Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis.

Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps of 33 colon samples spanning different stages of early neoplastic growth in persons with familial adenomatous polyposis (FAP). Our analysis revealed a substantial progressive loss of genome-wide cis-regulatory connectivity at early malignancy stages, correlating with nonlinear gene regulation effects.

Charge Distribution across Capped and Uncapped Infinite-Layer Neodymium Nickelate Thin Films.

Charge ordering (CO) phenomena have been widely debated in strongly-correlated electron systems mainly regarding their role in high-temperature superconductivity. Here, the structural and charge distribution in NdNiO thin films prepared with and without capping layers, and characterized by the absence and presence of CO are elucidated. The microstructural and spectroscopic analysis is done by scanning transmission electron microscopy-electron energy loss spectroscopy (STEM-EELS) and hard X-ray photoemission spectroscopy (HAXPES).

Novel gas exposure system for the controlled exposure of plants to gaseous hydrogen fluoride.

Plants can serve as sensitive bioindicators of the presence of contaminant vapors in the atmosphere. This work describes a novel laboratory-based gas exposure system capable of calibrating plants as bioindicators for the detection and delineation of the atmospheric contaminant hydrogen fluoride (HF) as a preparatory step for monitoring release emissions. To evaluate changes in plant phenotype and stress-induced physiological effects attributed to HF alone, the gas exposure chamber must have additional controls to simulate otherwise optimal plant growth conditions including variables such as light intensity, photoperiod, temperature, and irrigation.

Quarantine and serial testing for variants of SARS-CoV-2 with benefits of vaccination and boosting on consequent control of COVID-19.

Quarantine and serial testing strategies for a disease depend principally on its incubation period and infectiousness profile. In the context of COVID-19, these primary public health tools must be modulated with successive SARS CoV-2 variants of concern that dominate transmission. Our analysis shows that (1) vaccination status of an individual makes little difference to the determination of the appropriate quarantine duration of an infected case, whereas vaccination coverage of the population can have a substantial effect on this duration, (2) successive variants can challenge disease control efforts by their earlier and increased transmission in the disease time course relative to prior variants, and (3) sufficient vaccine boosting of a population substantially aids the suppression of local transmission through frequent serial testing.

An Oxygen Vacancy Memristor Ruled by Electron Correlations.

Resistive switching effects offer new opportunities in the field of conventional memories as well as in the booming area of neuromorphic computing. Here the authors demonstrate memristive switching effects produced by a redox-driven oxygen exchange in tunnel junctions based on NdNiO , a strongly correlated electron system characterized by the presence of a metal-to-insulator transition (MIT). Strikingly, a strong interplay exists between the MIT and the redox mechanism, which on the one hand modifies the MIT itself, and on the other hand radically affects the tunnel resistance switching and the resistance states' lifetime.

Charge and Spin Order Dichotomy in NdNiO_{2} Driven by the Capping Layer.

Superconductivity in infinite-layer nickelates holds exciting analogies with that of cuprates, with similar structures and 3d-electron count. Using resonant inelastic x-ray scattering, we studied electronic and magnetic excitations and charge density correlations in Nd_{1-x}Sr_{x}NiO_{2} thin films with and without an SrTiO_{3} capping layer. We observe dispersing magnons only in the capped samples, progressively dampened at higher doping.

Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation.

Background: Rapid antigen (RA) tests are being increasingly employed to detect SARS-CoV-2 infections in quarantine and surveillance. Prior research has focused on RT-PCR testing, a single RA test, or generic diagnostic characteristics of RA tests in assessing testing strategies.

Methods: We have conducted a comparative analysis of the post-quarantine transmission, the effective reproduction number during serial testing, and the false-positive rates for 18 RA tests with emergency use authorization from The United States Food and Drug Administration and an RT-PCR test.

Evolution of transcription factor binding through sequence variations and turnover of binding sites.

Variations in noncoding regulatory sequences play a central role in evolution. Interpreting such variations, however, remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in -regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, in which two related genomes are present within the same nucleus.

Environmental assessment of pediatric Lead exposure in Tehran; a prospective cross-sectional study.

Background: Ingestion and inhalation are common routes of exposure for lead in humans. Developing countries still have unacceptably high rates of lead toxicity, especially in children. Studies on probable risk factors of lead poisoning in Iranian children are insufficient.

Accumulation of cis- and trans-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species.

Gene regulatory variations accumulate during evolution and alter gene expression. While the importance of expression variation in phenotypic evolution is well established, the molecular basis remains largely unknown. Here, we examine two closely related yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus, which show phenotypical differences in morphology and cell cycle progression when grown in the same environment.

Optimal COVID-19 quarantine and testing strategies.

For COVID-19, it is vital to understand if quarantines shorter than 14 days can be equally effective with judiciously deployed testing. Here, we develop a mathematical model that quantifies the probability of post-quarantine transmission incorporating testing into travel quarantine, quarantine of traced contacts with an unknown time of infection, and quarantine of cases with a known time of exposure. We find that testing on exit (or entry and exit) can reduce the duration of a 14-day quarantine by 50%, while testing on entry shortens quarantine by at most one day.

