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  • Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation
    Lyu, Pengcheng; Jiang, Honglin (2024-03-12)
    Background: Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite cell proliferation and differentiation. Results: Using chromatin immunoprecipitation followed by sequencing, we identified 56,973 and 54,470 genomic regions marked with both the histone modifications H3K4me1 and H3K27ac, which were considered active enhancers, and 50,956 and 59,174 genomic regions marked with H3K27me3, which were considered repressed enhancers, in proliferating and differentiating bovine satellite cells, respectively. In addition, we identified 1,216 and 1,171 super-enhancers in proliferating and differentiating bovine satellite cells, respectively. Analyzing these enhancers showed that in proliferating bovine satellite cells, active enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation whereas repressed enhancers were associated with genes essential for myoblast differentiation, and that in differentiating satellite cells, active enhancers were associated with genes essential for myoblast differentiation or muscle contraction whereas repressed enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation. Active enhancers in proliferating bovine satellite cells were enriched with binding sites for many transcription factors such as MYF5 and the AP-1 family transcription factors; active enhancers in differentiating bovine satellite cells were enriched with binding sites for many transcription factors such as MYOG and TFAP4; and repressed enhancers in both proliferating and differentiating bovine satellite cells were enriched with binding sites for NF-kB, ZEB-1, and several other transcription factors. The role of TFAP4 in satellite cell or myoblast differentiation was previously unknown, and through gene knockdown and overexpression, we experimentally validated a critical role for TFAP4 in the differentiation and fusion of bovine satellite cells into myofibers. Conclusions: Satellite cell proliferation and differentiation are controlled by many transcription factors such as AP-1, TFAP4, NF-kB, and ZEB-1 whose roles in these processes were previously unknown in addition to those transcription factors such as MYF5 and MYOG whose roles in these processes are widely known.
  • Improving the performance of cryogenic calorimeters with nonlinear multivariate noise cancellation algorithms
    Vetter, K. J.; Beretta, M.; Capelli, C.; Corso, F. D.; Hansen, E. V.; Huang, R. G.; Kolomensky, Yu. G.; Marini, L.; Nutini, I.; Singh, V.; Torres, A.; Welliver, B.; Zimmermann, S.; Zucchelli, S. (2024-03-08)
    State-of-the-art physics experiments require high-resolution, low-noise, and low-threshold detectors to achieve competitive scientific results. However, experimental environments invariably introduce sources of noise, such as electrical interference or microphonics. The sources of this environmental noise can often be monitored by adding specially designed “auxiliary devices” (e.g. microphones, accelerometers, seismometers, magnetometers, and antennae). A model can then be constructed to predict the detector noise based on the auxiliary device information, which can then be subtracted from the true detector signal. Here, we present a multivariate noise cancellation algorithm which can be used in a variety of settings to improve the performance of detectors using multiple auxiliary devices. To validate this approach, we apply it to simulated data to remove noise due to electromagnetic interference and microphonic vibrations. We then employ the algorithm to a cryogenic light detector in the laboratory and show an improvement in the detector performance. Finally, we motivate the use of nonlinear terms to better model vibrational contributions to the noise in thermal detectors. We show a further improvement in the performance of a particular channel of the CUORE detector when using the nonlinear algorithm in combination with optimal filtering techniques.
