Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Providing the Uncertainty Information About a Tornado Occurrence on the Weather Recipients’ Cognition and Protective Action: Probabilistic Hazard Information Versus Deterministic Warnings

Currently, a binary alarm system is used in the United States to issue deterministic warning polygons in case of tornado events. To enhance the effectiveness of the weather information, a likelihood alarm system, which uses a tool called probabilistic hazard information (PHI), is being developed at National Severe Storms Laboratory to issue probabilistic information about the threat. This study aims to investigate the effects of providing the uncertainty information about a tornado occurrence through the PHI's graphical swath on laypeople's concern, fear, and protective action, as compared with providing the warning information with the deterministic polygon. The displays of color‐coded swaths and deterministic polygons were shown to subjects. Some displays had a blue background denoting the probability of any tornado formation in the general area. Participants were asked to report their levels of concern, fear, and protective action at randomly chosen locations within each of seven designated levels on each display. Analysis of a three‐stage nested design showed that providing the uncertainty information via the PHI would appropriately increase recipients’ levels of concern, fear, and protective action in highly dangerous scenarios, with a more than 60% chance of being affected by the threat, as compared with deterministic polygons. The blue background and the color‐coding type did not have a significant effect on the people's cognition of the threat and reaction to it. This study shows that using a likelihood alarm system leads to more conscious decision making by the weather information recipients and enhances the system safety.
Progression of Cystic Fibrosis Lung Disease from Childhood to Adulthood: Neutrophils, Neutrophil Extracellular Trap (NET) Formation, and NET Degradation

Genetic defects in cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene cause CF. Infants with CFTR mutations show a peribronchial neutrophil infiltration prior to the establishment of infection in their lung. The inflammatory response progressively increases in children that include both upper and lower airways. Infectious and inflammatory response leads to an increase in mucus viscosity and mucus plugging of small and medium-size bronchioles. Eventually, neutrophils chronically infiltrate the airways with biofilm or chronic bacterial infection. Perpetual infection and airway inflammation destroy the lungs, which leads to increased morbidity and eventual mortality in most of the patients with CF. Studies have now established that neutrophil cytotoxins, extracellular DNA, and neutrophil extracellular traps (NETs) are associated with increased mucus clogging and lung injury in CF. In addition to opportunistic pathogens, various aspects of the CF airway milieux (e.g., airway pH, salt concentration, and neutrophil phenotypes) influence the NETotic capacity of neutrophils. CF airway milieu may promote the survival of neutrophils and eventual pro-inflammatory aberrant NETosis, rather than the anti-inflammatory apoptotic death in these cells. Degrading NETs helps to manage CF airway disease; since DNAse treatment release cytotoxins from the NETs, further improvements are needed to degrade NETs with maximal positive effects. Neutrophil-T cell interactions may be important in regulating viral infection-mediated pulmonary exacerbations in patients with bacterial infections. Therefore, clarifying the role of neutrophils and NETs in CF lung disease and identifying therapies that preserve the positive effects of neutrophils, while reducing the detrimental effects of NETs and cytotoxic components, are essential in achieving innovative therapeutic advances.
The ENCePP Code of Conduct: A best practise for scientific independence and transparency in noninterventional postauthorisation studies

The ENCePP Code of Conduct provides a framework for scientifically independent and transparent pharmacoepidemiological research. Despite becoming a landmark reference, practical implementation of key provisions was still limited. The fourth revision defines scientific independence and clarifies uncertainties on the applicability to postauthorisation safety studies requested by regulators. To separate the influence of the funder from the investigator's scientific responsibility, the Code now requires that the lead investigator is not employed by the funding institution.
Proteomic Analysis of Histones H2A/H2B and Variant Hv1 in Tetrahymena thermophila Reveals an Ancient Network of Chaperones

