Miracle-dz/UniFAR-FTUs huggingface dataset:
An enhancer RNA recruits MLL1 to regulate transcription of Myb

The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for hematopoiesis. Distant enhancers of Myb form a hub of interactions with the Myb promoter. We identified a long non-coding RNA (Myrlin) originating from the −81 kb murine Myb enhancer. Myrlin and Myb are coordinately regulated during erythroid differentiation. Myrlin TSS deletion using CRISPR/Cas9 reduced Myrlin and Myb expression and LDB1 complex occupancy at the Myb enhancers, compromising enhancer contacts and reducing RNA Pol II occupancy in the locus. In contrast, CRISPRi silencing of Myrlin left LDB1 and the Myb enhancer hub unperturbed, although Myrlin and Myb expression were downregulated, decoupling transcription and chromatin looping. Myrlin interacts with the MLL1 complex. Myrlin CRISPRi compromised MLL1 occupancy in the Myb locus, decreasing CDK9 and RNA Pol II binding and resulting in Pol II pausing in the Myb first exon/intron. Thus, Myrlin directly participates in activating Myb transcription by recruiting MLL1.
Artomyces pyxidatus (Auriscalpiaceae, Fungi) in the Great Smoky Mountains National Park: Individuals and Populations

Artomyces pyxidatus is a North-temperate saprophytic coral fungus found in Europe, Asia, and North America. Collections from the Great Smoky Mountains National Park were used in this study to define the size of an individual and elucidate gene flow between three locations within the park (Greenbrier, Sugarlands, Cataloochee). Molecular techniques were used to determine the relationships between populations and among individuals. Two inter-simple sequence repeat (ISSR) primers amplified segments of DNA scattered throughout the genome and together produced 26 variable bands. ISSR analysis appeared to be a reliable technique for defining individuals, but should be used in conjunction with other techniques that are able to eliminate ambiguity and ensure accuracy. The nuclear ribosomal ITS 1-5.8S-ITS 2 (ITS) repeat provided a more defined genetic region and was studied using restriction fragment length polymorphisms (RFLP). An insertional element located within a Group I intron contained by the ribosomal 18S subunit was found in most eastern North American A. pyxidatus collections and was amplified and used to supplement the other molecular analyses by verifying the identity of individuals (Lickey 2002). Analyses based on genetic characterization of multiple fruitbodies from single logs indicated that several A. pyxidatus individuals could occupy a single substrate and that the mycelia could reach a measured size of 1.9 meters. Data also showed that the three GSMNP populations were not in Hardy-Weinberg equilibrium and were, therefore, not undergoing random gene exchange. A deficiency of heterozygotes suggested that the cause was inbreeding. The Greenbrier population appears to be the most genetically diverse based on Neighbor Joining and Principle Coordinates analyses. Both techniques
Height, autoimmune thyroid disease and thyroid cancer: a Mendelian randomisation study

Background Increased height has been associated with increased risk of hypothyroidism or thyroid cancer in epidemiological studies. However, the potential causal association between height and hypothyroidism or thyroid cancer have not been thoroughly explored. Autoimmune thyroid disease (AITD) mainly presents as hypothyroidism, thus, we aim to evaluate the causal relationship between height as exposure and its association with AITD or thyroid cancer. Methods Mendelian randomisation (MR) analyses were performed by using genetic instruments associated with height, which were selected from the largest genome-wide association meta-analysis for height in up to 5.4 million individuals. Summary-level data for AITD and thyroid cancer, including 30,234 and 3,001 cases respectively, were collected from the large available genome-wide association studies. Bidirectional MR was performed to test for reverse causal association between AITD and adult height. Results MR analyses showed that increased genetically predicted height was associated with a 4% increased risk of AITD ([95% CI 1.02, 1.07], pvalue=1.99E-03), per 1 standard deviation (SD) increase in genetically predicted height. The bidirectional MR did not show any causal association between AITD and adult height. Additionally, increased genetically predicted height was associated with 15% increased risk of thyroid cancer ([95% CI 1.07, 1.23], pvalue=2.32E-04), per 1-SD increase in height. Sensitivity analysis confirmed the main results. Conclusions This MR study showed that one standard deviation increased genetically predicted height was associated with increased risk of AITD and thyroid cancer. In contrast, there was no evidence of a causal association of genetically predicted AITD on height. These results could be further aiding the investigation of height-related pathways as a means for gaining new mechanistic insights into AITD and thyroid cancer.
Current Progress and Challenges in Large-Scale 3D Mitochondria Instance Segmentation