  • Enabling regulatory policy globally will promote realization of the potential of animal biotechnology
    Hallerman, Eric M.; Bredlau, Justin; Camargo, Luiz S. A.; Dagli, Maria L. Z.; Karembu, Margaret; Kovich, Daniel; Muia, Anne N.; Murrone, Mariana L.; Rocha-Salavarrieta, Pedro J.; Romero-Aldemita, Rhodora; Tizard, Mark; Walton, Mark; Wray-Cahen, Diane (2024-03-06)
    Animal biotechnologies have the potential to improve the sustainability and security of our global food systems. Government regulatory authorities are responsible for ensuring the safety of food their citizens consume, whether it is produced via conventional breeding methods or biotechnologies. While some countries have implemented animal biotechnology oversight policies, many countries have yet to develop theirs. Historically, regulatory approvals were required before products of biotechnology could enter the marketplace, and the high cost of the approval process limited the number and types of animal and plant products that sought approval. Only one biotech animal in the world that was developed for food production has reached the market under a GMO or rDNA approval process. The advent of genome editing techniques has revolutionized the scientific approach to introducing changes into DNA sequences and how biotechnology can be used to enhance agricultural breeding. Regulatory dialogs about biotechnology also have changed as a result of these new technologies. Regulatory agencies have begun to respond to these scientific advances, and a growing number of countries are looking to modernize regulatory approaches for these products, based on risk (or lack thereof) and similarity to organisms that could be produced via conventional breeding methods. Advances in animal biotechnology, especially genome editing, can accelerate the incorporation of valued phenotypes in animals, including enhanced yield, disease resistance, resilience to changing climate, and improved animal welfare, as well as food qualities valued by consumers. For animals with these biotechnology-introduced traits to enter agricultural production and reach consumers, clear risk-proportionate regulatory approaches must be in place, and to facilitate international trade of animal products, regulatory processes need to be aligned and compatible. Effective scientific public communication is crucial to build public trust in precision animal biotechnology and risk-proportionate regulatory approaches. An international workshop on regulatory approaches for animal biotechnology was convened in 2022 with 27 countries represented. We synthesize here technical progress, development of regulatory policy, and strategies for engagement with diverse publics on animal biotechnology reported in the workshop. Our goal is to encourage development and implementation of risk-proportionate regulatory approaches and policies in a global context.
  • Introduction of a formative assessment tool in a post-graduate training program in India: a mixed methods evaluation
    Douglass, Katherine; Ahluwalia, Tania; McKiernan, Brianna; Patel, Heena; Powell, Natasha; Keller, Jacob; Toy, Serkan (2024-03-01)
    Background: Our institution has longstanding post-graduate education and training partnership programs in Emergency Medicine (EM) across India. A programmatic challenge has been the integration and uptake of evidence-based medicine and lifelong learning concepts. Formative assessment (FA) is intended to enable learners to monitor learning, identify strengths and weaknesses, and target areas of growth. As part of a program improvement initiative, we introduced an online FA tool to existing summative assessments. This study investigates how the FA tool was used and perceived by trainees. Methods: 246 trainees across 19 sites were given access to the FA tool. Usage metrics were monitored over 12 months. Semi-structured interviews were conducted in person with trainees using a purposive sampling methodology. A hybrid thematic analysis approach was used to determine themes. Interviews were coded independently by two blinded researchers using NVivo software. The study was deemed exempt by our institutional review board. Results: There was high variability in trainees’ utilization of the FA tool. Trainees who used the FA tool more performed better on summative exams (r = 0.35, p < 0.001). Qualitative analysis revealed that trainees were motivated to learn for improved clinical knowledge and to be a good physician, not only passing exams. Benefits of the tool included the relationship to clinical practice and thorough explanation of answers, while disadvantages included topics unrelated to India. Conclusion: The integration of a FA tool has provided positive outcomes for trainees in EM education programs in India. Lessons learned may apply globally to other contexts and programs.
  • Notes on gauging noninvertible symmetries. Part I. Multiplicity-free cases
    Perez-Lona, Alonso; Robbins, D.; Sharpe, E.; Vandermeulen, T.; Yu, X. (2024-02-21)
    In this paper we discuss gauging noninvertible zero-form symmetries in two dimensions. We specialize to certain gaugeable cases, specifically, fusion categories of the form for a suitable Hopf algebra (which includes the special case Rep(G) for G a finite group). We also specialize to the case that the fusion category is multiplicity-free. We discuss how to construct a modular-invariant partition function from a choice of Frobenius algebra structure on . We discuss how ordinary G orbifolds for finite groups G are a special case of the construction, corresponding to the fusion category Vec(G) = Rep(ℂ[G]*). For the cases Rep(S3), Rep(D4), and Rep(Q8), we construct the crossing kernels for general intertwiner maps. We explicitly compute partition functions in the examples of Rep(S3), Rep(D4), Rep(Q8), and , and discuss applications in c = 1 CFTs. We also discuss decomposition in the special case that the entire noninvertible symmetry group acts trivially.
