Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisiting Raup: exploring the influence of outcrop area on diversity in light of modern sample-standardization techniques

Abstract Since David Raup's seminal 1976 work, paleontologists have been aware of the relationship between outcrop area and diversity. By incorporating lithologic data derived from Alexander Ronov and coworkers into our own data on areas of mapped outcrops from worldwide geologic maps, we are able to establish a quantitative connection between area of sedimentary rock exposure and diversity from the same general depositional environments. Significant power-law relations are observed at both global and continental scales of consideration. The addition of data on areas of habitable area estimated from paleogeographic maps does not substantially affect these correlations between outcrop area and diversity, indicating that the relation between outcrop area and diversity is primarily a function of sampling and not a common cause such as sea level. We observe a significant diversity-area effect, first noted by Jack Sepkoski in the marine realm. Unlike Sepkoski's, however, our diversity-area effect appears to play a substantial role in influencing diversity through time; a true global diversity signal appears to be contained in the rock record despite the impacts of variable sampling. Greater outcrop area can serve to increase estimated diversity by increasing both the sample size and the range of habitats and biogeographic provinces sampled. After standardizing for pure sampling intensity by rarefying the number of taxon occurrences, outcrop area continues to explain a substantial portion of global marine diversity. This indicates that coverage, or sampling from multiple habitats and biogeographic provinces, is even more important than sampling intensity. If we remove the effect of outcrop area from our estimate of global biodiversity, we do not observe a net increase in diversity toward the present, lending support to other studies that have not supported a substantial, long-term global increase in biodiversity during the Phanerozoic.
Feature Based Multi-Resolution Registration of Blurred Images for Image Mosaic

Existing methods for the registration of blurred images are efficient for the artificially blurred images or a planar registration, but not suitable for the naturally blurred images existing in the real image mosaic process. In this paper, we attempt to resolve this problem and propose a method for a distortion-free stitching of naturally blurred images for image mosaic. It adopts a multi-resolution and robust feature based inter-layer mosaic together. In each layer, Harris corner detector is chosen to effectively detect features and RANSAC is used to find reliable matches for further calibration as well as an initial homography as the initial motion of next layer. Simplex and subspace trust region methods are used consequently to estimate the stable focal length and rotation matrix through the transformation property of feature matches. In order to stitch multiple images together, an iterative registration strategy is also adopted to estimate the focal length of each image. Experimental results demonstrate the performance of the proposed method.
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

SUMMARY Transcription and chromatin regulators, and histone modifications play essential roles in gene expression regulation. We have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. We have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells and papers. Finally, we provide users with summary statistics of ChIP-Seq and DNase-Seq studies.
Catalpol inhibits the proliferation, migration and metastasis of HCC cells by regulating miR-140-5p expression

Hepatocellular carcinoma (HCC) is a frequent malignant tumor. Catalpol is a Chinese medicine extract with a number of pharmacologically active properties. The present study aimed to investigate the effects and mechanisms of catalpol in HCC. HCC cells were treated with catalpol in the presence or absence of microRNA (miR)-140-5p inhibitor, and assays to determine cell viability, proliferation, invasion and migration were performed. Reverse transcription-quantitative PCR and western blotting were performed to determine the mRNA and protein expression levels of miR-140-5p, vimentin, N-Cadherin and E-Cadherin. Moreover, cells were treated with catalpol in the absence or presence of transforming growth factor (TGF)-β1, and the cell morphology was observed under a microscope. The results demonstrated that catalpol inhibited cell proliferation, invasion and migration, and decreased the expression levels of vimentin and N-cadherin, but increased the expression levels of E-cadherin and miR-140-5p. Catalpol inhibited morphological changes in epithelial-mesenchymal transformation (EMT) of cells induced by TGF-β1. Following inhibition of miR-140-5p expression, the proliferation, invasion and migration of HCC cells were promoted, E-cadherin expression was decreased, and the levels of vimentin and N-cadherin were increased. The miR-140-5p inhibitor effectively reversed the inhibitory effect of catalpol on cell proliferation, invasion and migration. Thus, the results suggested that the antitumor potential of catalpol in HCC may be exerted by regulating the expression of miR-140-5p to inhibit proliferation, invasion, migration and EMT of HCC cells.
Comprehensive analysis of circulating microRNAs as predictive biomarkers for sorafenib therapy outcome in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Clinical management has improved the prognosis of early HCC, but that of advanced HCC remains poor. Sorafenib, an oral multikinase inhibitor, provided a treatment option for advanced-stage HCC, and prolonged the survival and inhibited tumor progression as first-line therapy in patients with advanced HCC. In this study, we investigated if specific microRNAs could act as predictive biomarkers of sorafenib effectiveness and indicate the best time to switch to second-line therapies. Sorafenib inhibited the proliferation of the Li-7, Hep3B, HepG2 and Huh7 liver cancer cell lines (effective group), but not that of the HLE, HLF and ALEX cancer cell lines (non-effective group). A microRNA (miRNA/miR) analysis was performed comparing sorafenib-effective and non-effective cells lines as well as serum samples from patients with HCC from sorafenib-effective (complete response/partial response) and -non-effective (progressive disease) groups before sorafenib administration and detected three differentially-expressed miRNAs that were common among the in vivo and in vitro samples. The increase rate (effective/non-effective) of hsa-miR-30d in the medium was higher than that in the cancer cells. hsa-miR-30d was highly expressed in the serum and exosomes of patients with HCC in the effective group when compared to those of the non-effective group. Additionally, the hsa-miR-30d expression in the medium of cancer cell lines was highly upregulated in the effective group compared with the non-effective group. These results suggested that hsa-miR-30d might be secreted by the cancer cells to the serum through the exosomes. We identified a specific circulating miRNA that is related to refractory HCC under sorafenib therapy. Therefore, hsa-miR-30d might serve as a predictive biomarker for the efficacy of sorafenib therapy in HCC.
8-Hydroxyeicosapentaenoic Acid Decreases Plasma and Hepatic Triglycerides via Activation of Peroxisome Proliferator-Activated Receptor Alpha in High-Fat Diet-Induced Obese Mice

