Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.

Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PAPERCLIP.

An atlas of combinatorial transcriptional regulation in mouse and man.

Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.

Examining cognitive accessibility of the VIA Inventory of Strengths for adults with intellectual disability.

BACKGROUND: We evaluated cognitive accessibility of the VIA Inventory of Strengths Youth short form with adults with intellectual disability for use in strengths-based practice. METHODS: We conducted cognitive testing with adults with intellectual disability (n = 33; M age = 36.2; range: 20.4-64.2). Data were coded for the extent to which (1) items were interpreted correctly; (2) participants endorsed items as describing themselves. We calculated descriptive statistics to evaluate item interpretation and response scale use. RESULTS: On average, 59% of participants interpreted items correctly, 20% misinterpreted items, 14% had mixed interpretations. Positive item endorsement was most associated with the response 'Very much like me' (77%); mixed endorsement was most associated with 'Somewhat like me' (39%); and negative endorsement of items was most associated with 'Not at all like me' (54%). CONCLUSIONS: Revisions are necessary for several items to improve accessibility for adults with intellectual disability and should be made in collaboration with this population.

Interpretability and Clinical Utility of the Pediatric Evaluation of Disability Inventory - Patient Reported Outcome (PEDI-PRO) Score Report.

AIMS: Well-designed score reports can support therapists to accurately interpret assessments. We piloted a score report for the Pediatric Evaluation Disability Inventory-Patient Reported Outcome (PEDI-PRO) and evaluated: 1) To what extent can occupational and physical therapists (OT, PT) accurately interpret item-response theory (IRT)-based PEDI-PRO assessment results? 2) What is the perceived clinical utility of the pilot score report? METHODS: Exploratory, sequential mixed methods design. Focus groups with OT and PTs (n = 20) informed the development of the final score report; revisions were made in response to feedback. Next, OTs and PTs (n = 33) reviewed score reports from two fictional clients and answered survey questions about the interpretation of the PEDI-PRO results. Additional questions evaluated clinical utility. RESULTS: Focus groups: Visual cues supported score interpretation, but therapists requested additional explanations for advanced IRT measurement concepts. Survey: Therapists accurately interpreted foundational IRT concepts (e.g. identifying most/least difficult items, highest scores), but were less accurate when interpreting advanced concepts (e.g. fit, unexpected responses). Therapists anticipated sharing different components of the score report with family members, clinicians, and payers to support their clinical practice. CONCLUSIONS: The pilot PEDI-PRO score report was highly endorsed by therapists, but therapists may need additional training to interpret advanced IRT concepts.

Deciphering the "Art" in Modeling and Simulation of the Knee Joint: Assessing Model Calibration Workflows and Outcomes.

Model reproducibility is a point of emphasis for the National Institutes of Health (NIH) and in science, broadly. As the use of computational modeling in biomechanics and orthopedics grows, so does the need to assess the reproducibility of modeling workflows and simulation predictions. The long-term goal of the KneeHub project is to understand the influence of potentially subjective decisions, thus the modeler's "art", on the reproducibility and predictive uncertainty of computational knee joint models. In this paper, we report on the model calibration phase of this project, during which five teams calibrated computational knee joint models of the same specimens from the same specimen-specific joint mechanics dataset. We investigated model calibration approaches and decisions, and compared calibration workflows and model outcomes among the teams. The selection of the calibration targets used in the calibration workflow differed greatly between the teams and was influenced by modeling decisions related to the representation of structures, and considerations for computational cost and implementation of optimization. While calibration improved model performance, differences in the postcalibration ligament properties and predicted kinematics were quantified and discussed in the context of modeling decisions. Even for teams with demonstrated expertise, model calibration is difficult to foresee and plan in detail, and the results of this study underscore the importance of identification and standardization of best practices for data sharing and calibration.

'Being a part of something': Experiences and perceived benefits of young adult peer mentors with intellectual/developmental disabilities and co-occurring mental health conditions.

BACKGROUND: Peer-provided services are a common model for addressing mental health concerns. Peer providers report a range of benefits and challenges associated with their role. However, there is little information about the experiences of peer providers with intellectual/developmental disabilities. AIM: To explore the experiences of young adult peer-providers with intellectual/developmental disabilities in the context of a mental health intervention. METHODS: We conducted interviews with four young adults with intellectual/developmental disabilities and their parents and teachers to understand their experiences providing a peer mentoring mental health intervention. RESULTS: Young adult peer mentors perceived themselves as responsible for maintaining the mentoring relationship, delivering the intervention and acting as helpers and independent professionals. The experiences of young adult peer mentors were driven by the temporal, institutional and social contexts of their work. Peer mentoring was an enjoyable, social activity. Mentors, parents and teachers emphasised how taking on the peer mentoring role during the transition to adulthood and within the capital-rich university context led to a sense of pride and professional development. Further, these contexts may have led mentors to emphasise their intervention-delivery, helper and professional roles over relationship maintenance. DISCUSSION & CONCLUSION: Context may shape the perceived roles and benefits for young adult peer mentors with intellectual/developmental disabilities.