  • Characteristics of departments with high-use of active learning in introductory STEM courses: implications for departmental transformation
    Lau, Alexandra C.; Henderson, Charles; Stains, Marilyne; Dancy, Melissa; Merino, Christian; Apkarian, Naneh; Raker, Jeffrey R.; Johnson, Estrella (2024-02-12)
    Background: It is well established in the literature that active learning instruction in introductory STEM courses results in many desired student outcomes. Yet, regular use of high-quality active learning is not the norm in many STEM departments. Using results of a national survey, we identified 16 departments where multiple instructors reported using high levels of active learning in their introductory chemistry, mathematics, or physics courses. We conducted interviews with 27 instructors in these 16 departments to better understand the characteristics of such departments. Results: Using grounded theory methodology, we developed a model that highlights relevant characteristics of departments with high use of active learning instruction in their introductory courses. According to this model, there are four main, interconnected characteristics of such departments: motivated people, knowledge about active learning, opportunities, and cultures and structures that support active learning. These departments have one or more people who are motivated to promote the use of active learning. These motivated people have knowledge about active learning as well as access to opportunities to promote the use of active learning. Finally, these departments have cultures and structures that support the use of active learning. In these departments, there is a positive feedback loop that works iteratively over time, where motivated people shape cultures/structures and these cultures/structures in turn increase the number and level of commitment of the motivated people. A second positive feedback loop was found between the positive outcome of using active learning instruction and the strengthening of cultures/structures supportive of active learning. Conclusions: According to the model, there are two main take-away messages for those interested in promoting the use of active learning. The first is that all four components of the model are important. A weak or missing component may limit the desired outcome. The second is that desired outcomes are obtained and strengthened over time through two positive feedback loops. Thus, there is a temporal aspect to change. In all of the departments that were part of our study, the changes took at minimum several years to enact. While our model was developed using only high-use of active learning departments and future work is needed to develop the model into a full change theory, our results do suggest that change efforts may be made more effective by increasing the robustness of the four components and the connections between them.
  • Constraints on a generalization of geometric quantum mechanics from neutrino and B0- B 0 ¯ $$ \overline{B^0} $$ oscillations
    Bhatta, Nabin; Minic, Djordje; Takeuchi, Tatsu (2024-02-05)
    Abstract Nambu Quantum Mechanics, proposed in Phys. Lett. B536, 305 (2002), is a deformation of canonical Quantum Mechanics in which the manifold over which the “phase” of an energy eigenstate time evolves is modified. This generalization affects oscillation and interference phenomena through the introduction of two deformation parameters that quantify the extent of deviation from canonical Quantum Mechanics. In this paper, we constrain these parameters utilizing atmospheric neutrino oscillation data, and B0- B 0 ¯ $$ \overline{B^0} $$ oscillation data from Belle. Surprisingly, the bound from atmospheric neutrinos is stronger than the bound from Belle. Various features of Nambu Quantum Mechanics are also discussed.
