Miracle-dz/UniFAR-FTUs huggingface dataset:
Plastic Food Packaging from Five Countries Contains Endocrine- and Metabolism-Disrupting Chemicals

Plastics are complex chemical mixtures of polymers and various intentionally and non-intentionally added substances. Despite the well-established links between certain plastic chemicals (bisphenols, phthalates) and adverse health effects, the composition and toxicity of real-world mixtures of plastic chemicals is not well understood. To assess both, we analyzed the chemicals from 36 plastic food contact articles from five countries using nontarget high-resolution mass spectrometry and reporter gene assays for four nuclear receptors that represent key components of the endocrine and metabolic system. We found that chemicals activating the pregnane X receptor (PXR), peroxisome proliferator receptor gamma (PPARγ), estrogen receptor alpha (ERα) and inhibiting the androgen receptor (AR) are prevalent in plastic packaging. We detected up to 9936 chemical features in a single product but found that each product has a rather unique chemical fingerprint. To tackle this chemical complexity, we used stepwise partial least squares regressions and prioritized and tentatively identified the chemical features associated with receptor activity. Our findings demonstrate that most plastic food packaging contains endocrine and metabolism disrupting chemicals. This shows that plastics are a relevant source of exposure to toxic chemicals and further supports the notion that plastic products designed for food contact cannot be considered safe.
Networked proteins redundantly interact with VAP27 and RABG3 to regulate membrane tethering at the vacuole and beyond

Biological processes in eukaryotes depend on the spatio-temporal compartmentalization of their cells. Integrity and positioning of organelles on the other hand rely on the organization of the actin cytoskeleton. Previously, it has been shown that changes of the plants largest organelle, the vacuole, depend on a functional actin organization. The connection between actin filaments and the vacuole is established by the family of Networked (NET) 4 proteins and, consequently, altering NET4 abundance impacts vacuolar morphology. However, the precise regulatory mechanism is unknown and gene deletions of NET4 did not result in a global growth phenotype. Here, we show that NET4 functions redundantly with NET3, interacting with RABG3-GTPases at the vacuole to allow for homotypic fusion or, alternatively, the generation of endoplasmic reticulum (ER) - vacuole contact sites. We found that ER-resident NET3 is able to interact with RABG3 residing at the tonoplast and that NET4 interacts with the contact site protein VAP27-1 at the ER. Generation of net3 net4 triple mutants by CRSIPR-guided mutagenesis helped us to overcome functional redundancy, resulting in impaired plant growth and development. Our results demonstrate how diversification of NET genes led to functional redundancy between different family members to create cellular plasticity of vascular plants. We hypothesize that establishment of a direct ER-vacuole connection enables direct lipid and protein transfer which is especially important in young and fast-growing cells. Availability of lipids would facilitate rapidly expanding vacuoles, which are the basis for high cell elongation rates and eventually fast plant growth.
Timing specific parental effects of ocean warming in a coral reef fish

Population and species persistence in a rapidly warming world will be determined by an organisms’ ability to acclimate to warmer conditions, especially across generations. There is potential for transgenerational acclimation, but the importance of ontogenetic timing in the transmission of environmentally induced parental effects remains mostly unknown. We aimed to disentangle the contributions of two critical ontogenetic stages (juvenile development and adult reproduction) to transgenerational plasticity, by exposing the coral reef fish Acanthochromis polyacanthus to simulated ocean warming with natural diel thermal fluctuations across two generations. By using hepatic transcriptomics, we discovered that the developmental environment of the offspring themselves had little effect on their acclimation potential at 2.5 months of life. Instead, the developmental experience of parents increased regulatory RNA production and protein synthesis, which could improve the offspring’s response to warming. Conversely, reproduction in warmer water elicited stress response mechanisms, with suppression of translation and mitochondrial respiration. Mismatches between temperatures in the parental ontogenetic thermal experience deeply affected offspring gene expression profiles, and detrimental effects were also evident when warming occurred both during parents’ development and reproduction. This study reveals that the previous generation’s developmental temperature contributes substantially to thermal acclimation potential during early life, however prolonged heat stress will likely have adverse effects on the species’ persistence.
"Why do you need 400 photographs of 400 different Lockheed Constellation?": Value Expressions by Contributors and Users of Wikimedia Commons

