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BACKGROUND: The use of electronic health record (EHR) data for research is limited by a lack of structure and a standard data model. The objective of the ICAREdata (Integrating Clinical Trials and Real-World Endpoints Data) project was to structure key research data elements in EHRs using a minimal Common Oncology Data Elements (mCODE) data model to extract and transmit data. METHODS: The ICAREdata project captured two EHR data elements essential to clinical trials: cancer disease status and treatment plan change. The project was implemented in clinical sites participating in Alliance for Clinical Trials in Oncology trials. Data were extracted from EHRs and sent by secure Fast Healthcare Interoperability Resource messaging (a standard for exchanging EHRs) to a database. Selected elements were compared with corresponding data from the trial's electronic data capture (EDC) system, Medidata Rave. RESULTS: By December 2023, data were extracted and transmitted from 10 sites for 35 patients, involving 367 clinical encounters across 15 clinical trials. Data through March 2023 demonstrated that concordance for the elements treatment plan change and cancer disease status was 79% and 34%, respectively. When disease evaluation was reported by both EHR and EDC (n = 15), there was 87% agreement on cancer disease status. CONCLUSIONS: Documentation, extraction, and aggregation of structured data elements in EHRs using mCODE and ICAREdata methods is feasible in multi-institutional cancer clinical trials. EDC as a reference data set allowed assessment of the completeness of EHR data capture. Future initiatives will focus on elements with shared definitions in clinical and research environments and efficient workflows. PLAIN LANGUAGE SUMMARY: Clinical trials use electronic case report forms to report data, and data must be manually entered on these forms, which is costly and time consuming. ICAREdata methods use structured, organized data from clinical trials that can be more easily shared instead having to enter free text into electronic health records.
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The interior of cellular nuclei, the nucleoplasm, is a crowded fluid that is pervaded by protein-decorated DNA polymers, the chromatin. Due to the complex architecture of chromatin and a multitude of associated nonequilibrium processes, e.g., DNA repair, the nucleoplasm can be expected to feature nontrivial material properties and hence anomalous transport phenomena. Here, we have used single-particle tracking on nuclear actin rods to probe such transport phenomena. Our analysis reveals that short actin rods in the nucleus show an intermittent, antipersistent subdiffusion with clear signatures of fractional Brownian motion. Moreover, the diffusive motion is heterogeneous with clear signatures of an intermittent switching of trajectories between at least two different mobilities, most likely due to transient associations with chromatin. In line with this interpretation, hyperosmotic stress is seen to stall the motion of nuclear actin rods, whereas hypo-osmotic conditions yield a reptationlike motion. Our data highlights the heterogeneity of transport in the nucleoplasm that needs to be taken into account for an understanding of nucleoplasmic organization and the mechanobiology of nuclei.
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Actinas , Núcleo Celular , Cromatina , Difusão , Actinas/metabolismo , Cromatina/metabolismo , Núcleo Celular/metabolismo , Animais , Modelos Biológicos , Pressão OsmóticaRESUMO
Birds, bats and ants are recognised as significant arthropod predators. However, empirical studies reveal inconsistent trends in their relative roles in top-down control across strata. Here, we describe the differences between forest strata in the separate effects of birds, bats and ants on arthropod densities and their cascading effects on plant damage. We implemented a factorial design to exclude vertebrates and ants in both the canopy and understorey. Additionally, we separately excluded birds and bats from the understorey using diurnal and nocturnal exclosures. At the end of the experiments, we collected all arthropods and assessed herbivory damage. Arthropods responded similarly to predator exclusion across forest strata, with a density increase of 81% on trees without vertebrates and 53% without both vertebrates and ants. Additionally, bird exclusion alone led to an 89% increase in arthropod density, while bat exclusion resulted in a 63% increase. Herbivory increased by 42% when vertebrates were excluded and by 35% when both vertebrates and ants were excluded. Bird exclusion alone increased herbivory damage by 28%, while the exclusion of bats showed a detectable but non-significant increase (by 22%). In contrast, ant exclusion had no significant effect on arthropod density or herbivory damage across strata. Our results reveal that the effects of birds and bats on arthropod density and herbivory damage are similar between the forest canopy and understorey in this temperate forest. In addition, ants were not found to be significant predators in our system. Furthermore, birds, bats and ants appeared to exhibit antagonistic relationships in influencing arthropod density. These findings highlight, unprecedentedly, the equal importance of birds and bats in maintaining ecological balance across different strata of a temperate forest.
