Miracle-dz/UniFAR-FTUs huggingface dataset:
Title: Targeted intragenic demethylation initiates chromatin rewiring for gene activation

: Aberrant DNA methylation in the region surrounding the transcription start site is a hallmark of gene silencing in cancer. Currently approved demethylating agents lack specificity and exhibit high toxicity. Herein we show, using the p16 gene as an example, that targeted demethylation of the promoter-exon 1-intron 1 (PrExI) region initiates an epigenetic wave of local chromatin remodeling and distal long-range interactions, culminating in gene-locus specific activation. Through development of CRISPR-DiR (DNMT1-interacting RNA), in which ad hoc edited guides block methyltransferase activity in a locus-specific fashion, we demonstrate that demethylation is coupled to epigenetic and topological changes. These results suggest the existence of a specialized “demethylation firing center (DFC)” which can be switched on by an adaptable and selective RNA-mediated approach for locus-specific transcriptional activation.
Transmission and Analytical Electron Microscopy Evidence for High Mg Contents of 1M Illite: Absence of 1M Polytypism in Normal Prograde Diagenetic Sequences of Pelitic Rocks

The normal prograde diagenetic and low-grade metamorphic sequence of dioctahedral clay minerals including illite-rich I-S and illite, as observed by TEM, proceeds from a partially disordered 1Md stacking sequence to 2M1; i.e. 1M does not normally occur as an intermediate polytype. Examples of 1M illite stacking sequences have been studied, however, from the Golden Cross gold deposit, New Zealand, the Broadlands-Ohaaki geothermal system, New Zealand, the Potsdam Sandstone, New York, and the Silverton Caldera, Colorado. Specific clay-mineral packets identified by TEM techniques as 1M illite were found to have anomalously high Mg contents. The Broadlands illite provides the most definitive data, as separate packets of 1M and 2M1 illite coexist. Average compositions for 1M and 2M1 illite are (K1.66Ca0.04)Σ1. 70(Al3.32Fe0.31Mg0.57Mn0.06)Σ4. 26(Si6.43Al1.57)Σ8O20(OH)4 and (K1.57Na0.31Ca0.03)Σ1. 91(Al3.58Fe0.05Mg0.29Mn0.01)Σ3. 93(Si6.70Al1.30)Σ8O20(OH)4, respectively. In addition, 1Mdillite, which is the polytype occurring in the common 1Mdto 2M1 prograde sequence, is relatively Mg poor, but coexists with Mg-rich illite in the Silverton Caldera sample.These data confirm that 1M stacking is caused by compositional anomalies, and thus explain the lack of the 1M stacking sequence in normal diagenetic sequences in pelitic rocks, as most illite in such environments has a relatively small phengitic component. The parameter Δz, a measure of the corrugation of the oxygen sheets, may be the key parameter reflecting the polytypic state of dioctahedral and trioctahedral micaceous minerals. Such composition-determined relations may be related to the occurrence of 1M polytypism in glauconite and celadonite, both dioctahedral 2:1 clay minerals having large Mg or Fe octahedral-cation components, and in trioctahedral micas. Insofar as the 1M stacking sequence does not have the same composition as 2M1 material, these data confirm that the different varieties of illite are not polytypes, sensu stricto.
Optimal Groundwater Remediation by Pump and Treat Using FEM- and EGA-Based Simulation-Optimization Model

AbstractGroundwater contamination is one of the most serious environmental problems in many parts of the world. For remediation of dissolved phase contaminants in groundwater, a pump-and-treat method is found to be a successful remediation technique. Developing an efficient and robust design to solve groundwater pollution remediation problems using a pump-and-treat method is very important because of the large construction and operating costs involved. In this study, an attempt is made to develop a coupled simulation-optimization model based on the finite-element method (FEM) and an evolutionary approach of an elitist genetic algorithm (EGA) for the optimal design of groundwater remediation by pump and treat. The model couples an EGA, a global search technique, with FEM for coupled flow, and a solute transport model to optimize the pump and treat groundwater pollution problems. The simulation-optimization model is used to optimize the remediation of a large-field unconfined aquifer polluted with total dis.
Moderate High Temperature is Beneficial or Detrimental Depending on Carbon Availability in the Green Alga Chlamydomonas reinhardtii

