Miracle-dz/UniFAR-FTUs huggingface dataset:
Conservation, Variability and the Modeling of Active Protein Kinases

The human proteome is rich with protein kinases, and this richness has made the kinase of crucial importance in initiating and maintaining cell behavior. Elucidating cell signaling networks and manipulating their components to understand and alter behavior require well designed inhibitors. These inhibitors are needed in culture to cause and study network perturbations, and the same compounds can be used as drugs to treat disease. Understanding the structural biology of protein kinases in detail, including their commonalities, differences and modes of substrate interaction, is necessary for designing high quality inhibitors that will be of true use for cell biology and disease therapy. To this end, we here report on a structural analysis of all available active-conformation protein kinases, discussing residue conservation, the novel features of such conservation, unique properties of atypical kinases and variability in the context of substrate binding. We also demonstrate how this information can be used for structure prediction. Our findings will be of use not only in understanding protein kinase function and evolution, but they highlight the flaws inherent in kinase drug design as commonly practiced and dictate an appropriate strategy for the sophisticated design of specific inhibitors for use in the laboratory and disease therapy.
STRUCTURE AND TOPOLOGY OF MASSIVE GRAPHS

Structure of massive graphs are highly Complex in nature. A complex network with non-trivial topological features often occurs in modeling real systems. Networks like World-Wide web, internet, Science collaboration graph, Cellular networks etc which are evolutionary and dynamic in nature. A common property of such large networks is that the vertex connections follow a scale free power law distribution. The scale-free nature of the link distributions indicates that collective phenomena play a vital role in the development of such networks. Here we illustrate different modeling approaches of such random graphs and its properties to analyze networks.
Framework for Vetting and Identifying Emulated Android Mobile Apps

Mobile apps emulation is increasing becoming serious threat. Criminals target popular apps that are used to carry sensitive user information like financial usernames and passwords. Criminals can download and repackage these apps with malicious codes which will help in stealing user information or send annoying adverts to user that will benefit the criminals. This paper focuses on XDroid Moss, an enhanced vetting framework to detect the emulated apps.
Multimodal Tomometry for Slug Detection in two Phase Flow

Electrical Capacitance and Resistance Tomometric (ECTm/ ERTm) approaches are attractive for measurement and control applications in the process industries. By using the time series of raw resistance and capacitance values R(i,j,t) and C(i,j,t) ( i=1, ., NR, j = 1, 2, ., NR and i ≠ j for ERT modules with NR electrodes; i=1, ., NC, j = 1, 2, ., NC and i ≠ j for ECT modules with NC electrodes), it is shown in this paper (with NR=16,NC=12) how the intermittent occurrence of slugs in a liquid/gas two phase flow can be detected using the time series data consisting of the measured resistances and capacitances R(i,j,t) and C(i,j,t). In a pipe transporting oil and gas, the slugs can be characterized by their sizes, occurring instants and frequencies. The signal processing employed to estimate these parameters associated with the slugs is based on the analysis of the pulse generated from the ECT/ERT module, both in time and frequency domains. Some measurements are also performed using high speed camera, thus making this effort multimodal. Due to the very much reduced estimation times involved in this process as compared to tomographic image processing, this tomometric method has many advantages in real time measurement and control applications. Signal processing of the volume ratio data of tomography systems and image analysis of high speed camera images can be done to extract various slug parameters. Slug length, velocity and frequency in a slightly inclined upward two phase water/air flow are estimated using fusion of data from the multimodal system. The results obtained are compared to verify the various parameters estimated using different modalities.
First-principles description of charge transfer in donor-acceptor compounds from self-consistent many-body perturbation theory

This work was supported by the European Research Council Advanced Grant DYNamo (ERC-2010-AdG-267374), the European Commission within the FP7 CRONOS project (ID 280879), Spanish Grant (FIS2010-21282-C02-01), Ikerbasque and Grupos Consolidados UPV/EHU del Gobierno Vasco (IT578-13).
Combining perturbation theories with halo models for the matter bispectrum

Aims. We investigate how unified models should be built to be able to predict the matter-density bispectrum (and power spectrum) from very large to small scales and that are at the same time consistent with perturbation theory at low k and with halo models at high k. Methods. We use a Lagrangian framework to decompose the bispectrum into “3-halo”, “2-halo”, and “1-halo” contributions, related to “perturbative” and “non-perturbative” terms. We describe a simple implementation of this approach and present a detailed comparison with numerical simulations. Results. We show that the 1-halo and 2-halo contributions contain counterterms that ensure their decay at low k, as required by physical constraints, and allow a better match to simulations. Contrary to the power spectrum, the standard 1-loop perturbation theory can be used for the perturbative 3-halo contribution because it does not grow too fast at high k. Moreover, it is much simpler and more accurate than two resummation schemes investigated in this paper. We obtain a good agreement with numerical simulations on both large and small scales, but the transition scales are poorly described by the simplest implementation. This cannot be amended by simple modifications to the halo parameters, but we show how it can be corrected for the power spectrum and the bispectrum through a simple interpolation scheme that is restricted to this intermediate regime. Then, we reach an accuracy on the order of 10% on mildly and highly nonlinear scales, while an accuracy on the order of 1% is obtained on larger weakly nonlinear scales. This also holds for the real-space two-point correlation function.
Study on Effect of Different Plant Extracts on Microbial Biofilms

