Showing papers by "University of Bologna published in 2016"
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TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.
For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.
Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.
5,187 citations
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TL;DR: The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015) as discussed by the authors was used to estimate the incidence, prevalence, and years lived with disability for diseases and injuries at the global, regional, and national scale over the period of 1990 to 2015.
5,050 citations
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TL;DR: The Global Burden of Disease 2015 Study provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015, finding several countries in sub-Saharan Africa had very large gains in life expectancy, rebounding from an era of exceedingly high loss of life due to HIV/AIDS.
4,804 citations
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TL;DR: In this paper, un estudio en donde se proporciona una revision extensa de la literatura de las two ultimas decadas, con el proposito de captar las principales caracteristicas y perspectivas of la CE (Economia circular): origenes, principios basicos, ventajas and desventajas, Modelado e implementacion of CE in los diferentes niveles (micro, meso, and macro) in todo el world.
3,121 citations
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Mayo Clinic1, University of Navarra2, Harvard University3, Cedars-Sinai Medical Center4, Memorial Sloan Kettering Cancer Center5, Emory University6, National and Kapodistrian University of Athens7, Mount Sinai Hospital8, University of Turin9, University of Texas MD Anderson Cancer Center10, Heidelberg University11, Alfred Hospital12, University Health System13, Carolinas Healthcare System14, University of Bologna15, Aalborg University16, Dalhousie University17, Erasmus University Rotterdam18, Roswell Park Cancer Institute19, Columbia University20, University of Toulouse21
TL;DR: Several aspects of disease response assessment are clarified, along with endpoints for clinical trials, and future directions for disease response assessments are highlighted, to allow uniform reporting within and outside clinical trials.
Abstract: Treatment of multiple myeloma has substantially changed over the past decade with the introduction of several classes of new effective drugs that have greatly improved the rates and depth of response. Response criteria in multiple myeloma were developed to use serum and urine assessment of monoclonal proteins and bone marrow assessment (which is relatively insensitive). Given the high rates of complete response seen in patients with multiple myeloma with new treatment approaches, new response categories need to be defined that can identify responses that are deeper than those conventionally defined as complete response. Recent attempts have focused on the identification of residual tumour cells in the bone marrow using flow cytometry or gene sequencing. Furthermore, sensitive imaging techniques can be used to detect the presence of residual disease outside of the bone marrow. Combining these new methods, the International Myeloma Working Group has defined new response categories of minimal residual disease negativity, with or without imaging-based absence of extramedullary disease, to allow uniform reporting within and outside clinical trials. In this Review, we clarify several aspects of disease response assessment, along with endpoints for clinical trials, and highlight future directions for disease response assessments.
1,681 citations
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Nicholas J Kassebaum1, Megha Arora1, Ryan M Barber1, Zulfiqar A Bhutta2 +679 more•Institutions (268)
TL;DR: In this paper, the authors used the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015) for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive HALE and DALYs by sex for 195 countries and territories from 1990 to 2015.
1,533 citations
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TL;DR: Bone scintigraphy enables the diagnosis of cardiac ATTR amyloidosis to be made reliably without the need for histology in patients who do not have a monoclonal gammopathy, and proposes noninvasive diagnostic criteria that are applicable to the majority of patients with this disease.
Abstract: Background—Cardiac transthyretin (ATTR) amyloidosis is a progressive and fatal cardiomyopathy for which several promising therapies are in development. The diagnosis is frequently delayed or missed...
1,185 citations
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University of Pittsburgh1, University of Bologna2, Hospital of the University of Pennsylvania3, University of Pisa4, Brigham and Women's Hospital5, Mount Sinai Health System6, Institut Gustave Roussy7, Kindai University8, University of Michigan9, University of São Paulo10, University of California, San Francisco11, University Health Network12, University of Texas MD Anderson Cancer Center13, New York University14, University of Wisconsin-Madison15, Harvard University16, University of Turin17, University of Portsmouth18, Tufts University19, Memorial Sloan Kettering Cancer Center20, Massachusetts Eye and Ear Infirmary21
TL;DR: Thyroid tumors currently diagnosed as noninvasive EFVPTC have a very low risk of adverse outcome and should be termed NIFTP, and this reclassification will affect a large population of patients worldwide and result in a significant reduction in psychological and clinical consequences associated with the diagnosis of cancer.