Developing and evaluating a toolkit of strategies to support remote inclusive research teams.

Research teams must collaborate with people with intellectual and developmental disabilities to identify effective and inclusive responses to the COVID-19 pandemic and other public health emergencies. Collaborating remotely requires telecommunication and other technologies. We designed and evaluated a digital "Toolkit for Remote Inclusive Research" to provide research teams with evidence-informed strategies to make remote research accessible to and inclusive of people with intellectual and developmental disabilities. First, we completed a rapid scoping review to identify technology used by people with intellectual and developmental disabilities on collaborative research teams. Second, we designed a digital toolkit featuring 23 strategies identified in the review. Third, six inclusive researchers evaluated the toolkit. We illustrate how our team used these evidence-informed strategies during the past year to develop this and other tools to support inclusive research.

Supporting young adults with intellectual/developmental disabilities to deliver a peer mentoring intervention: Evaluating fidelity and resources required.

BACKGROUND: Peer-delivered interventions are a best practice in mental health, yet no such intervention exists for young adults (YA) with intellectual/developmental disabilities with co-occurring mental health conditions. We evaluated YA with intellectual/developmental disabilities' ability to deliver a novel peer mentoring intervention with fidelity and the supports received. METHODS: We coded audio-recorded mentoring sessions to evaluate if 4 mentors adhered to 'content' (e.g., psychoeducation) and 'quality' (e.g., validation) fidelity criteria (codes: yes/no). We conducted content analysis of mentor support logs and interviews with mentors', mentors' parents and teachers to describe the supports mentors received. RESULTS: Average fidelity for content criteria (M = 73.3%) was higher than quality criteria (M = 60.0%). Weekly support addressed logistics, delivering content, interpersonal interactions, emotional support, professionalism, and organisation. Family members and teachers rarely provided additional support. CONCLUSIONS: With support, YA can deliver a peer mentoring intervention addressing mental health. Additional training activities will be developed to improve fidelity.

How people with intellectual and developmental disabilities on collaborative research teams use technology: A rapid scoping review.

BACKGROUND: We conducted a rapid scoping review to identify how inclusive research teams use technology during the research process that could support remote collaboration during public health emergencies like the COVID-19 pandemic. METHOD: We searched three databases and conducted a hand search. Two independent reviewers screened 1498 abstracts and titles for inclusion criteria; 81 full text articles were further reviewed; 47 were included. We extracted information about each type of technology, categorised technology used during the research process, and documented described accommodations. RESULTS: We identified 47 articles and 94 examples of technologies used by people with intellectual and developmental disabilities throughout the research process: team formation and team function (38), data collection (19), data analysis (17) and dissemination (20). CONCLUSIONS: Technology use by team members with intellectual and developmental disabilities demonstrates promise for remote research collaborations during public health and climate emergencies and teams with members living in diverse locations.

Neutrophil to lymphocyte ratio and risk of neoplastic progression in patients with Barrett's esophagus.

BACKGROUND: Patient's with Barrett's esophagus (BE) are at risk of progression to esophageal adenocarcinoma (EAC). Neutrophil to lymphocyte ratio (NLR) was found to be a predictor of poor prognosis in patients with EAC; however, its performance in premalignant esophageal lesions is vague. We aimed to evaluate the utility of NLR as a predictor of histologic progression in patients with BE. METHODS : A prospective cohort of patients with proven BE in a tertiary referral center was retrospectively analyzed. All biopsies were reviewed by an expert gastrointestinal pathologist. The discriminatory capacity of NLR was evaluated by area under the receiver operating characteristic (AUC) curve analysis and Cox regression analysis. RESULTS: 324 patients (mean age 62.3 years, 241 [74.4 %] males) were included in the final analysis. Overall, 13 patients demonstrated histologic progression to neoplasia over a mean follow-up of 3.7 years (progression risk 1.0 % per year). The AUC of NLR for progression to high grade dysplasia (HGD) or EAC was 0.88 (95 % confidence interval [CI] 0.83 - 0.96), and baseline NLR was associated with a 3-fold increase of progression to HGD and EAC during follow-up (hazard ratio [HR] 3.2, 95 %CI 1.5 - 5.8; P < 0.001). Notably, in a subgroup analysis of patients with nondysplastic BE (NDBE) at presentation, NLR was also a risk factor for histologic progression (HR 2.4, 95 %CI 1.7 - 3.4; P < 0.001). CONCLUSION: NLR predicted histologic progression in patients with BE. Patients with NDBE and NLR above 2.4 can be considered for specific surveillance programs with shorter intervals between sessions.