High temperatures impair plant and algal growth and reduce food and biofuel production, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is a superior model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and/or with the externally supplied organic carbon source, acetate. Most of the published research about Chlamydomonas heat responses used acetate-containing medium. Understanding how organic carbon sources affect heat responses is important for the algal industry but understudied. We cultivated Chlamydomonas wild-type cultures under highly controlled conditions in photobioreactors at control of 25°C, moderate high temperature of 35°C, or acute high temperature of 40°C with and without constant acetate supply for 1- or 4-days. Our results showed that 35°C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35°C could be explained by induced carbon metabolism, including acetate uptake and assimilation, glyoxylate cycle, gluconeogenesis pathways, and glycolysis. Acute high temperature at 40°C for more than 2 days was lethal to algal cultures with and without constant acetate supply. Our research provides insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells. Highlight We revealed the overlooked, dynamic effects of moderate high temperature in algae depending on carbon availability and demonstrated the importance of carbon metabolism in thermotolerance of photosynthetic cells.
Keratinocyte Stem Cells: Role in Aging

Stem cells located in the skin are responsible for continual regeneration, wound healing, and differentiation of different cell lineages of the skin. The three main locations of skin stem cells are the epidermis, dermis, and hair follicles. The keratinocyte stem cells are located in the epidermal basal layer (the interfollicular stem cells), hair follicle bulge region (the hair follicle stem cells), and sebaceous glands (the sebaceous gland stem cells) and are responsible for the epidermal proliferation, differentiation, and apoptosis. The interfollicular (IF) stem cells are responsible for epidermis regeneration by proliferating basal cells that attach to the underlying basement membrane and with time they exit from the cell cycle, start terminal differentiation, and move upward to form the spinous, the granular, and the stratum corneum layers. The hair follicle (HF) stem cells are responsible for hair regeneration and these stem cells undergo a cycle consists three stages; growth cycles (anagen), degeneration (catagen), and relative resting phase (telogen). The sebaceous gland (SG) stem cells located in between the hair follicle bulge and the gland and are responsible for producing the entire sebaceous gland which secretes oils to moisture our skin. The role of epidermal stem cells is extremely crucial because they produce enormous numbers of keratinocytes over a lifetime to maintain epidermal homeostasis. However, the age-associated changes in the skin; for example; alopecia, reduced hair density, gray or thin hair, reduced wound healing capacity are related to skin stem cells’ decline functionality with age.
Amazonian Floodplain Forests. Ecophysiology, Biodiversity and Sustainable Management