Abstract: Importance Although growing evidence points to highly indolent behavior of encapsulated follicular variant of papillary thyroid carcinoma (EFVPTC), most patients with EFVPTC are treated as having conventional thyroid cancer. Objective To evaluate clinical outcomes, refine diagnostic criteria, and develop a nomenclature that appropriately reflects the biological and clinical characteristics of EFVPTC. Design, Setting, and Participants International, multidisciplinary, retrospective study of patients with thyroid nodules diagnosed as EFVPTC, including 109 patients with noninvasive EFVPTC observed for 10 to 26 years and 101 patients with invasive EFVPTC observed for 1 to 18 years. Review of digitized histologic slides collected at 13 sites in 5 countries by 24 thyroid pathologists from 7 countries. A series of teleconferences and a face-to-face conference were used to establish consensus diagnostic criteria and develop new nomenclature. Main Outcomes and Measures Frequency of adverse outcomes, including death from disease, distant or locoregional metastases, and structural or biochemical recurrence, in patients with noninvasive and invasive EFVPTC diagnosed on the basis of a set of reproducible histopathologic criteria. Results Consensus diagnostic criteria for EFVPTC were developed by 24 thyroid pathologists. All of the 109 patients with noninvasive EFVPTC (67 treated with only lobectomy, none received radioactive iodine ablation) were alive with no evidence of disease at final follow-up (median [range], 13 [10-26] years). An adverse event was seen in 12 of 101 (12%) of the cases of invasive EFVPTC, including 5 patients developing distant metastases, 2 of whom died of disease. Based on the outcome information for noninvasive EFVPTC, the name “noninvasive follicular thyroid neoplasm with papillary-like nuclear features” (NIFTP) was adopted. A simplified diagnostic nuclear scoring scheme was developed and validated, yielding a sensitivity of 98.6% (95% CI, 96.3%-99.4%), specificity of 90.1% (95% CI, 86.0%-93.1%), and overall classification accuracy of 94.3% (95% CI, 92.1%-96.0%) for NIFTP. Conclusions and Relevance Thyroid tumors currently diagnosed as noninvasive EFVPTC have a very low risk of adverse outcome and should be termed NIFTP. This reclassification will affect a large population of patients worldwide and result in a significant reduction in psychological and clinical consequences associated with the diagnosis of cancer.
1,080 citations
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TL;DR: High-level consumption of plant foodstuffs consistent with an MD is associated with beneficial microbiome-related metabolomic profiles in subjects ostensibly consuming a Western diet, as well as higher urinary trimethylamine oxide levels in individuals with lower adherence to the MD.
Abstract: Objectives Habitual diet plays a major role in shaping the composition of the gut microbiota, and also determines the repertoire of microbial metabolites that can influence the host. The typical Western diet corresponds to that of an omnivore; however, the Mediterranean diet (MD), common in the Western Mediterranean culture, is to date a nutritionally recommended dietary pattern that includes high-level consumption of cereals, fruit, vegetables and legumes. To investigate the potential benefits of the MD in this cross-sectional survey, we assessed the gut microbiota and metabolome in a cohort of Italian individuals in relation to their habitual diets. Design and results We retrieved daily dietary information and assessed gut microbiota and metabolome in 153 individuals habitually following omnivore, vegetarian or vegan diets. The majority of vegan and vegetarian subjects and 30% of omnivore subjects had a high adherence to the MD. We were able to stratify individuals according to both diet type and adherence to the MD on the basis of their dietary patterns and associated microbiota. We detected significant associations between consumption of vegetable-based diets and increased levels of faecal short-chain fatty acids, Prevotella and some fibre-degrading Firmicutes, whose role in human gut warrants further research. Conversely, we detected higher urinary trimethylamine oxide levels in individuals with lower adherence to the MD. Conclusions High-level consumption of plant foodstuffs consistent with an MD is associated with beneficial microbiome-related metabolomic profiles in subjects ostensibly consuming a Western diet. Trial registration number This study was registered at clinical trials.gov as NCT02118857.
1,031 citations
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University of Paris1, Centre national de la recherche scientifique2, Academia Sinica3, California Institute of Technology4, Institute for the Physics and Mathematics of the Universe5, University of Cambridge6, University of Geneva7, Valparaiso University8, Smithsonian Astrophysical Observatory9, University of Edinburgh10, Niels Bohr Institute11, University of Rochester12, Space Telescope Science Institute13, ETH Zurich14, University of Bologna15, Max Planck Society16, University of Zagreb17, Kindai University18, University of the Western Cape19
TL;DR: The COSMOS2015(24) catalog as mentioned in this paper contains precise photometric redshifts and stellar masses for more than half a million objects over the 2deg(2) COSmOS field, which is highly optimized for the study of galaxy evolution and environments in the early universe.