PPARs regulate the expression of genes involved in lipid homeostasis. PPARs serve as molecular sensors of fatty acids, and their activation can act against obesity and metabolic syndromes. 8-Hydroxyeicosapentaenoic acid (8-HEPE) acts as a PPAR ligand and has higher activity than EPA. However, to date, the PPAR ligand activity of 8-HEPE has only been demonstrated in vitro. Here, we investigated its ligand activity in vivo by examining the effect of 8-HEPE treatment on high fat diet-induced obesity in mice. After the 4-week treatment period, the levels of plasma and hepatic triglycerides in the 8-HEPE-fed mice were significantly lower than those in the HFD-fed mice. The expression of genes regulated by PPARα was significantly increased in 8-HEPE-fed mice compared to those that received only HFD. Additionally, the level of hepatic palmitic acid in 8-HEPE-fed mice was significantly lower than in HFD-fed mice. These results suggested that intake of 8-HEPE induced PPARα activation and increased catabolism of lipids in the liver. We found no significant differences between EPA-fed mice and HFD-fed mice. We demonstrated that 8-HEPE has a larger positive effect on metabolic syndrome than EPA and that 8-HEPE acts by inducing PPARα activation in the liver.
Sheffield Economic Research Paper Series SERP Number : 2003002

This paper presents estimates of price functions for beef, lamb and pork for the UK economy which allow for the effects of the 1996 BSE crisis. Our estimates illustrate the importance of allowing for the joint endogeneity of prices in these markets. We show that the effects of this crisis had a significant negative effect on the price of beef and a positive and significant effect on the price of lamb. However, there appears to have been little effect on the price of pork.
Evolution of the southern margin of Tethys (North Australian region) from early Permian to late Cretaceous

Abstract A mid-Permian rifting episode appears to have removed continental blocks (now forming parts of Asia) from Australian Gondwana, but the present continental margin of Northern Australia-central New Guinea was formed by a later episode of rifting during the Jurassic. With the exception of the north-west Australian offshore region west of the Scott Plateau, this rifted continental margin has been greatly modified during the Cainozoic by collisions with arc-trench systems. Collision resulted in fold and thrust mountains, locally with ophiolite emplacements, that now characterize most of northern New Guinea and the Banda Arc. The identification of the Australia-New Guinea rifted continental margin in what is now the fold and thrust mountain belt of New Guinea, islands of the Outer Banda Arc, East Sulawesi, and Buton, rests largely on stratigraphic correlation and the recognition of the pre-rift sequence, breakup unconformity, and the post-breakup marine transgression and prolonged subsidence in these now highly deformed rocks. One implication of the Jurassic continental rifting is that the pre-rift rocks of the region accumulated in an intracratonic basin of eastern Gondwana. Another important implication is that the continental blocks rifted from the Northern Australia-central New Guinea margin must have drifted northwards towards Asia as the Mesozoic Tethys ocean spread across the tropics and equatorial region. These continental fragments of Gondwana collided with parts of south-east Asia that had been derived from Gondwana in an earlier phase of rifting.
SLOPE STABILITY ANALYSIS OF DANDOT PLATEAU, PUNJAB PAKISTAN

