Miracle-dz/UniFAR-FTUs huggingface dataset:
Species-Selective Killing of Bacteria by Antimicrobial Peptide-PNAs

Broad-spectrum antimicrobials kill indiscriminately, a property that can lead to negative clinical consequences and an increase in the incidence of resistance. Species-specific antimicrobials that could selectively kill pathogenic bacteria without targeting other species in the microbiome could limit these problems. The pathogen genome presents an excellent target for the development of such antimicrobials. In this study we report the design and evaluation of species-selective peptide nucleic acid (PNA) antibacterials. Selective growth inhibition of B. subtilis, E. coli, K. pnuemoniae and S. enterica serovar Typhimurium in axenic or mixed culture could be achieved with PNAs that exploit species differences in the translation initiation region of essential genes. An S. Typhimurium-specific PNA targeting ftsZ resulted in elongated cells that were not observed in E. coli, providing phenotypic evidence of the selectivity of PNA-based antimicrobials. Analysis of the genomes of E. coli and S. Typhimurium gave a conservative estimate of >150 PNA targets that could potentially discriminate between these two closely related species. This work provides a basis for the development of a new class of antimicrobial with a tuneable spectrum of activity.
Parallel Implementation of Pre-stack Least-squares Migration for Distributed Systems

Summary Least-squares wave-equation pre-stack depth migration is a computationally expensive algorithm, requiring repeated application of wave-field modeling and migration algorithms. We describe a parallel implementation of least-squares migration for distributed parallel computing systems using MPI. The implementation distributes both the storage and processing requirements. In storage, the migrated data is distributed across the memory spaces of the MPI processes using the depth dimension. Likewise, the data (before migration) is distributed across the memory spaces of the MPI processes using the frequency dimension. In processing, the computational work is shared across MPI processes by partitioning the frequency dimension. We apply the algorithm to the Marmousi finite difference data-set, and find that the computation time of the algorithm scales with the number of MPI processes.
Fundamentals of real exchange rate determination: what role in the peso crisis?

We examine the role of structural factors in the Mexican real exchange rate experience since 1970, particularly in the crisis of December, 1994. We find that “fundamental" determinants of the real exchange--omitted from previous research--are cointegrated with nominal exchange rates and relative prices, while tests of PPP alone fail. The cointegrating equation indicates a severe undervaluation during the 1980s and only modest overvaluation in the period immediately preceding the devaluation in December, 1994. Nothing in the fundamentals can account for magnitude of the blow Mexico suffered at that time.
Strategic union delegation and incentives for merger

A unionized duopoly model to analyse how unions affect the incentives for merger is considered. It is found that both firms will merge if and only if unions are weak. However, once surplus-maximizing unions have the option to delegate the wage bargaining to wage-maximizing delegates (such as senior union members), both firms may have incentives to merge even if the union bargaining power is strong. Moreover, the option of strategic delegation may harm both the unions and the firms.
Learning Relations and Information Extraction Rules for Protein Annotation

Protein annotation is a task that describes protein X in terms of topic Y Until now, most of protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever rapidly, manual annotation becomes difficult, and there is increasing need to automate the protein annotation process. Recently, Information Extraction (IE) has been used to solve this problem. Typically, IE requires pre-defined relations and hand-crafted IE rules or annotated corpora, and these requirements are difficult to satisfy in real world domains such as the biomedical domain. In this paper, we describe an IE system which requires only sentences labeled relevant or not to a given topic by domain experts.
Tetracysteine-Based Fluorescent Tags to Study Protein Localization and Trafficking in Plasmodium falciparum-Infected Erythrocytes

