Miracle-dz/UniFAR-FTUs huggingface dataset:
Manganese targets m‐aconitase and activates iron regulatory protein 2 in AF5 GABAergic cells

Studies suggest that disturbances of amino acid metabolism and cellular iron regulation are important mechanisms underlying manganese (Mn) neurotoxicity, although the targets underlying these disturbances are poorly defined. Using the AF5 neural‐derived cell line, which displays GABAergic properties, we showed that Mn significantly increased glutamate release to 174%–214% of that of the control and that the effects of Mn exposure on the metabolism of glutamate, glutamine, alanine, and GABA resembled the effects of fluorocitrate, an inhibitor of aconitase, but not the effects of other toxicants including paraquat, rotenone, or 3‐nitropropionic acid. Consistent with this, Mn inhibited aconitase activity in AF5 cells, resulting in a 90% increase in intracellular citrate; an in vitro assay revealed that m‐aconitase was significantly more sensitive to inhibition by Mn than was c‐aconitase. RNA mobility shift assay and Western blot showed that Mn treatment caused c‐aconitase to be converted to iron regulatory protein 1 (IRP1) and increased the abundance of IRP2, leading to reduced H‐ferritin expression, increased transferrin receptor expression, and increased uptake of transferrin. To determine the relative contributions of IRP1 and IRP2 in mediating the effects of Mn on iron homeostasis, we exposed transgenic fibroblasts lacking either c‐aconitase/IRP1 or IRP2 to Mn. Manganese exposure minimally altered ferritin levels in cells possessing only c‐aconitase/IRP1, whereas cells possessing only IRP2 showed a robust decrease in ferritin, indicating a dominant role of IRP2 in Mn‐induced alteration of iron homeostasis. Together, these results demonstrate that m‐aconitase is an important target of Mn and thatMn‐induced alteration of iron homeostasis is mediated predominantly through IRP2. © 2007 Wiley‐Liss, Inc.
Deriving Mobility Archetypes from Household Travel Survey Data

This article proposes a simple post hoc segmentation approach to revisit Household Travel Survey data and sketch archetypal mobility figures (clusters) that relate to people's daily mobility experiences. Describing the mobility behaviors of the different clusters and the distribution of the population between clusters is a powerful means to draw the mobility landscape of a metropolitan area and make comparisons over time and across places. Furthermore, clusters can be used to contextualize mobility behaviors in a variety of social inquiries and can be complementary to traditional quantitative mobility indicators or qualitative investigations.
Feedback interpretation based on facial expressions in human-robot interaction

In everyday conversation besides speech people also communicate by means of nonverbal cues. Facial expressions are one important cue, as they can provide useful information about the conversation, for instance, whether the interlocutor seems to understand or appears to be puzzled. Similarly, in human-robot interaction facial expressions also give feedback about the interaction situation. We present a Wizard of Oz user study in an object-teaching scenario where subjects showed several objects to a robot and taught the objects' names. Afterward, the robot should term the objects correctly. In a first evaluation, we let other people watch short video sequences of this study. They decided by looking at the face of the human whether the answer of the robot was correct (unproblematic situation) or incorrect (problematic situation). We conducted the experiments under specific conditions by varying the amount of temporal and visual context information and compare the results with related experiments described in the literature.
Elevated methane concentrations in trees of an upland forest

There is intense debate about whether terrestrial vegetation contributes substantially to global methane emissions. Although trees may act as a conduit for methane release from soils to atmosphere, the debate centers on whether vegetation directly produces methane by an uncharacterized, abiotic mechanism. A second mechanism of direct methane production in plants occurs when methanogens – microorganisms in the domain Archaea – colonize the wood of living trees. In the debate this biotic mechanism has largely been ignored, yet conditions that promote anaerobic activity in living wood, and hence potentially methane production, are prevalent across forests. We find average, growing season, trunk‐gas methane concentrations >15,000μL·L−1in common, temperate‐forest species. In upland habitat (where soils are not a significant methane source), concentrations are 2.3‐times greater than in lowland areas, and wood cores produce methane in anaerobic, lab‐assays. Emission rate estimates from our upland site are 52 ± 9.5 ng CH4 m−2 s−1; rates that are of a similar magnitude to the soil methane sink in temperate forest, and equivalent in global warming potential to ∼18% of the carbon likely sequestered by this forest. Microbial infection of one of the largest, biogenic sinks for carbon dioxide, living trees, might result in substantial, biogenic production of methane.
How do research institutes learn? Paper prepared for the 13th EGOS colloquium 'Organisational responses to radical environmental changes', Budapest, July 3-5, 1997