Abstract Epigenetic information, which can be passed on independently of the DNA sequence, is stored in part in the form of histone posttranslational modifications and specific histone variants. Although complexes necessary for deposition have been identified for canonical and variant histones, information regarding the chromatin assembly pathways outside of the Opisthokonts remains limited. Tetrahymena thermophila, a ciliated protozoan, is particularly suitable to study and unravel the chromatin regulatory layers due to its unique physical separation of chromatin states in the form of two distinct nuclei present within the same cell. Using a functional proteomics pipeline, we carried out affinity purification followed by mass spectrometry of endogenously tagged T. thermophila histones H2A, H2B and variant Hv1.We identified a set of interacting proteins shared among the three analyzed histones that includes the FACT-complex, as well as H2A- or Hv1-specific chaperones. We find that putative subunits of T. thermophila versions of SWR- and INO80-complexes, as well as transcription-related histone chaperone Spt6Tt specifically copurify with Hv1. We also identified importin β6 and the T. thermophila ortholog of nucleoplasmin 1 (cNpl1Tt) as H2A–H2B interacting partners. Our results further implicate Poly [ADP-ribose] polymerases in histone metabolism. Molecular evolutionary analysis, reciprocal affinity purification coupled to mass spectrometry experiments, and indirect immunofluorescence studies using endogenously tagged Spt16Tt (FACT-complex subunit), cNpl1Tt, and PARP6Tt underscore the validity of our approach and offer mechanistic insights. Our results reveal a highly conserved regulatory network for H2A (Hv1)–H2B concerning their nuclear import and assembly into chromatin.
Bidirectional, optical sign-dependent regulation of BMP2 gene expression in chick retinal pigment epithelium.

PURPOSE We explored the role of bone morphogenic protein 2 (BMP2) in defocus-induced ocular growth using gene expression changes in RPE as a surrogate. METHODS Young White-Leghorn chickens were used in this study. Normal gene expression of BMP2 and its receptors was examined in retina, RPE, and choroid, and BMP2 protein expression assessed in the same tissues using Western blots and immunohistochemistry. Quantitative PCR (qPCR) was used to assess the effects of short-term exposure (2 or 48 hours) to monocular +10 and -10 diopter (D) lenses, on RPE gene expression of BMP2 and its receptors. Ocular growth was assessed using A-scan ultrasonography. RESULTS In the eyes of untreated chickens, BMP2 mRNA was expressed more highly in RPE compared to retina and choroid and all three tissues expressed BMP2 protein. The gene expression for all three receptors also was detected in these tissues, with BMPR2 showing highest and BMPR1B lowest expression. BMP2 was up-regulated in the RPE from eyes wearing +10 D lenses, which exhibited shorter than normal vitreous chambers (VCDs) and thickened choroids, while BMP2 was down-regulated in the RPE from eyes wearing -10 D lenses, which developed enlarged VCDs. These treatments did not induce differential expression of BMP receptors in RPE. CONCLUSIONS That mRNA expression of BMP2 in chick RPE shows bidirectional, defocus sign-dependent changes is suggestive of a role for BMP2 in eye growth regulation, although the diffuse ocular expression of BMP2 and its receptors suggests complex growth-modulatory signal pathways.
Ocean Dumping of Containerized DDT Waste Was a Sloppy Process.

Industrial-scale dumping of organic waste to the deep ocean was once common practice, leaving a legacy of chemical pollution for which a paucity of information exists. Using a nested approach with autonomous and remotely operated underwater vehicles, a dumpsite offshore California was surveyed and sampled. Discarded waste containers littered the site and structured the suboxic benthic environment. Dichlorodiphenyltrichloroethane (DDT) was reportedly dumped in the area, and sediment analysis revealed substantial variability in concentrations of p, p-DDT and its analogs, with a peak concentration of 257 μg g-1, ∼40 times greater than the highest level of surface sediment contamination at the nearby DDT Superfund site. The occurrence of a conspicuous hydrocarbon mixture suggests that multiple petroleum distillates, potentially used in DDT manufacture, contributed to the waste stream. Application of a two end-member mixing model with DDTs and polychlorinated biphenyls enabled source differentiation between shelf discharge versus containerized waste. Ocean dumping was found to be the major source of DDT to more than 3000 km2 of the region's deep seafloor. These results reveal that ocean dumping of containerized DDT waste was inherently sloppy, with the contents readily breaching containment and leading to regional scale contamination of the deep benthos.
The Role of Toxins in the Pursuit for Novel Analgesics