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Early embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell-division timing and the subsequent mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo without breaking its eggshell. Compressing embryos to about two-thirds of their unperturbed diameter only resulted in markedly slower cell divisions. In contrast, compressing embryos to half of their native diameter frequently resulted in a loss of cytokinesis, yielding a non-natural syncytium that still allowed for multiple divisions of nuclei. Although the orientation of mitotic axes was strongly altered in the syncytium, key features of division timing and spatial arrangement of nuclei remained surprisingly similar to those of unperturbed embryos in the first few division cycles. This suggests that few, very robust mechanisms provide a basic and resilient program for safeguarding the early embryogenesis of C. elegans.
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Importance: There is substantial interest in capturing cancer treatment tolerability from the patient's perspective using patient-reported outcomes (PROs). Objective: To examine whether a PRO question, item 5 from the Functional Assessment of Cancer Therapy-General General Physical Wellbeing Scale (GP5), was associated with early treatment discontinuation (ETD) due to adverse events. Design, Setting, and Participants: This prospective survey study was conducted from February to April 2023. Among participants in the ECOG-ACRIN E1A11 trial (a phase 3, parallel design trial conducted between 2013 and 2019), patients with newly diagnosed multiple myeloma were randomized to receive bortezomib (VRd) or carfilzomib (KRd) plus lenalidomide and dexamethasone as induction therapy. The GP5 item was administered at baseline (pretreatment) and at 1 month, 2.8 months, and 5.5 months postbaseline. Eligible participants included patients with newly diagnosed multiple myeloma treated at community oncology practices or academic medical centers in the US. Exposures: GP5 response options were "very much," "quite a bit," "somewhat," "a little bit," and "not at all." Responses at each assessment while undergoing treatment (1 month, 2.8 months, and 5.5 months) were categorized as high adverse event bother (ie, "very much," and "quite a bit") and low adverse event bother (ie, "somewhat," "a little bit," or "not at all"). In addition, change from baseline to each assessment while undergoing treatment was calculated and categorized as worsening by 1 response category and 2 or more response categories. Main Outcome and Measure: ETD due to adverse events (yes vs no) was analyzed using logistic regression adjusting for treatment group, performance status, gender, race, and disease stage. Results: Of the 1087 participants in the original trial, 1058 (mean [SD] age 64 [9] years; 531 receiving VrD [50.2%]; 527 receiving KRd [49.8%]) responded to item GP5 and were included in the secondary analysis. A small proportion (142 patients [13.4%]) discontinued treatment early due to AEs. For those with high adverse-effect bother, GP5 while undergoing treatment was associated with ETD at 1 month (adjusted odds ratio [aOR], 2.20; 95% CI, 1.25-3.89), 2.8 months (aOR, 3.41; 95% CI, 2.01-5.80), and 5.5 months (aOR, 4.66; 95% CI, 1.69-12.83). Worsening by 2 or more response categories on the GP5 was associated with ETD at 2.8 months (aOR, 3.02; 95% CI, 1.64-5.54) and 5.5 months (aOR, 5.49; 95% CI, 1.45-20.76). Conclusions and Relevance: In this survey study of the E1A11 trial, worse GP5 response was associated with ETD. These findings suggest that simple assessment of adverse-effect bother while receiving treatment is an efficient way to indicate treatment tolerability and ETD risk.
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Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Mieloma Múltiplo , Humanos , Pessoa de Meia-Idade , Estudos Prospectivos , Bortezomib , Lenalidomida , Medidas de Resultados Relatados pelo PacienteRESUMO
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Tubulin polyglutamylation, catalysed by members of the tubulin tyrosine ligase-like (TTLL) protein family, is an evolutionarily highly conserved mechanism involved in the regulation of microtubule dynamics and function in eukaryotes. In the protozoan parasite Trypanosoma brucei, the microtubule cytoskeleton is essential for cell motility and maintaining cell shape. In a previous study, we showed that T. brucei TTLL6A and TTLL12B are required to regulate microtubule dynamics at the posterior cell pole. Here, using gene deletion, we show that the polyglutamylase TTLL1 is essential for the integrity of the highly organised microtubule structure at the cell pole, with a phenotype distinct from that observed in TTLL6A- and TTLL12B-depleted cells. Reduced polyglutamylation in TTLL1-deficient cells also leads to increased levels in tubulin tyrosination, providing new evidence for an interplay between the tubulin tyrosination and detyrosination cycle and polyglutamylation. We also show that TTLL1 acts differentially on specific microtubule doublets of the flagellar axoneme, although the absence of TTLL1 appears to have no measurable effect on cell motility.
