Miracle-dz/UniFAR-FTUs huggingface dataset:
The Protein Acetyltransferase PatZ from Escherichia coli Is Regulated by Autoacetylation-induced Oligomerization*

Background: PatZ is the main Escherichia coli acetyltransferase and controls acetyl-CoA synthetase (Acs) activity. Results: The kinetic and structural PatZ oligomer characteristics were determined. Conclusion: PatZ is a stable tetramer and forms an active octamer by autoacetylation to increase its stability. Significance: PTMs by acetylation have structural and functional roles in the cell. Lysine acetylation is an important post-translational modification in the metabolic regulation of both prokaryotes and eukaryotes. In Escherichia coli, PatZ (formerly YfiQ) is the only known acetyltransferase protein and is responsible for acetyl-CoA synthetase acetylation. In this study, we demonstrated PatZ-positive cooperativity in response to acetyl-CoA and the regulation of acetyl-CoA synthetase activity by the acetylation level. Furthermore, functional analysis of an E809A mutant showed that the conserved glutamate residue is not relevant for the PatZ catalytic mechanism. Biophysical studies demonstrated that PatZ is a stable tetramer in solution and is transformed to its octameric form by autoacetylation. Moreover, this modification is reversed by the sirtuin CobB. Finally, an in silico PatZ tetramerization model based on hydrophobic and electrostatic interactions is proposed and validated by three-dimensional hydrodynamic analysis. These data reveal, for the first time, the structural regulation of an acetyltransferase by autoacetylation in a prokaryotic organism.
Electrophoretic Profile of Serum Proteins in Opium and Heroin Dependents

Objectives: In this cross-sectional case-control study, albumin and globulin profile in the serum of opium and heroine addicts have been compared with correspondent values in a matched control group. Methods: Opioid consumption was confirmed by laboratory diagnostic tests on urine samples and protein electrophoresis of serum was performed to determine the concentration and profile of serum proteins. Results: There was no significant difference in albumin, alpha(1)-globulin, alpha(2)-globulin, and beta-globulin concentration among groups. Gamma-globulin concentration in opium and heroin addicts showed no significant difference, but it was significantly lower in comparison to the control group. Conclusion: This finding may be attributed to the higher probability of infectious diseases in opioids addicts.
The prevalence of immunohistochemically determined oestrogen receptor positivity in primary breast cancer is dependent on the choice of antibody and method of heat-induced epitope retrieval – prognostic implications?

Abstract Background. Oestrogen receptor (ER) status is important for the choice of systemic treatment of breast cancer patients. However, most data from randomised trials on the effect of adjuvant endocrine therapy according to ER status are based on the cytosol methods. Comparisons with immunohistochemical methods have given similar results. The aim of the present study was to examine whether different ER antibodies and heat-induced epitope retrieval (HIER) methods influence the prevalence of ER-positivity in primary breast cancer. Material and methods. This study is based on patients included in a clinical trial designed to compare the effect of two years of adjuvant tamoxifen versus no adjuvant systemic treatment in premenopausal women. From 1986 to 1991, 564 patients from two study centres in Sweden were enrolled and randomised. Patients were randomised independently of ER status. In the present study, ER status was assessed on tissue microarrays with the three different ER antibody/HIER combinations: 1D5 in citrate pH 6 (n = 390), SP1 in Tris pH 9 (n = 390) and PharmDx in citrate pH 6 (n = 361). Results. At cut-offs of 1% and 10%, respectively, the prevalence of ER-positivity was higher with SP1 (75% and 72%) compared with 1D5 (68% and 66%) and PharmDx (66% and 62%). At these cut-offs, patients in the discordant groups (SP1-positive and 1D5-negative) seem to have a prognosis intermediate between those of the double-positive and double-negative groups. Comparison with the ER status determined by the cytosol-based methods in the discordant group also showed an intermediate pattern. The repeatability was good for all antibodies and cut-offs, with overall agreement ≥ 93%. Conclusion. The present study shows that the choice of antibody and HIER method influences the prevalence of ER-positivity. We suggest that this be taken into consideration when choosing a cut-off for clinical decision making.
Stability of Equilibria in Games with Procedurally Rational Players