  • Neutrino amplitude decomposition, S matrix rephasing invariance, and reparametrization symmetry
    Minakata, Hisakazu (2024-02-07)
    Abstract The S matrix rephasing invariance is one of the fundamental principles of quantum mechanics that originates in its probabilistic interpretation. For a given S matrix which describes neutrino oscillation, one can define the two different rephased amplitudes S αβ Reph − 1 ≡ e i λ 1 / 2 E x S αβ $$ {S}_{\alpha \beta}^{\textrm{Reph}-1}\equiv {e}^{i\left({\lambda}_1/2E\right)x}{S}_{\alpha \beta} $$ and S αβ Reph − 2 ≡ e i λ 2 / 2 E x S αβ $$ {S}_{\alpha \beta}^{\textrm{Reph}-2}\equiv {e}^{i\left({\lambda}_2/2E\right)x}{S}_{\alpha \beta} $$ , which are physically equivalent to each other, where λk/2E denotes the energy eigenvalue of the k-th mass eigenstate. We point out that the transformation of the reparametrization (Rep) symmetry obtained with “Symmetry Finder” maps S αβ Reph − 1 $$ {S}_{\alpha \beta}^{\textrm{Reph}-1} $$ to S αβ Reph − 2 $$ {S}_{\alpha \beta}^{\textrm{Reph}-2} $$ , and vice versa, providing a local and manifest realization of the S matrix rephasing invariance by the Rep symmetry of the 1–2 state exchange type. It is strongly indicative of quantum mechanical nature of the Rep symmetry. The rephasing and Rep symmetry relation, though its all-order treatment remains incomplete, is shown to imply absence of the pure 1–3 exchange symmetry in Denton et al. perturbation theory. It then triggers a study of convergence of perturbation series.
  • Delayed presentation of food protein-induced enterocolitis syndrome (FPIES) to okra in a toddler
    Hall, Hunter; Anvari, Sara; Schultz, Fallon; Ojuola, Olubukola; Rider, Nicholas L. (2024-02-03)
    Background: Food protein-induced enterocolitis syndrome (FPIES) is a non-immunoglobulin E (IgE) -mediated food allergy predominantly observed in infants and characterized by the delayed onset of vomiting following ingestion of a trigger food. An increase in research and clinical consideration of FPIES has led to the discovery of unique deviations from the standard FPIES triggers and presentations. Case presentation: A 34-month-old female patient with a history of consuming okra daily presented to medical attention after developing classic FPIES symptoms to okra beginning at 14-months of age. Conclusions: Recently, awareness about the varied nature of FPIES clinical presentation has come to light. This case is the first to describe FPIES to the fruit okra that developed over a 12-month time span after previously tolerating the food. This case serves to emphasize the importance of understanding the range of FPIES symptoms to improve recognition and expedite best practice recommendations.
  • Immunoregulatory and neutrophil-like monocyte subsets with distinct single-cell transcriptomic signatures emerge following brain injury
    Gudenschwager Basso, Erwin K.; Ju, Jing; Soliman, Eman; de Jager, Caroline; Wei, Xiaoran; Pridham, Kevin J.; Olsen, Michelle L.; Theus, Michelle H. (2024-02-03)
    Monocytes represent key cellular elements that contribute to the neurological sequela following brain injury. The current study reveals that trauma induces the augmented release of a transcriptionally distinct CD115+/Ly6Chi monocyte population into the circulation of mice pre-exposed to clodronate depletion conditions. This phenomenon correlates with tissue protection, blood–brain barrier stability, and cerebral blood flow improvement. Uniquely, this shifted the innate immune cell profile in the cortical milieu and reduced the expression of pro-inflammatory Il6, IL1r1, MCP-1, Cxcl1, and Ccl3 cytokines. Monocytes that emerged under these conditions displayed a morphological and gene profile consistent with a subset commonly seen during emergency monopoiesis. Single-cell RNA sequencing delineated distinct clusters of monocytes and revealed a key transcriptional signature of Ly6Chi monocytes enriched for Apoe and chitinase-like protein 3 (Chil3/Ym1), commonly expressed in pro-resolving immunoregulatory monocytes, as well as granule genes Elane, Prtn3, MPO, and Ctsg unique to neutrophil-like monocytes. The predominate shift in cell clusters included subsets with low expression of transcription factors involved in monocyte conversion, Pou2f2, Na4a1, and a robust enrichment of genes in the oxidative phosphorylation pathway which favors an anti-inflammatory phenotype. Transfer of this monocyte assemblage into brain-injured recipient mice demonstrated their direct role in neuroprotection. These findings reveal a multifaceted innate immune response to brain injury and suggest targeting surrogate monocyte subsets may foster tissue protection in the brain.
