Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Purification of Protein from Skin and Muscles Homogenate of Labeo rohita (Rohu)

ISSN: 2319-7706 Volume 6 Number 8 (2017) pp. 1493-1500 Journal homepage: http://www.ijcmas. com India is endowed with an extensive network of fisheries resources; a long coast line of 1100 km along the Arabian Sea, supports a wide range of fish species with economic value and nutritional importance. Approximately 180 species of fish are found in fresh waters of India, majority of which are edible Antimicrobial proteins and peptides had been found from a wide variety of organisms in the last few years. These molecules have attracted much research interest because of their biochemical diversity, broad specificity on antiviral, anti-bacterial, anti-fungi, anti-protozoan parasites, anti-tumoural, and wound-healing effects. Antimicrobial proteins and peptides play key roles in innate immunity. They interact directly with bacteria and kill them. The present study was performed in order to isolate and purify the protein from skin and muscles homogenate of Labeo rohita (Rohu). Different studies are already performed which showed that bacteria and virus have caused high mortality in Labeo rohita cultures, but the endogenous antimicrobial peptides and proteins have not been explored till yet or less evidences are reported. As per the results observed, an antimicrobial component was obtained from the skin and muscles homogenate of L. rohita. It was observed that when the skin and muscles homogenate was digested with trypsin (proteolytic enzyme), its antimicrobial activity was lost, which confirmed that the antimicrobial component is a protein. The antimicrobial protein was further purified from the skin and muscles homogenate of Labeo rohita by successive ionexchange and gel filtration chromatography. The protein isolated was demonstrated to be single protein band by SDS-PAGE, with the apparent molecular weight of 46 KDa. The crude protein content in the mixed homogenate of the fish was found to be 20.5%. Although different feed content may also vary the nutritional significance of different biomolecules in the fish which is also another part of study. The protein fraction isolated was evaluated for antimicrobial activity. The protein fraction exhibited antimicrobial activity both for the Gram-positive bacteria, Staphylococcus aureus, Micrococcus luteus and Bacillus subtilis, and for the Gram-negative bacteria, Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio fluvialis, Pasteurella multocida, Aeromonas hydrophila, Escherichia coli, and Pseudomonas aeruginosa. Except A. hydrophila, P. aeruginosa, and E. coli (MIC>19 mol/L), most of the tested Gram-negative bacteria were sensitive to protein fraction (MIC<18 mol/L). Interestingly, the protein fraction showed potent antimicrobial activity against Gram-positive bacteria, S. aureus (MIC 5-10 mol/L) but comparatively weak antimicrobial activity against M. luteus and B. subtilis. The study thus suggests the presence of antimicrobial amino acids in the protein fraction which are needed to be isolated and characterization for further studies. K e y w o r d s
Open access database of raw ultrasonic signals acquired from malignant and benign breast lesions

Purpose: The aim of this paper is to provide access to a database consisting of the raw radio‐frequency ultrasonic echoes acquired from malignant and benign breast lesions. The database is freely available for study and signal analysis. Acquisition and validation methods: The ultrasonic radio‐frequency echoes were recorded from breast focal lesions of patients of the Institute of Oncology in Warsaw. The data were collected between 11/2013 and 10/2015. Patients were examined by a radiologist with 18 yr' experience in the ultrasonic examination of breast lesions. The set of data includes scans from 52 malignant and 48 benign breast lesions recorded in a group of 78 women. For each lesion, two individual orthogonal scans from the pathological region were acquired with the Ultrasonix SonixTouch Research ultrasound scanner using the L14‐5/38 linear array transducer. All malignant lesions were histologically assessed by core needle biopsy. In the case of benign lesions, part of them was histologically assessed and another part was observed over a 2‐year period. Data format and usage notes: The radio‐frequency echoes were stored in Matlab file format. For each scan, the region of interest was provided to correctly indicate the lesion area. Moreover, for each lesion, the BI‐RADS category and the lesion class were included. Two code examples of data manipulation are presented. The data can be downloaded via the Zenodo repository (https://doi.org/10.5281/zenodo.545928) or the website http://bluebox.ippt. gov.pl/˜hpiotrzk. Potential applications: The database can be used to test quantitative ultrasound techniques and ultrasound image processing algorithms, or to develop computer‐aided diagnosis systems.
Viability, biofilm formation, and MazEF expression in drug-sensitive and drug-resistant Mycobacterium tuberculosis strains circulating in Xinjiang, China

