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Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology
Gould, Elliot; Fraser, Hannah S.; Parker, Timothy H.; Nakagawa, Shinichi; Griffith, Simon C.; Vesk, Peter A.; Fidler, Fiona; Hamilton, Daniel G.; Abbey-Lee, Robin N.; Abbott, Jessica K.; Aguirre, Luis A.; Alcaraz, Carles; Aloni, Irith; Altschul, Drew; Arekar, Kunal; Atkins, Jeff W.; Atkinson, Joe; Baker, Christopher M.; Barrett, Meghan; Bell, Kristian; Bello, Suleiman K.; Beltrán, Iván; Berauer, Bernd J.; Bertram, Michael G.; Billman, Peter D.; Blake, Charlie K.; Blake, Shannon; Bliard, Louis; Bonisoli-Alquati, Andrea; Bonnet, Timothée; Bordes, Camille N. M.; Bose, Aneesh P. H.; Botterill-James, Thomas; Boyd, Melissa A.; Boyle, Sarah A.; Bradfer-Lawrence, Tom; Bradham, Jennifer; Brand, Jack A.; Brengdahl, Martin I.; Bulla, Martin; Bussière, Luc; Camerlenghi, Ettore; Campbell, Sara E.; Campos, Leonardo L. F.; Caravaggi, Anthony; Cardoso, Pedro; Carroll, Charles J. W.; Catanach, Therese A.; Chen, Xuan; Chik, Heung Y. J.; Choy, Emily S.; Christie, Alec P.; Chuang, Angela; Chunco, Amanda J.; Clark, Bethany L.; Contina, Andrea; Covernton, Garth A.; Cox, Murray P.; Cressman, Kimberly A.; Crotti, Marco; Crouch, Connor D.; D’Amelio, Pietro B.; de Sousa, Alexandra A.; Döbert, Timm F.; Dobler, Ralph; Dobson, Adam J.; Doherty, Tim S.; Drobniak, Szymon M.; Duffy, Alexandra G.; Duncan, Alison B.; Dunn, Robert P.; Dunning, Jamie; Dutta, Trishna; Eberhart-Hertel, Luke; Elmore, Jared A.; Elsherif, Mahmoud M.; English, Holly M.; Ensminger, David C.; Ernst, Ulrich R.; Ferguson, Stephen M.; Fernandez-Juricic, Esteban; Ferreira-Arruda, Thalita; Fieberg, John; Finch, Elizabeth A.; Fiorenza, Evan A.; Fisher, David N.; Fontaine, Amélie; Forstmeier, Wolfgang; Fourcade, Yoan; Frank, Graham S.; Freund, Cathryn A.; Fuentes-Lillo, Eduardo; Gandy, Sara L.; Gannon, Dustin G.; García-Cervigón, Ana I.; Garretson, Alexis C.; Ge, Xuezhen; Geary, William L.; Géron, Charly; Gilles, Marc; Girndt, Antje; Gliksman, Daniel; Goldspiel, Harrison B.; Gomes, Dylan G. E.; Good, Megan K.; Goslee, Sarah C.; Gosnell, J. S.; Grames, Eliza M.; Gratton, Paolo; Grebe, Nicholas M.; Greenler, Skye M.; Griffioen, Maaike; Griffith, Daniel M.; Griffith, Frances J.; Grossman, Jake J.; Güncan, Ali; Haesen, Stef; Hagan, James G.; Hager, Heather A.; Harris, Jonathan P.; Harrison, Natasha D.; Hasnain, Sarah S.; Havird, Justin C.; Heaton, Andrew J.; Herrera-Chaustre, María L.; Howard, Tanner J.; Hsu, Bin-Yan; Iannarilli, Fabiola; Iranzo, Esperanza C.; Iverson, Erik N. K.; Jimoh, Saheed O.; Johnson, Douglas H.; Johnsson, Martin; Jorna, Jesse; Jucker, Tommaso; Jung, Martin; Kačergytė, Ineta; Kaltz, Oliver; Ke, Alison; Kelly, Clint D.; Keogan, Katharine; Keppeler, Friedrich W.; Killion, Alexander K.; Kim, Dongmin; Kochan, David P.; Korsten, Peter; Kothari, Shan; Kuppler, Jonas; Kusch, Jillian M.; Lagisz, Malgorzata; Lalla, Kristen M.; Larkin, Daniel J.; Larson, Courtney L.; Lauck, Katherine S.; Lauterbur, M. E.; Law, Alan; Léandri-Breton, Don-Jean; Lembrechts, Jonas J.; L’Herpiniere, Kiara; Lievens, Eva J. P.; de Lima, Daniela O.; Lindsay, Shane; Luquet, Martin; MacLeod, Ross; Macphie, Kirsty H.; Magellan, Kit; Mair, Magdalena M.; Malm, Lisa E.; Mammola, Stefano; Mandeville, Caitlin P.; Manhart, Michael; Manrique-Garzon, Laura M.; Mäntylä, Elina; Marchand, Philippe; Marshall, Benjamin M.; Martin, Charles A.; Martin, Dominic A.; Martin, Jake M.; Martinig, April R.; McCallum, Erin S.; McCauley, Mark; McNew, Sabrina M.; Meiners, Scott J.; Merkling, Thomas; Michelangeli, Marcus; Moiron, Maria; Moreira, Bruno; Mortensen, Jennifer; Mos, Benjamin; Muraina, Taofeek O.; Murphy, Penelope W.; Nelli, Luca; Niemelä, Petri; Nightingale, Josh; Nilsonne, Gustav; Nolazco, Sergio; Nooten, Sabine S.; Novotny, Jessie L.; Olin, Agnes B.; Organ, Chris L.; Ostevik, Kate L.; Palacio, Facundo X.; Paquet, Matthieu; Parker, Darren J.; Pascall, David J.; Pasquarella, Valerie J.; Paterson, John H.; Payo-Payo, Ana; Pedersen, Karen