Miracle-dz/UniFAR-FTUs huggingface dataset:
Time and taxonomy

A cladistic approach, attempting to reconstruct phylogeny, is the most objective way of depicting relationships; whole-genome comparisons, such as DNA-DNA hybridisation, show that genetic similarity really does increase with recency of common ancestry. But if we aim to represent taxonomically every dichotomy in the cladogram, more and more taxonomic division will be required, and this has led to the current trend towards unranked taxonomies. To preserve the undoubted advantages of a ranked system, I propose that we retain the modified Linnaean ranking system and its associated “subs” and “supers,” while inserting unranked taxa at whatever point in the system is required. Moreover, to introduce full objectivity, we should try to link at least the modified Linnaean ranks (order, family, tribe, genus), except for species, to time since common ancestry; these time slots can be determined by looking at available fossil and/or molecular information on separation times of mammalian taxa in general, and applying criteria that do least violence to widely accepted taxonomic ranks.
Combined therapy: rifaximin-α and arabinogalactan with lactoferrin combination effectively prevents recurrences of symptomatic uncomplicated diverticular disease.

INTRODUCTION Background: Diverticulosis is the most common finding in the GI tract. Nearly half of the people with diverticula experience symptomatic uncomplicated diverticular disease (SUDD). AIMS The primary endpoints of our study were to assess the effectiveness of combined therapy with rifaximin-α and arabinogalactan-lactoferrin in symptom reduction and normalization of bowel movements. The secondary endpoints were an assessment of efficacy in SUDD recurrence prevention and patients' compliance to the combined therapy. METHODS A retrospective observational survey study was performed in 2019 among physicians experienced in diverticular disease (DD) treatment in Poland. Patients with previous episodes of recurrences treated with combined therapy (cyclic rifaximin-α at least 400 mg b.i.d/7 days/every month and continuous arabinogalactan-lactoferrin supplementation 1 sachet daily) were assessed after 3 and 6 months regarding symptoms' resolution in the three-point scale. The patients' SUDD history, diagnostic methods, treatment, and results, as well as patients' compliance were evaluated. RESULTS 281 patients met inclusion criteria, and were further evaluated (67.6% women, median age 65 years). After 6 months of combined treatment, there was a statistically significant reduction in the total severity score (median from 1.7 [max 3 points] to 0.26; P < 0.0001; sum from 8.5 [max 15 points] to 1.28; P < 0.0001) and improvement in each symptom score. Stool frequency statistically normalized in every group. As many as 31.7% had complete symptom resolution. Patients' compliance with the therapy was very good and good in 92.9% of cases. C onclusions and discussion: Combination therapy with cyclic rifaximin-α and continuous arabinogalactan combined with lactoferrin are effective in SUDD treatment in terms of symptom resolution, bowel movement normalization, prevention of recurrences with very good patient's compliance.
Line Drawings for Face Portraits From Photos Using Global and Local Structure Based GANs

Despite significant effort and notable success of neural style transfer, it remains challenging for highly abstract styles, in particular line drawings. In this paper, we propose APDrawingGAN++, a generative adversarial network (GAN) for transforming face photos to artistic portrait drawings (APDrawings), which addresses substantial challenges including highly abstract style, different drawing techniques for different facial features, and high perceptual sensitivity to artifacts. To address these, we propose a composite GAN architecture that consists of local networks (to learn effective representations for specific facial features) and a global network (to capture the overall content). We provide a theoretical explanation for the necessity of this composite GAN structure by proving that any GAN with a single generator cannot generate artistic styles like APDrawings. We further introduce a classification-and-synthesis approach for lips and hair where different drawing styles are used by artists, which applies suitable styles for a given input. To capture the highly abstract art form inherent in APDrawings, we address two challenging operations—(1) coping with lines with small misalignments while penalizing large discrepancy and (2) generating more continuous lines—by introducing two novel loss terms: one is a novel distance transform loss with nonlinear mapping and the other is a novel line continuity loss, both of which improve the line quality. We also develop dedicated data augmentation and pre-training to further improve results. Extensive experiments, including a user study, show that our method outperforms state-of-the-art methods, both qualitatively and quantitatively.
Risk of death, relapse or progression, and loss of life expectancy at different progression-free survival milestones in primary central nervous system lymphoma