Part I - Amazonian Floodplain Forests and the Environment 1. An Introduction to South American Wetland Forests: Distribution, Definitions and General Characterization 2. Development of the Amazon Valley during the Middle to Late Quaternary: Sedimentological and Climatological Observations 3. Remote Sensing of the Distribution and Extent of Wetlands in the Amazon Basin 4. Phytogeography, Species Diversity, Community Structure and Dynamics of Central Amazonian Floodplain Forests Part II - Ecological and Ecophysiological Aspects of Amazonian Floodplain Forests 5. Tree Phenology in Amazonian Floodplain Forests 6. Biochemistry of Amazonian Floodplain trees 7. The Morphology and Anatomy of Tree Roots and their Aeration Strategies 8. Fine Root Systems and Mycorrhizal Associations in Two Central Amazonian Inundation Forests - Igapo and Varzea 9. Morphology and Anatomy of Leaves 10. Gas Exchange and Photosynthesis 11. Sap Flow and Stem Respiration 12. Fruit and Seed Chemistry, Biomass and Dispersal 13. Seed Germination and Seedling Establishment of Amazonian Floodplain Trees 14. Nitrogen Balance of a Floodplain Forest of the Amazon River: the Role of Nitrogen Fixation 15. Genetic Variability, Divergence and Speciation in Trees of Periodically Flooded Forests of the Amazon: a Case Study of Himatanthus sucuuba (SPRUCE) WOODSON 16 . The Importance of Amazonian Floodplain Forests for Animal Biodiversity: Beetles in Canopies of Floodplain and Upland Forests Part III - Sustainable Management of Amazonian Floodplain Forests 17. Wood Anatomy, Tree Ring Structure of the Stem and their Importance for Tropical Dendrochronology. 18. Biomass and Net Primary Production of Central Amazonian Floodplain Forests 19. Use of Amazonian Floodplain Trees 20. Traditional Timber Harvesting in the Central Amazonian Floodplain Forests 21. Growth-Orientated Logging (GOL): The Use of Species Specific Growth Information for Forest Management in Central Amazonian Floodplains Part IV - Discussion and conclusions 22. Protected Areas in the Amazonian Varzea and their Role in its Conservation: the Case of Mamiraua Sustainable Development Reserve (MSDR) 23. The Role of Floodplain Forests in an Integrated Sustainable Management Concept of the Natural Resources of the Central Amazonian Varzea. 24 Ecophysiology, Biodiversity and Sustainable Management of Central Amazonian Floodplain Forests: a Synthesis
Supplementary Material for Cloud-Device Collaborative Adaptation to Continual Changing Environments in the Real-world A. Overview

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Genesis of Ultramafic Lamprophyres and Carbonatites at Aillik Bay, Labrador: a Consequence of Incipient Lithospheric Thinning beneath the North Atlantic Craton

Numerous dykes of ultramafic lamprophyre (aillikite, mela-aillikite, damtjernite) and subordinate dolomite-bearing carbonatite with U–Pb perovskite emplacement ages of 590–555Ma occur in the vicinity of Aillik Bay, coastal Labrador. The ultramafic lamprophyres principally consist of olivine and phlogopite phenocrysts in a carbonateor clinopyroxene-dominated groundmass. Ti-rich primary garnet (kimzeyite and Ti-andradite) typically occurs at the aillikite type locality and is considered diagnostic for ultramafic lamprophyre–carbonatite suites. Titanian aluminous phlogopite and clinopyroxene, as well as comparatively Al-enriched but Cr–Mg-poor spinel (Cr-number < 0.85), are compositionally distinct from analogous minerals in kimberlites, orangeites and olivine lamproites, indicating different magma geneses. The Aillik Bay ultramafic lamprophyres and carbonatites have variable but overlapping Sr/Sri ratios (0 70369–0 70662) and show a narrow range in initial «Nd (þ0 1 to þ1 9) implying that they are related to a common type of parental magma with variable isotopic characteristics. Aillikite is closest to this primary magma composition in terms of MgO ( 15–20wt %) and Ni ( 200–574 ppm) content; the abundant groundmass carbonate has dCPDB between 5 7 and 5‰, similar to primary mantle-derived carbonates, and dOSMOW from 9 4 to 11 6‰. Extensive melting of a garnet peridotite source region containing carbonateand phlogopite-rich veins at 4–7 GPa triggered by enhanced lithospheric extension can account for the volatile-bearing, potassic, incompatible element enriched and MgO-rich nature of the proto-aillikite magma. It is argued that low-degree potassic silicate to carbonatitic melts from upwelling asthenosphere infiltrated the cold base of the stretched lithosphere and solidified as veins, thereby crystallizing calcite and phlogopite that were not in equilibrium with peridotite. Continued Late Neoproterozoic lithospheric thinning, with progressive upwelling of the asthenosphere beneath a developing rift branch in this part of the North Atlantic craton, caused further veining and successive remelting of veins plus volatile-fluxed melting of the host fertile garnet peridotite, giving rise to long-lasting hybrid ultramafic lamprophyre magma production in conjunction with the break-up of the Rodinia supercontinent. Proto-aillikite magma reached the surface only after coating the uppermost mantle conduits with glimmeritic material, which caused minor alkali loss. At intrusion level, carbonate separation from this aillikite magma resulted in
Indicadores de Innovación en Uruguay (1998-2000): balance metodológico y principales resultados empíricos