M.; Perez, Grégoire; Perry, Kayla I.; Pottier, Patrice; Proulx, Michael J.; Proulx, Raphaël; Pruett, Jessica L.; Ramananjato, Veronarindra; Randimbiarison, Finaritra T.; Razafindratsima, Onja H.; Rennison, Diana J.; Riva, Federico; Riyahi, Sepand; Roast, Michael J.; Rocha, Felipe P.; Roche, Dominique G.; Román-Palacios, Cristian; Rosenberg, Michael S.; Ross, Jessica; Rowland, Freya E.; Rugemalila, Deusdedith; Russell, Avery L.; Ruuskanen, Suvi; Saccone, Patrick; Sadeh, Asaf; Salazar, Stephen M.; Sales, Kris; Salmón, Pablo; Sánchez-Tójar, Alfredo; Santos, Leticia P.; Santostefano, Francesca; Schilling, Hayden T.; Schmidt, Marcus; Schmoll, Tim; Schneider, Adam C.; Schrock, Allie E.; Schroeder, Julia; Schtickzelle, Nicolas; Schultz, Nick L.; Scott, Drew A.; Scroggie, Michael P.; Shapiro, Julie T.; Sharma, Nitika; Shearer, Caroline L.; Simón, Diego; Sitvarin, Michael I.; Skupien, Fabrício L.; Slinn, Heather L.; Smith, Grania P.; Smith, Jeremy A.; Sollmann, Rahel; Whitney, Kaitlin S.; Still, Shannon M.; Stuber, Erica F.; Sutton, Guy F.; Swallow, Ben; Taff, Conor C.; Takola, Elina; Tanentzap, Andrew J.; Tarjuelo, Rocío; Telford, Richard J.; Thawley, Christopher J.; Thierry, Hugo; Thomson, Jacqueline; Tidau, Svenja; Tompkins, Emily M.; Tortorelli, Claire M.; Trlica, Andrew; Turnell, Biz R.; Urban, Lara; Van de Vondel, Stijn; van der Wal, Jessica E. M.; Van Eeckhoven, Jens; van Oordt, Francis; Vanderwel, K. M.; Vanderwel, Mark C.; Vanderwolf, Karen J.; Vélez, Juliana; Vergara-Florez, Diana C.; Verrelli, Brian C.; Vieira, Marcus V.; Villamil, Nora; Vitali, Valerio; Vollering, Julien; Walker, Jeffrey; Walker, Xanthe J.; Walter, Jonathan A.; Waryszak, Pawel; Weaver, Ryan J.; Wedegärtner, Ronja E. M.; Weller, Daniel L.; Whelan, Shannon; White, Rachel L.; Wolfson, David W.; Wood, Andrew; Yanco, Scott W.; Yen, Jian D. L.; Youngflesh, Casey; Zilio, Giacomo; Zimmer, Cédric; Zimmerman, Gregory M.; Zitomer, Rachel A. (2025-02-06)
Abstract Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.
The surgical time-out: the relationship between perceptions of a safety-task anchor and surgical team workflow
Zagarese, Vivian J.; Hernandez, Ivan; Hauenstein, Neil M. A.; Foti, Roseanne J.; Parker, Sarah H. (2025-02-05)
Background The surgical time-out is a critical safety measure used in the operating room (OR). We examined the mediating relationship of the length of the time-out between team perceived usefulness of the time-out, and the rate at which the circulating nurse left the OR to retrieve instruments. Methods 60 cardiac surgical teams were observed performing their work. The length of the time-out and the rate at which the circulating nurse left the OR was obtained by observation of the surgical team. We administered a survey with a 7-point Likert scale to assess the surgical staff’s perceived usefulness of the time-out at the end of the surgery. An analysis was conducted to test if length of the time-out mediated the relationship between perceived usefulness of the time-out and rate at which the nurse leaves the OR to retrieve an instrument useful for the surgery. Results The relationship of the length of the time-out with the rate at which the nurse leaves the OR was non-significant (β = 0.089, p = .496). However, the relationship between perceived usefulness of the time-out with the length of the time-out was significant (β = 0.346, p < .05) and the effect between perceived usefulness of the time-out and the rate at which the nurse left the OR was statistically significant (β= − 0.424, p = < 0.001). Conclusion In this study we explore how surgical teams’ attitudes towards the usefulness of the time-out affect its utilization, and how attitudes about time-outs are related to the important process measure of rate at which the circulating nurse leaves the OR. The full mediation model was not supported by the data; however, there appears to be a relationship between the perceived usefulness of the time-out and the rate at which the circulating nurse leaves the OR.