  • Identifying sensors-based parameters associated with fall risk in community-dwelling older adults: an investigation and interpretation of discriminatory parameters
    Wang, Xuan; Cao, Junjie; Zhao, Qizheng; Chen, Manting; Luo, Jiajia; Wang, Hailiang; Yu, Lisha; Tsui, Kwok-Leung; Zhao, Yang (2024-02-01)
    Background: Falls pose a severe threat to the health of older adults worldwide. Determining gait and kinematic parameters that are related to an increased risk of falls is essential for developing effective intervention and fall prevention strategies. This study aimed to investigate the discriminatory parameter, which lay an important basis for developing effective clinical screening tools for identifying high-fall-risk older adults. Methods: Forty-one individuals aged 65 years and above living in the community participated in this study. The older adults were classified as high-fall-risk and low-fall-risk individuals based on their BBS scores. The participants wore an inertial measurement unit (IMU) while conducting the Timed Up and Go (TUG) test. Simultaneously, a depth camera acquired images of the participants’ movements during the experiment. After segmenting the data according to subtasks, 142 parameters were extracted from the sensor-based data. A t-test or Mann-Whitney U test was performed on the parameters for distinguishing older adults at high risk of falling. The logistic regression was used to further quantify the role of different parameters in identifying high-fall-risk individuals. Furthermore, we conducted an ablation experiment to explore the complementary information offered by the two sensors. Results: Fifteen participants were defined as high-fall-risk individuals, while twenty-six were defined as low-fall-risk individuals. 17 parameters were tested for significance with p-values less than 0.05. Some of these parameters, such as the usage of walking assistance, maximum angular velocity around the yaw axis during turn-to-sit, and step length, exhibit the greatest discriminatory abilities in identifying high-fall-risk individuals. Additionally, combining features from both devices for fall risk assessment resulted in a higher AUC of 0.882 compared to using each device separately. Conclusions: Utilizing different types of sensors can offer more comprehensive information. Interpreting parameters to physiology provides deeper insights into the identification of high-fall-risk individuals. High-fall-risk individuals typically exhibited a cautious gait, such as larger step width and shorter step length during walking. Besides, we identified some abnormal gait patterns of high-fall-risk individuals compared to low-fall-risk individuals, such as less knee flexion and a tendency to tilt the pelvis forward during turning.
  • Quantum cohomology from mixed Higgs-Coulomb phases
    Gu, Wei; Melnikov, Ilarion V.; Sharpe, Eric (2024-02-01)
    We generalize Coulomb-branch-based gauged linear sigma model (GLSM)–computations of quantum cohomology rings of Fano spaces. Typically such computations have focused on GLSMs without superpotential, for which the low energy limit of the GLSM is a pure Coulomb branch, and quantum cohomology is determined by the critical locus of a twisted one-loop effective superpotential. We extend these results to cases for which the low energy limit of the GLSM includes both Coulomb and Higgs branches, where the latter is a Landau-Ginzburg orbifold. We describe the state spaces and products of corresponding operators in detail, comparing a geometric phase description, where the operator product ring is quantum cohomology, to the description in terms of Coulomb and Higgs branch states. As a concrete test of our methods, we compare to existing mathematics results for quantum cohomology rings of hypersurfaces in projective spaces.