Optimal COVID-19 quarantine and testing strategies.

As economic woes of the COVID-19 pandemic deepen, strategies are being formulated to avoid the need for prolonged stay-at-home orders, while implementing risk-based quarantine, testing, contact tracing and surveillance protocols. Given limited resources and the significant economic, public health, and operational challenges of the current 14-day quarantine recommendation, it is vital to understand if shorter but equally effective quarantine and testing strategies can be deployed. To quantify the probability of post-quarantine transmission upon isolation of a positive test, we developed a mathematical model in which we varied quarantine duration and the timing of molecular tests for three scenarios of entry into quarantine.

Independent evolution of transcript abundance and gene regulatory dynamics.

Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels, but providing limited information about variation across different conditions.

Assessment of GFP Tag Position on Protein Localization and Growth Fitness in Yeast.

While protein tags are ubiquitously utilized in molecular biology, they harbor the potential to interfere with functional traits of their fusion counterparts. Systematic evaluation of the effect of protein tags on function would promote accurate use of tags in experimental setups. Here we examine the effect of green fluorescent protein tagging at either the N or C terminus of budding yeast proteins on subcellular localization and functionality.

Examples of coupled human and environmental systems from the extractive industry and hydropower sector interfaces.

Large-scale corporate projects, particularly those in extractive industries or hydropower development, have a history from early in the twentieth century of creating negative environmental, social, and health impacts on communities proximal to their operations. In many instances, especially for hydropower projects, the forced resettlement of entire communities was a feature in which local cultures and core human rights were severely impacted. These projects triggered an activist opposition that progressively expanded and became influential at both the host community level and with multilateral financial institutions.

Reactive Oxygen Species Tune Root Tropic Responses.

The default growth pattern of primary roots of land plants is directed by gravity. However, roots possess the ability to sense and respond directionally to other chemical and physical stimuli, separately and in combination. Therefore, these root tropic responses must be antagonistic to gravitropism.

Experience and lessons from health impact assessment for human rights impact assessment.

As globalisation has opened remote parts of the world to foreign investment, global leaders at the United Nations and beyond have called on multinational companies to foresee and mitigate negative impacts on the communities surrounding their overseas operations. This movement towards corporate impact assessment began with a push for environmental and social inquiries. It has been followed by demands for more detailed assessments, including health and human rights.

Baseline malaria vector transmission dynamics in communities in Ahafo mining area in Ghana.

Background: Malaria vector dynamics are relevant prior to commencement of mining activities. A baseline entomology survey was conducted in Asutifi and Tano (referred to as Ahafo) in the Brong-Ahafo geo-political region of Ghana during preparatory stages for mining by Newmont Ghana Gold Limited.

Methods: Between November 2006 and August 2007, eight Centre for Disease Control light traps were set daily (Monday-Friday) to collect mosquitoes.

Multinational corporations and infectious disease: Embracing human rights management techniques.

Background: Global health institutions have called for governments, international organisations and health practitioners to employ a human rights-based approach to infectious diseases. The motivation for a human rights approach is clear: poverty and inequality create conditions for infectious diseases to thrive, and the diseases, in turn, interact with social-ecological systems to promulgate poverty, inequity and indignity. Governments and intergovernmental organisations should be concerned with the control and elimination of these diseases, as widespread infections delay economic growth and contribute to higher healthcare costs and slower processes for realising universal human rights.

The State of Alaska's early experience with institutionalization of health impact assessment.

Background: Many nations routinely include health impact assessments (HIA) in public policy decisions. Institutionalization of HIA formally integrates health considerations into a governmental decision-making process. We describe an example of institutionalization in the United States through Alaska's early experience with institutionalization of HIA.

Untapped potential of health impact assessment.

The World Health Organization has promoted health impact assessment (HIA) for over 20 years. At the 2012 United Nations Conference on Sustainable Development (Rio+20), HIA was discussed as a critical method for linking health to "green economy" and "institutional framework" strategies for sustainable development. In countries having a high human development index (HDI), HIA has been added to the overall assessment suite that typically includes potential environmental and social impacts, but it is rarely required as part of the environmental and social impact assessment for large development projects.

Enhancing impact: visualization of an integrated impact assessment strategy.

The environmental impact assessment process is over 40 years old and has dramatically expanded. Topics, such as social, health and human rights impact are now included. The main body of an impact analysis is generally hundreds of pages long and supported by countless technical appendices.

Health impact assessment of industrial development projects: a spatio-temporal visualization.

Development and implementation of large-scale industrial projects in complex eco-epidemiological settings typically require combined environmental, social and health impact assessments. We present a generic, spatio-temporal health impact assessment (HIA) visualization, which can be readily adapted to specific projects and key stakeholders, including poorly literate communities that might be affected by consequences of a project. We illustrate how the occurrence of a variety of complex events can be utilized for stakeholder communication, awareness creation, interactive learning as well as formulating HIA research and implementation questions.