Miracle-dz/UniFAR-FTUs huggingface dataset:
Residues Essential for Catalysis and Stability of the Active Site of Escherichia coli Adenylosuccinate Synthetase as Revealed by Directed Mutation and Kinetics*

Examined here by directed mutation, circular dichroism spectroscopy, and kinetics are the relationships of five residues, Asp13, Glu14, Lys16, His41, and Arg131, to the catalytic function and structural organization of adenylosuccinate synthetase from Escherichia coli. The D13A mutant has no measurable activity. Mutants E14A and H41N exhibit 1% of the activity of the wild-type enzyme and 2–7-fold increases in theK m of substrates. The mutant K16Q has 34% of the activity of wild-type enzyme and K m values for substrates virtually unchanged from those of the wild-type system. Mutation of Arg131 to leucine caused only a 4-fold increase in the K m for aspartate relative to the wild-type enzyme. The dramatic effects of the D13A, E14A, and H41N mutations onk cat are consistent with the putative roles assigned to Asp13 (catalytic base), His41(catalytic acid), and Glu14 (structural organization of the active site). The modest effect of the R131L mutation on the binding of aspartate is also in harmony with recent crystallographic investigations, which suggests that Arg131 stabilizes the conformation of the loop that binds the β-carboxylate of aspartate. The modest effect of the K16Q mutation, however, contrasts with significant changes brought about by the mutation of the corresponding lysines in the P-loop of other GTP- and ATP-binding proteins. Crystallographic structures place Lys16 in a position of direct interaction with the γ-phosphate of GTP. Furthermore, lysine is present at corresponding positions in all known sequences of adenylosuccinate synthetase. We suggest that along with a modest role in stabilizing the transition state of the phosphotransfer reaction, Lys16 may stabilize the enzyme structurally. In addition, the modest loss of catalytic activity of the K16Q mutant may confer such a selective disadvantage to E. coli that this seemingly innocuous mutation is not tolerated in nature.
A new method of preparing gold probes for multiple-labeling cytochemistry.

A new method is described for preparing colloidal gold particles in any size between approximately 3 and 17 nm for electron microscopy. The gold particles are homogeneous in size (homodisperse). When bound to various proteins (e.g. IgG and protein A), the complexes were stable for long periods and suitable for affinity cytochemistry. We demonstrated the usefulness of the new gold probes bound to protein A for multiple labeling in a current immunocytochemical study on receptor mediated transport of IgA in human duodenal crypt cells. Other gold-protein complexes were useful for studying macromolecular arrangements at high resolution.
Collaborative filtering using non-negative matrix factorisation

Collaborative filtering is a popular strategy in recommender systems area. This approach gathers users’ ratings and then predicts what users will rate based on their similarity to other users. However, most of the collaborative filtering methods have faced problems such as sparseness and scalability. This paper presents a non-negative matrix factorisation method to alleviate these problems via decomposing rating matrix into user matrix and item matrix. This method tries to find two non-negative user matrix and item matrix whose product can well estimate the rating matrix. This approach proposes updated rules to learn the latent factors for factorising the rating matrix. The proposed method can estimate all the unknown ratings and its computational complexity is very low. Empirical studies on benchmark datasets show that the proposed method is more tolerant of the sparseness and scalability problems.
BIOLOGICAL AND MOLECULAR CHARACTERIZATIONS OF TOXOPLASMA GONDII STRAINS OBTAINED FROM SOUTHERN SEA OTTERS (ENHYDRA LUTRIS NEREIS)

Toxoplasma gondii was isolated from brain or heart tissue from 15 southern sea otters (Enhydra lutris nereis) in cell cultures. These strains were used to infect mice that developed antibodies to T. gondii as detected in the modified direct agglutination test and had T. gondii tissue cysts in their brains at necropsy. Mouse brains containing tissue cysts from 4 of the strains were fed to 4 cats. Two of the cats excreted T. gondii oocysts in their feces that were infectious for mice. Molecular analyses of 13 strains indicated that they were all type II strains, but that they were genetically distinct from one another.
Buoyancy induced convection in a narrow open-ended annulus

