@article{young_weese_stallrich_smucker_edwards_2024, title={A graphical comparison of screening designs using support recovery probabilities}, volume={5}, ISSN={["2575-6230"]}, DOI={10.1080/00224065.2024.2356127}, abstractNote={A screening experiment attempts to identify a subset of important effects using a relatively small number of experimental runs. Given the limited run size and a large number of possible effects, penalized regression is a popular tool used to analyze screening designs. In particular, an automated implementation of the Gauss-Dantzig selector has been widely recommended to compare screening design construction methods. Here, we illustrate potential reproducibility issues that arise when comparing two-level screening designs via simulation, and recommend a graphical method, based on screening probabilities, which compares designs by evaluating them along the penalized regression solution path. This method can be implemented using simulation, or, in the case of lasso, by using exact local lasso sign recovery probabilities. Our approach circumvents the need to specify tuning parameters associated with regularization methods, leading to more reliable design comparisons. This article contains Supplementary Materials including code to implement the proposed methods.}, journal={JOURNAL OF QUALITY TECHNOLOGY}, author={Young, Kade and Weese, Maria L. and Stallrich, Jonathan W. and Smucker, Byran J. and Edwards, David J.}, year={2024}, month={May} } @article{stallrich_mckibben_2024, title={Optimal designs for two-stage inference}, volume={5}, ISSN={["2575-6230"]}, DOI={10.1080/00224065.2024.2351878}, abstractNote={The analysis of screening experiments is often done in two stages, starting with factor selection via an analysis under a main effects model. The success of this first stage is influenced by three components: (1) main effect estimators' variances and (2) bias, and (3) the estimate of the noise variance. Component (3) has only recently been given attention with design techniques that ensure an unbiased estimate of the noise variance. In this paper, we propose a design criterion based on expected confidence intervals of the first stage analysis that balances all three components. To address model misspecification, we propose a computationally-efficient all-subsets analysis and a corresponding constrained design criterion based on lack-of-fit. Scenarios found in existing design literature are revisited with our criteria and new designs are provided that improve upon existing methods.}, journal={JOURNAL OF QUALITY TECHNOLOGY}, author={Stallrich, Jonathan and McKibben, Michael}, year={2024}, month={May} } @article{stallrich_allen-moyer_jones_2023, title={D- and A- Optimal Screening Designs}, volume={65}, ISSN={0040-1706 1537-2723}, url={http://dx.doi.org/10.1080/00401706.2023.2183262}, DOI={10.1080/00401706.2023.2183262}, abstractNote={Abstract In practice, optimal screening designs for arbitrary run sizes are traditionally generated using the D-criterion with factor settings fixed at ±1, even when considering continuous factors with levels in . This article identifies cases of undesirable estimation variance properties for such D-optimal designs and argues that generally A-optimal designs tend to push variances closer to their minimum possible value. New insights about the behavior of the criteria are gained through a study of their respective coordinate-exchange formulas. The study confirms the existence of D-optimal designs comprised only of settings ±1 for both main effect and interaction models for blocked and unblocked experiments. Scenarios are also identified for which arbitrary manipulation of a coordinate between leads to infinitely many D-optimal designs each having different variance properties. For the same conditions, the A-criterion is shown to have a unique optimal coordinate value for improvement. We also compare how Bayesian versions of the A- and D-criteria balance minimization of estimation variance and bias. Multiple examples of screening designs are considered for various models under Bayesian and non-Bayesian versions of the A- and D-criteria.}, number={4}, journal={Technometrics}, publisher={Informa UK Limited}, author={Stallrich, Jonathan and Allen-Moyer, Katherine and Jones, Bradley}, year={2023}, month={Apr}, pages={492–501} } @article{larsen_stallrich_sengupta_deng_kohavi_stevens_2023, title={Statistical Challenges in Online Controlled Experiments: A Review of A/B Testing Methodology}, volume={78}, ISSN={0003-1305 1537-2731}, url={http://dx.doi.org/10.1080/00031305.2023.2257237}, DOI={10.1080/00031305.2023.2257237}, abstractNote={The rise of internet-based services and products in the late 1990's brought about an unprecedented opportunity for online businesses to engage in large scale data-driven decision making. Over the past two decades, organizations such as Airbnb, Alibaba, Amazon, Baidu, Booking, Alphabet's Google, LinkedIn, Lyft, Meta's Facebook, Microsoft, Netflix, Twitter, Uber, and Yandex have invested tremendous resources in online controlled experiments (OCEs) to assess the impact of innovation on their customers and businesses. Running OCEs at scale has presented a host of challenges requiring solutions from many domains. In this paper we review challenges that require new statistical methodologies to address them. In particular, we discuss the practice and culture of online experimentation, as well as its statistics literature, placing the current methodologies within their relevant statistical lineages and providing illustrative examples of OCE applications. Our goal is to raise academic statisticians' awareness of these new research opportunities to increase collaboration between academia and the online industry.}, number={2}, journal={The American Statistician}, publisher={Informa UK Limited}, author={Larsen, Nicholas and Stallrich, Jonathan and Sengupta, Srijan and Deng, Alex and Kohavi, Ron and Stevens, Nathaniel T.}, year={2023}, month={Oct}, pages={135–149} } @article{holter_stallrich_2023, title={Tuning parameter selection for penalized estimation via R2}, volume={183}, ISSN={["1872-7352"]}, url={https://doi.org/10.1016/j.csda.2023.107729}, DOI={10.1016/j.csda.2023.107729}, abstractNote={The tuning parameter selection strategy for penalized estimation is crucial to identify a model that is both interpretable and predictive. However, popular strategies (e.g., minimizing average squared prediction error via cross-validation) tend to select models with more predictors than necessary. A simple yet powerful cross validation strategy is proposed which is based on maximizing the squared correlation between the observed and predicted values, rather than minimizing squared error loss for the purposes of support recovery. The strategy can be applied to all penalized least-squares estimators and, under certain conditions, the metric implicitly performs a bias adjustment named the α-modification. When applied to the Lasso estimator, the α-modification is closely related to the relaxed Lasso estimator. The approach is demonstrated on a functional variable selection problem to identify optimal placement of surface electromyogram sensors to control a robotic hand prosthesis.}, journal={COMPUTATIONAL STATISTICS & DATA ANALYSIS}, author={Holter, Julia C. and Stallrich, Jonathan W.}, year={2023}, month={Jul} } @article{li_liu_si_stallrich_huang_2023, title={Hierarchical Optimization for Control of Robotic Knee Prostheses Toward Improved Symmetry of Propulsive Impulse}, volume={70}, ISSN={["1558-2531"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85142785855&partnerID=MN8TOARS}, DOI={10.1109/TBME.2022.3224026}, abstractNote={Automatically personalizing complex control of robotic prostheses to improve gait performance, such as gait symmetry, is challenging. Recently, human-in-the-loop (HIL) optimization and reinforcement learning (RL) have shown promise in achieving optimized control of wearable robots for each individual user. However, HIL optimization methods lack scalability for high-dimensional space, while RL has mostly focused on optimizing robot kinematic performance. Thus, we propose a novel hierarchical framework to personalize robotic knee prosthesis control and improve overall gait performance. Specifically, in this study the framework was implemented to simultaneously design target knee kinematics and tune 12 impedance control parameters for improved symmetry of propulsive impulse in walking. In our proposed framework, HIL optimization is used to identify an optimal target knee kinematics with respect to symmetry improvement, while RL is leveraged to yield an optimal policy for tuning impedance parameters in high-dimensional space to match the kinematics target. The proposed framework was validated on human subjects, walking with robotic knee prosthesis. The results showed that our design successfully shaped the target knee kinematics as well as configured 12 impedance control parameters to improve propulsive impulse symmetry of the human users. The knee kinematics that yielded best propulsion symmetry did not preserve the normative knee kinematics profile observed in non-disabled individuals, suggesting that restoration of normative joint biomechanics in walking does not necessarily optimize the gait performance of human-prosthesis systems. This new framework for prosthesis control personalization may be extended to other wearable devices or different gait performance optimization goals in the future.