Stony Brook University

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. Results for the final phase of the 1000 Genomes Project are presented including whole-genome sequencing, targeted exome sequencing, and genotyping on high-density SNP arrays for 2,504 individuals across 26 populations, providing a global reference data set to support biomedical genetics. The 1000 Genomes Project has sought to comprehensively catalogue human genetic variation across populations, providing a valuable public genomic resource. The data obtained so far have found applications ranging from association studies and fine mapping studies to the filtering of likely neutral variants in rare-disease cohorts. The authors now report on the final phase of the project, phase 3, which covers previously uncharacterized areas of human genetic diversity in terms of the populations sampled and categories of characterized variation. The sample now includes more than 2,500 individuals from 26 global populations, with low coverage whole-genome and deep exome sequencing, as well as dense microarray genotyping. They find that while most common variants are shared across populations, rarer variants are often restricted to closely related populations. The authors also demonstrate the use of the phase 3 dataset as a reference panel for imputation to improve the resolution in genetic association studies.

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.

A search for the Standard Model Higgs boson in proton-proton collisions with the ATLAS detector at the LHC is presented. The datasets used correspond to integrated luminosities of approximately 4.8 fb^-1 collected at sqrt(s) = 7 TeV in 2011 and 5.8 fb^-1 at sqrt(s) = 8 TeV in 2012. Individual searches in the channels H->ZZ^(*)->llll, H->gamma gamma and H->WW->e nu mu nu in the 8 TeV data are combined with previously published results of searches for H->ZZ^(*), WW^(*), bbbar and tau^+tau^- in the 7 TeV data and results from improved analyses of the H->ZZ^(*)->llll and H->gamma gamma channels in the 7 TeV data. Clear evidence for the production of a neutral boson with a measured mass of 126.0 +/- 0.4(stat) +/- 0.4(sys) GeV is presented. This observation, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7x10^-9, is compatible with the production and decay of the Standard Model Higgs boson.

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

Prediction of species’ distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence‐only data to fit models, and independent presence‐absence data to evaluate the predictions. Along with well‐established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species’ distributions. These include machine‐learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species’ occurrence data. Presence‐only data were effective for modelling species’ distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.

We present DeepWalk, a novel approach for learning latent representations of vertices in a network. These latent representations encode social relations in a continuous vector space, which is easily exploited by statistical models. DeepWalk generalizes recent advancements in language modeling and unsupervised feature learning (or deep learning) from sequences of words to graphs.

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. This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease. The goal of the NIH Roadmap Epigenomics Consortium was to generate a reference collection of human epigenomes for primary cells and tissues. This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. The results show that disease and trait-associated genetic variants are enriched in predicted 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.

The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over-stabilization of alpha-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "Amber" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in Amber of two sets of backbone phi/psi dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the phi/psi dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems.

For the purposes of classification, it should be specified whether osteoarthritis (OA) of the knee is of unknown origin (idiopathic, primary) or is related to a known medical condition or event (secondary). Clinical criteria for the classification of idiopathic OA of the knee were developed through a multicenter study group. Comparison diagnoses included rheumatoid arthritis and other painful conditions of the knee, exclusive of referred or para-articular pain. Variables from the medical history, physical examination, laboratory tests, and radiographs were used to develop sets of criteria that serve different investigative purposes. In contrast to prior criteria, these proposed criteria utilize classification trees, or algorithms.

Assessment in clinical psychology typically relies on global retrospective self-reports collected at research or clinic visits, which are limited by recall bias and are not well suited to address how behavior changes over time and across contexts. Ecological momentary assessment (EMA) involves repeated sampling of subjects' current behaviors and experiences in real time, in subjects' natural environments. EMA aims to minimize recall bias, maximize ecological validity, and allow study of microprocesses that influence behavior in real-world contexts. EMA studies assess particular events in subjects' lives or assess subjects at periodic intervals, often by random time sampling, using technologies ranging from written diaries and telephones to electronic diaries and physiological sensors. We discuss the rationale for EMA, EMA designs, methodological and practical issues, and comparisons of EMA and recall data. EMA holds unique promise to advance the science and practice of clinical psychology by shedding light on the dynamics of behavior in real-world settings.

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 2,143 new measurements from 709 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on Machine Learning, and one on Spectroscopy of Light Meson Resonances. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 97 review articles. Volume 2 consists of the Particle Listings and contains also 23 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print, as a web version optimized for use on phones, and as an Android app.