Understanding the values that collaborators bring to a collaboration is important for the design of new systems. In collaborative systems understanding differing values could help design solutions to mitigate conflicts and more effectively coordinate collaboration. We review prior studies of Commons-Based Peer Production (CBPP) identifying four common value dimensions previously noted as present in CBPP: usage value, social value, ideological value, and monetary value. We use this synthetic framework to analyze a dataset of 32 interviews with contributors to Wikimedia Commons and editors of Wikipedia who use Commons resources. Our analysis supports the prior values categories while expanding how some dimensions are expressed by participants. We also highlight four additional value dimensions that were not previously identified in CBPP: cultural heritage value, rarity value, aesthetic value, and administrative value. We discuss the implications of our findings for the design of collaborative systems.
FLOW OF HEAT IN THE FRONT RANGE, COLORADO

Modern conceptions of the structure of the earth9s crust and of the distribution of radioactivity lead to an expectation of a greater flow of heat to the surface in mountains than in lowlands. An exceptional opportunity for testing this expectation is provided by the data obtained by the geologists of the Bureau of Reclamation during the construction of the Alva B. Adams Tunnel under Rocky Mountain National Park. This tunnel, 13 miles long, at a mean altitude of 8300 feet, passes under the Continental Divide, more than 12,000 feet above sea level. Some 70 observations of temperature have been reduced with the purpose of finding the flow of heat. Corrections have been applied for the topography on several different hypotheses regarding the physiographic history. The corrected vertical gradient of temperature lies between 24°C/km, on the assumption that the present topography has persisted indefinitely, and 20°C/km, on the assumption that the surface features have been derived from an old-age surface by erosion and by uplift of 7000 feet uniformly distributed over the last million years. If the time of evolution is taken as 4 million years, the corrected gradient is 22°C/km. An uncertainty of about 1°C/km results from lack of reliable data concerning the surface temperature. Thermal conductivity has been measured in the laboratory for 123 samples of rock from the tunnel; these rocks are chiefly granites, gneisses, and schists. The variations of conductivity with rock type and with position along the tunnel are found to be insignificant; the mean value of conductivity is 0.008 cal/cm·sec·deg. The heat flow is then computed as between 1.6 and 1.9 microcal/cm 2 ·sec, with a “best value” of 1.7 microcal/cm 2 ·sec. This is believed to differ significantly from the best values for a “normal” sea-level crust, which fall close to 1.1 microcal/cm 2 ·sec. With conventional assumptions as to thickness and density of the layers of the normal crust, the difference of heat flow may be accounted for in terms of mountain roots having a mean radioactivity of the same order as that of granites or intermediate rocks. The observed heat flow is consistent with the doctrine of mountain roots and with an approximately uniform distribution of radioactivity throughout the “granitic” layer. A few of the other possible interpretations are briefly discussed.
Prenatal Arsenite Exposure Alters Maternal Cardiac Remodeling During Late Pregnancy

Exposure to inorganic arsenic through drinking water is widespread and has been linked to many chronic diseases, including cardiovascular disease. Arsenic exposure has been shown to alter hypertrophic signaling in the adult heart, as well as in-utero offspring development. However, the effect of arsenic on maternal cardiac remodeling during pregnancy has not been studied. As such, there is a need to understand how environmental exposure contributes to adverse pregnancy-related cardiovascular events. This study seeks to understand the impact of trivalent inorganic arsenic exposure during gestation on maternal cardiac remodeling in late pregnancy, as well as offspring outcomes. C57BL/6J mice were exposed to 0 (control), 100 or 1000 µg/L sodium arsenite (NaAsO2) beginning at embryonic day (E) 2.5 and continuing through E17.5. Maternal heart function and size were assessed via transthoracic echocardiography, gravimetric measurement, and histology. Transcript levels of hypertrophic markers were probed via qRT-PCR and confirmed by western blot. Offspring outcomes were assessed through echocardiography and gravimetric measurement. We found that exposure to 1000 µg/L iAs abrogated normal physiologic growth of the maternal heart during late pregnancy and reduced transcript levels of estrogen receptor alpha (ERα), progesterone receptor membrane component 1 (Pgrmc1) and progesterone receptor membrane component 2 (Pgrmc2). Both 100 and 1000 µg/L iAs also reduced transcription of protein kinase B (Akt) and atrial natriuretic peptide (ANP). Akt protein expression was also significantly reduced after 1000 µg/L iAs exposure in the maternal heart with no change in activating phosphorylation. This significant abrogation of maternal cardiac hypertrophy suggests that arsenic exposure during pregnancy can potentially contribute to cardiovascular disease. Taken together, our findings further underscore the importance of reducing arsenic exposure during pregnancy and indicate that more research is needed to assess the impact of arsenic and other environmental exposures on the maternal heart and adverse pregnancy events.
Peer Produced Friction: How Page Protection on Wikipedia Affects Editor Engagement and Concentration

