Showing papers by "University of Southern California published in 2015"
TL;DR: This paper reviews the principles and practice of purposeful sampling in implementation research, summarizes types and categories of purposefully sampling strategies and provides a set of recommendations for use of single strategy or multistage strategy designs, particularly for state implementation research.
Abstract: Purposeful sampling is widely used in qualitative research for the identification and selection of information-rich cases related to the phenomenon of interest. Although there are several different purposeful sampling strategies, criterion sampling appears to be used most commonly in implementation research. However, combining sampling strategies may be more appropriate to the aims of implementation research and more consistent with recent developments in quantitative methods. This paper reviews the principles and practice of purposeful sampling in implementation research, summarizes types and categories of purposeful sampling strategies and provides a set of recommendations for use of single strategy or multistage strategy designs, particularly for state implementation research.
5,601 citations
Alexander A. Aarts, Joanna E. Anderson1, Christopher J. Anderson2, Peter Raymond Attridge3 +287 more•Institutions (116)
TL;DR: A large-scale assessment suggests that experimental reproducibility in psychology leaves a lot to be desired, and correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
Abstract: Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
5,532 citations
Massachusetts Institute of Technology1, Broad Institute2, University of California, Los Angeles3, University of British Columbia4, Baylor College of Medicine5, Howard Hughes Medical Institute6, University of Washington7, Ludwig Institute for Cancer Research8, University of California, San Francisco9, University of Connecticut10, University of Zagreb11, University of Texas at Austin12, Washington University in St. Louis13, University of Queensland14, Harvard University15, Cold Spring Harbor Laboratory16, University of Southern California17, University of California, Santa Cruz18, Simon Fraser University19, Morgridge Institute for Research20, University of Texas at Dallas21, National Institutes of Health22
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
Abstract: The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.
5,037 citations
University Hospital Bonn1, University of California, Riverside2, Harvard University3, Case Western Reserve University4, University of Illinois at Chicago5, European Institute6, VA Palo Alto Healthcare System7, Stanford University8, Spanish National Research Council9, Cleveland Clinic Lerner Research Institute10, Hong Kong University of Science and Technology11, University of California, Los Angeles12, University of Southern Denmark13, University of Cambridge14, University of the Basque Country15, Ikerbasque16, University of Manchester17, RIKEN Brain Science Institute18, University of Eastern Finland19, University of Massachusetts Medical School20, University of Bonn21, Center of Advanced European Studies and Research22, University of Southern California23, University of South Florida24, Duke University25, Southampton General Hospital26, University of Southampton27, Moorgreen Hospital28, Louisiana State University29, Imperial College London30, Centre national de la recherche scientifique31, Karolinska Institutet32, Max Planck Society33, University of Tübingen34, University of Groningen35, University of Colorado Denver36, Douglas Mental Health University Institute37
TL;DR: Genome-wide analysis suggests that several genes that increase the risk for sporadic Alzheimer's disease encode factors that regulate glial clearance of misfolded proteins and the inflammatory reaction.
Abstract: Increasing evidence suggests that Alzheimer's disease pathogenesis is not restricted to the neuronal compartment, but includes strong interactions with immunological mechanisms in the brain. Misfolded and aggregated proteins bind to pattern recognition receptors on microglia and astroglia, and trigger an innate immune response characterised by release of inflammatory mediators, which contribute to disease progression and severity. Genome-wide analysis suggests that several genes that increase the risk for sporadic Alzheimer's disease encode factors that regulate glial clearance of misfolded proteins and the inflammatory reaction. External factors, including systemic inflammation and obesity, are likely to interfere with immunological processes of the brain and further promote disease progression. Modulation of risk factors and targeting of these immune mechanisms could lead to future therapeutic or preventive strategies for Alzheimer's disease.
3,947 citations
Michael S. Lawrence1, Carrie Sougnez1, Lee Lichtenstein1, Kristian Cibulskis1 +306 more•Institutions (26)
TL;DR: It is shown that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1.
