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Editorial for the General Issue 6 (number 1) 2024, entitled ' Publishing & the Supporting the Academic'; written by David Allan, Judith Enrioquez, and Craig Hammond

For some individuals, rates of destructive behavior change in a predictable manner, irrespective of the contingencies programmed. Identifying such cyclical patterns can lead to better prediction of destructive behavior and may allow for the identification of relevant biological processes. However, identifying cyclical patterns of behavior can be difficult when using traditional methods of visual analysis. We describe a data-manipulation method, called data smoothing, in which one averages the data across time points within a specified window (e.g., 3, 5, or 7 days). This approach minimizes variability in the data and can increase the saliency of cyclical behavior patterns. We describe two cases for which we identified cyclical patterns in daily occurrences of destructive behavior, and we demonstrate the importance of analyzing smoothed data across various windows when using this approach. We encourage clinicians to analyze behavioral data in this way when rates vary independently of programmed contingencies and other potentially controlling variables have been ruled out (e.g., behavior variability related to sleep behavior). [ABSTRACT FROM AUTHOR]

This is the editorial article for the PRISM General Issue: Volume 5, Issue 1 (2023)

Neoantigen immunogenicity prediction is a highly challenging problem in the development of personalised medicines. Low reactivity rates in called neoantigens result in a difficult prediction scenario with limited training datasets. Here we describe ImmugenX, a modular protein language modelling approach to immunogenicity prediction for CD8+ reactive epitopes. ImmugenX comprises of a pMHC encoding module trained on three pMHC prediction tasks, an optional TCR encoding module and a set of context specific immunogenicity prediction head modules. Compared with state-of-the-art models for each task, ImmugenX's encoding module performs comparably or better on pMHC binding affinity, eluted ligand prediction and stability tasks. ImmugenX outperforms all compared models on pMHC immunogenicity prediction (Area under the receiver operating characteristic curve = 0.619, average precision: 0.514), with a 7% increase in average precision compared to the next best model. ImmugenX shows further improved performance on immunogenicity prediction with the integration of TCR context information. ImmugenX performance is further analysed for interpretability, which locates areas of weakness found across existing immunogenicity models and highlight possible biases in public datasets. Author summary: Accurate prediction of neoantigen immunogenicity has the potential to greatly improve the effectiveness of targeted therapies for cancer. While there are a number of associated tasks, such as peptide-HLA elution prediction, which can be now predicted with high accuracy by a number of published models, direct prediction of which epitopes will produce an immune response has proven more difficult. In this paper we demonstrate a modular protein language model approach which is trained iteratively to include data from related sub-tasks and can be extended to include information such as candidate TCRs of interest when available. There is a relatively small amount of immunogenicity data available, with even less data available with paired TCRs. This makes directly training a model to predict immunogenicity challenging. Our approach has the advantage of utilising data from sub-tasks and masked language modelling to allow for training a highly performant model with a small dataset. Using a cancer-specific benchmarking dataset we show this approach improves on existing state-of-the-art models and can be improved further with the addition of TCR context. This provides a framework that can serve as the basis for utilising additional information sources and datasets as they become available. [ABSTRACT FROM AUTHOR]

Pancarpal arthrodesis was performed in 21 dogs, using orthogonal (cranial/dorsal and medial) plates without postoperative rigid external coaptation. Short-term and long-term outcomes, arthrodesis progression, and complications were assessed using a retrospective review of case records and radiographs. Three of 21 (14.2%) dogs required a revision surgery: 2 had total implant explantation and 1 had a screw removed. Other complications were managed successfully medically. One of 21 (4.8%) dogs had confirmed deep surgical site infection requiring implant removal, and 4 of 21 (19%) had suspected (not confirmed on microbiology) superficial surgical site infections that resolved with medical management. Long-term outcomes were assessed via owner questionnaire (Canine Brief Pain Inventory) and were available for nine dogs at a mean of 26.78 mo after surgery. The mean score for the first part (assessment of pain) was 7.83/40, which is classified as no pain to mild pain. The mean score for the second part (assessment of function) was 12.67/60, which is classified as very good. The last part (overall impression) was defined as excellent in four dogs (44.44%), very good in one dog (11.11%), and good in the other four dogs (44.44%). This retrospective study documents a suitable technique for pancarpal arthrodesis in dogs with carpal injuries. [ABSTRACT FROM AUTHOR]

