Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural insights into the T6SS effector protein Tse3 and the Tse3–Tsi3 complex from Pseudomonas aeruginosa reveal a calcium‐dependent membrane‐binding mechanism

The opportunistic pathogen Pseudomonas aeruginosa uses the type VI secretion system (T6SS) to deliver the muramidase Tse3 into the periplasm of rival bacteria to degrade their peptidoglycan (PG). Concomitantly, P. aeruginosa uses the periplasm‐localized immunity protein Tsi3 to prevent potential self‐intoxication caused by Tse3, and thus gains an edge over rival bacteria in fierce niche competition. Here, we report the crystal structures of Tse3 and the Tse3–Tsi3 complex. Tse3 contains an annexin repeat‐like fold at the N‐terminus and a G‐type lysozyme fold at the C‐terminus. One loop in the N‐terminal domain (Loop 12) and one helix (α9) from the C‐terminal domain together anchor Tse3 and the Tse3–Tsi3 complex to membrane in a calcium‐dependent manner in vitro, and this membrane‐binding ability is essential for Tse3's activity. In the C‐terminal domain, a Y‐shaped groove present on the surface likely serves as the PG binding site. Two calcium‐binding motifs are also observed in the groove and these are necessary for Tse3 activity. In the Tse3–Tsi3 structure, three loops of Tsi3 insert into the substrate‐binding groove of Tse3, and three calcium ions present at the interface of the complex are indispensable for the formation of the Tse3–Tsi3 complex.
Indoors radio channel simulator

We have developed a program to obtain, by simulation, the impulse response of the indoor wideband radio channel. The program generates a sequence, in successive runs, of channel impulse responses, over different transmitter-receiver separation distances. The amplitudes, delays and phases are generated; based on a statistical model, the model parameters of the paths arriving at the receiver are introduced by the user, matching the simulation to the desired environment. The transmitter and receiver antenna gains, the operating wavelength and the receiver sensitivity are also user entries. The program is implemented in MATLab/spl trade/ 6.5 and it has a user-friendly interface, operating by means of easy to use menus, where the user introduces the parameters and data. As result, one simulator run obtains an impulse response graphic, amplitudes vs. arrival times, and a file that contains, in a results table, amplitude, arrival time and phase for every simulated path. Successive runs obtain, in other results tables, the radio channel parameters, such as total multipath gain, path loss, RMS delay spread and excess delay.
Synthesis and Preliminary Biological Evaluation of 1,3,5-Triazine Amino Acid Derivatives to Study Their MAO Inhibitors

Three series of 4,6-dimethoxy-, 4,6-dipiperidino- and 4,6-dimorpholino-1,3,5-triazin-2-yl) amino acid derivatives were synthesized and characterized. A preliminary study for their monoamine oxidase inhibitory activity showed that compounds 7, 18, and 25 had MAO-A inhibition activity comparable to that of the standard clorgyline, with apparently more selective inhibitory activity toward MAO-A than MAO-B and no significant acute toxicity.
Thompson Sampling in Switching Environments with Bayesian Online Change Point Detection

Thompson Sampling has recently been shown to achieve the lower bound on regret in the Bernoulli Multi-Armed Bandit setting. This bandit problem assumes stationary distributions for the rewards. It is often unrealistic to model the real world as a stationary distribution. In this paper we derive and evaluate algorithms using Thompson Sampling for a Switching Multi-Armed Bandit Problem. We propose a Thompson Sampling strategy equipped with a Bayesian change point mechanism to tackle this problem. We develop algorithms for a variety of cases with constant switching rate: when switching occurs all arms change (Global Switching), switching occurs independently for each arm (PerArm Switching), when the switching rate is known and when it must be inferred from data. This leads to a family of algorithms we collectively term Change-Point Thompson Sampling (CTS). We show empirical results in 4 articial environments, and 2 derived from real world data: news click-through[Yahoo! , 2011] and foreign exchange data[Dukascopy, 2012], comparing them to some other bandit algorithms. In real world data CTS is the most eective.
Lattice based Least Fixed Point Logic

As software systems become more complex, there is an increasing need for new static analyses. Thanks to the declarative style, logic programming is an attractive formalism for specifying them. However, prior work on using logic programming for static analysis focused on analyses defined over some powerset domain, which is quite limiting. In this paper we present a logic that lifts this restriction, called Lattice based Least Fixed Point Logic (LLFP), that allows interpretations over any complete lattice satisfying Ascending Chain Condition. The main theoretical contribution is a Moore Family result that guarantees that there always is a unique least solution for a given problem. Another contribution is the development of solving algorithm that computes the least model of LLFP formulae guaranteed by the Moore Family result.
Robust Matrix Decomposition With Sparse Corruptions