Abstract: The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1 Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22 A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53 Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours Therapeutic candidate alterations were identified in most HNSCCs
2,997 citations
TL;DR: This briefer article should be read as an addendum to the previous full account on the management of hyperglycemia, which described the need to individualize both treatment targets and treatment strategies with an emphasis on patient-centered care and shared decision making.
Abstract: In 2012, the American Diabetes Association (ADA) and the European Association for the Study of Diabetes (EASD) published a position statement on the management of hyperglycemia in patients with type 2 diabetes (1,2). This was needed because of an increasing array of antihyperglycemic drugs and growing uncertainty regarding their proper selection and sequence. Because of a paucity of comparative effectiveness research on long-term treatment outcomes with many of these medications, the 2012 publication was less prescriptive than prior consensus reports. We previously described the need to individualize both treatment targets and treatment strategies, with an emphasis on patient-centered care and shared decision making, and this continues to be our position, although there are now more head-to-head trials that show slight variance between agents with regard to glucose-lowering effects. Nevertheless, these differences are often small and would be unlikely to reflect any definite differential effect in an individual patient.
The ADA and EASD have requested an update to the position statement incorporating new data from recent clinical trials. Between June and September of 2014, the Writing Group reconvened, including one face-to-face meeting, to discuss the changes. An entirely new statement was felt to be unnecessary. Instead, the group focused on those areas where revisions were suggested by a changing evidence base. This briefer article should therefore be read as an addendum to the previous full account (1,2).
Glucose control remains a major focus in the management of patients with type 2 diabetes. However, this should always be in the context of a comprehensive cardiovascular risk factor reduction program, to include smoking cessation and the adoption of other healthy lifestyle habits, blood pressure control, lipid management with priority to statin medications, and, in some circumstances, antiplatelet therapy. Studies have conclusively determined that reducing hyperglycemia decreases the onset and progression of …
2,553 citations
TL;DR: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided in this paper, covering approximately the last seven years, including developments in density functional theory and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces.
Abstract: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr_2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.
2,396 citations
TL;DR: CD19-CAR T cell therapy is feasible, safe, and mediates potent anti-leukaemic activity in children and young adults with chemotherapy-resistant B-precursor acute lymphoblastic leukaemia and non-Hodgkin lymphoma.
2,394 citations
TL;DR: Future directions such as the "print-it-all" paradigm, that have the potential to re-imagine current research and spawn completely new avenues for exploration are pointed out.
Abstract: Additive manufacturing (AM) is poised to bring about a revolution in the way products are designed, manufactured, and distributed to end users. This technology has gained significant academic as well as industry interest due to its ability to create complex geometries with customizable material properties. AM has also inspired the development of the maker movement by democratizing design and manufacturing. Due to the rapid proliferation of a wide variety of technologies associated with AM, there is a lack of a comprehensive set of design principles, manufacturing guidelines, and standardization of best practices. These challenges are compounded by the fact that advancements in multiple technologies (for example materials processing, topology optimization) generate a "positive feedback loop" effect in advancing AM. In order to advance research interest and investment in AM technologies, some fundamental questions and trends about the dependencies existing in these avenues need highlighting. The goal of our review paper is to organize this body of knowledge surrounding AM, and present current barriers, findings, and future trends significantly to the researchers. We also discuss fundamental attributes of AM processes, evolution of the AM industry, and the affordances enabled by the emergence of AM in a variety of areas such as geometry processing, material design, and education. We conclude our paper by pointing out future directions such as the "print-it-all" paradigm, that have the potential to re-imagine current research and spawn completely new avenues for exploration. The fundamental attributes and challenges/barriers of Additive Manufacturing (AM).The evolution of research on AM with a focus on engineering capabilities.The affordances enabled by AM such as geometry, material and tools design.The developments in industry, intellectual property, and education-related aspects.The important future trends of AM technologies.