}, number={5}, journal={IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING}, author={Li, Minhan and Liu, Wentao and Si, Jennie and Stallrich, Jonathan W. and Huang, He}, year={2023}, month={May}, pages={1634–1642} } @article{arulalan_huayta_stallrich_san-miguel_2021, title={Antagonistic effects of chemical mixtures on the oxidative stress response are silenced by heat stress and reversed under dietary restriction}, volume={1}, ISSN={2635-2265}, url={http://dx.doi.org/10.1093/exposome/osab005}, DOI={10.1093/exposome/osab005}, abstractNote={Abstract Chemical agents released into the environment can induce oxidative stress in organisms, which is detrimental for health. Although environmental exposures typically include multiple chemicals, organismal studies on oxidative stress derived from chemical agents commonly study exposures to individual compounds. In this work, we explore how chemical mixtures drive the oxidative stress response under various conditions in the nematode Caenorhabditis elegans, by quantitatively assessing levels of gst-4 expression. Our results indicate that naphthoquinone mixtures drive responses differently than individual components, and that altering environmental conditions, such as increased heat and reduced food availability, result in dramatically different oxidative stress responses mounted by C. elegans. When exposed to heat, the oxidative stress response is diminished. Notably, when exposed to limited food, the oxidative stress response specific to juglone is significantly heightened, while identified antagonistic interactions between some naphthoquinone components in mixtures are abolished. This implies that organismal responses to xenobiotics are confounded by environment and stressor interactions. Given the high number of variables under study, and their potential combinations, a simplex centroid design was used to capture such non-trivial response over the design space. This makes the case for the adoption of Design of Experiments (DoE) approaches as they can greatly expand the experimental space probed in noisy biological readouts, and in combinatorial experiments. Our results also reveal gaps in our current knowledge of the organismal oxidative stress response, which can be addressed by employing sophisticated DoE approaches to identify significant interactions.}, number={1}, journal={Exposome}, publisher={Oxford University Press (OUP)}, author={Arulalan, Karthik Suresh and Huayta, Javier and Stallrich, Jonathan W and San-Miguel, Adriana}, year={2021}, month={Jan} } @article{estes_enomoto_moutos_carson_toth_eggert_stallrich_willard_veis_little_et al._2021, title={Biological resurfacing in a canine model of hip osteoarthritis}, volume={7}, ISSN={["2375-2548"]}, url={https://doi.org/10.1126/sciadv.abi5918}, DOI={10.1126/sciadv.abi5918}, abstractNote={A 3D woven scaffold seeded with MSCs was used to resurface the canine hip, reducing pain and improving joint function.}, number={38}, journal={SCIENCE ADVANCES}, publisher={American Association for the Advancement of Science (AAAS)}, author={Estes, Bradley T. and Enomoto, Masataka and Moutos, Franklin T. and Carson, Megan A. and Toth, Jeffrey M. and Eggert, Peter and Stallrich, Jonathan and Willard, Vincent P. and Veis, Deborah J. and Little, Dianne and et al.}, year={2021}, month={Sep} } @article{bergh_morrison_stallrich_short_cullum_leskey_2021, title={Border Habitat Effects on Captures of Halyomorpha halys (Hemiptera: Pentatomidae) in Pheromone Traps and Fruit Injury at Harvest in Apple and Peach Orchards in the Mid-Atlantic, USA}, volume={12}, ISSN={["2075-4450"]}, DOI={10.3390/insects12050419}, abstractNote={The invasive Halyomorpha halys invades crop fields from various bordering habitats, and its feeding on crops has caused significant economic losses. Thus, H. halys is considered a perimeter-driven threat, and research on alternative management tactics against it has focused on intervention at crop edges. Woodlands adjacent to crop fields contain many hosts of H. halys and are therefore considered “riskiest” in terms of pest pressure and crop injury. However, tree fruit orchards in the Mid-Atlantic, USA, are often bordered on one or more sides by woodlands and other habitats, including other tree fruit blocks, and field crops. Monitoring H. halys using pheromone traps has most often focused on the crop–woodland interface, but the relative effects of woodlands and other habitats bordering orchards on pest pressure and crop injury have not been examined. A two-year study comparing seasonal captures of H. halys and fruit injury among different habitats bordering commercial apple and peach orchards in the Mid-Atlantic revealed that while woodland borders often posed the greatest risk, other border habitats also contributed significantly to captures and injury in numerous instances. The relevance of these findings to refining and optimizing perimeter-based monitoring and management approaches for H. halys is discussed.}, number={5}, journal={INSECTS}, author={Bergh, James Christopher and Morrison, William R. I. I. I. I. I. I. and Stallrich, Jon W. and Short, Brent D. and Cullum, John P. and Leskey, Tracy C.}, year={2021}, month={May} } @article{allen-moyer_stallrich_2021, title={Incorporating Minimum Variances into Weighted Optimality Criteria}, volume={76}, ISSN={0003-1305 1537-2731}, url={http://dx.doi.org/10.1080/00031305.2021.1947375}, DOI={10.1080/00031305.2021.1947375}, abstractNote={Abstract Weighted optimality criteria allow an experimenter to express hierarchical interest across estimable functions through a concise weighting system. We show how such criteria can be implicitly influenced by the estimable functions’ minimum variances, leading to nonintuitive variance properties of the optimal designs. To address this, we propose a new optimality and evaluation approach that incorporates these minimum variances. A modified c-optimality criterion is introduced to calculate an estimable function’s minimum variance while requiring estimability of all other functions of interest. These minimum variances are then incorporated into a standardized weighted A-criterion that has an intuitive weighting system. We argue that optimal designs under this criterion tend to satisfy the conditions of a new design property we call weight adherence that sets appropriate expectations for how a given weighting system will influence variance properties. A practical, exploratory approach is then described for weighted optimal design generation and evaluation. Examples of the exploratory approach and weight adherence are provided for two types of factorial experiments.