In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 1,986 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that: 1) challenge metric was permissive with the false positive predictions; and 2) size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download.
Evaluation of the relationship among gene expressions and enzyme activities with antioxidant role and presenilin 1 expression in Alzheimer's disease

It is known that oxidative stress originating from reactive oxygen species plays a role in the pathogenesis of Alzheimer's disease. In this study, the role of antioxidant status associated with oxidative stress in Alzheimer's disease was investigated. Peripheral blood samples were obtained from 28 healthy individuals (as control) and 28 Alzheimer's patients who met the National Institute of Neurological and Communicative Diseases and Stroke/Alzheimer's Disease and Related Disorders Association criteria. Catalase, glutathione S‐transferase and paraoxonase 1 enzyme activities in blood plasma and glutathione S‐transferase enzyme activities in erythrocytes were determined by spectrophotometer. Catalase, glutathione S‐transferase and presenilin 1 gene expressions in leukocytes were determined using qRT‐PCR. Data were analysed with SPSS one‐way anova, a LSD post hoc test at p < 0.05. The activity of each enzyme was significantly reduced in Alzheimer's patients compared to control. The catalase gene expression level did not change compared to the control. Glutathione S‐transferase and presenilin 1 gene expression levels were increased compared to the control.
The everglades handbook: understanding the ecosystem.

BACKGROUND. The Everglades in space and time. An ecosystem overview. ENVIRONMENTS OF THE EVERGLADES REGION. Freshwater marshes: Water, weather, and fire. Tree Islands. Tropical hardwood hammocks. Pinelands. The Big Cypress Swamp. Mangrove swamps. Coastal lowland vegetation! and hurricanes! Coastal estuarine and marine waters. Lake Okeechobee and the Everglades' headwaters. THE FLORA AND FAUNA OF SOUTHERN FLORIDA. Origins of the flora and fauna. Invertebrates. Freshwater fishes. Marine and estuarine fishes. Amphibians. Reptiles. Mammals. Birds. Synthesis--Ecological relationships and processes in the Everglades region. ENVIRONMENTAL IMPACTS. Man and the Everglades.
Subduction initiation at passive margins: Numerical modeling

[1] Subduction is a key process for terrestrial plate tectonics, but its initiation is still not entirely understood. In particular, despite the abundance of both passive and active continental margins on Earth, no obvious cases of transition between them have been identified so far. It has been shown that at most passive margins, elastic and frictional forces exceed gravitational instability and ridge-push forces, which precludes subduction initiation. Therefore additional factors are needed to start subduction there. We investigated numerically in two dimensions factors controlling passive margins' stability such as age of the oceanic plate, thickness of the continental lithosphere and crust, and density contrast between subcontinental and suboceanic lithospheric mantles. Our numerical experiments show that three subsequent tectonic regimes can develop at a passive margin: (1) stable margin, (2) overthrusting, and (3) subduction. Transition from stable margin to the overthrusting regime is mainly controlled by ductile strength of the lower continental crust. Further transition from overthrusting to the subduction regime is governed by the ductile strength of the subcontinental lithospheric mantle and its chemical density contrast with the suboceanic lithospheric mantle. Our experiments also demonstrate that the age of the oceanic plate is a factor of secondary importance for subduction initiation and only plays a role if other parameters are of critical values. Favorable conditions for subduction initiation thus correspond to passive margins where chemically buoyant (depleted) continental lithosphere becomes thin and hot (Moho temperature >660°C). This situation can be occasionally created by superimposed external processes such as rifting and/or thermal-chemical plume activity.
Spatial and temporal distribution of diagenetic alterations in siliciclastic rocks: implications for mass transfer in sedimentary basins