  • Twisted Fibrations in M/F-theory
    Anderson, Lara B.; Gray, James; Oehlmann, Paul-Konstantin (2024-01-04)
    In this work we investigate 5-dimensional theories obtained from M-theory on genus one fibered threefolds which exhibit twisted algebras in their fibers. We provide a base-independent algebraic description of the threefolds and compute light 5D BPS states charged under finite sub-algebras of the twisted algebras. We further construct the Jacobian fibrations that are associated to 6-dimensional F-theory lifts, where the twisted algebra is absent. These 6/5-dimensional theories are compared via twisted circle reductions of F-theory to M-theory. In the 5-dimensional theories we discuss several geometric transitions that connect twisted with untwisted fibrations. We present detailed discussions of 𝔢(2)6,𝔰𝔬(3)8 and 𝔰𝔲(2)3 twisted fibers and provide several explicit example threefolds via toric constructions. Finally, limits are considered in which gravity is decoupled, including Little String Theories for which we match 2-group symmetries across twisted T-dual theories.
  • Multi-tier dynamic sampling weak RF signal estimation theory
    Smith, Brett; Lanzerotti, Mary (2024-01-06)
    This paper presents a theoretical analysis in discrete time for a multi-tier weak radiofrequency (RF) signal estimation process with N simultaneous signals. Discrete time dynamic sampling is introduced and is shown to provide the capability to extract signal parameter values with increased accuracy compared with accuracy of estimates obtained in prior work. This paper advances phase measurement approaches by proposing discrete time dynamic sampling which our paper shows offers the desirable capability for more accurate weak signal parameter estimates. For N = 2 simultaneous signals with a strong signal at 850 MHz and a weak signal at 855 MHz, the results show that dynamically sampling the instantaneous frequency at 24 times the Nyquist rate provides weak signal frequency estimates that are within 1.7 x 10 -5 of the actual weak signal frequency and weak signal amplitude estimates that are within 428 PPM of the actual weak signal amplitude. Results are also presented for situations with N = 2 simultaneous 5G signals. In one case, the strong signal is 3950 MHz, and the weak signal is 3955 MHz; in the other case the strong case is 5950 MHz, and the weak signal is 5955 MHz. The results for these cases show that estimates obtained with dynamic sampling are more accurate than estimates provided using a single sample rate of 65 MSPS. This work has promising applications for weak signal parameters estimation using instantaneous frequency measurements.
  • Constraints on directionality effect of nuclear recoils in a liquid argon time projection chamber
    (2024-01-10)
    The direct search for dark matter in the form of weakly interacting massive particles (WIMP) is performed by detecting nuclear recoils produced in a target material from the WIMP elastic scattering. The experimental identification of the direction of the WIMP-induced nuclear recoils is a crucial asset in this field, as it enables unmistakable modulation signatures for dark matter. The Recoil Directionality (ReD) experiment was designed to probe for such directional sensitivity in argon dual-phase time projection chambers (TPC), that are widely considered for current and future direct dark matter searches. The TPC of ReD was irradiated with neutrons at the INFN Laboratori Nazionali del Sud. Data were taken with nuclear recoils of known directions and kinetic energy of 72 keV, which is within the range of interest for WIMP-induced signals in argon. The direction-dependent liquid argon charge recombination model by Cataudella et al. was adopted and a likelihood statistical analysis was performed, which gave no indications of significant dependence of the detector response to the recoil direction. The aspect ratio R of the initial ionization cloud is R < 1.072 with 90% confidence level.