Background Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is one of the most common chronic infectious amphixenotic diseases worldwide. Prevention and control of TB are greatly difficult, due to the increase in drug-resistant TB, particularly multidrug-resistant TB. We speculated that there were some differences between drug-sensitive and drug-resistant MTB strains and that mazEF3,6,9 toxin–antitoxin systems (TASs) were involved in MTB viability. This study aimed to investigate differences in viability, biofilm formation, and MazEF expression between drug-sensitive and drug-resistant MTB strains circulating in Xinjiang, China, and whether mazEF3,6,9 TASs contribute to MTB viability under stress conditions. Materials and methods Growth profiles and biofilm-formation abilities of drug-sensitive, drug-resistant MTB strains and the control strain H37Rv were monitored. Using molecular biology experiments, the mRNA expression of the mazF3, 6, and 9 toxin genes, the mazE3, 6, and 9 antitoxin genes, and expression of the MazF9 protein were detected in the different MTB strains, H37RvΔmazEF3,6,9 mutants from the H37Rv parent strain were generated, and mutant viability was tested. Results Ex vivo culture analyses demonstrated that drug-resistant MTB strains exhibit higher survival rates than drug-sensitive strains and the control strain H37Rv. However, there was no statistical difference in biofilm-formation ability in the drug-sensitive, drug-resistant, and H37Rv strains. mazE3,6 mRNA-expression levels were relatively reduced in the drug-sensitive and drug-resistant strains compared to H37Rv. Conversely, mazE3,9 expression was increased in drug-sensitive strains compared to drug-resistant strains. Furthermore, compared with the H37Rv strain, mazF3,6 expression was increased in drug-resistant strains, mazF9 expression was increased in drug-sensitive strains, and mazF9 exhibited reduced expression in drug-resistant strains compared with drug-sensitive strains. Protein expression of mazF9 was increased in drug-sensitive and drug-resistant strains compared to H37Rv, while drug-resistant strains exhibited reduced mazF9 expression compared to drug-sensitive strains. Compared to H37Rv, H37RvΔmazEF3,6,9-deletion mutants grew more slowly under both stress conditions, and their ability to survive in host macrophages was also weaker. Furthermore, the host macrophage-apoptosis rate was higher after infection with any of the H37RvΔmazEF3,6,9 mutants than with the H37Rv strain. Conclusion The increased viability of MTB drug-resistant strains compared with drug-sensitive strains is likely to be related to differential MazEF mRNA and protein expression. mazEF3,6,9 TASs contribute to MTB viability under stress conditions.
Compact location encodings for scalable Internet routing

The Internet is facing the double-challenge of accelerating growth of routing table size and ever higher reliability requirements. Considerable progress has been made toward the scalability and reliability of the Internet. However, most of the proposals are only partial solutions that address some of the challenges. In this paper, we present a new addressing encoding scheme and a corresponding forwarding mechanism for Internet routing to solve the aforementioned problems. Underlying our design is a succinct data structure that allows us to compactly embed a set of addresses into packet headers. At the same time, the structure allows the data plane to efficiently extract multiple address information for the same destination without decompression. We provide time and space complexity analysis, and present experimental results evaluating the performance of our encoding method. It shows that the proposed encoding method can achieve a good compression factor without degrading packet-forwarding performance.
Fundamentals of Wireless Information and Power Transfer: From RF Energy Harvester Models to Signal and System Designs

Radio waves carry both energy and information simultaneously. Nevertheless, radio-frequency (RF) transmissions of these quantities have traditionally been treated separately. Currently, the community is experiencing a paradigm shift in wireless network design, namely, unifying wireless transmission of information and power so as to make the best use of the RF spectrum and radiation as well as the network infrastructure for the dual purpose of communicating and energizing. In this paper, we review and discuss recent progress in laying the foundations of the envisioned dual purpose networks by establishing a signal theory and design for wireless information and power transmission (WIPT) and identifying the fundamental tradeoff between conveying information and power wirelessly. We start with an overview of WIPT challenges and technologies, namely, simultaneous WIPT (SWIPT), wirelessly powered communication networks (WPCNs), and wirelessly powered backscatter communication (WPBC). We then characterize energy harvesters and show how WIPT signal and system designs crucially revolve around the underlying energy harvester model. To that end, we highlight three different energy harvester models, namely, one linear model and two nonlinear models, and show how WIPT designs differ for each of them in single-user and multi-user deployments. Topics discussed include rate-energy region characterization, transmitter and receiver architectures, waveform design, modulation, beamforming and input distribution optimizations, resource allocation, and RF spectrum use. We discuss and check the validity of the different energy harvester models and the resulting signal theory and design based on circuit simulations, prototyping, and experimentation. We also point out numerous directions that are promising for future research.
In Silico Study on Binding Specificity of Gonadotropins and Their Receptors: Design of a Novel and Selective Peptidomimetic for Human Follicle Stimulating Hormone Receptor