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Trypanosoma brucei brucei , Tubulina (Proteína) , Tubulina (Proteína)/metabolismo , Trypanosoma brucei brucei/genética , Trypanosoma brucei brucei/metabolismo , Microtúbulos/metabolismo , Neurônios/metabolismoRESUMO
Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical trial updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.In 2003, the Eastern Cooperative Oncology Group initiated a randomized phase III clinical trial (E4402) comparing two different rituximab dosing strategies for patients with previously untreated low-tumor burden follicular lymphoma. Rituximab-responsive patients (n = 299) were randomly assigned to either a retreatment rituximab (RR) strategy or a maintenance rituximab (MR) strategy. Each dosing strategy was continued until treatment failure. The primary end point of the study was time to treatment failure (TTF). In the original report, there was no difference in TTF between the two dosing strategies. Here, we report on the long-term outcomes for secondary end points of time to first cytotoxic therapy, duration of response, and overall survival (OS). At 7 years, 83% of MR patients had not required first chemotherapy compared with 63% of RR patients (hazard ratio, 2.37 [95% CI, 1.5 to 3.76]). At 7 years, 71% of MR remained in their first remission compared with 37% of RR patients. Despite the improved first remission length with MR, there was no difference in OS at 10 years (83% v 84%). With mature long-term data, we confirm that prolonged maintenance rituximab does not confer an OS advantage in low-tumor burden follicular lymphoma.
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Antineoplásicos , Linfoma Folicular , Humanos , Rituximab , Linfoma Folicular/patologia , Antineoplásicos/uso terapêutico , Seguimentos , Carga Tumoral , Protocolos de Quimioterapia Combinada Antineoplásica/efeitos adversosRESUMO
Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of four specific genomic loci. MATAC-Seq relies on preferential modification of accessible DNA by methyltransferases combined with Nanopore-Sequencing for direct readout of methylated DNA-bases. Applying MATAC-Seq to selected early-efficient and late-inefficient yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an accessible nucleosome-free region in combination with well-positioned +1 and +2 nucleosomes as a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during eukaryotic DNA replication. Consequently, our single-molecule chromatin accessibility assay will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.
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Origem de Replicação , Saccharomyces cerevisiae , Cromatina/genética , DNA , Replicação do DNA , Nucleossomos/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismoRESUMO
Acute myeloid leukaemia (AML) relapse after allogeneic haematopoietic cell transplantation (allo-HCT) is often driven by immune-related mechanisms and associated with poor prognosis. Immune checkpoint inhibitors combined with hypomethylating agents (HMA) may restore or enhance the graft-versus-leukaemia effect. Still, data about using this combination regimen after allo-HCT are limited. We conducted a prospective, phase II, open-label, single-arm study in which we treated patients with haematological AML relapse after allo-HCT with HMA plus the anti-PD-1 antibody nivolumab. The response was correlated with DNA-, RNA- and protein-based single-cell technology assessments to identify biomarkers associated with therapeutic efficacy. Sixteen patients received a median number of 2 (range 1-7) nivolumab applications. The overall response rate (CR/PR) at day 42 was 25%, and another 25% of the patients achieved stable disease. The median overall survival was 15.6 months. High-parametric cytometry documented a higher frequency of activated (ICOS+ , HLA-DR+ ), low senescence (KLRG1- , CD57- ) CD8+ effector T cells in responders. We confirmed these findings in a preclinical model. Single-cell transcriptomics revealed a pro-inflammatory rewiring of the expression profile of T and myeloid cells in responders. In summary, the study indicates that the post-allo-HCT HMA/nivolumab combination induces anti-AML immune responses in selected patients and could be considered as a bridging approach to a second allo-HCT. Trial-registration: EudraCT-No. 2017-002194-18.
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In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive 'identity code' that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.
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Replicação do DNA , Origem de Replicação , Animais , Origem de Replicação/genética , Replicação do DNA/genética , Cromatina/genética , DNA , Saccharomyces cerevisiae/genéticaRESUMO
Technological advances and a burst of new microscopy methods have boosted the use of quantitative tracking experiments, in Soft Matter and Biological Physics but also in the Life Sciences. However, in contrast to highly advanced measurement techniques and tracking tools, subsequent analyses of trajectories frequently do not exploit the data's full potential. Aiming especially at experimental laboratories and early-career scientists, we introduce, discuss, and apply in this Tutorial Review a large set of versatile measures that have proven to be useful for analyzing trajectories from single-particle tracking experiments, beyond a simple extraction of diffusion constants from mean squared displacements. To support a direct test and application of these measures, we supplement the text with a download package that comprises a low-threshold toolbox of ready-to-use routines and training data sets, hence relaxing the need to develop home-brewed solutions and/or to create suitable benchmark data.
