Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Plant Litter in Driving Plant-Soil Feedbacks

Most studies focusing on plant-soil feedbacks (PSFs) have considered direct interactions between plants, abiotic conditions (e. g., soil nutrients) and rhizosphere communities (e.g., pathogens, mutualists). However, few studies have addressed the role of indirect interactions mediated by plant litter inputs. This is problematic because it has left a major gap in our understanding of PSFs in natural ecosystems, where plant litter is a key component of feedback effects. Here, we propose a new conceptual framework that integrates rhizosphere- and litter-mediated PSF effects. Our framework provides insights into the relative contribution of direct effects mediated by interactions between plants and soil rhizosphere organisms, and indirect effects between plants and decomposer organisms mediated by plant root and shoot litter. We distinguish between three pathways through which senesced root and shoot litter may influence PSFs. Specifically, we examine: (1) physical effects of litter (layer) traits on seed germination, soil structure, and plant growth; (2) chemical effects of litter on concentrations of soil nutrients and secondary metabolites (e.g., allelopathic chemicals); and (3) biotic effects of saprotrophic soil communities that can perform different functional roles in the soil food web, or that may have specialized interactions with litter types, thereby altering soil nutrient cycling. We assess the role of litter in PSF effects via physical, chemical and biotic pathways to address how litter-mediated feedbacks may play out relative to, and in interaction with, feedbacks mediated through the plant rhizosphere. We also present one of the first experimental studies to show the occurrence and species-specificity of litter-mediated feedbacks and we identify critical research gaps. By formally incorporating the plant-litter feedback pathway into PSF experiments, we will further our understanding of PSFs under natural conditions.
Cancer Sample Biobanking at the Next Level: Combining Tissue With Living Cell Repositories to Promote Precision Medicine

Biorespositories of formalin-fixed and paraffin-embedded (FFPE) or fresh frozen human tissues from malignant diseases generated as integral part of the diagnostic workup in many pathology departments have been pivotal resources for translational cancer studies. However, such tissue biobanks have traditionally contained only non-viable specimens and thus cannot enable functional assays for the discovery and validation of therapeutic targets or the assessment of drug responses and resistance to treatment. To overcome these limitations, we have developed a next-generation comprehensive biobanking platform that includes the generation of patient-derived in vitro cell models from colorectal, pancreatic and kidney cancers among others. As such patient-derived cell (PDC) models retain important features of the original human tumors, they have emerged as relevant tools for more dynamic clinical and experimental analyses of cancer. Here, we describe details of the complex processes of acquisition and processing of patient-derived samples, propagation, annotation, characterization and distribution of resulting cell models and emphasize the requirements of quality assurance, organizational considerations and investment into resources. Taken together, we show how clinical tissue collections can be taken to the next level thus promising major new opportunities for understanding and treating cancer in the context of precision medicine.
Psychedelic drugs—a new era in psychiatry? 

This article covers the renaissance of classical psychedelic drugs such as psilocybin and LSD plus 3,4-methylene dioxymethamphetamine (MDMA—ecstasy) in psychiatric research. These drugs were used quite extensively before they became prohibited. This ban had little impact on recreational use, but effectively stopped research and clinical treatments, which up to that point had looked very promising in several areas of psychiatry. In the past decade a number of groups have been working to re-evaluate the utility of these substances in medicine. So far highly promising preliminary data have been produced with psilocybin in anxiety, depression, smoking, alcoholism, and with MDMA for post-traumatic stress disorder (PTSD) and alcoholism. These findings have led to the European Medicines Agency approving psilocybin for a phase 3 study in treatment-resistant depression and the Food and Drug Administration for PTSD with MDMA. Both trials should read out in 2020, and if the results are positive we are likely to see these medicines approved for clinical practice soon afterwards.
The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses

Background Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were small. Methods In this study, we analyzed the phylogenetic interrelationship of Desmostylia based on a new data matrix that includes larger numbers of characters and taxa than in any previous studies. The new data matrix was compiled mainly based on data matrices of previous studies and included three outgroups and 13 desmostylian ingroup taxa. Analyses were carried out using five kinds of parsimonious methods. Results Strict consensus trees of the most parsimonious topologies obtained in all analyses supported the monophyly of Desmostylidae and paraphyly of traditional Paleoparadoxiidae. Based on these results, we propose phylogenetic definitions of the clades Desmostylidae and Paleoparadoxiidae based on common ancestry.
Bivalirudin Versus Heparin During Percutaneous Coronary Intervention in Patients With Acute Myocardial Infarction

