Miracle-dz/UniFAR-FTUs huggingface dataset:
PolyADP-Ribosylation Is Involved in Neurotrophic Activity

PolyADP-ribosylation is a transient posttranslational modification of proteins, mainly catalyzed by poly(ADP-ribose)polymerase-1 (PARP-1). This highly conserved nuclear protein is activated rapidly in response to DNA nick formation and promotes a fast DNA repair. Here, we examine a possible association between polyADP-ribosylation and the activity of neurotrophins and neuroprotective peptides taking part in life-or-death decisions in mammalian neurons. The presented results indicate an alternative mode of PARP-1 activation in the absence of DNA damage by neurotrophin-induced signaling mechanisms. PARP-1 was activated in rat cerebral cortical neurons briefly exposed to NGF-related nerve growth factors and to the neuroprotective peptides NAP (the peptide NAPVSIPQ, derived from the activity-dependent neuroprotective protein ADNP) and ADNF-9 (the peptide SALLRSIPA, derived from the activity-dependent neurotrophic factor ADNF) In addition, polyADP-ribosylation was involved in the neurotrophic activity of NGF-induced and NAP-induced neurite outgrowth in differentiating pheochromocytoma 12 cells as well as in the neuroprotective activity of NAP in neurons treated with the Alzheimer's disease neurotoxin β-amyloid. A fast loosening of the highly condensed chromatin structure by polyADP-ribosylation of histone H1, which renders DNA accessible to transcription and repair, may underlie the role of polyADP-ribosylation in neurotrophic activity.
Geostrophic transport variability along the Aves Ridge in the eastern Caribbean Sea during 1985–1986

Data from five cruises during 1985–1986 along 63.55°W, across the eastern Caribbean Sea, are examined for seasonal variability of gcostrophic transport. A biannual maximum transport signal appears to correspond to that measured in the Florida Straits as well as to variations in the regional wind stress curl. Similar seasonal variations in the properties of water masses, entering the eastern margin of the basin and concentrated through the passages of the Lesser Antilles, are also indicated. A permanent system of strong westward flowing streams, interspersed by weaker eastward flowing streams, is shown to exist.
Enhanced initial cell responses to chemically modified anodized titanium.

BACKGROUND Previously, we reported that anodized porous titanium implants have photocatalytic hydrophilicity. However, this effect was not always sufficient for the significant improvement of bone apposition. PURPOSE The purpose of this study was to improve the photocatalytic properties of porous titanium implants by the fluoride modification of the anodized titanium dioxide (TiO(2)), and to investigate the initial cell response to it. MATERIALS AND METHODS The ideal concentration of ammonium hydrogen fluoride (NH(4)F-HF(2)) used in this study was determined by a static water contact angle assay. The ideal concentration of NH(4)F-HF(2) was 0.175%, and experimental disks were treated with this concentration. A pluripotent mesenchymal cell line, C2C12, was cultured on the disks in order to investigate cell attachment, morphology, and proliferation. RESULTS Cell attachment after 30 minutes of culturing was significantly higher for the ultraviolet-irradiated, fluoride-modified anodized TiO(2) (p < .05), and the simultaneous scanning electron microscope observation showed a rather flattened and extended cell morphology. The proliferation rate after 24 hours was also significantly higher for the fluoride-modified anodized TiO(2). CONCLUSION Fluoride chemical modification enhances the hydrophilic property of the anodized TiO(2) and improves the initial cell response to it.
MirrorBot: Using human-inspired mirroring behavior to pass a turing test

Believability of automated characters in virtual worlds has posed a challenge for many years. In this paper, the author discusses a novel approach of using human-inspired mirroring behavior in MirrorBot, an Unreal Tournament 2004 game bot which crossed the humanness barrier and won the 2K BotPrize 2012 competition with the score of 52.2%, a record in the five year history of this contest. A comparison with past contest entries is presented and the relevance of the mirroring behavior as a humanness improvement factor is argued. The modules that compose MirrorBot's architecture are presented along with a discussion of the advantages of this approach and proposed solutions for its drawbacks. The contribution continues with a discussion of the bot's results in humanness and judging accuracy.
Cigarette smoking and depression: a question of causation

Summary Cigarette smokers frequently describe the anxiolytic and antidepressant effects of smoking, but evidence suggests that cigarette smoking may itself increase negative affect, so that the causal direction of this association remains unclear. Although increasingly sophisticated analyses of epidemiological data may help to answer this question, observational data can never unequivocally provide evidence of causation. Here we discuss the potential utility of genetic information in determining the causal basis of the relationship of cigarette smoking and depression.
Genetic affinities of inbred mouse strains of uncertain origin.

