Miracle-dz/UniFAR-FTUs huggingface dataset:
Secretagogue-induced Exocytosis Recruits G Protein-gated K+ Channels to Plasma Membrane in Endocrine Cells*

Stimulation-regulated fusion of vesicles to the plasma membrane is an essential step for hormone secretion but may also serve for the recruitment of functional proteins to the plasma membrane. While studying the distribution of G protein-gated K+ (KG) channels in the anterior pituitary lobe, we found KG channel subunits Kir3.1 and Kir3.4 localized on the membranes of intracellular dense core vesicles that contained thyrotropin. Stimulation of these thyrotroph cells with thyrotropin-releasing hormone provoked fusion of vesicles to the plasma membrane, increased expression of Kir3.1 and Kir3.4 subunits in the plasma membrane, and markedly enhanced KG currents stimulated by dopamine and somatostatin. These data indicate a novel mechanism for the rapid insertion of functional ion channels into the plasma membrane, which could form a new type of negative feedback control loop for hormone secretion in the endocrine system.
Integrating Linguistic Primitives in Learning Context-Dependent Representation

The paper presents an explicit connectionist-inspired, language learning model in which the process of settling on a particular interpretation for a sentence emerges from the interaction of a set of "soft" lexical, semantic, and syntactic primitives. We address how these distinct linguistic primitives can be encoded from different modular knowledge sources but strongly involved in an interactive processing in such a way as to make implicit linguistic information explicit. The learning of a quasi-logical form called context-dependent representation, is inherently incremental and dynamical in such a way that every semantic interpretation will be related to what has already been presented in the context created by prior utterances. With the aid of the context-dependent representation, the capability of the language learning model in text understanding is strengthened. This approach also shows how the recursive and compositional role of a sentence as conveyed in the syntactic structure can be modeled in a neurobiologically motivated linguistics based on dynamical systems rather on combinatorial symbolic architecture. Experiments with more than 2000 sentences in different languages illustrating the influences of the context-dependent representation on semantic interpretation, among other issues, are included.
Hemoglobin &agr;/eNOS Coupling at Myoendothelial Junctions Is Required for Nitric Oxide Scavenging During Vasoconstriction

Objective— Hemoglobin &agr; (Hb &agr;) and endothelial nitric oxide synthase (eNOS) form a macromolecular complex at myoendothelial junctions; the functional role of this interaction remains undefined. To test if coupling of eNOS and Hb &agr; regulates nitric oxide signaling, vascular reactivity, and blood pressure using a mimetic peptide of Hb &agr; to disrupt this interaction. Approach and Results— In silico modeling of Hb &agr; and eNOS identified a conserved sequence of interaction. By mutating portions of Hb &agr;, we identified a specific sequence that binds eNOS. A mimetic peptide of the Hb &agr; sequence (Hb &agr; X) was generated to disrupt this complex. Using in vitro binding assays with purified Hb &agr; and eNOS and ex vivo proximity ligation assays on resistance arteries, we have demonstrated that Hb &agr; X significantly decreased interaction between eNOS and Hb &agr;. Fluorescein isothiocyanate labeling of Hb &agr; X revealed localization to holes in the internal elastic lamina (ie, myoendothelial junctions). To test the functional effects of Hb &agr; X, we measured cyclic guanosine monophosphate and vascular reactivity. Our results reveal augmented cyclic guanosine monophosphate production and altered vasoconstriction with Hb &agr; X. To test the in vivo effects of these peptides on blood pressure, normotensive and hypertensive mice were injected with Hb &agr; X, which caused a significant decrease in blood pressure; injection of Hb &agr; X into eNOS-/- mice had no effect. Conclusions— These results identify a novel sequence on Hb &agr; that is important for Hb &agr;/eNOS complex formation and is critical for nitric oxide signaling at myoendothelial junctions.
Rebelling for a Reason: Protein Structural “Outliers”

Analysis of structural variation in domain superfamilies can reveal constraints in protein evolution which aids protein structure prediction and classification. Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families. Some superfamily members show large structural differences which are functionally relevant. This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database. Functional annotations within superfamilies, with structural outliers or ‘rebels’, are discussed in the context of structural variations. Overall, these data reinforce the idea that functional similarities cannot be extrapolated from mere structural conservation. The implication for fold-function prediction is that the functional annotations can only be inherited with very careful consideration, especially at low sequence identities.
Cdkn2a Is an Atherosclerosis Modifier Locus That Regulates Monocyte/Macrophage Proliferation