264 for the range of Rayleigh numbers considered (7.09 X 70 s s Ra* =s 4.76 X W 9 ) in the experiments. In the numerical investigation, solutions to the three-dimensional time-averaged (Reynolds) steady-state equations of fluid motion and heat transfer were obtained using a finite element analysis. Results of the conjugate study including the local temperature distributions, heat transfer coefficients, and the flow field showing the interactions between the ambient and cavity flow fields agree favorably with experimental results. An investigation was also carried out to study the effect of axial length and the gap width of the annulus. A correlation for the average Nusselt number as a function of Rayleigh number, axial length and gap width has been obtained. The present work provides, for the first time, an experimental and numerical study of turbulent buoyancy induced flows in a narrow open-ended annulus.
Power loss analysis and comparision of DC and AC side decoupling module in a H-bridge inverter

In single-phase inverters, a considerable amount of low-frequency ripples appear on the DC side due to the instantaneous power imbalance between the DC side and AC side. Recently, active methods using film capacitors or inductors as ripple power storage components introduced at the DC or AC side are applied to ease this issue. Nevertheless, there is lack of research regarding the selection of DC side or AC side power decoupling. This paper investigates the power losses of key components in both AC side and DC side active power decoupling solutions and compares their performance from an efficiency perspective. The analytical power loss models are derived based on the operation principles of the active power decoupling methods. A comparative study is performed based on a 500 W single-phase H-bridge inverter study case with 400 V DC-link voltage level. The results provide a guideline to justify whether or not to apply active power decoupling methods or which active power decoupling method to choose for a given application.
Identification of bone edema , erosions and synovitis on MRI of hand and wrist in early rheumatoid arthritis in different variants of the disease

Address: Diana Vershynina Ivano-Frankivsk National Medical University, Radiology Department Galytska Str. 2, 76019, Ivano-Frankivsk, Ukraine. Tel. +380978920964 E-mail: dizi-girl@yandex.ru Abstract Magnetic-resonance tomography (MRT) is used to examine hands in patients with early rheumatoid arthritis (RA). 32 patients meeting the new PA ACR/EULAR 2010 criteria were involved in the study. In all the examined bone edema and synovitis were detected. In 17 patients out of 32 erosions were identified whose presence correlated with the disease activity. Analysis was made of relationship between bone edema, synovitis and erosion diagnostics and seropositiveness as per antibodies to citrullinated peptides. Bone edema, erosions and synovitis are important diagnostically significant MRT-symptoms in case of early RA. Detection of these lesions using MRT at the early stage of the process may play important role in management of these patients and determination of treatment tactics.
Robust Adaptive Constrained Motion Tracking Control of Piezo-Actuated Flexure-Based Mechanisms for Micro/Nano Manipulation

This paper presents a robust adaptive constrained motion tracking control methodology for piezo-actuated flexure-based micro/nano manipulation mechanisms. This unique control approach is established for the tracking of desired motion trajectories in a constrained environment exhibiting some degree of uncertain stiffness. The control methodology is also formulated to accommodate not only the parametric uncertainties and unknown force conversion function, but also nonlinearities including the hysteresis effect and external disturbances in the motion systems. In this paper, the equations for the dynamic modeling of a flexure-hinged four-bar micro/nano manipulation mechanism operating in a constrained environment are established. A lumped parameter dynamic model that combines the piezoelectric actuator and the micro/nano manipulation mechanism is developed for the formulation of the control methodology. Stability analysis of the proposed closed-loop system is conducted and the convergence of the motion tracking errors is proven theoretically. Furthermore, precise motion tracking ability in following a desired motion trajectory is demonstrated in the experimental study. An important advantage of this control approach is that it does not require the exact values for the system parameters and the force conversion function in the physical realization. This proposed constrained motion tracking control methodology is very useful for applications demanding high-precision motion tracking with force sensing and feedback.
Corpus Resources and Minority Language Engineering