1,792 citations
University of Texas Health Science Center at Houston1, Medical College of Wisconsin2, Oregon Health & Science University3, University of Washington4, University of California, San Francisco5, University of Tennessee Health Science Center6, University of Southern California7, University of Alabama at Birmingham8, University of Cincinnati9, University of Arizona10, University of Toronto11, University of Maryland, Baltimore12, Sunnybrook Health Sciences Centre13, American College of Surgeons14, National Institutes of Health15
TL;DR: In this article, the effectiveness and safety of transfusing patients with severe trauma and major bleeding using plasma, platelets, and red blood cells in a 1:1:1 ratio compared with a 1 :1:2 ratio was evaluated.
Abstract: Importance Severely injured patients experiencing hemorrhagic shock often require massive transfusion. Earlier transfusion with higher blood product ratios (plasma, platelets, and red blood cells), defined as damage control resuscitation, has been associated with improved outcomes; however, there have been no large multicenter clinical trials. Objective To determine the effectiveness and safety of transfusing patients with severe trauma and major bleeding using plasma, platelets, and red blood cells in a 1:1:1 ratio compared with a 1:1:2 ratio. Design, Setting, and Participants Pragmatic, phase 3, multisite, randomized clinical trial of 680 severely injured patients who arrived at 1 of 12 level I trauma centers in North America directly from the scene and were predicted to require massive transfusion between August 2012 and December 2013. Interventions Blood product ratios of 1:1:1 (338 patients) vs 1:1:2 (342 patients) during active resuscitation in addition to all local standard-of-care interventions (uncontrolled). Main Outcomes and Measures Primary outcomes were 24-hour and 30-day all-cause mortality. Prespecified ancillary outcomes included time to hemostasis, blood product volumes transfused, complications, incidence of surgical procedures, and functional status. Results No significant differences were detected in mortality at 24 hours (12.7% in 1:1:1 group vs 17.0% in 1:1:2 group; difference, −4.2% [95% CI, −9.6% to 1.1%]; P = .12) or at 30 days (22.4% vs 26.1%, respectively; difference, −3.7% [95% CI, −10.2% to 2.7%]; P = .26). Exsanguination, which was the predominant cause of death within the first 24 hours, was significantly decreased in the 1:1:1 group (9.2% vs 14.6% in 1:1:2 group; difference, −5.4% [95% CI, −10.4% to −0.5%]; P = .03). More patients in the 1:1:1 group achieved hemostasis than in the 1:1:2 group (86% vs 78%, respectively; P = .006). Despite the 1:1:1 group receiving more plasma (median of 7 U vs 5 U, P P Conclusions and Relevance Among patients with severe trauma and major bleeding, early administration of plasma, platelets, and red blood cells in a 1:1:1 ratio compared with a 1:1:2 ratio did not result in significant differences in mortality at 24 hours or at 30 days. However, more patients in the 1:1:1 group achieved hemostasis and fewer experienced death due to exsanguination by 24 hours. Even though there was an increased use of plasma and platelets transfused in the 1:1:1 group, no other safety differences were identified between the 2 groups. Trial Registration clinicaltrials.gov Identifier:NCT01545232
1,643 citations
TL;DR: The results suggest that sleep-disordered breathing is highly prevalent, with important public health outcomes, and that the definition of the disorder should be revised.
Memorial Sloan Kettering Cancer Center1, University of Lausanne2, University of North Carolina at Chapel Hill3, Rutgers University4, Harvard University5, University of Southern California6, Broad Institute7, Washington University in St. Louis8, Buck Institute for Research on Aging9, University of British Columbia10, Van Andel Institute11, The Chinese University of Hong Kong12, University of Utah13, Stanford University14, University of California, San Francisco15, United States Department of Veterans Affairs16, University of Pittsburgh17, University of Texas MD Anderson Cancer Center18, BC Cancer Agency19
TL;DR: This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options, suggesting differential modulation of ER activity in I LC and IDC.
TL;DR: In this article, the authors review recent progress in OAM beam generation/detection, multiplexing/demultiplexing, and its potential applications in different scenarios including free-space optical communications, fiber-optic communications, and RF communications.