Plasmodium falciparum (Pf) malaria parasites remodel host erythrocytes by placing membranous structures in the host cell cytoplasm and inserting proteins into the surrounding erythrocyte membranes. Dynamic imaging techniques with high spatial and temporal resolutions are required to study the trafficking pathways of proteins and the time courses of their delivery to the host erythrocyte membrane. Methodology and Findings Using a tetracysteine (TC) motif tag and TC-binding biarsenical fluorophores (BAFs) including fluorescein arsenical hairpin (FlAsH) and resorufin arsenical hairpin (ReAsH), we detected knob-associated histidine-rich protein (KAHRP) constructs in Pf-parasitized erythrocytes and compared their fluorescence signals to those of GFP (green fluorescent protein)-tagged KAHRP. Rigorous treatment with BAL (2, 3 dimercaptopropanol; British anti-Lewisite) was required to reduce high background due to nonspecific BAF interactions with endogenous cysteine-rich proteins. After this background reduction, similar patterns of fluorescence were obtained from the TC- and GFP-tagged proteins. The fluorescence from FlAsH and ReAsH-labeled protein bleached at faster rates than the fluorescence from GFP-labeled protein. Conclusion While TC/BAF labeling to Pf-infected erythrocytes is presently limited by high background signals, it may offer a useful complement or alternative to GFP labeling methods. Our observations are in agreement with the currently-accepted model of KAHRP movement through the cytoplasm, including transient association of KAHRP with Maurer's clefts before its incorporation into knobs in the host erythrocyte membrane.
CUDA-Based Linear Solvers for Stable Fluids

In the field of computer graphics, physically-based fluids simulations (i.e., simulations that solve the equations that govern fluids behavior) are performed using, among others, Stam's stable fluids method. This method requires the solution of two sparse linear systems that can be solved using an iterative solver (e.g., Jacobi, Gauss-Seidel, conjugate gradient, etc.). Focusing on real-time 3D applications, we provide and analyze the performance of the parallel GPU-based (using CUDA) algorithms of the Jacobi, Gauss-Seidel, and conjugate gradient solvers.
Human sperm capacitation induced by biological fluids and progesterone, but not by NADH or NADPH, is associated with the production of superoxide anion.

Recent evidence indicated that human sperm capacitation is associated with an increased production of superoxide anion (O2.-). To further study the role and importance of O2. - in capacitation, we investigated whether the O2. - generation is a general feature of capacitating spermatozoa, irrespective of the inducer used, and is correlated with capacitation levels and increased tyrosine phosphorylation of two sperm proteins (p105/p81). We also studied the time courses of O2. - production and action. Percoll-washed human spermatozoa were incubated in Ham's F-10 medium, supplemented or not supplemented with various capacitation inducers and in the presence or absence of superoxide dismutase (SOD). Sperm capacitation was measured by induction of the acrosome reaction with lysophosphatidylcholine, O2. - production was measured by chemiluminescence, and tyrosine phosphorylation was measured by immunodetection after electrophoresis and western blotting of sperm proteins. Progesterone and ultrafiltrates of human fetal cord serum, follicular fluid, and seminal plasma individually promoted sperm generation of O2. -, tyrosine phosphorylation of p105/p81, and capacitation. Fetal cord serum ultrafiltrate triggered a fivefold higher O2. - production than the other inducers (1,700 +/- 300 and 300 to 400 mV/10s/8 x 10(6) cells, respectively), a phenomenon possibly associated with the higher potency of this fluid to promote sperm hyperactivation. The production of O2. - by spermatozoa was rapid and transient. SOD prevented sperm capacitation triggered by the inducers mentioned above, but only when SOD was added at the beginning of incubation, and not after 30 minutes, indicating that the O2. - initiates a chain of early events leading to sperm capacitation. NADH and NADPH (5 mM) triggered sperm capacitation and phosphorylation of p105/p81, but these processes were not prevented by SOD or catalase, nor were they associated with an increased O2. - production. Therefore, these cofactors appeared to act by mechanisms different from those used by the other inducers studied. The sperm enzyme responsible for the O2. - generation may be very different from the NADPH oxidase of neutrophils.
’ s repository of research publications and other research outputs Adaptive Self-Configuration for Distributed Load in Sensor Networks Conference Item

