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.

Systematic differences between Cochrane and non-Cochrane meta-analyses on the same topic: a matched pair analysis

BACKGROUND: Meta-analyses conducted via the Cochrane Collaboration adhere to strict methodological and reporting standards aiming to minimize bias, maximize transparency/reproducibility, and improve the accuracy of summarized data. Whether this results in differences in the results reported by meta-analyses on the same topic conducted outside the Cochrane Collaboration is an open question. METHODS: We conducted a matched-pair analysis with individual meta-analyses as the unit of analysis, comparing Cochrane and non-Cochrane reviews. Using meta-analyses from the cardiovascular literature, we identified pairs that matched on intervention and outcome. The pairs were contrasted in terms of how frequently results disagreed between the Cochrane and non-Cochrane reviews, whether effect sizes and statistical precision differed systematically, and how these differences related to the frequency of secondary citations of those reviews. RESULTS: Our search yielded 40 matched pairs of reviews. The two sets were similar in terms of which was first to publication, how many studies were included, and average sample sizes. The paired reviews included a total of 344 individual clinical trials: 111 (32.3%) studies were included only in a Cochrane review, 104 (30.2%) only in a non-Cochrane review, and 129 (37.5%) in both. Stated another way, 62.5% of studies were only included in one or the other meta-analytic literature. Overall, 37.5% of pairs had discrepant results. The most common involved shifts in the width of 95% confidence intervals that would yield a different statistical interpretation of the significance of results (7 pairs). Additionally, 20% differed in the direction of the summary effect size (5 pairs) or reported greater than a 2-fold difference in its magnitude (3 pairs). Non-Cochrane reviews reported significantly higher effect sizes (P < 0.001) and lower precision (P < 0.001) than matched Cochrane reviews. Reviews reporting an effect size at least 2-fold greater than their matched pair were cited more frequently. CONCLUSIONS: Though results between topic-matched Cochrane and non-Cochrane reviews were quite similar, discrepant results were frequent, and the overlap of included studies was surprisingly low. Non-Cochrane reviews report larger effect sizes with lower precision than Cochrane reviews, indicating systematic differences, likely reflective of methodology, between the two types of reviews that could generate different interpretations of the interventions under question

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

Systematic differences between Cochrane and non-Cochrane meta-analyses on the same topic: a matched pair analysis

BACKGROUND: Meta-analyses conducted via the Cochrane Collaboration adhere to strict methodological and reporting standards aiming to minimize bias, maximize transparency/reproducibility, and improve the accuracy of summarized data. Whether this results in differences in the results reported by meta-analyses on the same topic conducted outside the Cochrane Collaboration is an open question. METHODS: We conducted a matched-pair analysis with individual meta-analyses as the unit of analysis, comparing Cochrane and non-Cochrane reviews. Using meta-analyses from the cardiovascular literature, we identified pairs that matched on intervention and outcome. The pairs were contrasted in terms of how frequently results disagreed between the Cochrane and non-Cochrane reviews, whether effect sizes and statistical precision differed systematically, and how these differences related to the frequency of secondary citations of those reviews. RESULTS: Our search yielded 40 matched pairs of reviews. The two sets were similar in terms of which was first to publication, how many studies were included, and average sample sizes. The paired reviews included a total of 344 individual clinical trials: 111 (32.3%) studies were included only in a Cochrane review, 104 (30.2%) only in a non-Cochrane review, and 129 (37.5%) in both. Stated another way, 62.5% of studies were only included in one or the other meta-analytic literature. Overall, 37.5% of pairs had discrepant results. The most common involved shifts in the width of 95% confidence intervals that would yield a different statistical interpretation of the significance of results (7 pairs). Additionally, 20% differed in the direction of the summary effect size (5 pairs) or reported greater than a 2-fold difference in its magnitude (3 pairs). Non-Cochrane reviews reported significantly higher effect sizes (P < 0.001) and lower precision (P < 0.001) than matched Cochrane reviews. Reviews reporting an effect size at least 2-fold greater than their matched pair were cited more frequently. CONCLUSIONS: Though results between topic-matched Cochrane and non-Cochrane reviews were quite similar, discrepant results were frequent, and the overlap of included studies was surprisingly low. Non-Cochrane reviews report larger effect sizes with lower precision than Cochrane reviews, indicating systematic differences, likely reflective of methodology, between the two types of reviews that could generate different interpretations of the interventions under question

Variability in the reported management of pulmonary metastases in osteosarcoma.