Abstract: Orbital angular momentum (OAM), which describes the “phase twist” (helical phase pattern) of light beams, has recently gained interest due to its potential applications in many diverse areas. Particularly promising is the use of OAM for optical communications since: (i) coaxially propagating OAM beams with different azimuthal OAM states are mutually orthogonal, (ii) inter-beam crosstalk can be minimized, and (iii) the beams can be efficiently multiplexed and demultiplexed. As a result, multiple OAM states could be used as different carriers for multiplexing and transmitting multiple data streams, thereby potentially increasing the system capacity. In this paper, we review recent progress in OAM beam generation/detection, multiplexing/demultiplexing, and its potential applications in different scenarios including free-space optical communications, fiber-optic communications, and RF communications. Technical challenges and perspectives of OAM beams are also discussed.
TL;DR: The data suggest that BBB breakdown is an early event in the aging human brain that begins in the hippocampus and may contribute to cognitive impairment.
TL;DR: The wellbeing of elderly people is an important objective for both economic and health policy and present new analyses about the pattern of wellbeing across ages and the association between wellbeing and survival at older ages.
TL;DR: Strong evidence for dust and no statistically significant evidence for tensor modes is found and various model variations and extensions are probe, including adding a synchrotron component in combination with lower frequency data, and find that these make little difference to the r constraint.
Abstract: We report the results of a joint analysis of data from BICEP2/Keck Array and Planck. BICEP2 and Keck Array have observed the same approximately 400 deg2 patch of sky centered on RA 0h, Dec. −57.5deg. The combined maps reach a depth of 57 nK deg in Stokes Q and U in a band centered at 150 GHz. Planck has observed the full sky in polarization at seven frequencies from 30 to 353 GHz, but much less deeply in any given region (1.2 μK deg in Q and U at 143 GHz). We detect 150×353 cross-correlation in B-modes at high significance. We fit the single- and cross-frequency power spectra at frequencies above 150 GHz to a lensed-ΛCDM model that includes dust and a possible contribution from inflationary gravitational waves (as parameterized by the tensor-to-scalar ratio r). We probe various model variations and extensions, including adding a synchrotron component in combination with lower frequency data, and find that these make little difference to the r constraint. Finally we present an alternative analysis which is similar to a map-based cleaning of the dust contribution, and show that this gives similar constraints. The final result is expressed as a likelihood curve for r, and yields an upper limit r0.05<0.12 at 95% confidence. Marginalizing over dust and r, lensing B-modes are detected at 7.0σ significance.
University of Washington1, Fred Hutchinson Cancer Research Center2, American Society of Clinical Oncology3, Cleveland Clinic4, University of British Columbia5, Pennsylvania State University6, Duke University7, Emory University8, University of Rochester9, University of North Carolina at Chapel Hill10, McMaster University11, University of Southern California12, University of California, San Francisco13, University of Michigan14
TL;DR: Current recommendations about the prophylaxis and treatment of venous thromboembolism (VTE) in patients with cancer and oncology professionals should educate patients about the signs and symptoms of VTE.
Abstract: Purpose To provide current recommendations about the prophylaxis and treatment of venous thromboembolism (VTE) in patients with cancer.
TL;DR: The new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined, and the challenges faced by the resource given the explosive growth in sequence data in recent years are discussed.
Abstract: The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012.
TL;DR: The experimental observation of highly anisotropic, bright excitons with large binding energy in monolayer black phosphorus opens avenues for the future explorations of many-electron physics in this unusual two-dimensional material, but also suggests its promising future in optoelectronic devices.
Abstract: Polarization-resolved photoluminescence measurements reveal the anisotropic character of excitons in monolayer black phosphorus, which are found to have a large binding energy.
TL;DR: The multifaceted biointerfacing enabled by the platelet membrane cloaking method provides a new approach in developing functional nanoparticles for disease-targeted delivery.