Peer production systems have frictions-mechanisms that make contributing more effortful-to prevent vandalism and protect information quality. Page protection on Wikipedia is a mechanism where the platform's core values conflict, but there is little quantitative work to ground deliberation. In this paper, we empirically explore the consequences of page protection on Internet Culture articles on Wikipedia (6,264 articles, 108 edit-protected). We first qualitatively analyzed 150 requests for page protection, finding that page protection is motivated by an article's (1) activity, (2) topic area, and (3) visibility. These findings informed a matching approach to compare protected pages and similar unprotected articles. We quantitatively evaluate the differences between protected and unprotected pages across two dimensions: editor engagement and contributor concentration. Protected articles show different trends in editor engagement and equity amongst contributors, affecting the overall disparity in the population. We discuss the role of friction in online platforms, new ways to measure it, and future work.
Non-coding 886 (nc886/vtRNA2-1), the epigenetic odd duck – implications for future studies

Non-coding 886 (nc886, VTRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability, and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNAs has been redefined multiple times and are still under debate and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Here, we aim to summarise the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, and reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the nc886 methylation pattern distribution is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.
"Keeping the Program Going": Technology Use by Community Organizations to Support the Social Connectedness of Older Adults During the COVID-19 Pandemic

Social programs run by community organizations provide an important outlet for social connectedness among older adults. However, these programs were disrupted by the COVID-19 pandemic restrictions. In this study, we aimed to understand how community organizations used digital technologies to continue running social programs online for older adults during COVID-19. We conducted semi-structured interviews with 12 staff members from local councils, libraries, community groups and care providers. We found that the use of technology benefited organizations by revealing new program delivery opportunities, and by strengthening their social bonds with older adults. However, organizations experienced challenges when transitioning social programs online. Some organizations lacked financial and human resources to support online programs; staff needed to upskill themselves and put significant effort into transferring older adults online; and it was difficult to replicate in-person experiences in online settings. Staff developed ad-hoc strategies to help older adults participate by providing extra guidance and training to increase digital literacy, and by offering accessible technical support. We discuss the significance of continuing online social programs beyond the pandemic and the importance of scaffolding to enable the online participation of older people in social programs. We outline design considerations for technology-mediated social programs run by community organizations.
"Connected to the people": Social Inclusion & Cohesion in Action through a Cultural Heritage Digital Tool

Current cultural policies are evolving from social inclusion (removing barriers and promoting equality for participation in culture) to social cohesion (fostering solid bonds between groups despite their differences). Digital interventions can create spaces that promote social inclusion and cohesion. In this paper, we report on the design and evaluation of a cultural heritage and digital storytelling application supporting a participatory approach to culture and hosting society. We evaluate our intervention in three marginalized communities with different social-cultural contexts: migrant women in Barcelona, a community living in a priority neighbourhood in Paris and second and third-generation migrants in Lisbon. Through an analysis of their application use, our findings point at their needs and desires, highlighting how the app can support social inclusion as the first step towards cohesion, but that these are heterogeneous concepts susceptible to nuanced appropriations by the different communities.
Sex- and caste-specific developmental responses to juvenile hormone in an ant with maternal caste determination

Queen-worker caste polyphenism in social insects is a prime example for developmental plasticity. Most of what we know about caste development comes from studies of the honeybee, in which female caste is determined during larval development and workers retain functional ovaries. The ant genus Cardiocondyla is one of only few genera in which complete worker sterility has evolved, so that adult workers completely lack reproductive organs. In C. obscurior, queen- and worker-destined individuals are distinct in their development by late-embryogenesis, and castes can be distinguished in a non-invasive manner from this stage onwards. This provides the opportunity to investigate the degree of flexibility in caste development in a species with early caste determination. Using topical juvenile hormone treatment, a method known to influence caste determination and differentiation in some species, we investigated whether hormone manipulation affects the development and growth of queen and worker-destined late-stage embryos and larvae, as well as of early-stage embryos which cannot yet be distinguished by caste. We found no effect of hormone treatment on female caste ratios or body sizes in any of the treated stages, even though individuals reacted to heightened hormone availability with increases in the expression of krüppel-homolog 1, a conserved JH first-response gene. In contrast, hormone treatment resulted in the emergence of significantly larger males. These results show that in C. obscurior, early, presumably maternal caste determination leads to irreversible and highly-canalized caste-specific development and growth.
Neural Evidence of Functional Compensation for Fluid Intelligence in Healthy Ageing

