Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated glycopeptide analysis - review of current state and future directions

Glycosylation of proteins is involved in immune defense, cell-cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural analysis of glycoproteins-glycoproteomics-remains in its infancy due to the scarcity of high-throughput analytical platforms capable of determining glycopeptide composition and structure, especially platforms for complex biological mixtures. Glycopeptide composition and structure can be determined with high mass-accuracy mass spectrometry, particularly when combined with chromatographic separation, but the sheer volume of generated data necessitates computational software for interpretation. This review discusses the current state of glycopeptide assignment software-advances made to date and issues that remain to be addressed. The various software and algorithms developed so far provide important insights into glycoproteomics. However, there is currently no freely available software that can analyze spectral data in batch and unambiguously determine glycopeptide compositions for N- and O-linked glycopeptides from relevant biological sources such as human milk and serum. Few programs are capable of aiding in structural determination of the glycan component. To significantly advance the field of glycoproteomics, analytical software and algorithms are required that: (i) solve for both N- and O-linked glycopeptide compositions, structures and glycosites in biological mixtures; (ii) are high-throughput and process data in batches; (iii) can interpret mass spectral data from a variety of sources and (iv) are open source and freely available.
Bridging Institutional Entrepreneurship and the Creation of New Organizational Forms: A Multilevel Model

The question of how new organizational forms are created remains an unsolved problem in new institutional theory. We argue that one important way that new organizational forms emerge is through a process of bridging institutional entrepreneurship, which involves an institutional entrepreneur combining aspects of established institutional logics to create a new type of organization underpinned by a new, hybrid logic. Building on an in-depth case study of a social enterprise in the United Kingdom, we present a model of the institutional work required for this type of institutional entrepreneurship. The model highlights the multilevel nature of bridging institutional entrepreneurship, showing that it entails institutional work at the micro-, meso-, and macrolevels. The study contributes to the literature by examining an important way that institutional entrepreneurs create new organizational forms; shedding light on the relationship between individual, organizational, and societal level institutional processes; and exploring the relationship between entrepreneurship and institutional entrepreneurship.
Wavelet neural network based short term load forecasting of electric power system commercial load

In an electric power system, the system load consists of domestic, commercial, industrial and municipal load sectors. This paper presents an approach for predicting electric power system commercial load using a wavelet neural network. Morlet and Mexican hat wavelets are used to generate the transfer functions of hidden layer nodes of the neural network. A wavelet neural network is trained for a particular power system load. Results show that wavelet neural networks may outperform traditional architectures in approximation and forecasting problems related to electric power system.
Component-based development process and component lifecycle

In recent years component-based development has become an established approach. Component-based Software Engineering (cid:0) CBSE (cid:1) that deals with the entire lifecycle of component-based products has been focused on technologies related to design and implementation of software components and systems built from software components. The experience has shown that pure technologies alone are not enough. A CBSE approach requires certain changes in development and life cycle processes. However, very few CBSE works, either research or practical, have addressed these topics. This paper describes principle differences of component-based and non-component based processes. Also we give an overview of a case study from a company that applies component-based approach.
Identification of Autoantibody-Negative Autoimmune Type 2 Diabetic Patients

OBJECTIVE Islet autoimmunity has long been recognized in the pathogenesis of type 1 diabetes and is becoming increasingly acknowledged as a component in the pathogenesis of type 2 diabetes. Islet reactive T cells and autoantibodies have been demonstrated in type 1 diabetes, whereas islet autoimmunity in type 2 diabetes has been limited to islet autoantibodies. In this study, we investigated whether islet reactive T cells might also be present in type 2 diabetic patients and how islet reactive T cells correlate with β-cell function. RESEARCH DESIGN AND METHODS Adult phenotypic type 2 diabetic patients (n = 36) were screened for islet reactive T-cell responses using cellular immunoblotting and five islet autoantibodies (islet cell antibody, GADA, insulin autoantibody, insulinoma-associated protein-2 autoantibody, and zinc transporter autoantibody). RESULTS We identified four subgroups of adult phenotypic type 2 diabetic patients based on their immunological status (Ab−T−, Ab+T−, Ab−T+, and Ab+T+). The Ab−T+ type 2 diabetic patients demonstrated T-cell responses similar to those of the Ab+T+ type 2 diabetic patients. Data were adjusted for BMI, insulin resistance, and duration of diabetes. Significant differences (P < 0.02) were observed among groups for fasting and glucagon-stimulated C-peptide responses. T-cell responses to islet proteins were also demonstrated to fluctuate less than autoantibody responses. CONCLUSIONS We have identified a group of adult autoimmune phenotypic type 2 diabetic patients who are Ab−T+ and thus would not be detected using autoantibody testing alone. We conclude that islet autoimmunity may be more prevalent in adult phenotypic type 2 diabetic patients than previously estimated.
Treatment of neovascular age-related macular degeneration in patients with diabetes