One approach to the modeling of bounded rationality in strategic environments is based on the dynamics of evolution and learning in games. An entirely different approach has been developed recently by Osborne and Rubinstein (1998). This latter approach is static and equilibrium based, but relies on less stringent assumptions regarding the knowledge and understanding of players than does the standard theory of Nash equilibrium. This paper formalizes Osborne and Rubinstein's dynamic interpretation of their equilibrium concept and thereby facilitates a comparison of this approach with the explicitly dynamic approach of evolutionary game theory. It turns out that the two approaches give rise to radically different static and dynamic predictions. For instance, dynamically stable equilibria can involve the playing of strictly dominated actions, and equilibria in which strictly actions are played with probability 1 can be unstable. Sufficient conditions for the instability of equilibria are provided for symmetric and asymmetric games.
Prevalence of depression and anxiety among cancer patients

Background: Depression and anxiety had negative effects on the quality of life of cancer patients, thus hospital anxiety and depression scale (HADS) is a useful instrument for screening these problems. This research was performed to assess the prevalence of their anxiety and depression. Methods: From 2012-2013, one hundred fifty patients with recent diagnosis of different cancers in Babol, Iran were assessed. A presumptive diagnosis of anxiety and depression was based on a four point 14-item HADS. The score of 0-7 means without clinical symptoms of anxiety or depression, 8-10 mild and 11-21 symptomatic anxiety or depression. The data were collected and analyzed. Results: Forty-four (29.3%) patients had mild anxiety, 25 (16.7%) symptomatic anxiety but mild and symptomatic depression were seen in 40 (26.7%) and 32 (21.3%) patients, respectively. There were significant relationships between anxiety, depression and the age group of the patients with higher frequency in older ages. There were significant relationships between anxiety and depression with the type of cancer and type of treatment. Breast and stomach cancer patients had the highest prevalence of anxiety and depression and the higher prevalence was observed in the patients who received chemotherapy as the single treatment. Conclusion: The results show that patients with breast and stomach cancer had the highest prevalence of anxiety and depression among all others cancer patients.
3D-PatchMatch: An optimization algorithm for point cloud completion

Point cloud completion is an indispensible process for handling the occlusion problem occurring during the data acquisition. For completion, 3D point clouds generate a much larger searching space than 2D images while searching for the best match for boundary patches. To handle the searching speed bottleneck, this paper proposed a novel optimization algorithm which is called the 3D-PatchMatch algorithm for 3D point cloud completion. Inspired by the nature coherence of the point cloud data, the proposed algorithm use a random initialization process and a propagation process to reduce the convergence time. Furthermore, a random guess process is proposed to make sure the proposed algorithm has the ability of escaping from the local minima. Experimental results show significant time reduction rate for this method compared to brute-force search. Furthermore, the completion results with comparisons indicate that the proposed algorithm is rarely trapped in the local minima.
Choice of θ and its effects on stability in the stochastic θ-method of stochastic delay differential equations

The second author's work [F. Wu, X. Mao, and L. Szpruch, Almost sure exponential stability of numerical solutions for stochastic delay differential equations, Numer. Math. 115 (2010), pp. 681–697] and Mao's papers [D.J. Higham, X. Mao, and C. Yuan, Almost sure and moment exponential stability in the numerical simulation of stochastic differential equations, SIAM J. Numer. Anal. 45 (2007), pp. 592–607; X. Mao, Y. Shen, and G. Alison, Almost sure exponential stability of backward Euler–Maruyama discretizations for hybrid stochastic differential equations, J. Comput. Appl. Math. 235 (2011), pp. 1213–1226] showed that the backward Euler–Maruyama (BEM) method may reproduce the almost sure stability of stochastic differential equations (SDEs) without the linear growth condition of the drift coefficient and the counterexample shows that the Euler–Maruyama (EM) method cannot. Since the stochastic θ-method is more general than the BEM and EM methods, it is very interesting to examine the interval in which the stochastic θ-method can capture the stability of exact solutions of SDEs. Without the linear growth condition of the drift term, this paper concludes that the stochastic θ-method can capture the stability for θ∈(1/2, 1]. For θ∈[0, 1/2), a counterexample shows that the stochastic θ-method cannot reproduce the stability of the exact solution. Finally, two examples are given to illustrate our conclusions.
A Location-Dependent Recommender System for the Web