Comparison of anesthetic effects of xylazine combined with alfaxalone or ketamine and maintained with isoflurane in captive Formosan Reeve’s Muntjac (Muntiacus reevesi micrurus)
Chang, Li-Jen; Wang, Zixuan; Lien, Chen-Yeh; Wen, Amanda H. (2025-02-08)
Formosan Reeve’s muntjac is a Cervidae species endemic to Southeast China and Taiwan. However, research on different anesthetic protocols, their effects, and their safety in Formosan Reeve’s muntjac is limited. This study evaluated the effects of ketamine-xylazine (KX) and alfaxalone-xylazine (AX) administered via blow darts to nine muntjacs. Induction and recovery times as well as the quality were assessed by a blinded observer. Peripheral oxygen saturation (SpO2), heart rate, respiratory rate, and rectal temperature were recorded for at least 30 min. Tolazoline (4 mg/kg) was used post-procedure to reverse xylazine’s effects. The mean doses were 4.68 ± 2.18 mg/kg for ketamine and 3.22 ± 1.33 mg/kg for xylazine in the KX group. In the AX group, the mean doses were 4.38 ± 0.31 mg/kg for alfaxalone and 1.19 ± 0.26 mg/kg for xylazine. The median induction times were 339.5 s (range 180.0-375.0) for KX and 125.0 s (range 71.0–334.0) for AX, with both groups scoring 3.0 for induction quality. The recovery times were 507.5 s (range 266.0–1081.0) for KX and 243.0 s (range 92.0–480.0) for AX, with recovery scores of 2.3 and 3.0, respectively, showing no significant difference. Hypoxemia (SpO2 < 90%) was more severe in the KX group when compared to the AX group (SpO2 > 92%), and rectal temperatures were higher in the former during the first 15 min. Heart and respiratory rates showed no significant differences between groups. Our findings demonstrate that both anesthetic combinations achieve reliable induction and satisfactory recovery in Formosan Reeve’s muntjac, with the ketamine-xylazine combination causing a more profound hypoxemia post-induction compared to the alfaxalone-xylazine combination.
Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress
Huang, Dan; Liao, Jingqiu; Balcazar, Jose L.; Ye, Mao; Wu, Ruonan; Wang, Dongsheng; Alvarez, Pedro J. J.; Yu, Pingfeng (BioMed Central, 2025-01-31)
Background: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress. Results: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities. Conclusions: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation.
Stabilizing milk-derived extracellular vesicles (mEVs) through lyophilization: a novel trehalose and tryptophan formulation for maintaining structure and Bioactivity during long-term storage
Dogan, Alan B.; Marsh, Spencer R.; Tschetter, Rachel J.; Beard, Claire E.; Amin, Md R.; Jourdan, L. Jane; Gourdie, Robert G. (2025-01-13)
Extracellular vesicles (EVs) are widely investigated for their implications in cell-cell signaling, immune modulation, disease pathogenesis, cancer, regenerative medicine, and as a potential drug delivery vector. However, maintaining integrity and bioactivity of EVs between Good Manufacturing Practice separation/filtration and end-user application remains a consistent bottleneck towards commercialization. Milk-derived extracellular vesicles (mEVs), separated from bovine milk, could provide a relatively low-cost, scalable platform for large-scale mEV production; however, the reliance on cold supply chain for storage remains a logistical and financial burden for biologics that are unstable at room temperature. Herein, we aim to characterize and engineer a freeze-dried, mEV formulation that can be stored at room temperature without sacrificing structure/bioactivity and can be reconstituted before delivery. In addition to undertaking established mEV assays of structure and function on our preparations, we introduce a novel, efficient, high throughput assay of mEV bioactivity based on Electric Cell Substrate Impedance Sensing (ECIS) in Human dermal fibroblast monolayers. By adding appropriate excipients, such as trehalose and tryptophan, we describe a protective formulation that preserves mEV bioactivity during long-term, room temperature storage. Our identification of the efficacy of tryptophan as a novel additive to mEV lyophilization solutions could represent a significant advancement in stabilizing small extracellular vesicles outside of cold storage conditions.
Associations between maternal personality dysfunction and emotion suppression and adolescent emotion suppression
Phillips, Jennifer J.; Smith, Cynthia L.; Bell, Martha A. (2024-11-27)
Background: Adaptive strategies of emotion regulation are important for adolescents, as maladaptive strategies of such can manifest as psychopathology that is sometimes severe. Individual biological characteristics and influences from peers have been shown to have an effect on the development of emotion regulation strategies in adolescents. Maternal factors, however, have received less attention in this age group regarding how they might predict emotion regulation in adolescents. Given that prior work has demonstrated that certain maternal factors, like emotion regulation and personality, play a crucial role in the development of emotion regulation strategies in early childhood, we sought to examine these associations in adolescents in our current study. Methods: Adolescents and their mothers (n = 123) both self-reported data on their own emotion regulation, and mothers also self-reported data on their own personality dysfunction. We operationalized maternal and adolescent emotion regulation as emotion suppression, a maladaptive emotion regulation strategy that is commonly used by adolescents. Results: Our data demonstrated that both maternal emotion suppression and interpersonal personality dysfunction were positively associated with adolescent emotion suppression. No associations among maternal intrapersonal personality functioning and adolescent emotion suppression were detected. Conclusions: Maternal personality dysfunction and emotion suppression both independently predicted adolescent emotion suppression use. These results support the idea that maternal characteristics play a role in shaping emotion regulation in adolescence.