A Method to Compare Heterogeneous Types of Bone and Cartilage Meshes.

Accurately capturing the bone and cartilage morphology and generating a mesh remains a critical step in the workflow of computational knee joint modeling. Currently, there is no standardized method to compare meshes of different element types and nodal densities, making comparisons across research teams a significant challenge. The aim of this paper is to describe a method to quantify differences in knee joint bone and cartilages meshes, independent of bone and cartilage mesh topology. Bone mesh-to-mesh distances, subchondral bone boundaries, and cartilage thicknesses from meshes of any type of mesh are obtained using a series of steps involving registration, resampling, and radial basis function fitting after which the comparisons are performed. Subchondral bone boundaries and cartilage thicknesses are calculated and visualized in a common frame of reference for comparison. The established method is applied to models developed by five modeling teams. Our approach to obtain bone mesh-to-mesh distances decreased the divergence seen in selecting a reference mesh (i.e., comparing mesh A-to-B versus mesh B-to-A). In general, the bone morphology was similar across teams. The cartilage thicknesses for all models were calculated and the mean absolute cartilage thickness difference was presented, the articulating areas had the best agreement across teams. The teams showed disagreement on the subchondral bone boundaries. The method presented in this paper allows for objective comparisons of bone and cartilage geometry that is agnostic to mesh type and nodal density.

Deciphering the "Art" in Modeling and Simulation of the Knee Joint: Variations in Model Development.

The use of computational modeling to investigate knee joint biomechanics has increased exponentially over the last few decades. Developing computational models is a creative process where decisions have to be made, subject to the modelers' knowledge and previous experiences, resulting in the "art" of modeling. The long-term goal of the KneeHub project is to understand the influence of subjective decisions on the final outcomes and the reproducibility of computational knee joint models. In this paper, we report on the model development phase of this project, investigating model development decisions and deviations from initial modeling plans. Five teams developed computational knee joint models from the same dataset, and we compared each teams' initial uncalibrated models and their model development workflows. Variations in the software tools and modeling approaches were found, resulting in differences such as the representation of the anatomical knee joint structures in the model. The teams consistently defined the boundary conditions and used the same anatomical coordinate system convention. However, deviations in the anatomical landmarks used to define the coordinate systems were present, resulting in a large spread in the kinematic outputs of the uncalibrated models. The reported differences and similarities in model development and simulation presented here illustrate the importance of the "art" of modeling and how subjective decision-making can lead to variation in model outputs. All teams deviated from their initial modeling plans, indicating that model development is a flexible process and difficult to plan in advance, even for experienced teams.

Adoption of patient-reported outcome measures with youth with intellectual/developmental disabilities: Contextual influences and practice patterns.

BACKGROUND: The purpose of this study was to identify potential barriers to patient reported outcome measure (PROM) adoption with youth and young adults with intellectual and/or developmental disabilities (IDD) and to understand current PROM adoption patterns of paediatric practitioners working with this population. METHODS: We used a web-based survey to collect data from paediatric practitioners who work with youth with IDD about factors influencing the adoption of PROMs and the frequency of PROM use across age groups (elementary, middle school and high school/transition age) and practice settings (school and rehabilitation). RESULTS: A total of 113 paediatric practitioners (occupational therapist = 48, physical therapist = 32, physician = 16, other = 17) responded to the survey with an average of 15 years of experience working with youth ages 8-21 with IDD. Accessibility and appropriateness, psychometric evidence, and time were most frequently ranked among the top three factors that influence practitioners' adoption of PROMs. Practitioners reported 'never or rarely' using PROMs 39%-65% of the time across age groups. CONCLUSIONS: Our results suggest that paediatric practitioners may be infrequently using PROMs with youth with IDD because of perceived inaccessibility and time requirements of PROMs and practice-environment barriers, including access to evidence and caseload demands. Because PROMs can facilitate client-centred care, addressing these potential barriers to adoption may improve paediatric rehabilitation.

Usability and Reliability of an Accessible Patient-Reported Outcome Measure (PROM) Software: The Pediatric Evaluation of Disability Inventory-Patient-Reported Outcome (PEDI-PRO).

