta features changed for at least ten patients at week 2 of treatment and increased to 61 at week 3, 79 at week 4 and 85 at week 5. There was 93% overlap between features selected at week 3 and the other weeks. Conclusions: This study describes a feature selection methodology for longitudinal radiomics that is able to select reproducible delta radiomics features that are informative due to their change during treatment, which can potentially be used for treatment decisions concerning adaptive radiotherapy. Nonetheless, the prognostic value of the selected delta radiomic features should be investigated in future studies.
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

Abstract The total‐evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model‐based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total‐evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total‐evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth‐death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total‐evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ∼12.7 Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem‐fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2. org with packages SA (version at least 1.1.4) and morph‐models (version at least 1.0.4) installed.
Frailty Score on Admission Predicts Outcomes in Elderly Burn Injury

With longer life expectancy, the number of burn injuries in the elderly continues to increase. Prediction of outcomes for the elderly is complicated by preinjury physical fitness and comorbid illness. The authors hypothesize that admission frailty assessment would be predictive of outcomes in the elderly burn population. Our primary aim was to determine if higher frailty scores were associated with higher risk of mortality for elderly burn patients. The secondary aims were to assess if higher frailty scores were associated with increased length of stay, increased needs for mechanical ventilation and poor discharge disposition. A 2-year retrospective chart review was performed of all admitted acute burn patients 65 years or older. Data collected included: age, gender, %TBSA of burn injury, presence of inhalation injury, in hospital mortality, hospital length of stay, ventilator days, ICU length of stay, surgical procedures, insurance status, and discharge disposition. Frailty scores were assessed from admission data and calculated using the Canadian Study of Health and Aging clinical frailty scale. A total of 89 patients met entry criteria. Mean age was 75.3 ± 8.1 years and consisted of 62 men and 27 women. Mean %TBSA was 9.6 ± 9.1% and mean frailty score (FS) was 4.5 ± 1.2. Eighty patients survived to discharge and nine died. Nonsurvivors had significantly higher FS compared to survivors (5.2 ± 1.2 vs 4.4 ± 1.2). FS were also significantly higher in patients discharged to skilled nursing facilities (SNF) (5.34 ± 0.9) compared to those who were discharged home (4.1 ± 1.2) or to physical rehabilitation facilities (4 ± 1.5). Multivariate linear regression analysis revealed that age (B = 0.04) and discharge to SNF (B = 1.2) are independently associated with higher FS. However, survivors were independently associated with a significantly lower FS (B = −1.3). Multivariate logistic regression analysis revealed high admission FS independently increased the risk of discharge to SNF (odds ratio of 2.5 [1.3–4.8, 95% confidence interval]) and increased the risk of mortality (odds ratio of 1.67 [1.01–2.7, 95% confidence interval]). Frailty scores on admission allow for a more complete assessment of elderly patients and can be used to establish benchmark models for burn injury outcomes. In addition FS can be used as a research tool to improve outcomes for elderly burn injured patients.
Pediatric Gastroesophageal Reflux Clinical Practice Guidelines: Joint Recommendations of the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN)

Objective: To develop a North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) and European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) international consensus on the diagnosis and management of gastroesophageal reflux and gastroesophageal reflux disease in the pediatric population. Methods: An international panel of 9 pediatric gastroenterologists and 2 epidemiologists were selected by both societies, which developed these guidelines based on the Delphi principle. Statements were based on systematic literature searches using the best-available evidence from PubMed, Cumulative Index to Nursing and Allied Health Literature, and bibliographies. The committee convened in face-to-face meetings 3 times. Consensus was achieved for all recommendations through nominal group technique, a structured, quantitative method. Articles were evaluated using the Oxford Centre for Evidence-based Medicine Levels of Evidence. Using the Oxford Grades of Recommendation, the quality of evidence of each of the recommendations made by the committee was determined and is summarized in appendices. Results: More than 600 articles were reviewed for this work. The document provides evidence-based guidelines for the diagnosis and management of gastroesophageal reflux and gastroesophageal reflux disease in the pediatric population. Conclusions: This document is intended to be used in daily practice for the development of future clinical practice guidelines and as a basis for clinical trials.
Meaningless comparisons lead to false optimism in medical machine learning

A new trend in medicine is the use of algorithms to analyze big datasets, e.g. using everything your phone measures about you for diagnostics or monitoring. However, these algorithms are commonly compared against weak baselines, which may contribute to excessive optimism. To assess how well an algorithm works, scientists typically ask how well its output correlates with medically assigned scores. Here we perform a meta-analysis to quantify how the literature evaluates their algorithms for monitoring mental wellbeing. We find that the bulk of the literature (∼77%) uses meaningless comparisons that ignore patient baseline state. For example, having an algorithm that uses phone data to diagnose mood disorders would be useful. However, it is possible to explain over 80% of the variance of some mood measures in the population by simply guessing that each patient has their own average mood—the patient-specific baseline. Thus, an algorithm that just predicts that our mood is like it usually is can explain the majority of variance, but is, obviously, entirely useless. Comparing to the wrong (population) baseline has a massive effect on the perceived quality of algorithms and produces baseless optimism in the field. To solve this problem we propose “user lift” that reduces these systematic errors in the evaluation of personalized medical monitoring.