}, number={3}, journal={The American Statistician}, publisher={Informa UK Limited}, author={Allen-Moyer, Katherine and Stallrich, Jonathan}, year={2021}, month={Aug}, pages={262–269} } @article{gajjar_stallrich_pasquinelli_king_2021, title={Process-Property Relationships for Melt-Spun Poly(lactic acid) Yarn}, volume={6}, ISSN={["2470-1343"]}, url={https://doi.org/10.1021/acsomega.1c01557}, DOI={10.1021/acsomega.1c01557}, abstractNote={Poly(lactic acid) (PLA) is an attractive biomaterial due to its biocompatibility, biodegradability, and fiber-forming ability. However, the polymer is highly susceptible to both hydrolytic and thermal degradation during processing. Melt processing conditions typically involve high temperature and shear, whereas to prevent premature degradation, PLA needs to be processed under the mildest conditions that still yield the desired yarn properties. Thus, there is a need to determine the optimum processing conditions to achieve the desired properties of extruded PLA yarn. This study focuses on the effect of melt-spinning process parameters on the mechanical and physicochemical properties of the resulting PLA yarn and to derive their process–property relationships. The study compares the effect of process parameters like melt temperature, throughput through the spinneret, take-up speed at the wind-up roller, draw ratio, and drawing temperature on the yarn properties such as the yarn size (linear mass density), tenacity, elongation at break, crystallinity, and molecular weight. Depending on the combination of process parameters, the resulting PLA yarn had a yarn size ranging from 6.2 to 101.6 tex, tenacity ranging from 2.5 to 34.1 gf/tex, elongation at break ranging from 4 to 480%, and degree of crystallinity ranging from 14.6 to 62.2%. Certain combinations of processing parameters resulted in higher process-induced degradation, as evident from the reduction in molecular weight, ranging from 7.6% reduction to 20.5% reduction. Findings from this study increase our understanding on how different process parameters can be utilized to achieve the desired properties of the as-spun and drawn PLA yarn while controlling process-induced premature degradation.}, number={24}, journal={ACS OMEGA}, publisher={American Chemical Society (ACS)}, author={Gajjar, Chirag R. and Stallrich, Jon W. and Pasquinelli, Melissa A. and King, Martin W.}, year={2021}, month={Jun}, pages={15920–15928} } @article{stallrich_islam_staicu_crouch_pan_huang_2020, title={OPTIMAL EMG PLACEMENT FOR A ROBOTIC PROSTHESIS CONTROLLER WITH SEQUENTIAL, ADAPTIVE FUNCTIONAL ESTIMATION (SAFE)}, volume={14}, ISSN={["1932-6157"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85091110385&partnerID=MN8TOARS}, DOI={10.1214/20-AOAS1324}, abstractNote={Robotic hand prostheses require a controller to decode muscle contraction information, such as electromyogram (EMG) signals, into the user’s desired hand movement. State-of-the-art decoders demand extensive training, require data from a large number of EMG sensors, and are prone to poor predictions. Biomechanical models of a single movement degree-of-freedom tell us that relatively few muscles, and hence fewer EMG sensors, are needed to predict movement. We propose a novel decoder based on a dynamic, functional linear model with velocity or acceleration as its response and the recent past EMG signals as functional covariates. The effect of each EMG signal varies with the recent position to account for biomechanical features of hand movement, increasing the predictive capability of a single EMG signal compared to existing decoders. The effects are estimated with a multi-stage, adaptive estimation procedure we call Sequential Adaptive Functional Estimation (SAFE). Starting with 16 potential EMG sensors, our method correctly identifies the few EMG signals that are known to be important for an able-bodied subject. Furthermore, the estimated effects are interpretable and can significantly improve understanding and development of robotic hand prostheses.}, number={3}, journal={ANNALS OF APPLIED STATISTICS}, publisher={Institute of Mathematical Statistics}, author={Stallrich, Jonathan and Islam, Md Nazmul and Staicu, Ana-Maria and Crouch, Dustin and Pan, Lizhi and Huang, He}, year={2020}, month={Sep}, pages={1164–1181} } @article{winkel_stallrich_storlie_reich_2021, title={Sequential Optimization in Locally Important Dimensions}, volume={63}, ISSN={["1537-2723"]}, url={http://dx.doi.org/10.1080/00401706.2020.1714738}, DOI={10.1080/00401706.2020.1714738}, abstractNote={Abstract Optimizing an expensive, black-box function is challenging when its input space is high-dimensional. Sequential design frameworks first model with a surrogate function and then optimize an acquisition function to determine input settings to evaluate next. Optimization of both and the acquisition function benefit from effective dimension reduction. Global variable selection detects and removes input variables that do not affect across the input space. Further dimension reduction may be possible if we consider local variable selection around the current optimum estimate. We develop a sequential design algorithm called sequential optimization in locally important dimensions (SOLID) that incorporates global and local variable selection to optimize a continuous, differentiable function. SOLID performs local variable selection by comparing the surrogate’s predictions in a localized region around the estimated optimum with the p alternative predictions made by removing each input variable. The search space of the acquisition function is further restricted to focus only on the variables that are deemed locally active, leading to greater emphasis on refining the surrogate model in locally active dimensions. A simulation study across multiple test functions and an application to the Sarcos robot dataset show that SOLID outperforms conventional approaches. Supplementary materials for this article are available online.}, number={2}, journal={TECHNOMETRICS}, publisher={Informa UK Limited}, author={Winkel, Munir A. and Stallrich, Jonathan W. and Storlie, Curtis B. and Reich, Brian J.}, year={2021}, month={Apr}, pages={236–248} } @article{weese_stallrich_smucker_edwards_2021, title={Strategies for Supersaturated Screening: Group Orthogonal and Constrained Var(s) Designs}, volume={63}, ISSN={["1537-2723"]}, url={http://dx.doi.org/10.1080/00401706.2020.1850529}, DOI={10.1080/00401706.2020.1850529}, abstractNote={Abstract Despite the vast amount of literature on supersaturated designs (SSDs), there is a scant record of their use in practice. We contend this imbalance is due to conflicting recommendations regarding SSD use in the literature as well as the designs’ inabilities to meet practitioners’ analysis expectations. To address these issues, we first summarize practitioner concerns and expectations of SSDs as determined via an informal questionnaire. Next, we discuss and compare two recent SSDs that pair a design construction method with a particular analysis method. The choice of a design/analysis pairing is shown to depend on the screening objective. Group orthogonal SSDs, when paired with our new, modified analysis, are demonstrated to have high power even with many active factors. Constrained positive Var(s)-optimal designs, when paired with the Dantzig selector, are recommended when effect directions can be credibly specified in advance; this strategy reasonably controls Type I error rates while still identifying a high proportion of active factors.}, number={4}, journal={TECHNOMETRICS}, publisher={Informa UK Limited}, author={Weese, Maria L. and Stallrich, Jonathan W. and Smucker, Byran J. and Edwards, David J.}, year={2021}, month={Oct}, pages={443–455} } @article{jones_lekivetz_majumdar_nachtsheim_stallrich_2020, title={Construction, Properties, and Analysis of Group-Orthogonal Supersaturated Designs}, volume={62}, ISSN={["1537-2723"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85073934534&partnerID=MN8TOARS}, DOI={10.1080/00401706.2019.1654926}, abstractNote={Abstract In this article, we propose a new method for constructing supersaturated designs that is based on the Kronecker product of two carefully chosen matrices. The construction method leads to a partitioning of the factors of the design such that the factors within a group are correlated to the others within the same group, but are orthogonal to any factor in any other group. We refer to the resulting designs as group-orthogonal supersaturated designs. We leverage this group structure to obtain an unbiased estimate of the error variance, and to develop an effective, design-based model selection procedure. Simulation results show that the use of these designs, in conjunction with our model selection procedure enables the identification of larger numbers of active main effects than have previously been reported for supersaturated designs. The designs can also be used in group screening; however, unlike previous group-screening procedures, with our designs, main effects in a group are not confounded. Supplementary materials for this article are available online.}, number={3}, journal={TECHNOMETRICS}, author={Jones, Bradley and Lekivetz, Ryan and Majumdar, Dibyen and Nachtsheim, Christopher J. and Stallrich, Jonathan W.