With the emergence of strains resistant to conventional antibiotics, it is important to carry studies using alternative methods to control these microorganisms causing important infections, such as the use of products of plant origin that has demonstrated effective antimicrobial activity besides biocompatibility. Therefore, in the present study an attempt has been made to screen different plant extracts against microbial biofilms. Out of 33 isolates BF5 was found to be a high biofilm producer by crystal violet assay with high hydrophobicity. On studying the factors influencing biofilm production increase in glucose concentration, acidic and alkaline pH, high osmolarity and low iron concentration promoted BF 5 biofilm formation. Among the different plant extracts tested, turmeric showed 100% efficacy against BF5 followed by cloves (97%), Indian borage (91%) and Aloe vera (84%). Turmeric and cloves extracts exhibited 50% antibiofilm activity against preformed biofilm.
Financial performance and social goals of microfinance institutions

Critics argue that there has been a trend among Microfinance Institutions (MFI) to focus on profitability in order to stay financially sustainable. This made some institutions neglect the social mission of microfinancing. In this paper I intend to examine if empirical evidence supports this so called mission drift hypothesis as well as other claims in this context. Using the global panel data set of the MIX (Microfinance Information Exchange), which gathers from 1995 to 2010 and contains up to 1400 institutions with a high variety of organizational forms, I was able to identify a world-wide mission drift effect in their social goal of reaching out the poorest part of the population. Furthermore, I find that, on average, the outreach of an MFI has a significant negative influence on its short and long term financial performance. Despite that, I eventually proved that the probability that an MFI worsens its social performance substantially increases if its profitability has decreased in the previous years.
A Study of Phytochemical Composition of a Few Tribal Medicinal Plants from Sriharikota

SRIHARIKOTA acquired importance botanically because of rich Island vegetation and due to installation of Rocket Launching Station by Indian Space Research Organisation (ISRO). A few Tribal colonies are domiciled there. Some aged tribal men conversed with herbal medicines and practices. With a fear that this tribal medicinal knowledge of the island may be lost, if urgently not pursued in a recorded manner for the benefit of modern society, a project on Ethnobotany and tribal medicines of Sriharikota Island is taken up three years back in 1996. Regular field tours are conducted covering all the seasons and about 300 medicinal plants are collected along with ample field notes on folklore medicinal uses with the support of local aged tribal men. Out of these, a few plants are selected on the basis of endemism and utility and subjected to phytochemical analysis. Investigation for 11 chemical components is made in 21 samples. All the data is recorded in this paper. The results are mostly in conformity with the medicinal uses and they are discussed.
Responses to Referee #1

General comments: The manuscript evaluates the ambient ammonia concentrations over southern Ontario as observed with passive samplers and calculated by the STILT-Chem v0.8 model. Three different dry deposition schemes were tested and validated with the observations. Two of the three dry deposition schemes were already present in the STILT-Chem model and were uni-directional. The third dry deposition scheme is bi-directional. For this deposition scheme different values are set for the stomatal and ground emission potentials for different land-use categories and for low-N and high-N canopies. Model results are evaluated using many different types of statistical approaches. However, it is questionable if all these statistics are really necessary and useful in the evaluation of the model results. Simple scatter plots with linear regression statistics are missing in this manuscript. Plots like Fig. 4 in Wen et al. (2013) are desirable in this paper as well (By the way, I can hardly believe that the regression line in the left panel of Fig. 4 of Wen et al. 2013 is correct? ). In this way, Figure 3, 4, and 6 can be combined, while much more information is obtained about the spatial correlation between model results and observations. Different symbols could be used for forest and agricultural sites, while different colors can be used for the different model simulations.
Development of Pd Alloy Hydrogen Separation Membranes with Dense/Porous Hybrid Structure for High Hydrogen Perm-Selectivity

