Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial heterogeneity of within‐stream methane concentrations

Streams, rivers, and other freshwater features may be significant sources of CH4 to the atmosphere. However, high spatial and temporal variabilities hinder our ability to understand the underlying processes of CH4 production and delivery to streams and also challenge the use of scaling approaches across large areas. We studied a stream having high geomorphic variability to assess the underlying scale of CH4 spatial variability and to examine whether the physical structure of a stream can explain the variation in surface CH4. A combination of high‐resolution CH4 mapping, a survey of groundwater CH4 concentrations, quantitative analysis of methanogen DNA, and sediment CH4 production potentials illustrates the spatial and geomorphic controls on CH4 emissions to the atmosphere. We observed significant spatial clustering with high CH4 concentrations in organic‐rich stream reaches and lake transitions. These sites were also enriched in the methane‐producing mcrA gene and had highest CH4 production rates in the laboratory. In contrast, mineral‐rich reaches had significantly lower concentrations and had lesser abundances of mcrA. Strong relationships between CH4 and the physical structure of this aquatic system, along with high spatial variability, suggest that future investigations will benefit from viewing streams as landscapes, as opposed to ecosystems simply embedded in larger terrestrial mosaics. In light of such high spatial variability, we recommend that future workers evaluate stream networks first by using similar spatial tools in order to build effective sampling programs.
Experimenting with graphical user interfaces for structured document retrieval

Standard Information Retrieval (IR) deals with documents as they were atomic entities, indexing and retrieving them as single objects. However, modern IR needs to be able to deal with more elaborate document representations, like for example structured documents, that is documents that are organised around a well defined structure. The increasingly popular SGML, HTML, or XML are formalisms that enable to represent and describe such documents. These new standards in structured document representation compel IR to design and implement models and tools to index and retrieve documents according to the given document structure. This means that documents should no longer be considered as atomic entities, but as aggregates of interrelated objects that need to be indexed, retrieved, and presented both as a whole and separately, in relation to the their structure and the user’s needs. Given the complexity of the IR task, interactivity has been widely recognised as a very effective way of improving information access performance. A good user interface enables the IR process to be highly interactive. In structured document retrieval, the need for a good interface between user and system becomes even more pressing. Structured documents are often long and complex and it has been observed that a certain form of disorientation occurs in situations where the user does not understand why certain documents appear in the retrieved list [1]. This user disorientation makes the task of query reformulation much harder, since the user has first to understand the response of the system and then to decide if any of the retrieved document is a good enough representation of the information need to provide the system with precise relevance feedback. This added difficulties obviously increase the cognitive load of the user and decrease the quality of the interaction with the system. An approach to this problem consists in providing the IR system with a graphical user interface (GUI) with explana-
Circulating Tumor Cells in Patients with Breast Cancer Dormancy

Purpose: The purpose of this study was to test the hypothesis that circulating tumor cells (CTCs) are present in patients many years after mastectomy without evidence of disease and that these CTCs are shed from persisting tumor in patients with breast cancer dormancy. Experimental Design: We searched for CTCs in 36 dormancy candidate patients and 26 age-matched controls using stringent criteria for cytomorphology, immunophenotype, and aneusomy. Results: Thirteen of 36 dormancy candidates, 7 to 22 years after mastectomy and without evidence of clinical disease, had CTCs, usually on more than one occasion. Only 1 of 26 controls had a possible CTC (no aneusomy). The statistical difference of these two distributions was significant (exact P = 0.0043). The CTCs in patients whose primary breast cancer was just removed had a half-life measured in 1 to 2.4 hours. Conclusions: The CTCs that are dying must be replenished every few hours by replicating tumor cells somewhere in the tissues. Hence, there appears to be a balance between tumor replication and cell death for as long as 22 years in dormancy candidates. We conclude that this is one mechanism underlying tumor dormancy.
De simbólicos vs. subsimbólicos, a los robots etoinspirados