espanolEste trabajo presenta, en la primera parte, los principales elementos conceptuales y metodologicos que guiaron la realizacion de la Encuesta de Actividades de Innovacion en la Industria en Uruguay, durante el periodo 1998-2000. En la segunda parte, se muestran los principales resultados empiricos que surgen de este ejercicio y se esbozan algunas caracteristicas de la conducta tecnologica de Ias firmas uruguayas EnglishThe first part of this work presents the main conceptual and methodological aspects that guided the execution of the Survey on Innovation Activities at the Industry in Uruguay, along the period 1998-2000. The second part shows the main empirical results arising from this exercise and outlines some characteristics of the technological behaviour of the Uruguayan firms.
WHY ARE BEVERIDGE-NELSON AND UNOBSERVED-COMPONENT DECOMPOSITIONS OF GDP SO DIFFERENT ?

Washington University in St. Louis, University of Washington, and University of Washington, respectively. The authors acknowledge with thanks support from the National Science Foundation under grants SES-9818789 and SBR-9711301 and from the Van Voorhis and Ensley endowments at the University of Washington. We received helpful comments from many individuals and particularly Charles Engel, Andrew Harvey, Chang-Jin Kim, Chris Murray, Jeremy Piger, Simon Potter, Glenn Rudebusch, Richard Startz, James Stock, and Mark Wohar, but responsibility for errors is entirely the authors'. Kyongwook Choi provided valuable research assistance.
Occurrence of zoned uvarovite—grossular garnet in a rodingite from the Vumba Schist Belt, Botswana, Africa: implications for the origin of rodingites

Abstract Based on petrographic, mineralogical and geochemical data, two groups of rodingites have been documented from the polymetamorphic Vumba Schist Belt of Botswana. Group I rodingites contain relict chromite grains with zoned uvarovite-grossular + clinopyroxene + epidote/zoisite ± quartz, whereas group II rodingites contain no chromite and uvarovite. Although the presence of chromite with Cr/(Cr + Al + Fe3+) ratio > 90, similar to chromites found in komatiites, suggests a possible komatiitic origin of group I rodingites, the major and trace element chemical data of most analysed basic rocks from this belt indicate that the protoliths of both groups of rodingites are related to basalt/gabbro of komatiitic affinity. The rodingites formed during the M3 phase of metamorphism.
Assessing the uncertainty in distributed model predictions using observed binary pattern information within GLUE

In this paper we extend the generalized likelihood uncertainty estimation (GLUE) technique to estimate spatially distributed uncertainty in models conditioned against binary pattern data contained in flood inundation maps. Untransformed binary pattern data already have been used within GLUE to estimate domain‐averaged (zero‐dimensional) likelihoods, yet the pattern information embedded within such sources has not been used to estimate distributed uncertainty. Where pattern information has been used to map distributed uncertainty it has been transformed into a continuous function prior to use, which may introduce additional errors. To solve this problem we use here ‘raw’ binary pattern data to define a zero‐dimensional global performance measure for each simulation in a Monte Carlo ensemble. Thereafter, for each pixel of the distributed model we evaluate the probability that this pixel was inundated. This probability is then weighted by the measure of global model performance, thus taking into account how well a given parameter set performs overall. The result is a distributed uncertainty measure mapped over real space. The advantage of the approach is that it both captures distributed uncertainty and contains information on global likelihood that can be used to condition predictions of further events for which observed data are not available. The technique is applied to the problem of flood inundation prediction at two test sites representing different hydrodynamic conditions. In both cases, the method reveals the spatial structure in simulation uncertainty and simultaneously enables mapping of flood probability predicted by the model. Spatially distributed uncertainty analysis is shown to contain information over and above that available from global performance measures. Overall, the paper highlights the different types of information that may be obtained from mappings of model uncertainty over real and n‐dimensional parameter spaces. Copyright © 2002 John Wiley & Sons, Ltd.
A perturbation simulation of CO2 uptake in an ocean general circulation model