  • Piloting a one-day parent-only intervention in the treatment of youth with anxiety disorders: child and family-level outcomes
    Cobham, Vanessa E.; Radtke, Sarah R.; Hawkins, Ingrid; Jordan, Michele; Ali, Nasriah R.; Ollendick, Thomas H.; Sanders, Matthew R. (2024-01-13)
    Objective: Parent-only cognitive-behavioural therapy (CBT) interventions have promise for youth with anxiety disorders. Fear-Less Triple P (FLTP) is one such intervention that has been found comparable to child-focused CBT. Although traditionally administered in six sessions, a one-day workshop format of FLTP was developed to improve accessibility. The current study compared the effectiveness of the six-session and one-day workshop formats. Method: Seventy-three youth (mean age, 8.4 years; 74% male) were randomized to traditional FLTP (6-week group) or the one-day workshop format. Anxiety diagnostic status, self- and parent-reported anxiety symptoms scores, independent evaluator-rated improvement, treatment satisfaction, and measures of family functioning were included to assess treatment outcome. Data were collected prior to treatment, and 1-week, 6-months, and 12-months following treatment. Results: Both conditions resulted in significant improvement in child anxiety symptom scores per parent report (on both questionnaire and diagnostic interview measures). Furthermore, significant decreases in sibling anxiety were observed in both treatment conditions. There were no statistically significant differences between conditions on any outcome measure. Conclusions: Results of this study add to the growing evidence that brief, low-intensity, parent-only interventions can effectively target child psychopathology. These brief interventions are ideal for families for whom the resources and time required to commit to a standard multi-week intervention are prohibitive.
  • Local studies provide a global perspective of the impacts of climate change on Indigenous Peoples and local communities
    Reyes-García, Victoria; García-Del-Amo, David; Porcuna-Ferrer, Anna; Schlingmann, Anna; Abazeri, Mariam; Attoh, Emmanuel M. N. A. N.; Vieira da Cunha Ávila, Julia; Ayanlade, Ayansina; Babai, Daniel; Benyei, Petra; Calvet-Mir, Laura; Carmona, Rosario; Caviedes, Julián; Chah, Jane; Chakauya, Rumbidzayi; Cuní-Sanchez, Aida; Fernández-Llamazares, Álvaro; Galappaththi, Eranga K.; Gerkey, Drew; Graham, Sonia; Guillerminet, Théo; Huanca, Tomás; Ibarra, José T.; Junqueira, André B.; Li, Xiaoyue; López-Maldonado, Yolanda; Mattalia, Giulia; Samakov, Aibek; Schunko, Christoph; Seidler, Reinmar; Sharakhmatova, Victoria; Singh, Priyatma; Tofighi-Niaki, Adrien; Torrents-Ticó, Miquel (2024-01-08)
    Indigenous Peoples and local communities with nature-dependent livelihoods are disproportionately affected by climate change impacts, but their experience, knowledge and needs receive inadequate attention in climate research and policy. Here, we discuss three key findings of a collaborative research consortium arising from the Local Indicators of Climate Change Impacts project. First, reports of environmental change by Indigenous Peoples and local communities provide holistic, relational, placed-based, culturally-grounded and multi-causal understandings of change, largely focused on processes and elements that are relevant to local livelihoods and cultures. These reports demonstrate that the impacts of climate change intersect with and exacerbate historical effects of socioeconomic and political marginalization. Second, drawing on rich bodies of inter-generational knowledge, Indigenous Peoples and local communities have developed context-specific responses to environmental change grounded in local resources and strategies that often absorb the impacts of multiple drivers of change. Indigenous Peoples and local communities adjust in diverse ways to impacts on their livelihoods, but the adoption of responses often comes at a significant cost due to economic, political, and socio-cultural barriers operating at societal, community, household, and individual levels. Finally, divergent understandings of change challenge generalizations in research examining the human dimensions of climate change. Evidence from Indigenous and local knowledge systems is context-dependent and not always aligned with scientific evidence. Exploring divergent understandings of the concept of change derived from different knowledge systems can yield new insights which may help prioritize research and policy actions to address local needs and priorities.