Abstract: Development of functional nanoparticles can be encumbered by unanticipated material properties and biological events, which can affect nanoparticle effectiveness in complex, physiologically relevant systems. Despite the advances in bottom-up nanoengineering and surface chemistry, reductionist functionalization approaches remain inadequate in replicating the complex interfaces present in nature and cannot avoid exposure of foreign materials. Here we report on the preparation of polymeric nanoparticles enclosed in the plasma membrane of human platelets, which are a unique population of cellular fragments that adhere to a variety of disease-relevant substrates. The resulting nanoparticles possess a right-side-out unilamellar membrane coating functionalized with immunomodulatory and adhesion antigens associated with platelets. Compared to uncoated particles, the platelet membrane-cloaked nanoparticles have reduced cellular uptake by macrophage-like cells and lack particle-induced complement activation in autologous human plasma. The cloaked nanoparticles also display platelet-mimicking properties such as selective adhesion to damaged human and rodent vasculatures as well as enhanced binding to platelet-adhering pathogens. In an experimental rat model of coronary restenosis and a mouse model of systemic bacterial infection, docetaxel and vancomycin, respectively, show enhanced therapeutic efficacy when delivered by the platelet-mimetic nanoparticles. The multifaceted biointerfacing enabled by the platelet membrane cloaking method provides a new approach in developing functional nanoparticles for disease-targeted delivery.
TL;DR: In this article, the authors discuss the potential of black phosphorus (black P) as a 2D layered material for nanoelectronics and nanophotonics, and give their perspectives on future 2D and thin-film black P research directions.
Abstract: One hundred years after its first successful synthesis in the bulk form in 1914, black phosphorus (black P) was recently rediscovered from the perspective of a 2D layered material, attracting tremendous interest from condensed matter physicists, chemists, semiconductor device engineers, and material scientists. Similar to graphite and transition metal dichalcogenides (TMDs), black P has a layered structure but with a unique puckered single-layer geometry. Because the direct electronic band gap of thin film black P can be varied from 0.3 eV to around 2 eV, depending on its film thickness, and because of its high carrier mobility and anisotropic in-plane properties, black P is promising for novel applications in nanoelectronics and nanophotonics different from graphene and TMDs. Black P as a nanomaterial has already attracted much attention from researchers within the past year. Here, we offer our opinions on this emerging material with the goal of motivating and inspiring fellow researchers in the 2D materials community and the broad readership of PNAS to discuss and contribute to this exciting new field. We also give our perspectives on future 2D and thin film black P research directions, aiming to assist researchers coming from a variety of disciplines who are desirous of working in this exciting research field.
TL;DR: Associations between inherited cellular transport gene variants and risk of EOC histologic subtypes are revealed on a large cohort of women.
Abstract: BACKGROUND: Defective cellular transport processes can lead to aberrant accumulation of trace elements, iron, small molecules and hormones in the cell, which in turn may promote the formation of reactive oxygen species, promoting DNA damage and aberrant expression of key regulatory cancer genes. As DNA damage and uncontrolled proliferation are hallmarks of cancer, including epithelial ovarian cancer (EOC), we hypothesized that inherited variation in the cellular transport genes contributes to EOC risk. METHODS: In total, DNA samples were obtained from 14,525 case subjects with invasive EOC and from 23,447 controls from 43 sites in the Ovarian Cancer Association Consortium (OCAC). Two hundred seventy nine SNPs, representing 131 genes, were genotyped using an Illumina Infinium iSelect BeadChip as part of the Collaborative Oncological Gene-environment Study (COGS). SNP analyses were conducted using unconditional logistic regression under a log-additive model, and the FDR q<0.2 was applied to adjust for multiple comparisons. RESULTS: The most significant evidence of an association for all invasive cancers combined and for the serous subtype was observed for SNP rs17216603 in the iron transporter gene HEPH (invasive: OR = 0.85, P = 0.00026; serous: OR = 0.81, P = 0.00020); this SNP was also associated with the borderline/low malignant potential (LMP) tumors (P = 0.021). Other genes significantly associated with EOC histological subtypes (p<0.05) included the UGT1A (endometrioid), SLC25A45 (mucinous), SLC39A11 (low malignant potential), and SERPINA7 (clear cell carcinoma). In addition, 1785 SNPs in six genes (HEPH, MGST1, SERPINA, SLC25A45, SLC39A11 and UGT1A) were imputed from the 1000 Genomes Project and examined for association with INV EOC in white-European subjects. The most significant imputed SNP was rs117729793 in SLC39A11 (per allele, OR = 2.55, 95% CI = 1.5-4.35, p = 5.66x10-4). CONCLUSION: These results, generated on a large cohort of women, revealed associations between inherited cellular transport gene variants and risk of EOC histologic subtypes.
