Miracle-dz/UniFAR-FTUs huggingface dataset:
Acetylcholine Receptors Direct Rapsyn Clusters to the Neuromuscular Synapse in Zebrafish

Clustering of nicotinic muscle acetylcholine receptors (AChRs) requires association with intracellular rapsyn, a protein with an intrinsic ability to self-cluster. Previous studies on sofa potato (sop), an AChR null line of zebrafish, have suggested that AChRs may play an active role in subsynaptic localization of rapsyn clusters. To test this proposal directly, we identified and cloned the gene responsible for the sop phenotype and then attempted to rescue subsynaptic localization of the receptor-rapsyn complex in mutant fish. sop contains a leucine to proline mutation at position 28, near the N terminus of the zebrafish AChR δ subunit. Transient expression of mutant δ subunit in sop fish was unable to restore surface expression of muscle AChRs. In contrast, expression of wild-type δ subunit restored the ability of muscle to assemble surface receptors along with the ability of fish to swim. Most importantly, the ability of rapsyn clusters to localize effectively to subsynaptic sites also was rescued in large part. Our results point to direct involvement of the AChR molecule in restricting receptor-rapsyn clusters to the synapse.
Loss and Gain of Function in SERPINB11: An Example of a Gene under Selection on Standing Variation, with Implications for Host-Pathogen Interactions

Serine protease inhibitors (SERPINs) are crucial in the regulation of diverse biological processes including inflammation and immune response. SERPINB11, located in the 18q21 gene cluster, is a polymorphic gene/pseudogene coding for a non-inhibitory SERPIN. In a genome-wide scan for recent selection, SERPINB11 was identified as a potential candidate gene for adaptive evolution in Yoruba. The present study sought a better understanding of the evolutionary history of SERPINB11, with special focus on evaluating its selective signature. Through the resequencing of coding and noncoding regions of SERPINB11 in 20 Yorubans and analyzing primate orthologous sequences, we identified a full-length SERPINB11 variant encoding a non-inhibitory SERPIN as the putative candidate of selection – probably driven to higher frequencies by an adaptive response using preexisting variation. In addition, we detected contrasting evolutionary features of SERPINB11 in primates: While primate phylogeny as a whole is under purifying selection, the human lineage shows evidence of positive selection in a few codons, all associated with the active SERPINB11. Comparative modeling studies suggest that positively selected codons reduce SERPINB11's ability to undergo the conformational changes typical of inhibitory SERPINs – suggesting that it is evolving towards a new non-inhibitory function in humans. Significant correlations between SERPINB11 variants and the environmental variables, pastoralism and pathogen richness, have led us to propose a selective advantage through host-pathogen interactions, possibly linked to an adaptive response combating the emergence of infectious diseases in recent human evolution. This work represents the first description of a resurrected gene in humans, and may well exemplify selection on standing variation triggered by drastic ecological shifts.
Drug resistance-associated changes in sphingolipids and ABC transporters occur in different regions of membrane domains Published, JLR Papers in Press, September 8, 2005. DOI 10.1194/jlr.M500070-JLR200

We have recently shown that two ATP binding cassette (ABC) transporters are enriched in Lubrol-resistant noncaveolar membrane domains in multidrug-resistant human cancer cells [Hinrichs, J. W. J., K. Klappe, I. Hummel, and J. W. Kok. 2004. ATP-binding cassette transporters are enriched in non-caveolar detergent-insoluble glycosphingolipid-enriched membrane domains (DIGs) in human multidrug-resistant cancer cells. J. Biol. Chem. 279: 5734–5738]. Here, we show that aminophospholipids are relatively enriched in Lubrol-resistant membrane domains compared with Triton X-100-resistant membrane domains, whereas sphingolipids are relatively enriched in the latter. Moreover, Lubrol-resistant membrane domains contain more protein and lipid mass. Based on these results, we postulate a model for detergent-insoluble glycosphingolipid-enriched membrane domains consisting of a Lubrol-insoluble/Triton X-100-insoluble region and a Lubrol-insoluble/Triton X-100-soluble region. The latter region contains most of the ABC transporters as well as lipids known to be necessary for their efflux activity. Compared with drug-sensitive cells, the detergent-insoluble glycosphingolipid-enriched membrane domains (DIGs) in drug-resistant cells differ specifically in sphingolipid content and not in protein, phospholipid, or cholesterol content. In drug-resistant cells, sphingolipids with specific fatty acids (especially C24:1) are enriched in these membrane domains. Together, these data show that multidrug resistance-associated changes in both sphingolipids and ABC transporters occur in DIGs, but in different regions of these domains.
Searching for Grammar Right