IMPORTANCE: Patient-reported outcome measures (PROMs) are used in rehabilitation to evaluate outcomes. We integrated a new PROM for transition-age youth with intellectual and/or developmental disabilities (IDD), the Pediatric Evaluation of Disability Inventory-Patient-Reported Outcome (PEDI-PRO), with a computer-delivered survey platform (Accessible Testing Learning and Assessment System) to enhance cognitive accessibility. OBJECTIVE: To evaluate the usability of the PEDI-PRO software and to investigate its reliability and acceptability to transition-age youth with IDD. DESIGN: Clinical field testing and a survey; repeated-observation test-retest design. SETTING: Clinicians evaluated the PEDI-PRO's usability in school and health care contexts; research staff conducted reliability and acceptability testing in natural settings. PARTICIPANTS: Occupational therapists (n = 12) and physical therapists (n = 2) administered the PEDI-PRO to 39 youths with IDD. Fifty-five transition-age youth with IDD (M age = 19.7) completed the PEDI-PRO twice. OUTCOMES AND MEASURES: Clinicians completed the System Usability Survey (SUS) and open-ended feedback. Youth provided feedback via a brief survey. RESULTS: The mean SUS rating was 84.00 (SD = 11.68), exceeding the industry standard. Intraclass correlations ranged from .80 to .83 across the three PEDI-PRO domains. Internal reliability (α) was .86-.90 across domains. Youth reported that they liked the accessibility features: interface images, button sounds, read-aloud audio, and rating category choices (M = 88.8%, SD = 5.1%). CONCLUSIONS AND RELEVANCE: The PEDI-PRO supported transition-age youth with IDD to reliably report perceived functional performance. The accessible software was favorably perceived by both clinicians and youth. WHAT THIS ARTICLE ADDS: Design features of the PEDI-PRO make it easy to use in practice with transition-age youth with IDD. The PEDI-PRO's cognitively accessible administrative design, including step-by-step instructions for teaching PROM use and a self-reflective questioning technique, could serve as a training model for this and other PROMs.

"That Felt Like Real Engagement": Fostering and Maintaining Inclusive Research Collaborations With Individuals With Intellectual Disability.

People with intellectual disability (ID) are increasingly involved in stakeholder-engaged research, such as "inclusive research" (IR). To understand the processes that foster and maintain IR with individuals with ID, we used a narrative interview approach with co-researchers with ID (n = 6) and academic researchers (n = 8). We analyzed the data using grounded theory principles. We then developed a model describing how contextual factors and team-level factors and processes coalesce to foster and maintain IR collaborations. We observed that team members' values and characteristics are foundational to IR and drive a commitment to accessibility. Contextual factors, including funding and partnership duration, influence teams' processes and structures. These processes and structures influence the extent to which co-researchers perceive the IR team to be cofacilitated or academic-facilitated. Co-researcher involvement is partially maintained by perceived personal and societal benefits. Optimizing the relationship between these factors may support involvement of people with ID in stakeholder-engaged research projects.

Stakeholder-driven approach to developing a peer-mentoring intervention for young adults with intellectual/developmental disabilities and co-occurring mental health conditions.

BACKGROUND: Young adults with intellectual/developmental disabilities and co-occurring mental health conditions (IDD-MH) experience significant mental health disparities. Barriers to services include transportation and stigma associated with services. Peer mentoring (PM) may be one solution to these barriers. METHODS: We conducted exploratory research to develop a PM intervention for young adults with IDD-MH by partnering with 3 young adults with IDD-MH and a seven-member advisory board. In addition, we conducted focus groups with mental health clinicians (n = 10), peer providers (n = 9), and transition specialists (n = 20) to identify the desired PM outcomes and features and content that may facilitate these outcomes. RESULTS: Prioritized outcome: identifying and utilizing leisure activities as coping strategies. PM features: mentors should use relationship- and outcome-driven actions to operationalize a mentee-centred approach. Features and content considerations: safety, mentor matching, degree of structure, mentor training and support, and collaboration with mentees' support teams. DISCUSSION: Findings are aligned with previous research on PM.

Non-contact photoacoustic imaging using laser speckle contrast analysis.

A novel method for non-contact and continuous detection of photoacoustic signals is presented and experimentally demonstrated. The approach is based on analysis of the contrast of time-varying speckle patterns, and suggests a more robust alternative in respect to interferometric and refractometric available solutions.

Youth's Perspective of Responsibility: Exploration of a Construct for Measurement with Youth with Developmental Disabilities.