  • The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes
    Ryazansky, Sergei S.; Chen, Chujia; Potters, Mark; Naumenko, Anastasia N.; Lukyanchikova, Varvara; Masri, Reem A.; Brusentsov, Ilya I.; Karagodin, Dmitriy A.; Yurchenko, Andrey A.; dos Anjos, Vitor L.; Haba, Yuki; Rose, Noah H.; Hoffman, Jinna; Guo, Rong; Menna, Theresa; Kelley, Melissa; Ferrill, Emily; Schultz, Karen E.; Qi, Yumin; Sharma, Atashi; Deschamps, Stéphane; Llaca, Victor; Mao, Chunhong; Murphy, Terence D.; Baricheva, Elina M.; Emrich, Scott; Fritz, Megan L.; Benoit, Joshua B.; Sharakhov, Igor V.; McBride, Carolyn S.; Tu, Zhijian; Sharakhova, Maria V. (2024-01-25)
    Background: Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. Methods: In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. Results: We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. Conclusion: The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
  • Genotype-by-environment interactions for feed efficiency traits in Nellore cattle based on bi-trait reaction norm models
    Silva Neto, João B.; Mota, Lucio F. M.; Amorim, Sabrina T.; Peripolli, Elisa; Brito, Luiz F.; Magnabosco, Claudio U.; Baldi, Fernando (2023-12-14)
    Background: Selecting animals for feed efficiency directly impacts the profitability of the beef cattle industry, which contributes to minimizing the environmental footprint of beef production. Genetic and environmental factors influence animal feed efficiency, leading to phenotypic variability when exposed to different environmental conditions (i.e., temperature and nutritional level). Thus, our aim was to assess potential genotype-by-environment (G × E) interactions for dry matter intake (DMI) and residual feed intake (RFI) in Nellore cattle (Bos taurus indicus) based on bi-trait reaction norm models (RN) and evaluate the genetic association between RFI and DMI across different environmental gradient (EG) levels. For this, we used phenotypic information on 12,958 animals (young bulls and heifers) for DMI and RFI recorded during 158 feed efficiency trials. Results: The heritability estimates for DMI and RFI across EG ranged from 0.26 to 0.54 and from 0.07 to 0.41, respectively. The average genetic correlations (± standard deviation) across EG for DMI and RFI were 0.83 ± 0.19 and 0.81 ± 0.21, respectively, with the lowest genetic correlation estimates observed between extreme EG levels (low vs. high) i.e. 0.22 for RFI and 0.26 for DMI, indicating the presence of G × E interactions. The genetic correlation between RFI and DMI across EG levels decreased as the EG became more favorable and ranged from 0.79 (lowest EG) to 0.52 (highest EG). Based on the estimated breeding values from extreme EG levels (low vs. high), we observed a moderate Spearman correlation of 0.61 (RFI) and 0.55 (DMI) and a selection coincidence of 53.3% and 40.0% for RFI and DMI, respectively. Conclusions: Our results show evidence of G × E interactions on feed efficiency traits in Nellore cattle, especially in feeding trials with an average daily gain (ADG) that is far from the expected of 1 kg/day, thus increasing reranking of animals.
  • Generating synthetic as-built additive manufacturing surface topography using progressive growing generative adversarial networks
    Seo, Junhyeon; Rao, Prahalada; Raeymaekers, Bart (2023-12-04)
    Numerically generating synthetic surface topography that closely resembles the features and characteristics of experimental surface topography measurements reduces the need to perform these intricate and costly measurements. However, existing algorithms to numerically generated surface topography are not well-suited to create the specific characteristics and geometric features of as-built surfaces that result from laser powder bed fusion (LPBF), such as partially melted metal particles, porosity, laser scan lines, and balling. Thus, we present a method to generate synthetic as-built LPBF surface topography maps using a progressively growing generative adversarial network. We qualitatively and quantitatively demonstrate good agreement between synthetic and experimental as-built LPBF surface topography maps using areal and deterministic surface topography parameters, radially averaged power spectral density, and material ratio curves. The ability to accurately generate synthetic as-built LPBF surface topography maps reduces the experimental burden of performing a large number of surface topography measurements. Furthermore, it facilitates combining experimental measurements with synthetic surface topography maps to create large data-sets that facilitate, e.g. relating as-built surface topography to LPBF process parameters, or implementing digital surface twins to monitor complex end-use LPBF parts, amongst other applications.