Impact of protein and small molecule interactions on kinase conformations.

Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.

The influence of scaffolding on intrinsic motivation and autonomous adherence to a game-based, sparsely supervised home rehabilitation program for people with upper extremity hemiparesis due to stroke. A randomized controlled trial.

BACKGROUND: This parallel, randomized controlled trial examined intrinsic motivation, adherence and motor function improvement demonstrated by two groups of subjects that performed a 12-week, home-based upper extremity rehabilitation program. Seventeen subjects played scaffolded games, presenting eight to twelve discrete levels of increasing difficulty. Sixteen subjects performed the same activities controlled by success algorithms that modify game difficulty incrementally. METHODS: 33 persons 20-80 years of age, at least 6 months post stroke with moderate to mild hemiparesis were randomized using a random number generator into the two groups. They were tested using the Action Research Arm Test, Upper Extremity Fugl Meyer Assessment, Stroke Impact Scale and Intrinsic Motivation Inventory pre and post training. Adherence was measured using timestamps generated by the gaming system. Subjects had the Home Virtual Rehabilitation System (Qiu in J Neuroeng Rehabil 17: 1-10, 2020) placed in their homes and were taught to perform rehabilitation games using it. Subjects were instructed to train twenty minutes per day but were allowed to train as much as they chose. Subjects trained for 12 weeks without appointments and received intermittent support from study staff. Group outcomes were compared using ANOVA. Correlations between subject demographics and adherence, as well as motor outcome, were evaluated using Pearson Correlation Coefficients. RESULTS: There were 5 dropouts and no adverse events. The main effect of time was statistically significant for four of the five clinical outcome measures. There were no significant training group by time interactions. Measures of adherence did not differ significantly between groups. The combined groups improved their UEFMA scores on average by 5.85 (95% CI 4.73-6.98). 21 subjects from both groups demonstrating improvements in UEFMA scores of at least 5 points, exceeding the minimal clinically important difference of 4.25. IMI scores were stable pre to post training. CONCLUSIONS: Scaffolding challenges during game based rehabilitation did not elicit higher levels of adherence when compared to algorithm control of game difficulty. Both sparsely supervised programs of game-based treatment in the home were sufficient to elicit statistically significant, clinically meaningful improvements in motor function and activities of daily living. TRIAL REGISTRATION: Clinical Trials.gov-NCT03985761, Registered June 14, 2019.

A qualitative exploration and a Fuzzy Delphi validation of high-risk scaffolding tasks and fatigue-related safety behavioural deviation among scaffolders.

Background: Most construction mishaps were caused by scaffolding incidents despite implementing various safety measures, and the association with human factors like fatigue has been widely reported. This study aims to identify all high-risk task sequences involved during the erection of the most commonly used scaffold; the deviation from the standard protocol led to a substandard fatigue state, followed by content validation using the Fuzzy Delphi Method. Methods: Qualitative exploration was conducted via focal group discussions (FGDs) involving 30 certified experts. The findings generated from FGDs were further validated by utilising the Fuzzy Delphi Method (FDM) by consulting 19 experts with extensive practical experience and leadership roles in scaffolding safety. Results: The FGDs identified a total of 7 constructs and 50 items for task sequences involved in the tubular scaffold erection, namely construct Instruction (3 items), Preparation (3 items), Foundation (10 items), First Lift (8 items), Working Platform (7 items), Guardrails (5 items) and Second Lift (14 items). In the FDM validation process, the experts' consensus for each construct was fulfilled with a threshold value (d) ≤ 0.2; thus, all constructs were accepted. Experts' consensus for all items achieved an expert agreement of 75 % and above. Items ranking was conducted using average fuzzy numbers. The highest average fuzzy number documented was 0.8, while the lowest was 0.588. None of the items with the lowest ranking was discarded as all items perfectly fulfilled the second prerequisite and obtained excellent experts' agreement. Conclusions: The tool generated will help guide the development of a protocol for scaffolding safety management.