For the commercial applications of hydrogen separation membranes, both high hydrogen selectivity and permeability (i.e., perm-selectivity) are required. However, it has been difficult to fabricate thin, dense Pd alloy composite membranes on porous metal support that have a pore-free surface and an open structure at the interface between the Pd alloy films and the metal support in order to obtain the required properties simultaneously. In this study, we fabricated Pd alloy hydrogen separation membranes with dense/porous hybrid structure for high hydrogen perm-selectivity. The hydrogen selectivity of this membrane increased owing to the dense and pore-free microstructure of the membrane surface. The hydrogen permeation flux also was remarkably improved by the formation of an open microstructure with numerous open voids at the interface and by an effective reduction in the membrane thickness as a result of the porous structure formed within the Pd alloy films.
A strategic approach for the visualisation of the low abundance protein fatty acid binding protein 7

Fatty acid binding protein 7 (FABP7) is a 15kDa protein that plays a role in fatty acid transport, solubilisation and metabolism. It has been found to be overexpressed in triple negative/basal like breast cancer patients. The role of FABP7 in these breast cancers is not fully understood; in order to better understand how it may be involved with breast cancer prognosis cell line models are needed for mechanistic studies. However using a standard western blotting protocol FABP7 was not detectable in a selection of breast cancer cell lines and mRNA was in low abundance. This paper outlines the approach of modifying a western blot protocol and presents an optimised western blot protocol for the detection of FABP7 in breast cancer cell lines. The main areas considered during optimisation were, titration of primary and secondary antibodies, choice of protein lysis buffer, lysate preparation and a comparison between in-house 12% polyacrylamide gels and commercially available gradient polyacrylamide gels. This strategy could be used for other low abundant and small proteins.
Characteristics and usefulness of interfascicular contacts in peripheral nerve recording

by ILYA KOLB Neural interfaces have been used in conjunction with source separation algorithms to address the challenge of extracting useful command signals from nerves. A peripheral nerve interface is generally useful for signal extraction if it (1) exhibits favorable recording characteristics such as signal-to-noise ratio and (2) provides as many independent channels of neural information as possible. We investigated the usefulness of novel interfascicular electrodes in acute experiments on the rabbit sciatic nerve (n = 4). Directed interfascicular contacts were found to record compound action potentials (CAPs) with an ̅̅ ̅̅ ̅̅ (mean SNR at p = 0.05) of 24.5 dB with respect to interference sources. Contacts that (1) faced opposite directions and (2) were placed in various positions within the epineurium were found to record independent information from the nerve (mixing matrix | ( )| for all electrode configurations). This neural information recorded using interfascicular electrodes may potentially be useful for command signal extraction algorithms.
Sustainability of Solar Electricity: The Role of Endogenous Resource Substitution and Market Mediated Responses

This study seeks to understand how materials scarcity and competition from alternative uses affects the potential for widespread deployment of solar electricity in the long run, in light of related technology and policy uncertainties. Simulation results of a computable partial equilibrium model predict a considerable expansion of solar electricity generation worldwide in the near decades, as generation technologies improve and production costs fall. Increasing materials scarcity becomes a significant constraint for further expansion of solar generation, which grows considerably slower in the second half of the coming century. Solar generation capacity increases with higher energy demand, squeezing consumption in industries that compete for scarce minerals. Stringent climate policies hamper growth in intermittent solar photovoltaics backed by fossil fuel powered plants, but lead to a small increase in non-intermittent concentrated solar power technology. By the end of the coming century, solar electricity remains a marginal source of global electricity supply even in the world of higher energy demand, strict carbon regulations, and generation efficiency improvements.
LEARNING CURVES EXPERIMENTED OVER A VIRTUAL PORT: SIMULATION TRAINING AND ITS IMPACT IN TERMINAL ACTIVITIES

This work is introduce the definition of a a Learning Curve (LC) for STVP simulator by witch evaluating the effectiveness of the training process and predicting the amount of activity that are needed to reach a predetermined level of skills. LC has been calculated with data collected from trainees with different background and different previous experience with that kind of simulator. In order to do that, the ability of a group of students doing a repetitive task with the virtual equipment have been monitored and a first mathematical formulation for LC is purposed. Finally, since port operations can be very dangerous in reality, errors and accidents during the activities have been converted into time penalties in order to define a LC that takes in account the quality of the training.
Design and Implementation of Cascade LQR Controller for Stabilization of Two-Wheeled Robot

Abstract In this paper the developed two-wheeled robot and cascade LQR controller, Kalman filters, PI and PID controllers are presented. The cascade LQR controller stabilizes the two-wheeled robot in upright position. The PID controller ensures good tracking of wheel position reference and the PI controller steers two-wheeled robot rotation around the vertical axis. A software in MATLAB®/Simulink environment intended for design and generation of control code which is embedded in a Texas Instruments Digital Signal Controller is developed. Simulation and experimental results of system performance are given that confirm the efficiency of the control system developed.
Creating auditory displays with multiple loudspeakers using VBAP: a case study with DIVA project