Suppose a given observation matrix can be decomposed as the sum of a low-rank matrix and a sparse matrix, and the goal is to recover these individual components from the observed sum. Such additive decompositions have applications in a variety of numerical problems including system identification, latent variable graphical modeling, and principal components analysis. We study conditions under which recovering such a decomposition is possible via a combination of ℓ1 norm and trace norm minimization. We are specifically interested in the question of how many sparse corruptions are allowed so that convex programming can still achieve accurate recovery, and we obtain stronger recovery guarantees than previous studies. Moreover, we do not assume that the spatial pattern of corruptions is random, which stands in contrast to related analyses under such assumptions via matrix completion.
Snakes and Strings: New Robotic Components for Rescue Operations

The International Rescue System Institute has been established in Japan to promote research and development of key technologies for the realization of practical search-and-rescue robots, anticipating future large-scale earthquakes and other catastrophic disasters. In this paper we propose a new paradigm called “snakes and strings”, for developing practical mobile robot systems that may be useful in such situations. “Snakes” stands for snake-like robots, which can skillfully move among the debris of the collapsed buildings. “Strings”, on the other hand, means robotic systems using strings or tethers, such as proposed in the “hyper-tether” research. Tethers can continuously supply energy, accomplish reliable communication links, and also exhibit high traction force. In this paper we present many new mechanical implementations of snake-like robots developed in our laboratory, and we also explain in detail the new paradigm.
Excitatory Actions of GABA after Neuronal Trauma

GABA is the dominant inhibitory neurotransmitter in the CNS. By opening Cl− channels, GABA generally hyperpolarizes the membrane potential, decreases neuronal activity, and reduces intracellular Ca2+ of mature neurons. In the present experiment, we show that after neuronal trauma, GABA, both synaptically released and exogenously applied, exerted a novel and opposite effect, depolarizing neurons and increasing intracellular Ca2+. Different types of trauma that were effective included neurite transection, replating, osmotic imbalance, and excess heat. The depolarizing actions of GABA after trauma increased Ca2+ levels up to fourfold in some neurons, occurred in more than half of the severely injured neurons, and was long lasting (>1 week). The mechanism for the reversed action of GABA appears to be a depolarized Cl− reversal potential that results in outward rather than inward movement of Cl−, as revealed by gramicidin-perforated whole-cell patch-clamp recording. The consequent depolarization and resultant activation of the nimodipine sensitive L- and conotoxin-sensitive N-type voltage-activated Ca2+channel allows extracellular Ca2+ to enter the neuron. The long-lasting capacity to raise Ca2+may give GABA a greater role during recovery from trauma in modulating gene expression, and directing and enhancing outgrowth of regenerating neurites. On the negative side, by its depolarizing actions, GABA could increase neuronal damage by raising cytosolic Ca2+ levels in injured cells. Furthermore, the excitatory actions of GABA after neuronal injury may contribute to maladaptive signal transmission in affected GABAergic brain circuits.
The Diabetes Detection Initiative: a pilot program of selective screening.

OBJECTIVE To identify adults who might have undiagnosed type 2 diabetes. METHODS Using social marketing methods, we identified the characteristics and preferences of the pilot communities. Risk assessment tests were developed to reflect these preferences. Clinics with registries provided quantitative evaluation data and all clinics shared qualitative data. RESULTS Baseline and intervention period data showed that the number of newly detected cases of diabetes increased by 11.5 per month for the 8 registry clinics. CONCLUSION Findings have advanced our understanding of screening by identifying ways of improving the identification of undiagnosed diabetes.
Lesion site patterns in severe, nonverbal aphasia to predict outcome with a computer-assisted treatment program.

OBJECTIVE To test whether lesion site patterns in patients with chronic, severe aphasia who have no meaningful spontaneous speech are predictive of outcome following treatment with a nonverbal, icon-based computer-assisted visual communication (C-ViC) program. DESIGN Retrospective study in which computed tomographic scans performed 3 months after onset of stroke and aphasia test scores obtained before C-ViC therapy were reviewed for patients after receiving C-ViC treatment. SETTING A neurology department and speech pathology service of a Department of Veterans Affairs medical center and a university aphasia research center. PATIENTS Seventeen patients with stroke and severe aphasia who began treatment with C-ViC from 3 months to 10 years after onset of stroke. MAIN OUTCOME MEASURE Level of ability to use C-ViC on a personal computer to communicate. RESULTS All patients with bilateral lesions failed to learn C-ViC. For patients with unilateral left hemisphere lesion sites, statistical analyses accurately discriminated between those who could initiate communication with C-ViC from those who were only able to answer directed questions. The critical lesion areas involved temporal lobe structures (Wernicke cortical area and the subcortical temporal isthmus), supraventricular frontal lobe structures (supplementary motor area or cingulate gyrus 24), and the subcortical medial subcallosal fasciculus, deep to the Broca area. Specific lesion sites were also identified for appropriate candidacy for C-ViC. CONCLUSIONS Lesion site patterns on computed tomographic scans are helpful to define candidacy for C-ViC training, and to predict outcome level. A practical method is presented for clinical application of these lesion site results in combination with aphasia test scores.
A framework for research into business-IT alignment: a cognitive emphasis