Maptcha: an efficient parallel workflow for hybrid genome scaffolding.

BACKGROUND: Genome assembly, which involves reconstructing a target genome, relies on scaffolding methods to organize and link partially assembled fragments. The rapid evolution of long read sequencing technologies toward more accurate long reads, coupled with the continued use of short read technologies, has created a unique need for hybrid assembly workflows. The construction of accurate genomic scaffolds in hybrid workflows is complicated due to scale, sequencing technology diversity (e.g., short vs. long reads, contigs or partial assemblies), and repetitive regions within a target genome. RESULTS: In this paper, we present a new parallel workflow for hybrid genome scaffolding that would allow combining pre-constructed partial assemblies with newly sequenced long reads toward an improved assembly. More specifically, the workflow, called Maptcha, is aimed at generating long scaffolds of a target genome, from two sets of input sequences-an already constructed partial assembly of contigs, and a set of newly sequenced long reads. Our scaffolding approach internally uses an alignment-free mapping step to build a ⟨ contig,contig ⟩ graph using long reads as linking information. Subsequently, this graph is used to generate scaffolds. We present and evaluate a graph-theoretic "wiring" heuristic to perform this scaffolding step. To enable efficient workload management in a parallel setting, we use a batching technique that partitions the scaffolding tasks so that the more expensive alignment-based assembly step at the end can be efficiently parallelized. This step also allows the use of any standalone assembler for generating the final scaffolds. CONCLUSIONS: Our experiments with Maptcha on a variety of input genomes, and comparison against two state-of-the-art hybrid scaffolders demonstrate that Maptcha is able to generate longer and more accurate scaffolds substantially faster. In almost all cases, the scaffolds produced by Maptcha are at least an order of magnitude longer (in some cases two orders) than the scaffolds produced by state-of-the-art tools. Maptcha runs significantly faster too, reducing time-to-solution from hours to minutes for most input cases. We also performed a coverage experiment by varying the sequencing coverage depth for long reads, which demonstrated the potential of Maptcha to generate significantly longer scaffolds in low coverage settings ( 1 × - 10 × ).

Maneuvering between cultures: The reception of hospice care in the Chinese medical community.

The expansion of hospice care worldwide has been received differently by medical communities in different societies. Nonetheless, existing efforts to explain how culture affects the reception of hospice care are inadequate. On the basis of fieldwork conducted in Chinese medical institutions and care facilities between 2017 and 2022, this paper draws on a theoretical framework that distinguishes between declarative culture and nondeclarative culture at the personal level to explain the discrepancies between healthcare professionals' beliefs regarding the value of hospice care and their daily healthcare practice. Moreover, this paper uses the concept of cultural scaffolding to demonstrate that the culture of hospice care and the culture of medical institutions are not separate, independent entities but rather evolve together to produce new and local forms of hospice care in the Chinese context. This analysis helps clarify the obstacles and opportunities associated with hospice care in China and contributes to existing research on the reception of hospice care worldwide.

Early Family Experiences and Neural Activity in Rural Pakistani Children: The Differential Role of Gender.

Adversity within low- and middle-income countries (LMICs) poses severe threats to neurocognitive development, which can be partially mitigated by high-quality early family experiences. Specifically, maternal scaffolding and home stimulation can buffer cognitive development in LMIC, possibly by protecting underlying neural functioning. However, the association between family experiences and neural activity remains largely unexplored in LMIC contexts. This study explored the relation of early family experiences to later cognitive skills and absolute gamma power (21-45 Hz), a neural marker linked to higher-order cognitive skills. Drawing data from the PEDS trial, a longitudinal study in rural Pakistan, we examined maternal scaffolding at 24 months and home stimulation quality at 18 months as predictors of verbal IQ, executive functions, and absolute gamma at 48 months for 105 mother-child dyads (52 girls). Maternal scaffolding interacted with gender to predict absolute gamma power, such that higher maternal scaffolding was related to higher gamma more strongly for girls. Maternal scaffolding also interacted with absolute gamma to predict executive functions, such that higher gamma was related to better executive functions only when maternal scaffolding was average to high. Individual differences in early family experiences may partially buffer the neural underpinnings of cognitive skills from adversity in LMIC.