AIMS: There is a need to develop self-reports that measure youth's responsibility for major life tasks. We examined if the Pediatric Evaluation of Disability Inventory-Computer Adaptive Test's (PEDI-CAT) operationalization of responsibility is salient to youth with developmental disabilities (DD). The PEDI-CAT defines responsibility as, "the extent to which the young person…take[s] control over organizing and managing major life tasks." METHODS: During six focus groups (n = 43), youth generated examples of behaviors and actions that demonstrated responsibility. Data were coded as "responsibility" or "discrete skills" per PEDI-CAT definitions. We reviewed examples in both categories and compared and contrasted how youth described responsibility. RESULTS: Youth's descriptions of responsibility aligned with the PEDI-CAT's responsibility construct 42.75% of the time. In these instances, youth perceived themselves as causal agents who had to make decisions and self-regulate to manage and organize major life tasks. Otherwise, youth described themselves as causal agents who adhered to rules, social norms, and expectations of others during the execution of discrete skills. CONCLUSIONS: Youth perceive themselves as responsible, causal agents during both the coordination and management of major life tasks and during the execution of discrete skills. As this is not aligned with the PEDI-CAT's operationalization of responsibility, there is a need to further explore youth's perceptions of responsibility prior to developing a self-report.

Patient-reported outcome measures for young people with developmental disabilities: incorporation of design features to reduce cognitive demands.

Use of patient-reported outcome measures (PROMs) may increase the involvement of young people with developmental disabilities in their healthcare decisions and healthcare-related research. Young people with developmental disabilities may have difficulty completing PROMs because of extraneous assessment demands that require additional cognitive processes. However, PROM design features may mitigate the impact of these demands. We identified and evaluated six pediatric PROMs of self-care and domestic life tasks for the incorporation of suggested design features that can reduce cognitive demands. PROMs incorporated an average of 6 out of 11 content, 7 out of 14 layout, and 2 out of 9 administration features. This critical review identified two primary gaps in PROM design: (1) examples and visuals were not optimized to reduce cognitive demands; and (2) administration features that support young people's motivation and self-efficacy and reduce frustration were underutilized. Because assessment demands impact the validity of PROMs, clinicians should prospectively consider the impact of these demands when selecting PROMs and interpreting scores. WHAT THIS PAPER ADDS: Patient-reported outcome measure (PROM) design features can reduce assessment demands related to cognitive processes. Pediatric PROMs underutilize design features that decrease cognitive demands of self-reporting.

Initial evaluation of the effects of an environmental-focused problem-solving intervention for transition-age young people with developmental disabilities: Project TEAM.

AIM: Project TEAM (Teens making Environment and Activity Modifications) teaches transition-age young people with developmental disabilities, including those with co-occurring intellectual or cognitive disabilities, to identify and resolve environmental barriers to participation. We examined its effects on young people's attainment of participation goals, knowledge, problem-solving, self-determination, and self-efficacy. METHOD: We used a quasi-experimental, repeated measures design (initial, outcome, 6-week follow-up) with two groups: (1) Project TEAM (28 males, 19 females; mean age 17y 6mo); and (2) goal-setting comparison (21 males, 14 females; mean age 17y 6mo). A matched convenience sample was recruited in two US states. Attainment of participation goals and goal attainment scaling (GAS) T scores were compared at outcome. Differences between groups for all other outcomes were analyzed using linear mixed effects models. RESULTS: At outcome, Project TEAM participants demonstrated greater knowledge (estimated mean difference: 1.82; confidence interval [CI]: 0.90, 2.74) and ability to apply knowledge during participation (GAS: t[75]=4.21; CI: 5.21, 14.57) compared to goal-setting. While both groups achieved significant improvements in knowledge, problem-solving, and self-determination, increases in parent reported self-determination remained at 6-week follow-up only for Project TEAM (estimated mean difference: 4.65; CI: 1.32, 7.98). Significantly more Project TEAM participants attained their participation goals by follow-up (Project TEAM=97.6%, goal-setting=77.1%, p=0.009). INTERPRETATION: Both approaches support attainment of participation goals. Although inconclusive, Project TEAM may uniquely support young people with developmental disabilities to act in a self-determined manner and apply an environmental problem-solving approach over time. WHAT THIS PAPER ADDS: Individualized goal-setting, alone or during Project TEAM (Teens making Environment and Activity Modifications) appears to support attainment of participation goals. Project TEAM appears to support young people with developmental disabilities to apply an environmental problem-solving approach to participation barriers. Parents of young people with developmental disabilities report sustained changes in self-determination 6 weeks after Project TEAM.