A relevant piece of information in many context-aware applications for wireless and mobile users is the user's current location. Knowledge of the position, when combined with the user preferences, permits efficient service (or product) location, location-dependent alerting, and location-aware recommendation systems. We propose a recommendation system that is based on a standard web browser and where models determining the relevance of a given URL in a given region are derived in an automated and adaptive way through the collaboration of users of the system. With respect to existing location-dependent recommendation systems, the advantage of our proposal lies in the reduced effort required for system development and in the increased independence of the recommendation from the services (or products) owners. After an initial tuning phase, a specific URL will be recommended to a user in a given location in a way that considers where and how often it was accessed by the previous users. In detail, a new middleware layer, the "location broker", collects a historic database where user positions and links used in the past are analyzed to develop models relating resources to their spatial usage pattern and to calculate a preference metric when the current user is asking for recommendations. The focus of this work is on scalability issues. When the system is used in a wide area (possibly covering a sizable fraction of the entire web), the size of the database and the complexity of the models increase very rapidly. In an ubiquitous computing scenario where a multitude of wirelessly interconnected system surround a mobile user, the number of resources in an explored region may easily grow to contain thousands or millions of items. We describe a suitable data structure that permits scalability and analyze the empirical computational complexity both on a simulated scenario and in a real-world context in our province.
Mechanical properties of phosphorene nanotubes: a density functional tight-binding study

Using the density functional tight-binding method, we studied the elastic properties, deformation and failure of armchair (AC) and zigzag (ZZ) phosphorene nanotubes (PNTs) under uniaxial tensile strain. We found that the deformation and failure of PNTs are very much anisotropic. For ZZ PNTs, three deformation phases are recognized: the primary linear elastic phase—which is associated with interactions between neighboring puckers, succeeded by the bond rotation phase—where the puckered configuration of phosphorene is smoothed via bond rotation, and lastly the bond elongation phase—where the P–P bonds are directly stretched up to the maximally allowed limit and failure is initiated by the rupture of the most stretched bonds. For AC PNTs, the applied strain stretches the bonds up to the maximally allowed limit, causing their ultimate failure. For both AC and ZZ PNTs, their failure strain and failure stress are sensitive— while the Young’s modulus, flexural rigidity, radial Poisson’s ratio and thickness Poisson’s ratio are relatively insensitive—to the tube diameter. More specifically, for AC PNTs, the failure strain decreases from 0.40 to 0.25 and the failure stress increases from 13 GPa to 21 GPa when the tube diameter increases from 13.3 Å to 32.8 Å; while for ZZ PNTs, the failure strain decreases from 0.66 to 0.55 and the failure stress increases from 4 GPa to 9 GPa when the tube diameter increases from 13.2 Å to 31.1 Å. The Young’s modulus, flexural rigidity, radial and thickness Poisson ratios are 114.2 GPa, 0.019 eV · nm2, 0.47 and 0.11 for AC PNTs, and 49.2 GPa, 0.071 eV · nm2, 0.07 and 0.21 for ZZ PNTs, respectively. The present findings provide valuable references for the design and application of PNTs as device elements.
Thermal Properties and Thermal Degradation of Cellulose Tri-Stearate (CTs)

Cellulose tri-stearate (CTs) was synthesized employing triﬂuoroacetic anhydride (TFAA), stearic acid (SA), with microcrystal cellulose (MCC) and characterized with FT-IR and 1H-NMR. The degree of substitution of CTs was determined by the traditional saponiﬁcation method and 1H-NMR. The thermal properties of CTs were investigated by the thermogravimetric analysis (TGA) under Ar flow in dynamic heating conditions. Thermal stability, activation energy, as well as the degradation mechanism of the decomposition process were revealed. The results showed that the thermal stability of CTs is superior to that of raw materials-MCC, and that the degradation of CTs in argon is a first-order weight loss; the initial decomposition temperature and the temperature corresponding to maximum degradation rate (Tp) increase with an increase in heating rate. The activation energy values were calculated with the Ozawa method, Coats-Redfern method and Kinssinger method, respectively. Analyses of experimental results suggest that the degradation mechanism 0.10 0.80. The degradation mechanism of CTs in the whole conversion range is a complex mechanism, and is the combination of A3, F2 and R3.
The Bacterial Type III Secretion System as a Target for Developing New Antibiotics