This paper describes our ongoing work in and thoughts on developing a grammar learning system based on a construction grammar formalism. Necessary modules are presented and first results and challenges in formalizing the grammar are shown up. Furthermore, we point out the major reasons why we chose construction grammar as the most fitting formalism for our purposes. Then our approach and ideas of learning new linguistic phenomena, ranging from holophrastic constructions to compositional ones, is presented.
BLEnd: Practical Continuous Neighbor Discovery for Bluetooth Low Energy

Identifying "who is around" is key in a plethora of smart scenarios. While many solutions exist, they often take a theoretical approach, reasoning about protocol behavior with an abstract model that makes simplifying assumptions about the environment. This approach creates a gap between protocol implementations and the models used during design and analysis. In this paper, we take a system approach to continuous neighbor discovery: starting with the concrete technology of Bluetooth Low Energy (BLE) we build a protocol, called BLEnd, tailored to its constraints. Moreover, we also consider the very real effects of packet collisions, to our knowledge a first in this domain. Our ultimate goal is to directly empower developers with the ability to determine the optimal protocol configuration for their applications; in this respect, the slotless operation of BLEnd offers richer alternatives than state-of-the-art protocols. Developers specify the minimum discovery probability, the target discovery latency, and the maximum expected node density; these are used by an optimizer tool to parameterize the BLEnd implementation towards maximum lifetime. This paper shows that BLEnd not only achieves the user-specified goals, but does so more efficiently than analogous configurations of competing protocols.
Comparative Endocrinology of Aging and Longevity Regulation

Hormones regulate growth, development, metabolism, and other complex processes in multicellular animals. For many years it has been suggested that hormones may also influence the rate of the aging process. Aging is a multifactorial process that causes biological systems to break down and cease to function in adult organisms as time passes, eventually leading to death. The exact underlying causes of the aging process remain a topic for debate, and clues that may shed light on these causes are eagerly sought after. In the last two decades, gene mutations that result in delayed aging and extended longevity have been discovered, and many of the affected genes have been components of endocrine signaling pathways. In this review we summarize the current knowledge on the roles of endocrine signaling in the regulation of aging and longevity in various animals. We begin by discussing the notion that conserved systems, including endocrine signaling pathways, “regulate” the aging process. Findings from the major model organisms: worms, flies, and rodents, are then outlined. Unique lessons from studies of non-traditional models: bees, salmon, and naked mole rats, are also discussed. Finally, we summarize the endocrinology of aging in humans, including changes in hormone levels with age, and the involvement of hormones in aging-related diseases. The most well studied and widely conserved endocrine pathway that affects aging is the insulin/insulin-like growth factor system. Mutations in genes of this pathway increase the lifespan of worms, flies, and mice. Population genetic evidence also suggests this pathway’s involvement in human aging. Other hormones including steroids have been linked to aging only in a subset of the models studied. Because of the value of comparative studies, it is suggested that the aging field could benefit from adoption of additional model organisms.
Shape Grammar applied to urban morphology studies: land subdivision in urbanized areas.