Blackout Poetry: Eclipsing With Words and Images to Illuminate Ideas.

Integrating literacy practices in science classrooms can help students read complex scientific text, write arguments as part of shared cross-disciplinary practices, and engage with content. In the Linking Science, Mathematics, and Literacy for All Learners program, middle school science, mathematics, ELA, and special education teachers have been implementing multimodal STEM text sets that include a range of texts and scaffolds that support instruction and students' content learning. One of these strategies combines reading and writing in unique and creative ways: poetry writing! Blackout and found poems are accessible approaches to help students focus on key words and ideas in a complex text, pull out those words to work with them, and then reconstruct them into a poem. This approach can be used in a variety of ways, and in some of the examples provided, students include an altered page from a scientific article on which they find their words, black out the rest of the text, and then illustrate the entire document to help show their message.

Hydrogels for Neural Regeneration: Exploring New Horizons.

Nerve injury can significantly impair motor, sensory, and autonomic functions. Understanding nerve degeneration, particularly Wallerian degeneration, and the mechanisms of nerve regeneration is crucial for developing effective treatments. This manuscript reviews the use of advanced hydrogels that have been researched to enhance nerve regeneration. Hydrogels, due to their biocompatibility, tunable properties, and ability to create a supportive microenvironment, are being explored for their effectiveness in nerve repair. Various types of hydrogels, such as chitosan-, alginate-, collagen-, hyaluronic acid-, and peptide-based hydrogels, are discussed for their roles in promoting axonal growth, functional recovery, and myelination. Advanced formulations incorporating growth factors, bioactive molecules, and stem cells show significant promise in overcoming the limitations of traditional therapies. Despite these advancements, challenges in achieving robust and reliable nerve regeneration remain, necessitating ongoing research to optimize hydrogel-based interventions for neural regeneration.

The Evolving Role of Bruton's Tyrosine Kinase Inhibitors in B Cell Lymphomas.

Bruton's tyrosine kinase (BTK), a non-receptor tyrosine kinase crucial for B cell development and function, acts downstream of the B cell receptor (BCR) in the BCR pathway. Other kinases involved downstream of the BCR besides BTK such as Syk, Lyn, PI3K, and Mitogen-activated protein (MAP) kinases also play roles in relaying signals from the BCR to provide pro-survival, activation, and proliferation cues. BTK signaling is implicated in various B-cell lymphomas such as mantle cell lymphoma, Waldenström Macroglobulinemia, follicular lymphoma, and diffuse large B cell lymphoma, leading to the development of transformative treatments like ibrutinib, the first-in-class covalent BTK inhibitor, and pirtobrutinib, the first-in-class noncovalent BTK inhibitor. However, kinase-deficient mutations C481F, C481Y, C481R, and L528W in the BTK gene confer resistance to both covalent and non-covalent BTK inhibitors, facilitating B cell survival and lymphomagenesis despite kinase inactivation. Further studies have revealed BTK's non-catalytic scaffolding function, mediating the assembly and activation of proteins including Toll-like receptor 9 (TLR9), vascular cell adhesion protein 1 (VCAM-1), hematopoietic cell kinase (HCK), and integrin-linked kinase (ILK). This non-enzymatic role promotes cell survival and proliferation independently of kinase activity. Understanding BTK's dual roles unveils opportunities for therapeutics targeting its scaffolding function, promising advancements in disrupting lymphomagenesis and refining B cell lymphoma treatments.

Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast.