Abstract: We present the COSMOS2015(24) catalog, which contains precise photometric redshifts and stellar masses for more than half a million objects over the 2deg(2) COSMOS field. Including new YJHK(s) images from the UltraVISTA-DR2 survey, Y-band images from Subaru/Hyper-Suprime-Cam, and infrared data from the Spitzer Large Area Survey with the Hyper-Suprime-Cam Spitzer legacy program, this near-infrared-selected catalog is highly optimized for the study of galaxy evolution and environments in the early universe. To maximize catalog completeness for bluer objects and at higher redshifts, objects have been detected on a chi(2) sum of the YJHK(s) and z(++) images. The catalog contains similar to 6 x 10(5) objects in the 1.5 deg(2) UltraVISTA-DR2 region and similar to 1.5 x 10(5) objects are detected in the “ultra-deep stripes” (0.62 deg(2)) at K-s \textless= 24.7 (3 sigma, 3 `', AB magnitude). Through a comparison with the zCOSMOS-bright spectroscopic redshifts, we measure a photometric redshift precision of sigma(Delta z(1) (+ zs)) = 0.007 and a catastrophic failure fraction of eta = 0.5%. At 3 \textless z \textless 6, using the unique database of spectroscopic redshifts in COSMOS, we find sigma(Delta z(1) (+ zs)) = 0.021 and eta = 13.2%. The deepest regions reach a 90% completeness limit of 10(10)M(circle dot) to z = 4. Detailed comparisons of the color distributions, number counts, and clustering show excellent agreement with the literature in the same mass ranges. COSMOS2015 represents a unique, publicly available, valuable resource with which to investigate the evolution of galaxies within their environment back to the earliest stages of the history of the universe. The COSMOS2015 catalog is distributed via anonymous ftp and through the usual astronomical archive systems (CDS, ESO Phase 3, IRSA).
1,002 citations
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TL;DR: The rate of complete remission was higher with inotuzumab ozogamicin than with standard therapy, and a higher percentage of patients in the inotzumabozogamic in group had results below the threshold for minimal residual disease.
Abstract: BackgroundThe prognosis for adults with relapsed acute lymphoblastic leukemia is poor. We sought to determine whether inotuzumab ozogamicin, an anti-CD22 antibody conjugated to calicheamicin, results in better outcomes in patients with relapsed or refractory acute lymphoblastic leukemia than does standard therapy. MethodsIn this phase 3 trial, we randomly assigned adults with relapsed or refractory acute lymphoblastic leukemia to receive either inotuzumab ozogamicin (inotuzumab ozogamicin group) or standard intensive chemotherapy (standard-therapy group). The primary end points were complete remission (including complete remission with incomplete hematologic recovery) and overall survival. ResultsOf the 326 patients who underwent randomization, the first 218 (109 in each group) were included in the primary intention-to-treat analysis of complete remission. The rate of complete remission was significantly higher in the inotuzumab ozogamicin group than in the standard-therapy group (80.7% [95% confidence in...
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TL;DR: The study significantly adds to the understanding of mental health symptoms and their role in addictive use of modern technology, and suggests that the concept of Internet use disorder (i.e., "Internet addiction") as a unified construct is not warranted.
Abstract: Over the last decade, research into "addictive technological behaviors" has substantially increased. Research has also demonstrated strong associations between addictive use of technology and comorbid psychiatric disorders. In the present study, 23,533 adults (mean age 35.8 years, ranging from 16 to 88 years) participated in an online cross-sectional survey examining whether demographic variables, symptoms of attention-deficit/hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), anxiety, and depression could explain variance in addictive use (i.e., compulsive and excessive use associated with negative outcomes) of two types of modern online technologies: social media and video games. Correlations between symptoms of addictive technology use and mental disorder symptoms were all positive and significant, including the weak interrelationship between the two addictive technological behaviors. Age appeared to be inversely related to the addictive use of these technologies. Being male was significantly associated with addictive use of video games, whereas being female was significantly associated with addictive use of social media. Being single was positively related to both addictive social networking and video gaming. Hierarchical regression analyses showed that demographic factors explained between 11 and 12% of the variance in addictive technology use. The mental health variables explained between 7 and 15% of the variance. The study significantly adds to our understanding of mental health symptoms and their role in addictive use of modern technology, and suggests that the concept of Internet use disorder (i.e., "Internet addiction") as a unified construct is not warranted.
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TL;DR: In patients with HCV-related cirrhosis, DAA-induced resolution of HCV infection does not seem to reduce occurrence of HCC, and patients previously treated for HCC have still a high risk of tumour recurrence in the short term, despite DAA treatment.
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TL;DR: In this paper, the authors exploit the unprecedented statistics provided by the Baryon Oscillation Spectroscopic Survey (BOSS) Data Release 9 to provide new constraints on the Hubble parameter H(z) using the cosmic chronometers approach.