Low density languages are typically viewed as those for which few language resources are available. Work relating to low density languages is becoming a focus of increasing attention within language engineering (e.g. Charoenporn, 1997, Hall and Hudson, 1997, Somers, 1997, Nirenberg and Raskin, 1998, Somers, 1998). However, much work related to low density languages is still in its infancy, or worse, work is blocked because the resources needed by language engineers are not available. In response to this situation, the MILLE (Minority Language Engineering) project was established by the Engineering and Physical Sciences Research Council in the UK to discover what language corpora should be built to enable language engineering work on non-indigenous minority languages in the UK, most of which are typically lowdensity languages. This paper summarises some of the major findings of
Analyzing the impact of business interoperability on the performance of cooperative supply chain networks

The originality of this paper consists in proposing a model that can be used to simulate the manner in which companies interoperate in cooperative supply chain networks. The objective is to develop a model that enables the analysis of the impact of business interoperability on the performance of cooperative supply chain networks. The analysis of the impact is based on the agent-based simulation method. To test the proposed theoretical model, an application scenario regarding a reverse supply chain network is presented.
Biological variation of oxidative stress biomarkers and lactic dehydrogenase in mice.

This is the first report, we aimed to determine the biological variations, analytical quality specifications of oxidative stress biomarkers such as glucose-6-phosphate dehydrogenase (G6PD), catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase (GST), reduced glutathione (GSH), malondialdehyde (MDA), and also lactic dehydrogenase (LDH) in mice. In the our study, Mus musculus albino mice, forty-one adult (female 20, male 21), weighing between 23 and 40 g were enrolled for biological variation study during 30-day period. Samples were stored and then tested at the same time. Results were assessed in duplicate and coefficients of variation for each analyte which were isolated to distinguish variation such as within-, and between-individual variations. From these results, an index of individuality were determined for each analyte. The analytical, within-individual, between-individual variations were assessed in apparently healthy mice and were found to be; 1.19%, 22.51% and 7.38% for G6PD, 14.09%, 23.03% and 29.42% for CAT, 6.18%, 11.12% and 21.14% for SOD, 9.13%, 12.00% and 12.58% for GST, 4.12%, 23.40% and 11.20% for GSH, 2.11%, 16.45% and 11.27% for LDH, 4.75%, 9.03% and 31.55% for MDA, respectively. As a result, while population-based reference intervals for G6PD, GSH and LDH were appropriate, Subject-based reference intervals for SOD and MDA were more appropriate. CAT and GST had intermediate individuality so population-based reference intervals should be used with caution.
Improvements on Vibe algorithm for detecting foreground objects

In order to improve the execution efficiency of Vibe algorithm in the process of background model updating, a time and space integrated method is proposed, which can not only take the advantage of previous memoryless updating strategy, but also improve the execution efficiency of the algorithm by combining both with-memory and memoryless methods. To remove the ghost in the initialization phase of Vibe algorithm, we present a method which combines Vibe algorithm and saliency map. For the Conservative update mechanism of Vibe algorithm, a foreground life mechanism based on the life cycle of foreground blobs is applied, so that wrongly updatings of big and slow objects can be avoided. The experiments show that the above three proposed algorithms give better performance compared with classical Vibe algorithm.
Muscle Strength Assessment From Functional Performance Tests: Role of Body Size

The aim of the study was to test the hypothesis that the body size plays an important role in assessment of muscle ability to exert force by standard functional performance tests. Twenty-one male students were tested on maximal isometric lift, one leg rising, vertical jump, and box lift tests, and the maximal isokinetic strength of hip and knee extensors was also recorded. When indices of the 4 functional performance tests were related to the strength of each of the 2 leg extensor muscle groups, only maximal isometric lift demonstrated positive correlation with knee extensors strength. When muscle strength was corrected for body mass, however, the aforementioned relationship became insignificant, but the 1 leg rising performance demonstrated a positive relationship with knee extensor strength. In addition, maximal isometric lift and 1 leg rising test performance provided positive and negative correlation, respectively, with body mass. The obtained findings were in line with the effects of scale applied on the tested performance. We generally conclude that the assessment of muscle capability to exert force based on some standard functional performance tests could be confounded by the body size effect.
An Optimization of Closed Frequent Subgraph Mining Algorithm

