Massachusetts Institute of Technology

This paper describes a computational approach to edge detection. The success of the approach depends on the definition of a comprehensive set of goals for the computation of edge points. These goals must be precise enough to delimit the desired behavior of the detector while making minimal assumptions about the form of the solution. We define detection and localization criteria for a class of edges, and present mathematical forms for these criteria as functionals on the operator impulse response. A third criterion is then added to ensure that the detector has only one response to a single edge. We use the criteria in numerical optimization to derive detectors for several common image features, including step edges. On specializing the analysis to step edges, we find that there is a natural uncertainty principle between detection and localization performance, which are the two main goals. With this principle we derive a single operator shape which is optimal at any scale. The optimal detector has a simple approximate implementation in which edges are marked at maxima in gradient magnitude of a Gaussian-smoothed image. We extend this simple detector using operators of several widths to cope with different signal-to-noise ratios in the image. We present a general method, called feature synthesis, for the fine-to-coarse integration of information from operators at different scales. Finally we show that step edge detector performance improves considerably as the operator point spread function is extended along the edge.

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

I. Introduction, 65. — II. A model of long-run growth, 66. — III. Possible growth patterns, 68. — IV. Examples, 73. — V. Behavior of interest and wage rates, 78. — VI. Extensions, 85. — VII. Qualifications, 91.

Finite systems of deterministic ordinary nonlinear differential equations may be designed to represent forced dissipative hydrodynamic flow. Solutions of these equations can be identified with trajectories in phase space. For those systems with bounded solutions, it is found that nonperiodic solutions are ordinarily unstable with respect to small modifications, so that slightly differing initial states can evolve into considerably different states. Systems with bounded solutions are shown to possess bounded numerical solutions. A simple system representing cellular convection is solved numerically. All of the solutions are found to be unstable, and almost all of them are nonperiodic. The feasibility of very-long-range weather prediction is examined in the light of these results.

Non-randomised studies of the effects of interventions are critical to many areas of healthcare evaluation, but their results may be biased. It is therefore important to understand and appraise their strengths and weaknesses. We developed ROBINS-I (“Risk Of Bias In Non-randomised Studies - of Interventions”), a new tool for evaluating risk of bias in estimates of the comparative effectiveness (harm or benefit) of interventions from studies that did not use randomisation to allocate units (individuals or clusters of individuals) to comparison groups. The tool will be particularly useful to those undertaking systematic reviews that include non-randomised studies.

This paper describes a simple method of calculating a heteroskedasticity and autocorrelation consistent covariance matrix that is positive semi-definite by construction. It also establishes consistency of the estimated covariance matrix under fairly general conditions.

Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.

On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-Wave Observatory simultaneously observed a transient gravitational-wave signal. The signal sweeps upwards in frequency from 35 to 250 Hz with a peak gravitational-wave strain of 1.0×10(-21). It matches the waveform predicted by general relativity for the inspiral and merger of a pair of black holes and the ringdown of the resulting single black hole. The signal was observed with a matched-filter signal-to-noise ratio of 24 and a false alarm rate estimated to be less than 1 event per 203,000 years, equivalent to a significance greater than 5.1σ. The source lies at a luminosity distance of 410(-180)(+160) Mpc corresponding to a redshift z=0.09(-0.04)(+0.03). In the source frame, the initial black hole masses are 36(-4)(+5)M⊙ and 29(-4)(+4)M⊙, and the final black hole mass is 62(-4)(+4)M⊙, with 3.0(-0.5)(+0.5)M⊙c(2) radiated in gravitational waves. All uncertainties define 90% credible intervals. These observations demonstrate the existence of binary stellar-mass black hole systems. This is the first direct detection of gravitational waves and the first observation of a binary black hole merger.

Wireless distributed microsensor systems will enable the reliable monitoring of a variety of environments for both civil and military applications. In this paper, we look at communication protocols, which can have significant impact on the overall energy dissipation of these networks. Based on our findings that the conventional protocols of direct transmission, minimum-transmission-energy, multi-hop routing, and static clustering may not be optimal for sensor networks, we propose LEACH (Low-Energy Adaptive Clustering Hierarchy), a clustering-based protocol that utilizes randomized rotation of local cluster based station (cluster-heads) to evenly distribute the energy load among the sensors in the network. LEACH uses localized coordination to enable scalability and robustness for dynamic networks, and incorporates data fusion into the routing protocol to reduce the amount of information that must be transmitted to the base station. Simulations show the LEACH can achieve as much as a factor of 8 reduction in energy dissipation compared with conventional outing protocols. In addition, LEACH is able to distribute energy dissipation evenly throughout the sensors, doubling the useful system lifetime for the networks we simulated.

We have developed a near-real-time computer system that can locate and track a subject's head, and then recognize the person by comparing characteristics of the face to those of known individuals. The computational approach taken in this system is motivated by both physiology and information theory, as well as by the practical requirements of near-real-time performance and accuracy. Our approach treats the face recognition problem as an intrinsically two-dimensional (2-D) recognition problem rather than requiring recovery of three-dimensional geometry, taking advantage of the fact that faces are normally upright and thus may be described by a small set of 2-D characteristic views. The system functions by projecting face images onto a feature space that spans the significant variations among known face images. The significant features are known as "eigenfaces," because they are the eigenvectors (principal components) of the set of faces; they do not necessarily correspond to features such as eyes, ears, and noses. The projection operation characterizes an individual face by a weighted sum of the eigenface features, and so to recognize a particular face it is necessary only to compare these weights to those of known individuals. Some particular advantages of our approach are that it provides for the ability to learn and later recognize new faces in an unsupervised manner, and that it is easy to implement using a neural network architecture.