Abstract: Deriving the expansion history of the Universe is a major goal of modern cosmology. To date, the most accurate measurements have been obtained with Type Ia Supernovae (SNe) and Baryon Acoustic Oscillations (BAO), providing evidence for the existence of a transition epoch at which the expansion rate changes from decelerated to accelerated. However, these results have been obtained within the framework of specific cosmological models that must be implicitly or explicitly assumed in the measurement. It is therefore crucial to obtain measurements of the accelerated expansion of the Universe independently of assumptions on cosmological models. Here we exploit the unprecedented statistics provided by the Baryon Oscillation Spectroscopic Survey (BOSS, [1-3]) Data Release 9 to provide new constraints on the Hubble parameter H(z) using the cosmic chronometers approach. We extract a sample of more than 130000 of the most massive and passively evolving galaxies, obtaining five new cosmology-independent H(z) measurements in the redshift range 0.3 < z < 0.5, with an accuracy of ~11–16% incorporating both statistical and systematic errors. Once combined, these measurements yield a 6% accuracy constraint of H(z = 0.4293) = 91.8 ± 5.3 km/s/Mpc. The new data are crucial to provide the first cosmology-independent determination of the transition redshift at high statistical significance, measuring zt = 0.4 ± 0.1, and to significantly disfavor the null hypothesis of no transition between decelerated and accelerated expansion at 99.9% confidence level. This analysis highlights the wide potential of the cosmic chronometers approach: it permits to derive constraints on the expansion history of the Universe with results competitive with standard probes, and most importantly, being the estimates independent of the cosmological model, it can constrain cosmologies beyond—and including—the ΛCDM model.
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Memorial Sloan Kettering Cancer Center1, Humanitas University2, Harvard University3, University of Bologna4, University of California, Los Angeles5, Mayo Clinic6, University of Texas MD Anderson Cancer Center7, Princess Margaret Cancer Centre8, Emory University9, Churchill Hospital10, Charles University in Prague11, Bristol-Myers Squibb12, Brigham and Women's Hospital13
TL;DR: Nivolumab resulted in frequent responses with an acceptable safety profile in patients with classical Hodgkin's lymphoma who progressed after autologous stem-cell transplantation and brentuximab vedotin, and might be a new treatment option for a patient population with a high unmet need.
Abstract: Summary Background Malignant cells of classical Hodgkin's lymphoma are characterised by genetic alterations at the 9p24.1 locus, leading to overexpression of PD-1 ligands and evasion of immune surveillance. In a phase 1b study, nivolumab, a PD-1-blocking antibody, produced a high response in patients with relapsed and refractory classical Hodgkin's lymphoma, with an acceptable safety profile. We aimed to assess the clinical benefit and safety of nivolumab monotherapy in patients with classical Hodgkin's lymphoma after failure of both autologous stem-cell transplantation and brentuximab vedotin. Methods In this ongoing, single-arm phase 2 study, adult patients (aged ≥18 years) with recurrent classical Hodgkin's lymphoma who had failed to respond to autologous stem-cell transplantation and had either relapsed after or failed to respond to brentuximab vedotin, and with an Eastern Cooperative Oncology Group performance status score of 0 or 1, were enrolled from 34 hospitals and academic centres across Europe and North America. Patients were given nivolumab intravenously over 60 min at 3 mg/kg every 2 weeks until progression, death, unacceptable toxicity, or withdrawal from study. The primary endpoint was objective response following a prespecified minimum follow-up period of 6 months, assessed by an independent radiological review committee (IRRC). All patients who received at least one dose of nivolumab were included in the primary and safety analyses. This trial is registered with ClinicalTrials.gov, number NCT02181738. Findings Among 80 treated patients recruited between Aug 26, 2014, and Feb 20, 2015, the median number of previous therapies was four (IQR 4–7). At a median follow-up of 8·9 months (IQR 7·8–9·9), 53 (66·3%, 95% CI 54·8–76·4) of 80 patients achieved an IRRC-assessed objective response. The most common drug-related adverse events (those that occurred in ≥15% of patients) included fatigue (20 [25%] patients), infusion-related reaction (16 [20%]), and rash (13 [16%]). The most common drug-related grade 3 or 4 adverse events were neutropenia (four [5%] patients) and increased lipase concentrations (four [5%]). The most common serious adverse event (any grade) was pyrexia (three [4%] patients). Three patients died during the study; none of these deaths were judged to be treatment related. Interpretation Nivolumab resulted in frequent responses with an acceptable safety profile in patients with classical Hodgkin's lymphoma who progressed after autologous stem-cell transplantation and brentuximab vedotin. Therefore, nivolumab might be a new treatment option for a patient population with a high unmet need. Ongoing follow-up will help to assess the durability of response. Funding Bristol-Myers Squibb.