The uptake of anthropogenic CO2 by the ocean is simulated using a perturbation approach in a three-dimensional global general circulation model. Atmospheric pCO2 is prescribed for the period 1750–1990 using the combined Siple ice core and Mauna Loa records. For the period 1980 to 1989, the average flux of CO2 into the ocean is 1.9 GtC/yr. However the bomb radiocarbon simulation of Toggweiler et al. (1989b) shows that the surface to deep ocean exchange in this model is too sluggish. Hence the CO2 uptake calculated by the model is probably below the actual value. The observed atmospheric increase in 1980 to 1989 is 3.2 GtC/yr, for a combined atmosphere-ocean total of 5.1 GtC/yr. This is comparable to the estimated fossil CO2 production of 5.4 GtC/yr, implying that other sources and sinks (such as from deforestation, enhanced growth of land biota, and changes in the ocean carbon cycle) must be approximately in balance. The sensitivity of the uptake to the gas exchange rate is small: a 100% increase in gas exchange rate gives only a 9.2% increase in cumulative oceanic uptake. Details of the penetration into different oceanic regions are discussed.
Estimating Nonpoint Source Pollution in the Upper Yangtze River Using the Export Coefficient Model, Remote Sensing, and Geographical Information System

Recently, increasing nutrient (i.e., nitrogen and phosphorus) concentrations have been observed in the surface water of many countries and this nonpoint source (NPS) pollution has become an important factor in the deterioration of water quality in the upper reach of the Yangtze River Basin. In this paper, the NPS pollution loads in the upper reach of Yangtze River Basin in the year 2000 were estimated using export coefficient model and remote sensing techniques. The spatial distributions of the NPS loads within the watershed were then displayed using geographical information system. Results indicated that the total nitrogen load was 1.947× 106 t and the total phosphorus load was 8.364× 104 t . Important source areas for the nutrients were croplands in the Jinsha R. and Jialing R. watershed, as well as the Chongqing municipality.
Nutrient Uptake and Short-Term Responses of Phytoplankton and Benthic Algal Communities from a Subarctic Pond to Experimental Nutrient Enrichment in Microcosms

Abstract Climate warming is anticipated to affect high-latitude regions, including abundant ponds of the Hudson Bay Lowlands (HBL). However, it remains unclear if associated increased frequency of nutrient pulses will be rapidly consumed by aquatic biota and sediment or lead to a rise in pond-water nutrient concentrations. Here, we performed a nutrient-amendment experiment to examine short-term (≤72 h) nutrient uptake and identify the consumers of the added nutrients (planktonic vs. benthic communities). Microcosms (1 L) with and without sediment were experimentally amended with inorganic nitrogen (nitrate, ammonium) with and without phosphate. Amended nitrate and ammonium concentrations remained high in microcosms without sediments, and phytoplankton biomass did not change relative to the un-amended control. However, phosphate concentration declined significantly in microcosms without sediment, resulting in significant increase of phytoplankton biomass after 72 h. In the presence of sediment, amended nutrients were rapidly removed from the water, stimulating benthic algal biomass when phosphate was co-amended with ammonium or nitrate. Phytoplankton biomass was significantly elevated in microcosms with sediment compared to those without sediment, regardless of whether nutrients were amended or not, indicating that sediment and associated benthic biofilm stimulate phytoplankton growth, likely via supply of nutrients to the overlying water column. A key outcome of the experiment is that pulsed nutrients were taken up rapidly and primarily by the benthic community. Findings suggest that shallow ponds in the HBL are capable of rapidly consuming pulsed nutrient supplies, as may occur due to hydroclimatic events, climate warming and other disturbances.