Resumen En la Inteligencia Artificial, desde sus oŕigenes, han existido dos corrientes basicas, la simbolica y la subsimbolica. Estas dos aproximaciones han tenido gran influencia tambien en la robotica. En este articulo queremos presentar un enfoque menos conocido, el de la etoloǵia, y en concreto su aplicacion a la generacion de comportamiento autonomo en robots moviles. Para ello presentamos los fundamentos de la ”Jerarquia Dinamica de Esquemas”, una arquitectura para el control de robots moviles, basada en la composicion de unidades simples denominadas ”esquemas”siguiendo las teoŕias etologicas de Arbib. Igualmente se presentan experimentos preliminares que validan esta aproximacion y se discute su viabilidad y se presentan los trabajos previstos para continuar investigando en esta ĺinea.
Gender differences regarding barriers and motivators of HIV status disclosure among HIV-positive service users

There are inconsistent findings about the relation between gender and HIV status disclosure. We conducted a facility-based cross-sectional study, using qualitative and quantitative data collection methods, to explore gender differences in HIV-positive status disclosure among service users in south-west Ethiopia. Among 705 participants, an equal number of men and women (94.6% men v. 94.3%, women) indicated that they had disclosed their result to someone, and the majority (90.9% men v. 90.7% women) to their current main partner. ‘It is customary to tell my partner everything’ was the most frequently cited reason for disclosing (62.5% men v. 68.5% women). Reasons for non-disclosure varied by gender: men were concerned about their partner's worry and exposure of their own unfaithfulness. Women feared physical violence, and social and economic pressure in raising their children. Factors that influenced disclosure also indicated gender variation. For men, disclosure of HIV results to a sexual partner was positively associated with knowing the partner's HIV status and discussion about HIV testing prior to seeking services, while for women it was associated with knowing the partner's HIV status, advanced disease stage, having no more than primary education, being married, and perceiving the current relationship as long-lasting. There was no significant difference in the proportion of HIV status disclosure among men and women. However, the contextual barriers and motivators of disclosure varied by gender. Therefore it is important that clinicians, counsellors, and health educators underscore the importance of gender-specific interventions in efforts to dispel barriers to HIV status disclosure.
Traditional and Modern Uses of Natural Honey in Human Diseases: A Review

Honey is a by-product of flower nectar and the upper aero-digestive tract of the honey bee, which is concentrated through a dehydration process inside the bee hive. Honey has a very complex chemical composition that varies depending on the botanical source. It has been used both as food and medicine since ancient times. Human use of honey is traced to some 8000 years ago as depicted by Stone Age paintings. In addition to important role of natural honey in the traditional medicine, during the past few decades, it was subjected to laboratory and clinical investigations by several research groups and it has found a place in modern medicine. Honey has been reported to have an inhibitory effect on around 60 species of bacteria, some species of fungi and viruses. Antioxidant capacity of honey is important in many disease conditions and is due to a wide range of compounds including phenolics, peptides, organic acids, enzymes, and Maillard reaction products. Honey has also been used in some gastrointestinal, cardiovascular, inflammatory and neoplastic states. This review covers the composition, physico-chemical properties and the most important uses of natural honey in human diseases.
Deniable authentication and key exchange

We extend the definitional work of Dwork,Naor and Sahai from deniable authentication to deniable key-exchange protocols. We then use these definitions to prove the deniability features of SKEME and SIGMA, two natural and efficient protocols which serve as basis for the Internet Key Exchange (IKE)protocol.SKEME is an encryption-based protocol for which we prove full deniability based on the plaintext awareness of the underlying encryption scheme. Interestingly SKEME's deniability is possibly the first "natural" application which essentially requires plaintext awareness (until now this notion has been mainly used as a tool for proving chosen-ciphertext security). SIGMA, on the other hand,uses non-repudiable signatures for authentication and hence cannot be proven to be fully deniable. Yet we are able to prove a weaker, but meaningful, "partial deniability" property: a party may not be able to deny that it was "alive" at some point in time but can fully deny the contents of its communications and the identity of its interlocutors.We remark that the deniability of SKEME and SIGMA holds in a concurrent setting and does not essentially rely on the random oracle model.
Examining the response of top marine predators to ecological change using stable isotope proxies