The spatial and temporal distribution of diagenetic alterations in siliciclastic sequences is controlled by a complex array of interrelated parameters that prevail during eodiagenesis, mesodiagenesis and telodiagenesis. The spatial distribution of near‐surface eogenetic alteration is controlled by depositional facies, climate, detrital composition and relative changes in sea‐level. The most important eogenetic alterations in continental sediments include silicate dissolution and the formation of kaolinite, smectite, calcrete and dolocrete. In marine and transitional sediments, eogenetic alterations include the precipitation of carbonate, opal, microquartz, Fe‐silicates (glaucony, berthierine and nontronite), sulphides and zeolite. The eogenetic evolution of marine and transitional sediments can probably be developed within a predictable sequence stratigraphic context. Mesodiagenesis is strongly influenced by the induced eogenetic alterations, as well as by temperature, pressure and the composition of basinal brines. The residence time of sedimentary sequences under certain burial conditions is of key importance in determining the timing, extent and patterns of diagenetic modifications induced. The most important mesogenetic alterations include feldspar albitization, illitization and chloritization of smectite and kaolinite, dickitization of kaolinite, chemical compaction as well as quartz and carbonate cementation. Various aspects of deep‐burial mesodiagenesis are still poorly understood, such as: (i) whether reactions are accomplished by active fluid flow or by diffusion; (ii) the pattern and extent of mass transfer between mudrocks and sandstones; (iii) the role of hydrocarbon emplacement on sandstone diagenesis; and (iv) the importance and origin of fluids involved in the formation of secondary inter‐ and intragranular porosity during mesodiagenesis. Uplift and incursion of meteoric waters induce telogenetic alterations that include kaolinitization and carbonate‐cement dissolution down to depths of tens to a few hundred metres below the surface.
Proceedings of the 11th ACM conference on Electronic commerce

The papers in these proceedings represent the technical contributions to the 11th ACM Conference on Electronic Commerce -- EC'10, held June 7-11, 2010, at Harvard University in Cambridge, Massachusetts, USA. Since its inception in 1999, ACM EC has served as the leading scientific conference on advances in theory, systems, and applications for electronic commerce. The natural focus of the conference is on computer science issues, but the conference is interdisciplinary in nature, addressing a number of facets of electronic commerce including (1) theory and foundations; (2) languages; (3) automation, personalization, and targeting; (4) security, privacy, encryption, and digital rights; (5) applications and empirical studies; and (6) social factors. In addition to the main technical program, EC'10 features two workshops, four tutorials, and invited keynote presentations from MIT Sloan School of Management Professor Erik Brynjolfsson and Microsoft's General Manager for Experimentation Platform Ronny Kohavi. EC'10 is also co-located this year with the 9th Workshop on the Economics of Information Security (WEIS 2010), the Trading Agent Competition (TAC 2010) and the 25th IEEE Conference on Computational Complexity (CCC 2010). The call for papers attracted 136 submissions from authors in academia and industry from around the world, including Africa, Asia, Canada, Europe, the Middle East, and the United States. Each paper was reviewed by at least three program committee members and one senior program committee member on the basis of scientific novelty, technical quality, and importance to the field. After discussion and deliberation among the program committee, senior program committee and program chairs, 45 papers were selected for presentation at the conference; most of these papers appear in these proceedings. For a few accepted papers and at the authors' request, only abstracts are included along with pointers to full versions of these "working papers. " This accommodates the practices of fields outside of computer science in which journal rather than conference publishing is the norm and conference publishing sometimes precludes journal publishing. It is expected that many of the papers in these proceedings will appear in a more polished and complete form in scientific journals in the future.
MANAGING A DISASTER IN THE VETERINARY FIELD