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Katholieke Universiteit Leuven1, University of Bologna2, Royal Prince Alfred Hospital3, University of California, Davis4, University of Milan5, Radboud University Nijmegen6, Scripps Health7, Curie Institute8, University of Amsterdam9, Medical University of Vienna10, Newcastle University11, University of Padua12, Ludwig Maximilian University of Munich13, Virginia Commonwealth University14, Utrecht University15, Autonomous University of Barcelona16, Université de Montréal17, University of Birmingham18, University Health Network19, Erasmus University Rotterdam20, University of Gothenburg21, Intercept Pharmaceuticals22
TL;DR: Obeticholic acid administered with ursodiol or as monotherapy for 12 months in patients with primary biliary cholangitis resulted in decreases from baseline in alkaline phosphatase and total bilirubin levels that differed significantly from the changes observed with placebo.
Abstract: Background Primary biliary cholangitis (formerly called primary biliary cirrhosis) can progress to cirrhosis and death despite ursodiol therapy. Alkaline phosphatase and bilirubin levels correlate with the risk of liver transplantation or death. Obeticholic acid, a farnesoid X receptor agonist, has shown potential benefit in patients with this disease. Methods In this 12-month, double-blind, placebo-controlled, phase 3 trial, we randomly assigned 217 patients who had an inadequate response to ursodiol or who found the side effects of ursodiol unacceptable to receive obeticholic acid at a dose of 10 mg (the 10-mg group), obeticholic acid at a dose of 5 mg with adjustment to 10 mg if applicable (the 5-10-mg group), or placebo. The primary end point was an alkaline phosphatase level of less than 1.67 times the upper limit of the normal range, with a reduction of at least 15% from baseline, and a normal total bilirubin level. Results Of 216 patients who underwent randomization and received at least one dose of obeticholic acid or placebo, 93% received ursodiol as background therapy. The primary end point occurred in more patients in the 5-10-mg group (46%) and the 10-mg group (47%) than in the placebo group (10%; P Conclusions Obeticholic acid administered with ursodiol or as monotherapy for 12 months in patients with primary biliary cholangitis resulted in decreases from baseline in alkaline phosphatase and total bilirubin levels that differed significantly from the changes observed with placebo. There were more serious adverse events with obeticholic acid. (Funded by Intercept Pharmaceuticals; POISE ClinicalTrials.gov number, NCT01473524; Current Controlled Trials number, ISRCTN89514817.).
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TL;DR: The analyses, carried out using a novel open source software capable of performing an automatic image analysis of 3D tumor colonies, showed that a number of morphology parameters affect the response of large spheroidids to treatment and indicate the need for a pre-selection of tumor spheroids of homogeneous volume and shape before use in a cytotoxicity test.
Abstract: The potential of a spheroid tumor model composed of cells in different proliferative and metabolic states for the development of new anticancer strategies has been amply demonstrated. However, there is little or no information in the literature on the problems of reproducibility of data originating from experiments using 3D models. Our analyses, carried out using a novel open source software capable of performing an automatic image analysis of 3D tumor colonies, showed that a number of morphology parameters affect the response of large spheroids to treatment. In particular, we found that both spheroid volume and shape may be a source of variability. We also compared some commercially available viability assays specifically designed for 3D models. In conclusion, our data indicate the need for a pre-selection of tumor spheroids of homogeneous volume and shape to reduce data variability to a minimum before use in a cytotoxicity test. In addition, we identified and validated a cytotoxicity test capable of providing meaningful data on the damage induced in large tumor spheroids of up to diameter in 650 μm by different kinds of treatments.
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TL;DR: In this article, the main objectives of the KM3NeT Collaboration are (i) the discovery and subsequent observation of high-energy neutrino sources in the Universe and (ii) the determination of the mass hierarchy of neutrinos.
Abstract: The main objectives of the KM3NeT Collaboration are (i) the discovery and subsequent observation of high-energy neutrino sources in the Universe and (ii) the determination of the mass hierarchy of neutrinos. These objectives are strongly motivated by two recent important discoveries, namely: (1) the high-energy astrophysical neutrino signal reported by IceCube and (2) the sizable contribution of electron neutrinos to the third neutrino mass eigenstate as reported by Daya Bay, Reno and others. To meet these objectives, the KM3NeT Collaboration plans to build a new Research Infrastructure consisting of a network of deep-sea neutrino telescopes in the Mediterranean Sea. A phased and distributed implementation is pursued which maximises the access to regional funds, the availability of human resources and the synergistic opportunities for the Earth and sea sciences community. Three suitable deep-sea sites are selected, namely off-shore Toulon (France), Capo Passero (Sicily, Italy) and Pylos (Peloponnese, Greece). The infrastructure will consist of three so-called building blocks. A building block comprises 115 strings, each string comprises 18 optical modules and each optical module comprises 31 photo-multiplier tubes. Each building block thus constitutes a three-dimensional array of photo sensors that can be used to detect the Cherenkov light produced by relativistic particles emerging from neutrino interactions. Two building blocks will be sparsely configured to fully explore the IceCube signal with similar instrumented volume, different methodology, improved resolution and complementary field of view, including the galactic plane. One building block will be densely configured to precisely measure atmospheric neutrino oscillations.