IDSA/ATS Guidelines for CAP in Adults • CID 2007:44 (Suppl 2) • S31 33.A longer duration of therapy may be needed if initial therapy was not active against the identified pathogen or if it was complicated by extrapulmonary infection, such as meningitis or endocarditis.(Weak recommendation; level III evidence.)Other Treatment Considerations 34.Patients with CAP who have persistent septic shock despite adequate fluid resuscitation should be considered for treatment with drotrecogin alfa activated within 24 h of admission.(Weak recommendation; level II evidence.)35.Hypotensive, fluid-resuscitated patients with severe CAP should be screened for occult adrenal insufficiency.(Moderate recommendation; level II evidence.)36.Patients with hypoxemia or respiratory distress should receive a cautious trial of noninvasive ventilation unless they require immediate intubation because of severe hypoxemia (PaO 2 /FiO 2 ratio, !150) and bilateral alveolar infiltrates.(Moderate recommendation; level I evidence.)37. Low-tidal-volume ventilation (6 cm 3 /kg of ideal body weight) should be used for patients undergoing ventilation who have diffuse bilateral pneumonia or acute respiratory distress syndrome.(Strong recommendation; level I evidence.)Management of Nonresponding Pneumonia Definitions and classification.38.The use of a systematic classification of possible causes of failure to respond, based on time of onset and type of failure (table 11), is recommended.(Moderate recommendation; level II evidence.)As many as 15% of patients with CAP may not respond appropriately to initial antibiotic therapy.A systematic approach to these patients (table 11) will help to determine the cause.Because determination of the cause of failure is more accurate if the original microbiological etiology is known, risk factors for nonresponse or deterioration (table 12) figure prominently in the list of situations in which more aggressive and/ or extensive initial diagnostic testing is warranted (table 5).Prevention (see table 13) 39.All persons у50 years of age, others at risk for influenza complications, household contacts of high-risk persons, and health care workers should receive inactivated influenza vaccine as recommended by the Advisory Committee on Immunization Practices, Centers for Disease Control and Prevention.(Strong recommendation; level I evidence.)40.The intranasally administered live attenuated vaccine is an alternative vaccine formulation for some persons 5-49 years of age without chronic underlying diseases, including immunodeficiency, asthma, or chronic medical conditions.(Strong recommendation; level I evidence.)41.Health care workers in inpatient and outpatient settings and long-term care facilities should receive annual influenza immunization.(Strong recommendation; level I evidence.)42.Pneumococcal polysaccharide vaccine is recommended for persons у65 years of age and for those with selected high-risk concurrent diseases, according to current Advisory Committee on Immunization Practices guidelines.(Strong recommendation; level II evidence.)43.Vaccination status should be assessed at the time of hospital admission for all patients, especially those with medical illnesses.(Moderate recommendation; level III evidence.)44.Vaccination may be performed either at hospital discharge or during outpatient treatment.(Moderate recommendation; level III evidence.)45.Influenza vaccine should be offered to persons at hospital discharge or during outpatient treatment during the fall and winter.(Strong recommendation; level III evidence.)46.Smoking cessation should be a goal for persons hospitalized with CAP who smoke.(Moderate recommendation; level III evidence.)47.Smokers who will not quit should also be vaccinated for both pneumococcus and influenza.(Weak recommendation; level III evidence.)48.Cases of pneumonia that are of public health concern should be reported immediately to the state or local health department.(Strong recommendation; level III evidence.)49.Respiratory hygiene measures, including the use of hand hygiene and masks or tissues for patients with cough, should be used in outpatient settings and EDs as a means to reduce the spread of respiratory infections.(Strong recommendation; level III evidence.)

The primary function of the skin is to serve as a protective barrier against the environment. Loss of the integrity of large portions of the skin as a result of injury or illness may lead to major disability or even death. Every year in the United States more than 1.25 million people have burns1 and 6.5 million have chronic skin ulcers caused by pressure, venous stasis, or diabetes mellitus.2 The primary goals of the treatment of wounds are rapid wound closure and a functional and aesthetically satisfactory scar. Recent advances in cellular and molecular biology have greatly expanded our understanding . . .

Fatigue is a prominent disabling symptom in a variety of medical and neurologic disorders. To facilitate research in this area, we developed a fatigue severity scale, subjected it to tests of internal consistency and validity, and used it to compare fatigue in two chronic conditions: systemic lupus erythematosus and multiple sclerosis. Administration of the fatigue severity scale to 25 patients with multiple sclerosis, 29 patients with systemic lupus erythematosus, and 20 healthy adults revealed that the fatigue severity scale was internally consistent, correlated well with visual analogue measures, clearly differentiated controls from patients, and could detect clinically predicted changes in fatigue over time. Fatigue had a greater deleterious impact on daily living in patients with multiple sclerosis and systemic lupus erythematosus compared with controls. The results further showed that fatigue was largely independent of self-reported depressive symptoms and that several characteristics could differentiate fatigue that accompanies multiple sclerosis from fatigue that accompanies systemic lupus erythematosus. This study demonstrates (1) the clinical and research applications of a scale that measures fatigue severity and (2) helps to identify features that distinguish fatigue between two chronic medical disorders.