Monitoring the response of upper trophic level animals to ecological change is important to understanding the state and stability of ecosystems. Marine predators integrate information over large geographical scales and are relatively long-lived; furthermore, many of these organisms are restricted to terrestrial or freshwater habitats at certain times during their life history and are accessible to researchers. This thesis investigated the response of marine predators to ecological change at a variety of spatial and temporal scales using stable isotope ratio methods with the aims of developing meaningful proxies, or indices, of variability in marine ecosystems. The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental) factors important to modulating variation in the stable isotope ratios of C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the Southern Ocean. In the second study, long-term records of variation in d15N and d13C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus) tooth dentin provided evidence for large-scale climate forcing across the eastern North Atlantic. In the following study, a more detailed examination of intraand inter-individual stable isotope variation in Atlantic salmon within a single year was undertaken in an attempt to better understand recent declines in somatic condition of these fish. The last two studies were concerned with the development of high resolution sampling of fish otoliths using secondary mass spectrometry (SIMS) and the application of this technique to reconstructing the thermal and metabolic histories of individual Atlantic salmon from intra-otolith d13C and d18O values. Stable isotope proxies can be used to document shifts in trophic dynamics and animal movement that may be associated with ecological change. Using multiple tissues, elements and species, such studies provide unique monitoring tools at a range of spatial and temporal scales.
Imprinting at the PLAGL1 domain is contained within a 70-kb CTCF/cohesin-mediated non-allelic chromatin loop

Paternal duplications of chromosome 6q24, a region that contains the imprinted PLAGL1 and HYMAI transcripts, are associated with transient neonatal diabetes mellitus. A common feature of imprinted genes is that they tend to cluster together, presumably as a result of sharing common cis-acting regulatory elements. To determine the extent of this imprinted cluster in human and mouse, we have undertaken a systematic analysis of allelic expression and DNA methylation of the genes mapping within an ∼1.4-Mb region flanking PLAGL1/Plagl1. We confirm that all nine neighbouring genes are biallelically expressed in both species. In human we identify two novel paternally expressed PLAGL1 coding transcripts that originate from unique promoter regions. Chromatin immunoprecipitation for CTCF and the cohesin subunits RAD21 and SMC3 reveals evolutionarily conserved binding sites within unmethylated regions ∼5 kb downstream of the PLAGL1 differentially methylated region and within the PLAGL1 3′ untranslated region (UTR). Higher-order chromatin looping occurs between these regions in both expressing and non-expressing tissues, forming a non-allelic chromatin loop around the PLAGL1/Plagl1 gene. In placenta and brain tissues, we identify an additional interaction between the PLAGL1 P3/P4 promoters and the unmethylated element downstream of the PLAGL1 differentially methylated region that we propose facilitates imprinted expression of these alternative isoforms.
Relevance Preserving Projection and Ranking for Web Image Search Reranking With Hierarchical Topic Awareness

: Image Search re-ranking is as an effective way to improve the retrieval precision. Image search re-ranking has recently been proposed to refine image search results obtained from text-based image search engines. Most of the traditional re-ranking methods cannot capture both relevance and diversity of the search results at the same time. Or they ignore the hierarchical topic structure of search result. Each topic is treated equally and for certain queries are naturally in hierarchical organization, rather than simple parallel relation. Image Search Reranking (ISR) technique aims at refining text-based search results by mining images’ visual content. Feature extraction and ranking function design are two key steps in ISR. Here a new re-ranking method “Topic -Aware Re-ranking (TARerank)” is proposed. TARerank describes the hierarchical topic structure of search results in one model, and seamlessly captures both relevance and diversity of the image search results simultaneously. By set of carefully designed features, through a structured learning framework, relevance and diversified images are modeled in TARerank, and then the model is learned from human-labeled training sample. The learned model is expected to predict re-ranking results with high relevance and diversity for testing queries. We collect an image search dataset and conduct the comparison experiments on it to verify the effectiveness of the proposed method. The experimental results demonstrate that the proposed TARerank outperforms the existing relevance-based and diversified re-ranking methods. Extensive experimental results on real-world datasets show that the proposed algorithms are effective. Moreover, the fact that only relevant images are required to be labeled makes it has a strong practical significance.
Slow inward current and contraction of sheep cardiac Purkinje fibers

