Principles for data analysis workflows.

A systematic and reproducible "workflow"-the process that moves a scientific investigation from raw data to coherent research question to insightful contribution-should be a fundamental part of academic data-intensive research practice. In this paper, we elaborate basic principles of a reproducible data analysis workflow by defining 3 phases: the Explore, Refine, and Produce Phases. Each phase is roughly centered around the audience to whom research decisions, methodologies, and results are being immediately communicated. Importantly, each phase can also give rise to a number of research products beyond traditional academic publications. Where relevant, we draw analogies between design principles and established practice in software development. The guidance provided here is not intended to be a strict rulebook; rather, the suggestions for practices and tools to advance reproducible, sound data-intensive analysis may furnish support for both students new to research and current researchers who are new to data-intensive work.

Ten simple rules on writing clean and reliable open-source scientific software.

Functional, usable, and maintainable open-source software is increasingly essential to scientific research, but there is a large variation in formal training for software development and maintainability. Here, we propose 10 "rules" centered on 2 best practice components: clean code and testing. These 2 areas are relatively straightforward and provide substantial utility relative to the learning investment. Adopting clean code practices helps to standardize and organize software code in order to enhance readability and reduce cognitive load for both the initial developer and subsequent contributors; this allows developers to concentrate on core functionality and reduce errors. Clean coding styles make software code more amenable to testing, including unit tests that work best with modular and consistent software code. Unit tests interrogate specific and isolated coding behavior to reduce coding errors and ensure intended functionality, especially as code increases in complexity; unit tests also implicitly provide example usages of code. Other forms of testing are geared to discover erroneous behavior arising from unexpected inputs or emerging from the interaction of complex codebases. Although conforming to coding styles and designing tests can add time to the software development project in the short term, these foundational tools can help to improve the correctness, quality, usability, and maintainability of open-source scientific software code. They also advance the principal point of scientific research: producing accurate results in a reproducible way. In addition to suggesting several tips for getting started with clean code and testing practices, we recommend numerous tools for the popular open-source scientific software languages Python, R, and Julia.

Ferromagnetic Mott state in Twisted Graphene Bilayers at the Magic Angle.

We address the effective tight-binding Hamiltonian that describes the insulating Mott state of twisted graphene bilayers at a magic angle. In that configuration, twisted bilayers form a honeycomb superlattice of localized states, characterized by the appearance of flat bands with fourfold degeneracy. After calculating the maximally localized superlattice Wannier wave functions, we derive the effective spin model that describes the Mott state. We suggest that the system is an exotic ferromagnetic Mott insulator, with well-defined experimental signatures.

Spectral Dynamics of Nitro Derivatives of Xanthione in Solutions.

Nitro derivatives of xanthione, 2,7-dinitro-9 H-xanthene-9-thione and 2,4,7-trinitro-9 H-xanthene-9-thione, have been first synthesized and their stationary and transient spectra have been measured. The stationary spectra show that the attachment of the nitro groups to the xanthione scaffold leads to strong quenching of S2 → S0 fluorescence and the decrease of the oscillator strength of the S2 ← S0 electronic transition. Analysis of the transient absorption spectra uncovers the ultrafast stimulated emission quenching from the second excited state, S2, in the both derivatives. A kinetic scheme has been suggested to rationalize the complex spectral dynamics of the transient absorption signal. The kinetic scheme is deduced from the analysis of the transient spectra and supported by the quantum-chemical calculations, which predict the existence of a dark state and S2 state splitting into two close levels. The ultrafast transitions between S2 state sublevels and the transition into the dark state play a crucial role in spectral dynamics. These new features discovered in the nitro derivatives of xanthione distinguish essentially their spectral dynamics from that observed in xanthione.

A seven-Gene Signature assay improves prognostic risk stratification of perioperative chemotherapy treated gastroesophageal cancer patients from the MAGIC trial.