The ecological and evolutionary success of multicellular lineages is due in no small part to their increased size relative to unicellular ancestors. However, large size also poses biophysical challenges, especially regarding the transport of nutrients to all cells; these constraints are typically overcome through multicellular innovations (e.g., a circulatory system). Here we show that an emergent biophysical mechanism - spontaneous fluid flows arising from metabolically-generated density gradients - can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Surprisingly, beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This work demonstrates how simple physical mechanisms can act as a 'biophysical scaffold' to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations. More broadly, our findings highlight how co-option of conserved physical processes is a crucial but underappreciated facet of evolutionary innovation across scales.

New mechanism of LncRNA: In addition to act as a ceRNA.

Long non-coding RNAs (LncRNAs) are a class of RNA molecules with nucleic acid lengths ranging from 200 bp to 100 kb that cannot code for proteins, which are diverse and widely expressed in both animals and plants. Scholars have found that lncRNAs can regulate human physiological processes at the gene and protein levels, mainly through the regulation of epigenetic, transcriptional and post-transcriptional levels of genes and proteins, as well as in the immune response by regulating the expression of immune cells and inflammatory factors, and thus participate in the occurrence and development of a variety of diseases. From the downstream targets of lncRNAs, we summarize the new research progress of lncRNA mechanisms other than miRNA sponges in recent years, aiming to provide new ideas and directions for the study of lncRNA mechanisms.

Caveolin-1 differentially regulates the transforming growth factor-ß and epidermal growth factor signaling pathways in MDCK cells.

Caveolin-1 is critical for interacting with the TGF-ß receptor (TGFßR) and EGF receptor (EGFR) signaling, often observed in advanced cancers and tissue fibrosis. However, the mechanism underlying caveolin-1-mediated transactivation of TGFßR and EGFR signaling remains unclear. Therefore, we sought to determine whether caveolin-1 is involved in canonical and non-canonical TGFßR and EGFR signaling transactivation in this study. Methyl-ß-cyclodextrin (MßCD) was used to disrupt the cholesterol-containing membranes domains, and the caveolin-1 scaffolding domain (CSD) peptide was used to mimic the CSD of caveolin-1. Additionally, we transfected the Madin-Darby canine kidney cells with wild-type or phosphorylation-defective caveolin-1. We discovered that tyrosine 14 of caveolin-1 was critical for the negative regulation of TGFßR and EGFR canonical signaling. On the contrary, caveolin-1 inhibited TGF-ß1-induced ERK2 activation independent of tyrosine 14 phosphorylation. Although EGF failed to induce Smad3 phosphorylation in caveolin-1 knockdown cells, it activated Smad3 upon MßCD co-treatment, indicating that caveolin-1 indirectly regulated the non-canonical pathway of EGF. In conclusion, caveolin-1 differentially modulates TGFßR and EGFR signaling. Thus, targeting caveolin-1 is a potential strategy for treating diseases involving TGF-ß1 and EGF signaling.

Scaffolding fundamentals and recent advances in sustainable scaffolding techniques for cultured meat development.

In cultured meat (CM) production, Scaffolding plays an important role by aiding cell adhesion, growth, differentiation, and alignment. The existence of fibrous microstructure in connective and muscle tissues has attracted considerable interest in the realm of tissue engineering and triggered the interest of researchers to implement scaffolding techniques. A wide array of research efforts is ongoing in scaffolding technologies for achieving the real meat structure on the principality of biomedical research and to replace serum free CM production. Scaffolds made of animal-derived biomaterials are found efficient in replicating the extracellular matrix (ECM), thus focus should be paid to utilize animal byproducts for this purpose. Proper identification and utilization of plant-derived scaffolding biomaterial could be helpful to add diversified options in addition to animal derived sources and reduce in cost of CM production through scaffolds. Furthermore, techniques like electrospinning, modified electrospinning and 3D bioprinting should be focused on to create 3D porous scaffolds to mimic the ECM of the muscle tissue and form real meat-like structures. This review discusses recent advances in cutting edge scaffolding techniques and edible biomaterials related to structured CM production.

