Miracle-dz/UniFAR-FTUs huggingface dataset:
Xvent‐1 mediates BMP‐4‐induced suppression of the dorsal‐lip‐specific early response gene XFD‐1′ in Xenopus embryos

Ectopic expression of the ventralizing morphogen BMP‐4 (bone morphogenetic protein‐4) in the dorsal lip (Spemann organizer) of Xenopus embryos blocks transcription of dorsal‐lip‐specific early response genes. We investigated the molecular mechanism underlying the BMP‐4‐induced inhibition of the fork head gene XFD‐1′. The promoter of this gene contains a BMP‐triggered inhibitory element (BIE) which prevents activation of this gene at the ventral/vegetal side of the embryo in vivo. In the present study, we show that BMP‐4‐induced inhibition is not direct but indirect, and is mediated by Xvent homeobox proteins. Micro‐injections of Xvent‐1 RNA and XFD‐1′ promoter deletion mutants demonstrate that Xvent‐1 mimics the effect of BMP‐4 signalling not only by suppression of the XFD‐1′ gene, but also by utilizing the BIE. Suppression could be reverted using a dominant‐negative Xvent‐1 mutant. The repressor domain was localized to the N‐terminal region of the protein. Gel‐shift and footprint analyses prove that Xvent‐1 binds to the BIE. Moreover, PCR‐based target‐site selection for the Xvent‐1 homeodomain confirms distinct motifs within the BIE as preferential binding sites. Thus, biological and molecular data suggest that Xvent‐1 acts as direct repressor for XFD‐1′ transcription and mediates BMP‐4‐induced inhibition.
Pericytes, Mesenchymal Stem Cells and the Wound Healing Process

Pericytes are cells that reside on the wall of the blood vessels and their primary function is to maintain the vessel integrity. Recently, it has been realized that pericytes have a much greater role than just the maintenance of vessel integrity essential for the development and formation of a vascular network. Pericytes also have stem cell-like properties and are seemingly able to differentiate into adipocytes, chondrocytes, osteoblasts and granulocytes, leading them to be identified as mesenchymal stem cells (MSCs). More recently it has been suggested that pericytes play a key role in wound healing, whereas the beneficial effects of MSCs in accelerating the wound healing response has been recognized for some time. In this review, we collate the most recent data on pericytes, particularly their role in vessel formation and how they can affect the wound healing process.
A Pseudorandom Generator from any One-way Function

Pseudorandom generators are fundamental to many theoretical and applied aspects of computing. We show how to construct a pseudorandom generator from any one-way function. Since it is easy to construct a one-way function from a pseudorandom generator, this result shows that there is a pseudorandom generator if and only if there is a one-way function.
Automated healing approach in cloud base-station with high load using RRUs cooperation

The cloud base-station realizes base station baseband unit (BBU) centralized on a universal cloud computing platform and connected the remote radio units (RRUs) with fiber. Automated healing of the cloud base-station applies to detect and compensate the outage RRU automatically by the adjacent RRUs cooperation. It aims at providing temporary alleviation of coverage, capacity and service quality caused by the outage. This paper proposes an automated healing with the RRUs cooperation compensation (AHCC) approach which adjusts antenna downtilt angles of the adjacent RRUs to expand the coverage after the outage detection. The approach is an objective increment method and online iterative process. Numerical results show that it can achieve remarkable performance recovery as well as fast convergence.
Analyzing the dust storm in Iraq using meteorological satellite data during the Iraq war

The Iraq war has passed about three years. This paper introduces the analysis of the huge dust storm happened in the middle of the Arabia Peninsula on 25-27 March 2003, in course of Iraq war, with remote sensing technology, and shows that the weather condition is one of the important factors parameters in Modern warfare. The result of analysis is based on two kinds of meteorological satellite data, geostationary orbit satellite and polar orbit satellite, and shows that the FY-1C/LDPT data and the Metosate-5 images, have great effect on analyzing the dust storm.
A fast algorithm for parameter estimation of multi-component LFM signal at low SNR

