Address to the pious and benevolent, proposing an annual subscription for the support of missionaries in the Highlands and adjacent islands of Scotland, the isles of Jersey, Guernsey, and Newfoundland, the West Indies, and the provinces of Nova Scotia and Quebec.

Reproduction of copy held by Special Collections, Bridewell Library, Perkins School of Theology, Southern Methodist University. Includes both DjVu and PDF files for download. Mode of access: World Wide Web.

OPEN DOORS AND OPEN MINDS: WHAT FACULTY AUTHORS CAN DO TO ENSURE OPEN ACCESS TO THEIR WORK THROUGH THEIR INSTITUTION

The Internet has brought unparalleled opportunities for expanding availability of research by bringing down economic and physical barriers to sharing. The digitally networked environment promises to democratize access, carry knowledge beyond traditional research niches, accelerate discovery, encourage new and interdisciplinary approaches to ever more complex research challenges, and enable new computational research strategies. However, despite these opportunities for increasing access to knowledge, the prices of scholarly journals have risen sharply over the past two decades, often forcing libraries to cancel subscriptions. Today even the wealthiest institutions cannot afford to sustain all of the journals needed by their faculties and students. To take advantage of the opportunities created by the Internet and to further their mission of creating, preserving, and disseminating knowledge, many academic institutions are taking steps to capture the benefits of more open research sharing. Colleges and universities have built digital repositories to preserve and distribute faculty scholarly articles and other research outputs. Many individual authors have taken steps to retain the rights they need, under copyright law, to allow their work to be made freely available on the Internet and in their institutionâ s repository. And, faculties at some institutions have adopted resolutions endorsing more open access to scholarly articles. Most recently, on February 12, 2008, the Faculty of Arts and Sciences (FAS) at Harvard University took a landmark step. The faculty voted to adopt a policy requiring that faculty authors send an electronic copy of their scholarly articles to the universityâ s digital repository and that faculty authors automatically grant copyright permission to the university to archive and to distribute these articles unless a faculty member has waived the policy for a particular article. Essentially, the faculty voted to make open access to the results of their published journal articles the default policy for the Faculty of Arts and Sciences of Harvard University. As of March 2008, a proposal is also under consideration in the University of California system by which faculty authors would commit routinely to grant copyright permission to the university to make copies of the facultyâ s scholarly work openly accessible over the Internet. Inspired by the example set by the Harvard faculty, this White Paper is addressed to the faculty and administrators of academic institutions who support equitable access to scholarly research and knowledge, and who believe that the institution can play an important role as steward of the scholarly literature produced by its faculty. This paper discusses both the motivation and the process for establishing a binding institutional policy that automatically grants a copyright license from each faculty member to permit deposit of his or her peer-reviewed scholarly articles in institutional repositories, from which the works become available for others to read and cite.

Complying with the NIH Public Access Policy - Copyright Considerations and Options