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TL;DR: The theoretical background of MD and enhanced sampling methods is reviewed, focusing on free-energy perturbation, metadynamics, steered MD, and other methods most consistently used to study drug-target binding.
Abstract: Molecular dynamics (MD) and related methods are close to becoming routine computational tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and entropic effects. This allows a more accurate estimate of the thermodynamics and kinetics associated with drug-target recognition and binding, as better algorithms and hardware architectures increase their use. Here, we review the theoretical background of MD and enhanced sampling methods, focusing on free-energy perturbation, metadynamics, steered MD, and other methods most consistently used to study drug-target binding. We discuss unbiased MD simulations that nowadays allow the observation of unsupervised ligand-target binding, assessing how these approaches help optimizing target affinity and drug residence time toward improved drug efficacy. Further issues discussed include allosteric modulation and the role of water molecules in ligand binding and optimization. We conclude by calling for more prospective studies to attest to these methods' utility in discovering novel drug candidates.
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Vardan Khachatryan1, Albert M. Sirunyan1, Armen Tumasyan1, Wolfgang Adam +2283 more•Institutions (141)
TL;DR: Combined fits to CMS UE proton–proton data at 7TeV and to UEProton–antiproton data from the CDF experiment at lower s, are used to study the UE models and constrain their parameters, providing thereby improved predictions for proton-proton collisions at 13.
Abstract: New sets of parameters ("tunes") for the underlying-event (UE) modeling of the PYTHIA8, PYTHIA6 and HERWIG++ Monte Carlo event generators are constructed using different parton distribution functions. Combined fits to CMS UE data at sqrt(s) = 7 TeV and to UE data from the CDF experiment at lower sqrt(s), are used to study the UE models and constrain their parameters, providing thereby improved predictions for proton-proton collisions at 13 TeV. In addition, it is investigated whether the values of the parameters obtained from fits to UE observables are consistent with the values determined from fitting observables sensitive to double-parton scattering processes. Finally, comparisons of the UE tunes to "minimum bias" (MB) events, multijet, and Drell-Yan (q q-bar to Z / gamma* to lepton-antilepton + jets) observables at 7 and 8 TeV are presented, as well as predictions of MB and UE observables at 13 TeV.
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Nicholas J Kassebaum1, Ryan M Barber1, Zulfiqar A Bhutta2, Zulfiqar A Bhutta3 +613 more•Institutions (272)
TL;DR: In this article, the authors quantified maternal mortality throughout the world by underlying cause and age from 1990 to 2015 for ages 10-54 years by systematically compiling and processing all available data sources from 186 of 195 countries and territories.
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University of Tübingen1, Queen Mary University of London2, University of Bologna3, Tohoku University4, University of California, Los Angeles5, Heidelberg University6, Cornell University7, University of Belgrade8, Technische Universität München9, University of Gothenburg10, University of Nottingham11
TL;DR: The past decade has seen remarkable progress in the understanding of functional bowel disorders such as IBS that will be summarized in this Primer.
Abstract: A 28-year-old woman presents with a 7-month history of recurrent, crampy pain in the left lower abdominal quadrant, bloating with abdominal distention, and frequent, loose stools. She reports having had similar but milder symptoms since childhood. She spends long times in the bathroom because she is worried about uncontrollable discomfort and fecal soiling if she does not completely empty her bowels before leaving the house. She feels anxious and fatigued and is frustrated that her previous physician did not seem to take her distress seriously. Physical examination is unremarkable except for tenderness over the left lower quadrant. How should her case be evaluated and treated?
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TL;DR: These final results from the DASISION trial continue to support dasatinib 100 mg once daily as a safe and effective first-line therapy for the long-term treatment of CML-CP.
Abstract: PurposeWe report the 5-year analysis from the phase III Dasatinib Versus Imatinib Study in Treatment-Naive Chronic Myeloid Leukemia Patients (DASISION) trial, evaluating long-term efficacy and safety outcomes of patients with chronic myeloid leukemia (CML) in chronic phase (CP) treated with dasatinib or imatinib.Patients and MethodsPatients with newly diagnosed CML-CP were randomly assigned to receive dasatinib 100 mg once daily (n = 259) or imatinib 400 mg once daily (n = 260).ResultsAt the time of study closure, 61% and 63% of dasatinib- and imatinib-treated patients remained on initial therapy, respectively. Cumulative rates of major molecular response and molecular responses with a 4.0- or 4.5-log reduction in BCR-ABL1 transcripts from baseline by 5 years remained statistically significantly higher for dasatinib compared with imatinib. Rates for progression-free and overall survival at 5 years remained high and similar across treatment arms. In patients who achieved BCR-ABL1 ≤ 10% at 3 months (dasatin...