}, year={2020}, month={Jul}, pages={403–414} } @article{brandt_riddick_stallrich_lewek_huang_2019, title={Effects of extended powered knee prosthesis stance time via visual feedback on gait symmetry of individuals with unilateral amputation: a preliminary study}, volume={16}, ISSN={["1743-0003"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85072172371&partnerID=MN8TOARS}, DOI={10.1186/s12984-019-0583-z}, abstractNote={AbstractBackgroundEstablishing gait symmetry is a major aim of amputee rehabilitation and may be more attainable with powered prostheses. Though, based on previous work, we postulate that users transfer a previously-learned motor pattern across devices, limiting the functionality of more advanced prostheses. The objective of this study was to preliminarily investigate the effect of increased stance time via visual feedback on amputees’ gait symmetry using powered and passive knee prostheses.MethodsFive individuals with transfemoral amputation or knee disarticulation walked at their self-selected speed on a treadmill. Visual feedback was used to promote an increase in the amputated-limb stance time. Individuals were fit with a commercially-available powered prosthesis by a certified prosthetist and practiced walking during a prior visit. The same protocol was completed with a passive knee and powered knee prosthesis on separate days. We used repeated-measures, two-way ANOVA (alpha = 0.05) to test for significant effects of the feedback and device factors. Our main outcome measures were stance time asymmetry, peak anterior-posterior ground reaction forces, and peak anterior propulsion asymmetry.ResultsIncreasing the amputated-limb stance time via visual feedback significantly improved the stance time symmetry (p = 0.012) and peak propulsion symmetry (p = 0.036) of individuals walking with both prostheses. With the powered knee prosthesis, the highest feedback target elicited 36% improvement in stance time symmetry, 22% increase in prosthesis-side peak propulsion, and 47% improvement in peak propulsion symmetry compared to a no feedback condition. The changes with feedback were not different with the passive prosthesis, and the main effects of device/ prosthesis type were not statistically different. However, subject by device interactions were significant, indicating individuals did not respond consistently with each device (e.g. prosthesis-side propulsion remained comparable to or was greater with the powered versus passive prosthesis for different subjects). Overall, prosthesis-side peak propulsion averaged across conditions was 31% greater with the powered prosthesis and peak propulsion asymmetry improved by 48% with the powered prosthesis.ConclusionsIncreasing prosthesis-side stance time via visual feedback favorably improved individuals’ temporal and propulsive symmetry. The powered prosthesis commonly enabled greater propulsion, but individuals adapted to each device with varying behavior, requiring further investigation.}, number={1}, journal={JOURNAL OF NEUROENGINEERING AND REHABILITATION}, author={Brandt, Andrea and Riddick, William and Stallrich, Jonathan and Lewek, Michael and Huang, He Helen}, year={2019}, month={Sep} } @article{webster_marcellin-little_koballa_stallrich_harrysson_2019, title={Evaluation of the geometric accuracy of computed tomography and microcomputed tomography of the articular surface of the distal portion of the radius of cats}, volume={80}, ISSN={["1943-5681"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85072655250&partnerID=MN8TOARS}, DOI={10.2460/ajvr.80.10.976}, abstractNote={Abstract OBJECTIVE To evaluate accuracy of articular surfaces determined by use of 2 perpendicular CT orientations, micro-CT, and laser scanning. SAMPLE 23 cat cadavers. PROCEDURES Images of antebrachia were obtained by use of CT (voxel size, 0.6 mm) in longitudinal orientation (CTLO images) and transverse orientation (CTTO images) and by use of micro-CT (voxel size, 0.024 mm) in a longitudinal orientation. Images were reconstructed. Craniocaudal and mediolateral length, radius of curvature, and deviation of the articular surface of the distal portion of the radius of 3-D renderings for CTLO, CTTO, and micro-CT images were compared with results of 3-D renderings acquired with a laser scanner (resolution, 0.025 mm). RESULTS Measurement of CTLO and CTTO images overestimated craniocaudal and mediolateral length of the articular surface by 4% to 10%. Measurement of micro-CT images underestimated craniocaudal and mediolateral length by 1%. Measurement of CTLO and CTTO images underestimated mediolateral radius of curvature by 15% and overestimated craniocaudal radius of curvature by > 100%; use of micro-CT images underestimated them by 3% and 5%, respectively. Mean ± SD surface deviation was 0.26 ± 0.09 mm for CTLO images, 0.30 ± 0.28 mm for CTTO images, and 0.04 ± 0.02 mm for micro-CT images. CONCLUSIONS AND CLINICAL RELEVANCE Articular surface models derived from CT images had dimensional errors that approximately matched the voxel size. Thus, CT cannot be used to plan conforming arthroplasties in small joints and could lack precision when used to plan the correction of a limb deformity or repair of a fracture. }, number={10}, journal={AMERICAN JOURNAL OF VETERINARY RESEARCH}, author={Webster, Caroline E. and Marcellin-Little, Denis J. and Koballa, Erin M. and Stallrich, Jonathan W. and Harrysson, Ola L. A.}, year={2019}, month={Oct}, pages={976–984} } @article{martin_stallrich_bereman_2019, title={Mixture designs to investigate adverse effects upon co-exposure to environmental cyanotoxins}, volume={421}, ISSN={0300-483X}, url={http://dx.doi.org/10.1016/J.TOX.2019.04.013}, DOI={10.1016/j.tox.2019.04.013}, abstractNote={The goal of this study was to implement powerful mixture design techniques, commonly used in process optimization, to investigate enhanced adverse effects upon co-exposure to environmental cyanotoxins. Exposure to cyanobacteria, which are found ubiquitously in environmental water reservoirs, have been linked to several neurodegenerative diseases. Despite the known co-occurrence of various cyanotoxins, the majority of studies investigating this link have focused on the investigation of a single cyanotoxin, a noncanonical amino acid called β-methylamino-L-alanine (BMAA), which poorly recapitulates an actual environmental exposure. Interactions amongst cyanotoxic compounds is an area of great concern and remains poorly understood. To this end, we describe the use of a simplex axial mixture design to screen for interactive adverse effects of cyanotoxic mixtures. Using a combination of basic toxicity assays coupled with contemporary proteomic techniques, our results show the existence of a significant (p ≤ 0.01) interaction between BMAA and its isomers aminoethyl glycine (AEG) and 2,4-diaminobutyric acid (2,4DAB). Cyanotoxic mixtures significantly decreased cell viability by an average of 19% and increased caspases 3/7 activities by an average of 110% when compared to individual cyanotoxins (p ≤ 0.05). Cyanotoxic mixtures perturbed various biological pathways associated with neurodegeneration, including inhibition of protective autophagy and activation of mitochondrial dysfunction (z-score >|2|). Additionally, exposure to mixtures perturbed important upstream regulators involved in cellular dysfunction, morbidity, and development. Taken together, our results highlight: (1) the need to study combinations of cyanotoxins when investigating the link between cyanobacteria and neurodegenerative pathologies and (2) the application of design of experiment (DoE) as an efficient methodology to study mixtures of relevant environmental toxins.}, journal={Toxicology}, publisher={Elsevier BV}, author={Martin, Rubia M. and Stallrich, Jonathan and Bereman, Michael S.}, year={2019}, month={Jun}, pages={74–83} } @article{crouch_pan_filer_stallings_huang_2018, title={Comparing Surface and Intramuscular Electromyography for Simultaneous and Proportional Control Based on a Musculoskeletal Model: A Pilot Study}, volume={26}, ISSN={["1558-0210"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85050633647&partnerID=MN8TOARS}, DOI={10.1109/TNSRE.2018.2859833}, abstractNote={Simultaneous and proportional control (SPC) of neural-machine interfaces uses magnitudes of smoothed electromyograms (EMG) as control inputs. Though surface EMG (sEMG) electrodes are common for clinical neural-machine interfaces, intramuscular EMG (iEMG) electrodes may be indicated in some circumstances (e.g., for controlling many degrees of freedom). However, differences in signal characteristics between sEMG and iEMG may influence SPC performance. We conducted a pilot study to determine the effect of electrode type (sEMG and iEMG) on real-time task performance with SPC based on a novel 2-degree-of-freedom EMG-driven musculoskeletal model of the wrist and hand. Four able-bodied subjects and one transradial amputee performed a virtual posture matching task with either sEMG or iEMG. There was a trend of better task performance with sEMG than iEMG for both able-bodied and amputee subjects, though the difference was not statistically significant. Thus, while iEMG may permit targeted recording of EMG, its signal characteristics may not be as ideal for SPC as those of sEMG. The tradeoff between recording specificity and signal characteristics is an important consideration for development and clinical implementation of SPC for neural-machine interfaces.