On January 11, 2008, the National Institutes of Health ('NIH') adopted a revised Public Access Policy for peer-reviewed journal articles reporting research supported in whole or in part by NIH funds. Under the revised policy, the grantee shall ensure that a copy of the author's final manuscript, including any revisions made during the peer review process, be electronically submitted to the National Library of Medicine's PubMed Central ('PMC') archive and that the person submitting the manuscript will designate a time not later than 12 months after publication at which NIH may make the full text of the manuscript publicly accessible in PMC. NIH adopted this policy to implement a new statutory requirement under which: The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law. This White Paper is written primarily for policymaking staff in universities and other institutional recipients of NIH support responsible for ensuring compliance with the Public Access Policy. The January 11, 2008, Public Access Policy imposes two new compliance mandates. First, the grantee must ensure proper manuscript submission. The version of the article to be submitted is the final version over which the author has control, which must include all revisions made after peer review. The statutory command directs that the manuscript be submitted to PMC 'upon acceptance for publication.' That is, the author's final manuscript should be submitted to PMC at the same time that it is sent to the publisher for final formatting and copy editing. Proper submission is a two-stage process. The electronic manuscript must first be submitted through a process that requires input of additional information concerning the article, the author(s), and the nature of NIH support for the research reported. NIH then formats the manuscript into a uniform, XML-based format used for PMC versions of articles. In the second stage of the submission process, NIH sends a notice to the Principal Investigator requesting that the PMC-formatted version be reviewed and approved. Only after such approval has grantee's manuscript submission obligation been satisfied. Second, the grantee also has a distinct obligation to grant NIH copyright permission to make the manuscript publicly accessible through PMC not later than 12 months after the date of publication. This obligation is connected to manuscript submission because the author, or the person submitting the manuscript on the author's behalf, must have the necessary rights under copyright at the time of submission to give NIH the copyright permission it requires. This White Paper explains and analyzes only the scope of the grantee's copyright-related obligations under the revised Public Access Policy and suggests six options for compliance with that aspect of the grantee's obligation. Time is of the essence for NIH grantees. As a practical matter, the grantee should have a compliance process in place no later than April 7, 2008. More specifically, the new Public Access Policy applies to any article accepted for publication on or after April 7, 2008 if the article arose under (1) an NIH Grant or Cooperative Agreement active in Fiscal Year 2008, (2) direct funding from an NIH Contract signed after April 7, 2008, (3) direct funding from the NIH Intramural Program, or (4) from an NIH employee. In addition, effective May 25, 2008, anyone submitting an application, proposal or progress report to the NIH must include the PMC reference number when citing articles arising from their NIH funded research. (This includes applications submitted to the NIH for the May 25, 2008 and subsequent due dates.) Conceptually, the compliance challenge that the Public Access Policy poses for grantees is easily described. The grantee must depend to some extent upon the author(s) to take the necessary actions to ensure that the grantee is in compliance with the Public Access Policy because the electronic manuscripts and the copyrights in those manuscripts are initially under the control of the author(s). As a result, any compliance option will require an explicit understanding between the author(s) and the grantee about how the manuscript and the copyright in the manuscript are managed. It is useful to conceptually keep separate the grantee's manuscript submission obligation from its copyright permission obligation because the compliance personnel concerned with manuscript management may differ from those responsible for overseeing the author's copyright management. With respect to copyright management, the grantee has the following six options: (1) rely on authors to manage copyright but also to request or to require that these authors take responsibility for amending publication agreements that call for transfer of too many rights to enable the author to grant NIH permission to make the manuscript publicly accessible ('the Public Access License'); (2) take a more active role in assisting authors in negotiating the scope of any copyright transfer to a publisher by (a) providing advice to authors concerning their negotiations or (b) by acting as the author's agent in such negotiations; (3) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License; (4) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License and also grants a license to the grantee to make certain uses of the article, including posting a copy in the grantee's publicly accessible digital archive or repository and authorizing the article to be used in connection with teaching by university faculty; (5) negotiate a more systematic and comprehensive agreement with the biomedical publishers to ensure either that the publisher has a binding obligation to submit the manuscript and to grant NIH permission to make the manuscript publicly accessible or that the author retains sufficient rights to do so; or (6) instruct NIH-funded authors to submit manuscripts only to journals with binding deposit agreements with NIH or to journals whose copyright agreements permit authors to retain sufficient rights to authorize NIH to make manuscripts publicly accessible.

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Background Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE. Results We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0~1%. Conclusions Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.

A Laminar Cortical Model for 3D Perception of Slanted and Curved Surfaces and of 2D Images: Developement, attention, and Bistability

A model of laminar visual cortical dynamics proposes how 3D boundary and surface representations of slated and curved 3D objects and 2D images arise. The 3D boundary representations emerge from interactions between non-classical horizontal receptive field interactions with intracorticcal and intercortical feedback circuits. Such non-classical interactions contextually disambiguate classical receptive field responses to ambiguous visual cues using cells that are sensitive to angles and disparity gradients with cortical areas V1 and V2. These cells are all variants of bipole grouping cells. Model simulations show how horizontal connections can develop selectively to angles, how slanted surfaces can activate 3D boundary representations that are sensitive to angles and disparity gradients, how 3D filling-in occurs across slanted surfaces, how a 2D Necker cube image can be represented in 3D, and how bistable Necker cuber percepts occur. The model also explains data about slant aftereffects and 3D neon color spreading. It shows how habituative transmitters that help to control developement also help to trigger bistable 3D percepts and slant aftereffects, and how attention can influence which of these percepts is perceived by propogating along some object boundaries.

How Does the Cerebral Cortex Work? Developement, Learning, Attention, and 3D Vision by Laminar Circuits of Visual Cortex

A key goal of behavioral and cognitive neuroscience is to link brain mechanisms to behavioral functions. The present article describes recent progress towards explaining how the visual cortex sees. Visual cortex, like many parts of perceptual and cognitive neocortex, is organized into six main layers of cells, as well as characteristic sub-lamina. Here it is proposed how these layered circuits help to realize the processes of developement, learning, perceptual grouping, attention, and 3D vision through a combination of bottom-up, horizontal, and top-down interactions. A key theme is that the mechanisms which enable developement and learning to occur in a stable way imply properties of adult behavior. These results thus begin to unify three fields: infant cortical developement, adult cortical neurophysiology and anatomy, and adult visual perception. The identified cortical mechanisms promise to generalize to explain how other perceptual and cognitive processes work.