Advancing implementation science in community settings: the implementation strategies applied in communities (ISAC) compilation
Balis, Laura E.; Houghtaling, Bailey; Clausen, Whitney; Lane, Hannah; Wende, Marilyn E.; Pereira, Emiliane; McLoughlin, Gabriella M.; Harden, Samantha M. (2024-11-26)
Background: Implementation strategies have predominantly been operationalized and studied in clinical settings. Implementation strategies are also needed to improve evidence-based intervention (EBI) integration in community settings, but there is a lack of systematic characterization of their use, which limits generalizability of findings. The goals of this study were to determine which implementation strategies are most used to deliver primary prevention EBIs in community settings, develop a compilation and pragmatic strategy selection process with accompanying guidance tools, and understand practitioners’ preferences for dissemination. Methods: Purposive and snowball sampling was used to recruit community setting researchers and practitioners delivering primary prevention EBIs (nutrition, physical activity, tobacco prevention) in community settings: education, social services, city planning and transportation, workplaces, recreation/sport, faith-based, and other public health organizations. Semi-structured interviews were conducted using a guide based on the reach, effectiveness, adoption, implementation, maintenance (RE-AIM) framework. Participants were asked to describe barriers experienced and strategies used to overcome them within each RE-AIM dimension. Practitioners were also asked about preferred dissemination strategies, prompted by Diffusion of Innovations theory concepts of sources (who provides information) and channels (how information is provided). A rapid deductive approach was used to analyze findings with a coding matrix aligned with the interview guide. Results: Researchers (n = 10) and practitioners (n = 8) across all targeted settings and intervention outcomes completed interviews. Interviewees shared unique implementation strategies (N = 40) which were used to overcome barriers related to multiple RE-AIM dimensions, most commonly implementation (n = 29) and adoption (n = 27). Most frequently mentioned implementation strategies were conduct pragmatic evaluation (n = 31), provide training (n = 26), change adaptable program components (n = 26), and leverage funding sources (n = 21). Webinars (n = 6) and listservs/newsletters (n = 5) were the most mentioned dissemination channels; national public health organizations (n = 13) were the most mentioned sources. Conclusions: Results reflect commonly used implementation strategies in community settings (e.g., training, technical assistance) and add novel strategies not reflected in current taxonomies. Dissemination preferences suggest the need to involve broad-reaching public health organizations. The resultant compilation (Implementation Strategies Applied in Communities) and strategy selection process provide resources to assist researchers and practitioners in applying strategies and improving EBI delivery in community settings.
Assessing the impact of COVID-19 on outpatient psychiatric population well-being and symptomology utilizing COVID-19 Events Checklist (CEC) and Measurement Based Care
Jones, Sydney B.; Ko, Hayoung; Gatto, Alyssa J.; Kablinger, Anita S.; Sharp, Hunter D.; Cooper, Lee D.; Tenzer, Martha M.; O’Brien, Virginia C.; McNamara, Robert S. (2024-11-21)
Background: This study examines the impact of SARS-CoV-2 (i.e., coronavirus, COVID, COVID-19) using data from a measurement-based care (MBC) system utilized in an outpatient psychiatric clinic providing telemedicine care. A novel Patient Rated Outcome Measure (PROM), the COVID-19 Events Checklist (CEC) was administered in a hospital system based ambulatory clinic beginning April 2020 to track COVID-19-19’s impact on patients’ mental, emotional, and health-related behaviors during the pandemic. The study (1) provides descriptive CEC data, and (2) compares CEC results with PROMs evaluating anxiety (Generalized Anxiety Disorder-7; GAD-7), depression (Patient Health Questionnaire; PHQ-9), and psychological distress (Brief Adjustment Scale-6; BASE-6). Methods: This retrospective observational study included patient intake data collected from April 2020 to March 2021. Patient (N = 842) reports on the CEC’s five domain questions were aggregated to calculate average reports of COVID-19 related impacts at intake over the initial 12 months of the pandemic. Trends in COVID-19 related impacts were examined, and non-aggregated scores on the PHQ-9, GAD-7, and BASE-6 were compared to primary dichotomous (yes/no) CEC survey questions via Wilcoxon rank- sum testing. Results: Results capture the relationship between COVID-19 exposure, COVID-19- related sequelae and behaviors, and psychological symptom severity. Specifically, Wilcoxon rank-sum tests indicate that social determinants of health (SDOH), negative mental health impacts, and positive coping skill use were significantly associated with psychological symptomatology including overall psychological functioning via the BASE-6, anxiety via the GAD-7, and depressive symptoms via the PHQ-9. Results regarding SDOH were as follows: BASE-6 (w = 44,005, p < 0.001), GAD-7 (w = 44,116, p < 0.001), and PHQ-9 (w = 43,299, p < 0.001). Regarding negative mental health outcomes, the results were: BASE-6 (w = 38,374, p < 0.001), GAD-7 (w = 39,511, p < 0.001), and PHQ-9 (w = 40,154, p < 0.001). As the initial year of the pandemic elapsed, incoming patients demonstrated increased rates of suspected or confirmed exposure to COVID-19, (+2.29%, t = 3.19, p = 0.01), reported fewer negative impacts of COVID-19 on SDOH (−3.53%, t= −2.45, p = 0.034), and less engagement in positive coping strategies (−1.47%, t = −3.14, p = 0.010). Conclusions: Psychosocial factors related to COVID-19 are discussed, as well as opportunities for further research on the relationship between psychological symptomatology and the impact of COVID-19 on health-related behaviors.