A technique called optical coherence tomography (OCT) has been developed for noninvasive cross-sectional imaging in biological systems. OCT uses low-coherence interferometry to produce a two-dimensional image of optical scattering from internal tissue microstructures in a way that is analogous to ultrasonic pulse-echo imaging. OCT has longitudinal and lateral spatial resolutions of a few micrometers and can detect reflected signals as small as approximately 10(-10) of the incident optical power. Tomographic imaging is demonstrated in vitro in the peripapillary area of the retina and in the coronary artery, two clinically relevant examples that are representative of transparent and turbid media, respectively.

In this paper we show how to divide data D into n pieces in such a way that D is easily reconstructable from any k pieces, but even complete knowledge of k - 1 pieces reveals absolutely no information about D . This technique enables the construction of robust key management schemes for cryptographic systems that can function securely and reliably even when misfortunes destroy half the pieces and security breaches expose all but one of the remaining pieces.

An encryption method is presented with the novel property that publicly revealing an encryption key does not thereby reveal the corresponding decryption key. This has two important consequences: Couriers or other secure means are not needed to transmit keys, since a message can be enciphered using an encryption key publicly revealed by the intended recipient. Only he can decipher the message, since only he knows the corresponding decryption key. A message can be “signed” using a privately held decryption key. Anyone can verify this signature using the corresponding publicly revealed encryption key. Signatures cannot be forged, and a signer cannot later deny the validity of his signature. This has obvious applications in “electronic mail” and “electronic funds transfer” systems. A message is encrypted by representing it as a number M, raising M to a publicly specified power e, and then taking the remainder when the result is divided by the publicly specified product, n , of two large secret prime numbers p and q. Decryption is similar; only a different, secret, power d is used, where e * d = 1(mod (p - 1) * (q - 1)). The security of the system rests in part on the difficulty of factoring the published divisor, n .

The prefrontal cortex has long been suspected to play an important role in cognitive control, in the ability to orchestrate thought and action in accordance with internal goals. Its neural basis, however, has remained a mystery. Here, we propose that cognitive control stems from the active maintenance of patterns of activity in the prefrontal cortex that represent goals and the means to achieve them. They provide bias signals to other brain structures whose net effect is to guide the flow of activity along neural pathways that establish the proper mappings between inputs, internal states, and outputs needed to perform a given task. We review neurophysiological, neurobiological, neuroimaging, and computational studies that support this theory and discuss its implications as well as further issues to be addressed

Accelerating the discovery of advanced materials is essential for human welfare and sustainable, clean energy. In this paper, we introduce the Materials Project (www.materialsproject.org), a core program of the Materials Genome Initiative that uses high-throughput computing to uncover the properties of all known inorganic materials. This open dataset can be accessed through multiple channels for both interactive exploration and data mining. The Materials Project also seeks to create open-source platforms for developing robust, sophisticated materials analyses. Future efforts will enable users to perform ‘‘rapid-prototyping’’ of new materials in silico, and provide researchers with new avenues for cost-effective, data-driven materials design.

We develop and analyze low-complexity cooperative diversity protocols that combat fading induced by multipath propagation in wireless networks. The underlying techniques exploit space diversity available through cooperating terminals' relaying signals for one another. We outline several strategies employed by the cooperating radios, including fixed relaying schemes such as amplify-and-forward and decode-and-forward, selection relaying schemes that adapt based upon channel measurements between the cooperating terminals, and incremental relaying schemes that adapt based upon limited feedback from the destination terminal. We develop performance characterizations in terms of outage events and associated outage probabilities, which measure robustness of the transmissions to fading, focusing on the high signal-to-noise ratio (SNR) regime. Except for fixed decode-and-forward, all of our cooperative diversity protocols are efficient in the sense that they achieve full diversity (i.e., second-order diversity in the case of two terminals), and, moreover, are close to optimum (within 1.5 dB) in certain regimes. Thus, using distributed antennas, we can provide the powerful benefits of space diversity without need for physical arrays, though at a loss of spectral efficiency due to half-duplex operation and possibly at the cost of additional receive hardware. Applicable to any wireless setting, including cellular or ad hoc networks-wherever space constraints preclude the use of physical arrays-the performance characterizations reveal that large power or energy savings result from the use of these protocols.

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome. The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

Although cancer classification has improved over the past 30 years, there has been no general approach for identifying new cancer classes (class discovery) or for assigning tumors to known classes (class prediction). Here, a generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring and suggest a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge.

A low-density parity-check code is a code specified by a parity-check matrix with the following properties: each column contains a small fixed number <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j \geq 3</tex> of l's and each row contains a small fixed number <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k &gt; j</tex> of l's. The typical minimum distance of these codes increases linearly with block length for a fixed rate and fixed <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j</tex> . When used with maximum likelihood decoding on a sufficiently quiet binary-input symmetric channel, the typical probability of decoding error decreases exponentially with block length for a fixed rate and fixed <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j</tex> . A simple but nonoptimum decoding scheme operating directly from the channel a posteriori probabilities is described. Both the equipment complexity and the data-handling capacity in bits per second of this decoder increase approximately linearly with block length. For <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j &gt; 3</tex> and a sufficiently low rate, the probability of error using this decoder on a binary symmetric channel is shown to decrease at least exponentially with a root of the block length. Some experimental results show that the actual probability of decoding error is much smaller than this theoretical bound.