The aim of this paper is to contribute to the theory of organisational learning (OL) by developing a middle range theory of how research institutes learn. Because of a research institute’s specific division of labour in the organisation-environment interactions, the means of mediation between individual and organisational learning are of particular interest. To study these means, a secondary analysis of interviews with scientists of four newly founded East German research institutes was carried out. The early development of these institutes was determined by the necessity to learn as fast as possible in order to achieve quick integration into the German research landscape. The results of the empirical analysis show (1) the importance of ‘unconventional’ OL by hiring West German scientists who are experienced in the relevant contexts in which the institute has to operate; (2) the close connection between the modes of ‘loose coupling’, on the one hand, and, on the other hand, the mediation between individual learning and OL; and (3) the need to enrich analyses of research institutes by introducing a variable describing the fragmentation of an institute’s technical core, thus going beyond the classical variables for describing organisations’ technologies (task uncertainty and complexity).
IMPACT OF REPEATED APPLICATIONS OF ALPHA- CYPERMETHRIN ON ELDANA SACCHARINA (LEPIDOPTERA:PYRALIDAE) AND ON ARTHROPODS ASSOCIATED WITH SUGARCANE

In five field–scale insecticide trials, the repeated application of the synthetic pyrethroid alphacypermethrin to carry-over cane, reduced damage caused by the sugarcane borer Eldana saccharina Walker (Lepidoptera: Pyralidae) to the crop. The insecticide was applied with mistblowers at a rate of 200 ml formulation/ha in 350 L water/ha, once every two weeks for 16 weeks, commencing when the crop was 6-9 months old. At harvest, average damage and larval numbers were reduced by 72% and 73% respectively. ERC % cane increased by an average of 28%. Arthropods were monitored in two of the trials by means of pitfall trapping. Results showed that there was some impact of the treatment on abundance and diversity, primarily over the period of treatment application. However, at crop harvest, five months after treatment application ended, there was no significant effect. The impact on ants, considered important predators of eldana, was similar. It is concluded that this approach to suppressing borer infestations may have commercial value.
The Globular Tail Domain of Myosin Va Functions as an Inhibitor of the Myosin Va Motor*

The actin-activated ATPase activity of full-length mammalian myosin Va is well regulated by Ca2+, whereas that of truncated myosin Va without the C-terminal globular tail domain (GTD) is not. Here, we have found that exogenous GTD is capable of inhibiting the actin-activated ATPase activity of GTD-deleted myosin Va. A series of truncated constructs of myosin Va further showed that the entire length of the first coiled-coil (coil-1) of the tail domain is critical for GTD-dependent regulation of myosin Va and that deletion of 58 residues from the C-terminal end of coil-1 markedly hampered regulation. Negative staining electron microscopy revealed that GTD-deleted myosin Va formed a “Y”-shaped structure, which was converted to a triangular shape, similar to the structure of full-length myosin Va in the inhibited state, by addition of exogenous GTD. In contrast, the triangular shape was not observed when the C-terminal 58 residues of coil-1 were deleted, even in the presence of exogenous GTD. Based on these results, we propose a model for the formation of the inhibited state of myosin Va. GTD binds to the C-terminal end of coil-1. The neck-tail junction of myosin Va is flexible, and the long neck enables the head domain to reach the GTD associated with the end of coil-1. Once the head interacts with the GTD, the triangular inhibited conformation is stabilized. Consistent with this model, we found that shortening of the neck of myosin Va by two IQ motifs abolished the regulation by GTD, whereas regulation was partially restored by shortening of coil-1 by an amount comparable to that of the two IQ motifs.
Gateless patterning of epitaxial graphene by local intercalation