Non-trivial area operators require non-local magic
Cao, ChunJun (2024-11-19)
We show that no stabilizer codes over any local dimension can support a non-trivial area operator for any bipartition of the physical degrees of freedom even if certain code subalgebras contain non-trivial centers. This conclusion also extends to more general quantum codes whose logical operators satisfy certain factorization properties, including any complementary code that encodes qubits and supports transversal logical gates that form a nice unitary basis. These results support the observation that some desirable conditions for fault tolerance are in tension with emergent gravity and suggest that non-local “magic” would play an important role in reproducing features of gravitational back-reaction and the quantum extremal surface formula. We comment on conditions needed to circumvent the no-go result and examine some simple instances of non-stabilizer codes that do have non-trivial area operators.
Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh
Carnegie, L.; McCrone, J. T.; du Plessis, L.; Hasan, M.; Ali, M.Z.; Begum, R.; Hassan, M.Z.; Islam, S.; Rahman, M.H.; Uddin, A.S.M.; Sarker, M.S.; Das, T.; Hossain, M.; Khan, M.; Razu, M.H.; Akram, A.; Arina, S.; Hoque, E.; Molla, M.M.A.; Nafisaa, T.; Angra, P.; Rambaut, A.; Pullan, S.T.; Osman, K.L.; Hoque, M.A.; Biswas, P.; Flora, M.S.; Raghwani, J.; Fournié, G.; Samad, M.A.; Hill, S.C. (2024-11-13)
Background: Genomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world’s least developed countries (LDCs). Methods: To begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the country’s first COVID-19 wave by analysing case reports and whole-genome sequences from all eight divisions of the country. Results: We detected > 50 virus introductions to the country during the period, including during a period of national lockdown. Additionally, through discrete phylogeographic analyses, we identified that geographical distance and population -density and/or -size influenced virus spatial dispersal in Bangladesh. Conclusions: Overall, this study expands our knowledge of SARS-CoV-2 genomic epidemiology in Bangladesh, shedding light on crucial transmission characteristics within the country, while also acknowledging resemblances and differences to patterns observed in other nations.
Evaluating attachment-based family therapy in residential treatment in the United States: does adolescents’ increased attachment security to caregivers lead to decreases in depressive symptoms?
Diamond, Guy; Rivers, Alannah S.; Winston-Lindeboom, Payne; Russon, Jody M.; Roeske, Michael (2024-11-13)
Background: The inclusion of family therapy in residential treatment centers (RTCs) has increased over time. However, there is little data on whether empirically-supported family therapies (ESFTs) are being adopted and if they contribute to treatment effectiveness. This study aimed to test whether Attachment-Based Family Therapy (ABFT), an ESFT integrated into a large residential psychiatric system, would improve perceived attachment insecurity (anxiety and avoidance) and contribute to decreases in depression for adolescents. Method: ABFT was integrated into the clinical program of a large, residential psychiatric system. All family therapists were trained to a level of certification. Improvement was measured by changes in adolescent’s perceived attachment to caregivers and reduction in depressive symptoms. The sample included 4786 patients. Attachment insecurity and depressive symptoms were measured at intake, week 3, and week 5. A random-intercept, cross-lagged panel model was used to examine the relationships between attachment and depression over time. Results: The results generally supported hypotheses. Attachment insecurity and depressive symptoms improved over the five weeks of treatment. Improvements in attachment avoidance preceded improvements in depressive symptoms within subjects, over time. Simultaneously, improvements in depressive symptoms preceded those in both dimensions of attachment. Thus, improvement in perceived attachment was associated with a reduction in depressive symptoms. Conclusion: RTCs that can generate improvements in attachment insecurity and depressive symptoms, via ABFT or other ESFTs, might improve treatment outcomes, and ideally, adolescents’ successful transition back home to families. More research is needed to disentangle the contribution of ABFT and other treatment elements in a multimodal, residential treatment program. The study supports the call for increased incorporation of families into the RTC treatment process.
Generalized symmetries in 2D from string theory: SymTFTs, intrinsic relativeness, and anomalies of non-invertible symmetries
Franco, Sebastián; Yu, Xingyang (2024-11-05)
Generalized global symmetries, in particular non-invertible and categorical symmetries, have become a focal point in the recent study of quantum field theory (QFT). In this paper, we investigate aspects of symmetry topological field theories (SymTFTs) and anomalies of non-invertible symmetries for 2D QFTs from a string theory perspective. Our primary focus is on an infinite class of 2D QFTs engineered on D1-branes probing toric Calabi-Yau 4-fold singularities. We derive 3D SymTFTs from the topological sector of IIB supergravity and discuss the resulting 2D QFTs, which can be intrinsically relative or absolute. For intrinsically relative QFTs, we propose a sufficient condition for them to exist. For absolute QFTs, we show that they exhibit non-invertible symmetries with an elegant brane origin. Furthermore, we find that these non-invertible symmetries can suffer from anomalies, which we discuss from a top-down perspective. Explicit examples are provided, including theories for Y(p,k)(ℙ2), Y(2,0)(ℙ1 × ℙ1), and ℂ4/ℤ4 geometries.
