Harvard University

About: Harvard University is a education organization based out in Cambridge, Massachusetts, United States. It is known for research contribution in the topics: Population & Cancer. The organization has 208150 authors who have published 530388 publications receiving 38152182 citations. The organization is also known as: Harvard & University of Harvard.

limma powers differential expression analyses for RNA-sequencing and microarray studies

Abstract: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.

The magical number seven, plus or minus two: some limits on our capacity for processing information

Abstract: First, the span of absolute judgment and the span of immediate memory impose severe limitations on the amount of information that we are able to receive, process, and remember. By organizing the stimulus input simultaneously into several dimensions and successively into a sequence or chunks, we manage to break (or at least stretch) this informational bottleneck. Second, the process of recoding is a very important one in human psychology and deserves much more explicit attention than it has received. In particular, the kind of linguistic recoding that people do seems to me to be the very lifeblood of the thought processes. Recoding procedures are a constant concern to clinicians, social psychologists, linguists, and anthropologists and yet, probably because recoding is less accessible to experimental manipulation than nonsense syllables or T mazes, the traditional experimental psychologist has contributed little or nothing to their analysis. Nevertheless, experimental techniques can be used, methods of recoding can be specified, behavioral indicants can be found. And I anticipate that we will find a very orderly set of relations describing what now seems an uncharted wilderness of individual differences. Third, the concepts and measures provided by the theory of information provide a quantitative way of getting at some of these questions. The theory provides us with a yardstick for calibrating our stimulus materials and for measuring the performance of our subjects. In the interests of communication I have suppressed the technical details of information measurement and have tried to express the ideas in more familiar terms; I hope this paraphrase will not lead you to think they are not useful in research. Informational concepts have already proved valuable in the study of discrimination and of language; they promise a great deal in the study of learning and memory; and it has even been proposed that they can be useful in the study of concept formation. A lot of questions that seemed fruitless twenty or thirty years ago may now be worth another look. In fact, I feel that my story here must stop just as it begins to get really interesting. And finally, what about the magical number seven? What about the seven wonders of the world, the seven seas, the seven deadly sins, the seven daughters of Atlas in the Pleiades, the seven ages of man, the seven levels of hell, the seven primary colors, the seven notes of the musical scale, and the seven days of the week? What about the seven-point rating scale, the seven categories for absolute judgment, the seven objects in the span of attention, and the seven digits in the span of immediate memory? For the present I propose to withhold judgment. Perhaps there is something deep and profound behind all these sevens, something just calling out for us to discover it. But I suspect that it is only a pernicious, Pythagorean coincidence.

The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis.

Abstract: The revised criteria for the classification of rheumatoid arthritis (RA) were formulated from a computerized analysis of 262 contemporary, consecutively studied patients with RA and 262 control subjects with rheumatic diseases other than RA (non-RA). The new criteria are as follows: 1) morning stiffness in and around joints lasting at least 1 hour before maximal improvement; 2) soft tissue swelling (arthritis) of 3 or more joint areas observed by a physician; 3) swelling (arthritis) of the proximal interphalangeal, metacarpophalangeal, or wrist joints; 4) symmetric swelling (arthritis); 5) rheumatoid nodules; 6) the presence of rheumatoid factor; and 7) radiographic erosions and/or periarticular osteopenia in hand and/or wrist joints. Criteria 1 through 4 must have been present for at least 6 weeks. Rheumatoid arthritis is defined by the presence of 4 or more criteria, and no further qualifications (classic, definite, or probable) or list of exclusions are required. In addition, a "classification tree" schema is presented which performs equally as well as the traditional (4 of 7) format. The new criteria demonstrated 91-94% sensitivity and 89% specificity for RA when compared with non-RA rheumatic disease control subjects.

Soft self-consistent pseudopotentials in a generalized eigenvalue formalism.

Abstract: A new approach to the construction of first-principles pseudopotentials is described. The method allows transferability to be improved systematically while holding the cutoff radius fixed, even for large cutoff radii. Novel features are that the pseudopotential itself becomes charge-state dependent, the usual norm-conservation constraint does not apply, and a generalized eigenproblem is introduced. The potentials have a separable form well suited for plane-wave solid-state calculations, and show promise for application to first-row and transition-metal systems.