Antibiotic resistance in pathogens requires new targets for developing novel antibacterials. The bacterial type III secretion system (T3SS) is an attractive target for developing antibacterials as it is essential in the pathogenesis of many Gram‐negative bacteria. The T3SS consists of structural proteins, effectors, and chaperones. Over 20 different structural proteins assemble into a complex nanoinjector that punctures a hole on the eukaryotic cell membrane to allow the delivery of effectors directly into the host cell cytoplasm. Defects in the assembly and function of the T3SS render bacteria non‐infective. Two major classes of small molecules, salicylidene acylhydrazides and thiazolidinones, have been shown to inhibit multiple genera of bacteria through the T3SS. Many additional chemically and structurally diverse classes of small molecule inhibitors of the T3SS have been identified as well. While specific targets within the T3SS of a few inhibitors have been suggested, the vast majority of specific protein targets within the T3SS remain to be identified or characterized. Other T3SS inhibitors include polymers, proteins, and polypeptides mimics. In addition, T3SS activity is regulated by its interaction with biologically relevant molecules, such as bile salts and sterols, which could serve as scaffolds for drug design.
Dynamic Analysis of Model Steel Structures Retrofitted with GFRP Composites under Microtremor Vibration

There are many varieties of the structural and architectural structures strengthened with different FRP composites are gaining popularity, and there is a growing need to understand and compare the behavior of these structures before-after GFRP composite strengthening. In this study, model steel structure was tested on the bench-scale earthquake simulator (The Quanser Shake Table) using ambient vibration, to determine the dynamic response. After this, slabs of the model steel structure was strengthened with GFRP composite, and tested on the bench-scale earthquake simulator (The Quanser Shake Table) using ambient vibration, to determine the dynamic behavior. Finally, dynamic responses of model steel structure before and after GFRP composite strengthening, such as displacements and maximum-minimum acceleration, were compared. At the end of the study, it is seen that displacements had decreased along the height of the model steel structure. Also, it is seen from the earthquake analyses that GFRP strengthening is very effective on the dynamic responses of the model steel structure.
Exposure Data 1 . 1 Cell and tissue tropism

Merkel cell polyomavirus (MCV) was first discovered clonally integrated in Merkel cell carcinoma (MCC) (Feng et al., 2008). Merkel cells reside in the basal layers of the skin and express dual epithelial/neuroendocrine phenotypic markers. In conjunction with sensory afferent neurites, Merkel cells normally function as mechanoreceptors. A comprehensive initial study by Loyo and colleagues showed that MCV DNA can be detected, in varying amounts, in specimens from a wide range of different tissues (Loyo et al., 2010). The highest amounts of MCV DNA are detected in oral samples and are shed from apparently healthy skin surfaces in the form of assembled virions (Wieland et al., 2009; Loyo et al., 2010; Schowalter et al., 2010). Kidney and bladder specimens carry a much lower level of MCV DNA, indicating that the urinary tract is unlikely to be a major site of productive MCV infection, as it is for BK polyomavirus (BKV) and JC polyomavirus (JCV). It appears that MCV DNA can be readily detected in environments occupied by humans (Foulongne et al., 2011). The possibility of environmental contamination should be considered a very serious concern for polymerase chain reaction (PCR)-based studies of MCV (Cohen & Enserink, 2011). 1.2 Methods for the detection of MCV
Machine learning for decoding listeners’ attention from electroencephalography evoked by continuous speech