Abstract In this study, we analyzed the evolution of the prognosis of primary central nervous system lymphoma (PCNSL) patients as they reach selected progression-free survival (PFS) milestones after high-dose methotrexate (HD-MTX)-based therapy. In total, 258 and 146 patients were included from Denmark and British Columbia, respectively. All patients were diagnosed during 2000–2017. The 5-year PFS was 27% (95% CI 23; 32); however, for patients reaching 5 years of PFS, this increased to 71% (95% CI 57; 86). Within the first 5 years after diagnosis, patients lost 2.0 years (95% CI 1.8; 2.2) when compared to a similar background population. This reduced to 0.5 years (95% CI 0.2; 0.9) for patients reaching 5 years of PFS. Treatment with rituximab was associated with improved outcomes. The prognosis of patients with PCNSL treated with HD-MTX-based regimens in this cohort is poor, although it improves as patients survive without progression/relapse. However, survival does not conclusively normalize to that of a similar background population.
Impact of previous left atrial ablation procedures on the mechanism of left atrial flutter: A single‐centre experience

Left atrial flutter predominantly occurs after surgical or ablation procedures but this entity has also been recently reported in individuals without previous interventions. The use of high‐density electroanatomical mapping‐systems (HDM) has improved the understanding of underlying mechanisms beyond entrainment maneuvers and substrate analyses. We aimed to evaluate the mechanism of left atrial (LA) flutters in preablated vs ablation‐naïve individuals and sought to assess the efficacy of empiric ablations sets in these groups.
Impact of Epstein-Barr virus coinfection in Mycoplasma pneumoniae pneumonia

Abstract Mycoplasma pneumoniae (MP) is one of the most common pathogens of respiratory infection in children, while Epstein-Barr virus (EBV) infection is usually subclinical in immunocompetent children. Although single MP infection is common enough, MP and EBV coinfection have received little attention. Especially, the pathogenic role of EBV in lung when coinfection with MP, has not been clarified. The purpose of this study was to investigate the impact of EBV on MP pneumonia (MPP) in hospitalized children. We retrospectively reviewed the clinical data of MPP children who underwent screening for EBV by polymerase chain reaction in bronchoalveolar lavage fluid during hospitalization in 2014. Of total 147 patients, 68 patients were in the MP group and 79 were in the MP/EBV coinfection group. We found longer fever duration and higher CRP, IgA, IgG, interleukin-2 (IL-2), percentage of peripheral neutrophils levels, higher incidence of pulmonary consolidation and percentage of refractory MPP in coinfection group, when compared to those in MP group. In ROC curve analysis, IL-2 was useful for differentiating patients with coinfection from those with MP infection. Logistic regression analysis showed that the IL-2 ≥ 3.35 pg/ml (OR = 3.677) was a significant predictor regarding to MP/EBV coinfection. In conclusion, coinfection of EBV and MP poses a higher risk for prolonged symptoms. IL-2 could be used as a good predictor of coinfection.
Patient Perception of Cardiovascular Risk in Rheumatoid Arthritis

Patients with rheumatoid arthritis (RA) have higher incidence of cardiovascular diseases (CVDs) compared with age‐ and sex‐matched controls. The objective of our study was to measure the knowledge of patients with RA about the association between their disease and cardiovascular (CV) risk and to measure the frequency of counseling by physicians based on patient report.
An unprecedented cluster of Australian bat lyssavirus in Pteropus conspicillatus indicates pre‐flight flying fox pups are at risk of mass infection

In November 2017, two groups of P. conspicillatus pups from separate locations in Far North Queensland presented with neurological signs consistent with Australian bat lyssavirus (ABLV) infection. These pups (n = 11) died over an 11‐day period and were submitted to a government laboratory for testing where ABLV infection was confirmed. Over the next several weeks, additional ABLV cases in flying foxes in Queensland were also detected. Brain tissue from ABLV‐infected flying foxes during this period, as well as archived brain tissue, was selected for next‐generation sequencing. Phylogenetic analysis suggests that the two groups of pups were each infected from single sources. They were likely exposed while in crèche at night as their dams foraged. This study identifies crèche‐age pups at a potentially heightened risk for mass ABLV infection.
A randomized crossover trial

