Users Guide for SnadiOpt: A Package Adding Automatic Differentiation to Snopt

SnadiOpt is a package that supports the use of the automatic differentiation package ADIFOR with the optimization package Snopt. Snopt is a general-purpose system for solving optimization problems with many variables and constraints. It minimizes a linear or nonlinear function subject to bounds on the variables and sparse linear or nonlinear constraints. It is suitable for large-scale linear and quadratic programming and for linearly constrained optimization, as well as for general nonlinear programs. The method used by Snopt requires the first derivatives of the objective and constraint functions to be available. The SnadiOpt package allows users to avoid the time-consuming and error-prone process of evaluating and coding these derivatives. Given Fortran code for evaluating only the values of the objective and constraints, SnadiOpt automatically generates the code for evaluating the derivatives and builds the relevant Snopt input files and sparse data structures.Comment: pages i-iv, 1-2

accuracy: Tools for Accurate and Reliable Statistical Computing

Most empirical social scientists are surprised that low-level numerical issues in software can have deleterious effects on the estimation process. Statistical analyses that appear to be perfectly successful can be invalidated by concealed numerical problems. We have developed a set of tools, contained in accuracy, a package for R and S-PLUS, to diagnose problems stemming from numerical and measurement error and to improve the accuracy of inferences. The tools included in accuracy include a framework for gauging the computational stability of model results, tools for comparing model results, optimization diagnostics, and tools for collecting entropy for true random numbers generation.

The Impact and Limitations of the NHS Bowel Cancer Screening Programme in the North East of England

This thesis analyses the impact of the NHS Bowel Cancer Screening Programme (BCSP) since its national implementation. A regional cancer registry (Northern Colorectal Cancer Audit Group, NORCCAG, database) and the regional BCSP database were combined to obtain the full screening history for all patients diagnosed with a colorectal cancer (CRC) in the North East of England, out of the population eligible for screening. The CRCs in the screening population between April 2007 and March 2010 were identified and classified into four groups: control (diagnosed before first screening invite), screen-detected, interval (diagnosed between screening rounds, after a negative screening episode), and non-uptake (declined screening). Patient demographics, tumour characteristics and survival were compared between groups. In all, 511 out of 1336 (38.2%) CRCs were controls; 825 (61.8%) were in individuals invited for screening of which 322 (39.0%) were screen-detected, 311 (37.7%) were in the non-uptake group, and 192 (23.3%) were interval cancers. Compared with the control and interval cancer group, the screen-detected group had a higher proportion of men, left colon tumours, and superior survival, implying the guaiac-based faecal occult blood test (FOBt) is more effective at detecting cancers in these groups. There was no difference in demographics, tumour location/stage, or survival between control and interval groups. A cost-effectiveness analysis of altering the screening pathway by lowering the minimum criteria for an abnormal FOBt was performed and raises potential opportunities that the screening programme could develop in order to minimise on the number of missed cancers

Conformations of biopolymers in the gas phase: a new mass spectrometric method

A method is developed for measuring collision cross sections of gas-phase biomolecules using a slightly modified commercial triple quadrupole instrument. The modifications allow accurate stopping potentials to be measured for ions exiting the collision region of the instrument. A simple model allows these curves to be converted to cross sections. In order to account for certain poorly defined experimental parameters (exact ion energy, absolute pressure in the collision cell, etc.) variable parameters are included in the model. These parameters are determined on a case by case basis by normalizing the results to the well known cross section of singly charged bradykinin, Two relatively large systems were studied (cytochrome c and myoglobin) so comparisons could be made to literature values. A number of new peptide systems were then studied in the 9 -14 residue range. These included singly and doubly charged ions of luteinizing hormone releasing hormone (LHRH) substance P, and bombesin in addition to bradykinin. The experimental cross sections were in very good agreement with predictions from extensive molecular dynamics modeling. One interesting result was the experimental observation that the cross section of the doubly charged ions of LHRH, substance P, and bombesin were all smaller than those of the corresponding singly charged ions. Molecular dynamics did not reproduce this result, predicting doubly charged cross sections of the same magnitude or slightly larger than for the singly charged species. The experimental results appear to be correct, however. Possible shortcomings in the modeling procedure for multiply charged ions were suggested that might account for the discrepancy

Measuring and mitigating AS-level adversaries against Tor

The popularity of Tor as an anonymity system has made it a popular target for a variety of attacks. We focus on traffic correlation attacks, which are no longer solely in the realm of academic research with recent revelations about the NSA and GCHQ actively working to implement them in practice. Our first contribution is an empirical study that allows us to gain a high fidelity snapshot of the threat of traffic correlation attacks in the wild. We find that up to 40% of all circuits created by Tor are vulnerable to attacks by traffic correlation from Autonomous System (AS)-level adversaries, 42% from colluding AS-level adversaries, and 85% from state-level adversaries. In addition, we find that in some regions (notably, China and Iran) there exist many cases where over 95% of all possible circuits are vulnerable to correlation attacks, emphasizing the need for AS-aware relay-selection. To mitigate the threat of such attacks, we build Astoria--an AS-aware Tor client. Astoria leverages recent developments in network measurement to perform path-prediction and intelligent relay selection. Astoria reduces the number of vulnerable circuits to 2% against AS-level adversaries, under 5% against colluding AS-level adversaries, and 25% against state-level adversaries. In addition, Astoria load balances across the Tor network so as to not overload any set of relays.Comment: Appearing at NDSS 201

