Miracle-dz/UniFAR-FTUs huggingface dataset:
Starvation and recovery in the deep‐sea methanotroph Methyloprofundus sedimenti

In the deep ocean, the conversion of methane into derived carbon and energy drives the establishment of diverse faunal communities. Yet specific biological mechanisms underlying the introduction of methane‐derived carbon into the food web remain poorly described, due to a lack of cultured representative deep‐sea methanotrophic prokaryotes. Here, the response of the deep‐sea aerobic methanotroph Methyloprofundus sedimenti to methane starvation and recovery was characterized. By combining lipid analysis, RNA analysis, and electron cryotomography, it was shown that M. sedimenti undergoes discrete cellular shifts in response to methane starvation, including changes in headgroup‐specific fatty acid saturation levels, and reductions in cytoplasmic storage granules. Methane starvation is associated with a significant increase in the abundance of gene transcripts pertinent to methane oxidation. Methane reintroduction to starved cells stimulates a rapid, transient extracellular accumulation of methanol, revealing a way in which methane‐derived carbon may be routed to community members. This study provides new understanding of methanotrophic responses to methane starvation and recovery, and lays the initial groundwork to develop Methyloprofundus as a model chemosynthesizing bacterium from the deep sea.
Link quality based association mechanism in IEEE 802.11 h compliant wireless LANs

When deploying IEEE 802.11 LANs, it is important from the performance perspective to associate the users to the available access points in an efficient way. The efficiency of an association relates to the average rates that the users can achieve with the particular association. Current implementations of 802.11 LANs do not take into account physical channel information in making association decisions. This usually results in much lower user rates than what can be ideally achieved. In this paper, we propose a new user association control framework for infrastructure-based wireless LANs compliant with the IEEE 802.11h specification in light of these issues. By using the new information that is implicitly provided by 802.11h specifications, our framework, takes into account the channel conditions when associating stations with the access points. Simulation results show that the proposed schemes improve the throughput of the network, compared with the static allocation without channel quality information. This improvement is significant, especially in an environment where external interference is present.
Enzymatic Characterization of 5-Methylthioribose 1-Phosphate Isomerase from Bacillus subtilis

The product of the mtnA gene of Bacillus subtilis catalyzes the isomerization of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). The catalysis of MtnA is a novel isomerization of an aldose phosphate harboring a phosphate group on the hemiacetal group. This enzyme is distributed widely among bacteria through higher eukaryotes. The isomerase reaction analyzed using the recombinant B. subtilis enzyme showed a Michaelis constant for MTR-1-P of 138 μM, and showed that the maximum velocity of the reaction was 20.4 μmol min−1 (mg protein)−1. The optimum reaction temperature and reaction pH were 35 °C and 8.1. The activation energy of the reaction was calculated to be 68.7 kJ mol−1. The enzyme, with a molecular mass of 76 kDa, was composed of two subunits. The equilibrium constant in the reversible isomerase reaction [MTRu-1-P]/[MTR-1-P] was 6. We discuss the possible reaction mechanism.
Refined crystal structures of "aged" and "non-aged" organophosphoryl conjugates of gamma-chymotrypsin.

"Aged" organophosphoryl conjugates of serine hydrolases differ from the corresponding "non-aged" conjugates in their striking resistance to nucleophilic reactivation. The refined X-ray structures of "aged" and "non-aged" organophosphoryl conjugates of gamma-chymotrypsin were compared in order to understand the molecular basis for this resistance of "aged" conjugates. "Aged" and "non-aged" crystalline organophosphoryl-gamma-chymotrypsin conjugates were obtained by prolonged soaking of native gamma-chymotrypsin crystals with appropriate organophosphates. Thus, a representative "non-aged" conjugate, diethylphosphoryl-gamma-chymotrypsin, was obtained by soaking native crystals with paraoxon (diethyl-p-nitrophenyl phosphate), and a closely related "aged" conjugate, monoisopropyl-gamma-chymotrypsin, was obtained by soaking with diisopropylphosphorofluoridate. In both crystalline conjugates, the refined structures clearly reveal a high occupancy of the active site by the appropriate organophosphoryl moiety within covalent bonding distance of Ser195 O gamma. Whereas in the "non-aged" conjugate both ethyl groups can be visualized clearly, in the putative "aged" conjugate, as expected, only one isopropyl group is present. There is virtually no difference between the "aged" and "non-aged" conjugates either with respect to the conformation of the polypeptide backbone as a whole or with respect to the positioning of the side-chains within the active site. In the "aged" conjugate, however, close proximity (2.6 A) of the negatively charged phosphate oxygen atom of the dealkylated organophosphoryl group to His57 N epsilon 2 indicates the presence of a salt bridge between these two moieties. In contrast, in the "non-aged" conjugate the DEP moiety retains its two alkyl groups; thus, lacking a negative oxygen atom, it does not enter into such a charge-charge interaction and its nearest oxygen atom is 3.6 A away from His57 N epsilon 2. It is suggested that steric constraints imposed by the salt bridge in the "aged" conjugate lie at the basis of its resistance to reactivation.
Efficient Video Encryption by Image Key Based on Hyper-chaos System

In this paper, an efficient video encryption scheme is constructed by image key and is based on hyper-chaos system. The chaotic lattices are used to generate pseudorandom sequences and then selected pixel and bit pixel of image key encrypt frame blocks one by one. By iterating chaotic maps for certain times, the generated pseudorandom sequences obtain high initial-value sensitivity and good randomness. The pseudorandom-bits in each lattice are used to select pixel and bit pixel of image key and then encrypt the Direct Current coefficient (DC) and the signs of the Alternating Current coefficients (ACs). Theoretical analysis and experimental results show that the scheme has good cryptographic security and perceptual security, and it does not affect the compression efficiency apparently. These properties make the scheme a suitable choice for practical applications.
Roles of DNA-dependent protein kinase and ATM in cell-cycle-dependent radiation sensitivity in human cells

Purpose : The roles of DNA-dependent protein kinase (DNA-PK) and ATM in the cell-cycle-dependent radiosensitivity in human cells were investigated. Methods and materials : A DNA-PK activity-deficient human glioblastoma cell line M059J, ataxia telangiectasia cell lines AT3BISV and AT5BIVA, and control cell lines were used. Wortmannin inhibited DNA-PK and ATM activities. Cells were synchronized by hydroxyurea. Progression through the cell cycle was analysed by flow cytometry. Results : M059J exhibited hyper-radiosensitivity throughout the cell cycle, with extreme hyper-radiosensitivity in G to early S-phase compared with the control cell line M059K. AT3BISV and AT5BIVA exhibited hyper-radiosensitivity throughout the cell cycle but showed a similar pattern of cell-cycle-dependent radiosensitivity to that observed in LM217 or HeLa cells. In AT3BISV and AT5BIVA, radiosensitization by wortmannin was observed throughout the cell cycle and was most prominent in G 1 to early S-phase. Wortmannin did not sensitize M059J to ionizing radiation in any cell-cycle phase. DNA-PK activities were not different throughout the cell cycle. Conclusion : The results suggest that (1) non-homologous endjoining plays a dominant role in G 1 to early S-phase and a minor role in late S to G 2 -phase in repairing DNA double-strand breaks, (2) the role of ATM in repairing double-strand breaks may be almost cell-cycle-independent and (3) the dominant role of non-homologous end-joining during G 1 to early S-phase is not due to cell-cycle-dependent fluctuations in DNA-PK activity.
Mismatched Decoding: Error Exponents, Second-Order Rates and Saddlepoint Approximations

This paper considers the problem of channel coding with a given (possibly suboptimal) maximum-metric decoding rule. A cost-constrained random-coding ensemble with multiple auxiliary costs is introduced, and is shown to achieve error exponents and second-order coding rates matching those of constant-composition random coding, while being directly applicable to channels with infinite or continuous alphabets. The number of auxiliary costs required to match the error exponents and second-order rates of constant-composition coding is studied, and is shown to be at most two. For independent identically distributed random coding, asymptotic estimates of two well-known non-asymptotic bounds are given using saddlepoint approximations. Each expression is shown to characterize the asymptotic behavior of the corresponding random-coding bound at both fixed and varying rates, thus unifying the regimes characterized by error exponents, second-order rates, and moderate deviations. For fixed rates, novel exact asymptotics expressions are obtained to within a multiplicative 1+o(1) term. Using numerical examples, it is shown that the saddlepoint approximations are highly accurate even at short block lengths.
Non-linearly quantized moment shadow maps

Moment shadow maps enable direct filtering to accomplish proper antialiasing of dynamic hard shadows. For each texel, the moment shadow map stores four powers of the depth in either 64 or 128 bits. After filtering, this information enables a heuristic reconstruction. However, the rounding errors introduced at 64 bits per texel necessitate a bias that strengthens light leaking artifacts noticeably. In this paper, we propose a non-linear transform which maps the four moments to four quantities describing the depth distribution more directly. These quantities can then be quantized to a total of 32 or 64 bits. At 64 bits, the results are virtually indistinguishable from moment shadow mapping at 128 bits per texel. Even at 32 bits, there is hardly any additional light leaking but banding artifacts may occur. At the same time, the computational overhead for the reconstruction is reduced. As a prerequisite for the use of these quantization schemes, we propose a compute shader that applies a resolve for a multisampled shadow map and a 92 two-pass Gaussian filter in shared memory. The quantized moments are written back to device memory only once at the very end. This approach makes our technique roughly as fast as variance shadow mapping with 32 bits per texel. Since hardware-accelerated bilinear filtering is incompatible with non-linear quantization, we employ blue noise dithering as inexpensive alternative to manual bilinear filtering.
Synchronization of Wind Farm Power System to Utility Grid Under Voltage and Frequency Variations

The high penetration of micro-grid (MG) based on renewable distributed generators (DG) in the electrical network has brought about new issues on the stability and the transient operation of the grid. However, the disconnection and the reconnection of these local networks may give rise to undesired transient overcurrents and other damage that have to be avoided. In order to solve this problem, this paper presents a novel synchronization method for a DG grid connection. This synchronization method has been implemented in a grid-connected power converter that acts as an intelligent connection agent and adapts the magnitude, the frequency and the phase angle of the MG voltage at the point of common coupling (PCC) to be equal to those of the main voltage, despite the grid frequency and voltage variations. The system is simulated using MATLAB software and results are discussed in order to prove the performance and the robustness of this synchronization technique.
New Exact and Approximation Algorithms for the Star Packing Problem in Undirected Graphs

By a T-star we mean a complete bipartite graph K1,t for some t T. For an undirected graph G, a T-star packing is a collection of node-disjoint T-stars in G. For example, we get ordinary matchings for T = 1 and packings of paths of length 1 and 2 for T = 2. Hereinafter we assume that T 2. Hell and Kirkpatrick devised an ad-hoc augmenting algorithm that finds a T-star packing covering the maximum number of nodes. The latter algorithm also yields a min-max formula. We show that T-star packings are reducible to network flows, hence the above problem is solvable in O(m p n) time (hereinafter n denotes the number of nodes in G, and m — the number of edges). For the edge-weighted case (in which weights may be assumed positive) finding a maximum T-packing is NP-hard. A novel 9 T T+1 -factor approximation algorithm is presented. For non-negative node weights the problem reduces to a special case of a max-cost flow. We develop a divide-and-conquer approach that solves it in O(m p n logn) time. The node-weighted problem with arbitrary weights is more dicult. We prove that it is NP-hard for T 3 and is
Infrared–ultrasonic sensor fusion for support vector machine–based fall detection

This article presents an infrared–ultrasonic sensor fusion approach for support vector machine–based fall detection, often required by elderly healthcare. Its detection algorithms and performance evaluation are detailed. The location, size, and temperature profile of the user can be estimated based on a novel sensory fusion algorithm. Different feature sets of the support vector machine–based machine learning algorithm are analyzed and their impact on fall detection accuracy is evaluated and compared empirically. Experiments study three non-fall activities, standing, sitting, and stooping, and two fall actions, forward falling and sideway falling, to simulate daily activities of the elderly. Fall detection accuracy studies are performed based on discretely and continuously (closer to reality) recorded experimental data, respectively. For the discrete data recording, an average accuracy of 92.2% is achieved when the stand-alone Grid-EYE is used and the accuracy is increased to 96.7% when sensor fusion is used. For the continuous data recording (180 training sets, 60 test sets at each distance), an average accuracy less than 70.0% is achieved when the stand-alone Grid-EYE is used and the accuracy is increased to around 90.3% after sensor fusion. New features will be explored in the next step to further increase detection accuracy.
Position and velocity sensitivity of muscle spindles in the cat. 3. Static fusimotor single-fibre activation of primary and secondary endings.

During the tetanic stimulation of single static fusimotor fibres, primary and secondary endings in ankle extensor and flexor muscles of the cat have been subjected to ‘triangular’ length changes. Position and velocity sensitivities were determined and compared with those obtained in non-activated endings. Two types of action of static fibre stimulation on the position sensitivity have been observed both in primary and secondary endings: it was either unchanged, or it decreased with increasing rate of stimulation (type I effect); it increased with increasing rate of stimulation (type II effect). The distribution of the two types was different to primary and secondary endings and to extensor and flexor endings. During stimulation of most static fibres, irrespective of their type, the velocity responses of both primary and secondary endings resembled those of non-activated secondary endings. The ‘quick’ component of the velocity response was usually larger in primary than in secondary endings, while the ‘slow’ components were about the same. Comparisons made in secondary endings between the velocity responses during static activation and in the non-activated state showed that the ‘quick’ component was reduced and the ‘slow’ component increased by the stimulation. ‘Exceptional’ velocity responses were observed in type I activation of some primary endings.
A comparison of visual and haptic object representations based on similarity

Do we judge similarity between two objects to be the same using touch and vision? We investigated this using psychophysical experiments in which subjects rated the similarity between objects presented either visually or haptically. The stimuli were a family of novel, three-dimensional objects whose microgeometry ("texture") and macrogeometry ("shape") were parametrically varied. Multidimensional scaling of the similarity data was used to reconstruct haptic and visual perceptual spaces. For both modalities, a two-dimensional perceptual space was found whose dimensions clearly corresponded to shape and texture. Interestingly, shape dominated in visual space, whereas both shape and texture were important in haptic space. Furthermore, stimuli clusters were observed in this space, suggesting the emergence of category structure based on similarity relationships. The same category boundaries were confirmed in a visual free sorting experiment. This study reveals differences in object processing across modality and demonstrates an approach for analyzing such differences in multisensory visualizations.
Evaluation of mechanical behaviour of unidirectional fibre-reinforced composites considering the void morphology

Voids are one of the most common defects in fibre-reinforced composite materials. Insightful understandings of the correlation between void morphology and material properties can benefit the desired performance of industrial products. A two-level analysis method for unidirectional fibre-reinforced composites containing voids is developed based on micromechanical modelling. Representative volume cells at different levels are developed based on the description of fibre distribution and void geometry. Finite element analysis was performed on the representative volume cell to determine the effective elastic moduli. Good agreements are found among the finite element analysis results, theoretical results of Halpin–Tsai equation and experimental characterization from literature. Results show that the mechanical properties of composites are significantly affected by void morphology. Larger width–height aspect ratio leads to a less modulus reduction of in-plane modulus, but it produces larger reduction of out-of-plane modulus. Moreover, the finite element analysis results can give good explanation to the discreteness of the experimental characterization. It indicates that typical voids that are formed in the autoclave process have significant impact on the out-of-plane modulus. The study considered the temperature effect on the composite containing voids. Results show that there is no coupling effect between porosity and temperature.
Selection of full‐length IgGs by tandem display on filamentous phage particles and Escherichia coli fluorescence‐activated cell sorting screening

Phage display of antibody libraries is a powerful tool for antibody discovery and evolution. Recombinant antibodies have been displayed on phage particles as scFvs or Fabs, and more recently as bivalent F(ab′)2. We recently developed a technology (E‐clonal) for screening of combinatorial IgG libraries using bacterial periplasmic display and selection by fluorescence‐activated cell sorting (FACS) [Mazor Y et al. (2007) Nat Biotechnol25, 563–565]. Although, as a single‐cell analysis technique, FACS is very powerful, especially for the isolation of high‐affinity binders, even with state of the art instrumentation the screening of libraries with diversity > 108 is technically challenging. We report here a system that takes advantage of display of full‐length IgGs on filamentous phage particles as a prescreening step to reduce library size and enable subsequent rounds of FACS screening in Escherichia coli. For the establishment of an IgG phage display system, we utilized phagemid‐encoded IgG with the fUSE5–ZZ phage as a helper phage. These phage particles display the Fc‐binding ZZ protein on all copies of the phage p3 coat protein, and are exploited as both helper phages and anchoring surfaces for the soluble IgG. We demonstrate that tandem phage selection followed by FACS allows the selection of a highly diversified profile of binders from antibody libraries without undersampling, and at the same time capitalizes on the advantages of FACS for real‐time monitoring and optimization of the screening process.
Metallic hydrophobic surface fabrication and wettability study

Hydrophobic surfaces can be designed to have useful properties such as self-cleaning, anti-icing, and flow drag reduction. Research interests in this area have been growing with rising demands from various industries. Hydrophobic surfaces can be fabricated by coating, micro or nano-scale texturing, or a combination of the two. For industrial applications, methods for mass production of hydrophobic surfaces are desired. This thesis investigated two hydrophobic surface fabrication methods, laser machining and sandblasting, and conducted wettability analysis of the fabricated surfaces. In the laser machining, four microscale surface structures including channel, pillar, varied channel and varied pillar, are designed and fabricated. The static contact angles of all laser-machined samples are close to 130° without any coating. In sandblasting fabrication, three standoff distances (10 mm, 20 mm and 30 mm) between the spray nozzle and target surfaces are tested. For stainless steel, lower standoff distance leads to increased water contact angle on the sandblasted surfaces. For carbon steel, sandblasting increases wettability of the carbon steel, with lower contact angle from lower standoff distance. A low energy coating (Aculon) is applied on the samples from both fabrication methods. In the analysis, samples are divided into two groups, one for coated samples, and the other for the uncoated ones. Overall, the coating increases static contact angle and decreases hysteresis in all laser-machined samples and sandblasted ones. The difference in wettability of the samples from the two fabrication methods is analyzed in details. Sandblasted samples can reach 113°±4° without any coating, compared with static contact angle of 128°±5° from the laser-machined sample with pillar. After coating, the water contact angle of sandblasted samples increases to 137°±3° compared with 142°±4° on laser machined samples with pillar. The results of contact angle hysteresis are nearly same for the two methods before coating. After coating, contact angle hysteresis on sandblasted samples is overall lower than that on laser-machined samples.