We present a technique to pattern the charge density of a large-area epitaxial graphene sheet locally without using metallic gates. Instead, local intercalation of the graphene–substrate interface can selectively be established in the vicinity of graphene edges or predefined voids. It provides changes of the work function of several hundred meV, corresponding to a conversion from n-type to p-type charge carriers. This assignment is supported by photoelectron spectroscopy, scanning tunneling microscopy, scanning electron microscopy and Hall effect measurements. The technique introduces materials contrast to a graphene sheet in a variety of geometries and thus allows for novel experiments and novel functionalities.
Late-Quaternary vegetation history of Tasmania from pollen records

Vegetation forms the major living characteristic of a landscape that solicits inquiry into the history of its changes during the late Quaternary and the major factors that have influenced the changes. Early studies considered ecological factors would cause vegetation to develop until a stable climatic climax formation was attained (Clements 1936). The concept of an area developing a potential natural vegetation in the absence of humans was similar (Tuxen 1956). Both ideas held that the vegetation of an area would develop to a stable condition that would change little. However, the vegetation of a region never remains in stasis, but develops dynamically through time, influenced by changing dominant factors (Chiarucci et al. 2010).
Semi-Supervised Multi-Label Learning with Incomplete Labels

The problem of incomplete labels is frequently encountered in many application domains where the training labels are obtained via crowd-sourcing. The label incompleteness significantly increases the difficulty of acquiring accurate multi-label prediction models. In this paper, we propose a novel semi-supervised multi-label method that integrates low-rank label matrix recovery into the manifold regularized vector-valued prediction framework to address multi-label learning with incomplete labels. The proposed method is formulated as a convex but non-smooth joint optimization problem over the latent label matrix and the prediction model parameters. We then develop a fast proximal gradient descent with continuation algorithm to solve it for a global optimal solution. The efficacy of the proposed approach is demonstrated on multiple multi-label datasets, comparing to related methods that handle incomplete labels.
Experimental Inoculation of Egyptian Rousette Bats (Rousettus aegyptiacus) with Viruses of the Ebolavirus and Marburgvirus Genera

The Egyptian rousette bat (Rousettus aegyptiacus) is a natural reservoir for marburgviruses and a consistent source of virus spillover to humans. Cumulative evidence suggests various bat species may also transmit ebolaviruses. We investigated the susceptibility of Egyptian rousettes to each of the five known ebolaviruses (Sudan, Ebola, Bundibugyo, Taï Forest, and Reston), and compared findings with Marburg virus. In a pilot study, groups of four juvenile bats were inoculated with one of the ebolaviruses or Marburg virus. In ebolavirus groups, viral RNA tissue distribution was limited, and no bat became viremic. Sudan viral RNA was slightly more widespread, spurring a second, 15-day Sudan virus serial euthanasia study. Low levels of Sudan viral RNA disseminated to multiple tissues at early time points, but there was no viremia or shedding. In contrast, Marburg virus RNA was widely disseminated, with viremia, oral and rectal shedding, and antigen in spleen and liver. This is the first experimental infection study comparing tissue tropism, viral shedding, and clinical and pathologic effects of six different filoviruses in the Egyptian rousette, a known marburgvirus reservoir. Our results suggest Egyptian rousettes are unlikely sources for ebolaviruses in nature, and support a possible single filovirus—single reservoir host relationship.
A Greedy Two-stage Gibbs Sampling Method for Motif Discovery in Biological Sequences