}, number={9}, journal={IEEE TRANSACTIONS ON NEURAL SYSTEMS AND REHABILITATION ENGINEERING}, author={Crouch, Dustin L. and Pan, Lizhi and Filer, William and Stallings, Jonathan W. and Huang, He}, year={2018}, month={Sep}, pages={1735–1744} } @article{reich_pacifici_stallings_2018, title={Integrating auxiliary data in optimal spatial design for species distribution modelling}, volume={9}, ISSN={["2041-2096"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85044859013&partnerID=MN8TOARS}, DOI={10.1111/2041-210X.13002}, abstractNote={Abstract Traditional surveys used to create species distribution maps and estimate ecological relationships are expensive and time consuming. Citizen science offers a way to collect a massive amount of data at negligible cost and has been shown to be a useful supplement to traditional analyses. However, there remains a need to conduct formal surveys to firmly establish ecological relationships and trends. In this paper, we investigate the use of auxiliary (e.g. citizen science) data as a guide to designing more efficient ecological surveys. Our aim is to explore the use of opportunistic data to inform spatial survey design through a novel objective function that minimizes misclassificaton rate (i.e. false positives and false negatives) of the estimated occupancy maps. We use an initial occupancy estimate from auxiliary data as the prior in a Bayesian spatial occupancy model, and an efficient posterior approximation that accounts for spatial dependence, covariate effects, and imperfect detection in an exchange algorithm to search for the optimal set of sampling locations to minimize misclassification rate. We examine the optimal design as a function of the detection rate and quality of the citizen‐science data, and compare this optimal design with several common ad hoc designs via an extensive simulation study. We then apply our method to eBird data for the brown‐headed nuthatch in the Southeast US. We argue that planning a survey with the use of auxiliary data improves estimation accuracy and may significantly reduce the costs of sampling. }, number={6}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Reich, Brian J. and Pacifici, Krishna and Stallings, Jonathan W.}, year={2018}, month={Jun}, pages={1626–1637} } @article{rahman_stallings_williams_2018, title={Poster: Defect Prediction Metrics for Infrastructure as Code Scripts in DevOps}, ISSN={["2574-1926"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85049668341&partnerID=MN8TOARS}, DOI={10.1145/3183440.3195034}, abstractNote={Use of infrastructure as code (IaC) scripts helps software teams manage their configuration and infrastructure automatically. Information technology (IT) organizations use IaC scripts to create and manage automated deployment pipelines to deliver services rapidly. IaC scripts can be defective, resulting in dire consequences, such as creating wide-scale service outages for end-users. Prediction of defective IaC scripts can help teams to mitigate defects in these scripts by prioritizing their inspection efforts. The goal of this paper is to help software practitioners in prioritizing their inspection efforts for infrastructure as code (IaC) scripts by proposing defect prediction model-related metrics. IaC scripts use domain specific languages (DSL) that are fundamentally different from object-oriented programming (OOP) languages. Hence, the OOP-based metrics that researchers used in defect prediction might not be applicable for IaC scripts. We apply Constructivist Grounded Theory (CGT) on defect-related commits mined from version control systems to identify metrics suitable for IaC scripts. By applying CGT, we identify 18 metrics. Of these metrics, 13 are related to IaC, for example, count of string occurrences in a script. Four of the identified metrics are related to churn, and one metric is lines of code.}, journal={PROCEEDINGS 2018 IEEE/ACM 40TH INTERNATIONAL CONFERENCE ON SOFTWARE ENGINEERING - COMPANION (ICSE-COMPANION}, author={Rahman, Akond and Stallings, Jonathan and Williams, Laurie}, year={2018}, pages={414–415} } @article{terrell_kofink_middleton_rainear_murphy-hill_parnin_stallings_2017, title={Gender differences and bias in open source: Pull request acceptance of women versus men}, volume={2017}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85028652618&partnerID=MN8TOARS}, DOI={10.7717/peerj-cs.111}, abstractNote={Biases against women in the workplace have been documented in a variety of studies. This paper presents a large scale study on gender bias, where we compare acceptance rates of contributions from men versus women in an open source software community. Surprisingly, our results show that women’s contributions tend to be accepted more often than men’s. However, for contributors who are outsiders to a project and their gender is identifiable, men’s acceptance rates are higher. Our results suggest that although women on GitHub may be more competent overall, bias against them exists nonetheless.}, number={5}, journal={PeerJ Computer Science}, author={Terrell, J. and Kofink, A. and Middleton, J. and Rainear, C. and Murphy-Hill, E. and Parnin, C. and Stallings, J.}, year={2017} } @article{brandt_wen_liu_stallings_huang_2017, title={Interactions Between Transfemoral Amputees and a Powered Knee Prosthesis During Load Carriage}, volume={7}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/S41598-017-14834-7}, DOI={10.1038/s41598-017-14834-7}, abstractNote={AbstractMachines and humans become mechanically coupled when lower limb amputees walk with powered prostheses, but these two control systems differ in adaptability. We know little about how they interact when faced with real-world physical demands (e.g. carrying loads). Here, we investigated how each system (i.e. amputee and powered prosthesis) responds to changes in the prosthesis mechanics and gravitational load. Five transfemoral amputees walked with and without load (i.e. weighted backpack) and a powered knee prosthesis with two pre-programmed controller settings (i.e. for load and no load). We recorded subjects’ kinematics, kinetics, and perceived exertion. Compared to the no load setting, the load setting reduced subjects’ perceived exertion and intact-limb stance time when they carried load. When subjects did not carry load, their perceived exertion and gait performance did not significantly change with controller settings. Our results suggest transfemoral amputees could benefit from load-adaptive powered knee controllers, and controller adjustments affect amputees more when they walk with (versus without) load. Further understanding of the interaction between powered prostheses, amputee users, and various environments may allow researchers to expand the utility of prostheses beyond simple environments (e.g. firm level ground without load) that represent only a subset of real-world environments.}, number={1}, journal={Scientific Reports}, publisher={Springer Nature}, author={Brandt, Andrea and Wen, Yue and Liu, Ming and Stallings, Jonathan and Huang, He Helen}, year={2017}, month={Nov} } @article{morgan_stallings_2017, title={Optimal experimental design that targets meaningful information}, volume={9}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85011665599&partnerID=MN8TOARS}, DOI={10.1002/wics.1393}, abstractNote={Computer generation of experimental designs, for reasons including flexibility, speed, and ease of access, is the first line of approach for many experimentalists. The algorithms generating designs in many popular software packages employ optimality functions to measure design effectiveness. These optimality functions make implicit assumptions about the goals of the experiment that are not always considered and which may be inappropriate as the basis for design selection. General weighted optimality criteria address this problem by tailoring design selection to a practitioner's research questions. Implementation of weighted criteria in some popular design software is easily accomplished. The technique is demonstrated for factorial designs and for designing experiments with a control treatment. WIREs Comput Stat 2017, 9:e1393. doi: 10.1002/wics.1393 This article is categorized under: Statistical Learning and Exploratory Methods of the Data Sciences > Knowledge Discovery}, number={2}, journal={Wiley Interdisciplinary Reviews: Computational Statistics}, author={Morgan, J.P. and Stallings, J.