A "slow" inward current (Is) has been identified in ventricular muscle and Purkinje fibers of several mammalian species. The two- microelectrode voltage clamp technique is used to examine some of the relationships between Is and contraction of the sheep cardiac Purkinje fiber. "Tails" of inward current occurring on repolarization and extrapolation of Is recovery each show that the Is system may not inactivate completely during prolonged depolarization. The rate of recovery of Is after a depolarization is slow, and when a train of 300- ms clamps (frequency 1 s-1) is begun after a rest, Is is larger for the first clamp than it is for succeedings clamps. For the first clamp after a rest, the thresholds for Is and tension are the same and there is a direct correlation between peak tension and peak Is for clamp voltages between threshold and minus 40 mV. After a clamp, however, the ability to contract recovers much more slowly than does Is. Therefore, since Is may occur under certain conditions without tension, the realtionship between Is and tension must be indirect. Calcium entering the cell via this current may replenish or augment an intracellular calcium pool.
Shear band propagation in soils and dynamics of tsunamigenic landslides

This publication discusses a mechanism to overcome the underestimation of the real height of a tsunami wave. It is based on the phenomenon of shear band propagation along the failure surface of the landslide, as well as based on the energy balance (FMEB) approach from fracture mechanics. A main advantage of this approach is it allows a distinction to be made between progressive and catastrophic shear band propagation. The aim of this thesis is to validate the FMEB approach with physical tests and develop an analytical solution of the mechanism of tsunamigenic landslides, taking into account dynamic effects taking place during the failure process. When this method is applied to recent and historic landslides, it is possible to produce the initial landslide velocities, which significantly affect tsunami wave height predictions. This publication is divided into sections as follows: (1) Introduction; (2) Overview and State of the Art (Tsunamis and their Sources, Mechanics, Failure in Soils); (3) Progressive Shear Band Propagation in Trapdoor Tests; (4) Progressive Shear Band Propagation in Shear Blade Tests; (5) Catastrophic Shear Band Propagation in Biaxial Tests; (6) A Dynamic Solution of the Shear Band Propagation in Submerged Landslides; (7) Application to Historic and Recent Tsunamigenic Landslides; and (8) Summary and Outlook.
New Model of Macrophage Acquisition of the Lymphatic Endothelial Phenotype