Chronic pain is a major medical issue which reduces the quality of life of millions and inflicts a significant burden on health authorities worldwide. Currently, management of chronic pain includes first-line pharmacological therapies that are inadequately effective, as in just a portion of patients pain relief is obtained. Furthermore, most analgesics in use produce severe or intolerable adverse effects that impose dose restrictions and reduce compliance. As the majority of analgesic agents act on the central nervous system (CNS), it is possible that blocking pain at its source by targeting nociceptors would prove more efficient with minimal CNS-related side effects. The development of such analgesics requires the identification of appropriate molecular targets and thorough understanding of their structural and functional features. To this end, plant and animal toxins can be employed as they affect ion channels with high potency and selectivity. Moreover, elucidation of the toxin-bound ion channel structure could generate pharmacophores for rational drug design while favorable safety and analgesic profiles could highlight toxins as leads or even as valuable therapeutic compounds themselves. Here, we discuss the use of plant and animal toxins in the characterization of peripherally expressed ion channels which are implicated in pain.
Modulation of Polar Lipid Profiles in Chlorella sp. in Response to Nutrient Limitation

We evaluate the effects of nutrient limitation on cellular composition of polar lipid classes/species in Chlorella sp. using modern polar lipidomic profiling methods (liquid chromatography–tandem mass spectrometry; LC-MS/MS). Total polar lipid concentration was highest in nutrient-replete (HN) cultures with a significant reduction in monogalactosyldiacylglycerol (MGDG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE) class concentrations for nutrient-deplete (LN) cultures. Moreover, reductions in the abundance of MGDG relative to total polar lipids versus an increase in the relative abundance of digalactosyldiacylglycerol (DGDG) were recorded in LN cultures. In HN cultures, polar lipid species composition remained relatively constant throughout culture with high degrees of unsaturation associated with acyl moieties. Conversely, in LN cultures lipid species composition shifted towards greater saturation of acyl moieties. Multivariate analyses revealed that changes in the abundance of a number of species contributed to the dissimilarity between LN and HN cultures but with dominant effects from certain species, e.g., reduction in MGDG 34:7 (18:3/16:4). Results demonstrate that Chlorella sp. significantly alters its polar lipidome in response to nutrient limitation, and this is discussed in terms of physiological significance and polar lipids production for applied microalgal production systems.
Accurate On-line Support Vector Regression

Batch implementations of support vector regression (SVR) are inefficient when used in an on-line setting because they must be retrained from scratch every time the training set is modified. Following an incremental support vector classification algorithm introduced by Cauwenberghs and Poggio (2001), we have developed an accurate on-line support vector regression (AOSVR) that efficiently updates a trained SVR function whenever a sample is added to or removed from the training set. The updated SVR function is identical to that produced by a batch algorithm. Applications of AOSVR in both on-line and cross-validation scenarios are presented.Inbothscenarios, numerical experiments indicate that AOSVR is faster than batch SVR algorithms with both cold and warm start.
Inhibition of tumor necrosis factor alpha and increased of interleukin 10 by Lactobacillus: a molecular mechanism protection against TNBS-induced ulcerative colitis in chicks