A fast method for parameter estimation of the multi-component linear frequency modulated (multi-LFM) signal is proposed. The signal detector and chirp rate estimator are based on the modulus square of the fractional autocorrelation. By using the estimated chirp rate, an approach based on the fractional Fourier transform (FrFT) is employed for estimation of the amplitude and centre frequency. The proposed algorithm reduces two-dimensional searches, widely used in the time-frequency based method, FrFT and chirp Fourier transform, into two one-dimensional searches. By utilizing the discrete FrFT, along with the fast Fourier transform (FFT) algorithm, the proposed method is a computationally fast alternative for LFM signal detection and parameter estimation. Analysis of the multi-LFM signal is performed using the CLEAN technique as well. Finally, computer simulations are provided to illustrate the performance of the proposed algorithm.
Spectral gamma ray characterization of high resolution sequence stratigraphy: examples from Upper Carboniferous fluvio-deltaic systems, County Clare, Ireland

Abstract The application of high resolution sequence stratigraphy requires the ability to recognize key surfaces which record fluctuations in relative sea-level. In sub-surface studies, gamma ray logs have been used to identify maximum flooding surfaces, but their full potential has not been realized. Gamma ray profiles produced using a portable spectrometer on exposed Upper Carboniferous fluvio-deltaic deposits in western Ireland reveal that key surfaces and systems tracts can be characterized more comprehensively and recognized with greater confidence if spectral gamma ray data (K, U, Th and their respective ratios) are used in conjunction with traditional total count data. Maximum flooding surfaces can be distinguished from lesser flooding surfaces by a distinctive U peak (> 5 ppm) and low Th/U ratio (< 2.5). Erosional unconformities and their associated incised valley fills are characterized by consistently low total counts (40–50 cps) and high Th/K ratios (> 6). Laterally correlative interfluves are represented by distinctive palaeosols that can be clearly identified in spectral gamma ray data by their anomalously low K content (<0.4%) and exceptionally high Th/K ratio (> 17). Finally, the stacking pattern of parasequence sets can be identified using the trends of Th/K ratios from sandstones in successive parasequences. These results have widespread implications for the recognition of high resolution sequence stratigraphic signatures in the stratigraphic record, with particular reference to the subsurface analysis of fluvio-deltaic deposits.
Verifying epistemic protocols under common knowledge

Epistemic protocols are communication protocols aiming at transfer of knowledge in a controlled way. Typically, the preconditions or goals for protocol actions depend on the knowledge of agents, often in nested form. Informal epistemic protocol descriptions for muddy children, coordinated attack, dining cryptographers, Russian cards, secret key exchange are well known. The contribution of this paper is a formal study of a natural requirement on epistemic protocols, that the contents of the protocol can be assumed to be common knowledge. By formalizing this requirement we can prove that there can be no unbiased deterministic protocol for the Russian cards problem. For purposes of our formal analysis we introduce an epistemic protocol language, and we show that its model checking problem is decidable.
A Happening-Based Encoding for Nonlinear PDDL+ Planning

Hybrid planning with nonlinear continuous change is a significant challenge for existing planners. Prior works limit their scope to linear change or base their formalisms in model checking frameworks with inherent limitations. We address nonlinear PDDL+ planning with a new encoding in ﬁrst order logic over real valued functions. Our planner, PluReal , translates PDDL+ to this logical encoding and applies the dReal Satisﬁability Modulo Theories (SMT) solver to construct plans. Unlike prior work that uses dReal in the hybrid system model checking tradition, PluReal is based in the planning as satisﬁability (SAT) heritage. Adopting the SAT approach helps lift several unnatural restrictions that are imposed by the translation through hybrid systems and leads to improved scalability even without SMT solver variable selection heuristics.
Towards the automatic evolution of reengineering tools