For the motif discovery problem of DNA sequences, a greedy two-stage Gibbs sampling algorithm is presented, and the related software package is called Greedy MotifSAM. Based on position weight matrix (PWM) motif model, a greedy strategy for choosing the initial parameters of PWM is employed. Two sampling methods, site sampler and motif sampler, are used. Site sampler is used to find one occurrence per sequence of the motif in the dataset. Motif sampler is used to find zero or more non-overlapping occurrences of the motif in each sequence. The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset. We use the binding sites (motif) information of eukaryotic transcription factors stored in TRANSFAC database to test our methods. The prediction accuracy, scalability and reliability are compared to several other methods.
Anatomy of the Aortic Valvar Complex and Its Implications for Transcatheter Implantation of the Aortic Valve

The books and articles devoted to the anatomy of the aortic valvar complex are numerous. Until now, however, little consideration has been given to understanding the anatomy with percutaneous valvar replacement in mind. It is axiomatic that knowledge of the anatomy of the valve is fundamental in understanding key principles involved in valvar replacement. Such an appreciation of the anatomy helps better understand the optimal positioning for the prosthetic valve within the root of the aortia with respect to the coronary arteries, mitral valve, and the conduction system and may circumvent complications that can arise during its implantation. In this review, therefore, we describe the anatomy of the trifoliate aortic valvar complex and its implications for percutaneous valvar replacement.
A Model for Switching Traps in Amorphous Oxides

Negative Bias Temperature Instability (NBTI) is frequently suspected to arise from a delicate interplay between some sort of hole trapping and an interface generation mechanism. In a recently suggested model the E′ center along with its second form as an Si−Si dimer are supposed to play a key role. Despite of its successful application to a large amount of experimental data, this model relies on a classical determination of the bandedge energy diagram and the carrier concentrations. The occurrence of subbands in the inversion layer shifts the initial energy level for charge trapping and may thus strongly impact the trapping dynamics. We evaluate the new model against measurement data in order to investigate the impact of quantization effects on the model parameters.
Mouse strain dependent variation in diet-induced obesity and insulin resistance Running title : Genetic background and insulin resistance

Aims/hypothesis: Metabolic disorders are commonly investigated using knockout and transgenic mouse models. A variety of mouse strains have been used for this purpose. However, mouse strains can differ in their inherent propensities to develop metabolic disease, which may affect the experimental outcomes of metabolic studies. We have investigated strain-dependent differences in the susceptibility to diet-induced obesity and insulin resistance in five commonly used inbred mouse strains (C57BL/6J, 129X1/SvJ, BALB/c, DBA/2 and FVB/N). Methods: Mice were fed either a low-fat or a high-fat diet (HFD) for 8 weeks. Whole-body energy expenditure and body composition were then determined. Tissues were used to measure markers of mitochondrial metabolism, inflammation, oxidative stress and lipid accumulation. Results: BL6, 129X1, DBA/2 and FVB/N mice were all susceptible to varying degrees to HFD-induced obesity, glucose intolerance and insulin resistance, but BALB/c mice exhibited some protection from these detrimental effects. This protection could not be explained by differences in mitochondrial metabolism or oxidative stress in liver or muscle, or inflammation in adipose tissue. Interestingly, in contrast with the other strains, BALB/c mice did not accumulate excess lipid (triacylglycerols and diacylglycerols) in the liver; this is potentially related to lower fatty acid uptake rather than differences in lipogenesis or lipid oxidation. Conclusions/interpretation: Collectively, our findings indicate that most mouse strains develop metabolic defects on an HFD. However, there are inherent differences between strains, and thus the genetic background needs to be considered carefully in metabolic studies.
Peer-to-Peer Grid Databases for Web Service Discovery

