Miracle-dz/UniFAR-FTUs huggingface dataset:
Formation of a N2-dG:N2-dG Carbinolamine DNA Cross-link by the trans-4-Hydroxynonenal-Derived (6S,8R,11S) 1,N2-dG Adduct

Michael addition of trans-4-hydroxynonenal (HNE) to deoxyguanosine yields diastereomeric 1,N2-dG adducts in DNA. When placed opposite dC in the 5′-CpG-3′ sequence, the (6S,8R,11S) diastereomer forms a N2-dG:N2-dG interstrand cross-link [Wang, H. ; Kozekov, I. D. ; Harris, T. M. ; Rizzo, C. J. J. Am. Chem. Soc.2003, 125, 5687–5700]. We refined its structure in 5′-d(G1C2T3A4G5C6X7A8G9T10C11C12)-3′·5′-d(G13G14A15C16T17C18Y19C20T21A22G23C24)-3′ [X7 is the dG adjacent to the C6 carbon of the cross-link or the α-carbon of the (6S,8R,11S) 1,N2-dG adduct, and Y19 is the dG adjacent to the C8 carbon of the cross-link or the γ-carbon of the HNE-derived (6S,8R,11S) 1,N2-dG adduct; the cross-link is in the 5′-CpG-3′ sequence]. Introduction of 13C at the C8 carbon of the cross-link revealed one 13C8→H8 correlation, indicating that the cross-link existed predominantly as a carbinolamine linkage. The H8 proton exhibited NOEs to Y19 H1′, C20 H1′, and C20 H4′, orienting it toward the complementary strand, consistent with the (6S,8R,11S) configuration. An NOE was also observed between the HNE H11 proton and Y19 H1′, orienting the former toward the complementary strand. Imine and pyrimidopurinone linkages were excluded by observation of the Y19N2H and X7 N1H protons, respectively. A strong H8→H11 NOE and no 3J(13C→H) coupling for the 13C8–O–C11–H11 eliminated the tetrahydrofuran species derived from the (6S,8R,11S) 1,N2-dG adduct. The (6S,8R,11S) carbinolamine linkage and the HNE side chain were located in the minor groove. The X7N2 and Y19N2 atoms were in the gauche conformation with respect to the linkage, maintaining Watson–Crick hydrogen bonds at the cross-linked base pairs. A solvated molecular dynamics simulation indicated that the anti conformation of the hydroxyl group with respect to C6 of the tether minimized steric interaction and predicted hydrogen bonds involving O8H with C20O2 of the 5′-neighbor base pair G5·C20 and O11H with C18O2 of X7·C18. These may, in part, explain the stability of this cross-link and the stereochemical preference for the (6S,8R,11S) configuration.
Fast alternating volume maximization algorithm for blind separation of non-negative sources

We recently reported an iterative non-negative blind source separation (nBSS) method, called convex analysis of mixtures of nonnegative sources via alternating volume maximization (CAMNSAVM) [1], and demonstrated that it provides promising separation performance in image analysis. Nonetheless, the amount of data may be quite large in practical applications, and this may limit the real-time applicability of CAMNS-AVM. In this paper, we propose a fast CAMNS-AVM algorithm involving three complexity reduction methods, specifically problem equivalence, redundant constraints removal, and customized algorithm implementation. The problem equivalence provides sufficiency in solving one linear program (LP) for each partial volume maximization problem, rather than the two LPs required by the original CAMNS-AVM. Then, we remove redundant constraints of each LP involved in CAMNS-AVM by using Quickhull algorithm to enumerate all the extreme points of the constraint-set-constructed convex hull. Finally, we implement a customized primal-dual interior-point method (IPM) for LP. Some Monte Carlo simulation results demonstrate that the fast CAMNS-AVM algorithm is thirty times more computationally efficient than the original CAMNS-AVMalgorithm, without any performance loss.
Pre-echo reduction in the ITU-T G.729.1 embedded coder