Abstract Graph mining isamajor area of interest within the field of data mining in recent years. Akey aspect of graph mining is frequent subgraph mining. Central to the entire discipline of frequent subgraph mining is the concept of subgraph isomorphism. One major issue in early subgraph isomorphism research concerns computational complexity. Normally, the subgraph isomorphism problem is NP-complete. Previous studies of frequent subgraph mining have not solved NP-complete problem in the subgraph isomorphism. In this paper, we proposeanew algorithm which can deal with this problem. The proposed algorithm can solve the subgraph isomorphism in polynomial time in some settings. Moreover, the new algorithm is proved theoretically more effective than previous studies in closed frequent subgraph mining.
Chronic hyperammonemia alters the circadian rhythms of corticosteroid hormone levels and of motor activity in rats

Patients with liver cirrhosis may present hepatic encephalopathy with a wide range of neurological disturbances and alterations in sleep quality and in the sleep‐wake circadian rhythm. Hyperammonemia is a main contributor to the neurological alterations in hepatic encephalopathy. We have assessed, in an animal model of chronic hyperammonemia without liver failure, the effects of hyperammonemia per se on the circadian rhythms of motor activity, temperature, and plasma levels of adrenal corticosteroid hormones. Chronic hyperammonemia alters the circadian rhythms of locomotor activity and of cortisol and corticosterone levels in blood. Different types of motor activity are affected differentially. Hyperammonemia significantly alters the rhythm of spontaneous ambulatory activity, reducing strongly ambulatory counts and slightly average velocity during the night (the active phase) but not during the day, resulting in altered circadian rhythms. In contrast, hyperammonemia did not affect wheel running at all, indicating that it affects spontaneous but not voluntary activity. Vertical activity was affected only very slightly, indicating that hyperammonemia does not induce anxiety. Hyperammonemia abolished completely the circadian rhythm of corticosteroid hormones in plasma, completely eliminating the peaks of cortisol and corticosterone present in control rats at the start of the dark period. The data reported show that chronic hyperammonemia, similar to that present in patients with liver cirrhosis, alters the circadian rhythms of corticosteroid hormones and of motor activity. This suggests that hyperammonemia would be a relevant contributor to the alterations in corticosteroid hormones and in circadian rhythms in patients with liver cirrhosis. © 2009 Wiley‐Liss, Inc.
Electrospun Polycaprolactone 3D Nanofibrous Scaffold with Interconnected and Hierarchically Structured Pores for Bone Tissue Engineering

For the first time, electrospun polycaprolactone (PCL) 3D nanofibrous scaffold has been developed by an innovative and convenient approach (i.e., thermally induced nanofiber self‐agglomeration followed by freeze drying), and the scaffold possesses interconnected and hierarchically structured pores including macropores with sizes up to ≈300 μm. The novel PCL 3D scaffold is soft and elastic with very high porosity of ≈96.4%, thus it is morphologically/structurally similar to natural extracellular matrix and well suited for cell functions and tissue formation. The in vitro studies reveal that the scaffold can lead to high cell viability; more importantly, it is able to promote more potent BMP2‐induced chondrogenic than osteogenic differentiation of mouse bone marrow mesenchymal stem cells. Consistent to the in vitro findings, the in vivo results indicate that the electrospun PCL 3D scaffold acts as a favorable synthetic extracellular matrix for functional bone regeneration through the physiological endochondral ossification process.
Dropped personal pronoun recovery in Chinese SMS*