Currently, the land regulation plans define the urban micro-scale, producing standardized and pre-dimensioned blocks and lots, generating monotony, poor urban quality and high infrastructure costs. In the quest for sustainability, studies point to a density and a certain degree of population density to enable urban infrastructures with qualitative and quantitative gains, through concepts of compactness, completeness and connectivity. This study presents possibilities of batch sizing using the Grammatical method of the Form, through morphological configurations and rules presents possibilities of generation of new formats, distribution of urban lots in the neighborhood Valentina, in João Pessoa PB and discusses results.
Improving the Prediction Efficiency for MultiView Video Coding Using Histogram Matching

Abstract. Applications for video data recorded with a setup of several cameras are currently attracting increasing interest. For such multi-view sequences, efficient coding is crucial to handle the enormous amount of data. However, significant luminance and chrominance variations between the different views, which often originate from imperfect camera calibration, are able to reduce the coding efficiency and the rendering quality. In this paper, we suggest the usage of histogram matching to compensate these differences in a pre-filtering step. After a description of the proposed algorithm, it is explained how histogram matching can be applied to multi-view video data. The effect of histogram matching on the coding performance is evaluated by statistically analysing prediction from temporal as well as from spatial references. For several test sequences, results are shown which indicate that the amount of spatial prediction across different camera views can be increased by applying histogram matching. Index Terms – multi-view video, video coding, image filtering
Hyperventilation in Craniotomy for Brain Tumor

The effect of the method of pulmonary ventilation on cerebrospinal fluid pressure (CSF), brain tension, and blood gas changes was investigated in 20 patients undergoing craniotomy for brain tumor. Five different methods of ventilation were successively employed in the same patient during halothane/oxygen anesthesia. Assisted ventilation gave the highest values for CSF pressure (average = 238 mm. of water). Intermittent positive pressure breathing caused a moderate fall in CSF pressure (mean = 212 mm. of water). Positive-negative pressure breathing at minute volumes equal to or less than 15 liters per minute resulted in the lowest values for CSF pressure (mean = 115 mm. of water), and clinically was associated with a slack brain. When a minute ventilation volume greater than 15 liters per minute was employed, CSF pressure tended to rise (mean = 179 mm. of water), while the brain became tight and congested. This occurred in spite of respiratory alkalosis and a negative phase during expiration. Large ventilatory volumes were also associated with a progressive increase in cerebral arterialvenous oxygen difference and fall in oxygen saturation of blood sampled from the sagittal sinus. The data indicate that brain tension and CSF pressure can be modified by varying the method of ventilation under halothane/oxygen anesthesia.
SNARE Assembly and Membrane Fusion, a Kinetic Analysis*

SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) assembly may promote intracellular membrane fusion, an essential process for vesicular transport in cells. Core complex formation between vesicle-associated SNARE and target membrane SNARE perhaps drives the merging of two membranes into a single bilayer. Using spin-labeling EPR, trans-SNARE complex formation was monitored “locally” at four different core locations of recombinant yeast SNAREs, which are individually reconstituted into phospholipid vesicles. The results indicate that the time scales of core formation are virtually the same at all four locations throughout the core region, indicating the possibility of a single step core assembly, which appears to be somewhat different from what has been postulated by the “zipper” model. The EPR data were then compared with the kinetics of the lipid mixing measured with the fluorescence assay. The analysis suggests that SNARE core assembly occurs on a much faster time scale than the lipid mixing, providing a new insight into the timing of individual events in SNARE-induced membrane fusion.
Energy–Robustness Tradeoff in Cellular Network Power Control

In the seminal paper by Foschini and Miljanic in 1993, a distributed power control algorithm was developed to meet SIR targets with minimal powers in cellular network uplinks. Since the SIR on an active link may dip below the SIR target during the transient after a new user enters the cell, Bambos proposed an active link protection algorithm to provide robustness, at the expense of higher energy consumption. This paper examines the tradeoff between energy and robustness. An optimization problem is formulated where robustness is captured in the constraint and the price of robustness penalized in the objective function. A distributed algorithm is developed to solve this problem. Local convergence and optimality of equilibrium are proved for the algorithm. The objective function modulates the tradeoff between energy and robustness, and between energy and speed of admission, as illustrated through a series of numerical experiments. A parameterized family of objective functions is constructed to control the transient and equilibrium properties of robust distributed power control.
Robustness and stability optimization of power generating kite systems in a periodic pumping mode