Arrestin-3-assisted activation of JNK3 mediates dopaminergic behavioral sensitization.

In rodents with unilateral ablation of neurons supplying dopamine to the striatum, chronic treatment with the dopamine precursor L-DOPA induces a progressive increase of behavioral responses, a process known as behavioral sensitization. This sensitization is blunted in arrestin-3 knockout mice. Using virus-mediated gene delivery to the dopamine-depleted striatum of these mice, we find that the restoration of arrestin-3 fully rescues behavioral sensitization, whereas its mutant defective in c-Jun N-terminal kinase (JNK) activation does not. A 25-residue arrestin-3-derived peptide that facilitates JNK3 activation in cells, expressed ubiquitously or selectively in direct pathway striatal neurons, also fully rescues sensitization, whereas an inactive homologous arrestin-2-derived peptide does not. Behavioral rescue is accompanied by the restoration of JNK3 activity, as reflected by JNK-dependent phosphorylation of the transcription factor c-Jun in the dopamine-depleted striatum. Thus, arrestin-3-assisted JNK3 activation in direct pathway neurons is a critical element of the molecular mechanism underlying sensitization upon dopamine depletion and chronic L-DOPA treatment.

Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus ß-carboxysome.

Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO2-concentrating mechanism (CCM). Biogenesis of carboxysome requires the fine organization of thousands of individual proteins; however, the packaging pattern of internal RuBisCOs remains largely unknown. Here we purified the intact ß-carboxysomes from Synechococcus elongatus PCC 7942 and identified the protein components by mass spectrometry. Cryo-electron tomography combined with subtomogram averaging revealed the general organization pattern of internal RuBisCOs, in which the adjacent RuBisCOs are mainly arranged in three distinct manners: head-to-head, head-to-side, and side-by-side. The RuBisCOs in the outermost layer are regularly aligned along the shell, the majority of which directly interact with the shell. Moreover, statistical analysis enabled us to propose an ideal packaging model of RuBisCOs in the ß-carboxysome. These results provide new insights into the biogenesis of ß-carboxysomes and also advance our understanding of the efficient carbon fixation functionality of carboxysomes.

Usability of Standards for Scaffolding in a Health Sciences Programme: A feasibility Study.

BACKGROUND: Standards contribute to comprehensive and programmatic implementation of educational strategies, such as scaffolding. Although the development of educational standards follows a rigorous consensus approach, they are socially constructed and could result in varied interpretations by users. Reports of varied implementation of standards in health professions education underscore the need to test the developed standards for scaffolding in health sciences programmes. Usability entails determining whether a product like standards works as intended under the expected conditions and contexts. This study aimed to describe the usability of standards for scaffolding in a health sciences programme through a pilot study. METHODS: A multi-method design employing user and expert-based usability evaluation techniques sought to describe the usability of the standards for scaffolding in a three-year pre-registration nursing programme. The user sample of nurse educators drawn from the programme, conducted a self-assessment on scaffolding practices in the programme using a developed standards checklist. For the expert sample, three-panel members with an understanding of the discipline and programme context were purposively sampled. These panelists studied the users' self-assessment reports before completing an author-generated heuristics checklist to support or refute any of the standards. Descriptive statistics, comparative and content analysis were applied to analyse data from users' interviews and expert's completed heuristics checklist, determining the standards' usability, and identifying the usability flaws or strengths. RESULTS: The users had three or more years of teaching experience in the competency-based curriculum for nursing. The experts shared an average of 16 years of experience in teaching in higher education, and seven years of experience in quality assurance and programme accreditation. The four standards had a usability score of above average (68%). Seven usability strengths and four usability flaws were identified. Usability flaws related to misinterpretation of some criteria statements and terminologies, multiple meanings, and users' challenges in generating evidence for some criteria. CONCLUSIONS: The pilot study revealed the context-based 'truth' regarding the fidelity of a health sciences programme evaluation on scaffolding, as well as identifying the ideal contextual conditions in which the standards for scaffolding health sciences programmes would work best. The identified usability flaws highlighted the need for further revisions of the standards. Future research on the feasibility of the standards in other health sciences programmes and contexts is recommended.