Kinematic analysis was performed to assess the stability of mountainous limestone deposits of Dandot plateau being used as raw material for cement manufacturing process. The discontinuity data was collected for analysis using DIPS computer program to ascertain the stability of the limestone quarry site of M/s Dandot Cement Company Limited. The geological discontinuities in the area show the likelihood of plane and toppling failures at various slope face orientations. Furthermore, susceptibility of wedge failure is unlikely as indicated by the attitude of major discontinuities. It was assessed that recent failures of slopes were of circular type. It is recommended that prior analysis of the discontinuity data with the new face orientations must be conducted at each step in order to assure the stability of quarry slopes.
Conservation Efforts and Natural History of a Prairie Habitat at Jennings Environmental Education Center, Pennsylvania

Abstract The habitat consideted in this study is a 19.8-acre (8.0-hectare) prairie relict, which is part of the Z96-acre (lZO­ hectare) park (Jennings Environmental Education Center), and it is located in northwest Pennsylvania (Butler County). This prairie remnant is one of the easternmost existing relicts of the once widespread post~glacial prairies. The focus of this paper is to present an overview of the natural history of the Jennings Prairie with emphasis on preser~ vation practices that have occurred since its discovery, in 1905, and management approaches aimed at the conserva; tion of this habitat. The maintenance of its 225 native plant species requires human intervention in order to avoid its succession into a forest ecosystem, which is typical for this bioregion. Pedologic data are presented briefly as a frame; work used to justify decision;making in common land management practices. The conservation of the Jennings Prairie (the only one remaining of a few prairies dislocated through the landscape of western Pennsylvania) remains a unique habitat unit to demonstrate ecosystem diversity in the region.
Soil compaction and water content effects on lodgepole pine seedling growth in British Columbia

Increased mechanization during timber harvesting activities has led to concerns that compaction may negatively affect the long-term productivity of soil. A greenhouse study was carried out to determine the effects of soil compaction under three levels of soil water content. Mineral soil was collected from a landing in central British Columbia, Canada and lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) seedlings were grown in pots for 12 weeks. Pots were compacted to densities that corresponded to 67, 72 and 76% of the Proctor maximum bulk density (1798 kg m-3) for the soil. Volumetric water contents of 0.10-0.15, 0.20-0.30 and 0.30-0.35 cm3cm-3 were maintained by weighing the pots, determining the gravimetric water content and adding the required water. Compaction only had an effect on seedling growth at low water content. Diameter growth and total shoot biomass were significantly smaller for 76% compaction compared to 67% compaction. At low water content, 76% and 72% compaction caused decreases in new root biomass and 76% compaction increased shoot macronutrient concentrations. The findings of this study imply that, for the compaction levels observed, water content had a greater impact on seedling growth than compaction.
Norwegian Experiences with Steel Piles to Rock

Synopsis The Paper reviews 25 years of Norwegian experience in the use of steel piles for foundations. The condition of soft clay overlying a hard and oftensteeply inclined rock surface which is common in Norway creates a number of problems in the design and driving of point bearing piles to bedrock. Methods of pile driving which have been evolved to ensure a satisfactory sealing of the pile point into rock are described in detail. The problems of the buckling of piles under load and of the corrosion of steel piles in the ground are discussed in the light of recorded experience. Finally, the settlements of single piles and of buildings are discussed.The settlement of a successful single pile is found approximately equal to the elastic compression of the pile, whereas observations indicate that thesettlements of buildings are two to four times this value. L'article passe en revue 25 ans d'experience norvegienne dans I'emploi de pieux en acier pour fondations. Les conditions souvent rencontrees en Norvege, .
Learning in Networks: a survey

This paper presents a survey of research on learning with a special focus on the structure of interaction between individual entities. The structure is formally modelled as a network: the nodes of the network are individuals while the arcs admit a variety of interpretations (ranging from information channels to social and economic ties). I first examine the nature of learning about optimal actions for a given network architecture. I then discuss learning about optimal links and actions in evolving networks.
GeneTUKit: a software for document-level gene normalization

Motivation: Linking gene mentions in an article to entries of biological databases can facilitate indexing and querying biological literature greatly. Due to the high ambiguity of gene names, this task is particularly challenging. Manual annotation for this task is cost expensive, time consuming and labor intensive. Therefore, providing assistive tools to facilitate the task is of high value. Results: We developed GeneTUKit, a document-level gene normalization software for full-text articles. This software employs both local context surrounding gene mentions and global context from the whole full-text document. It can normalize genes of different species simultaneously. When participating in BioCreAtIvE III, the system obtained good results among 37 runs: the system was ranked first, fourth and seventh in terms of TAP-20, TAP-10 and TAP-5, respectively on the 507 full-text test articles. Availability and implementation: The software is available at http://www.qanswers. net/GeneTUKit/. Contact: aihuang@tsinghua.edu. cn
The Difference Engine