SUMMARY Grids are collaborative distributed Internet systems characterized by large scale, heterogeneity, lack of central control, multiple autonomous administrative domains, unreliable components and frequent dynamic change. In such systems, it is desirable to maintain and query dynamic and timely information about active participants such as services, resources and user communities. The web services vision promises that programs are made more flexible, adaptive and powerful by querying Internet databases (registries) at runtime in order to discover information and network attached building blocks, enabling the assembly of distributed higher-level components. In support of this vision, we introduce the Web Service Discovery Architecture (WSDA), which subsumes an array of disparate concepts, interfaces and protocols under a single semi-transparent umbrella. WSDA specifies a small set of orthogonal multi-purpose communication primitives (building blocks) for discovery, covering service identification, service description retrieval, data publication as well as minimal and powerful query support. The individual primitives can be combined and plugged together by specific clients and services to yield a wide range of behaviors and emerging synergies. Based on WSDA, we introduce the hyper registry, which is a centralized database node for discovery of dynamic distributed content. It supports XQueries over a tuple set from a dynamic XML data model. We address the problem of maintaining dynamic and timely information populated from a large variety of unreliable, frequently changing, autonomous and heterogeneous remote data sources. However, in a large cross-organizational system, the set of information tuples is partitioned over many such distributed nodes, for reasons including autonomy, scalability, availability, performance and security. This suggests the use of Peer-to-Peer (P2P) query technology. Consequently, we propose the WSDA based Unified Peer-to-Peer Database Framework (UPDF) and its corresponding Peer Database Protocol (PDP). They are unified in the sense that they allow to express specific discovery applications for a wide range of data types, node topologies (e.g. ring, tree, graph), query languages (e.g. XQuery, SQL), query response modes (e.g. Routed, Direct and Referral Response), neighbor selection policies, pipelining, timeout and scope policies. We describe the first steps towards the convergence of Grid Computing, Peer-toPeer Computing, Distributed Databases and Web Services. The uniformity and wide applicability of our approach is distinguished from related work, which (1) addresses some but not all problems, and (2) does not propose a unified framework.
Dualistic nature of adhesive protein function: fibronectin and its biologically active peptide fragments can autoinhibit fibronectin function

Fibronectin and certain polypeptide regions of this adhesive glycoprotein mediate cell attachment and spreading on various substrates. We explored the theoretical prediction that this adhesive protein could become a competitive inhibitor of fibronectin-mediated processes if present in solution at appropriately high concentrations. Fibronectin function was inhibited by purified plasma fibronectin at 5- 10 mg/ml, by a 75,000-dalton cell-interaction fragment of the protein at 0.5-1 mg/ml, and even by two synthetic peptides containing a conserved, hydrophilic amino acid sequence at 0.1-0.5 mg/ml. Inhibition of fibronectin-dependent cell spreading was dose dependent, noncytotoxic, and reversible. It was competitive in nature, since increased quantities of substrate-adsorbed fibronectin or longer incubation periods decreased the inhibition. A peptide inhibitory for fibronectin-mediated cell spreading also inhibited fibronectin-mediated attachment of cells to type I collagen, but it did not affect concanavalin A-mediated spreading. These results demonstrate the potential of a cell adhesion molecule and its biologically active peptide fragments to act as competitive inhibitors, and they suggest that fibronectin may act by binding to a saturable cell surface receptor.
Current challenges and future applications for protein maps and post‐translational vector maps in proteome projects

5 6 Introduction . 2-D gel electrophoresis allows the creation of reference maps . 2-D reference maps as a tool for proteome studies . Global quantitation of proteins . Study of post-translational modifications “Vector Maps” of 2-D gels . “Shotgun” approaches to proteome analysis . Analysis of protein heterogeneity . Current challenges to 2-D technology Low copy number proteins . Very basic and large proteins Optimal size for 2-D gels . Sample preparation . Protein modifications resulting from electrophoresis . Conclusions . References . 830
A comparison of state-of-the-art technologies for irreversible compression of large medical datasets

In this work we compare state-of-the-art 3D coding technologies which are suitable for compression of 3D (volumetric) medical imagery. Our aim is to assess the usage of these methods on representative large datasets, also keeping into account relevant features related to modern application requirements. This work wants to be a useful reference for those interested in medical image coding technologies evaluation and, more in general, in the interdisciplinary debate about the usage of irreversible compression technologies for an improved and cost effective handling of diagnostic imaging processes and infrastructures (PACS, teleradiology) involving large datasets. Reproducibility and possible extension of this study are guaranteed by the use of publicly available reference software and datasets.