Research studies worldwide show that due to different factors as climate change, poverty, urbanization, etc., there is a tendency of increasing the frequency and severity of both natural and man-made disasters. As the occurrence of natural disasters is a consequence of various preconditions, this work focuses on biological hazards which lead to epidemics and pandemics (including epizootics and panzootics). An analysis is made of legislative and official documents such as recommendations, strategies, regulations, etc. (from the international, European and Bulgarian legislative framework) with emphasis on reducing risks in the veterinary field in Bulgaria. Some suggestions are given for improvement of the systems for risk and disaster management of veterinary activities in the country.
MINERALOGY OF MEDIEVAL SLAGS FROM LEAD AND SILVER SMELTING (BOHUTÍN, PŘÍBRAM DISTRICT, CZECH REPUBLIC): TOWARDS ESTIMATION OF HISTORICAL SMELTING CONDITIONS*

Slags from the Pb/Ag medieval (14th century) smelting plant located at Bohutin, Přibram district, Czech Republic, were studied from the mineralogical and geochemical points of view. Two types of slags were distinguished: (i) quenched slags formed mainly by Pb-rich glass and unmelted residual grains of SiO2 and feldspars, and (ii) crystallized slags mainly composed of Fe-rich olivine (fayalite) and glass. The mean log viscosity value of the slags calculated for 1200°C was 2.119 Pa s. The morphology of olivine crystals was used to estimate the cooling rates of the melt, for some slags indicating rates > 1450°C/h. The projection of the bulk composition of slags onto the SiO2–PbO–FeO ternary system was used for rough temperature estimates of slag formation, lying probably between 800 and 1200°C.
On the Geotectonics of Southern China

The tectonic nature of southern China has changed again and again in the Phanerozoic. In the Caledonian cycle, there existed three tectonic units-the Yangtze paraplatform, Indosinian-South China Sea paraplatforrn and Caledonian South China fold belt, of which the last unit is not a collisional orogenic belt but a scissor-shaped aulacogen- type geosyncline opening towards Yunnan and Vietnam. In the Indosinian cycle, South China belonged to the Tethyan tectonic domain, and no abyssal oceanic basin existed there. Since the Late Triassic, especially in the Yanshanian orogenic stage, it became a component part of the peri-Pacific continental-margin activation belt of eastern Asia. No Alpine-type orogenic belt occurs in the interior of the continent of southern China.
A plate tectonic model of the Palaeozoic tectonic history of New South Wales

Abstract An updated∗ tectonic model for the Palaeozoic tectonic history of New South Wales, based on actualistic models of plate tectonics, has resulted from tectonic analyses and syntheses during the compilation of the Tectonic Map of New South Wales. Most emphasis is given to marginal seas, which characterize Pacific marginal mobile zones. Marginal seas form in the regime of lithospheric tension under the influence of retrograde motion of the Benioff zone, and during the formation of a new Benioff zone, or during formation of spheno‐ and rhombochasms. Additional mechanisms for obduction zone formation are suggested: the development of an obduction zone at the originally coupled continental margin is important. Three basic types of volcanic chains are distinguished: volcanic arcs, volcanic arches, and volcanic rifts, in the formation of which both primary subduction zones at major plate margins, and secondary subduction zones which develop in marginal seas may be concerned. During the Palaeozoic the east.
Combining Open Channel Flow at Right Angled Junctions

In combining open channel flow, the rise in the upstream flow depth due to the effect of lateral inflow from the branch channel can be significant. For right‐angled, sharp‐edged junctions of rectangular channels, a relation between the depth of flow at the junction and the ratio of the lateral discharge to the total discharge is derived on the basis of the momentum principle. Using this relationship, one can predict the rise in the flow depth when the undisturbed flow conditions in the channels are specified. In the proposed model, the contribution of the momentum transfer from the branch channel to the main channel is included, as this factor can be significant when the lateral discharge is relatively large. The proposed relationship is verified with the results of experiments related to combining flows for which the flow conditions downstream of the junction are both critical and unsubmerged. The study of combining flow at right angle junctions has a direct application in drainage network systems and ri.
Improving the performance of industrial mixers that are used in agricultural technologies via chaotic systems and artificial intelligence techniques