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Aix-Marseille University1, University of Oklahoma2, University of Iowa3, Azerbaijan National Academy of Sciences4, Université Paris-Saclay5, University of Amsterdam6, University of California, Santa Cruz7, University of Sussex8, Tel Aviv University9, Technion – Israel Institute of Technology10, University of Oregon11, Stockholm University12, King's College London13, International Centre for Theoretical Physics14, AGH University of Science and Technology15, Brookhaven National Laboratory16, Northern Illinois University17, Ludwig Maximilian University of Munich18, Rutherford Appleton Laboratory19, University of Liverpool20, University of Belgrade21, University of Göttingen22, University of Granada23, Boston University24, Joint Institute for Nuclear Research25, University of Rome Tor Vergata26, Lund University27, University of Bologna28, University of Victoria29, University of Grenoble30, National University of La Plata31, CERN32, National Technical University of Athens33, University of Salento34, University of Chicago35, Columbia University36, University of Birmingham37, University of Naples Federico II38, University of Copenhagen39, University of Washington40, University of Valencia41, Lawrence Berkeley National Laboratory42, Federal University of Rio de Janeiro43, Brandeis University44, University of Michigan45, University of Coimbra46, University of Lisbon47, University of Sheffield48, University of Geneva49, University of Texas at Austin50, Heidelberg University51, University of Milan52, National and Kapodistrian University of Athens53, Dresden University of Technology54, Novosibirsk State University55, IFAE56
TL;DR: In this article, a combined ATLAS and CMS measurements of the Higgs boson production and decay rates, as well as constraints on its couplings to vector bosons and fermions, are presented.
Abstract: Combined ATLAS and CMS measurements of the Higgs boson production and decay rates, as well as constraints on its couplings to vector bosons and fermions, are presented. The combination is based on the analysis of five production processes, namely gluon fusion, vector boson fusion, and associated production with a $W$ or a $Z$ boson or a pair of top quarks, and of the six decay modes $H \to ZZ, WW$, $\gamma\gamma, \tau\tau, bb$, and $\mu\mu$. All results are reported assuming a value of 125.09 GeV for the Higgs boson mass, the result of the combined measurement by the ATLAS and CMS experiments. The analysis uses the CERN LHC proton--proton collision data recorded by the ATLAS and CMS experiments in 2011 and 2012, corresponding to integrated luminosities per experiment of approximately 5 fb$^{-1}$ at $\sqrt{s}=7$ TeV and 20 fb$^{-1}$ at $\sqrt{s} = 8$ TeV. The Higgs boson production and decay rates measured by the two experiments are combined within the context of three generic parameterisations: two based on cross sections and branching fractions, and one on ratios of coupling modifiers. Several interpretations of the measurements with more model-dependent parameterisations are also given. The combined signal yield relative to the Standard Model prediction is measured to be 1.09 $\pm$ 0.11. The combined measurements lead to observed significances for the vector boson fusion production process and for the $H \to \tau\tau$ decay of $5.4$ and $5.5$ standard deviations, respectively. The data are consistent with the Standard Model predictions for all parameterisations considered.
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Haidong Wang1, Zulfiqar A Bhutta2, Zulfiqar A Bhutta3, Matthew M Coates1 +610 more•Institutions (263)
TL;DR: The Global Burden of Disease 2015 Study provides an analytical framework to comprehensively assess trends for under-5 mortality, age-specific and cause-specific mortality among children under 5 years, and stillbirths by geography over time and decomposed the changes in under- 5 mortality to changes in SDI at the global level.
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Columbia University1, University of Amsterdam2, University of Bologna3, University of Mainz4, University of Coimbra5, Weizmann Institute of Science6, New York University Abu Dhabi7, University of Zurich8, Stockholm University9, Rensselaer Polytechnic Institute10, Max Planck Society11, University of Münster12, University of Bern13, Purdue University14, École des mines de Nantes15, University of California, Los Angeles16, Rice University17
TL;DR: In this article, the expected sensitivity of the Xenon1T experiment to the spin-independent WIMP-nucleon interaction cross section was investigated based on Monte Carlo predictions of the electronic and nuclear recoil backgrounds.