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Because it lacks a lymphatic circulation, the brain must clear extracellular proteins by an alternative mechanism. The cerebrospinal fluid (CSF) functions as a sink for brain extracellular solutes, but it is not clear how solutes from the brain interstitium move from the parenchyma to the CSF. We demonstrate that a substantial portion of subarachnoid CSF cycles through the brain interstitial space. On the basis of in vivo two-photon imaging of small fluorescent tracers, we showed that CSF enters the parenchyma along paravascular spaces that surround penetrating arteries and that brain interstitial fluid is cleared along paravenous drainage pathways. Animals lacking the water channel aquaporin-4 (AQP4) in astrocytes exhibit slowed CSF influx through this system and a ~70% reduction in interstitial solute clearance, suggesting that the bulk fluid flow between these anatomical influx and efflux routes is supported by astrocytic water transport. Fluorescent-tagged amyloid β, a peptide thought to be pathogenic in Alzheimer's disease, was transported along this route, and deletion of the Aqp4 gene suppressed the clearance of soluble amyloid β, suggesting that this pathway may remove amyloid β from the central nervous system. Clearance through paravenous flow may also regulate extracellular levels of proteins involved with neurodegenerative conditions, its impairment perhaps contributing to the mis-accumulation of soluble proteins.

1 Introduction 2 Groundwork 3 Convolution 4 Notation for Some Useful Functions 5 The Impulse Symbol 6 The Basic Theorems 7 Obtaining Transforms 8 The Two Domains 9 Waveforms, Spectra, Filters and Linearity 10 Sampling and Series 11 The Discrete Fourier Transform and the FFT 12 The Discrete Hartley Transform 13 Relatives of the Fourier Transform 14 The Laplace Transform 15 Antennas and Optics 16 Applications in Statistics 17 Random Waveforms and Noise 18 Heat Conduction and Diffusion 19 Dynamic Power Spectra 20 Tables of sinc x, sinc2x, and exp(-71x2) 21 Solutions to Selected Problems 22 Pictorial Dictionary of Fourier Transforms 23 The Life of Joseph Fourier

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,324 new measurements from 878 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on High Energy Soft QCD and Diffraction and one on the Determination of CKM Angles from B Hadrons. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 98 review articles. Volume 2 consists of the Particle Listings and contains also 22 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print and as a web version optimized for use on phones as well as an Android app.

This paper presents the results of a functional-integral approach to the dynamics of a two-state system coupled to a dissipative environment. It is primarily an extended account of results obtained over the last four years by the authors; while they try to provide some background for orientation, it is emphatically not intended as a comprehensive review of the literature on the subject. Its contents include (1) an exact and general prescription for the reduction, under appropriate circumstances, of the problem of a system tunneling between two wells in the presence of a dissipative environment to the "spin-boson" problem; (2) the derivation of an exact formula for the dynamics of the latter problem; (3) the demonstration that there exists a simple approximation to this exact formula which is controlled, in the sense that we can put explicit bounds on the errors incurred in it, and that for almost all regions of the parameter space these errors are either very small in the limit of interest to us (the "slow-tunneling" limit) or can themselves be evaluated with satisfactory accuracy; (4) use of these results to obtain quantitative expressions for the dynamics of the system as a function of the spectral density $J(\ensuremath{\omega})$ of its coupling to the environment. If $J(\ensuremath{\omega})$ behaves as ${\ensuremath{\omega}}^{s}$ for frequencies of the order of the tunneling frequency or smaller, the authors find for the "unbiased" case the following results: For $s<1$ the system is localized at zero temperature, and at finite $T$ relaxes incoherently at a rate proportional to $\mathrm{exp}\ensuremath{-}{(\frac{{T}_{0}}{T})}^{1\ensuremath{-}s}$. For $s>2$ it undergoes underdamped coherent oscillations for all relevant temperatures, while for $11$) the behavior is an incoherent relaxation at a rate proportional to ${T}^{2\ensuremath{\alpha}\ensuremath{-}1}$, but for low $T$ and $0<\ensuremath{\alpha}<\frac{1}{2}$ the authors predict a combination of damped coherent oscillation and incoherent background which appears to disagree with the results of all previous approximations. The case of finite bias is also discussed.

We present an analysis of atmospheric neutrino data from a 33.0 kton yr (535-day) exposure of the Super-Kamiokande detector. The data exhibit a zenith angle dependent deficit of muon neutrinos which is inconsistent with expectations based on calculations of the atmospheric neutrino flux. Experimental biases and uncertainties in the prediction of neutrino fluxes and cross sections are unable to explain our observation. The data are consistent, however, with two-flavor ${\ensuremath{\nu}}_{\ensuremath{\mu}}\ensuremath{\leftrightarrow}{\ensuremath{\nu}}_{\ensuremath{\tau}}$ oscillations with ${sin}^{2}2\ensuremath{\theta}>0.82$ and $5\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}<\ensuremath{\Delta}{m}^{2}<6\ifmmode\times\else\texttimes\fi{}1{0}^{\ensuremath{-}3}\mathrm{eV}{}^{2}$ at 90% confidence level.