Building reverse engineering or reengineering tools often requires parsers for many different programming languages. The diffusion of dialects and variants makes many available parsers almost useless. While manual grammar maintenance is feasible, it can be a long, tedious and expensive task. This paper proposes to adopt genetic algorithms to evolve existing grammars inferring changes from examples written using the dialect. Applying grammar inference from scratch may lead to a useless grammar, while the proposed approach simply applies changes to the original grammar when needed, thus producing a meaningful grammar. The paper reports some preliminary results related to the evolution of a C grammar.
Heuristics for Traffic Grooming in WDM Optical Networks with Shared Path Protection

The emergence of wavelength division multiplexing (WDM) technology has significantly increased the transmission capacity of a link in today's optical networks. In WDM networks, the bandwidth request of a traffic stream is usually much lower than the capacity of a wavelength. Traffic grooming can aggregate low-rate connections onto high-capacity optical fibers to make an efficient use of the bandwidth and, also to increase the network throughput. In addition, since huge amount data can flow at a very high speed in a WDM optical network, survivability of such a network against any fault, especially, in the optical fiber link, is of prime concern. Survivable traffic grooming in WDM optical networks has become a topic that is gaining more and more research and commercial attention. In this paper we present a survey of recent research on traffic grooming in WDM optical networks. We have tried to review the research papers that are focused on survivable traffic grooming in WDM mesh networks with an emphasis on shared-path protection, which uses less network resources than dedicated-path protection.
A role for the common GTP-binding protein in coupling of chromosome replication to cell growth and cell division.

Homologues of CgtA, the common GTP-binding protein of Vibrio harveyi, are present in diverse organisms ranging from bacteria to humans. In bacteria, proteins homologous to CgtA form a subfamily of small GTP-binding proteins, called Obg/Gtp1. Similarity between bacterial members of this subfamily and their eukaryotic homologues is as high as about 50%. Nevertheless, specific functions of these proteins remain largely unknown. Genes coding for CgtA-like proteins are essential in almost all species of bacteria. The only known exception is V. harveyi, whose cells survive disruption of the cgtA gene. Therefore, the V. harveyi cgtA insertional mutant is a very useful tool for studies on functions of CgtA. Here we demonstrate that under normal growth conditions, cells of the cgtA mutant are slightly larger than wild-type cells, whereas indirect inhibition of DNA replication initiation by addition of rifampicin results in significantly higher differences in average cell size between these two strains as measured by flow cytometry. These differences decreased when cell division was inhibited by cephalexin. DNA synthesis per cell mass was found to be increased in the cgtA mutant relative to wild-type V. harveyi strain, whereas the mutant cells grew slower than bacteria with functional cgtA gene. Kinetics of DNA replication after inhibition of cell division was also considerably different in wild-type and cgtA mutant strains. These results suggest that the cgtA gene product plays a role in coupling of DNA replication to cell growth and cell division.
Alpha‐synuclein in the appendiceal mucosa of neurologically intact subjects

Parkinson's disease is characterized by the pathological aggregation of Alpha‐synuclein. The dual‐hit hypothesis proposed by Braak implicates the enteric nervous system as an initial site of α‐synuclein aggregation with subsequent spread to the central nervous system. Regional variations in the spatial pattern or levels of α‐synuclein along the enteric nervous system could have implications for identifying sites of onset of this pathogenic cascade. We performed immunohistochemical staining for α‐synuclein on gastrointestinal tissue from patients with no history of neurological disease using the established LB509 antibody and a new clone, MJFR1, characterized for immunohistochemistry here. We demonstrate that the vermiform appendix is particularly enriched in α‐synuclein–containing axonal varicosities, concentrated in its mucosal plexus rather than the classical submucosal and myenteric plexuses. Unexpectedly, intralysosomal accumulations of α‐synuclein were detected within mucosal macrophages of the appendix. The abundance and accumulation of α‐synuclein in the vermiform appendix implicate it as a candidate anatomical locus for the initiation of enteric α‐synuclein aggregation and permits the generation of testable hypotheses for Parkinson's disease pathogenesis. © 2013 International Parkinson and Movement Disorder Society
Formation of supported bilayers on silica substrates.