TL;DR: In this article, a nonconvex formulation of the phase retrieval problem was proposed and a concrete solution algorithm was presented. But the main contribution is that this algorithm is shown to rigorously allow the exact retrieval of phase information from a nearly minimal number of random measurements.
Abstract: We study the problem of recovering the phase from magnitude measurements; specifically, we wish to reconstruct a complex-valued signal $ \boldsymbol {x}\in \mathbb {C}^{n}$ about which we have phaseless samples of the form $y_{r} = \left |{\langle \boldsymbol {a}_{r}, \boldsymbol {x} \rangle }\right |^{2}$ , $r = 1,\ldots , m$ (knowledge of the phase of these samples would yield a linear system). This paper develops a nonconvex formulation of the phase retrieval problem as well as a concrete solution algorithm. In a nutshell, this algorithm starts with a careful initialization obtained by means of a spectral method, and then refines this initial estimate by iteratively applying novel update rules, which have low computational complexity, much like in a gradient descent scheme. The main contribution is that this algorithm is shown to rigorously allow the exact retrieval of phase information from a nearly minimal number of random measurements. Indeed, the sequence of successive iterates provably converges to the solution at a geometric rate so that the proposed scheme is efficient both in terms of computational and data resources. In theory, a variation on this scheme leads to a near-linear time algorithm for a physically realizable model based on coded diffraction patterns. We illustrate the effectiveness of our methods with various experiments on image data. Underlying our analysis are insights for the analysis of nonconvex optimization schemes that may have implications for computational problems beyond phase retrieval.
Bjarni J. Vilhjálmsson1, Jian Yang2, Hilary K. Finucane3, Alexander Gusev4 +391 more•Institutions (14)
TL;DR: LDpred is introduced, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel, and outperforms the approach of pruning followed by thresholding, particularly at large sample sizes.
Abstract: Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred outperforms the approach of pruning followed by thresholding, particularly at large sample sizes. Accordingly, predicted R(2) increased from 20.1% to 25.3% in a large schizophrenia dataset and from 9.8% to 12.0% in a large multiple sclerosis dataset. A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase.
TL;DR: The clearance systems of the brain as they relate to proteins implicated in AD pathology are described, with the main focus on Aβ.
Abstract: Accumulation of toxic protein aggregates-amyloid-β (Aβ) plaques and hyperphosphorylated tau tangles-is the pathological hallmark of Alzheimer disease (AD). Aβ accumulation has been hypothesized to result from an imbalance between Aβ production and clearance; indeed, Aβ clearance seems to be impaired in both early and late forms of AD. To develop efficient strategies to slow down or halt AD, it is critical to understand how Aβ is cleared from the brain. Extracellular Aβ deposits can be removed from the brain by various clearance systems, most importantly, transport across the blood-brain barrier. Findings from the past few years suggest that astroglial-mediated interstitial fluid (ISF) bulk flow, known as the glymphatic system, might contribute to a larger portion of extracellular Aβ (eAβ) clearance than previously thought. The meningeal lymphatic vessels, discovered in 2015, might provide another clearance route. Because these clearance systems act together to drive eAβ from the brain, any alteration to their function could contribute to AD. An understanding of Aβ clearance might provide strategies to reduce excess Aβ deposits and delay, or even prevent, disease onset. In this Review, we describe the clearance systems of the brain as they relate to proteins implicated in AD pathology, with the main focus on Aβ.
TL;DR: The mechanisms regulating the formation and maintenance of the BBB and functions of BBB-associated cell types are examined and the growing evidence associating BBB breakdown with the pathogenesis of inherited monogenic neurological disorders and complex multifactorial diseases, including Alzheimer's disease is discussed.
TL;DR: It is demonstrated that low-dose 5-AZA-CdR targets colorectal cancer-initiating cells (CICs) by inducing viral mimicry, and the MDA5/MAVS/IRF7 pathway is highlighted as a potentially druggable target against CICs.