Background The aim of the study was to compare the efficacy and safety of bivalirudin versus unfractionated heparin (UFH) in patients with acute myocardial infarction who undergo percutaneous coronary intervention (PCI). Earlier trials comparing bivalirudin and UFH during PCI demonstrated that bivalirudin caused less bleeding with more stent thrombosis. Since then, adjunct antiplatelet strategies have evolved. Improved upstream platelet inhibition with potent P2Y12 inhibitors decreased the need for routine glycoprotein IIb/IIIa inhibitor (GPI), resulting in similar outcomes among UFH and bivalirudin. Therefore, the role of bivalirudin in modern PCI practices is questionable. Methods We utilized Cochrane Review Manager (RevMan) 5.3 to perform a meta-analysis of seven randomized controlled trials (RCTs) with 22,844 patients to compare bivalirudin to UFH in patients with acute myocardial infarction requiring revascularization. Results There was no difference between bivalirudin and UFH regarding major adverse cardiac events (MACE), risk ratio (RR) 0.99, 95% confidence interval (CI) 0.87 - 1.12; P = 0.83) or cardiovascular mortality (RR 0.87, 95% CI 0.71 - 1.07; P = 0.18). Bivalirudin increased acute stent thrombosis (RR 2.77, 95% CI 1.49 - 5.13; P = 0.001), which was only significant among ST-elevation myocardial infarction (STEMI) only trials. Bivalirudin caused less major bleeding (RR 0.66, 95% CI 0.49 - 0.90; P = 0.007), which was negated when GPI was used provisionally (RR 0.93, 95% CI 0.64 - 1.33; P = 0.67). Conclusions Among patients with acute myocardial infarction who underwent PCI, bivalirudin and UFH demonstrated similar MACE and cardiovascular mortality. Bivalirudin increased acute stent thrombosis, which was more remarkable among STEMI. Bivalirudin decreased major bleeding, but this benefit was negated when GPI was used provisionally.
Influence of the Lung Microbiota Dysbiosis in Chronic Obstructive Pulmonary Disease Exacerbations: The Controversial Use of Corticosteroid and Antibiotic Treatments and the Role of Eosinophils as a Disease Marker

Chronic obstructive pulmonary disease (COPD) is a debilitating lung disease associated with loss of lung function, poorer quality of life, co-morbidities, significant mortality, and higher health care costs. Frequent acute exacerbations of COPD are sudden worsening of symptoms, the nature of which is associated with bacterial or viral infections. However, one-third of exacerbations remain of undetermined origin. Although it is largely discussed and controversial, current guidelines recommend treatment of exacerbations with bronchodilators, antibiotics, and systemic corticosteroids; this is despite being associated with limited benefits in term of reducing mortality, side effects and without paying attention to the heterogeneity of these exacerbations. Increasing evidence suggests that the lung microbiota plays an important role in COPD and numerous studies have reported differences in the microbiota between healthy and disease states, as well as between exacerbations and stable COPD, leading to the hypothesis that frequent acute exacerbation is more likely to experience significant changes in lung microbiota composition. These findings will need further examination to explain the causes of lung dysbiosis, namely microbial composition, the host response, including the recruitment of eosinophils, lifestyle, diet, cigarette smoking and the use of antibiotics and corticosteroids. It is now important to assess: 1) Whether alterations in the lung microbiota contribute to disease pathogenesis, especially in exacerbations of unknown origin; 2) The role of eosinophils; and 3) Whether the microbiota of the lung can be manipulated therapeutically to improve COPD exacerbation event and disease progression. In summary, we hypothesize that the alterations of the lung microbiota may explain the undetermined origins of exacerbations and that there is an urgent need to facilitate the design of intervention studies that aim at conserving the lung microbial flora.
Exploring aspects of the cognitive behavioural model of physical hoarding in relation to digital hoarding behaviours

While the hoarding of physical objects has been extensively explored, there is little research relating to the hoarding of digital materials. The research that has been conducted suggests that digital hoarding (DH) behaviours appear to have some similarities with physical hoarding (PH) behaviours, and can be just as psychologically distressing. This study uses the framework of the cognitive behavioural model of PH to explore DH behaviours, including possible similarities regarding emotional attachment to digital possessions, and possible links with Obsessive Compulsive Disorder (OCD) and indecisiveness. For the study, 282 participants completed an online survey which measured levels of digital and physical hoarding, compulsive acquisition, OCD, indecisiveness and mood. Strong emotional attachments to particular types of digital possessions were evident: this was especially true for photographs and videos. Significant positive relationships were found between all the variables measured. However, a regression analysis revealed that only OCD and PH scores were significant predictors of DH. DH thus appears to share some of the features of PH. Implications, limitations and future research possibilities are discussed.
Efficacy of Physical Activity in Prevention of Muscle Weakness in Patients With Chronic Liver Disease