Objective—Common genetic variants in a 58-kb region of chromosome 9p21, near the CDKN2A/CDKN2B tumor suppressor locus, are strongly associated with coronary artery disease. However, the underlying mechanism of action remains unknown. Methods and Results—We previously reported a congenic mouse model harboring an atherosclerosis susceptibility locus and the region of homology with the human 9p21 locus. Microarray and transcript-specific expression analyses showed markedly decreased Cdkn2a expression, including both p16INK4a and p19ARF, but not Cdkn2b (p15INK4b), in macrophages derived from congenic mice compared with controls. Atherosclerosis studies in subcongenic strains revealed genetic complexity and narrowed 1 locus to a small interval including Cdkn2a/b. Bone marrow (BM) transplantation studies implicated myeloid lineage cells as the culprit cell type, rather than resident vascular cells. To directly test the role of BM-derived Cdkn2a transcripts in atherogenesis and inflammatory cell proliferation, we performed a transplantation study using Cdkn2a+/− cells in the Ldlr−/− mouse model. Cdkn2a-deficient BM recipients exhibited accelerated atherosclerosis, increased Ly6Chi proinflammatory monocytes, and increased monocyte/macrophage proliferation compared with controls. Conclusion—These data provide a plausible mechanism for accelerated atherogenesis in susceptible congenic mice, involving decreased expression of Cdkn2a and increased proliferation of monocyte/macrophages, with possible relevance to the 9p21 human locus.
Clocking design and analysis for a 600 MHz Alpha microprocessor

The clocking methodology for the 600 MHz Alpha microprocessor allows increased performance goals to be met through multi-level buffering. In addition power savings are realized through reduced metal usage and conditional clocks. Two distinct analysis methods are required to verify the clock design. One is used for large, globally distributed clocks and the other is applied to small, locally distributed clocks. The clock is generated from an 80-200 MHz reference clock multiplied by an on-chip phase-locked loop (PLL) to a nominal frequency of 600 MHz. The clock distribution network up to and including the global clock (GCLK) is included in the feedback loop of the PLL to control phase alignment. GCLK is the primary timing reference for the chip. The generation of GCLK begins at the PLL and is routed through a high-gain buffer network to a central point on the die. From there the clock is driven through buffered X, H and RC trees to distributed GCLK drivers located in a windowpane pattern across the chip. The final physical stage of the global clock distribution network is a grid of upper-level low-impedance metal that covers the entire die.
Variation of Microbial Communities in Soil, Rhizosphere, and Rhizoplane in Response to Crop Species, Soil Type, and Crop Development

ABSTRACT We investigated the influence of plant species, soil type, and plant development time on the shaping of microbial communities in soil and in association with roots. The sample group consisted of a total of 32 microcosms in three habitats: soil, rhizosphere, and rhizoplane. Communities were represented by the patterns of a sequence-specific separation of rRNA target sequences. Effects of experimental parameters were classified by a cluster analysis of pattern similarities. The type of plant species (clover, bean, or alfalfa) had the greatest effect in plant-associated habitats and also affected soil patterns. Plant development had a minor habitat-dependent effect that was partly obscured by replicate variation. The results stress the applicability of biased community representations in an analysis of induced variation.
Automatic Clustering with Self-Organizing Maps and Genetic Algorithms

The analysis of data sets of unknown characteristics usually demands that subsets (or clusters) of the data are identified in such a way that the members of any one such cluster display common (in some sense) characteristics. In order to do this we must determine a) The number of clusters, b) The clusters themselves and c) The labeling of every element in the data set such that each element belongs uniquely to one of the clusters. We discuss an algorithm which allows us to solve (b) and (c); we assume that (a) is given. We show that the so-called labeling problem may be solved by minimizing an adequate measure of distance. We discuss several such metrics, the corresponding minimization (genetic) algorithm and offer some results derived from its application.
Use of nucleic acid probes to identify mycobacteria directly from Difco ESP-Myco bottles

Mycobacterial isolates were identified directly from positive ESP-Myco bottles by use of nucleic acid probes. Retrospective analysis of 360 cultures which grew either Mycobacterium tuberculosis, M. avium complex, or M. gordonae showed that 87% were identified by direct testing of an aliquot obtained at the time a positive culture was detected. Another 12% of these cultures gave results in the equivocal range, with only 1% of the isolates yielding negative results on initial testing.
Fast Synthesis of Reversible Circuits using a Sorting Algorithm and Optimization