Expanding methods to address RE-AIM metrics in hybrid effectiveness-implementation studies
Harden, Samantha M.; Galaviz, Karla I.; Estabrooks, Paul A. (2024-11-04)
Background: Dissemination and implementation science is an evolving field that focuses on the strategies and mechanisms by which scientific evidence is adopted, used, and sustained in clinical and community practice. Main body: Implementation scientists are confronted by the challenge to balance rigor and generalizability in their work while also attempting to speed the translation of evidence into clinical and community practice. Hybrid Effectiveness-Implementation studies and the RE-AIM framework were conceptualized to address these challenges. Hybrid Effectiveness-Implementation (HEI) studies provide methods of examining the effectiveness of health promoting interventions while concurrently assessing the utility of dissemination and implementation strategies designed to enhance the application of evidence-based principles in practice. RE-AIM provides a set of planning and evaluation dimensions that can be assessed with a goal to balance internal and external validity. The purpose of this commentary is to provide clarity on definitions of each approach and how to effectively use them together to answer research questions that will advance dissemination and implementation science for health promotion. Conclusions: We provide examples of concerted use of RE-AIM within HEI studies from the literature and focus on language to provide a clarity and consistency across research questions, designs, and settings. We share how to operationalize RE-AIM dimensions in HEI studies for both dissemination and implementation strategies. Future directions include refining, defining, and evaluating each RE-AIM dimension within hybrid studies.
The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation
Kosch, Tiffany A.; Torres-Sánchez, María; Liedtke, H. C.; Summers, Kyle; Yun, Maximina H.; Crawford, Andrew J.; Maddock, Simon T.; Ahammed, Md. S.; Araújo, Victor L. N.; Bertola, Lorenzo V.; Bucciarelli, Gary M.; Carné, Albert; Carneiro, Céline M.; Chan, Kin O.; Chen, Ying; Crottini, Angelica; da Silva, Jessica M.; Denton, Robert D.; Dittrich, Carolin; Espregueira Themudo, Gonçalo; Farquharson, Katherine A.; Forsdick, Natalie J.; Gilbert, Edward; Che, Jing; Katzenback, Barbara A.; Kotharambath, Ramachandran; Levis, Nicholas A.; Márquez, Roberto; Mazepa, Glib; Mulder, Kevin P.; Müller, Hendrik; O’Connell, Mary J.; Orozco-terWengel, Pablo; Palomar, Gemma; Petzold, Alice; Pfennig, David W.; Pfennig, Karin S.; Reichert, Michael S.; Robert, Jacques; Scherz, Mark D.; Siu-Ting, Karen; Snead, Anthony A.; Stöck, Matthias; Stuckert, Adam M. M.; Stynoski, Jennifer L.; Tarvin, Rebecca D.; Wollenberg Valero, Katharina C. (2024-11-01)
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.
Quantitative ultrasound assessment of fatty infiltration of the rotator cuff muscles using backscatter coefficient
Toto-Brocchi, Marco; Wu, Yuanshan; Jerban, Saeed; Han, Aiguo; Andre, Michael; Shah, Sameer B.; Chang, Eric Y. (2024-10-22)
Background: To prospectively evaluate ultrasound backscatter coefficients (BSCs) of the supraspinatus and infraspinatus muscles and compare with Goutallier classification on magnetic resonance imaging (MRI). Methods: Fifty-six participants had shoulder MRI exams and ultrasound exams of the supraspinatus and infraspinatus muscles. Goutallier MRI grades were determined and BSCs were measured. Group means were compared and the strength of relationships between the measures were determined. Using binarized Goutallier groups (0–2 versus 3–4), areas under the receiver operating characteristic curves (AUROCs) were calculated. The nearest integer cutoff value was determined using Youden’s index. Results: BSC values were significantly different among most Goutallier grades for the supraspinatus and infraspinatus muscles (both p < 0.001). Strong correlations were found between the BSC values and Goutallier grades for the supraspinatus (τb = 0.72, p < 0.001) and infraspinatus (τb = 0.79, p < 0.001) muscles. BSC showed excellent performance for classification of the binarized groups (0–2 versus 3–4) for both supraspinatus (AUROC = 0.98, p < 0.0001) and infraspinatus (AUROC = 0.98, p < 0.0001) muscles. Using a cutoff BSC value of −17 dB, sensitivity, specificity, and accuracy for severe fatty infiltration were 87.0%, 90.0%, and 87.5% for the supraspinatus muscle, and 93.6%, 87.5%, and 92.7% for the infraspinatus muscle. Conclusion: BSC can be applied to the rotator cuff muscles for assessment of fatty infiltration. For both the supraspinatus and infraspinatus muscles, BSC values significantly increased with higher Goutallier grades and showed strong performance in distinguishing low versus high Goutallier grades. Relevance statement: Fatty infiltration of the rotator cuff muscles can be quantified using BSC values, which are higher with increasing Goutallier grades. Key Points Ultrasound BSC measurements are reliable for the quantification of muscle fatty infiltration. BCS values increased with higher Goutallier MRI grades. BCS values demonstrated high performance for distinguishing muscle fatty infiltration groups.