Background: Following neoadjuvant chemotherapy for operable gastroesophageal cancer, lymph node metastasis is the only validated prognostic variable; however, within lymph node groups there is still heterogeneity with risk of relapse. We hypothesized that gene profiles from neoadjuvant chemotherapy treated resection specimens from gastroesophageal cancer patients can be used to define prognostic risk groups to identify patients at risk for relapse. Patients and methods: The Medical Research Council Adjuvant Gastric Infusional Chemotherapy (MAGIC) trial (n = 202 with high quality RNA) samples treated with perioperative chemotherapy were profiled for a custom gastric cancer gene panel using the NanoString platform. Genes associated with overall survival (OS) were identified using penalized and standard Cox regression, followed by generation of risk scores and development of a NanoString biomarker assay to stratify patients into risk groups associated with OS. An independent dataset served as a validation cohort. Results: Regression and clustering analysis of MAGIC patients defined a seven-Gene Signature and two risk groups with different OS [hazard ratio (HR) 5.1; P < 0.0001]. The median OS of high- and low-risk groups were 10.2 [95% confidence interval (CI) of 6.5 and 13.2 months] and 80.9 months (CI: 43.0 months and not assessable), respectively. Risk groups were independently prognostic of lymph node metastasis by multivariate analysis (HR 3.6 in node positive group, P = 0.02; HR 3.6 in high-risk group, P = 0.0002), and not prognostic in surgery only patients (n = 118; log rank P = 0.2). A validation cohort independently confirmed these findings. Conclusions: These results suggest that gene-based risk groups can independently predict prognosis in gastroesophageal cancer patients treated with neoadjuvant chemotherapy. This signature and associated assay may help risk stratify these patients for post-surgery chemotherapy in future perioperative chemotherapy-based clinical trials.

Investigating the feasibility of tumour molecular profiling in gastrointestinal malignancies in routine clinical practice.

Background: Targeted capture sequencing can potentially facilitate precision medicine, but the feasibility of this approach in gastrointestinal (GI) malignancies is unknown. Patients and methods: The FOrMAT (Feasibility of a Molecular Characterisation Approach to Treatment) study was a feasibility study enrolling patients with advanced GI malignancies from February 2014 to November 2015. Targeted capture sequencing (mainly using archival formalin-fixed paraffin-embedded diagnostic/resection samples) was carried out to detect mutations, copy number variations and translocations in up to 46 genes which had prognostic/predictive significance or were targets in current/upcoming clinical trials. Results: Of the 222 patients recruited, 215 patients (96.8%) had available tissue samples, 125 patients (56.3%) had ≥16 genes successfully sequenced and 136 patients (61.2%) had ≥1 genes successfully sequenced. Sample characteristics influenced the proportion of successfully sequenced samples, e.g. tumour type (colorectal 70.9%, biliary 52.6%, oesophagogastric 50.7%, pancreas 27.3%, P = 0.002), tumour cellularity (high versus low: 78.3% versus 13.3%, P ≤ 0.001), tumour content (high versus low: 78.6% versus 27.3%, P = 0.001) and type of sample (resection versus biopsy: 82.4% versus 47.6%, P ≤ 0.001). Currently, actionable alterations were detected in 90 (40.5%) of the 222 patients recruited (66% of the 136 patients sequenced) and 2 patients subsequently received a targeted therapy. The most frequently detected currently actionable alterations were mutations in KRAS, BRAF, TP53 and PIK3CA. For the 205 patients with archival samples, the median time to obtain sequencing results was 18.9 weeks, including a median of 4.9 weeks for sample retrieval and 5.1 weeks for sequencing. Conclusions: Targeted sequencing detected actionable alterations in formalin-fixed paraffin-embedded samples, but tissue characteristics are of critical importance in determining sequencing success. Routine molecular profiling of GI tumours outside of clinical trials is not an effective use of healthcare resources unless more targeted drugs become available. ClinicalTrials.gov identifier: NCT02112357.

Theory of Liquid Film Growth and Wetting Instabilities on Graphene.

We investigate wetting phenomena near graphene within the Dzyaloshinskii-Lifshitz-Pitaevskii theory for light gases of hydrogen, helium, and nitrogen in three different geometries where graphene is either affixed to an insulating substrate, submerged or suspended. We find that the presence of graphene has a significant effect in all configurations. When placed on a substrate, the polarizability of graphene can increase the strength of the total van der Waals force by a factor of 2 near the surface, enhancing the propensity towards wetting. In a suspended geometry unique to two-dimensional materials, where graphene is able to wet on only one side, liquid film growth becomes arrested at a critical thickness, which may trigger surface instabilities and pattern formation analogous to spinodal dewetting. The existence of a mesoscopic critical film with a tunable thickness provides a platform for the study of a continuous wetting transition, as well as the engineering of custom liquid coatings. These phenomena are robust to some mechanical deformations and are also universally present in doped graphene and other two-dimensional materials, such as monolayer dichalcogenides.

Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer.

Background: Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but lack of chronological references makes dating the exact onset of tumours very challenging. Patients and methods: Here, we describe the case of a colorectal cancer (CRC) patient presenting with synchronous lung metastasis and metachronous thyroid, chest wall and urinary tract metastases over the course of 5 years. The chest wall metastasis was caused by needle tract seeding, implying a known time of onset. Using whole genome sequencing data from primary and metastatic sites we inferred the complete chronology of the cancer by exploiting the time of needle tract seeding as an in vivo 'stopwatch'. This approach allowed us to follow the progression of the disease back in time, dating each ancestral node of the phylogenetic tree in the past history of the tumour. We used a Bayesian phylogenomic approach, which accounts for possible dynamic changes in mutational rate, to reconstruct the phylogenetic tree and effectively 'carbon date' the malignant progression. Results: The primary colon cancer emerged between 5 and 8 years before the clinical diagnosis. The primary tumour metastasized to the lung and the thyroid within a year from its onset. The thyroid lesion presented as a tumour-to-tumour deposit within a benign Hurthle adenoma. Despite rapid metastatic progression from the primary tumour, the patient showed an indolent disease course. Primary cancer and metastases were microsatellite stable and displayed low chromosomal instability. Neo-antigen analysis suggested minimal immunogenicity. Conclusion: Our data provide the first in vivo experimental evidence documenting the timing of metastatic progression in CRC and suggest that genomic instability might be more important than the metastatic potential of the primary cancer in dictating CRC fate.

Prognostic role of the LCS6 KRAS variant in locally advanced rectal cancer: results of the EXPERT-C trial.

BACKGROUND: Lethal-7 (let-7) is a tumour suppressor miRNA which acts by down-regulating several oncogenes including KRAS. A single-nucleotide polymorphism (rs61764370, T > G base substitution) in the let-7 complementary site 6 (LCS-6) of KRAS mRNA has been shown to predict prognosis in early-stage colorectal cancer (CRC) and benefit from anti-epidermal growth factor receptor monoclonal antibodies in metastatic CRC. PATIENTS AND METHODS: We analysed rs61764370 in EXPERT-C, a randomised phase II trial of neoadjuvant CAPOX followed by chemoradiotherapy, surgery and adjuvant CAPOX plus or minus cetuximab in locally advanced rectal cancer. DNA was isolated from formalin-fixed paraffin-embedded tumour tissue and genotyped using a PCR-based commercially available assay. Kaplan-Meier method and Cox regression analysis were used to calculate survival estimates and compare treatment arms. RESULTS: A total of 155/164 (94.5%) patients were successfully analysed, of whom 123 (79.4%) and 32 (20.6%) had the LCS-6 TT and LCS-6 TG genotype, respectively. Carriers of the G allele were found to have a statistically significantly higher rate of complete response (CR) after neoadjuvant therapy (28.1% versus 10.6%; P = 0.020) and a trend for better 5-year progression-free survival (PFS) [77.4% versus 64.5%: hazard ratio (HR) 0.56; P = 0.152] and overall survival (OS) rates (80.3% versus 71.9%: HR 0.59; P = 0.234). Both CR and survival outcomes were independent of the use of cetuximab. The negative prognostic effect associated with KRAS mutation appeared to be stronger in patients with the LCS-6 TT genotype (HR PFS 1.70, P = 0.078; HR OS 1.79, P = 0.082) compared with those with the LCS-6 TG genotype (HR PFS 1.33, P = 0.713; HR OS 1.01, P = 0.995). CONCLUSION: This analysis suggests that rs61764370 may be a biomarker of response to neoadjuvant treatment and an indicator of favourable outcome in locally advanced rectal cancer possibly by mitigating the poor prognosis of KRAS mutation. In this setting, however, this polymorphism does not appear to predict cetuximab benefit.

Erratum: Publisher Correction: wMel replacement of dengue-competent mosquitoes is robust to near-term climate change.

[This corrects the article DOI: 10.1038/s41558-023-01746-w.].

Thermal conductivity of a laser plasma.