Linking Attention to Learning, Expectation, Competition, and Consciousness

The concept of attention has been used in many senses, often without clarifying how or why attention works as it does. Attention, like consciousness, is often described in a disembodied way. The present article summarizes neural models and supportive data and how attention is linked to processes of learning, expectation, competition, and consciousness. A key them is that attention modulates cortical self-organization and stability. Perceptual and cognitive neocortex is organized into six main cell layers, with characteristic sub-lamina. Attention is part of unified design of bottom-up, horizontal, and top-down interactions among indentified cells in laminar cortical circuits. Neural models clarify how attention may be allocated during processes of visual perception, learning and search; auditory streaming and speech perception; movement target selection during sensory-motor control; mental imagery and fantasy; and hallucination during mental disorders, among other processes.

Neural Dynamics of Autistic Behaviors: Cognitive, Emotional, and Timing Substrates

What brain mechanisms underlie autism and how do they give rise to autistic behavioral symptoms? This article describes a neural model, called the iSTART model, which proposes how cognitive, emotional, timing, and motor processes may interact together to create and perpetuate autistic symptoms. These model processes were originally developed to explain data concerning how the brain controls normal behaviors. The iSTART model shows how autistic behavioral symptoms may arise from prescribed breakdowns in these brain processes.

From Working Memory to Long-term Memory and Back: Linked but Distinct

Neural models have proposed how short-term memory (STM) storage in working memory and long-term memory (LTM) storage and recall are linked and interact, but are realized by different mechanisms that obey different laws. The authors' data can be understood in the light of these models, which suggest that the authors may have gone too far in obscuring the differences between these processes.

Linking brain to mind in normal behavior and schizophrenia

In order to understand schizophrenia, a linking hypothesis is needed that shows how brain mechanisms lead to behavioral functions in normals, and also how breakdown in these mechanisms lead to behavioral symptoms in schizophrenia. Such a linking hypothesis is now available that complements the discussion offered by Phillips and Silverstein.

Isoperimetric Graph Partitioning for Data Clustering and Image Segmentation

Spectral methods of graph partitioning have been shown to provide a powerful approach to the image segmentation problem. In this paper, we adopt a different approach, based on estimating the isoperimetric constant of an image graph. Our algorithm produces the high quality segmentations and data clustering of spectral methods, but with improved speed and stability.

A Neural Model of Surface Perception: Lightness, Anchoring, and Filling-in

This article develops a neural model of how the visual system processes natural images under variable illumination conditions to generate surface lightness percepts. Previous models have clarified how the brain can compute the relative contrast of images from variably illuminate scenes. How the brain determines an absolute lightness scale that "anchors" percepts of surface lightness to us the full dynamic range of neurons remains an unsolved problem. Lightness anchoring properties include articulation, insulation, configuration, and are effects. The model quantatively simulates these and other lightness data such as discounting the illuminant, the double brilliant illusion, lightness constancy and contrast, Mondrian contrast constancy, and the Craik-O'Brien-Cornsweet illusion. The model also clarifies the functional significance for lightness perception of anatomical and neurophysiological data, including gain control at retinal photoreceptors, and spatioal contrast adaptation at the negative feedback circuit between the inner segment of photoreceptors and interacting horizontal cells. The model retina can hereby adjust its sensitivity to input intensities ranging from dim moonlight to dazzling sunlight. A later model cortical processing stages, boundary representations gate the filling-in of surface lightness via long-range horizontal connections. Variants of this filling-in mechanism run 100-1000 times faster than diffusion mechanisms of previous biological filling-in models, and shows how filling-in can occur at realistic speeds. A new anchoring mechanism called the Blurred-Highest-Luminance-As-White (BHLAW) rule helps simulate how surface lightness becomes sensitive to the spatial scale of objects in a scene. The model is also able to process natural images under variable lighting conditions.