Decomposition squared
Sharpe, Eric R.; Zhang, H. (2024-10-23)
Abstract In this paper, we test and extend a proposal of Gu, Pei, and Zhang for an application of decomposition to three-dimensional theories with one-form symmetries and to quantum K theory. The theories themselves do not decompose, but, OPEs of parallel one-dimensional objects (such as Wilson lines) and dimensional reductions to two dimensions do decompose, sometimes in two independent ways. We apply this to extend conjectures for quantum K theory rings of gerbes (realized by three-dimensional gauge theories with one-form symmetries) via both orbifold partition functions and gauged linear sigma models.
Demonstration of neutron identification in neutrino interactions in the MicroBooNE liquid argon time projection chamber
Abratenko, P.; Alterkait, O.; Aldana, D. A.; Arellano, L.; Asaadi, J.; Ashkenazi, A.; Balasubramanian, S.; Baller, B.; Barnard, A.; Barr, G.; Barrow, D.; Barrow, J.; Basque, V.; Bateman, J.; Rodrigues, O. B.; Berkman, S.; Bhanderi, A.; Bhat, A.; Bhattacharya, M.; Bishai, M.; Blake, A.; Bogart, B.; Bolton, T.; Book, J. Y.; Brunetti, M. B.; Camilleri, L.; Cao, Y.; Caratelli, D.; Cavanna, F.; Cerati, G.; Chappell, A.; Chen, Y.; Conrad, J. M.; Convery, M.; Cooper-Troendle, L.; Crespo-Anadón, J. I.; Cross, R.; Del Tutto, M.; Dennis, S. R.; Detje, P.; Diurba, R.; Djurcic, Z.; Dorrill, R.; Duffy, K.; Dytman, S.; Eberly, B.; Englezos, P.; Ereditato, A.; Evans, J. J.; Fine, R.; Foreman, W.; Fleming, B. T.; Franco, D.; Furmanski, A. P.; Gao, F.; Garcia-Gamez, D.; Gardiner, S.; Ge, G.; Gollapinni, S.; Gramellini, E.; Green, P.; Greenlee, H.; Gu, L.; Gu, W.; Guenette, R.; Guzowski, P.; Hagaman, L.; Handley, M. D.; Hen, O.; Hilgenberg, C.; Horton-Smith, G. A.; Imani, Z.; Irwin, B.; Ismail, M. S.; James, C.; Ji, X.; Jo, J. H.; Johnson, R. A.; Jwa, Y.-J.; Kalra, D.; Kamp, N.; Karagiorgi, G.; Ketchum, W.; Kirby, M.; Kobilarcik, T.; Kreslo, I.; Lane, N.; Li, J.-Y.; Li, Y.; Lin, K.; Littlejohn, B. R.; Liu, H.; Louis, W. C.; Luo, X.; Mariani, Camillo; Marsden, D.; Marshall, J.; Martinez, N.; Caicedo, D. A. M.; Martynenko, S.; Mastbaum, A.; Mawby, I.; McConkey, N.; Meddage, V.; Mendez, J.; Micallef, J.; Miller, K.; Mogan, A.; Mohayai, T.; Mooney, M.; Moor, A. F.; Moore, C. D.; Lepin, L. M.; Moudgalya, M. M.; Mulleriababu, S.; Naples, D.; Navrer-Agasson, A.; Nayak, N.; Nebot-Guinot, M.; Nguyen, C.; Nowak, J.; Oza, N.; Palamara, O.; Pallat, N.; Paolone, V.; Papadopoulou, A.; Papavassiliou, V.; Parkinson, H. B.; Pate, S. F.; Patel, N.; Pavlovic, Z.; Piasetzky, E.; Pletcher, K.; Pophale, I.; Qian, X.; Raaf, J. L.; Radeka, V.; Rafique, A.; Reggiani-Guzzo, M.; Ren, L.; Rochester, L.; Rondon, J. R.; Rosenberg, M.; Ross-Lonergan, M.; Safa, I.; Schmitz, D. W.; Schukraft, A.; Seligman, W.; Shaevitz, M. H.; Sharankova, R.; Shi, J.; Snider, E. L.; Soderberg, M.; Söldner-Rembold, S.; Spitz, J.; Stancari, M.; John, J. S.; Strauss, T.; Szelc, A. M.; Tang, W.; Taniuchi, N.; Terao, K.; Thorpe, C.; Torbunov, D.; Totani, D.; Toups, M.; Trettin, A.; Tsai, Y.-T.; Tyler, J.; Uchida, M. A.; Usher, T.; Viren, B.; Wang, J.; Weber, M.; Wei, H.; White, A. J.; Wolbers, S.; Wongjirad, T.; Wospakrik, M.; Wresilo, K.; Wu, W.; Yandel, E.; Yang, T.; Yates, L. E.; Yu, H. W.; Zeller, G. P.; Zennamo, J.; Zhang, C. (2024-10-14)
A significant challenge in measurements of neutrino oscillations is reconstructing the incoming neutrino energies. While modern fully-active tracking calorimeters such as liquid argon time projection chambers in principle allow the measurement of all final state particles above some detection threshold, undetected neutrons remain a considerable source of missing energy with little to no data constraining their production rates and kinematics. We present the first demonstration of tagging neutrino-induced neutrons in liquid argon time projection chambers using secondary protons emitted from neutron-argon interactions in the MicroBooNE detector. We describe the method developed to identify neutrino-induced neutrons and demonstrate its performance using neutrons produced in muon-neutrino charged current interactions. The method is validated using a small subset of MicroBooNE’s total dataset. The selection yields a sample with 60 % of selected tracks corresponding to neutron-induced secondary protons. At this purity, the integrated efficiency is 8.4% for neutrons that produce a detectable proton.