Pre-echo is a well-known artefact of transform coding at low bit rates. In this paper we present a new method to address this problem. The input signal is assumed to be coded in two stages: in time domain first, and then in transform domain. This is for instance the case in CELP+transform embedded coding. The first stage reconstructs a signal that is usually free of pre-echo. Therefore transform coding can exploit this reconstructed signal as side information for pre-echo detection and reduction. The proposed method is implemented as an adaptive limiter at the decoder side and does not need transmission of auxiliary data. It is part of the recently standardized ITU-T G.729. 1 coder, in which it is used in two separate subbands. Experimental test results show that this method has a significant impact on quality in G.729. 1 with very small complexity.
Protective Properties of Tin‐ and Manganese‐Centered Porphyrins Against Hydrogen Peroxide‐Mediated Injury in Rat Astroglial Cells

Abstract: Tin‐mesoporphyrin (tin‐mp), a potent inhibitor of heme oxygenase, and manganese (III) tetrakis(1‐methyl‐4‐pyridyl)porphyrin (MnTMPyP), a potent superoxide dismutase mimetic, reduced H2O2 toxicity in cultures of transformed rat astroglial cells if added 30 min before, or at the same time as, H2O2. Reduced toxicity was not observed if treatment was delayed for 60 min, the time by which H2O2 was essentially eliminated from cultures. Coadministration of tin‐mp and MnTMPyP did not increase protection over either compound administered individually. Tin‐mp, but not MnTMPyP, was stable in culture. MnCl2 was not protective, suggesting that protection by MnTMPyP was not dependent on manganous ion, a by‐product of MnTMPyP breakdown. Protection by tin‐mp and MnTMPyP was not associated with metalloporphyrin‐mediated induction of heme oxygenase‐1 or with changes in heme oxygenase‐2 on western blots. Whereas protective concentrations of tin‐mp did not have superoxide dismutase‐mimetic properties in vitro, protective concentrations of MnTMPyP partially inhibited heme oxygenase. The data support the hypothesis that heme oxygenase inhibition is protective against acute oxidative injury.
Association of HLA alleles with Plasmodium falciparum severity in Malian children

Pre-erythrocytic immunity to Plasmodium falciparum malaria is likely to be mediated by T-cell recognition of malaria epitopes presented on infected host cells via class I and II major histocompatibility complex (MHC) antigens. To test for associations of human leukocyte antigen (HLA) alleles with disease severity, we performed high-resolution typing of HLA class I and II loci and compared the distributions of alleles of HLA-A, -B, -C and -DRB1 loci in 359 Malian children of Dogon ethnicity with uncomplicated or severe malaria. We observed that alleles A*30:01 and A*33:01 had higher frequency in the group of patients with cerebral disease compared to patients with uncomplicated disease [A*30:01: gf = 0.2031 vs gf = 0.1064, odds ratio (OR) = 3.17, P = 0.004, confidence interval (CI) (1.94–5.19)] and [A*33:01: gf = 0.0781 vs gf = 0.0266, 4.21, P = 0.005, CI (1.89–9.84)], respectively. The A*30:01 and A*33:01 alleles share some sequence motifs and A*30:01 appears to have a unique peptide binding repertoire compared to other A*30 group alleles. Computer algorithms predicted malaria peptides with strong binding affinity for HLA-A*30:01 and HLA-A*33:01 but not to closely related alleles. In conclusion, we identified A*30:01 and A*33:01 as potential susceptibility factors for cerebral malaria, providing further evidence that polymorphism of MHC genes results in altered malaria susceptibility.
Fundamentals of Throughput Maximization With Random Arrivals for M2M Communications

For wireless systems in which randomly arriving devices attempt to transmit a fixed payload to a central receiver, we develop a framework to characterize the system throughput as a function of arrival rate and per-device data rate. The framework considers both coordinated transmission (where devices are scheduled) and uncoordinated transmission (where devices communicate on a random access channel and a provision is made for retransmissions). Our main contribution is a novel characterization of the optimal throughput for the case of uncoordinated transmission and a strategy for achieving this throughput that relies on overlapping transmissions and joint decoding. Simulations for a noise-limited cellular network show that the optimal strategy provides a factor of four improvement in throughput compared with slotted ALOHA. We apply our framework to evaluate more general system-level designs that account for overhead signaling. We demonstrate that, for small payload sizes relevant for machine-to-machine (M2M) communications (200 bits or less), a one-stage strategy, where identity and data are transmitted optimally over the random access channel, can support at least twice the number of devices compared with a conventional strategy, where identity is established over an initial random-access stage and data transmission is scheduled.
Plenoptic path and its applications