Background Sarcopenia is a prognostic factor for patients with liver cirrhosis and hepatocellular carcinoma, and it affects the onset of hepatic encephalopathy. Therefore, the prevention of sarcopenia contributes to the improvement of the prognosis of patients with chronic liver disease (CLD). We focused on changes of hand grip strength (HGS), one of the indicators of sarcopenia. However, there are little data investigating the impact of physical activity (PA) on HGS in patients with CLD. This study aimed to clarify whether PA contributes to the prevention of muscle weakness in patients with CLD. Methods This was a prospective observational study. We examined the effect of PA on changes in HGS from the baseline to the endpoint in each group. Metabolic equivalents-hour/week (METs-h/w) was used to evaluate PA. In total, 183 outpatients with CLD were analyzed. We divided participants into four groups (low PA in younger patients (n = 20), high PA in younger patients (n = 33), low PA in elderly patients (n = 47), and high PA in elderly patients (n = 83)). Results Fifty-eight percent of patients were men, and the median (interquartile range) age was 69.0 (63.0, 75.0) years. The most common etiology of liver disease was hepatitis C (38%). The frequency of living alone and low exercise habit was significantly high, and sarcopenia was more obvious in elderly patients with low PA than in those with high PA. Additionally, the elderly with low PA showed significantly reduced HGS compared to that of the elderly with high PA (-1.00 (-2.27, 0.55) kg vs. 0.10 (-1.40, 1.10) kg, P < 0.05). However, changes in HGS in younger patients were not significant (-0.02 (1.83, 1.47) kg vs. 0.25 (-2.45, 2.05) kg, P = 0.96). Logistic regression analyses identified PA as the independent factor for prevention of decrease in HGS (odds ratio: 1.91, 95% confidence interval: 1.00 - 3.62, P = 0.049). Conclusions Young patients with low PA were characterized by a long sedentary time; however, there was no loss of HGS. In contrast, elderly patients with CLD and low PA had significantly reduced HGS compared to that in elderly patients with CLD and high PA.
Comparison between two- and three-dimensional scoring of zebrafish response to psychoactive drugs: identifying when three-dimensional analysis is needed

Zebrafish (Danio rerio) have recently emerged as a valuable laboratory species in the field of behavioral pharmacology, where they afford rapid and precise high-throughput drug screening. Although the behavioral repertoire of this species manifests along three-dimensional (3D), most of the efforts in behavioral pharmacology rely on two-dimensional (2D) projections acquired from a single overhead or front camera. We recently showed that, compared to a 3D scoring approach, 2D analyses could lead to inaccurate claims regarding individual and social behavior of drug-free experimental subjects. Here, we examined whether this conclusion extended to the field of behavioral pharmacology by phenotyping adult zebrafish, acutely exposed to citalopram (30, 50, and 100 mg/L) or ethanol (0.25%, 0.50%, and 1.00%), in the novel tank diving test over a 6-min experimental session. We observed that both compounds modulated the time course of general locomotion and anxiety-related profiles, the latter being represented by specific behaviors (erratic movements and freezing) and avoidance of anxiety-eliciting areas of the test tank (top half and distance from the side walls). We observed that 2D projections of 3D trajectories (ground truth data) may introduce a source of unwanted variation in zebrafish behavioral phenotyping. Predictably, both 2D views underestimate absolute levels of general locomotion. Additionally, while data obtained from a camera positioned on top of the experimental tank are similar to those obtained from a 3D reconstruction, 2D front view data yield false negative findings.
Sirtuin 1 alleviates endoplasmic reticulum stress-mediated apoptosis of intestinal epithelial cells in ulcerative colitis

BACKGROUND Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing. AIM To investigate the role of SIRT1 in intestinal epithelial cells (IECs) in UC and further explore the underlying mechanisms. METHODS We developed a coculture model using macrophages and Caco-2 cells. After treatment with the SIRT1 activator SRT1720 or inhibitor nicotinamide (NAM), the expression of occludin and zona occludens 1 (ZO-1) was assessed by Western blot analysis. Annexin V-APC/7-AAD assays were performed to evaluate Caco-2 apoptosis. Dextran sodium sulfate (DSS)-induced colitis mice were exposed to SRT1720 or NAM for 7 d. Transferase-mediated dUTP nick-end labeling (TUNEL) assays were conducted to assess apoptosis in colon tissues. The expression levels of glucose-regulated protein 78 (GRP78), CCAAT/enhancer-binding protein homologous protein (CHOP), caspase-12, caspase-9, and caspase-3 in Caco-2 cells and the colon tissues of treated mice were examined by quantitative real-time PCR and Western blot. RESULTS SRT1720 treatment increased the protein levels of occludin and ZO-1 and inhibited Caco-2 apoptosis, whereas NAM administration caused the opposite effects. DSS-induced colitis mice treated with SRT1720 had a lower disease activity index (P < 0.01), histological score (P < 0.001), inflammatory cytokine levels (P < 0.01), and apoptotic cell rate (P < 0.01), while exposure to NAM caused the opposite effects. Moreover, SIRT1 activation reduced the expression levels of GRP78, CHOP, cleaved caspase-12, cleaved caspase-9, and cleaved caspase-3 in Caco-2 cells and the colon tissues of treated mice. CONCLUSION SIRT1 activation reduces apoptosis of IECs via the suppression of endoplasmic reticulum stress-mediated apoptosis-associated molecules CHOP and caspase-12. SIRT1 activation may be a potential therapeutic strategy for UC.
Fundamental niche unfilling and potential invasion risk of the slider turtle Trachemys scripta