}, year={2017} } @inproceedings{riaz_stallings_singh_slankas_williams_2016, title={DIGS}, volume={08-09-September-2016}, ISBN={9781450344272}, url={http://dx.doi.org/10.1145/2961111.2962599}, DOI={10.1145/2961111.2962599}, abstractNote={Context: The security goals of a software system provide a foundation for security requirements engineering. Identifying security goals is a process of iteration and refinement, leveraging the knowledge and expertise of the analyst to secure not only the core functionality but the security mechanisms as well. Moreover, a comprehensive security plan should include goals for not only preventing a breach, but also for detecting and appropriately responding in case a breach does occur. Goal: The objective of this research is to support analysts in security requirements engineering by providing a framework that supports a systematic and comprehensive discovery of security goals for a software system. Method: We develop a framework, Discovering Goals for Security (DIGS), that models the key entities in information security, including assets and security goals. We systematically develop a set of security goal patterns that capture multiple dimensions of security for assets. DIGS explicitly captures the relations and assumptions that underlie security goals to elicit implied goals. We map the goal patterns to NIST controls to help in operationalizing the goals. We evaluate DIGS via a controlled experiment where 28 participants analyzed systems from mobile banking and human resource management domains. Results: Participants considered security goals commensurate to the knowledge available to them. Although the overall recall was low given the empirical constraints, participants using DIGS identified more implied goals and felt more confident in completing the task. Conclusion: Explicitly providing the additional knowledge for the identification of implied security goals significantly increased the chances of discovering such goals, thereby improving coverage of stakeholder security requirements, even if they are unstated.}, booktitle={Proceedings of the 10th ACM/IEEE International Symposium on Empirical Software Engineering and Measurement - ESEM '16}, publisher={ACM Press}, author={Riaz, Maria and Stallings, Jonathan and Singh, Munindar P. and Slankas, John and Williams, Laurie}, year={2016} } @article{brown_stallings_clay_rhoads_2016, title={Erratum: Periconceptional heat stress of holstein dams is associated with differences in daughter milk production and composition during multiple lactations (PLoS ONE (2016) 11:2)}, volume={11}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84960517181&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0150049}, number={2}, journal={PLoS ONE}, author={Brown, B.M. and Stallings, J.W. and Clay, J.S. and Rhoads, M.L.}, year={2016} } @article{bergh_stallings_2016, title={Field evaluations of the contribution of predators and the parasitoid, Aphelinus mali, to biological control of woolly apple aphid, Eriosoma lanigerum, in Virginia, USA}, volume={61}, ISSN={["1573-8248"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84960343039&partnerID=MN8TOARS}, DOI={10.1007/s10526-016-9714-7}, number={2}, journal={BIOCONTROL}, author={Bergh, J. Christopher and Stallings, Jon W.}, year={2016}, month={Apr}, pages={155–165} } @article{brown_stallings_clay_rhoads_2016, title={Periconceptional Heat Stress of Holstein Dams Is Associated with Differences in Daughter Milk Production during Their First Lactation}, volume={11}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84958998801&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0148234}, abstractNote={The fertility of lactating Holstein cows is severely reduced during periods of heat stress. Despite this reduction in fertility, however, some inseminations conducted during heat stress result in successful pregnancies from which heifer calves are born. Many of these heifer calves are retained and raised to enter the milking herd as replacement animals. Heat stress experienced by these females around the time they were conceived may confer long-lasting effects that alter subsequent milk production capacity. The objective of this study was to examine the relationship between periconceptional heat stress and subsequent milk production of primiparous cows. National Dairy Herd Improvement Association data was obtained from Dairy Records Management Systems. Records included Holstein cows that had completed at least one lactation in one of three states with large populations of dairy cattle and which are known for having hot, humid summers: Georgia, Florida or Texas. Dates of conception were calculated by subtracting 276 d from the recorded birth date of each individual cow. Records for cows conceived within the months of June, July, and August were retained as heat stress-conceived (HSC) cows (n = 94,440); cows conceived within the months of December, January, and February were retained as thermoneutral-conceived (TNC) contemporaries (n = 141,365). In order to account for the effects of environmental conditions on total milk production for a given lactation, cows were blocked by season of calving (winter, spring, summer or fall). Adjusted 305-day mature-equivalent milk production was evaluated with a mixed model ANOVA using SAS, in which random effects were used to account for variability between herds. Of the cows that calved in the summer, fall and winter, TNC cows had higher milk yield than the HSC cows in all states. Interestingly, the cows that calved in the spring presented a unique relationship, with HSC cows producing more milk. Overall however, heat stress at the time of conception is associated with lower milk production during the first lactation. While this association does not prove cause and effect, it does provide justification for additional investigation into whether heat stress around the time of conception results in long-term, detrimental consequences for the conceptus.}, number={2}, journal={PLOS ONE}, author={Brown, Britni M. and Stallings, Jon W. and Clay, John S. and Rhoads, Michelle L.}, year={2016}, month={Feb} } @inproceedings{mcnamara_verma_stallings_staddon_2016, title={Predicting mobile app privacy preferences with psychographics}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84999040303&partnerID=MN8TOARS}, DOI={10.1145/2994620.2994631}, abstractNote={Using a multi-country data set of over 600 survey participants, we show that psychographics and various attributes of the mobile app context are predictive of user privacy preferences. In particular, we find that a user's decision-making style is predictive of their privacy preferences, with users who are more independent decision makers tending to be more conservative about sharing personal information. We also provide additional insights into several of the privacy preference clusters identified in Lin et al.\@ 2014 by finding that users who are more privacy-concerned tend to be more knowledgeable of app privacy risks and more attentive to app permissions requests, and those individuals with less concern are more likely to trust well-known app companies.}, booktitle={WPES 2016 - Proceedings of the 2016 ACM Workshop on Privacy in the Electronic Society, co-located with CCS 2016}, author={McNamara, A. and Verma, A. and Stallings, J. and Staddon, J.