Background: Pelvic exenteration for rectal cancer involves a radical multi‐visceral resection to improve complete surgical clearance, and access is limited within Queensland. Methods: A retrospective review of a prospective database of the referrals to the pelvic exenteration service in the Royal Brisbane and Women's Hospital from 2009 to2023. Geographic, as well as clinical and demographic information was collected. Results: One hundred and seventy six patients were referred to the pelvic exenterations service. In total 93 patients were referred from a major city, 52 from inner regional areas, and 31 from outer regional or remote areas. One hundred and three referred patients (58.5%) proceeded to surgery, significantly more of whom were referred from a major city (P < 0.001). Of the patients referred from outer regional, inner regional, and major cities, a similar proportion of patients proceeded to surgery (55%, 52%, and 63.4%). Patients not proceeding to surgery in major cities and inner regional areas were most commonly unfit to proceed, whereas in outer regional areas most patients decided against surgery (61.5%). In the 14‐year period, overall referrals increased, with inner regional referrals increasing the most over time. Overall survival was not significantly impacted by remoteness. Conclusion: Awareness of the pelvic exenteration service in regional Queensland may have resulted in less referrals to the service. It is important to confirm a broad‐reaching service to optimize patient care. [ABSTRACT FROM AUTHOR]

In treatments based on differential reinforcement of alternative behavior, applied researchers and clinicians often provide multiple, qualitatively different reinforcers (i.e., synthesized reinforcement) rather than a single reinforcer (i.e., isolated reinforcement) contingent on alternative behavior. Some research shows that providing synthesized reinforcement for alternative responses within such treatments produces more rapid and complete suppression of target behavior; however, there is limited research evaluating the durability of these effects during treatment disruptions. Conceptual explanations of resurgence (e.g., resurgence as choice, context theory) suggest that treatments that include synthesized alternative reinforcement may lead to more resurgence of target behavior when alternative reinforcement is disrupted relative to treatments using isolated reinforcement. We evaluated this hypothesis within a three‐phase resurgence evaluation. We exposed rats to isolated or synthesized reinforcement for alternative responding in the second phase, and we exposed rats to extinction in the third phase. Synthesized alternative reinforcement produced more rapid and complete suppression of target behavior than did isolated reinforcement in the second phase; however, exposure to extinction following synthesized reinforcement produced more resurgence. We discuss these results in terms of their implications for applied research and their support for current conceptual explanations for resurgence. [ABSTRACT FROM AUTHOR]

Highlights Accurate discharge estimation is important when evaluating edge-of-field conservation practices. V-notch weir equations were developed for three sizes of subsurface drainage water level control structures. Compound weir equations were developed for subsurface drainage water level control structures. The compound weir equation accurately estimates discharge for flows within and overtopping the V-notch. Numerous edge-of-field conservation practices use subsurface drainage water level control structures to monitor water levels and estimate discharge. In a control structure, procedures for calculating discharge when flow depth (head) exceeds the V-notch depth and overflows in the rectangular portion of the compound weir (CW) are ambiguous. In this study, we developed calibration equations for V-notch weirs in Agri Drain inline water level control structures of different sizes for flows within the V-notch and overtopping flow events. The discharge equation for overtopping events (QCW, L s-1) was determined as: QCW = a1(hb1-h1b1)+a2(We-Wv)h1b2, where h and h1 are heads above vertex/bottom and top of V-notch (cm), respectively, W is the effective crest width of rectangular weir (cm), Wv is the top width of V-notch (cm), a1 and b1 are parameters for V-notch weir obtained by calibration, and a2 and b2 are calibration parameters for rectangular weir obtained from literature. Results were compared with a weir equation available in the literature (QV+R), which combines a V-notch equation with a head equal to V-depth and a rectangular weir equation for flow above V-depth. Discharge at overflow was estimated with high accuracy with QCW, whereas QV+R underestimated discharge (e.g., PBIAS of 0.67% vs. 17.82% for a 15.2 cm structure). An example using QV+R resulted in a 14% lower annual estimation of nitrate-N load diverted to a saturated buffer than QCW due to underestimation of drainage discharge during overflow events. Results suggest that the developed equation (QCW) accurately estimates discharge and will thus improve the estimated N load compared to QV+R. [ABSTRACT FROM AUTHOR]

Researchers have investigated several schedule‐thinning approaches during functional communication training (FCT), including FCT with delay schedules (Delay FCT), FCT with discriminative stimuli (Signaled FCT), and FCT with delay‐and‐denial tolerance training (DDTT). Despite many publications on these approaches, it is unclear how regularly, how often, and under what conditions behavior analysts use these FCT thinning strategies. We analyzed survey data from 129 board‐certified behavior analysts® to determine (a) how often they use the three thinning approaches during FCT, (b) their most preferred thinning method, and (c) the variables (e.g., years of experience, treatment setting) associated with their most used and preferred approaches. DDTT was the most commonly implemented and preferred FCT thinning strategy. Relative to DDTT, Signaled FCT was more frequently used and preferred by doctoral‐level behavior analysts and those working in clinical settings. However, regardless of approach, behavior analysts reported several challenges that hold implications for practice and research. [ABSTRACT FROM AUTHOR]