Contemporary empirical research into business-IT alignment is almost entirely behavioral in its focus. It explores the alignment issue by examining the ways in which organisations behave. In contrast, few studies have attempted to investigate the issue from a cognitive perspective. Managerial cognition is an area of growing interest and importance in strategic management. This chapter proposes a framework to guide research into business-IT alignment. It reviews alignment research and also considers some of the cognitive theories and methodologies that may be appropriate for the study of alignment.
Performance analysis of several back-end database architectures

The growing acceptance of database systems makes their performance increasingly more important. One way to gain performance is to off-load some of the functions of the database system to aback-end computer. The problem is what functions should be off-loaded to maximize the benefits of distributed processing. Our approach to this problem consisted of constructing several variants of an existing relational database system. INGRES, that partition the database system software into two parts, and assigning these two parts to two computers connected by a local area network. For the purposes of this experiment, six different variants of the database software were constructed to test the sir most interesting functional subdivisions. Each variant was then benchmarked using two different databases and query streams. The communication medium and the communication software were also benchmarked to measure their contribution to the performance of each configuration. Combining the database and network measurement results, various conclusions were reached about the viability of the configurations, the desirable properties of the communications mechanisms to he used, the operating system interface and overhead, and the performance of the database system. The variants to be preferred depend on the hardware technology, operating system features, database system internal structure, and network software overhead.
Low-cost, fast and accurate reconstruction of robotic and human postures via IMU measurements

In this paper, we present a method to reconstruct the configurations of kinematic trees of rigid bodies not using measurements of relative angles (such as, e.g. rotary encoders at joints) but absolute posture sensors (such as IMUs) along with suitable filter algorithms. We argue that the relatively larger inaccuracies shown by absolute sensors can be compensated by suitable processing, such as a passive complementary filters exploiting the Mahony-Hamel formulation. The proposed method is applicable to systems where measurements of relative angles is not feasible or convenient, or where the joint kinematics are not lower pairs: for example, human body parts or soft robotic devices. In the paper, we make explicit reference to the reconstruction of posture of the compliant, underactuated Pisa/IIT SoftHand. Quantitative comparisons with ground truth data in grasping tests are used to validate the proposed method. The resulting hardware design is mechanically robust, cheap and can be easily adapted to robotic hands with different structures, as well as to sensorizing gloves for studying human grasping strategies.
Application of voice conversion to hearing-impaired Mandarin speech enhancement

This paper studies the application of voice conversion to hearing-impaired Mandarin speech enhancement. The system is based on the combined use of a sinusoidal analysis-synthesis model and a priori knowledge about Mandarin syllable phonetic structures. We propose a time-scale modification algorithm that finds accurate alignments between hearing-impaired and normal utterances. Using the alignments, spectral conversion is performed by a continuous probabilistic transform based on a Gaussian mixture model. Simulation results indicate that the proposed system can improve the intelligibility of hearing-impaired Mandarin speech.
Towards a unified gesture description language

Proliferation of novel types of gesture-based user interfaces has led to considerable fragmentation, both in terms of program code and in terms of the gestures themselves. Consequently, it is difficult for developers to build on previous work, thereby consuming valuable development time. Moreover, the flexibility of the resulting user interface is limited, particularly in respect to users wishing to customize the interface. To address this problem, we present a generic and extensible formal language to describe gestures. This language is applicable to a wide variety of input devices, such as multi-touch surfaces, pen-based input, tangible objects and even free-hand gestures. It enables the development of a generic gesture recognition engine which can serve as a backend to a wide variety of user interfaces. Moreover, rapid customization of the interface becomes possible by simply swapping gesture definitions - an aspect which has considerable advantages when conducting UI research or porting an existing application to a new type of input device. Developers will be able to benefit from the reduced amount of code, while users will be able to benefit from the increased flexibility through customization afforded by this approach.
Radio-Frequency Study of Dopant-Segregated n-Type SB-MOSFETs on Thin-Body SOI