Auditory displays containing an arbitrary number of loudspeakers in any positioning are created. The sound signals are positioned to the display using Vector Base Amplitude Panning (VBAP). The VBAP method is reviewed and a new automatic loudspeaker setup division routine is presented. The VBAP is used to create auditory display to the Digital Interactive Virtual Acoustics (DIVA) virtual environment system.
Parameterisation of transient evoked otoacoustic emissions

In this paper we compare the application of the discrete wavelet transform (DWT) and wavelet packets (WP) to transient evoked otoacoustic emissions (TEOAE) to conduct a differential diagnosis of frequency-specifc hearing loss. By parameterising the TEOAE with WP, we aim to improve the separation of groups with different hearing ability compared to a DWT parameterisation.
Investigating Attitudes of Prospective Mathematics Teachers towards the Use of Mobile Learning at a Higher Learning Institution

The aim of this study is to investigate the attitudes of prospective mathematics teachers towards mobile learning based on different variables and examine their opinions on this subject. This study used an exploratory design, which is a mixed design involving the analysis of qualitative and quantitative data collected together. The participants, which consisted of 181 prospective teachers, were selected by convenient sampling. The study was performed with a mixed method in which both qualitative and quantitative data were collected and analyzed together. The quantitative data of this study were collected by a mobile learning attitude scale, while the qualitative data were collected via a structured interview form. Independent samples t-test was used to analyze the quantitative data, while content analysis was used on the qualitative data. As a result of the study, it was found that the attitudes of the prospective teachers towards mobile learning were on a medium-level both in the general total and sub-factor (freedom, advantages, practicality and limitations) scores, and the attitudes of the male participants were higher than those of the female participants. On the other hand, it was found that the prospective mathematics teachers had positive views on mobile learning, most stated that this type of learning has advantages and disadvantages and it may be used in extracurricular environments and increases course success, but it is not economical.
Clinical correlation between the Point-of-care testing method and the traditional clinical laboratory diagnosis in the measure of the lipid profile in patients seen in medical offices

Introduction: Elevated plasma levels of lipids are considered the main modifiable risk factor for the cardiovascular disease. The Point-of-care testing (POCT) method provides quick results and allows anticipating diagnosis and treatment. Objective: To compare the lipid profile results obtained from both POCT and the traditional clinical laboratory. Methods: Fasting blood samples were collected from 111 patients who sought, for any reason, the private medical offices participating on this study. Capillary whole blood samples were analyzed in CardioChek® PA (CCPA) equipment, and the serum samples were analyzed in clinical laboratories (LAB) that have internal and external quality control, with certification. The mean values of each variable of the lipid profile obtained by CCPA and LAB were calculated. Linear regression was used to determine the existence of correlation between the two methods. Results: We observed a positive correlation between the values obtained by CCPA and LAB for all variables of the lipid profile. Our data, extracted from the routine use of CCPA in private medical offices, supports a substantial contribution of the POCT methodology in the detection of the main cardiovascular risk factors. Conclusion: The POCT CardioChek® PA Analyzer is an easy-to-operate tool, with adequate analytical performance and a good correlation with the results of the conventional laboratory method, therefore, considered a reliable method.
The harmony of programs package: Quasi-experimental evidence on deworming and canteen interventions in rural Senegal

This paper uses a unique and large-scale quasi-experimental data to study the effect of deworming and school meals programs as a package on educational outcomes pupils test scores aggregate, French or math; enrollment, promotion or dropout rates in rural Senegal. We extend the endogenous selection model la Heckman to incorporate a double-index selection mechanism. We also generalize the Roy model accordingly. We develop estimation strategies based on the full information maximum likelihood and the two-step method. We derive a wide and rich collection of treatment effects ranging from exclusive to relative effects including sequential and substitution effects. The results show that the combination of deworming and school meals programs is more beneficial to pupils achievements than taking programs separately. The sequence of implementation does matter. The two programs are complementary in increasing scores and promotion rates. However, they are substitutes in reducing dropouts. The cost-effectiveness analysis shows the deworming program is by far cheaper than the meals intervention. Implementing meals program before deworming is more cost-effective than the reverse. Lastly, unlike the deworming, meals program and the package deworming and meals have a welfare-enhancing effect on households.
Are Japanese Willing to Employ a Chinese Candidate with High Language Proficiency? An Experimental Study of Prejudice in Hiring Decisions

We investigated the extent to which Japanese hold prejudice attitudes toward Chinese. Japanese participants evaluated the personality and job qualifications of a male job candidate as a function of the candidate’s nationality (Japanese, Chinese, or simply Asian), the number of languages he speaks, and the level of the participants’ patriotism.The Japanese participants’ evaluation of the candidate was not influenced by the candidate’s nationality, but was influenced by the number of languages he speaks. The level of the participants’ patriotism also influenced their evaluation of the job candidate in expected and unexpected directions. Various implications of the results were discussed.