}, year={2016}, pages={47–58} } @article{king_stallings_riaz_williams_2017, title={To log, or not to log: using heuristics to identify mandatory log events - a controlled experiment}, volume={22}, ISSN={["1573-7616"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84983464748&partnerID=MN8TOARS}, DOI={10.1007/s10664-016-9449-1}, number={5}, journal={EMPIRICAL SOFTWARE ENGINEERING}, author={King, Jason and Stallings, Jon and Riaz, Maria and Williams, Laurie}, year={2017}, month={Oct}, pages={2684–2717} } @article{hickey_hatch_stallings_wolf_2016, title={Under-Trellis Cover Crop and Rootstock Affect Growth, Yield Components, and Fruit Composition of Cabernet Sauvignon}, volume={67}, ISSN={["1943-7749"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84977595594&partnerID=MN8TOARS}, DOI={10.5344/ajev.2016.15079}, abstractNote={We compared the effectiveness of an under-trellis cover crop treatment (CC, Festuca rubra) and an 85-cm-wide herbicide-treated strip treatment (HTS) and rootstock (101-14, 420-A, or riparia) for regulating vegetative growth and improving fruit composition in Cabernet Sauvignon over a six- to seven-year period of data collection. The cover crop reduced average vine pruning weight by 26% and increased fruit exposure by 35% compared to the HTS floor management scheme. Vines grafted to riparia rootstock had pruning weights that were lower than those of vines grafted to 101-14 in two years; however, effects of rootstock were insignificant when averaged over the seven-year experiment. There was a measurable crop yield penalty for the CC floor management: vines grown with CC averaged 610 kg/ha/year lower crop yields, and had reduced cluster weight, berries per cluster, and berry weight compared to vines in the HTS floor management. Riparia rootstock increased berry weight, cluster weight, and crop yield per vine compared to 101-14. Fruit from vines grown with CC averaged greater soluble solids compared to vines grown with HTS. Rootstock 420-A produced fruit with lower pH than fruit from 101-14 or riparia vines. Compared to 420-A, inconsistent increases in grape anthocyanins and phenolics were observed in riparia (both) and 101-14 (phenolics only). The use of an under-trellis cover crop favorably reduced vine size, especially during the earlier years of the experiment.}, number={3}, journal={AMERICAN JOURNAL OF ENOLOGY AND VITICULTURE}, author={Hickey, Cain C. and Hatch, Tremain A. and Stallings, Jonathan and Wolf, Tony K.}, year={2016}, month={Jul}, pages={281–295} } @article{stallings_morgan_2015, title={General weighted optimality of designed experiments}, volume={102}, ISSN={["1464-3510"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84950335855&partnerID=MN8TOARS}, DOI={10.1093/biomet/asv037}, abstractNote={The standard approach to finding optimal experimental designs employs conventional measures of design efficacy, such as the $A$, $E$, and $D$-criterion, that assume equal interest in all estimable functions of model parameters. This paper develops a general theory for weighted optimality, allowing precise design selection according to expressed relative interest in different functions in the estimation space. The approach employs a very general class of matrix-specified weighting schemes that produce easily interpretable weighted optimality criteria. In particular, for any set of estimable functions, and any selected corresponding weights, analogs of standard optimality criteria are found that guide design selection according to the weighted variances of estimators of those particular functions. The results are applied to solve the $A$-optimal design problem for baseline factorial effects in unblocked experiments.}, number={4}, journal={BIOMETRIKA}, author={Stallings, J. W. and Morgan, J. P.}, year={2015}, month={Dec}, pages={925–935} } @article{brown_stallings_clay_rhoads_2015, title={Periconceptional Heat Stress of Holstein Dams Is Associated with Differences in Daughter Milk Production and Composition during Multiple Lactations}, volume={10}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84949921083&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0133574}, abstractNote={Heat stress at the time of conception affects the subsequent milk production of primiparous Holstein cows; however, it is unknown whether these effects are maintained across multiple lactations. Therefore, the objective of the current study was to examine the relationship between periconceptional heat stress and measurements of milk production and composition in cows retained within a herd for multiple lactations. National Dairy Herd Improvement Association data was obtained from Dairy Records Management Systems. Records included milk production data and milk composition data from over 75,000 and 44,000 Holstein cows, respectively, born between 2000 and 2010 in Florida, Georgia, and Texas. Conception dates were calculated by subtracting 276 d from the recorded birth date. Records for cows conceived within the months of June, July, and August were retained as heat stress conceived (HSC) cows; cows conceived within the months of December, January, and February were retained as thermoneutral conceived (TNC) contemporaries. Adjusted 305-d mature equivalent milk, protein percent and fat percent were evaluated with a mixed model ANOVA using SAS. Milk production was significantly affected by periconceptional heat stress. When a significant difference or tendency for a difference was detected between the HSC and TNC cows, the TNC produced more milk in all but one comparison. The advantage in milk production for the TNC cows over the HSC cows ranged from 82 ± 42 to 399 ± 61 kg per lactation. Alterations in fat and protein percentage were variable and most often detected in first lactations (first > second or third). Overall, the most striking result of this study is the consistency of the relationship between HSC and milk production. The nature of this relationship suggests that heat stress at or around the time of conception impairs cow milk yield throughout her lifetime.}, number={10}, journal={PLOS ONE}, author={Brown, Britni M. and Stallings, Jon W. and Clay, John S. and Rhoads, Michelle L.}, year={2015}, month={Oct} } @article{trumbo_nislow_stallings_hudy_smith_kim_wiggins_dolloff_2014, title={Ranking Site Vulnerability to Increasing Temperatures in Southern Appalachian Brook Trout Streams in Virginia: An Exposure-Sensitivity Approach}, volume={143}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84892401567&partnerID=MN8TOARS}, DOI={10.1080/00028487.2013.835282}, abstractNote={Abstract Models based on simple air temperature–water temperature relationships have been useful in highlighting potential threats to coldwater‐dependent species such as Brook Trout Salvelinus fontinalis by predicting major losses of habitat and substantial reductions in geographic distribution. However, spatial variability in the relationship between changes in air temperature to changes in water temperature complicates predictions. We directly measured paired summer air and water temperatures over 2 years in a stratified representative sample of watersheds (<1–274 km 2 ) supporting wild Brook Trout throughout Virginia near the southern edge of the species distribution. We used the temperature data to rank streams in terms of two important components of habitat vulnerability: sensitivity (predicted change in water temperature per unit increase in air temperature) and exposure (predicted frequency, magnitude, and duration of threshold water temperatures). Across all sites, sensitivity was substantially lower (median sensitivity = 0.35°C) than the 0.80°C assumed in some previous models. Median sensitivity across all sites did not differ between the 2 years of the study. In contrast, median exposure was considerably greater in 2010 (a particularly warm summer) than in 2009, but exposure ranks of habitat patches were highly consistent. Variation in sensitivity and exposure among habitat patches was influenced by landscape metrics (percent forested riparian corridor, patch area, and elevation), but considerable unexplained variation in sensitivity and exposure among sites was likely due to local‐scale differences in the extent of groundwater influence. Overall, our direct measurement approach identified significantly more Brook Trout habitat patches with low sensitivity and low exposure that may persist under warming air temperatures than did previous large‐scale models. Our sensitivity and exposure classification should provide a useful general framework for managers in making investment decisions for protecting and restoring Brook Trout habitat.}, number={1}, journal={Transactions of the American Fisheries Society}, author={Trumbo, B.A. and Nislow, K.H. and Stallings, J. and Hudy, M. and Smith, E.P. and Kim, D.-Y. and Wiggins, B. and Dolloff, C.A.