The dynamic architecture of the network is monitored by exchanging so-called Network State Beacons (NSBs) between key network nodes. The Beacon Exchange rate and the network state define both the time and nature of a proactive action to combat network performance degradation at a time of crisis. It is thus essential to select and update the beacon exchange rate (FX) according to the variations in the load profile of the network. This paper presents a novel localized method that for selecting and updating the FX by adapting to the network load and energy constraints. The results indicating that the model reconfigures the network more effectively to achieve higher throughput as well as greater network integrity, with minimal resource overheads. KeywordsHigh Density Ad-hoc Networks, Self Configuration, Distributed Adaptive Optimization, Beacon Exchange Rate
Subcellular localization of myosin V in nerve growth cones and outgrowth from dilute-lethal neurons

Myosin V-null mice (dilute-lethal mutants) exhibit apparent neurological defects that worsen from birth until death in the third postnatal week. Although myosin V is enriched in brain, the neuronal function of myosin V is unclear and the underlying cause of the neurological defects in these mice is unknown. To aide in understanding myosin V function, we examined the distribution of myosin V in the rodent superior cervical ganglion (SCG) growth cone, a well characterized neuronal structure in which myosin V is concentrated. Using affinity purified, myosin V-specific antibodies in immunofluorescence and immunoelectron microscopy, we observed that myosin V is concentrated in organellerich regions of the growth cone. Myosin V is present on a distinct population of small (50-100 nm) organelles, and on actin filaments and the plasma membrane. Myosin V-associated organelles are present on both microtubules and actin filaments. These results indicate that myosin V may be carried as a passenger on organelles that are transported along microtubules, and that these organelles may also be capable of movement along actin filaments. In addition, we found no abnormalities in outgrowth, morphology, or cytoskeletal organization of SCG growth cones from dilute-lethal mice. These results indicate that myosin V is not necessary for the traction force needed for growth cone locomotion, for organization of the actin cytoskeleton, or for filopodial dynamics.
Equalized CR-dropping for Image Compression

This paper proposes a new idea for image compression that neither the additional information nor the complex formulas for image decompression are needed. Our method includes removing image pixel values from the equalized selected rows and columns for image compression and uses known adjacent pixel values to calculate unknown pixel values for image decompression. We experimentally found that the image quality after compression and decompression by our method is better than that applying joint photographic experts group (JPEG) method for image compression and decompression. Furthermore, the quality of the decompressed images can be higher than that of JPEG images even when the compression rate is higher. Considering the LENA image, when the compression rate is 25%, the image quality in our method is 33.45 dB and that of JPEG images is 32.83 dB, when the compression ratio is 6.25%, the image quality in our method is 27.93 dB and that of JPEG images is 27.49 dB.
A Hybrid Visual Servo Controller for Robust Grasping by Wheeled Mobile Robots

This paper develops a robust vision-based mobile manipulation system for wheeled mobile robots (WMRs). In particular, this paper addresses the retention of visual features in the field of view of the camera, which is an important robustness issue in visual servoing. First, the classical approach of image-based visual servoing (IBVS) for fixed-base manipulators is extended to WMRs and a control law with Lyapunov stability is determined. Second, in order to guarantee visibility of visual features, an innovative controller with machine learning using Q-learning is proposed, which can learn its behavior policy and autonomously improve its performance. Third, a hybrid controller for robust mobile manipulation is developed to integrate the IBVS controller and the Q-learning controller through a rule-based arbitrator. This is thought to be the first paper that integrates reinforcement learning or Q-learning with visual servoing to achieve robust operation. Experiments are carried out to validate the approaches developed in this paper. The experimental results show that the new hybrid controller developed here possesses the capabilities of self-learning and fast response, and provides a balanced performance with respect to robustness and accuracy.
Information-theoretical optimization techniques