Abstract The purpose of this study was to evaluate the effects and mechanism of Lactobacillus on ameliorating ulcerative colitis chicks induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS). There are three groups in this study, control, Lactobacillus and ulcerative colitis groups. 1-day-old chicks were fed with microcapsules containing Lactobacillus LA-5 daily for Lactobacillus group and clustered with 2,4,6-trinitrobenzene sulfonic acid (TNBS) to make the model of ulcerative colitis at ten-day-old. Chicks in control and ulcerative colitis groups were fed with empty microcapsules daily at 1-day-old and then chicks in ulcerative colitis group were induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS) for preparation of ulcerative colitis model at 10-day-old. We detected the changes of mRNA and protein expression of TNF-α and IL-10 in the colon by Real-Time PCR and Western Blot. Histopathology evaluation on colon was conducted. Results showed that chicks pretreated with Lactobacillus had striking injury improvement compared with ulcerative colitis group in histopathology. Compared with ulcerative colitis group, down-regulation of TNF-α and up-regulation of IL-10 were observed in Lactobacillus group chicks. Therefore, Lactobacillus could improve the injury of intestinal mucosa and reduce inflammatory response by regulating mRNA and protein expression levels of TNF-α and IL-10, respectively. In conclusion, Lactobacillus could ameliorate the effects on chicks of TNBS-induced ulcerative colitis by reducing the inflammation and regulating the expression of TNF-α and IL-10, respectively.
Power-Velocity and Power-Efficiency Implications in the Limitation of Ramp Incremental Cycle Ergometry: Reply to Morales-Alamo et al.

to the editor: We thank Morales-Alamo et al. ([5][1]) for raising important questions worthy of further discussion. A key concern of both our studies ([3][2], [4][3]) is whether the limit of tolerance (LoT) in ramp-incremental exercise is reached with a reserve in power producing capacity. To this
Rehospitalization for heart failure: predict or prevent?

Heart failure is the leading cause of hospitalization among adults >65 years of age in the United States. Annually, >1 million patients are hospitalized with a primary diagnosis of heart failure, accounting for a total Medicare expenditure exceeding $17 billion.1 Despite dramatic improvement in outcomes with medical therapy,2,3 admission rates following heart failure hospitalization remain high,4 with ≥50% patients readmitted to hospital within 6 months of discharge.5–7 Because reduction in readmission rates might simultaneously reduce costs and improve quality of care, public and private payers have increasingly targeted readmissions as a focus of pay-for-performance initiatives.8 In 2009, the US Center for Medicare & Medicaid Services began public reporting of all-cause readmission rates after heart failure hospitalization, and, in the following year, the Patient Protection and Affordable Care Act9 established financial penalties for hospitals with the highest readmission rates during the first 30 days after discharge. Increasing concern regarding the need to reduce readmissions has focused national research and hospital-driven efforts on the prediction of which patients with heart failure are likely to be readmitted and the design of interventions to prevent readmissions. Discharge from a heart failure hospitalization is followed by a readmission within 30 days in ≈24% of cases.5 Recurrent heart failure and related cardiovascular conditions account for only about half of readmissions in patients with heart failure, whereas other comorbid conditions account for the rest.10 Although the proportion of noncardiovascular admissions is higher in those with preserved ejection fraction (EF),11 overall readmission rates for heart failure remain similar whether the heart failure occurs with reduced or preserved EF.12 The rate and characteristics of readmission for patients with an initially low EF that recovers to ≥40% (heart failure with ‘better' EF) are yet to be …
The evolution of eye size in response to increased fish predation in Daphnia

Variation in eye size is ubiquitous across taxa. Increased eye size is correlated with improved vision and increased fitness via shifts in behavior. Tests of the drivers of eye size evolution have focused on macroevolutionary studies evaluating the importance of light availability. Predator‐induced mortality has recently been identified as a potential driver of eye size variation. Here, we tested the influence of increased predation by the fish predator, the alewife (Alosa pseudoharengus) on eye size evolution in waterfleas (Daphnia ambigua) from lakes in Connecticut. We quantified the relative eye size of Daphnia from lakes with and without alewife using wild‐caught and third‐generation laboratory reared specimens. This includes comparisons between lakes where alewife are present seasonally (anadromous) or permanently (landlocked). Wild‐caught specimens did not differ in eye size across all lakes. However, third‐generation lab reared Daphnia from lakes with alewife, irrespective of the form of alewife predation, exhibited significantly larger eyes than Daphnia from lakes without alewife. This genetically based increase in eye size may enhance the ability of Daphnia to detect predators. Alternatively, such shifts in eye size may be an indirect response to Daphnia aggregating at the bottom of lakes. To test these mechanisms, we collected Daphnia as a function of depth and found that eye size differed in Daphnia found at the surface versus the bottom of the water column between anadromous alewife and no alewife lakes. However, we found no evidence of Daphnia aggregating at the bottom of lakes. Such results indicate that the evolution of a larger eye may be explained by a connection between eyes and enhanced survival. We discuss the cause of the lack of concordance in eye size variation between our phenotypic and genetic specimens and the ultimate drivers of eye size.
Risk factors associated with Richter’s transformation in patients with chronic lymphocytic leukaemia: protocol for a retrospective population-based cohort study