Background How species colonize new environments is still a fundamental question in ecology and evolution, assessable by evaluating range characteristics of invasive species. Here we propose a model approach to evaluate environmental conditions and species features to predict niche changes in non-equilibrium contexts. It incorporates potentially range-limiting processes (fundamental niche), hence allowing for better predictions of range shifts, differentiation of analog and non-analog conditions between the native and non-native (invaded) ranges, and identification of environmental conditions not currently available but likely in the future. We apply our approach with the worldwide invasive slider-turtle Trachemys scripta. Methods We estimated the native and non-native realized niches of T. scripta and built its fundamental niche based on key features of the turtle’s temperature physiological tolerance limits and survival-associated factors. We next estimated response functions adjusted to the physiological predictor variables and estimated habitat suitability values, followed by a comprehensive set of analyses and simulations to compare the environmental conditions occupied by T. scripta (at its native and non-native ranges). Results Climatic space analysis showed that the T. scripta’s non-native realized niche is 28.6% greater than the native one. Response curves showed that it does not use its entire range of temperature tolerances (density curves for native: 5.3–23.7 °C and non-native: 1.7–28.4 °C ranges). Whether considering the mean temperature of the warmest or the coldest quarter, it occupies a wider range of temperatures along its non-native distribution. Results of the response curves for worldwide (global) and across Mexico (regional) comparisons showed it occupies analog and non-analog conditions between its native and invaded ranges, exhibiting also unoccupied suitable climatic conditions. Discussion We demonstrate that T. scripta occupies a wider subset of its fundamental niche along its non-native range (within its physiological tolerances), revealing that the species observed niche shift corresponds to a different subset of its fundamental niche (niche unfilling). We also identified suitable environmental conditions, globally and regionally, where the slider turtle could potentially invade. Our approach allows to accurately predict niche changes in novel or non-equilibrium contexts, which can improve our understanding about ecological aspects and geographic range boundaries in current and potential invasions.
Contrary to Myth, Older Adults Multitask With Media and Technologies, But Studying Their Multitasking Behaviors Can Be Challenging

Abstract Background and Objectives The study’s objective was to explore older adults’ (aged 65 or older) descriptions of behavior related to multitasking with traditional and newer media/information and communication technologies (ICTs) and perceived benefits of such behavior, along with older adults’ preference for research methods used to study their multitasking behaviors. Employing common media-use measures that heavily rely on self-reporting in populations of older adults is challenging, especially given that patterns of media/ICT use are becoming increasingly complex. Cumulatively, people spend more time using media than they are aware of because of the tendency to use some forms of media simultaneously. As cognitive ability deteriorates with age, self-reported recollection of complex patterns of media/ICT use, such as multitasking, among older adults increases the threat to data accuracy. Research Design and Methods: Twenty-eight community-dwelling older adults in a Midwestern U.S. state participated in in-depth interviews (average length was 40 minutes) to discuss their use of traditional and newer media/technologies in combination with other activities and outline methods researchers should use to study such behaviors. Results Participants reported they engaged in multitasking behaviors similar to those of younger generations, with the difference in the higher extent of using traditional media and ICTs. They talked about multitasking with radio and television for “background noise” as being a rewarding experience. They perceived the effects of multitasking to be detrimental to attention and performance and attributed this media-use habit to individual psychological and demographic differences. They preferred ethnographic observation and keeping a paper-and-pencil diary as research methods to study multitasking among their peers. Data-logging methods were less popular because they raised privacy concerns among interviewees. Discussion and Implications Different types of traditional and newer media and technologies could be used differently in situations that require older adults to focus, relax, or be efficient. The findings suggest that future researchers strive for a compromise between data access and data accuracy when they select a research method to study media use among older adults.