Background: There is considerable evidence that prolonged use of cervical collars potentially cause detrimental effects including increase in optic nerve sheath diameter (ONSD) among healthy volunteers. Different types of cervical collars immobilize cervical spine variably well and may presumably differently influence the venous compression and hence the intracranial pressure. We therefore aimed to evaluate the influence of cervical spine immobilization with 5 different types of cervical collars on ONSD measured noninvasively by ultrasound on healthy volunteers. Methods:We conducted a randomized crossover trial including 60 adult healthy volunteers. Control assessment of the optic nerve sheath thickness was performed in both sagittal and transverse planes. Patient was placed supine on a transport stretcher, cervical collar was placed, and ONSD measurement was performed after 5 and 20minutes. During the next days, the procedure was repeated with random allocation of participants and random cervical collar. Results: Sixty healthy volunteers were included in our study. ONSD left diameter [mm] for the baseline was 3.8 [interquartile range (IQR): 3.65–3.93)] mm. Using AMBU after 5min, ONSD was changed up to 4.505 (IQR 4.285–4.61; P< .001) mm. The largest change at 5minutes and 20minutes was using Philly 4.73 (IQR: 4.49–4.895; P< .001) and 4.925 (IQR: 4.65–5.06; P< .001), respectively. Necklite reported the lower change in ONSD: 3.92 (IQR: 3.795–4; P=1.0) mm in 5minutes and 3.995 (IQR: 3.875 – 4.1; P=1.0) mm in 20minutes. ONSD right diameter [mm] for the baseline was 3.8 (IQR 3.675–3.9) mm. Using AMBU after 5minutes, ONSD was changed up to 4.5 (IQR 4.21–4.6) mm. The largest change at 5minutes and 20minutes was using Philly 4.705 (IQR 4.455–4.9) and 4.93 (IQR 4.645–5.075), respectively. Necklite reported the lower change in ONSD -33.9 (IQR 3.795–3.99) mm in 5 minutes and 3.995 (IQR 3.86–4.09) mm in 20minutes. Conclusion:We report significant increase of ONSD from the baseline after cervical collar placement among healthy volunteers at 5minutes and 20minutes interval. In addition, no significant difference was noted between ONSD measurements at 5 and 20 minutes. Clinicians should take proactive steps to assess the actual need of cervical collar case by case basis. Nonetheless, when needed, Necklite moldable neck brace seems to be a reasonable option. Registration: ClinicalTrials database (www.clinicaltrials.gov, NCT03609879). Abbreviations: ANOVA = Analysis of variance, ICP = Intracranial pressure, IQR = Interquartile range, IRB = Institutional Review Board, ONSD = Optic nerve sheath diameter.
Innovations in research and clinical care using patient‐generated health data

Patient‐generated health data (PGHD), or health‐related data gathered from patients to help address a health concern, are used increasingly in oncology to make regulatory decisions and evaluate quality of care. PGHD include self‐reported health and treatment histories, patient‐reported outcomes (PROs), and biometric sensor data. Advances in wireless technology, smartphones, and the Internet of Things have facilitated new ways to collect PGHD during clinic visits and in daily life. The goal of the current review was to provide an overview of the current clinical, regulatory, technological, and analytic landscape as it relates to PGHD in oncology research and care. The review begins with a rationale for PGHD as described by the US Food and Drug Administration, the Institute of Medicine, and other regulatory and scientific organizations. The evidence base for clinic‐based and remote symptom monitoring using PGHD is described, with an emphasis on PROs. An overview is presented of current approaches to digital phenotyping or device‐based, real‐time assessment of biometric, behavioral, self‐report, and performance data. Analytic opportunities regarding PGHD are envisioned in the context of big data and artificial intelligence in medicine. Finally, challenges and solutions for the integration of PGHD into clinical care are presented. The challenges include electronic medical record integration of PROs and biometric data, analysis of large and complex biometric data sets, and potential clinic workflow redesign. In addition, there is currently more limited evidence for the use of biometric data relative to PROs. Despite these challenges, the potential benefits of PGHD make them increasingly likely to be integrated into oncology research and clinical care.
Comparison of third generation balloon-expandable Edwards Sapien 3 versus self-expandable Evolut R in transcatheter aortic valve implantation: a meta-analysis.