The Social Explanatory Styles Questionnaire: Assessing moderators of basic social-cognitive phenomena including spontaneous trait inference, the fundamental attribution error, and moral blame

Why is he poor? Why is she failing academically? Why is he so generous? Why is she so conscientious? Answers to such everyday questions—social explanations—have powerful effects on relationships at the interpersonal and societal levels. How do people select an explanation in particular cases? We suggest that, often, explanations are selected based on the individual\u27s pre-existing general theories of social causality. More specifically, we suggest that over time individuals develop general beliefs regarding the causes of social events. We refer to these beliefs as social explanatory styles. Our goal in the present article is to offer and validate a measure of individual differences in social explanatory styles. Accordingly, we offer the Social Explanatory Styles Questionnaire (SESQ), which measures three independent dimensions of social explanatory style: Dispositionism, historicism, and controllability. Studies 1–3 examine basic psychometric properties of the SESQ and provide positive evidence regarding internal consistency, factor structure, and both convergent and divergent validity. Studies 4–6 examine predictive validity for each subscale: Does each explanatory dimension moderate an important phenomenon of social cognition? Results suggest that they do. In Study 4, we show that SESQ dispositionism moderates the tendency to make spontaneous trait inferences. In Study 5, we show that SESQ historicism moderates the tendency to commit the Fundamental Attribution Error. Finally, in Study 6 we show that SESQ controllability predicts polarization of moral blame judgments: Heightened blaming toward controllable stigmas (assimilation), and attenuated blaming toward uncontrollable stigmas (contrast). Decades of research suggest that explanatory style regarding the self is a powerful predictor of self-functioning. We think it is likely that social explanatory styles—perhaps comprising interactive combinations of the basic dimensions tapped by the SESQ—will be similarly potent predictors of social functioning. We hope the SESQ will be a useful tool for exploring that possibility

Cavalry To Campfires: The Politics Of Preservation In Frontier Historical Park

Located on the bank of Big Creek in the Smoky Hills Region of the Great Plains is a small wooded park that contains a unique history. Today, the park is split into two sections, one being Frontier Park and the other being the Fort Hays State Historic Site that administers four original buildings from the active years of Fort Hays. Visitors from all states in the Union and many countries pass through Hays to visit the park. Whether to step back in time and experience life of the nineteenth century frontier or to absorb the quiet serenity of the state park’s natural area. Many visitors may not realize the political battle that took place in order to establish a state park located in Hays. From the time the military decided to place forts in the area in 1865, the land was known for its unique scenic quality due to the abundance of trees located along Big Creek, one of the few water sources in the region. For one hundred years the Fort Hays Military Reservation was at the heart of a political battle over the proper use of the land after the deactivation of the Post. During the active years of Fort Hays, military personnel worked to protect the trees along Big Creek. The post surgeon took part in a natural survey of the land, noting the unusual timber growth and variety of wildlife species. After the closing of Fort Hays in 1889, the land was turned over to the care of the Department of the Interior. Political debates arose in the wake of the fort’s closure in 1889. The seven thousand six hundred acres of the former military reservation rested in the hands of the federal government. Coinciding with the timing of the fort’s closure was the rising popularity of the conservation movement. While representatives from Kansas were in talks with the Interior Department about the right of the state to own the property, the development of a public park became one of the stipulations for the federal land transfer to the state of Kansas. The finalization of the land transfer agreement took place in 1901. From this point forward, a multitude of people from a variety of backgrounds worked to develop Frontier Historical Park as a modern state park in western Kansas. The goal of the park was to provide a place of relaxation, recreation, and historic interests to visitors traveling through the state of Kansas

Our Grandparents, Our Parents, Our Future Selves: Optimizing Function in Old Age.

Most of my research at Yale University School of Medicine over the past several years has focused on identifying older adults at risk of functional decline and disability, identifying events that may precipitate the transition from functional independence to disability, and developing strategies to postpone or reduce frailty and disability. As a result of the Precipitating Events Project (PEP) and other research conducted by the Yale Center on Aging/Pepper Center, we now realize that age is only a proxy for other factors that lead to disability, and that some of these factors can be modified to reduce the risk of disability. In fact, disability rates have been steadily declining among older adults for decades

Shaftesbury on the beauty of nature

Many people today glorify wild nature. This attitude is diametrically opposed to the denigration of wild nature that was common in the seventeenth century. One of the most significant initiators of the modern revaluation of nature was Anthony Ashley Cooper, the third Earl of Shaftesbury (1671–1713). I elucidate here Shaftesbury’s pivotal view of nature. I show how that view emerged as Shaftesbury’s solution to a problem he took to be of the deepest philosophical and personal importance: the problem of how worship of God can be both transportingly emotional and entirely rational. In section 1 I sketch the denigration of wild nature in two of Shaftesbury’s predecessors: Burnet and Locke. I next turn to Shaftesbury’s problem, describing in section 2 the love of God he aspired to and in section 3 his commitment to rational religion. I then explain Shaftesbury’s solution, describing in section 4 his view of beauty in general and in section 5 his view of the beauty of nature

A geometric proof of the Kochen-Specker no-go theorem

We give a short geometric proof of the Kochen-Specker no-go theorem for non-contextual hidden variables models. Note added to this version: I understand from Jan-Aake Larsson that the construction we give here actually contains the original Kochen-Specker construction as well as many others (Bell, Conway and Kochen, Schuette, perhaps also Peres).Comment: This paper appeared some years ago, before the author was aware of quant-ph. It is relevant to recent developments concerning Kochen-Specker theorem