Let (I, </) be a measurable space, referred to as the state space. The state space is discrete if I is countable and J consists of all subsets of I. By 77 we denote the set of countable decompositions of I in measurable sets, directed in the usual way by refinement. 770 denotes the subset of 17 consisting of finite decompositions. By a distribution we mean a probability measure on (/, J). The set of all distributions is denoted by M. For p.e M and n e II, \x | n denotes the restriction of \x to the ff-algebra generated by %. For a point function <p on I, <<p, /i> denotes the expectation of q> w.r. t. /. i. For a set function (p on «/, <<p, /*>„ denotes expectation of (p w.r.t. H | n, i.e. (<p,H->K = Z<l>(A)n(A).
Psychiatric Symptoms in Patients with Shiga Toxin-Producing E. coli O104:H4 Induced Haemolytic-Uraemic Syndrome

Background In May 2011 an outbreak of Shiga toxin-producing enterohaemorrhagic E. coli (STEC) O104:H4 in Northern Germany led to a high number of in-patients, suffering from post-enteritis haemolytic-uraemic syndrome (HUS) and often severe affection of the central nervous system. To our knowledge so far only neurological manifestations have been described systematically in literature. Aim To examine psychiatric symptoms over time and search for specific symptom clusters in affected patients. Methods 31 in-patients suffering from E. coli O104:H4 associated HUS, were examined and followed up a week during the acute hospital stay. Psychopathology was assessed by clinical interview based on the AMDP Scale, the Brief Symptom Inventory and the Clinical Global Impressions Scale. Results At baseline mental disorder due to known physiological condition (ICD-10 F06.8) was present in 58% of the examined patients. Patients suffered from various manifestations of cognitive impairment (n = 27) and hallucinations (n = 4). Disturbances of affect (n = 28) included severe panic attacks (n = 9). Psychiatric disorder was significantly associated with higher age (p<0.0001), higher levels of C-reactive protein (p<0.05), and positive family history of heart disease (p<0.05). Even within the acute hospital stay with a median follow up of 7 days, symptoms improved markedly over time (p <0.0001). Conclusions Aside from severe neurological symptoms the pathology in E.coli O104:H4 associated HUS frequently includes particular psychiatric disturbances. Long term follow up has to clarify whether or not these symptoms subside.
On the clustering phase transition in self-gravitating N-body systems

The thermodynamic behaviour of self-gravitating N-body systems has been worked out by borrowing a standard method from molecular dynamics. The link between dynamics and thermodynamics is made in the microcanonical ensemble of statistical mechanics. Through the computation of basic thermodynamic observables and of the equation of state in the plane, the clustering phase transition appears to be of the second-order type. The dynamical–microcanonical averages are compared with their corresponding canonical ensemble averages, obtained through standard Monte Carlo computations. The latter seem to have completely lost any information about the phase transition. Finally, our results – obtained in a ‘microscopic’ framework – are compared with some existing theoretical predictions – obtained in a ‘macroscopic’ (thermodynamic) framework: qualitative and quantitative agreement is found, with an interesting exception.
An Optimal Blind Temporal Motion Blur Deconvolution Filter

The frames of a video sequence can be improved by a spatial deconvolution of any motion blur not exceeding two pixels per frame. Yet, this requires an accurate blur estimation and local deconvolution, which is problematic for multiple local motions. We introduce an optimal temporal blur deconvolution filter restoring blindly any nonuniform motion blur with an amplitude below one pixel per frame. The discrete filter has a very low complexity of about 20 operations per pixel. Experiments illustrate the method on simulated data, real movies and on sequences from the Middlebury database.
Hydrogen bond dynamics in the active site of photoactive yellow protein

Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural studies provide limited insight into the conformational plasticity of individual hydrogen bonds or the dynamical coupling present within hydrogen bond networks. We report the NMR detection of the hydrogen-bonded protons donated by Tyr-42 and Glu-46 to the chromophore oxygen in the active site of the bacterial photoreceptor, photoactive yellow protein (PYP). We have used the NMR resonances for these hydrogen bonds to probe their conformational properties and ability to rearrange in response to nearby electronic perturbation. The detection of geometric isotope effects transmitted between the Tyr-42 and Glu-46 hydrogen bonds provides strong evidence for robust coupling of their equilibrium conformations. Incorporation of a modified chromophore containing an electron-withdrawing cyano group to delocalize negative charge from the chromophore oxygen, analogous to the electronic rearrangement detected upon photon absorption, results in a lengthening of the Tyr-42 and Glu-46 hydrogen bonds and an attenuated hydrogen bond coupling. The results herein elucidate fundamental properties of hydrogen bonds within the complex environment of a protein interior. Furthermore, the robust conformational coupling and plasticity of hydrogen bonds observed in the PYP active site may facilitate the larger-scale dynamical coupling and signal transduction inherent to the biological function that PYP has evolved to carry out and may provide a model for other coupled dynamic systems.
Speech Bandwidth Extension Based on GMM and Clustering Method

Conventional Gaussian mixture model (GMM) Speech Bandwidth Extension (BWE) methods often suffer from the overly smoothed problem. Thus, a method of BWE based on a cluster process and GMM whose parameters are determined by expectation-Maximization (EM) is proposed. Firstly, a cluster process is used to cluster the low frequency and high frequency parameters, and then the GMM for each cluster is established. Later on, the parameters of low frequency are transformed to the parameters of high frequency according to the learned mapping function of the corresponding GMM. Self-organization Feature Mapping (SOFM) and Vector Quantization (VQ) are applied as the cluster. It is shown by subjective evaluation and objective evaluation that, the proposed method improves the quality of the synthesized speech signals compared with the conventional GMM-based BWE method and overcomes the over-smoothed problem caused by the traditional GMM-based BWE method largely.
Fast spectrum sensing algorithm for 802.22 WRAN Systems

As the wireless communication services grow quickly, the seriousness of spectrum scarcity has been on the rise gradually. Recently, the FCC (Federal Communications Commission) announced very interesting reports. It pointed out that more than 70 % of radio spectrums are underutilized in certain times or geographic locations. This means that spectrum scarcity is not due to fundamental lack of spectrum but wasteful static spectrum allocations. In this context, IEEE 802.22 WG (working group) was organized in November 2004. Since it is originated by the secondary spectrum usage approach, its critical technology is spectrum sensing not to interfere with licensed users. Thus, in this paper, we propose the fast spectrum sensing algorithm based on the discrete wavelet packet transform focusing on the coarse detection. By simulations and complexity analysis, we verify our algorithm
An implementation technique for database query languages

Structured query languages, such as those available for relational databases, are becoming increasingly desirable for all database management systems. Such languages are applicative: there is no need for an assignment or update statement. A new technique is described that allows for the implementation of applicative query languages against most commonly used database systems. The technique involves “lazy” evaluation and has a number of advantages over existing methods: it allows queries and functions of arbitrary complexity to be constructed; it reduces the use of secondary storage; it provides a simple control structure through which interfaces to other programs may be constructed; and the implementation, including the database interface, is quite compact. Although the technique is presented for a specific functional programming system and for a CODASYL DBMS, it is general and may be used for other query languages and database systems.
Text-Independent Speaker Recognition for Ubiquitous Robot Companion

This paper describes text-independent speaker recognition system which is basic and essential for interaction between users and the robot in Ubiquitous Robot Companion environment. For comfortable interaction between users and the robot, we implement an online speaker enrollment module which trains a GMM for each speaker model and text-independent speaker recognition module which consists of text-independent speaker identification and verification. The task of this system is to recognize one of the family members consisting of four to five persons. A user-specific service can be provided from the results of speaker recognition. Finally, the speaker recognition system is evaluated on speech database collected in URC environment with various distances, and we discuss the results.