Functional compensation is a common notion in the neuroscience of healthy ageing, whereby older adults are proposed to recruit additional brain activity to compensate for reduced cognitive function. However, whether this additional brain activity in older participants actually helps their cognitive performance remains debated. We examined brain activity and cognitive performance in a human lifespan sample (N=223) while they performed a problem-solving task (based on Cattell’s test of fluid intelligence) during functional magnetic resonance imaging (fMRI). Whole-brain univariate analysis revealed that activity in bilateral cuneal cortex for hard vs. easy problems increased both with age and with performance, even when adjusting for an estimate of age-related differences in cerebrovascular reactivity. Multivariate Bayesian decoding further demonstrated that age increased the likelihood that activation patterns in this cuneal region provided non-redundant information about the two task conditions, beyond that of the multiple-demand network generally activated in this task. This constitutes some of the strongest evidence yet for functional compensation in healthy ageing, at least in this brain region during visual problem-solving.
ASSESSMENT OF STABILIZING FEEDBACK CONTROL OF WALKING, A TUTORIAL

Walking without falling requires stabilization of the trajectory of the body center of mass relative to the base of support. Model studies suggest that this requires active, feedback control, especially in the mediolateral direction. In older adults and in individuals with neurological or orthopedic disorders that affect walking ability, falls during gait are a common cause of injuries, hospitalization and loss of independence. In this tutorial, we illustrate how gait analysis can be used to assess the stabilizing feedback control of gait. We present methods ranging from those that require limited input data (e.g. position data of markers placed on the feet and pelvis only) to those that require full-body kinematics and electromyography. Analyses range from simple kinematics analyses to inverse dynamics. These methods assess stabilizing feedback control of human walking at three levels: 1) the level of center of mass movement and horizontal ground reaction forces, 2) the level of center of mass movement and foot placement and 3) the level of center of mass movement and the joint moments or muscle activity. We show how these can be calculated and provide a GitHub repository (https://github.com/VU-HMS/Tutorial-stabilizing-walking) which contains open access Matlab and Python code to calculate these. Finally, we discuss what information on feedback control can be learned from each of these.
Single-cell multimodal profiling of atherosclerosis identifies CD200 as a cell surface lineage marker of vascular smooth muscle cells and their derived cells

Vascular smooth muscle cells (VSMCs) play a central role in the development of atherosclerosis due in part to their capability to phenotypically transition into either a protective or harmful state. However, the ability to identify and trace VSMCs and their progeny in vivo is limited due to the lack of well-defined VSMC cell surface markers. Therefore, investigations into VSMC fate must utilize lineage-tracing mouse models, which are time-consuming and challenging to generate and not feasible in humans. Here, we employed CITE-seq to characterize the phenotypic expression of 119 cell surface proteins in mouse atherosclerosis. We found that CD200 is a highly expressed and specific marker of VSMCs, which persists even with phenotypic modulation. We validated our findings using a combination of flow cytometry, qPCR, and immunohistochemistry, all confirming that CD200 can identify and mark VSMCs and their derived cells in early to advanced mouse atherosclerotic lesions. Additionally, we describe a similar expression pattern of CD200 in human coronary and carotid atherosclerosis. Thus, our data support the use of CD200 as a lineage marker for VSMCs and VSMC-derived cells in mouse and human atherosclerosis.
Cannabidiol prevents the locomotor sensitization induced by cocaine and caffeine and upregulates genes of extracellular matrix and anti-inflammatory pathways in the nucleus accumbens: a transcriptome-wide analysis

Cannabidiol (CBD), a non-psychotomimetic phytocannabinoid found in the Cannabis plant, has emerged as a potential therapeutic agent for psychostimulant use disorders. In recent work, we demonstrated that CBD is able to attenuate the expression of locomotor sensitization and the enhanced metabolic activity in the nucleus accumbens (NAc) generated by the combination of cocaine and caffeine. CDB interacts directly or indirectly with several molecular targets, so the underlying mechanisms of its beneficial effects are hard to determine. Here we used high-throughput RNA-sequencing in mice’s NAc after a sensitization protocol with combined cocaine plus caffeine and a CBD pre-treatment, to identify the major pathways and genes involved in CBD attenuating behavioral effects. Results indicated that CBD pretreatment consistently reduced both the acquisition and expression of cocaine and caffeine locomotor sensitization. The transcriptome analysis revealed that CBD pre-treatment enriched genes and functional association between proteins mainly related to extracellular matrix (ECM) organization and cell interactions in the NAc. Moreover, the neuroinflammation and BDNF signaling pathways were also influenced by CBD. Some specially enriched genes such as Tnc were identified as interesting specific candidates for follow-up studies. These findings provide valuable and novel insights into molecular mechanisms of CBD putatively associated with a protective effect on psychostimulant actions. A better understanding of the therapeutic targets of CBD can open new avenues for psychostimulant use disorder treatment strategies.