TL;DR: An update on the latest advances in the clinical development of treatment strategies targeting cancer stem cells with rational combinations of agents to inhibit possible compensatory escape mechanisms is provided.
Abstract: During the past decade, cancer stem cells (CSCs) have been increasingly identified in many malignancies Although the origin and plasticity of these cells remain controversial, tumour heterogeneity and the presence of small populations of cells with stem-like characteristics is established in most malignancies CSCs display many features of embryonic or tissue stem cells, and typically demonstrate persistent activation of one or more highly conserved signal transduction pathways involved in development and tissue homeostasis, including the Notch, Hedgehog (HH), and Wnt pathways CSCs generally have slow growth rates and are resistant to chemotherapy and/or radiotherapy Thus, new treatment strategies targeting these pathways to control stem-cell replication, survival and differentiation are under development Herein, we provide an update on the latest advances in the clinical development of such approaches, and discuss strategies for overcoming CSC-associated primary or acquired resistance to cancer treatment Given the crosstalk between the different embryonic developmental signalling pathways, as well as other pathways, designing clinical trials that target CSCs with rational combinations of agents to inhibit possible compensatory escape mechanisms could be of particular importance We also share our views on the future directions for targeting CSCs to advance the clinical development of these classes of agents
TL;DR: In patients with refractory colorectal cancer, TAS-102, as compared with placebo, was associated with a significant improvement in overall survival, and this phase 3 trial was the first to report this result.
Abstract: BackgroundEarly clinical trials conducted primarily in Japan have shown that TAS-102, an oral agent that combines trifluridine and tipiracil hydrochloride, was effective in the treatment of refractory colorectal cancer. We conducted a phase 3 trial to further assess the efficacy and safety of TAS-102 in a global population of such patients. MethodsIn this double-blind study, we randomly assigned 800 patients, in a 2:1 ratio, to receive TAS-102 or placebo. The primary end point was overall survival. ResultsThe median overall survival improved from 5.3 months with placebo to 7.1 months with TAS-102, and the hazard ratio for death in the TAS-102 group versus the placebo group was 0.68 (95% confidence interval [CI], 0.58 to 0.81; P<0.001). The most frequently observed clinically significant adverse events associated with TAS-102 were neutropenia, which occurred in 38% of those treated, and leukopenia, which occurred in 21%; 4% of the patients who received TAS-102 had febrile neutropenia, and one death related...
TL;DR: This paper describes a recently created image database, TID2013, intended for evaluation of full-reference visual quality assessment metrics, and methodology for determining drawbacks of existing visual quality metrics is described.
Abstract: This paper describes a recently created image database, TID2013, intended for evaluation of full-reference visual quality assessment metrics. With respect to TID2008, the new database contains a larger number (3000) of test images obtained from 25 reference images, 24 types of distortions for each reference image, and 5 levels for each type of distortion. Motivations for introducing 7 new types of distortions and one additional level of distortions are given; examples of distorted images are presented. Mean opinion scores (MOS) for the new database have been collected by performing 985 subjective experiments with volunteers (observers) from five countries (Finland, France, Italy, Ukraine, and USA). The availability of MOS allows the use of the designed database as a fundamental tool for assessing the effectiveness of visual quality. Furthermore, existing visual quality metrics have been tested with the proposed database and the collected results have been analyzed using rank order correlation coefficients between MOS and considered metrics. These correlation indices have been obtained both considering the full set of distorted images and specific image subsets, for highlighting advantages and drawbacks of existing, state of the art, quality metrics. Approaches to thorough performance analysis for a given metric are presented to detect practical situations or distortion types for which this metric is not adequate enough to human perception. The created image database and the collected MOS values are freely available for downloading and utilization for scientific purposes. We have created a new large database.This database contains larger number of distorted images and distortion types.MOS values for all images are obtained and provided.Analysis of correlation between MOS and a wide set of existing metrics is carried out.Methodology for determining drawbacks of existing visual quality metrics is described.