Gonadotropins bind to specific receptors in spite of sharing a high level of sequence and structural similarity. This specific binding is crucial for maintaining the reproductive health of an organism. In this study, residues that dictate the receptor binding specificity of the gonadotropins (FSH and LH) have been identified using combination of in silico methods. Docking studies (ZDOCK), based on the systematic replacement of these residues, confirmed its importance in receptor binding. An interesting observation is that the relative positioning of the residues conferring binding specificity varied for the gonadotropin-receptor complexes. This spatial difference of the key residues could be exploited for design of specific modulators. Based on the identified residues, we have rationally designed a peptidomimetic (FSHP) that displays good binding affinity and specificity for hFSHR. FSHP was developed by screening 3.9 million compounds using pharmacophore-shape similarity followed by fragment-based approach. It was observed that FSHP and hFSHâ can share the same receptor binding site thereby mimicking the native hFSHR-FSH interactions. FSHP also displayed higher binding affinity to hFSHR as compared to two reported hFSHR antagonists. MD simulation studies on hFSHR-FSHP complex revealed that FSHP is conformationally rigid and the intermolecular interactions are maintained during the course of simulation.
Application of the Dynamic Time Warping Distance for the Student Drop-out Prediction on Time Series Data

It is reported by diﬀerent universities that over 40% of students do not complete their studies within 6 years. Especially in technical courses, the drop-out rate is already very high at the beginning. Therefore an automatic drop-out prediction is useful for a monitoring system. Since the study progress data can be sorted by time, we show how they can be transformed into a multivariate time series. Then we examine the dynamic time warping (DTW) distance in conjunction with the k-nn classiﬁer and show how DTW can be used as an SVM kernel for drop-out prediction on the time-series data. With this approach, we are able to recognize about 67% of the drop outs from the course of study after the ﬁrst semester and about 60% after the second semester.
Frequency of Thyroid Dysfunctions during Interferon Alpha Treatment of Single and Combination Therapy in Hepatitis C Virus-Infected Patients: A Systematic Review Based Analysis

Background Thyroid dysfunction is the commonest endocrinopathy associated with HCV infection due to interferon-based treatment. This comprehensive and systematic review presents the available evidence for newly developed thyroid antibodies and dysfunctions during interferon treatment (both single and combination) in HCV patients. Methodology/Principal Findings This systematic review was conducted in accordance with the PRISMA guidelines. The data generated were used to analyze the risk for thyroid dysfunctions during interferon (IFN) treatment in HCV patients. There was a wide range in the incidence of newly developed thyroid dysfunctions and thyroid antibodies in HCV patients during IFN treatment (both single and combination). The wide range of incidence also denoted the possibility of factors other than IFN treatment for thyroid-related abnormalities in HCV patients. These other factors include HCV viral factors, genetic predisposition, environmental factors, and patho-physiological factors. Variations in IFN dosage, treatment duration of IFN, definition/criteria followed in each study for thyroid dysfunction and irregular thyroid function testing during treatment in different studies influence the outcome of the single studies and jeopardise the validity of a pooled risk estimate of side effects of thyroid dysfunction. Importantly, reports differ as to whether the thyroid-related side effects disappear totally after withdrawal of the IFN treatment. Conclusions/Significance The present review shows that there is a wide range in the incidence of newly developed thyroid dysfunctions and thyroid antibodies in IFN treated HCV patients. This is a comprehensive attempt to collate relevant data from 56 publications across several nations about IFN (both mono and combination therapy) related thyroid dysfunction among HCV patients. The role of each factor in causing thyroid dysfunctions in HCV patients treated with IFN should be analyzed in detail in future studies, for a better understanding of the problem and sounder clinical management of the disease.
An ERP study of effects of regularity and consistency in delayed naming and lexicality judgment in a logographic writing system

Phonological access is an important component in theories and models of word reading. However, phonological regularity and consistency effects are not clearly separable in alphabetic writing systems. We investigated these effects in Chinese, where the two variables are operationally distinct. In this orthographic system, regularity is defined as the congruence between the pronunciation of a complex character (or phonogram), and that of its phonetic radical, while phonological consistency indexes the proportion of orthographic neighbors that share the same pronunciation as the phonogram. In the current investigation, regularity and consistency were contrasted in an event-related potential (ERP) study using a lexical decision (LD) task and a delayed naming (DN) task with native Chinese readers. ERP results showed that effects of regularity occurred early after stimulus onset and were long-lasting. Regular characters elicited larger N170, smaller P200, and larger N400 compared to irregular characters. In contrast, significant effects of consistency were only seen at the P200 and consistent characters showed a greater P200 than inconsistent characters. Thus, both the time course and the direction of the effects indicated that regularity and consistency operated under different mechanisms and were distinct constructs. Additionally, both of these phonological effects were only found in the DN task and absent in LD, suggesting that phonological access was non-obligatory for LD. The study demonstrated cross-language variability in how phonological information was accessed from print and how task demands could influence this process.
Bio-inspired controller achieving forward speed modulation with a 3D bipedal walker