Chern-Simons theory, decomposition, and the A model
Pantev, Tony; Sharpe, Eric; Yu, Xingyang (2024-10-15)
In this paper, we discuss how gauging one-form symmetries in Chern-Simons theories is implemented in an A-twisted topological open string theory. For example, the contribution from a fixed H/Z bundle on a three-manifold M, arising in a BZ gauging of H Chern-Simons, for Z a finite subgroup of the center of H, is described by an open string worldsheet theory whose bulk is a sigma model with target a Z-gerbe (a bundle of one-form symmetries) over T∗M, of characteristic class determined by the H/Z bundle. We give a worldsheet picture of the decomposition of one-form-symmetry-gauged Chern-Simons in three dimensions, and we describe how a target-space constraint on bundles arising in the gauged Chern-Simons theory has a natural worldsheet realization. Our proposal provides examples of the expected correspondence between worldsheet global higher-form symmetries, and target-space gauged higher-form symmetries.
Scintillation light in SBND: simulation, reconstruction, and expected performance of the photon detection system
Mariani, Camillo (2024-10-10)
SBND is the near detector of the Short-Baseline Neutrino program at Fermilab. Its location near to the Booster Neutrino Beam source and relatively large mass will allow the study of neutrino interactions on argon with unprecedented statistics. This paper describes the expected performance of the SBND photon detection system, using a simulated sample of beam neutrinos and cosmogenic particles. Its design is a dual readout concept combining a system of 120 photomultiplier tubes, used for triggering, with a system of 192 X-ARAPUCA devices, located behind the anode wire planes. Furthermore, covering the cathode plane with highly-reflective panels coated with a wavelength-shifting compound recovers part of the light emitted towards the cathode, where no optical detectors exist. We show how this new design provides a high light yield and a more uniform detection efficiency, an excellent timing resolution and an independent 3D-position reconstruction using only the scintillation light. Finally, the whole reconstruction chain is applied to recover the temporal structure of the beam spill, which is resolved with a resolution on the order of nanoseconds.
Connexin 43 regulates intercellular mitochondrial transfer from human mesenchymal stromal cells to chondrocytes
Irwin, Rebecca M.; Thomas, Matthew A.; Fahey, Megan J.; Mayán, María D.; Smyth, James W.; Delco, Michelle L. (2024-10-10)
Background: The phenomenon of intercellular mitochondrial transfer from mesenchymal stromal cells (MSCs) has shown promise for improving tissue healing after injury and has potential for treating degenerative diseases like osteoarthritis (OA). Recently MSC to chondrocyte mitochondrial transfer has been documented, but the mechanism of transfer is unknown. Full-length connexin 43 (Cx43, encoded by GJA1) and the truncated, internally translated isoform GJA1-20k have been implicated in mitochondrial transfer between highly oxidative cells, but have not been explored in orthopaedic tissues. Here, our goal was to investigate the role of Cx43 in MSC to chondrocyte mitochondrial transfer. In this study, we tested the hypotheses that (a) mitochondrial transfer from MSCs to chondrocytes is increased when chondrocytes are under oxidative stress and (b) MSC Cx43 expression mediates mitochondrial transfer to chondrocytes. Methods: Oxidative stress was induced in immortalized human chondrocytes using tert-Butyl hydroperoxide (t-BHP) and cells were evaluated for mitochondrial membrane depolarization and reactive oxygen species (ROS) production. Human bone-marrow derived MSCs were transduced for mitochondrial fluorescence using lentiviral vectors. MSC Cx43 expression was knocked down using siRNA or overexpressed (GJA1 + and GJA1-20k+) using lentiviral transduction. Chondrocytes and MSCs were co-cultured for 24 h in direct contact or separated using transwells. Mitochondrial transfer was quantified using flow cytometry. Co-cultures were fixed and stained for actin and Cx43 to visualize cell-cell interactions during transfer. Results: Mitochondrial transfer was significantly higher in t-BHP-stressed chondrocytes. Contact co-cultures had significantly higher mitochondrial transfer compared to transwell co-cultures. Confocal images showed direct cell contacts between MSCs and chondrocytes where Cx43 staining was enriched at the terminal ends of actin cellular extensions containing mitochondria in MSCs. MSC Cx43 expression was associated with the magnitude of mitochondrial transfer to chondrocytes; knocking down Cx43 significantly decreased transfer while Cx43 overexpression significantly increased transfer. Interestingly, GJA1-20k expression was highly correlated with incidence of mitochondrial transfer from MSCs to chondrocytes. Conclusions Overexpression of GJA1-20k in MSCs increases mitochondrial transfer to chondrocytes, highlighting GJA1-20k as a potential target for promoting mitochondrial transfer from MSCs as a regenerative therapy for cartilage tissue repair in OA.

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