Introduction Richter’s transformation (RT) refers to the development of an aggressive lymphoma in patients with chronic lymphocytic leukaemia (CLL) or small lymphocytic lymphoma. Studies have shown that 2–10% of patients with CLL develop RT including diffuse large B-cell lymphoma (DLBCL) and less common Hodgkin lymphoma (HL). This study aims to assess the risk factors for RT of CLL in a nationwide cohort. Additionally, we want to examine prognostic factors in patients with RT. These findings may guide management of treated as well as untreated patients with CLL in the risk of RT. Methods Clinical data for patients diagnosed with CLL between 2008 and 2016 will be retrieved from the Danish National CLL registry (DCLLR). Using the Danish unique person identification number, clinical data will be merged with histologically verified DLBCL and/or HL diagnoses retrieved from the Danish National Pathology Data Bank. This will ensure complete follow-up for all patients. The DCLLR includes data from more than 4000 patients with CLL ensuring a median follow-up of 3 years. With the reported incidences (2-10%) of RT, we expect to identify 80–200 CLL patients with RT enabling analysis of overall survival following RT. From time of CLL diagnosis, estimates of cumulative incidence of RT will be calculated using the Aalen-Johansen estimator. From time of RT diagnosis, survival analysis will be performed by Kaplan-Meier method. Cox proportional hazards models will be used for multivariable survival analysis. Ethics and dissemination Approvals for data collection and analysis was obtained from the Danish Data Protection Agency and the Danish Health Authorities. All data will be managed confidentially according to guidelines and legislation. The dissemination will include a publication of scientific papers and/or presentations of the study findings at international conferences.
Age-dependent co-dependency structure of biomarkers in the general population of the United States

Phenotypic biomarkers (e.g. cholesterol, weight, and glucose) are important to diagnose and treat diseases associated with aging. However, while many biomarkers are co-dependent (e.g. glycohemoglobin and glucose), it is generally unknown how age influences their co-dependence. In the following, we analyzed 50 biomarkers in 27,508 National Health and Nutrition Examination Survey (NHANES) participants (age range: 20 to 80, mean age: 46.3 years old, sexes: 48.9% males, 51.1% females, ethnicities: 46.0% Whites, 27.8% Hispanics, 20.0% non-Hispanic Blacks, 6.1% others) to investigate how the co-dependency structure of common biomarkers evolves with age and whether differences exist between sexes and ethnicities. First, we associated the change in correlations between biomarkers with chronological age. We identified six trends and replicated our top finding (height vs. systolic blood pressure) in participants of the UK Biobank (N=470,895). We found that, on average, correlations tend to decrease with age. Secondly, we examined how biomarkers predict other biomarkers in participants of different age groups. We found 17 (34%) biomarkers whose predictability decreases with age and 5 (10%) biomarkers whose predictability increases with age. A limitation of this study is that it cannot distinguish between biological changes related to aging and generational effects. Our results can be interactively explored here: http://apps.chiragjpgroup. org/Aging_Biomarkers_Co-Dependencies/.
Strategy for a globally coordinated response to a priority neglected tropical disease: Snakebite envenoming

In one of his final essays, statesman and former United Nations secretary general Kofi Annan said, ‘Snakebite is the most important tropical disease you’ve never heard of’ [1]. Mr. Annan firmly believed that victims of snakebite envenoming should be recognised and afforded greater efforts at improved prevention, treatment, and rehabilitation. During the last years of his life, he advocated strongly for the World Health Organisation (WHO) and the global community to give greater priority to this disease of poverty and its victims.