BACKGROUND The 3rd generations of transcatheter heart valve system, including Edwards SAPIEN S3 (ES3) and Medtronic's Evolut R, has been developed to specifically improve the safety of transcatheter aortic valve implantation (TAVI). The aim of this work was to provide a summary effect estimate of the peri-procedural characteristics and clinical outcome of patients treated with ES3 versus the Evolut R. METHODS We conducted a literature search of PubMed, Ovid and EMBASE (2002 to 2018). Two authors extracted the data independently. The safety and feasibility of Sapien 3 and Evolut R were compared by odds ratios (ORs) with 95% confidence intervals (CIs) in inverse variance method. RESULTS After a multi-step assessment, a total 6 studies were finally included, yielding 1,664 patients, of which, 768 (46%) used ES3 and 896 (54%) used Evolut R. There was no statistical difference with device success rate (OR 1.15, 95% CI: 0.70-1.91, I2 =0%), 30-day mortality [OR: 0.72 (0.33-1.57), I2 =0%], pre-dilation rate, 30-day stroke, bleeding complication (BC) (major and life-threating), major vascular complication (VC), and paravalvular leakage between the two groups. However, the ES3 group was associated with a higher risk of acute kidney injury (AKI), higher mean aortic valve gradient and better mean left ventricular ejection fraction (LVEF) after TAVR procedure. Moreover, the Evolut R group had a higher rate of post-dilation and new permanent pacemaker implantation (PPMI). CONCLUSIONS Both devices had demonstrated excellent procedural success rate and short-term safety. At 30-day follow-up, both devices shared similar rates of mortality, BC, VC, stroke, and paravalvular leakage (PVL). However, the rate of AKI was higher in the ES3 group, and the rate of PPM was higher in the Evolut R group.
PBR-Net: Imitating Physically Based Rendering Using Deep Neural Network

Physically based rendering has been widely used to generate photo-realistic images, which greatly impacts industry by providing appealing rendering, such as for entertainment and augmented reality, and academia by serving large scale high-fidelity synthetic training data for data hungry methods like deep learning. However, physically based rendering heavily relies on ray-tracing, which can be computational expensive in complicated environment and hard to parallelize. In this paper, we propose an end-to-end deep learning based approach to generate physically based rendering efficiently. Our system consists of two stacked neural networks, which effectively simulates the physical behavior of the rendering process and produces photo-realistic images. The first network, namely shading network, is designed to predict the optimal shading image from surface normal, depth and illumination; the second network, namely composition network, learns to combine the predicted shading image with the reflectance to generate the final result. Our approach is inspired by intrinsic image decomposition, and thus it is more physically reasonable to have shading as intermediate supervision. Extensive experiments show that our approach is robust to noise thanks to a modified perceptual loss and even outperforms the physically based rendering systems in complex scenes given a reasonable time budget.
Skin manifestations associated with irritable bowel syndrome

Irritable bowel syndrome (IBS) is a functional bowel disorder characterized by abdominal pain and/or discomfort, related to abnormal bowel habits, leading to profound alterations of quality of life. IBS patients are usually classified according to the predominance symptoms associated with abdominal pain; IBS with predominance of diarrhea (IBS-D), constipation (IBS-C) or mixed troubles (IBS-A). Several studies have suggested a higher prevalence of other comorbidities in IBS patients. Asthma, food, pollen and animal allergies, psoriasis and rheumatoid arthritis were found to be associated with IBS. A nationwide epidemiological study reported a slight, although statistically significant, increase of rosacea in patients with IBS.
PCARE and WASF3 regulate ciliary F-actin assembly that is required for the initiation of photoreceptor outer segment disk formation