Abstract In written Chinese, personal pronouns are commonly dropped when they can be inferred from context. This practice is particularly common in informal genres like Short Message Service messages sent via cell phones. Restoring dropped personal pronouns can be a useful preprocessing step for information extraction. Dropped personal pronoun recovery can be divided into two subtasks: (1) detecting dropped personal pronoun slots and (2) determining the identity of the pronoun for each slot. We address a simpler version of restoring dropped personal pronouns wherein only the person numbers are identified. After applying a word segmenter, we used a linear-chain conditional random field to predict which words were at the start of an independent clause. Then, using the independent clause start information, as well as lexical and syntactic information, we applied a conditional random field or a maximum-entropy classifier to predict whether a dropped personal pronoun immediately preceded each word and, if so, the person number of the dropped pronoun. We conducted a series of experiments using a manually annotated corpus of Chinese Short Message Service. Our approaches substantially outperformed a rule-based approach based partially on rules developed by Chung and Gildea (2010, Effects of Empty Categories on Machine Translation. Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP). Association for Computational Linguistics. pp. 636–45). Our approaches also outperformed (though by a considerably smaller margin) a machine-learning approach based closely on work by Yang, Liu, and Xue in (2015, Recovering Dropped Pronouns from Chinese Text Messages. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics (ACL). Association for Computational Linguistics. pp. 309–13). Features derived from parsing largely did not help our approaches. We conclude that, given independent clause start information, the parse information we used was largely superfluous for identifying dropped personal pronouns.
InLiDa: A 3D Lidar Dataset for People Detection and Tracking in Indoor Environments

The objective evaluation of people detectors and trackers is essential to develop high performance and general purpose solutions to these problems. This evaluation can be easily done thanks to the use of annotated datasets, but there are some combinations of sensors and scopes that have not been extensively explored. Namely, the application of large range 3D sensors in indoor environments for people detection purposes has been sparsely studied. To fill this gap, we propose InLiDa, a dataset that consists of six different sequences acquired in two different large indoor environments. The dataset is released with a set of tools valid for its use as benchmark for people detection and tracking proposals. Also baseline results obtained with state-of-the-art techniques for people detection and tracking are presented.
Repeatability of inspiratory capacity during incremental exercise in patients with severe COPD.

STUDY OBJECTIVE Estimating lung volume using inspiratory capacity (IC) maneuvers is a useful way of tracking dynamic hyperinflation. An understanding of the repeatability of the IC in a clinical setting is important when evaluating an individual's response to a therapeutic intervention that might influence lung volume. This is the first study to determine the repeatability of serial IC measurements of patients with severe COPD undergoing incremental exercise testing in a clinical setting. SUBJECTS AND METHODS Ten patients with severe COPD, inexperienced in exercise testing, cycled with power increased until they reached symptom limitation. Flow was measured at the mouth using a pneumotachograph. IC maneuvers were performed at 1-min to 3-min intervals. Subjects repeated the exercise test 2 days later. Three methods of calculating IC from flow have been described previously. To determine which method provided the best repeatability, we calculated the following: (1) IC calculated by the integration of inspired flow from the start to the end of the IC maneuver (ICINSP); (2) IC calculated from the difference between the drift-corrected peak inspiratory volume (total lung capacity [TLC]) and the drift-corrected end-expiratory lung volume (EELV) of the six breaths that preceded the IC prompt (ICREG); and (3) IC calculated, after correction of the expiratory part of the signal, as the difference between the mean EELV of the six breaths that preceded the IC prompt and the peak inspiratory volume (ICRATIO). Each individual's IC response was expressed as a function of exercise time and of ventilation. RESULTS There was a significant (p < 0.05) decrease in the expired volume of the breath before the IC maneuver (0.11 +/- 0.26 L) [mean +/- SD]. ICINSP (1.78 +/- 0.88 L) was significantly less than the IC calculated using the other two methods (ICREG, 1.88 +/- 0.89 L; ICRATIO, 1.86 +/- 0.87 L). ICRATIO improved the repeatability of the serial IC measures by as much as 60% over ICINSP and ICREG. CONCLUSION Calculating IC as the difference between EELV and TLC was unaffected by unsatisfactory technique, such as a change in breathing pattern immediately before the maneuver. Adjusting expiratory flow based on premaneuver inspiratory to expiratory volume ratio before estimating EELV improved the repeatability coefficient of the IC.