Previous research has shown that it is possible to predict which speaker is attended in a multispeaker scene by analyzing a listener's electroencephalography (EEG) activity. In this study, existing linear models that learn the mapping from neural activity to an attended speech envelope are replaced by a non‐linear neural network (NN). The proposed architecture takes into account the temporal context of the estimated envelope and is evaluated using EEG data obtained from 20 normal‐hearing listeners who focused on one speaker in a two‐speaker setting. The network is optimized with respect to the frequency range and the temporal segmentation of the EEG input, as well as the cost function used to estimate the model parameters. To identify the salient cues involved in auditory attention, a relevance algorithm is applied that highlights the electrode signals most important for attention decoding. In contrast to linear approaches, the NN profits from a wider EEG frequency range (1–32 Hz) and achieves a performance seven times higher than the linear baseline. Relevant EEG activations following the speech stimulus after 170 ms at physiologically plausible locations were found. This was not observed when the model was trained on the unattended speaker. Our findings therefore indicate that non‐linear NNs can provide insight into physiological processes by analyzing EEG activity.
Prediction of osteoporotic fractures by postural instability and bone density.

OBJECTIVE--To investigate the utility of risk factors such as bone mineral density, lifestyle, and postural stability in the prediction of osteoporotic fractures. DESIGN--Longitudinal, epidemiological, and population based survey. SETTING--City of Dubbo, New South Wales. SUBJECTS--All residents of Dubbo aged > or = 60 on 1 January 1989. MAIN OUTCOME MEASURE--Incidence of fracture for individual subjects. RESULTS--The overall incidence of atraumatic fractures in men and women was 1.9% and 3.1% per annum respectively. The predominant sites of fracture were hip (18.9%), distal radius (18.5%), ribs and humerus (11.9% in each case), and ankle and foot (9.1% and 6.6% respectively). Major predictors of fractures in men and women were femoral neck bone mineral density, body sway, and quadriceps strength. Age, years since menopause, height, weight, and lifestyle factors were also correlated with bone mineral density and body sway and hence were indirect risk factors for fracture. Discriminant function analysis correctly identified 96% and 93% (sensitivities 88% and 81%) of men and women, respectively, who subsequently developed atraumatic fractures. Predictions based on this model indicated that a woman with a bone mineral density in the lowest quartile in the hip together with high body sway had a 8.4% probability of fracture per annum. This represented an almost 14-fold increase in risk of fracture compared with a woman in the highest bone mineral density quartile with low postural sway. An individual with all three predictors in the "highest risk" quartile had a 13.1% risk of fracture per annum. CONCLUSIONS--Bone mineral density, body sway, and muscle strength are independent and powerful synergistic predictors of fracture incidence.
A Linear Algorithm for Finding the Invariant Edges of an Edge-Weighted Graph

Given an edge-weighted graph where all weights are nonnegative reals, an edge reweighting is an assignment of nonnegative reals to edges such that, for each vertex, the sums of given and new weights assigned to the edges incident on the vertex do coincide. An edge is then said to be invariant if its weight is the same for any edge reweighting. We show that the set of invariant edges of an arbitrary edge-weighted graph can be determined in time linear in the size of the underlying graph. Moreover, an application to the security of statistical data is discussed.
Control of switched reluctance drives for electric vehicle applications

Dynamic controllers of switched reluctance drives adjust at least three variables, i.e., current amplitude, turn-on, and turn-off angles. In electric vehicle (EV) applications high efficiency of the drive over a wide speed range, wide torque bandwidth, and low torque ripple under varying DC-bus voltage conditions are important design goals. Hence, controllers of switched reluctance drives for EVs usually have a complex structure. In this paper, the demands on control accuracy of switched reluctance machine traction drives and the traction controller sampling frequency, which are necessary to take advantage of the switched reluctance machine dynamic capabilities, are discussed. To integrate the traction drive, the control commands need to be actualized with a sampling frequency of at least 100 Hz to meet the high-dynamic requirements of modern vehicle control systems, e.g., active cruise control, antislip control, and active damping of mechanical drivetrain oscillations. It is found that the switching angles have to be adjusted within one-tenth of a mechanical degree. This study shows that switched reluctance drives can fulfill all requirements needed for electric propulsion using standard microcontrollers or digital signal processors.