Nearly 20% of patients with newly diagnosed osteosarcoma have detectable metastases at diagnosis; the majority of which occur in the lungs. There are no established recommendations for the timing and modality of metastasectomy. Members of the Connective Tissue Oncology Society (CTOS) were emailed an anonymous 10-min survey assessing their management practices for pulmonary findings at the time of an osteosarcoma diagnosis. The questionnaire presented three scenarios and discussed the choice to perform surgery, the timing of resection, and the choice of surgical procedure. Analyses were stratified by medical profession. One hundred and eighty-three physicians responded to our questionnaire. Respondents were comprised of orthopedic surgeons (37%), medical oncologists (31%), pediatric oncologists (22%), and other medical subspecialties (10%). There was variability among the respondents in the management of the pulmonary nodules. The majority of physicians chose to resect the pulmonary nodules following neoadjuvant chemotherapy (46-63%). Thoracotomy was the preferred technique for surgical resection. When only unilateral findings were present, the majority of physicians did not explore the contralateral lung. The majority of respondents did not recommend resection if the pulmonary nodule disappeared following chemotherapy. The survey demonstrated heterogeneity in the management of pulmonary metastases in osteosarcoma. Prospective trials need to evaluate whether these differences in management have implications for outcomes for patients with metastatic osteosarcoma

Effects of a single interprofessional simulation session on medical and nursing students’ attitudes toward interprofessional learning and professional identity: a questionnaire study

Background Participation in simulation-based interprofessional education (sim-IPE) may affect students’ attitudes towards interprofessional learning (through gaining experience with others) and their professional identity (by increasing the ‘fit’ of group membership). We examined this in two questionnaire studies involving students from four universities in two areas of the UK. Method Questionnaire data were collected before and after students took part in a sim-IPE session consisting of three acute scenarios. Questionnaires included the Readiness for Interprofessional Learning Scale (RIPLS) and measures of professional identity derived from the social identity theory literature. In Study 1, only identification with Professional Group (doctor or nurse) was measured, while in Study 2 identification with Student Group (medical or nursing student) and the immediate interprofessional Team worked with in the simulation were also measured. Linear mixed effects regression analysis examined the effect of the simulation session, and differences between medical and nursing students, sites and identity measures. Results A total of 194 medical and 266 nursing students completed questionnaires. A five-item subset of RIPLS (RIPLSCore) was used in analysis. In both studies RIPLSCore increased for all groups following participation in sim-IPE, although this was larger for nursing students in Study 1. Nursing students had consistently higher RIPLSCore scores than medical students at one site. Effects of the session on identity varied between sites, and dimensions of identity. Notably, while positive emotions associated with group membership (Ingroup Affect) increased for Student Group, Professional Group and Team, the sense of belonging (Ingroup Ties) and importance (Centrality) of the group increased only for Team. Nursing students had consistently higher identification scores than medical students. Conclusions Participation in a sim-IPE session can improve attitudes towards interprofessional learning. It can also enhance professional identity, particularly as related to emotional aspects of group membership, with possible benefits for wellbeing. Changes in identification with the immediate Team suggest positive psychological consequences of ad hoc Team formation in the workplace. Differences between medical and nursing students suggest their differing opportunities to work with other professions during training may change baseline attitudes and identity. However, a single sim-IPE session can still have an additive effect

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

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