}, year={2014}, pages={173–187} } @article{joseph_stallings_leskey_krawczyk_polk_butler_bergh_2014, title={Spatial Distribution of Brown Marmorated Stink Bug (Hemiptera: Pentatomidae) Injury at Harvest in Mid-Atlantic Apple Orchards}, volume={107}, ISSN={["1938-291X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84926656837&partnerID=MN8TOARS}, DOI={10.1603/ec14154}, abstractNote={ABSTRACT Brown marmorated stink bug, Halyomorpha halys (Stål), injury to late-season apple cultivars was measured at harvest in 2011 and 2012 in commercial orchards in four mid-Atlantic states. In each orchard block, a border zone (adjacent to woods), an interior zone (near orchard center), and an intermediate zone (between border and interior zones) comprised 1–3 tree rows per zone, depending on block size. Just before commercial harvest, 10 fruit were sampled from the upper, middle, and lower third of the canopy from five trees in each zone. After 3–5 wk in cold storage, fruit were examined for external and internal injury, and severity of internal injury (number of injury sites per fruit) from H. halys. A zero-inflated negative binomial model accounted for significant variation among the orchards and showed that apples from the upper canopy of border zone trees had the highest probability of experiencing external and internal injury. A minor interaction was detected among the orchards and zones for injury prevalence and severity, but there was no evidence of an orchard showing less expected injury in the border zone compared with other zones. Adjusting for orchard-to-orchard variation, differences in injury distributions among the zones and canopies were primarily due to injury prevalence rather than expected injury severity. The implications of these results to scouting and managing H. halys in eastern apple orchards are discussed.}, number={5}, journal={JOURNAL OF ECONOMIC ENTOMOLOGY}, author={Joseph, Shimat V. and Stallings, Jonathan W. and Leskey, Tracy C. and Krawczyk, Greg and Polk, Dean and Butler, Bryan and Bergh, J. Christopher}, year={2014}, month={Oct}, pages={1839–1848} } @article{stallings_2014, title={Type IV errors: How collaborations can lead to simpler analyses}, volume={440}, journal={AMSTAT News}, author={Stallings, J.W.}, year={2014}, pages={24–25} } @article{stallings_vance_yang_vannier_liang_pang_dai_ye_wang_2013, title={Determining scientific impact using a collaboration index}, volume={110}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84878999111&partnerID=MN8TOARS}, DOI={10.1073/pnas.1220184110}, abstractNote={Researchers collaborate on scientific projects that are often measured by both the quantity and the quality of the resultant peer-reviewed publications. However, not all collaborators contribute to these publications equally, making metrics such as the total number of publications and the H-index insufficient measurements of individual scientific impact. To remedy this, we use an axiomatic approach to assign relative credits to the coauthors of a given paper, referred to as the A-index for its axiomatic foundation. In this paper, we use the A-index to compute the weighted sums of peer-reviewed publications and journal impact factors, denoted as the C- and P-indexes for collaboration and productivity, respectively. We perform an in-depth analysis of bibliometric data for 186 biomedical engineering faculty members and from extensive simulation. It is found that these axiomatically weighted indexes better capture a researcher's scientific caliber than do the total number of publications and the H-index, allowing for fairer and sharper evaluation of researchers with diverse collaborative behaviors.}, number={24}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Stallings, J. and Vance, E. and Yang, J. and Vannier, M.W. and Liang, J. and Pang, L. and Dai, L. and Ye, I. and Wang, G.}, year={2013}, pages={9680–9685} } @article{neal_rossmeisl_robertson_arena_davis_singh_stallings_davalos_2013, title={Improved Local and Systemic Anti-Tumor Efficacy for Irreversible Electroporation in Immunocompetent versus Immunodeficient Mice}, volume={8}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0064559}, DOI={10.1371/journal.pone.0064559}, abstractNote={Irreversible electroporation (IRE) is a non-thermal focal ablation technique that uses a series of brief but intense electric pulses delivered into a targeted region of tissue, killing the cells by irrecoverably disrupting cellular membrane integrity. This study investigates if there is an improved local anti-tumor response in immunocompetent (IC) BALB/c versus immunodeficient (ID) nude mice, including the potential for a systemic protective effect against rechallenge. Subcutaneous murine renal carcinoma tumors were treated with an IRE pulsing protocol that used 60% of the predicted voltage required to invoke complete regressions in the ID mice. Tumors were followed for 34 days following treatment for 11 treated mice from each strain, and 7 controls from each strain. Mouse survival based on tumor burden and the progression-free disease period was substantially longer in the treated IC mice relative to the treated ID mice and sham controls for both strains. Treated IC mice were rechallenged with the same cell line 18 days after treatment, where growth of the second tumors was shown to be significantly reduced or prevented entirely. There was robust CD3+ cell infiltration in some treated BALB/C mice, with immunocytes focused at the transition between viable and dead tumor. There was no difference in the low immunocyte presence for untreated tumors, nude mice, and matrigel-only injections in both strains. These findings suggest IRE therapy may have greater therapeutic efficacy in immunocompetent patients than what has been suggested by immunodeficient models, and that IRE may invoke a systemic response beyond the targeted ablation region.}, number={5}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Neal, Robert E. and Rossmeisl, John H. and Robertson, John L. and Arena, Christopher B. and Davis, Erica M. and Singh, Ravi N. and Stallings, Jonathan and Davalos, Rafael V.}, editor={Rubinsky, BorisEditor}, year={2013}, month={May}, pages={e64559} } @article{morgan_stallings_2014, title={On the a criterion of experimental design}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84899925948&partnerID=MN8TOARS}, DOI={10.1080/15598608.2013.769922}, number={3}, journal={Journal of Statistical Theory and Practice}, author={Morgan, J.P. and Stallings, J.W.}, year={2014}, pages={418–422} } @article{wang_masters_hong_stallings_falkinham_edwards_pruden_2012, title={Effect of disinfectant, water age, and pipe material on occurrence and persistence of legionella, mycobacteria, pseudomonas aeruginosa, and two amoebas}, volume={46}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84868544334&partnerID=MN8TOARS}, DOI={10.1021/es303212a}, abstractNote={Opportunistic pathogens represent a unique challenge because they establish and grow within drinking water systems, yet the factors stimulating their proliferation are largely unknown. The purpose of this study was to examine the influence of pipe materials, disinfectant type, and water age on occurrence and persistence of three opportunistic pathogens (Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa), broader genera (Legionella and mycobacteria), and two amoeba hosts (Acanthamoeba spp. and Hartmanella vermiformis). Triplicate simulated distribution systems (SDSs) compared iron, cement, and PVC pipe materials fed either chlorinated or chloraminated tap water and were sampled at water ages ranging from 1 day to 5.7 days. Quantitative polymerase chain reaction quantified gene copies of target microorganisms in both biofilm and bulk water. Legionella, mycobacteria, P. aeruginosa, and both amoebas naturally colonized the six SDSs, but L. pneumophila and M. avium were not detected. Disinfectant type and dose was observed to have the strongest influence on the microbiota. Disinfectant decay was noted with water age, particularly in chloraminated SDSs (due to nitrification), generally resulting in increased microbial detection frequencies and densities with water age. The influence of pipe material became apparent at water ages corresponding to low disinfectant residual. Each target microbe appeared to display a distinct response to disinfectant type, pipe materials, water age, and their interactions. Differences between the first and the second samplings (e.g., appearance of Legionella, reduction in P. aeruginosa and Acanthamoeba) suggest a temporally dynamic drinking water microbial community.}, number={21}, journal={Environmental Science and Technology}, author={Wang, H. and Masters, S. and Hong, Y. and Stallings, J. and Falkinham, J.O. and Edwards, M.A. and Pruden, A.}, year={2012}, pages={11566–11574} }