Significance The photoreceptor outer segments are primary cilia, modified for phototransduction by incorporation of stacked opsin-loaded membrane disks that are continuously regenerated. This process is disrupted in several types of inherited retinal dystrophy, but the driving force remained unclear. We show that C2orf71/PCARE (photoreceptor cilium actin regulator), associated with inherited retinal dystrophy subtype RP54, efficiently recruits the Arp2/3 complex activator WASF3 to the cilium. This activates an actin dynamics-driven expansion of the ciliary tip, resembling membrane evagination in lamellipodia formation. Colocalization of this actin dynamics module to the base of the outer segments, and absence thereof in Pcare−/− mice, suggests PCARE-regulated actin dynamics as a critical process in outer segment disk formation. The outer segments (OS) of rod and cone photoreceptor cells are specialized sensory cilia that contain hundreds of opsin-loaded stacked membrane disks that enable phototransduction. The biogenesis of these disks is initiated at the OS base, but the driving force has been debated. Here, we studied the function of the protein encoded by the photoreceptor-specific gene C2orf71, which is mutated in inherited retinal dystrophy (RP54). We demonstrate that C2orf71/PCARE (photoreceptor cilium actin regulator) can interact with the Arp2/3 complex activator WASF3, and efficiently recruits it to the primary cilium. Ectopic coexpression of PCARE and WASF3 in ciliated cells results in the remarkable expansion of the ciliary tip. This process was disrupted by small interfering RNA (siRNA)-based down-regulation of an actin regulator, by pharmacological inhibition of actin polymerization, and by the expression of PCARE harboring a retinal dystrophy-associated missense mutation. Using human retinal organoids and mouse retina, we observed that a similar actin dynamics-driven process is operational at the base of the photoreceptor OS where the PCARE module and actin colocalize, but which is abrogated in Pcare−/− mice. The observation that several proteins involved in retinal ciliopathies are translocated to these expansions renders it a potential common denominator in the pathomechanisms of these hereditary disorders. Together, our work suggests that PCARE is an actin-associated protein that interacts with WASF3 to regulate the actin-driven expansion of the ciliary membrane at the initiation of new outer segment disk formation.
Nurses' views and practices regarding use of validated nutrition screening tools

Objective To explore nurses’ views and practices regarding use of the Malnutrition Screening Tool (MST) and the Malnutrition Universal Screening Tool (MUST) in acute hospital wards. Design The study used a combined methods design with both qualitative and quantitative techniques including focus groups and survey of patient records. Setting Four medical or surgical wards in three hospitals within a single health service in Melbourne, Victoria, Australia. Subjects Registered nurses (n=54). Main outcome measures Audit results and themes from narrative data. Results The initial screening rate was 25% and 61% on spot audit of two wards using the MUST, with only 4% (2/47) of patients screened in two wards using the MST. Application of screening was limited by priority of other nursing duties, a nurse’s skill in use of a tool, and interpretation of patients’ weight status. Some nurses applied individual judgment rather than a tool to assess malnutrition risk. After nurse education and support over four months in wards using the MUST, compliance improved to 46% and 70%, Barriers were identified in use of either tool. Conclusions Implementation of evidence‐based screening tools within patient admission procedures does not automatically translate into nursing practice. Nurses’ time and nutrition screening knowledge were the main barriers to efficient screening. This suggests a need for induction programs for new staff and increased feedback to nurses regarding screening practice. A nutrition screening team might provide leadership and advocate for such screening practice and enable development of an audit cycle, including regular performance reporting, to increase compliance. RESEARCH PAPER
Dimensions of social support in the experience of work engagement in middle age: A Northern Finland Birth Cohort 1966 Study.

So far, the relationship between the various dimensions of social support and work engagement has not been widely examined in the literature. In this study, we examined the relationship of social support at work (from a colleague or supervisor) and social support in one's private life (from a spouse, relative or friend) with various dimensions of work engagement (vigor, dedication and absorption). The participants (N = 5,259-5,376, 46 years-old, 52.7% women) came from the Northern Finland Birth Cohort 1966 study. Social support was evaluated with the Social Support Questionnaire (SSQ), and work engagement was assessed with a short version of the Utrecht Work Engagement Scale (UWES-9). The data were analyzed using linear regression analyses. The results showed that high social support at work (p < 0.001) and in one's private life (p < 0.001) were associated with higher total work engagement, higher vigor, higher dedication, and higher absorption. These findings were adjusted for gender, marital status, education and occupational status. The results were essentially unchanged when they were additionally adjusted for job strain and effort-reward imbalance. To conclude, our findings indicate that the experience of overall social support may play a role in the experience of work engagement.