@article{stallrich_allen-moyer_jones_2023, title={D- and A-Optimal Screening Designs}, ISSN={["1537-2723"]}, 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.}, journal={TECHNOMETRICS}, author={Stallrich, Jonathan and Allen-Moyer, Katherine and Jones, Bradley}, year={2023}, month={Apr} }
 @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{larsen_stallrich_sengupta_deng_kohavi_stevens_2023, title={Statistical Challenges in Online Controlled Experiments: A Review of A/B Testing Methodology}, volume={10}, ISSN={["1537-2731"]}, url={https://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.}, journal={AMERICAN STATISTICIAN}, author={Larsen, Nicholas and Stallrich, Jonathan and Sengupta, Srijan and Deng, Alex and Kohavi, Ron and Stevens, Nathaniel T.}, year={2023}, month={Oct} }
 @article{holter_stallrich_2023, title={Tuning parameter selection for penalized estimation via R2}, volume={183}, ISSN={["1872-7352"]}, 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{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}, ISSN={["1537-2731"]}, 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.}, journal={AMERICAN STATISTICIAN}, author={Allen-Moyer, Katherine and Stallrich, Jonathan}, year={2021}, month={Aug} }
 @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{winkel_stallrich_storlie_reich_2021, title={Sequential Optimization in Locally Important Dimensions}, volume={63}, ISSN={["1537-2723"]}, 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}, 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"]}, 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}, 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"]}, 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{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://dx.doi.org/10.1214/20-aoas1324}, 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{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={Abstract}, 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"]}, DOI={10.2460/ajvr.80.10.976}, abstractNote={Abstract}, 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{brandt_wen_liu_stallings_huang_2017, title={Interactions between transfemoral amputees and a powered knee prosthesis during load carriage}, volume={7}, journal={Scientific Reports}, author={Brandt, A. and Wen, Y. and Liu, M. and Stallings, J. and Huang, H. H.}, year={2017} }
 @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={https://doi.org/10.1007/s10664-016-9449-1}, 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{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"]}, 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"]}, 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} }
 @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"]}, 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"]}, 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"]}, 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{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"]}, 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} }