This paper studies synthesis and optimization of reversible circuits composed of Toffoli gates with negative and positive control lines. The proposed synthesis algorithm performs sorting among optimal implementations of certain functions called as essential functions to implement any reversible Boolean function. Essential functions comprise very small amount of all functions. For example, to implement 3 bit circuits, 28 essential functions out of all 40320 functions are needed. The proposed optimization algorithm considers both reversible and quantum circuit costs. First, reversible cost is reduced by considering adjacent gate pairs. Then, inner quantum structures of the gates are investigated and quantum optimization is performed. The proposed algorithms are evaluated on benchmark circuits in comparison with the results in the literature.
Immunoelectron Microscopic Evidence for Tetherin/BST2 as the Physical Bridge between HIV-1 Virions and the Plasma Membrane

Tetherin/BST2 was identified in 2008 as the cellular factor responsible for restricting HIV-1 replication at a very late stage in the lifecycle. Tetherin acts to retain virion particles on the plasma membrane after budding has been completed. Infected cells that express large amounts of tetherin display large strings of HIV virions that remain attached to the plasma membrane. Vpu is an HIV-1 accessory protein that specifically counteracts the restriction to virus release contributed by tetherin. Tetherin is an unusual Type II transmembrane protein that contains a GPI anchor at its C-terminus and is found in lipid rafts. The leading model for the mechanism of action of tetherin is that it functions as a direct physical tether bridging virions and the plasma membrane. However, evidence that tetherin functions as a physical tether has thus far been indirect. Here we demonstrate by biochemical and immunoelectron microscopic methods that endogenous tetherin is present on the viral particle and forms a bridge between virion particles and the plasma membrane. Endogenous tetherin was found on HIV particles that were released by partial proteolytic digestion. Immunoelectron microscopy performed on HIV-infected T cells demonstrated that tetherin forms an apparent physical link between virions and connects patches of virions to the plasma membrane. Linear filamentous strands that were highly enriched in tetherin bridged the space between some virions. We conclude that tetherin is the physical tether linking HIV-1 virions and the plasma membrane. The presence of filaments with which multiple molecules of tetherin interact in connecting virion particles is strongly suggested by the morphologic evidence.
De novo design of a transmembrane Zn2+-transporting four-helix bundle

The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn2+ and Co2+, but not Ca2+, across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn2+ ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties. Computational design yields a transmembrane protein that selectively transports zinc cations. [Also see Perspective by Lupas] Building transmembrane zinc transporters The ability to design proteins gives insight into the relation between a protein's fold and its function and also provides a path to custom proteins for bioengineering applications. Impressive strides have been made in the design of soluble proteins, but designing membrane proteins remains a challenge. Joh et al. achieve a milestone by designing a transmembrane Zn2+ transporter (see the Perspective by Lupas). The protein comprises four helices: Two tightly interacting pairs form a weaker interface that facilitates the transport of Zn2+ with concomitant reverse transport of protons. Science, this issue p. 1520; see also p. 1455
Surveillance of mobile objects using coordinated wireless sensor nodes

Surveillance of mobile office assets is made by attaching wireless sensor nodes to assets and to their authorized users. The wireless sensor nodes are monitored via radio base access points connected to a distributed application framework for analysis and coordination of security events. By logic rules applied to the event information, temporarily stored and accessible in a distributed tuple space, security decisions, alarms and other actions are implemented.
A model of best vitelliform macular dystrophy in rats.

PURPOSE The VMD2 gene, mutated in Best macular dystrophy (BMD) encodes bestrophin, a 68-kDa basolateral plasma membrane protein expressed in retinal pigment epithelial (RPE) cells. BMD is characterized by a depressed light peak (LP) in the electro-oculogram. Bestrophin is thought to be the Cl channel that generates the LP. The goal was to generate an animal model of BMD and to determine the effects of bestrophin overexpression on the RPE-generated components of the ERG. METHODS Bestrophin or bestrophin mutants (W93C or R218C) were overexpressed in the RPE of rats by injection of replication-defective adenovirus. Immunofluorescence microscopy and ERG recordings were used to study subsequent effects. RESULTS Bestrophin was confined to the basolateral plasma membrane of the RPE. Neither wild-type (wt) nor mutant bestrophin affected the a- or b-waves of the ERG. Wt bestrophin, however, increased the c-wave and fast oscillation (FO), but not the LP. In contrast, both mutants had little or no effect on the c-wave and FO, but did reduce LP amplitude. LP amplitudes across a range of stimuli were not altered by wt bestrophin, though the luminance response function was desensitized. LP response functions were unaffected by bestrophin R218C but were significantly altered by bestrophin W93C. CONCLUSIONS A model of BMD was developed in the present study. Because overexpression of wt bestrophin shifted luminance response but did not alter the range of LP response amplitudes, the authors conclude that the rate-limiting step for generating LP amplitude occurs before activation of bestrophin or that bestrophin does not directly generate the LP conductance.
Embodied Artificial Intelligence - On the role of morphology and materials in the emergence of cognitition