Phylogenetic analyses of genetic data arising from 144 gene loci are used to describe the interrelationships among 24 widely used inbred strains of mice. An unordered-parsimony analysis gives a cladogram that is virtually identical to the known genealogy of the mouse strains. A loss-parsimony analysis is used to evaluate the hypothesis that the observed patterns of genetic divergence among these 24 strains can be explained by the segregation of residual heterozygosity arising from a small population of highly heterozygous mice. The loss-parsimony cladogram is very similar to both the unordered-parsimony cladogram and the known genealogy of the mice. The phylogenetic analyses of these 144 loci are integrated with data on the type and origin of the Y chromosome. Inclusion of the Y-chromosome data provides additional insights into the genetic composition of several of the original stocks used to produce the current inbred strains of mice. Ten strains of uncertain origin are contained in these analyses, including AKR, BUB, CE, I, NZB, P, RF, SJL, ST, and SWR. SJL is hypothesized to have been derived from the same Swiss albino stock previously used to produce SWR. The BUB strain appears to have had a complex origin and shows closest genetic similarity to SWR and ST. AKR and RF are shown to be closely related, while the I strain shows greatest genetic similarity to DBA/2 for the 144 loci. However, I and DBA possess different types of Y chromosome. The NZB strain shows genetic similarity to several stocks of both U.S. and European origins. The power of the genetic data used in these analyses reiterates that inbred strains of mice can be a valuable paradigm for studies in evolutionary biology.
Investigation of MM-PBSA Rescoring of Docking Poses

Target-based virtual screening is increasingly used to generate leads for targets for which high quality three-dimensional (3D) structures are available. To allow large molecular databases to be screened rapidly, a tiered scoring scheme is often employed whereby a simple scoring function is used as a fast filter of the entire database and a more rigorous and time-consuming scoring function is used to rescore the top hits to produce the final list of ranked compounds. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approaches are currently thought to be quite effective at incorporating implicit solvation into the estimation of ligand binding free energies. In this paper, the ability of a high-throughput MM-PBSA rescoring function to discriminate between correct and incorrect docking poses is investigated in detail. Various initial scoring functions are used to generate docked poses for a subset of the CCDC/Astex test set and to dock one set of actives/inactives from the DUD data set. The effectiveness of each of these initial scoring functions is discussed. Overall, the ability of the MM-PBSA rescoring function to (i) regenerate the set of X-ray complexes when docking the bound conformation of the ligand, (ii) regenerate the X-ray complexes when docking conformationally expanded databases for each ligand which include "conformation decoys" of the ligand, and (iii) enrich known actives in a virtual screen for the mineralocorticoid receptor in the presence of "ligand decoys" is assessed. While a pharmacophore-based molecular docking approach, PhDock, is used to carry out the docking, the results are expected to be general to use with any docking method.
smartAR: a proposal of IP micro-mobility protocol for single and simultaneous movements scenario

In this paper, we analyze three solutions for the micro-mobility problem. The SIP solution requires SIP domains; the SCTP solution requires "slightly" update of the protocol stack of the devices. The third solution is based on the fact that in a subnetwork the access router is always present. Consequently, in our opinion it is better to equip the access router with more "intelligence" in order to handle all mobility scenarios. In this work, we firstly compare these solutions against the problems of both single and simultaneous movements of the end peers. Then, we show the basic mechanisms of our enhanced access router, we called as smartAR. By numerical simulations, we argue that smartAR can be a candidate for optimal solution in term of hand-off delay cost and network complexity.
Identifying Time-Lagged Gene Clusters on Gene Expression Data

Motivation: Analysis of gene expression data can provide insights into the time-lagged co-regulations of genes/gene clusters. However, existing methods such as Event Method and Edge Detection Method are inefficient as they only compare two genes each time. More importantly, they lose some important information due to their scoring criterion. In this paper, we propose an efficient algorithm to identify time-lagged co-regulated gene clusters. The algorithm facilitates localized comparison and processes several genes simultaneously to generate detailed and complete time-lagged information between genes/gene clusters. Results: We experimented with the time series Yeast gene dataset and compared our scheme with the Event Method. Our results show that our scheme is not only efficient, but delivers more reliable and detailed information of timelagged co-regulation between genes/gene clusters. Availability: The software is available upon request. Contact: {jiliping,tankl}@comp.nus.edu.sg Supplementary Information: Supplementary tables and figures for this paper can be found at http://www.comp.nus.edu.sg/∼jiliping/p2.htm.
Limb immobilization alters muscle activation patterns during a fatiguing isometric contraction