AIRSTREAM: A Neural Network Model of Auditory Scene Analysis and Source Segregation

Multiple sound sources often contain harmonics that overlap and may be degraded by environmental noise. The auditory system is capable of teasing apart these sources into distinct mental objects, or streams. Such an "auditory scene analysis" enables the brain to solve the cocktail party problem. A neural network model of auditory scene analysis, called the AIRSTREAM model, is presented to propose how the brain accomplishes this feat. The model clarifies how the frequency components that correspond to a give acoustic source may be coherently grouped together into distinct streams based on pitch and spatial cues. The model also clarifies how multiple streams may be distinguishes and seperated by the brain. Streams are formed as spectral-pitch resonances that emerge through feedback interactions between frequency-specific spectral representaion of a sound source and its pitch. First, the model transforms a sound into a spatial pattern of frequency-specific activation across a spectral stream layer. The sound has multiple parallel representations at this layer. A sound's spectral representation activates a bottom-up filter that is sensitive to harmonics of the sound's pitch. The filter activates a pitch category which, in turn, activate a top-down expectation that allows one voice or instrument to be tracked through a noisy multiple source environment. Spectral components are suppressed if they do not match harmonics of the top-down expectation that is read-out by the selected pitch, thereby allowing another stream to capture these components, as in the "old-plus-new-heuristic" of Bregman. Multiple simultaneously occuring spectral-pitch resonances can hereby emerge. These resonance and matching mechanisms are specialized versions of Adaptive Resonance Theory, or ART, which clarifies how pitch representations can self-organize durin learning of harmonic bottom-up filters and top-down expectations. The model also clarifies how spatial location cues can help to disambiguate two sources with similar spectral cures. Data are simulated from psychophysical grouping experiments, such as how a tone sweeping upwards in frequency creates a bounce percept by grouping with a downward sweeping tone due to proximity in frequency, even if noise replaces the tones at their interection point. Illusory auditory percepts are also simulated, such as the auditory continuity illusion of a tone continuing through a noise burst even if the tone is not present during the noise, and the scale illusion of Deutsch whereby downward and upward scales presented alternately to the two ears are regrouped based on frequency proximity, leading to a bounce percept. Since related sorts of resonances have been used to quantitatively simulate psychophysical data about speech perception, the model strengthens the hypothesis the ART-like mechanisms are used at multiple levels of the auditory system. Proposals for developing the model to explain more complex streaming data are also provided.

Adaptive Neural Models of Queuing and Timing in Fluent Action

Temporal structure in skilled, fluent action exists at several nested levels. At the largest scale considered here, short sequences of actions that are planned collectively in prefrontal cortex appear to be queued for performance by a cyclic competitive process that operates in concert with a parallel analog representation that implicitly specifies the relative priority of elements of the sequence. At an intermediate scale, single acts, like reaching to grasp, depend on coordinated scaling of the rates at which many muscles shorten or lengthen in parallel. To ensure success of acts such as catching an approaching ball, such parallel rate scaling, which appears to be one function of the basal ganglia, must be coupled to perceptual variables, such as time-to-contact. At a fine scale, within each act, desired rate scaling can be realized only if precisely timed muscle activations first accelerate and then decelerate the limbs, to ensure that muscle length changes do not under- or over-shoot the amounts needed for the precise acts. Each context of action may require a much different timed muscle activation pattern than similar contexts. Because context differences that require different treatment cannot be known in advance, a formidable adaptive engine-the cerebellum-is needed to amplify differences within, and continuosly search, a vast parallel signal flow, in order to discover contextual "leading indicators" of when to generate distinctive parallel patterns of analog signals. From some parts of the cerebellum, such signals controls muscles. But a recent model shows how the lateral cerebellum, such signals control muscles. But a recent model shows how the lateral cerebellum may serve the competitive queuing system (in frontal cortex) as a repository of quickly accessed long-term sequence memories. Thus different parts of the cerebellum may use the same adaptive engine system design to serve the lowest and the highest of the three levels of temporal structure treated. If so, no one-to-one mapping exists between levels of temporal structure and major parts of the brain. Finally, recent data cast doubt on network-delay models of cerebellar adaptive timing.

A Cortical and Cerebellar Parcellation System for Speech Studies

A neuroanatomical parcellation system is described which encompasses the entire cerebral cortex and the cerebellum. The cortical system modified version of the scheme described by Caviness et al. (1996) and is designed particularly for studies of speech processing. The cerebellum is parcellated into 6 cortical regions of interest (ROIs) and an ROI representing the deep cerebellar nuclei in each hemisphere. The boundaries of each ROI are based on individual anatomical markers that are clearly visible from standard structural MRI acquistions. The system permits averaginh of functional imaging data sets from multiple sujects while accounting for individual anatomical variability. Used in conjuction with region-of-interest analysis techniques such as that described by Nieto-Castanon et al. (2003), the parcellation system provides a more powerful means of analyzing functional data.