We present a model of the electron thermal conductivity of a laser-produced plasma. The model, supported by Vlasov-Fokker-Planck simulations, predicts that laser absorption reduces conductivity by forcing electrons out of a Maxwell-Boltzmann equilibrium, which results in the depletion of both low-velocity bulk electrons and high-velocity tail electrons. We show that both the bulk and tail electrons approximately follow super-Gaussian distributions, but with distinct exponents that each depend on the laser intensity and wavelength through the parameter α=Zv_{E}^{2}/v_{T}^{2}. For a value of α=0.5, tail depletion reduces the thermal conductivity to half its zero-intensity value. We present our results as simple analytic fits that can be readily implemented in any radiation-hydrodynamics code or used to correct the local limit of nonlocal conduction models.

wMel replacement of dengue-competent mosquitoes is robust to near-term change.

Rising temperatures are impacting the range and prevalence of mosquito-borne diseases. A promising biocontrol technology replaces wild mosquitoes with those carrying the virus-blocking Wolbachia bacterium. Because the most widely used strain, wMel, is adversely affected by heat stress, we examined how global warming may influence wMel-based replacement. We simulated interventions in two locations with successful field trials using Coupled Model Intercomparison Project Phase 5 climate projections and historical temperature records, integrating empirical data on wMel's thermal sensitivity into a model of Aedes aegypti population dynamics to evaluate introgression and persistence over one year. We show that in Cairns, Australia, climatic futures necessitate operational adaptations for heatwaves exceeding two weeks. In Nha Trang, Vietnam, projected heatwaves of three weeks and longer eliminate wMel under the most stringent assumptions of that symbiont's thermal limits. We conclude that this technology is generally robust to near-term (2030s) climate change. Accelerated warming may challenge this in the 2050s and beyond.

Spinodal de-wetting of light liquids on graphene.

We demonstrate theoretically the possibility of spinodal de-wetting in heterostructures made of light-atom liquids (hydrogen, helium, and nitrogen) deposited on suspended graphene. Extending our theory of film growth on two-dimensional (2D) materials to include analysis of surface instabilities via the hydrodynamic Cahn-Hilliard-type equation, we characterize in detail the spatial and temporal scales of the resulting spinodal de-wetting patterns. Both linear stability analysis and direct numerical simulations of the surface hydrodynamics show micron-sized (generally material dependent) patterns of 'dry' regions. The physical reason for the development of such instabilities on graphene can be traced back to the inherently weak van der Waals interactions between atomically thin materials and atoms in the liquid. Thus 2D materials could represent a new theoretical and technological platform for studies of spinodal de-wetting.

Thermodynamics of a gas of deconfined bosonic spinons in two dimensions.

We consider the quantum phase transition between a Néel antiferromagnet and a valence-bond solid (VBS) in a two-dimensional system of S = 1/2 spins. Assuming that the excitations of the critical ground state are linearly dispersing deconfined spinons obeying Bose statistics, we derive expressions for the specific heat C and the magnetic susceptibility χ at low temperature T in terms of a correlation length ξ(T). Comparing with quantum Monte Carlo results for the J-Q model, which is a candidate for a deconfined Néel-VBS transition, we obtain an almost perfect consistency between C, χ, and ξ. The corresponding expressions for magnon (triplet) excitations are not internally consistent, however, lending strong support for spinon excitations in the J-Q model.

Health Impacts of Climate Change as Contained in Economic Models Estimating the Social Cost of Carbon Dioxide.

The health impacts of climate change are substantial and represent a primary motivating factor to mitigate climate change. However, the health impacts in economic models that estimate the social cost of carbon dioxide (SC-CO2) have generally been made in isolation from health experts and have never been rigorously evaluated. Version 3.10 of the Framework for Uncertainty, Negotiation and Distribution (FUND) model was used to estimate the health-based portion of current SC-CO2 estimates across low-, middle-, and high-income regions. In addition to the base model, three additional experiments assessed the sensitivity of these estimates to changes in the socio-economic assumptions in the model. Economic impacts from adverse health outcomes represent ∼8.7% of current SC-CO2 estimates. The majority of these health impacts (74%) were attributable to diarrhea mortality (from both low- and high-income regions) followed by diarrhea morbidity (12%) and malaria mortality (11%); no other health impact makes a meaningful contribution to SC-CO2 estimates in current economic models. The results of the socio-economic experiments show that the health-based portion of SC-CO2 estimates are highly sensitive to assumptions regarding income elasticity of health effects, income growth, and use of equity weights. Improving the health-based portion of SC-CO2 estimates could have substantial impacts on magnitude of the SC-CO2. Incorporating additional health impacts not previously included in estimates of SC-CO2 will be a critical component of model updates. This effort will be most successful through coordination between economists and health researchers and should focus on updating the form and function of concentration-response functions.