The purpose of the study was to determine the role of excitation–contraction coupling in the increased endurance time for low‐force contractions after 4 weeks of elbow joint immobilization. Twelve subjects participated in a protocol that required immobilization of the elbow joint in a fiberglass cast for 4 weeks, and 4 subjects acted as controls. Measurements of muscle strength, contractile properties, and fatigability were performed before and after 4 weeks of limb immobilization, and after 4 weeks of recovery. The immobilization intervention produced significant reductions in the daily activity of the elbow flexor muscles, a 21% decline in the maximum voluntary contraction (MVC) force, and a 31% decrease in the maximum load that could be lifted once. Seven of the immobilized subjects exhibited an unusual pattern of muscle activity during the fatiguing contraction after immobilization, which was associated with an increase in the endurance time of the elbow flexor muscles (mean = 220%) in these subjects. The unusual pattern of muscle activity involved lower relative activity of the brachialis muscle, no increase in the amplitude of the electromyogram (EMG) for the elbow flexor muscles, and intermittent rather than continuous EMG. In contrast, the force–frequency relationship of biceps brachii was not altered by immobilization in these subjects, suggesting that adaptations in excitation–contraction coupling were not the primary cause of the prolonged endurance time after immobilization. Rather, the results suggest that the prolonged endurance time exhibited by some subjects after immobilization was largely due to adaptations within the nervous system. © 2000 John Wiley & Sons, Inc. Muscle Nerve 23: 1381–1392, 2000.
Credible ratings

This paper considers a model of a rating agency with multiple clients, in which each client has a separate market that forms a belief about the quality of the client after the agency issues a rating. When the clients are rated separately (individ-ual rating), the credibility of a good rating in an inﬂationary equilibrium of the signaling game is limited by the incentive of the agency to exaggerate the quality of the client. With a centralized rating, the agency rates all clients together and shares the rating information among all markets. This allows the agency to coordinate the ratings and achieve a higher average level of credibility for its good ratings than with individual rating. Under decentralized rating, the ratings are again shared among all markets, but each client is rated by a self-interested rater of the agency with no access to the quality information of other clients. When the underlying qualities of the clients are correlated, decentralized rating leads to a smaller degree of rating inﬂation and hence a greater level of credibility than under individual rating. Comparing centralized rating with decentralized rating, we ﬁnd that centralized rating dominates decentralized rating for the agency when the underlying qualities are weakly correlated, but the reverse holds when the qualities are strongly correlated.
A scalable monitoring approach for service level agreements validation

In order to detect violations of end-to-end service level agreements (SLA) and to isolate trouble links and nodes based on a unified framework, managers of a service provider network need to gather quality of service (QoS) measurements from multiple nodes in the network. For a network carrying over thousands of flows with end-to-end SLAs, the information exchanged between network nodes and a central network management system (NMS) could be substantial. Moreover in situations where only, a small number of flows violate their respective SLAs, simple polling mechanisms can lead to huge unnecessary overhead in identifying these ill-behaved flows. We propose an algorithm called (ARM) (Aggregation and Refinement based Monitoring) to reduce the amount of information exchange. (ARM) uses a histogram-based dynamic QoS data aggregation/refinement technique at each network node and a reasoning engine at the NMS to minimized the amount of data exchange between network nodes and NMS. (ARM) not only reduces unnecessary reporting through selective refinement, it also performs well across a wide range of traffic loads. Our simulation results show that (ARM) is at least an order of magnitude more efficient than a simple polling scheme. It also outperforms two centralized highly optimized schemes that cannot be implemented in practice.
An Alternative Path for the Evolution of Biological Nitrogen Fixation

Nitrogenase catalyzed nitrogen fixation is the process by which life converts dinitrogen gas into fixed nitrogen in the form of bioavailable ammonia. The most common form of nitrogenase today requires a complex metal cluster containing molybdenum (Mo), although alternative forms exist which contain vanadium (V) or only iron (Fe). It has been suggested that Mo-independent forms of nitrogenase (V and Fe) were responsible for N2 fixation on early Earth because oceans were Mo-depleted and Fe-rich. Phylogenetic- and structure-based examinations of multiple nitrogenase proteins suggest that such an evolutionary path is unlikely. Rather, our results indicate an evolutionary path whereby Mo-dependent nitrogenase emerged within the methanogenic archaea and then gave rise to the alternative forms suggesting that they arose later, perhaps in response to local Mo limitation. Structural inferences of nitrogenase proteins and related paralogs suggest that the ancestor of all nitrogenases had an open cavity capable of binding metal clusters which conferred reactivity. The evolution of the nitrogenase ancestor and its associated bound metal cluster was controlled by the availability of fixed nitrogen in combination with local environmental factors that influenced metal availability until a point in Earth’s geologic history where the most desirable metal, Mo, became sufficiently bioavailable to bring about and refine the solution (Mo-nitrogenase) we see perpetuated in extant biology.
Morphological and Functional Alterations in Ventricular Myocytes From Male Transgenic Mice With Hypertrophic Cardiomyopathy