: In this study, it is aimed to show how important to apply chaotic systems and Fuzzy Logic artificial intelligence technique to increase the production performance of industrial mixers used in agriculture in terms of important criteria such as product quality, homogeneity, time, and energy saving by using. A PLC (Programmable Logic Controller) controlled mixer whose all functions can be controlled by the HMI (Human Machine Interface) operator panel is designed and manufactured for experimental studies. Water, leonardite and potassium hydroxide (KOH) mixture components are mixed in a newly designed mixer in three different ways by using traditional, chaos, and artificial intelligence techniques in order to obtain liquid humic acid which is used as plant nutrition and soil modulator in agriculture. For the chaotic mixing option, chaotic systems with different dynamic features are chosen from the literature. After converting the time series values of chaotic systems to the frequency values with the program written on the PLC device, it is provided to rotate at variable speeds according to different chaotic systems of the mixer motor connected to the frequency inverter. Fuzzy Logic is chosen for the artificial intelligence mixing option. Fuzzy Logic membership functions and rules are established in accordance with the results of the chaotic systems mixing experiments and the data obtained from experts in humic acid production. Mixing experiments are carried out by using an interface program that makes the choice of chaotic systems and motor rotation speed range. By mixing humic acid components with traditional methods, the comparison is done in terms of product quality, solute ratio, pH values and total energy consumption. When the developed mixer is provided to operate with chaos and artificial intelligence methods, it is observed that more eﬀicient results are obtained in terms of criteria such as product quality, homogeneity, time, and energy savings compared to the traditional mixing methods.
Global distribution of total cloud cover and cloud type amounts over the ocean

This is the fourth of a series of atlases to result from a study of the global cloud distribution from ground-based observations. The first two atlases (NCAR/TN-201+STR and NCAR/TN-241+STR) described the frequency of occurrence of each cloud type and the co-occurrence of different types, but included no information about cloud amounts. The third atlas (NCAR/TN-273+STR) described, for the land areas of the earth, the average total cloud cover and the amounts of each cloud type, and their geographical, diurnal, seasonal, and interannual variations, as well as the average base heights of the low clouds. The present atlas does the same for the ocean areas of the earth.
Satellite observations of asymmetrical physical and biological responses to Hurricane Earl

Asymmetrical physical and biological responses to Hurricane Earl in 2010 are revealed with a combined data set of the Moderate Resolution Imaging Spectroradiometer (MODIS) ocean color and Advanced Microwave Scanning Radiometer EOS (AMSR‐E) SST observations onboard the satellite Aqua. Hurricane Earl induced broad SST drops and elevated chlorophyll‐a concentrations along its track. The ocean's physical and biological responses are notably right‐biased when the hurricane passed along the U.S. East Coast. In the ranges within 100 km off the track, the SST dropped 1.85°C and 1.23°C on the right and left sides, respectively. On the other hand, the ratios of the chlorophyll‐a concentration before and after the passage of Hurricane Earl are 2.04 on the right side and 1.33 on the left. In addition to the satellite‐observed sea surface changes, temperature and salinity profiles of an Argo float on Earl's track show the ocean's physical response occurred mostly within the mixed layer and thermocline in the upper 70 m water column.
Nonlinear Pricing

I survey the use of nonlinear pricing as a method of price discrimination, both with monopoly and oligopoly supply. Topics covered include an analysis of when it is pro(cid:133)table to o⁄er quantity discounts and bundle discounts, connections between second- and third-degree price discrimination, the use of market demand functions to calculate nonlinear tari⁄s, the impact of consumers with bounded rationality, bundling arrangements between separate sellers, and the choice of prices for upgrades and add-on products.