We have investigated the formation of phospholipid bilayers of the neutral (zwitterionic) lipid dimyristoyl-phosphatidylcholine (DMPC) on various glass surfaces from vesicles in various aqueous solutions and temperatures using a number of complementary techniques: the surface forces apparatus (SFA), quartz crystal microbalance (QCM), fluorescence recovery after photobleaching (FRAP), fluorescence microscopy, and streaming potential (SP) measurements. The process involves five stages: vesicle adhesion to the substrate surfaces via electrostatic and van der Waals forces, steric interactions with neighboring vesicles, rupture, spreading via hydrophobic fusion of bilayer edges, and ejection of excess lipid, trapped water, and ions into the solution. The forces between DMPC bilayers and silica were measured in the SFA in phosphate buffered saline (PBS), and the adhesion energy was found to be 0.5-1 mJ/m(2) depending on the method of bilayer preparation. This value is stronger than the expected adhesion predicted by van der Waals interactions. Theoretical analysis of the bilayer-silica interaction shows that the strong attraction is likely due to an attractive electrostatic interaction between the uncharged bilayer and negatively charged silica owing to the surfaces interacting at "constant potential. " However, the bilayer-silica interaction in distilled water was found to be repulsive at all distances, which is attributed to the surfaces interacting at "constant charge. " These results are consistent with QCM measurements that show vesicles readily forming bilayers on silica in high salt but only weakly adhering in low salt conditions. We conclude that the electrostatic interaction is the most important interaction in determining the adhesion between neutral bilayers and charged hydrophilic surfaces. SP and FRAP experiments gave insights into the bilayer formation process as well as information on the surface coverage, lateral diffusion of the lipid molecules, and surface potential of the bilayers during the spreading process.
Social Factors Driving Settlement and Relocation Decisions in a Solitary and Aggregative Spider

Both ecological and social factors play an important role in determining the structure of animal settlement patterns. While the ecological factors determining animal settlement are generally well known, the relative importance of social factors in mediating fine-scale settlement choices is poorly understood. As a result, we have little knowledge of why individuals choose to settle near specific neighbors. Here we used a web-building spider (Nephila plumipes) that settles both solitarily and next to neighbors within aggregations to examine the specific social factors that influence settlement decisions. Within experimental enclosures, we observed the settlement patterns of females pre- and postmale release. This allowed us to compare two models of aggregative settlement in lekking species—the hotshot and preferences models—to examine the relative importance of a female’s phenotype and mate attraction to further dissect settlement and relocation decisions. We show that mate attraction increased with aggregation size and that larger females were generally preferred, supporting both the hotshot and preference models of aggregative settlement. We further demonstrate that smaller females that attracted fewer males within an aggregation were most likely to relocate. Our results demonstrate how social feedback can affect initially state-dependent settlement decisions, thereby highlighting the dynamic nature of settlement.
Planning with PlaceMaker: Complex Indices for Sustainable Projects

Questions connected to urban analysis study aspects that are not unilaterally translated into objective facts with particular regard to three issues: (1) the scientificity, and so the objectivity of the results; (2) the repeatability of the method in different contexts; and (3) the updating capability, and so the possibility of adding new data in order to modify the existing data and to obtain other results; the times, and so the sustainable possibility of using the results with respect to the evolution of a sustainable programming and town planning process. To answer these questions the method of analysis called PlaceMaker and the associated software, which is actually under development, have the following main characteristics: flexibility, facility and rapidity of use, strong graphical impact, and indexing of the results. PlaceMaker is a method for analyzing the contemporary urban landscape that is designed to identify the elements that do not feature in traditional mapping and which constitute the contemporary identity of the places, representing them in a complex map that renders those places intelligible. Starting from these premises, the objective of this work is to investigate the construction of complex indices starting from data and symbols related to the place-identity. In order to support the study and the project of the sustainable urban landscapes, the symbols created for the elaboration of the complex map, the final result of the analysis, are translated by the PlaceMaker software into numerical indices. Owing to these characteristics, the prime users of PlaceMaker are urban planners, administrators, citizens and all people involved in construction of a sustainable city. To complete the work suitable case studies are presented.
Applying Ensemble Model for Identifying Uncertainty in the Species Distribution Models