Abstract— Familial hypertrophic cardiomyopathy (FHC) is a human genetic disorder caused by mutations in sarcomeric proteins. It is generally characterized by cardiac hypertrophy, fibrosis, and myocyte disarray. A transgenic mouse model of FHC with mutations in the actin-binding domain of the &agr;-myosin heavy chain (MyHC) gene displays many phenotypes similar to human FHC. At 4 months, male transgenic (TG) mice present with concentric cardiac hypertrophy that progresses to dilation with age. Accompanying this latter morphological change is systolic and diastolic dysfunction. Left ventricular (LV) myocytes from male TG and wild-type (WT) littermates at 5 and 12 months of age were isolated and used for morphological and functional studies. Myocytes from 5- and 12-month-old TG animals had shorter sarcomere lengths compared with WT. This sarcomere length difference was abolished in the presence of 2,3-butanedione monoxime, suggesting that the basal level of contractile element activation was increased in TG myocytes. Myocytes from 12-month-old TG mice were significantly longer than those from age-matched WT controls, and TG myocytes exhibited Z-band disorganization. When cells were paced at 0.5 Hz, TG myocyte relengthening and the fall in intracellular [Ca2+] were slowed when compared with cells from age-matched WT controls. Moreover, an increased amount of &bgr;-myosin heavy chain protein was found in hearts from TG compared with WT. Thus, myocytes from the &agr;-MyHC TG mouse model display many morphological and functional abnormalities that may help explain the LV dysfunction seen in this TG mouse model of FHC.
MGL Receptor and Immunity: When the Ligand Can Make the Difference

C-type lectin receptors (CLRs) on antigen-presenting cells (APCs) facilitate uptake of carbohydrate antigens for antigen presentation, modulating the immune response in infection, homeostasis, autoimmunity, allergy, and cancer. In this review, we focus on the role of the macrophage galactose type C-type lectin (MGL) in the immune response against self-antigens, pathogens, and tumor associated antigens (TAA). MGL is a CLR exclusively expressed by dendritic cells (DCs) and activated macrophages (MØs), able to recognize terminal GalNAc residues, including the sialylated and nonsialylated Tn antigens. We discuss the effects on DC function induced throughout the engagement of MGL, highlighting the importance of the antigen structure in the modulation of immune response. Indeed modifying Tn-density, the length, and steric structure of the Tn-antigens can result in generating immunogens that can efficiently bind to MGL, strongly activate DCs, mimic the effects of a danger signal, and achieve an efficient presentation in HLA classes I and II compartments.
A Resource-Search and Routing Algorithm within PCDN Autonomy Area

This paper studied a new type of network model; it is formed by the dynamic autonomy area, the structured source servers and the proxy servers. The new network model satisfies the dynamics within the autonomy area, where each node undertakes different tasks according to their different abilities, to ensure that each node has the load ability fit its own; it does not need to exchange information via the central servers, so it can carry out the efficient data transmission and routing search. According to the highly dynamics of the autonomy area, we established dynamic tree structure-proliferation system routing and resource-search algorithms and simulated these algorithms. Test results show the performance of the proposed network model and the algorithms are very stable.
ADAPTING WESTERN LANGUAGE RECOGNIZER FOR CHINESE RECOGNITION

In this paper, we will present a speaker-independent Mandarin Chinese recognition system. The system is designed to adapt an existing Western language recognizer in order to support Chinese recognition. We will only focus on the stage of acoustic recognition. Since Chinese has its special characteristic (a tonal language) comparing with Western languages, we will first develop a system special for tone recognition using pitch information. Then we will present two methods for the integration of tone information into the existing system.
MultiCalib: national-scale traffic model calibration in real time with multi-source incomplete data

Real-time traffic modeling at national scale is essential to many applications, but its calibration is extremely challenging due to its large spatial and fine temporal coverage. The existing work mostly is focused on urban-scale calibration with complete field data from single data sources (e.g., loop sensors or taxis), which cannot be generalized to national scale, because complete single-source field data at national scale are almost impossible to obtain. To address this challenge, in this paper, we design MultiCalib, a model calibration framework to optimize traffic models based on multiple incomplete data sources at national scale in real time. Instead of naively combining multi-source data, we theoretically formulate a multi-source model calibration problem based on real-world contexts and multi-view learning. More importantly, we implement and evaluate MultiCalib with two heterogeneous nationwide vehicle networks with 340,000 vehicles to infer traffic conditions on 36 expressways and 119 highways, along with 4 cities across China. The results show that MultiCalib outperforms state-of-the- art calibration by 25% on average with same input data.