Despite all the effort devoted to generating locomotion algorithms for bipedal walkers, robots are still far from reaching the impressive human walking capabilities, for instance regarding robustness and energy consumption. In this paper, we have developed a bio-inspired torque-based controller supporting the emergence of a new generation of robust and energy-efficient walkers. It recruits virtual muscles driven by reflexes and a central pattern generator, and thus requires no computationally intensive inverse kinematics or dynamics modeling. This controller is capable of generating energy-efficient and human-like gaits (both regarding kinematics and dynamics) across a large range of forward speeds, in a 3D environment. After a single off-line optimization process, the forward speed can be continuously commanded within this range by changing high-level parameters, as linear or quadratic functions of the target speed. Sharp speed transitions can then be achieved with no additional tuning, resulting in immediate adaptations of the step length and frequency. In this paper, we particularly embodied this controller on a simulated version of COMAN, a 95 cm tall humanoid robot. We reached forward speed modulations between 0.4 and 0.9 m/s. This covers normal human walking speeds once scaled to the robot size. Finally, the walker demonstrated significant robustness against a large spectrum of unpredicted perturbations: facing external pushes or walking on altered environments, such as stairs, slopes, and irregular ground.
Development and characterization of polypyrrole-polylactide conductive open-porous composites

In this study, conductive porous composites were fabricated using the host substrate with an interconnected porous network, followed by the penetration and deposition of polypyrrole (PPy) to create a continuous conductive network. The open-porous host substrate was processed using polylactide (PLA) with compression molding and salt leaching techniques. Three different salt contents were varied from 75 wt %, 85 wt %, and 90 wt %, which were referred to by their salt-to-polymer mass ratios of 3, 6, and 9, respectively. The porous network was made conductive by coating its interior surfaces through in situ polymerization of PPy using iron (III) chloride as the oxidant species. These porous composites were then characterized to analyze the relationships between their morphology and their physical, conductive, and mechanical properties. The mechanical properties were then fitted with numerically simulated results from finite element modeling (FEM). © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Analytic Expressions and Bounds for Special Functions and Applications in Communication Theory

This paper is devoted to the derivation of novel analytic expressions and bounds for a family of special functions that are useful in wireless communication theory. These functions are the well-known Nuttall Q-function, incomplete Toronto function, Rice Ie-function, and incomplete Lipschitz-Hankel integrals. Capitalizing on the offered results, useful identities are additionally derived between the above functions and Humbert, Φ1, function as well as for specific cases of the Kampé de Fériet function. These functions can be considered as useful mathematical tools that can be employed in applications relating to the analytic performance evaluation of modern wireless communication systems, such as cognitive radio, cooperative, and free-space optical communications as well as radar, diversity, and multiantenna systems. As an example, new closed-form expressions are derived for the outage probability over nonlinear generalized fading channels, namely, α-η-μ, α-λ-μ, and α-κ-μ as well as for specific cases of the η-μ and λ-μ fading channels. Furthermore, simple expressions are presented for the channel capacity for the truncated channel inversion with fixed rate and corresponding optimum cutoff signal-to-noise ratio for single-antenna and multiantenna communication systems over Rician fading channels. The accuracy and validity of the derived expressions is justified through extensive comparisons with respective numerical results.
The Role of AIRE in the Immunity Against Candida Albicans in a Model of Human Macrophages

Autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a primary immunodeficiency caused by mutations in the autoimmune regulator gene (AIRE). Patients with AIRE mutations are susceptible to Candida albicans infection and present with autoimmune disorders. We previously demonstrated that cytoplasmic AIRE regulates the Syk-dependent Dectin-1 pathway. In this study, we further evaluated direct contact with fungal elements, synapse formation, and the response of macrophage-like THP-1 cells to C. albicans hyphae to determine the role of AIRE upon Dectin receptors function and signaling. We examined the fungal synapse (FS) formation in wild-type and AIRE-knockdown THP-1 cells differentiated to macrophages, as well as monocyte-derived macrophages from APECED patients. We evaluated Dectin-2 receptor signaling, phagocytosis, and cytokine secretion upon hyphal stimulation. AIRE co-localized with Dectin-2 and Syk at the FS upon hyphal stimulation of macrophage-like THP-1 cells. AIRE-knockdown macrophage-like THP-1 cells exhibited less Dectin-1 and Dectin-2 receptors accumulation, decreased signaling pathway activity at the FS, lower C. albicans phagocytosis, and less lysosome formation. Furthermore, IL-1β, IL-6, or TNF-α secretion by AIRE-knockdown macrophage-like THP-1 cells and AIRE-deficient patient macrophages was decreased compared to control cells. Our results suggest that AIRE modulates the FS formation and hyphal recognition and help to orchestrate an effective immune response against C. albicans.