In this paper we formulate and solve optimal control problems for power generating kite systems. Here, the kite generates energy by periodically pulling a generator on the ground while flying fast in a crosswind direction. We are searching for an intrinsically open-loop stable trajectory such that the kite generates as much power as possible without needing feedback, while neither the kite nor the cable should touch the ground in the presence of wind turbulence. As the wind turbulences are unknown, robustness aspects need to be taken into account. The formulation of the associated optimal control problem makes use of periodic Lyapunov differential equations in order to guarantee local open-loop stability while robustness aspects are regarded in a linear approximation. The main result of this paper is that open-loop stable kite orbits exist and that open-loop stability only costs approximately 23% compared to the power-optimal unstable orbit.
Increasing Signal Specificity of the TOL Network of Pseudomonas putida mt-2 by Rewiring the Connectivity of the Master Regulator XylR

Prokaryotic transcription factors (TFs) that bind small xenobiotic molecules (e.g., TFs that drive genes that respond to environmental pollutants) often display a promiscuous effector profile for analogs of the bona fide chemical signals. XylR, the master TF for expression of the m-xylene biodegradation operons encoded in the TOL plasmid pWW0 of Pseudomonas putida, responds not only to the aromatic compound but also, albeit to a lesser extent, to many other aromatic compounds, such as 3-methylbenzylalcohol (3MBA). We have examined whether such a relaxed regulatory scenario can be reshaped into a high-capacity/high-specificity regime by changing the connectivity of this effector-sensing TF within the rest of the circuit rather than modifying XylR structure itself. To this end, the natural negative feedback loop that operates on xylR transcription was modified with a translational attenuator that brings down the response to 3MBA while maintaining the transcriptional output induced by m-xylene (as measured with a luxCDABE reporter system). XylR expression was then subject to a positive feedback loop in which the TF was transcribed from its own target promoters, each known to hold different input/output transfer functions. In the first case (xylR under the strong promoter of the upper TOL operon, Pu), the reporter system displayed an increased transcriptional capacity in the resulting network for both the optimal and the suboptimal XylR effectors. In contrast, when xylR was expressed under the weaker Ps promoter, the resulting circuit unmistakably discriminated m-xylene from 3MBA. The non-natural connectivity engineered in the network resulted both in a higher promoter activity and also in a much-increased signal-to-background ratio. These results indicate that the working regimes of given genetic circuits can be dramatically altered through simple changes in the way upstream transcription factors are self-regulated by positive or negative feedback loops.
An Improved Analytical Solution for the Temperature Profile of Ice Sheets

The one‐dimensional steady state analytical solution of the energy conservation equation obtained by Robin (1955, https://doi.org/10.3189/002214355793702028) is frequently used in glaciology. This solution assumes a linear change in surface velocity from a minimum value equal to minus the mass balance at the surface to zero at the bed. Here we show that this assumption of a linear velocity profile leads to large errors in the calculated temperature profile and especially in basal temperature. By prescribing a nonlinear power function of elevation above the bed for the vertical velocity profile arising from use of the Shallow Ice Approximation, we derive a new analytical solution for temperature. We show that the solution produces temperature profiles identical to numerical temperature solutions with the Shallow Ice Approximation vertical velocity near ice divides. We quantify the importance of strain heating and demonstrate that integrating the strain heating and adding it to the geothermal heat flux at the bed is a reasonable approximation for the interior regions. Our analytical solution does not include horizontal advection components, so we compare our solution with numerical solutions of a two‐dimensional advection‐diffusion model and assess the applicability and errors of the analytical solution away from the ice divide. We show that several parameters and assumptions impact the spatial extent of applicability of the new solution including surface mass balance rate and surface temperature lapse rate. We delineate regions of Greenland and Antarctica within which the analytical solution at any depth is likely within 2 K of the actual temperatures with horizontal advection.
Pathology of hepatitis C virus infection