Abstract: The XENON1T experiment is currently in the commissioning phase at the Laboratori Nazionali del Gran Sasso, Italy. In this article we study the experiment's expected sensitivity to the spin-independent WIMP-nucleon interaction cross section, based on Monte Carlo predictions of the electronic and nuclear recoil backgrounds. The total electronic recoil background in 1 tonne fiducial volume and (1, 12) keV electronic recoil equivalent energy region, before applying any selection to discriminate between electronic and nuclear recoils, is (1.80 ± 0.15) · 10(−)(4) (kg·day·keV)(−)(1), mainly due to the decay of (222)Rn daughters inside the xenon target. The nuclear recoil background in the corresponding nuclear recoil equivalent energy region (4, 50) keV, is composed of (0.6 ± 0.1) (t·y)(−)(1) from radiogenic neutrons, (1.8 ± 0.3) · 10(−)(2) (t·y)(−)(1) from coherent scattering of neutrinos, and less than 0.01 (t·y)(−)(1) from muon-induced neutrons. The sensitivity of XENON1T is calculated with the Profile Likelihood Ratio method, after converting the deposited energy of electronic and nuclear recoils into the scintillation and ionization signals seen in the detector. We take into account the systematic uncertainties on the photon and electron emission model, and on the estimation of the backgrounds, treated as nuisance parameters. The main contribution comes from the relative scintillation efficiency Script L(eff), which affects both the signal from WIMPs and the nuclear recoil backgrounds. After a 2 y measurement in 1 t fiducial volume, the sensitivity reaches a minimum cross section of 1.6 · 10(−)(47) cm(2) at m(χ) = 50 GeV/c(2).
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TL;DR: This work provides for the first time the phylogenetic microbiota analysis of semi-supercentenarians, i.e., 105-109 years old, in comparison to adults, elderly, and centenarian, thus reconstructing the longest available human microbiota trajectory along aging.
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TL;DR: Pembrolizumab treatment induced favorable responses in a heavily pretreated patient cohort, justifying further studies.
Abstract: Purpose Classical Hodgkin lymphoma (HL) frequently exhibits genetic alterations leading to overexpression of the programmed death-1 (PD-1) ligands, suggesting a possible vulnerability to PD-1 blockade. The phase Ib study KEYNOTE-013 (NCT01953692) tested the safety and efficacy of the anti-PD-1 antibody pembrolizumab in patients with hematologic malignancies. Based on its genetics, HL was included as an independent cohort. Methods We enrolled patients with relapsed or refractory HL whose disease progressed on or after treatment with brentuximab vedotin. Patients received pembrolizumab, 10 mg/kg every 2 weeks, until disease progression occurred. Response to treatment was assessed at week 12 and every 8 weeks thereafter. Principal end points were safety and complete remission (CR) rate. Results Thirty-one patients were enrolled; 55% had more than four lines of prior therapy, and 71% had relapsed after autologous stem cell transplantation. Five patients (16%) experienced grade 3 drug-related adverse events (AEs); there were no grade 4 AEs or deaths related to treatment. The CR rate was 16% (90% CI, 7% to 31%). In addition, 48% of patients achieved a partial remission, for an overall response rate of 65% (90% CI, 48% to 79%). Most of the responses (70%) lasted longer than 24 weeks (range, 0.14+ to 74+ weeks), with a median follow-up of 17 months. The progression-free survival rate was 69% at 24 weeks and 46% at 52 weeks. Biomarker analyses demonstrated a high prevalence of PD-L1 and PD-L2 expression, treatment-induced expansion of T cells and natural killer cells, and activation of interferon-γ, T-cell receptor, and expanded immune-related signaling pathways. Conclusions Pembrolizumab was associated with a favorable safety profile. Pembrolizumab treatment induced favorable responses in a heavily pretreated patient cohort, justifying further studies.
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University of Amsterdam1, University of Bologna2, University of Mainz3, University of Coimbra4, University of Bern5, Columbia University6, Weizmann Institute of Science7, New York University Abu Dhabi8, University of Zurich9, Rensselaer Polytechnic Institute10, Max Planck Society11, Stockholm University12, University of Nantes13, Karlsruhe Institute of Technology14, University of Münster15, University of Chicago16, Arizona State University17, Purdue University18, Rice University19, University of California, San Diego20, University of Freiburg21, Dresden University of Technology22, Imperial College London23, University of California, Los Angeles24
TL;DR: DARk matter WImp search with liquid xenoN (DARWIN) as mentioned in this paper is an experiment for the direct detection of dark matter using a multi-ton liquid xenon time projection chamber at its core.
Abstract: DARk matter WImp search with liquid xenoN (DARWIN(2)) will be an experiment for the direct detection of dark matter using a multi-ton liquid xenon time projection chamber at its core. Its primary g ...
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University of Barcelona1, Medical University of Graz2, Leiden University Medical Center3, Paris Diderot University4, University College London5, University of Padua6, University of Bologna7, Ludwig Maximilian University of Munich8, King's College London9, Katholieke Universiteit Leuven10, University of Bonn11, University of Paris-Sud12, Goethe University Frankfurt13, Université libre de Bruxelles14, University of Hamburg15
TL;DR: Patients with AD without ACLF showed very high baseline levels of inflammatory cytokines, HNA2, PRC, and PCC, and the strength of association of ACLF with SI was higher than with SCD, supporting SI as the primary driver of ACLf in cirrhosis.