Background Macrophage-derived lymphatic endothelial cell progenitors (M-LECPs) contribute to new lymphatic vessel formation, but the mechanisms regulating their differentiation, recruitment, and function are poorly understood. Detailed characterization of M-LECPs is limited by low frequency in vivo and lack of model systems allowing in-depth molecular analyses in vitro. Our goal was to establish a cell culture model to characterize inflammation-induced macrophage-to-LECP differentiation under controlled conditions. Methodology/Principal Findings Time-course analysis of diaphragms from lipopolysaccharide (LPS)-treated mice revealed rapid mobilization of bone marrow-derived and peritoneal macrophages to the proximity of lymphatic vessels followed by widespread (∼50%) incorporation of M-LECPs into the inflamed lymphatic vasculature. A differentiation shift toward the lymphatic phenotype was found in three LPS-induced subsets of activated macrophages that were positive for VEGFR-3 and many other lymphatic-specific markers. VEGFR-3 was strongly elevated in the early stage of macrophage transition to LECPs but undetectable in M-LECPs prior to vascular integration. Similar transient pattern of VEGFR-3 expression was found in RAW264.7 macrophages activated by LPS in vitro. Activated RAW264.7 cells co-expressed VEGF-C that induced an autocrine signaling loop as indicated by VEGFR-3 phosphorylation inhibited by a soluble receptor. LPS-activated RAW264.7 macrophages also showed a 68% overlap with endogenous CD11b+/VEGFR-3+ LECPs in the expression of lymphatic-specific genes. Moreover, when injected into LPS- but not saline-treated mice, GFP-tagged RAW264.7 cells massively infiltrated the inflamed diaphragm followed by integration into 18% of lymphatic vessels. Conclusions/Significance We present a new model for macrophage-LECP differentiation based on LPS activation of cultured RAW264.7 cells. This system designated here as the “RAW model” mimics fundamental features of endogenous M-LECPs. Unlike native LECPs, this model is unrestricted by cell numbers, heterogeneity of population, and ability to change genetic composition for experimental purposes. As such, this model can provide a valuable tool for understanding the LECP and lymphatic biology.
Quantitative Analysis of Near-Infrared Spectra by Wavelet-based Interferences Removal and Least Squares Support Vector Regression

A new hybrid algorithm named EODT-LS-SVR based on least squares support vector regression (LS-SVR) with wavelet-based EODT algorithm as preprocessed tools is proposed for removing the interferences and developing the quantitative models with high precision in near-infrared (NIR) spectra. EODT-LS-SVR algorithm is composed of two steps. In the first step, the preprocessing algorithm named EODT, which combines the ideas of wavelet packet transform (WPT), orthogonal signal correction (OSC) and information theory, is employed for the characteristic extraction of analyte information through multi-scale analysis. Entropy-based baseline signal removing (EBSR) algorithm is applied to remove the baseline of the spectra based on information theory with WPT-based analysis, and then the information orthogonal to the concentrations of analyte is removed by OSC algorithm in each frequency band of spectra. In the second step, LS-SVR method coupled with grid search and particle swarm optimization (PSO) technique for parameters optimization is used to enhancing the quality of regression models. EODT-LS-SVR algorithm was validated by two NIR spectral datasets, one used for measuring the fat concentration of milk and the other used for measuring the oil content of corn. The comparison of prediction results demonstrated that the performance of calibration models developed by EODT-LS-SVR algorithm is better than that developed by other conventional algorithms, showing the high efficiency and the high quality for quantitative model development in NIR spectra of complex samples.
The permeability of endplate channels to monovalent and divalent metal cations

The relative permeability of endplate channels to monovalent and divalent metal ions was determined from reversal potentials. Thallium is the most permeant ion with a permeability ratio relative to Na+ of 2.5. The selectivity among alkali metals is weak with a sequence, Cs+ greater than Rb+ greater than K+ greater than Na+ greater than Li+, and permeability ratios of 1.4, 1.3, 1.1, 1.0, and 0.9. The selectivity among divalent ions is also weak, with a sequence for alkaline earths of Mg++ greater than Ca++ greater than Ba++ greater than Sr++. The transition metal ions Mn++, Co++, Ni++, Zn++, and Cd++ are also permeant. Permeability ratios for divalent ions decreased as the concentration of divalent ion was increased in a manner consistent with the negative surface potential theory of Lewis (1979 J. Physiol. (Lond.). 286: 417--445). With 20 mM XCl2 and 85.5 mM glucosamine.HCl in the external solution, the apparent permeability ratios for the alkaline earth cations (X++) are in the range 0.18--0.25. Alkali metal ions see the endplate channel as a water-filled, neutral pore without high-field-strength sites inside. Their permeability sequence is the same as their aqueous mobility sequence. Divalent ions, however, have a permeability sequence almost opposite from their mobility sequence and must experience some interaction with groups in the channel. In addition, the concentrations of monovalent and divalent ions are increased near the channel mouth by a weak negative surface potential.