This paper reviews our current knowledge of hepatitis C virus, its structure, epidemiology and pathological effects in man. The histopathological features of acute and chronic hepatitis due to hepatitis C virus are detailed and illustrated. The possible pathogenetic mechanisms involved in the liver injury are outlined and the significance of genotypic subtypes of the virus and of host genetic predisposition in relation to the liver injury and the response to therapy are summarized.
Comparing knowledge about greenhouse effect and ozone layer among Norwegian pupils finishing compulsory education in 1989, 1993 and 2005

The greenhouse effect and the ozone layer have been in media’s focus more than two decades. In the same period Norwegian compulsory school have d three national curricula. Only the last one prescribes the two topics explicit. During the last two decades media and public debate might have been sources of information causi ng informal learning among pupils. Changing curricula, formal and informal learning ar e the background for examining the development of pupils’ knowledge about the greenhou se effect and ozone layer from 1989 to 2005. In 2005 the trends seem to be more pupils con fuse the greenhouse effect with the effects of the ozone layer. On the same time specif ic knowledge about the greenhouse effect is improving. The article will discuss some possibl e causes for the trends, and give some recommendations for teaching the topics. Introduction This article deals with five lines of evolution cro ssing each other in the classrooms of Norwegian schools: The evolution of 1.scientific kn owledge about the greenhouse effect and 2.the ozone layer; 3.actions to get control over at mospheric pollution concerning the greenhouse effect and 4.the ozone layer both heav ily reported in media; 5.the incorporation of knowledge about the greenhouse effect and the ef fects of the ozone layer in the national curriculum for compulsory education. The main focus in the article is the pupils’ knowledge about the greenhouse effect and the ozone layer at the time they finish their compulsory education. The evolution of scientific knowledge about the gre enhouse effect has lasted for almost two centuries, here exemplified by some highlights (for a more complete briefing see Houghton, 2004): • 1827 Fourier claimed that certain gasses in the atm osphere were holding back heat from the earth like the glasses in a greenhouse. This me taphor gave name to the ‘greenhouse effect’. • 1861 Tyndall showed that climate change might be a result of variation in atmospheric carbon dioxide (CO2) content. • 1890-ies Arrhenius worried about the extreme burnin g of coal as a consequence of the Industrial Revolution, and predicted that the avera g temperature on earth would raise 5-6 degrees if doubling the CO 2 content in the atmosphere. This statement raised a deb te on atmospheric pollution. • 1938 Callender determined that higher content of CO 2 had caused warmer temperatures in America and Europe, and that Arrhenius had underest imated the raise of temperature. Callender and Flohn discussed how the photo synthes is in trees and plants could take up some carbon dioxide and reduce the temperature rais .
Exploiting decision theory concepts within clinical guideline systems: Toward a general approach

Supporting therapy selection is a fundamental task for a system for computerized management of clinical guidelines (GL). To this end, decision theory concepts could provide significant advances. In this article, we propose a systematic analysis of the main GL representation primitives and of how they could be related to decision theory concepts. The knowledge representation contribution we provide can be seen as a basis for implementing a decision support tool within any of the systems described in the literature: As a matter of fact, at a sufficiently abstract level, the GL primitives we treat are shared by all of the systems. Such a tool could be adopted when executing a GL on a single patient (in clinical practice) and for simulation purposes. In particular, a decision theory tool based on this analysis is being implemented in the GLARE system. © 2006 Wiley Periodicals, Inc. Int J Int Syst 21: 585–599, 2006.