In this paper, we present a method for acquiring, spatially filtering and viewing annotated videos captured with a full field of view multihead camera moving along a path. We describe our tailored egomotion recovery algorithm used for calculating the trajectory path of the panoramic head. We then focus on sampling the plenoptic path efficiently according to geometric visibility events. Appropriate samplings allow us to filter and compress the panoramic images avoiding some redundancies in the image database. We present several applications and results of plenoptic paths either obtained from indoor shootings or perfectly rendered by computer graphics scripts.
CONSTRUCTING ONLINE TESTABLE CIRCUITS USING REVERSIBLE LOGIC

Testable fault tolerant system design has become vital for many safety critical applications. On the other hand, reversible logic is gaining interest in the recent past due to its less heat dissipating characteristics. Any Boolean logic function can be implemented using reversible gates. This paper proposes a technique to convert any reversible logic gate to a testable gate that is also reversible. The resultant reversible testable gate can detect online any single bit errors that include Single Stuck Faults and Single Event Upsets S.Karp et.al (1993). The proposed technique is illustrated using an example that converts a reversible decoder circuit to an online testable reversible decoder circuit.
FreeMMG: a hybrid peer-to-peer and client-server model for massively multiplayer games

A Massively Multiplayer Game (MMG) is an Internet-based distributed game (or multiplayer game) that supports a large amount of simultaneous players interacting, in real-time, in a persistent virtual world. Practically all of today's MMGs employ a client-server distribution approach where the client is trusted only to send interaction requests and receive updates about the current state of the virtual world (position updates, etc). One of the main reasons that drive this choice of a strongly centralized architecture is the protection it offers against player cheating. Examples of successful MMGs that routinely support several thousand simultaneous players include EverQuest and Lineage.
A location-based friend-assisted coding-aware routing protocol for wireless multihop networks

In this paper, we propose a location-based friend-assisted coding-aware routing protocol (LFCR) for wireless multihop networks. To achieve improved network throughout, LFCR performs inter-flow network coding based routing with the assistance of location information. Specifically, LFCR combines friend-assisted path discovery and coding-aware routing. Further, when making decision on next hop selection, LFCR takes into account both coding opportunities and forwarding progress in next hop selection and attempts to make a good tradeoff between them. Simulation results show that LFCR significantly outperforms existing work in terms of network throughput, packet delivery ratio, and coding frequency.
Nucleus-specific translation and assembly of acetylcholinesterase in multinucleated muscle cells

Multinucleated skeletal muscle fibers synthesize cell surface and secreted oligomeric forms of acetylcholinesterase (AChE) that accumulate at specialized locations on the cell surface, such as sites of nerve-muscle contact. Using allelic variants of the AChE polypeptide chains as genetic markers, we show that nuclei homozygous for either the alpha or beta alleles residing in chimeric myotubes preferentially translate their AChE mRNAs on their respective ERs. These results indicate that the events of transcription, translation, and assembly of this membrane protein are compartmentalized into nuclear domains in multinucleated cells, and provide the structural basis for the possible localized expression and regulation of synaptic components at the neuromuscular junctions of vertebrate skeletal muscle fibers.
Sidelobe Suppression and Agile Transmission Techniques for Multicarrier-based Cognitive Radio Systems