In the cognitivistic paradigm, intelligence was viewed as algorithmic, an approach that has lead to many impressive results and applications. However, this view turned out to be too limited: If we are to understand natural forms of intelligence, embodiment must be taken into account. In this paper we explore the implications of embodiment by providing a number of case studies. One concept that we will investigate is “ecological balance”, i.e. the interplay of morphology, materials, and neural processing. We develop a method of how this can be systematically investigated using artificial evolution and morphogenesis.
Two RPG Flow-graphs for Software Watermarking using Bitonic Sequences of Self-inverting Permutations

Software watermarking has received considerable attention and was adopted by the software development community as a technique to prevent or discourage software piracy and copyright infringement. A wide range of software watermarking techniques has been proposed among which the graph-based methods that encode watermarks as graph structures. Following up on our recently proposed methods for encoding watermark numbers $w$ as reducible permutation flow-graphs $F[\pi^*]$ through the use of self-inverting permutations $\pi^*$, in this paper, we extend the types of flow-graphs available for software watermarking by proposing two different reducible permutation flow-graphs $F_1[\pi^*]$ and $F_2[\pi^*]$ incorporating important properties which are derived from the bitonic subsequences composing the self-inverting permutation $\pi^*$. We show that a self-inverting permutation $\pi^*$ can be efficiently encoded into either $F_1[\pi^*]$ or $F_2[\pi^*]$ and also efficiently decoded from theses graph structures. The proposed flow-graphs $F_1[\pi^*]$ and $F_2[\pi^*]$ enrich the repository of graphs which can encode the same watermark number $w$ and, thus, enable us to embed multiple copies of the same watermark $w$ into an application program $P$. Moreover, the enrichment of that repository with new flow-graphs increases our ability to select a graph structure more similar to the structure of a given application program $P$ thereby enhancing the resilience of our codec system to attacks.
DynaFusion: a modeling system for interactive impossible objects

We describe DynaFusion, a modeling system for interactive impossible objects. Impossible objects are defined as multiple 3D polygonal meshes with edge visibility information and a set of constraints that define pointwise relationships between the meshes. A user can easily create such models with our modeling tool. The back-end of our system is a constraint solver that seamlessly combines multiple meshes in a projected 2D domain with 3D line orientations and that maintains coherence for each successive viewpoint, thereby allowing the user to rotate the impossible object without losing visual continuity of the edges. We believe that our system will stimulate the creation of innovative artworks.
PERIOD OF INFECTIVITY OF PATIENTS WITH HOMOLOGOUS SERUM JAUNDICE AND ROUTES OF INFECTION IN THIS DISEASE

1. Pooled specimens of serum obtained from 3 human volunteers three-fourths through their respective 56, 66, and 70 day incubation periods of homologous serum jaundice produced the disease in 1 out of 4 human volunteers following parenteral inoculation. 2. Serum specimens obtained from these same 3 patients during the acute, pre-icteric phase of their homologous serum jaundice produced the disease in 3 out of 4 human volunteers following parenteral inoculation. 3. These same sera, proven to be infectious by parenteral inoculation, failed to produce disease when ingested by 10 other human volunteers. 4. Pooled specimens of serum obtained in the convalescent phase (28 to 32 days after onset) of these 3 patients failed to produce apparent infection when inoculated parenterally into 5 human volunteers. 5. Pooled specimens of feces of 3 patients obtained in the acute phase of homologous serum jaundice, when virus was proven to be in the serum, were not demonstrably infectious when fed to 6 volunteers. 6. These findings are slightly different from those encountered in a similar study with infectious material from cases of infectious hepatitis.
Role of Glial Cells in Axonal Regeneration

Axonal regeneration is critical for functional recovery following neural injury. In addition to intrinsic differences between regenerative responses of axons in peripheral versus central nervous systems, environmental factors such as glial cells and related molecules in the extracellular matrix (ECM) play an important role in axonal regeneration. Schwann cells in the peripheral nervous system (PNS) are recognized as favorable factors that promote axonal regeneration, while astrocytes and oligodendrocytes in the central nervous system (CNS) are not. In this review, we evaluate the roles of Schwann cells and astrocytes in axonal regeneration and examine recent evidence that suggests a dual function of astrocytes in regenerative responses. We also discuss the role of Cdc2 pathways in axonal regeneration, which is commonly activated in Schwann cells and astrocytes. Greater insight on the roles of glial cells in axonal regeneration is key to establishing baseline interventions for improving functional recovery following neural injury.