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In the near future, humans will increasingly be required to offload tasks to artificial systems to facilitate daily as well as professional activities. Yet, research has shown that humans are often averse to offloading tasks to algorithms (so-called "algorithmic aversion"). In the present study, we asked whether this aversion is also present when humans act under high cognitive load. Participants performed an attentionally demanding task (a multiple object tracking (MOT) task), which required them to track a subset of moving targets among distractors on a computer screen. Participants first performed the MOT task alone (Solo condition) and were then given the option to offload an unlimited number of targets to a computer partner (Joint condition). We found that participants significantly offloaded some (but not all) targets to the computer partner, thereby improving their individual tracking accuracy (Experiment 1). A similar tendency for offloading was observed when participants were informed beforehand that the computer partner's tracking accuracy was flawless (Experiment 2). The present findings show that humans are willing to (partially) offload task demands to an algorithm to reduce their own cognitive load. We suggest that the cognitive load of a task is an important factor to consider when evaluating human tendencies for offloading cognition onto artificial systems.
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Algoritmos , Cognição , Humanos , Computadores , AfetoRESUMO
Self-organization of cells into higher-order structures is key for multicellular organisms, for example via repetitive replication of template-like founder cells or syncytial energids. Yet, very similar spatial arrangements of cell-like compartments ('protocells') are also seen in a minimal model system of Xenopus egg extracts in the absence of template structures and chromatin, with dynamic microtubule assemblies driving the self-organization process. Quantifying geometrical features over time, we show here that protocell patterns are highly organized with a spatial arrangement and coarsening dynamics similar to that of two-dimensional foams but without the long-range ordering expected for hexagonal patterns. These features remain invariant when enforcing smaller protocells by adding taxol, i.e. patterns are dominated by a single, microtubule-derived length scale. Comparing our data to generic models, we conclude that protocell patterns emerge by simultaneous formation of randomly assembling protocells that grow at a uniform rate towards a frustrated arrangement before fusion of adjacent protocells eventually drives coarsening. The similarity of protocell patterns to arrays of energids and cells in developing organisms, but also to epithelial monolayers, suggests generic mechanical cues to drive self-organized space compartmentalization.
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Células Artificiais , Modelos Biológicos , Microtúbulos , CromatinaRESUMO
mTOR inhibitors such as everolimus may cause oral stomatitis, often a dose-limiting toxicity. Prior clinical research has suggested that a dexamethasone mouth rinse might help prevent and/or treat this. Alliance A221701 was a randomized phase III trial of patients initiating 10 mg daily oral everolimus that compared dexamethasone mouthwash taken preventively (initial dexamethasone group) versus therapeutically (initial placebo group) to assess two coprimary endpoints: the incidence of mTOR inhibitor-associated stomatitis (mIAS), and the area under the curve (AUC) of mIAS-associated pain over an 8-week treatment period. A Fisher's exact test was used to compare the incidences while a Wilcoxon rank-sum test was used to compare the AUCs. In addition, we performed an exploratory analysis of the association of everolimus trough concentrations and toxicity using a Mann-Whitney U test. Due to slow accrual, this study closed after 39 patients were randomized (19 to upfront placebo and 20 to upfront dexamethasone). There were no significant differences between groups seen in either of the coprimary endpoints; furthermore, we found no association between whole blood everolimus trough concentrations and toxicity. Although limited by poor enrollment, the results of this study do not suggest that prophylactic dexamethasone mouthwash is superior to therapeutic dexamethasone mouthwash (initiated at the first sign of mouth pain) for reducing the incidence or severity of mIAS from everolimus.