With the advent of new high data rate wireless applications, as well as growth of existing wireless services, demand for additional bandwidth is rapidly increasing. Existing spectrum allocation policies of the Federal Communications Commission (FCC) prohibits unlicensed access to licensed spectrum, constraining them instead to several heavily populated, interference-prone frequency bands, which causes spectrum scarcity. However, it has been shown by several spectrum measurement campaigns that the current licensed spectrum usage across time and frequency is inefficient. Therefore, a concept of unlicensed users temporarily “borrowing” spectrum from incumbent license holders to improve the spectrum utilization, called “spectrum pooling”, which is based on dynamic spectrum access (DSA), is proposed. Cognitive radio is a communication paradigm that employs software-defined radio technology in order to perform DSA and offers versatile, powerful and portable wireless transceivers. Orthogonal frequency division multiplexing (OFDM) is a promising candidate for cognitive radio transmission. OFDM supports high data rates that are robust to channel impairments. In addition, some subcarriers can be deactivated which constitutes a non-contiguous OFDM (NC-OFDM) transmission. However, one of the biggest problems for OFDM transmission is high out-of-band (OOB) radiation, which is caused by sinc-type function representing the symbols during one time constant. Thus, high sidelobe may occur that will interfere with neighboring transmissions. This thesis presents two novel techniques for NC-OFDM sidelobe suppression. Another concern about cognitive radio systems is that the influence of frequency-selective fading channel. Consequently, this thesis also presents a combined approach employing power loading, bit allocation and sidelobe suppression for OFDM-based cognitive radio systems optimization.
Strategies for Exploiting Independent Cloud Implementations of Biometric Experts in Multibiometric Scenarios

Cloud computing represents one of the fastest growing areas of technology and offers a new computing model for various applications and services. This model is particularly interesting for the area of biometric recognition, where scalability, processing power, and storage requirements are becoming a bigger and bigger issue with each new generation of recognition technology. Next to the availability of computing resources, another important aspect of cloud computing with respect to biometrics is accessibility. Since biometric cloud services are easily accessible, it is possible to combine different existing implementations and design new multibiometric services that next to almost unlimited resources also offer superior recognition performance and, consequently, ensure improved security to its client applications. Unfortunately, the literature on the best strategies of how to combine existing implementations of cloud-based biometric experts into a multibiometric service is virtually nonexistent. In this paper, we try to close this gap and evaluate different strategies for combining existing biometric experts into a multibiometric cloud service. We analyze the (fusion) strategies from different perspectives such as performance gains, training complexity, or resource consumption and present results and findings important to software developers and other researchers working in the areas of biometrics and cloud computing. The analysis is conducted based on two biometric cloud services, which are also presented in the paper.
Maximal metabolic rates during voluntary exercise, forced exercise, and cold exposure in house mice selectively bred for high wheel-running

SUMMARY Selective breeding for high wheel-running activity has generated four lines of laboratory house mice (S lines) that run about 170% more than their control counterparts (C lines) on a daily basis, mostly because they run faster. We tested whether maximum aerobic metabolic rates (V̇O2max) have evolved in concert with wheel-running, using 48 females from generation 35. Voluntary activity and metabolic rates were measured on days 5+6 of wheel access (mimicking conditions during selection), using wheels enclosed in metabolic chambers. Following this, V̇O2max was measured twice on a motorized treadmill and twice during cold-exposure in a heliox atmosphere (HeO2). Almost all measurements, except heliox V̇O2max, were significantly repeatable. After accounting for differences in body mass (S<C) and variation in age at testing, S and C did not differ in V̇O2max during forced exercise or in heliox, nor in maximal running speeds on the treadmill. However, running speeds and V̇O2max during voluntary exercise were significantly higher in S lines. Nevertheless, S mice never voluntarily achieved the V̇O2max elicited during their forced treadmill trials, suggesting that aerobic capacity per se is not limiting the evolution of even higher wheel-running speeds in these lines. Our results support the hypothesis that S mice have genetically higher motivation for wheel-running and they demonstrate that behavior can sometimes evolve independently of performance capacities. We also discuss the possible importance of domestication as a confounding factor to extrapolate results from this animal model to natural populations.
Validation of reflex indicators for measuring vitality and predicting the delayed mortality of wild coho salmon bycatch released from fishing gears

Summary 1. Effective management of fish and wildlife populations benefits from an understanding of the effects of stressors on individual physiology. While physiological knowledge can provide a mechanistic understanding of organismal responses, its applied utility is limited because it cannot easily be used by stakeholders. 2. Reflex action mortality predictors (RAMP) is a method that involves checking for the presence or absence of natural animal reflexes to generate a condition (RAMP) score in response to stressors and to predict fate. The method has previously been validated with fishes in artificial laboratoryand field-based holding studies as a responsive measure of fisheries capture stress and a predictor of delayed mortality, but has not been evaluated in the wild. 3. We used radio telemetry to monitor migration success of 50 endangered coho salmon Oncorhynchus kisutch following incidental capture in an aboriginal beach seine fishery in the lower Fraser River (Canada). RAMP was used to measure the condition of fish at release and to predict migration success following capture. Biopsy of an additional 43 coho profiled physiological condition at time of release. 4. Individuals with greater reflex impairment (higher RAMP scores) at release experienced significantly higher rates of migration failure. RAMP scores were also significantly correlated with fishery handling time. Plasma variables showed that captured coho had experienced physiological stress characteristic of exhaustive exercise and hypoxia, with significantly elevated cortisol and lactate values for fish entangled longer in fishing gear. 5. Synthesis and applications. This is the first validation of RAMP in a wild setting. Based on our findings, fishers could use the method and make adjustments in fishing behaviour in real-time to improve fish condition and reduce the mortality of bycatch, and conservation practitioners could monitor animal condition and identify problems that deserve management attention. RAMP is an easy, rapid and inexpensive approach to predicting mortality and measuring vitality and performed better than traditional physiological tools that cannot easily be used by stakeholders.
GABAB Mediated Regulation of Sympathetic Preganglionic Neurons: Pre- and Postsynaptic Sites of Action

Modulatory influences on sympathetic nervous system activity are diverse and far reaching, acting at select points in the complex pathways controlling sympathetic outflow to enable subtle changes or more global effects. Changes in the degree of sympathetic neuromodulation can have serious consequences on homeostatic variables such as heart rate, blood pressure and gut motility. At the level of the spinal cord, the sympathetic preganglionic neurons (SPNs) can be modulated by activation of presynaptic GABAB heteroreceptors on glutamatergic terminals and by postsynaptic GABAB receptors. Here we show that a low concentration of the GABAB agonist baclofen (1 μM) attenuated GABAergic inhibitory postsynaptic potentials in SPNs elicited from stimulation of either the central autonomic area or descending fibers in the lateral funiculus. This low baclofen concentration also elicited three categories of postsynaptic response: a large hyperpolarization with a decrease in input resistance, a moderate hyperpolarization with no change in input resistance and no response. Using cesium-loaded, tetraethylammonium chloride containing electrodes (to block potassium conductance), baclofen elicited moderate hyperpolarizations with no change in input resistance in 50% of SPNs; the remainder were unaffected. These modest hyperpolarizations were reduced in Ca2+ free solution or cadmium. Hyperpolarizing responses were also observed in interneurons in the vicinity of SPNs. These studies provide the first evidence for GABAB autoreceptors involved in inhibitory GABAergic transmission onto SPNs and for postsynaptic GABAB receptors on interneurons. The data also indicate that there is heterogeneity in the postsynaptic responses of SPNs.
Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells*

Transcription factors of the nuclear factor of activated T cell (NFAT) family are essential for antigen-specific T cell activation and differentiation. Their cooperative DNA binding with other transcription factors, such as AP1 proteins (FOS, JUN, and JUNB), FOXP3, IRFs, and EGR1, dictates the gene regulatory action of NFATs. To identify as yet unknown interaction partners of NFAT, we purified biotin-tagged NFATc1/αA, NFATc1/βC, and NFATc2/C protein complexes and analyzed their components by stable isotope labeling by amino acids in cell culture-based mass spectrometry. We revealed more than 170 NFAT-associated proteins, half of which are involved in transcriptional regulation. Among them are many hitherto unknown interaction partners of NFATc1 and NFATc2 in T cells, such as Raptor, CHEK1, CREB1, RUNX1, SATB1, Ikaros, and Helios. The association of NFATc2 with several other transcription factors is DNA-dependent, indicating cooperative DNA binding. Moreover, our computational analysis discovered that binding motifs for RUNX and CREB1 are found preferentially in the direct vicinity of NFAT-binding motifs and in a distinct orientation to them. Furthermore, we provide evidence that mTOR and CHEK1 kinase activity influence NFAT's transcriptional potency. Finally, our dataset of NFAT-associated proteins provides a good basis to further study NFAT's diverse functions and how these are modulated due to the interplay of multiple interaction partners.