Composite image, optically encoded by escort-craft of the trans-Channel airship Lord Brunel: aerial view of suburban Cherbourg, October 14, 1905. A villa, a garden, a balcony. Erase the balcony's wrought-iron curves, exposing a bath-chair and its occupant. Reflected sunset glints from the nickel-plate of the chair's wheel-spokes. The occupant, owner of the villa, rests her arthritic hands upon fabric woven by a Jacquard loom. These hands consist of tendons, tissue, jointed bone. Through quiet processes of time and information, threads within the human cells have woven themselves into a woman. Her name is Sybil Gerard. Below her, in a neglected formal garden, leafless vines lace wooden trellises on whitewashed, flaking walls. From the open windows of her sickroom, a warm draft stirs the loose white hair at her neck, bringing scents of coal-smoke, jasmine, opium. Her attention is fixed upon the sky, upon a silhouette of vast and irresistible grace -metal, in her lifetime, having taught itself to fly. In advance of that magnificence, tiny unmanned aeroplanes dip and skirl against the red horizon. Like starlings, Sybil thinks. The airship's lights, square golden windows, hint at human warmth. Effortlessly, with the incomparable grace of organic function, she imagines a distant music there, the music of London: the passengers promenade, they drink, they flirt, perhaps they dance. Thoughts come unbidden, the mind weaving its perspectives, assembling meaning from emotion and memory. She recalls her life in London. Recalls herself, so long ago, making her way along the Strand, pressing past the crush at Temple Bar. Pressing on, the city of Memory winding itself about her -till, by the walls of Newgate, the shadow of her father's hanging falls . And Memory turns, deflected swift as light, down another byway -one where it is always evening . It is January 15, 1855. A room in Grand's Hotel, Piccadilly.
zbw Publikationsarchiv

Several Academic Social Networking Sites (ASNSs) have been launched in the last few years and their number of members is growing. Researchers using ASNSs come from very divergent scientific backgrounds and academic levels, prompting one to ask the question what kind of communication and self-presentation behaviors occur within these structures. The qualitative study presented in this article has analyzed the communication behavior of a selected sample on ResearchGate (RG). It investigates how researchers present themselves on their personal profile-sites and how they interact with other researchers. Overall, the results show that mostly young male academics without previous connections to each other (e.g., faculty colleges) use RG for their scholarly exchanges. In general, communication behavior is characterized by an objective, professional, unemotional choice of words and seldom the use of polite salutations or words of farewell. However, there seems to be a correlation between long discussion and an increased use of colloquial and emotional language. Based on our findings, we have derived preliminary practical recommendations for communications on
Spatial planning and place branding: rethinking relations and synergies

ABSTRACT Spatial planning and place branding are allies in the discovery and creation of place narratives and assets as well as in contributing to spatial transformation or the improvement of the socio-spatial and spatial-economic conditions of a place. However, the existing and potential linkages between spatial planning and place branding are yet to be explored by both scientists and policy-makers. The objective of this paper is twofold. First, we reflect upon the central themes of this special issue by placing them in the context of larger debates on the position of place branding and spatial planning in society. Secondly, we show that this requires attention to the many ways in which planning and branding can cross-fertilize each other and to the embedding of both in evolving spatial governance structures. We then conclude with a typology expanding the understanding of this linkage between spatial planning and place branding.
Recapitulation of morphogenetic cell shape changes enables wound re-epithelialisation

Wound repair is a fundamental, conserved mechanism for maintaining tissue homeostasis and shares many parallels with embryonic morphogenesis. Small wounds in simple epithelia rapidly assemble a contractile actomyosin cable at their leading edge, as well as dynamic filopodia that finally knit the wound edges together. Most studies of wound re-epithelialisation have focused on the actin machineries that assemble in the leading edge of front row cells and that resemble the contractile mechanisms that drive morphogenetic episodes, including Drosophila dorsal closure, but, clearly, multiple cell rows back must also contribute for efficient repair of the wound. Here, we examine the role of cells back from the wound edge and show that they also stretch towards the wound and cells anterior-posterior to the wound edge rearrange their junctions with neighbours to drive cell intercalation events. This process in anterior-posterior cells is active and dependent on pulses of actomyosin that lead to ratcheted shrinkage of junctions; the actomyosin pulses are targeted to breaks in the cell polarity protein Par3 at cell vertices. Inhibiting actomyosin dynamics back from the leading edge prevents junction shrinkage and inhibits the wound edge from advancing. These events recapitulate cell rearrangements that occur during germband extension, in which intercalation events drive the elongation of tissues.