We present a detailed direct current and radiofrequency study of fully depleted dopant-segregated Schottky barrier (SB) MOSFETs on thin-body Silicon-on-Insulator. On-wafer scattering-parameter measurements of n-type NiSi source/drain SB-MOSFETs provide an in-depth understanding of key device parameters (transconductances and capacitances) as a function of the implanted arsenic dose, i.e., different SB height. Devices with 80-nm-channel length show a high ON current of 1150 mA/mm and exhibit a unity-gain cutoff frequency of fT = 140 GHz.
Enterprise's WeChat use and its impact on firm performance - from the perspective of value co-creation

As an emerging social media, WeChat has brought a shock both theoretically and practically, which caused the shift of service mode and content. However, research on WeChat application and its impacts on performance at firm level are rare. This study examines how WeChat use influence firm performance through customer relationship management (CRM) capability, and value co-creation. Partial least squares (PLS) were used to analyze the 240 data collected. Results indicate that Wechat use has a significant impact on value co-creation, and both value co-creation and CRM capability are significantly related to firm performance. Implications and conclusions and discussed.
Merge or Separate?: Multi-job Scheduling for OpenCL Kernels on CPU/GPU Platforms

Computer systems are increasingly heterogeneous with nodes consisting of CPUs and GPU accelerators. As such systems become mainstream, they move away from specialized high-performance single application platforms to a more general setting with multiple, concurrent, application jobs. Determining how jobs should be dynamically best scheduled to heterogeneous devices is non-trivial. In certain cases, performance is maximized if jobs are allocated to a single device, in others, sharing is preferable. In this paper, we present a runtime framework which schedules multi-user OpenCL tasks to their most suitable device in a CPU/GPU system. We use a machine learning-based predictive model at runtime to detect whether to merge OpenCL kernels or schedule them separately to the most appropriate devices without the need for ahead-of-time profiling. We evaluate out approach over a wide range of workloads, on two separate platforms. We consistently show significant performance and turn-around time improvement over the state-of-the-art across programs, workload, and platforms.
A novel type of glutathione S-transferase in Onchocerca volvulus

Onchocerca volvulus is a pathogenic human filarial parasite which, like other helminth parasites, is capable of evading the host's immune responses by a variety of defense mechanisms which are likely to include the detoxification and repair mechanisms of the enzyme glutathione S-transferase (GST). In this study, we show that one of the previously described GSTs from O. volvulus appears to possess the characteristics of a secreted enzyme. When the complete O. volvulus GST1 (OvGST1) sequence presented here is compared with those of other GSTs, 50 additional residues at the N terminus are observed, the first 25 showing characteristics of a signal peptide. This is consistent with the N-terminal sequence data on the native mature enzyme which begins at amino acid 26, based on the deduced protein sequence from the cDNA. The native protein, without the signal peptide sequence, possesses a 24-amino-acid extension not present in other GSTs. The deduced amino acid sequence of the OvGST1 cDNA clone was shown to possess four potential N-glycosylation sites. Digestion of O. volvulus homogenate with endoglycosidase, followed by detection of OvGST1 with specific antibody, indicated that the enzyme possesses at least two N-linked oligosaccharide chains. Gel filtration of the Escherichia coli-produced recombinant OvGST1 showed that it is enzymatically active as a nonglycosylated dimer. OvGST1 is found in the media surrounding adult worms maintained in culture, indicating that, in vitro, this enzyme is released from the worm. The strongest immunostaining for OvGST1 was observed in the outer cellular covering of the adult worm body, the syncytial hypodermis, especially in the interchordal hypodermis, where the peripheral membrane forms a series of lamellae which run into the outer zone of the hypodermal cytoplasm.
Application of Microarray-Based Comparative Genomic Hybridization in Prenatal and Postnatal Settings: Three Case Reports

Microarray-based comparative genomic hybridization (array CGH) is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables the efficient detection of DNA copy number variations (a.k.a, cryptic genomic imbalances). The development and the clinical application of array CGH have revolutionized the diagnostic process in patients and has provided a clue to many unidentified or unexplained diseases which are suspected to have a genetic cause. In this paper, we present three clinical cases in both prenatal and postnatal settings. Among all, array CGH played a major discovery role to reveal the cryptic and/or complex nature of chromosome arrangements. By identifying the genetic causes responsible for the clinical observation in patients, array CGH has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner.
Efficiently Modeling 3D Scenes from a Single Image

A proposed system lets users create a 3D scene easily and quickly from a single image. The scene model consists of background and foreground objects whose coordinates the system calculates on the basis of a boundary between the ground plane and a wall plane. The system quickly extracts foreground objects by combining image segmentation and graph-cut-based optimization. It enables efficient modeling of foreground objects, easy creation of their textures, and rapid construction of scene models that are simple but produce sufficient 3D effects.