Species distribution models have been widely applied in order to assess biodiversity, design reserve, manage habitat and predict climate change. However, SDMs has been used restrictively to the public and policy sectors owing to model uncertainty. Recent studies on ensemble and consensus models have been increased to reduce model uncertainty. This paper was carried out single model and multi model for Corylopsis coreana and compares two models. First, model evaluation was used AUC, kappa and TSS. TSS was the most effective method because it was easy to compare several models and convert binary maps. Second, both single and ensemble model show good performance and RF, Maxent and GBM was evaluated higher, GAM and SRE was evaluated lower relatively. Third, ensemble model tended to overestimate over single model. This problem can be solved by the suitable model selection and weighting through collaboration between field experts and modeler. Finally, we should identify causes and magnitude of model uncertainty and improve data quality and model methods in order to apply special decision-making support system and conservation planning, and when we make policy decisions using SDMs, we should recognize uncertainty and risk.
Modeling with explicit spectral water and ice microphysics of a two‐layer cloud system of altostratus and cirrus observed during the FIRE Arctic Clouds Experiment

A one-dimensional version of a cloud model with an explicit microphysics scheme is used to simulate a case study of middle and upper level cloud formation and evolution that was observed during the FIRE Arctic Clouds Experiment. In the simulations, the midlevel altostratus cloud is initially liquid phase, then partially freezes, and exists in mixed phase for several hours with a relative equilibrium between the rate of drop production by condensation and their depletion by freezing. The dominant mode of cirrus formation was periodic homogeneous freezing of deliquescent submicron haze particles. These crystal layers form near the tropopause and, subsequently, precipitate into the middle troposphere, causing seeding of the underlying altostratus cloud. Sensitivity tests are conducted varying the initial humidity and nucleation schemes.
Association of X-ray Repair Cross Complementing Group 1 Arg399Gln Polymorphisms with the Risk of Squamous Cell Carcinoma of the Head and Neck: Evidence from an Updated Meta-Analysis

Background Epidemiologic studies have reported the association of X-ray repair cross-complementary group 1 (XRCC1) Arg399Gln polymorphisms with susceptibility to squamous cell carcinoma of the head and neck (HNSCC). However, the results were conflictive rather than conclusive. The purpose of this study was to clarify the association of XRCC1 Arg399Gln variants with HNSCC risk. Methods Systematic searches were performed through the search engines of PubMed, Elsevier, Science Direct, CNKI and Chinese Biomedical Literature Database. Summary odds ratio (OR) with 95% confidence intervals (CI) was computed to estimate the strength association. Results Overall, we did not observe any association of XRCC1 Arg399Gln polymorphisms with HNSCC risk in total population (OR = 0.95, 95% CI: 0.76–1.19 for Gln/Gln vs. Arg/Arg, OR = 1.05, 95% CI: 0.92–1.20 for Arg/Gln vs. Arg/Arg, and OR = 1.03, 95% CI: 0.90–1.18 for Gln/Gln+Arg/Gln vs. Arg/Arg) based on 18 studies including 3917 cases and 4560 controls. In subgroup analyses, we observed an increased risk of XRCC1 399 Arg/Gln genotype for HNSCC in Caucasians (OR = 1.20, 95% CI: 1.00–1.44) and Gln/Gln genotype for larynx squamous cell carcinoma (OR = 1.63, 95% CI: 1.10–2.40). We did not observe any association between XRCC1 Arg399Gln variants and HNSCC risk in additional subgroup analyses. Conclusion The results from this present meta-analysis suggest that XRCC1 Arg399Gln variants may contribute to HNSCC risk among Caucasians and to the risk of larynx squamous cell carcinoma. Further, well-designed studies with larger sample sizes are required to verify our findings.