Intratumor morphologic and transcriptomic heterogeneity in V600EBRAF-mutated metastatic colorectal adenocarcinomas.

BACKGROUND: Intratumor heterogeneity (ITH) is described as the presence of various clones within one tumor, each with their own unique features in terms of morphology, inflammation, genetics or transcriptomics. Heterogeneity provides the fuel for drug resistance; therefore, an accurate assessment of tumor heterogeneity is essential for the development of effective therapies. The purpose of this study was to dissect morphologic and molecular ITH in colorectal adenocarcinoma. MATERIALS AND METHODS: A series of 120 V600EBRAF-mutated (V600EBRAFmt) consecutive metastatic colorectal adenocarcinomas was assessed for morphologic heterogeneity. The two heterogeneous components of each specimen underwent a histopathological, immunohistochemical and molecular characterization to evaluate: histologic variant, grading, tumor-infiltrating lymphocytes (TILs), mismatch repair proteins' expression, KRAS/BRAF/NRAS mutations, microsatellite instability (MSI) status and consensus molecular subtype (CMS). RESULTS: Thirty-one out of 120 (25.8%) V600EBRAFmt primary colorectal adenocarcinomas presented a heterogeneous morphology. Among these, eight cases had adequate material for molecular profiling. Five out of the eight (62.5%) cases resulted instable at MSI testing. The majority (62.5%) of the samples showed a CMS4 phenotype based on gene expression profiling. Heterogeneity in CMS classification was observed in four out of eight cases. One out of eight cases presented significant heterogeneity in the number of TILs between the two components of the tumor. CONCLUSIONS: Although the distribution of the immune infiltrate appears relatively conserved among heterogeneous areas of the same tumor, changes in gene expression profile and CMS occur in 50% of V600EBRAFmt adenocarcinoma cases in our small series and might contribute to variability in response to anticancer therapy and clinical outcomes. Assessment of morphological and molecular ITH is needed to improve colorectal cancer classification and to tailor anticancer treatments and should be included in the pathology report.

Translating gene drive science to promote linguistic diversity in community and stakeholder engagement.

Information about genetic engineering (GE) for vector control in the United States is disseminated primarily in English, though non-English speakers are equally, and in some geographic regions even more affected by such technologies. Non-English-speaking publics should have equal access to such information, which is especially critical when the technology in question may impact whole communities. We convened an interdisciplinary workgroup to translate previously developed narrated slideshows on gene drive mosquitoes from English into Spanish, reviewing each iteration for scientific accuracy and accessibility to laypeople. Using the finalised stimuli, we conducted five online, chat-based focus groups with Spanish-speaking adults from California. Overall, participants expressed interest in the topic and were able to summarise the information presented in their own words. Importantly, participants asked for clarification and expressed scepticism about the information presented, indicating critical engagement with the material. Through collaboration with Spanish-speaking scientists engaged in the development of GE methods of vector control, we translated highly technical scientific information into Spanish that successfully engaged Spanish-speaking participants in conversations about this topic. In this manuscript, we document the feasibility of consulting Spanish-speaking publics about a complex emerging technology by drawing on the linguistic diversity of the scientific teams developing the technology.

Quantification of dispersion of Gd-DTPA from the initial area of enhancement into the peritumoral zone of edema in brain tumors.

To evaluate Gd-DTPA contrast enhancement of brain tumors over time and to describe the dispersion of contrast into the zone of peritumoral edema. We performed MR imaging with a dose of 0.4 mmol Gd-DTPA/kg on eleven patients diagnosed with 5 different supratentorial tumors. MR imaging was done at five intervals between 5 min and 6 h. The change in zone of enhancement was measured for each time point, and a linear measurement was made of the furthest dispersion of contrast from the original volume of enhancement. An increase in the zone of enhancement over time was seen for all tumors; the average increase in volume of contrast was 14.76 +/- 3.35 cm(3) (mean +/- standard deviation). The largest changes in the zone of contrast enhancement, 18.6 +/- 4.63 cm(3), were seen in glioblastoma multiforme. The expansion of contrast enhancement assumed the morphology of the surrounding edema. The dispersion of Gd-DTPA over time into the zone of peritumoral edema is a potential source of error in clinical settings when there is a delay between Gd-DTPA injection and scanning.