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Everolimo , Estomatite , Humanos , Everolimo/efeitos adversos , Antissépticos Bucais/uso terapêutico , Estomatite/induzido quimicamente , Estomatite/prevenção & controle , Estomatite/tratamento farmacológico , Dor/tratamento farmacológico , Dexametasona/uso terapêuticoRESUMO
The chromatin environment at origins of replication is thought to influence DNA replication initiation in eukaryotic genomes. However, it remains unclear how and which chromatin features control the firing of early-efficient (EE) or late-inefficient (LI) origins. Here, we use site-specific recombination and single-locus chromatin isolation to purify EE and LI replication origins in Saccharomyces cerevisiae. Using mass spectrometry, we define the protein composition of native chromatin regions surrounding the EE and LI replication start sites. In addition to known origin interactors, we find the microtubule-binding Ask1/DASH complex as an origin-regulating factor. Strikingly, tethering of Ask1 to individual origin sites advances replication timing (RT) of the targeted chromosomal domain. Targeted degradation of Ask1 globally changes RT of a subset of origins, which can be reproduced by inhibiting microtubule dynamics. Thus, our findings mechanistically connect RT and chromosomal organization via Ask1/DASH with the microtubule cytoskeleton.
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Proteínas Associadas aos Microtúbulos , Origem de Replicação , Proteínas de Saccharomyces cerevisiae , Cromatina/metabolismo , DNA/metabolismo , Replicação do DNA , Período de Replicação do DNA , Proteínas Associadas aos Microtúbulos/metabolismo , Complexos Multiproteicos/metabolismo , Proteômica , Origem de Replicação/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismoRESUMO
A panoply of new tools for tracking single particles and molecules has led to an explosion of experimental data, leading to novel insights into physical properties of living matter governing cellular development and function, health and disease. In this Perspective, we present tools to investigate the dynamics and mechanics of living systems from the molecular to cellular scale via single-particle techniques. In particular, we focus on methods to measure, interpret, and analyse complex data sets that are associated with forces, materials properties, transport, and emergent organisation phenomena within biological and soft-matter systems. Current approaches, challenges, and existing solutions in the associated fields are outlined in order to support the growing community of researchers at the interface of physics and the life sciences. Each section focuses not only on the general physical principles and the potential for understanding living matter, but also on details of practical data extraction and analysis, discussing limitations, interpretation, and comparison across different experimental realisations and theoretical frameworks. Particularly relevant results are introduced as examples. While this Perspective describes living matter from a physical perspective, highlighting experimental and theoretical physics techniques relevant for such systems, it is also meant to serve as a solid starting point for researchers in the life sciences interested in the implementation of biophysical methods.
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Disciplinas das Ciências Biológicas , Imagem Individual de Molécula , Biofísica , Disciplinas das Ciências Biológicas/métodosRESUMO
Integrated photonic circuits are key components for photonic quantum technologies and for the implementation of chip-based quantum devices. Future applications demand flexible architectures to overcome common limitations of many current devices, for instance the lack of tuneabilty or built-in quantum light sources. Here, we report on a dynamically reconfigurable integrated photonic circuit comprising integrated quantum dots (QDs), a Mach-Zehnder interferometer (MZI) and surface acoustic wave (SAW) transducers directly fabricated on a monolithic semiconductor platform. We demonstrate on-chip single photon generation by the QD and its sub-nanosecond dynamic on-chip control. Two independently applied SAWs piezo-optomechanically rotate the single photon in the MZI or spectrally modulate the QD emission wavelength. In the MZI, SAWs imprint a time-dependent optical phase and modulate the qubit rotation to the output superposition state. This enables dynamic single photon routing with frequencies exceeding one gigahertz. Finally, the combination of the dynamic single photon control and spectral tuning of the QD realizes wavelength multiplexing of the input photon state and demultiplexing it at the output. Our approach is scalable to multi-component integrated quantum photonic circuits and is compatible with hybrid photonic architectures and other key components for instance photonic resonators or on-chip detectors.
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Chromatin dynamics is key for cell viability and replication. In interphase, chromatin is decondensed, allowing the transcription machinery to access a plethora of DNA loci. Yet, decondensed chromatin occupies almost the entire nucleus, suggesting that DNA molecules can hardly move. Recent reports have even indicated that interphase chromatin behaves like a solid body on mesoscopic scales. To explore the local chromatin dynamics, we have performed single-particle tracking on telomeres under varying conditions. We find that mobile telomeres feature, under all conditions, a strongly subdiffusive, antipersistent motion that is consistent with the monomer motion of a Rouse polymer in viscoelastic media. In addition, telomere trajectories show intermittent accumulations in local niches at physiological conditions, suggesting that the surrounding chromatin reorganizes on these timescales. Reducing the temperature or exposing cells to osmotic stress resulted in a significant reduction of mobile telomeres and the number of visited niches. Altogether, our data indicate a vivid local chromatin dynamics, akin to a semidilute polymer solution, unless perturbations enforce a more rigid or entangled state of chromatin.