Use of a clinical reasoning scaffolding document improves student performance.

OBJECTIVE: Clinical reasoning is an essential skill set for practicing pharmacists to possess. Given its complex nature, optimal pedagogies for teaching clinical reasoning are largely unknown. The use of scaffolding to expand a student's zone of proximal development and improve clinical reasoning performance was assessed in this study. METHODS: This prospective, observational cohort study of second professional year (P2) students compared performance of those who were exposed to a clinical reasoning scaffolding tool (CRST) to historic control P2 students (No CRST) on FARMR notes in alignment with the Pharmacists' Patient Care Process. Student performance was assessed using an entrustment-like scale for each of 5 sections (Findings, Assessment and goals, Recommendations, Monitoring, and Rationale) of the FARMR to link classroom and experiential education settings. RESULTS: In total, 141 CRST students from 28 groups were compared to 77 No CRST students from 13 groups. CRST students performed significantly higher in Assessment and goals of therapy, Recommendations, Monitoring, Rationale sections but no difference in Findings. CONCLUSIONS: Scaffolding has been utilized successfully in other health professions education. This study provides evidence of it successfully improving student pharmacist clinical reasoning skills, an essential ability for successful pharmacy practitioners.

Why ask why? Toward coordinating knowledge of proximate and ultimate explanations in physiology.

In physiology education, students must learn to recognize and construct causal explanations. This challenges students, in part, because causal explanations in biology manifest in different varieties. Unlike other natural sciences, causal mechanisms in physiology support physiological functions and reflect biological adaptations. Therefore, students must distinguish between questions that prompt a proximate or an ultimate explanation. In the present investigation, we aimed to determine how these different varieties of student knowledge coordinate within students' written explanations. Prior research in science education demonstrates that students present specific challenges when distinguishing between proximate and ultimate explanations: students appear to conflate the two or construct other nonmechanistic explanations. This investigation, however, demonstrates that analytic frameworks can distinguish between students' proximate and ultimate explanations when they are provided explanatory scaffolds that contextualize questions. Moreover, these scaffolds and prompts help students distinguish between physiological functions and the cellular and molecular mechanisms that underpin them. Together, these findings deliver insight into the context-sensitive nature of student knowledge in physiology education and offer an analytic framework for identifying and characterizing student knowledge in physiology.NEW & NOTEWORTHY Why ask why? How questions posed in physiology task students with developing their mechanistic reasoning. Why questions sometimes undermine this reasoning. Prior research, however, also illustrates that framing the context of a question explicitly supports students in distinguishing between question types. We further illustrate how providing such context in the form of explanatory scaffolds and prompts allows students to tap different and useful varieties of knowledge when constructing written explanations.

From skeletons to screens: Transforming pedagogy in the age of remote learning.

This Educational Perspective explores the challenges and opportunities in Radiologic Technology education, focusing on the impact of active learning strategies and technological tools in enhancing asynchronous learning experiences. Radiologic Technology, a field reliant on hands-on experience and practical application, faced significant disruptions during the COVID-19 pandemic, necessitating a shift towards remote learning modalities. The Educational Perspective synthesizes the literature on the self-relevance effect, scaffolding, active learning, and metacognitive strategies to elucidate their role in promoting student engagement and success. The article offers recommendations to address the observed challenges, including creating scenario-based eLearning modules, providing immediate feedback and reflection opportunities, and incorporating gamification elements. These strategies aim to enrich asynchronous learning experiences, empowering radiology students to effectively adapt to changing educational landscapes and achieve optimal learning outcomes.

Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM.

DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications.