Miracle-dz/UniFAR-FTUs huggingface dataset:
MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection

MmeI is an unusual Type II restriction enzyme that is useful for generating long sequence tags. We have cloned the MmeI restriction-modification (R-M) system and found it to consist of a single protein having both endonuclease and DNA methyltransferase activities. The protein comprises an amino-terminal endonuclease domain, a central DNA methyltransferase domain and C-terminal DNA recognition domain. The endonuclease cuts the two DNA strands at one site simultaneously, with enzyme bound at two sites interacting to accomplish scission. Cleavage occurs more rapidly than methyl transfer on unmodified DNA. MmeI modifies only the adenine in the top strand, 5′-TCCRAC-3′. MmeI endonuclease activity is blocked by this top strand adenine methylation and is unaffected by methylation of the adenine in the complementary strand, 5′-GTYGGA-3′. There is no additional DNA modification associated with the MmeI R-M system, as is required for previously characterized Type IIG R-M systems. The MmeI R-M system thus uses modification on only one of the two DNA strands for host protection. The MmeI architecture represents a minimal approach to assembling a restriction-modification system wherein a single DNA recognition domain targets both the endonuclease and DNA methyltransferase activities.
Q-Learning for Policy Based SON Management in wireless Access Networks

Self organized networks has been one of the first concrete implementations of autonomic network management concept. Currently, several Self-Organizing-Network (SON) functions are developed by Radio Access Network (RAN) vendors and already deployed in many networks all around the world. These functions have been designed independently to replace different operational tasks. The concern of making these functions work together in a coherent manner has been studied later in particular in SEMAFOUR project where a Policy Based SON Management (PBSM) framework has been proposed to holistically manage a SON enabled network, namely a network with several individual SON functions. Enriching this PBSM framework with cognition capability is the next step towards the realization of the initial promise of SON concept: a unique self-managed network that responds autonomously and efficiently to the operator high level requirements and objectives. This paper proposes a cognitive PBSM system that enhances the SON management decisions by learning from past experience using Q-learning approach. Our approach is evaluated by simulation on a SON enabled Long-Term Evolution Advanced (LTE-A) network with several SON functions. The paper shows that the decisions are enhanced during the learning process and discusses the implementation options of this solution.
Role of Amino Acid Residues in Transmembrane Segments IS6 and IIS6 of the Na+ Channel α Subunit in Voltage-dependent Gating and Drug Block*

Alanine-scanning mutagenesis of transmembrane segments IS6 and IIS6 of the rat brain Nav1.2 channel α subunit identified mutations N418A in IS6 and L975A in IIS6 as causing strong positive shifts in the voltage dependence of activation. In contrast, mutations V424A in IS6 and L983A in IIS6 caused strong negative shifts. Most IS6 mutations opposed inactivation from closed states, but most IIS6 mutations favored such inactivation. Mutations L421C and L983A near the intracellular ends of IS6 and IIS6, respectively, exhibited significant sustained Na+ currents at the end of 30-ms depolarizations, indicating a role for these residues in Na+ channel fast inactivation. These residues, in combination with residues at the intracellular end of IVS6, are well situated to form an inactivation gate receptor. Mutation I409A in IS6 reduced the affinity of the local anesthetic etidocaine for the inactivated state by 6-fold, and mutations I409A and N418A reduced use-dependent block by etidocaine. No IS6 or IIS6 mutations studied affected inactivated-state affinity or use-dependent block by the neuroprotective drug sipatrigine (compound 619C89). These results suggest that the local anesthetic receptor site is formed primarily by residues in segments IIIS6 and IVS6 with the contribution of a single amino acid in segment IS6.
A NOVEL MATHEMATICAL MODEL AND NUMERICAL SIMULATION OF MASS AND HEAT TRANSFER IN BIOLEACHING PROCESS OF COPPER AGGLOMERATE.

The bioleaching unlike the leaching is a process catalyzed by bacteria to obtain copper. Generally, the material containing copper is previously agglomerated to build piles. A three dimensional mathematical model to describe the fluid mechanics, mass and heat transport that consider source terms for oxidation reaction, biological kinetic, and oxygen depletion due to methanogenic bacteria (15-45 oC), is presented. The results of computational simulations made with original programs using the proposed mathematical model, the finite volume method and RECT computational package were validated comparing it with experimental results obtained from a leaching pile of tailing agglomerated. These shown good concordances between them. When the effect of the catalyzing bacteria was included, is possible to predict their effect over the temperature, oxygen concentration and acid consume for a pile with bioleaching process.
An energy-based implicit co-scheduling model for Beowulf cluster

This paper introduces an implicit co-scheduling model called an energy-based model where a parallel system is considered as an RC electric circuit whose components are processes. The dynamical behavior of the system is represented by the charging and discharging of potentials of these components. The priorities of parallel processes are then adjusted accordingly. The model proposed falls into a framework of implicit co-scheduling techniques where the scheduler uses the recent traces of communication patterns to periodically calculate the priorities of processes. However, no previously proposed models incorporate the history of the communication and computation of the processes. The model is implemented as a highly portable Linux kernel module. The experiments using NAS benchmark show that the co-scheduling kernel modules substantially increase the speed of the parallel program execution. The improvement is better than the recent results reported in the literature.
Content Sharing Building Social User Experiences

People are increasingly interested in personally creating content, such as images, audio and videos, as well as sharing them in social networking services. Creating content has become increasingly common with state-of-art devices and technology. Sharing such content mediates rich social interactions between the users in social media services. This research aims to gain deeper understanding of personal content management from the user experience viewpoint. This research studies the design solutions supporting and motivating users in management and sharing of their personal content. Contribution of this work is to identify the motivations and needs that occur in media content sharing regardless of the content type and as a theoretical outcome Content Sharing Social User Experience framework is constructed.
Insect host–parasite coevolution in the light of experimental evolution

The many ways parasites can impact their host species have been the focus of intense study using a range of approaches. A particularly promising but under‐used method in this context is experimental evolution, because it allows targeted manipulation of known populations exposed to contrasting conditions. The strong potential of applying this method to the study of insect hosts and their associated parasites is demonstrated by the few available long‐term experiments where insects have been exposed to parasites. In this review, we summarize these studies, which have delivered valuable insights into the evolution of resistance in response to parasite pressure, the underlying mechanisms, as well as correlated genetic responses. We further assess findings from relevant artificial selection studies in the interrelated contexts of immunity, life history, and reproduction. In addition, we discuss a number of well‐studied Tribolium castaneum–Nosema whitei coevolution experiments in more detail and provide suggestions for research. Specifically, we suggest that future experiments should also be performed using nonmodel hosts and should incorporate contrasting experimental conditions, such as population sizes or environments. Finally, we expect that adding a third partner, for example, a second parasite or symbiont, to a host–parasite system could strongly impact (co)evolutionary dynamics.
Disaggregated memory for expansion and sharing in blade servers

Analysis of technology and application trends reveals a growing imbalance in the peak compute-to-memory-capacity ratio for future servers. At the same time, the fraction contributed by memory systems to total datacenter costs and power consumption during typical usage is increasing. In response to these trends, this paper re-examines traditional compute-memory co-location on a single system and details the design of a new general-purpose architectural building block-a memory blade-that allows memory to be "disaggregated" across a system ensemble. This remote memory blade can be used for memory capacity expansion to improve performance and for sharing memory across servers to reduce provisioning and power costs. We use this memory blade building block to propose two new system architecture solutions-(1) page-swapped remote memory at the virtualization layer, and (2) block-access remote memory with support in the coherence hardware-that enable transparent memory expansion and sharing on commodity-based systems. Using simulations of a mix of enterprise benchmarks supplemented with traces from live datacenters, we demonstrate that memory disaggregation can provide substantial performance benefits (on average 10X) in memory constrained environments, while the sharing enabled by our solutions can improve performance-per-dollar by up to 57% when optimizing memory provisioning across multiple servers.
An optimal quantized feedback strategy for scalar linear systems

We give an optimal (memoryless) quantized feedback strategy for stabilization of scalar linear systems, in the case of integral eigenvalue. As we do not require the quantization subsets to be intervals, this strategy has better performances than allowed by the lower bounds recently proved by Fagnani and Zampieri. We also describe a general setting, in which we prove a necessary and sufficient condition for the existence of a memoryless quantized feedback to achieve stability, and provide an analysis of Maxwell's demon in this context.
Regularized Interference Alignment Based on Weighted Sum-MSE Criterion for MIMO Interference Channels

The original interference alignment (IA) scheme provides poor sum-rate performance compared to simple orthogonal access schemes such as time-division multiple access (TDMA) in low-to-medium SNR under total power constraint. In this paper, we address this problem by proposing a method of regularizing the IA scheme with a criterion of minimizing the weighted sum of the mean square error (WMSE) function. To perform the regularization process efficiently, the weight terms in the WMSE metric should be computed from the optimal zero-forcing (ZF) schemes. Thus, we first prove the optimality of the enhanced IA algorithm introduced in our previous work in the ZF sense. From simulation results, it is shown that the proposed scheme outperforms the TDMA in overall SNR regime. We can further improve the performance by repeating the proposed regularization process iteratively. Moreover, we propose a modified design that provides robustness in the presence of channel uncertainty.
Performance of a Compliant Structure for a Thermal Resonant Microgyroscope

Realizing a structure that allows integration of actuation and sensing components operating at identical frequency is critical from functional standpoint of resonant microgyroscope. This paper presents the design and experimental test results of a compliant nickel structure for a microgyroscope. The device consists of three suspended proof masses supported by in-plane flexures anchored to the substrate thereby enabling to realize distinct driving and sensing components. Chevron-shaped beams driven electrothermally were employed for actuating drive component while parallel electrostatic combs were employed for sensing the Coriolis force induced rotation. Experimental investigation of the dynamic performance of the actuator and sensor structures revealed that their operating frequencies are very close (within 1%) thereby enabling to realize resonant microgyroscope with increased sensitivity. Comparison of the experimental results with the predictions made by analytical and finite-element models agreed well within 15%. Design guidelines for realizing microgyroscope with improved performance were briefly discussed highlighting the challenges associated with the frequency tuning.
Optimizing Sparse Matrix–Vector Product Computations Using Unroll and Jam

Large-scale scientific applications frequently compute sparse matrix–vector products in their computational core. For this reason, techniques for computing sparse matrix– vector products efficiently on modern architectures are important. In this paper we describe a strategy for improving the performance of sparse matrix–vector product computations using a loop transformation known as unrollandjam. We describe a novel sparse matrix representation that enables us to apply this transformation. Our approach is best suited for sparse matrices that have rows with a small number of predictable lengths. This work was motivated by sparse matrices that arise in SAGE, an application from Los Alamos National Laboratory. We evaluate the performance benefits of our approach using sparse matrices produced by SAGE for a pair of sample inputs. We show that our strategy is effective for improving sparse matrix–vector product performance using these matrices on MIPS R12000, Alpha Ev67, IBM Power 3, and Itanium 2 processors. Our measurements show that for this class of sparse matrices, our strategy improves sparse matrix–vector product performance from a low of 41% on MIPS to well over a factor of 2 on Itanium.
Electrical properties of a single p-type ZnO nanowire by Ga implantation with FIB

ZnO nanowires were implanted with Ga<sup>+</sup> ions with a dose of 10<sup>12</sup> cm<sup>−2</sup> and a field effect transistor (FET) device with a single Ga-doped ZnO nanowire was fabricated in a combined scanning-electron-microscope/focused-ion-beam (SEM/FIB) system. Resistance measurements performed on a single Ga-doped ZnO nanowire show the ohmic contact behavior in current-voltage curves. Moreover, resistance roughly tends to decrease with the gate voltage changes from 1V to −6V, indicating the p-type behavior. The electrical activation energy for the hole carriers due to thermal activation is estimated to be ∼229.5±2.8 meV.
The optimal blood pressure reduction

Optimal blood pressure reduction The optimal blood pressure reduction when treating arterial hypertension is obviously the one which causes the maximum achievable prevention of hypertension-associated cardiovascular morbidity and mortality. This goal has not yet been reached by present approaches to antihypertensive treatment Several large intervention trials in hypertension have shown that treated hypertensive patients still have an increased risk of cardiovascular morbidity and mortality in spite of receiving antihypertensive treatment. One possible explanation for this is that treated blood pressure is rarely, if ever, reduced to strictly normotensive levels. Another explanation, favored by proponents of the J-curve argument, is that excessive lowering of blood pressure may increase cardiovascular risks. Data available from intervention trials So far, two prospective intervention trials have addressed this problem, the Swedish BBB (Treat Blood pressure Better) study, for which results have been published, and the much larger Hypertension Optimal Treatment (HOT) study, which is still under way. Moreover, new epidemiological data from the Framingham Heart Study and the study of 50-year-old men in Gothenburg suggest that active intervention against arterial hypertension may change the pattern of blood pressure distribution in the population towards lower levels, also in untreated subjects, suggesting an additional and unexpected benefit from antihypertensive treatment.
Cholinergic elements in the zebrafish central nervous system: Histochemical and immunohistochemical analysis

Recently, the zebrafish has been extensively used for studying the development of the central nervous system (CNS). However, the zebrafish CNS has been poorly analyzed in the adult. The cholinergic/cholinoceptive system of the zebrafish CNS was analyzed by using choline acetyltransferase (ChAT) immunohistochemistry and acetylcholinesterase (AChE) histochemistry in the brain, retina, and spinal cord. AChE labeling was more abundant and more widely distributed than ChAT immunoreactivity. In the telencephalon, ChAT‐immunoreactive (ChAT‐ir) cells were absent, whereas AChE‐positive neurons were observed in both the olfactory bulb and the telencephalic hemispheres. The diencephalon was the region with the lowest density of AChE‐positive cells, mainly located in the pretectum, whereas ChAT‐ir cells were exclusively located in the preoptic region. ChAT‐ir cells were restricted to the periventricular stratum of the optic tectum, but AChE‐positive neurons were observed throughout the whole extension of the lamination except in the marginal stratum. Although ChAT immunoreactivity was restricted to the rostral tegmental, oculomotor, and trochlear nuclei within the mesencephalic tegmentum, a widespread distribution of AChE reactivity was observed in this region. The isthmic region showed abundant AChE‐positive and ChAT‐ir cells in the isthmic, secondary gustatory and superior reticular nucleus and in the nucleus lateralis valvulae. ChAT immunoreactivity was absent in the cerebellum, although AChE staining was observed in Purkinje and granule cells. The medulla oblongata showed a widespread distribution of AChE‐positive cells in all main subdivisions, including the octavolateral area, reticular formation, and motor nuclei of the cranial nerves. ChAT‐ir elements in this area were restricted to the descending octaval nucleus, the octaval efferent nucleus and the motor nuclei of the cranial nerves. Additionally, spinal cord motoneurons appeared positive to both markers. Substantial differences in the ChAT and AChE distribution between zebrafish and other fish species were observed, which could be important because zebrafish is widely used as a genetic or developmental animal model. J. Comp. Neurol. 474:75–107, 2004. © 2004 Wiley‐Liss, Inc.
Leveraging existing power control circuits and power delivery architecture for variability measurement

Embedded test structures are increasingly being used to measure and analyze performance and power variations in product chips to better understand the impact of process variations. In this work, we propose a minimally-invasive, low-overhead technique for characterizing within-die and die-to-die leakage variation. The proposed technique leverages existing power control circuitry added by designers to reduce the power consumption of inactive functional units. We manipulate these ‘sleep islands’ to isolate and measure their leakage current contribution to the chip-wide leakage current. The measured set of sleep island leakage currents reflect the leakage current variation across the chip at a coarse level of resolution. In order to improve resolution, we propose a multiple power supply port (MSP) measurement technique to provide ‘within-island’ leakage current measurements. A calibration technique is described that corrects for differences between the sleep island and MSP approaches, effectively enabling the same information to be obtained using either technique. We demonstrate the techniques on a set of test chips fabricated in 65-nm SOI technology. The results show that leakage current variations across a small test structure array have both a locally random and globally deterministic component that can be accurately mapped using the sleep island or MSP approaches.
Object Modelling with a Handheld RGB-D Camera

This work presents a flexible system to reconstruct 3D models of objects captured with an RGB-D sensor. A major advantage of the method is that our reconstruction pipeline allows the user to acquire a full 3D model of the object. This is achieved by acquiring several partial 3D models in different sessions that are automatically merged together to reconstruct a full model. In addition, the 3D models acquired by our system can be directly used by state-of-the-art object instance recognition and object tracking modules, providing object-perception capabilities for different applications, such as human-object interaction analysis or robot grasping. The system does not impose constraints in the appearance of objects (textured, untextured) nor in the modelling setup (moving camera with static object or a turn-table setup). The proposed reconstruction system has been used to model a large number of objects resulting in metrically accurate and visually appealing 3D models.
Hierarchies in Biomineral Structures

From sea urchin teeth to mammalian bones, the skeletons of organisms often contain several levels of structural hierarchy, designed to resist mechanical damage. In his Perspective, Currey describes several such hierarchical systems, highlighting in particular the high level of hierarchical organization in the skeleton of the deepwater sponge Euplectella (described by Aizenberg et al.). The complex structure of biomineralized systems probably serves mostly to avoid the traveling of cracks through the structure; Currey suggests that the chemistry of the mineral used in a skeleton is much less important than how this mineral is arranged in space.
Adhesion rings surround invadopodia and promote maturation

Summary Invasion and metastasis are aggressive cancer phenotypes that are highly related to the ability of cancer cells to degrade extracellular matrix (ECM). At the cellular level, specialized actin-rich structures called invadopodia mediate focal matrix degradation by serving as exocytic sites for ECM-degrading proteinases. Adhesion signaling is likely to be a critical regulatory input to invadopodia, but the mechanism and location of such adhesion signaling events are poorly understood. Here, we report that adhesion rings surround invadopodia shortly after formation and correlate strongly with invadopodium activity on a cell-by-cell basis. By contrast, there was little correlation of focal adhesion number or size with cellular invadopodium activity. Prevention of adhesion ring formation by inhibition of RGD-binding integrins or knockdown (KD) of integrin-linked kinase (ILK) reduced the number of ECM-degrading invadopodia and reduced recruitment of IQGAP to invadopodium actin puncta. Furthermore, live cell imaging revealed that the rate of extracellular MT1-MMP accumulation at invadopodia was greatly reduced in both integrin-inhibited and ILK-KD cells. Conversely, KD of MT1-MMP reduced invadopodium activity and dynamics but not the number of adhesion-ringed invadopodia. These results suggest a model in which adhesion rings are recruited to invadopodia shortly after formation and promote invadopodium maturation by enhancing proteinase secretion. Since adhesion rings are a defining characteristic of podosomes, similar structures formed by normal cells, our data also suggest further similarities between invadopodia and podosomes.