The number of patients with type 2 diabetes continues to rise; an anticipated 300 million people will be affected by 2025. The immense social and economic burden of the condition is exacerbated by the initial asymptomatic nature of type 2 diabetes, resulting in a high prevalence of micro-and macrovascular complications at presentation. Diabetic retinopathy, one of the potential microvascular complications associated with diabetes, and neovascular age-related macular degeneration (AMD) are the two most frequent retinal degenerative diseases, and are responsible for the majority of blindness due to retinal disease. Both conditions predominantly affect the central macula, and are associated with the presence of retinal edema and an aggressive inflammatory repair process that accelerates disease progression. The associated retinal edema and the inflammatory repair process are directly involved in the breakdown of the blood-retinal barrier (BRB). Yet, the underlying alterations to the BRB caused by the diseases are very different. The coexistence of the two conditions appears to be relatively uncommon, suggesting that diabetes may even protect patients from developing neovascular AMD. However, it is thought that the inflammatory repair responses associated with diabetic retinopathy and neovascular AMD may be cumulative and, in patients affected by both, could result in chronic diffuse cystoid edema. Treatment considerations in such patients should, therefore, include the role of retinal edema and the increased susceptibility of patients with diabetes to potential systemic side effects associated with agents administered repeatedly for neovascular AMD treatment.
Pxmp2 Is a Channel-Forming Protein in Mammalian Peroxisomal Membrane

Background Peroxisomal metabolic machinery requires a continuous flow of organic and inorganic solutes across peroxisomal membrane. Concerning small solutes, the molecular nature of their traffic has remained an enigma. Methods/Principal Findings In this study, we show that disruption in mice of the Pxmp2 gene encoding Pxmp2, which belongs to a family of integral membrane proteins with unknown function, leads to partial restriction of peroxisomal membrane permeability to solutes in vitro and in vivo. Multiple-channel recording of liver peroxisomal preparations reveals that the channel-forming components with a conductance of 1.3 nS in 1.0 M KCl were lost in Pxmp2 −/− mice. The channel-forming properties of Pxmp2 were confirmed with recombinant protein expressed in insect cells and with native Pxmp2 purified from mouse liver. The Pxmp2 channel, with an estimated diameter of 1.4 nm, shows weak cation selectivity and no voltage dependence. The long-lasting open states of the channel indicate its functional role as a protein forming a general diffusion pore in the membrane. Conclusions/Significance Pxmp2 is the first peroxisomal channel identified, and its existence leads to prediction that the mammalian peroxisomal membrane is permeable to small solutes while transfer of “bulky” metabolites, e.g., cofactors (NAD/H, NADP/H, and CoA) and ATP, requires specific transporters.
Identification and validation of reference genes for gene expression analysis in Aphidius gifuensis (Hymenoptera: Aphidiidae)

Reference genes have been utilized in estimating gene expression levels using quantitative reverse transcriptase-quantitative polymerase chain reaction (qRT-PCR) analysis. Aphidius gifuensis Ashmaed is one of the most widely used biological control agents for aphids. The biological properties of this species have been studied in detail, and current investigations are focused on elucidating the regulatory mechanisms in its host However, the appropriate reference genes for target gene expression studies have not been identified. In this study, the expression profiles of 12 candidate reference genes were evaluated under different experimental conditions(development stage, sex, tissue type, diet) by using dedicated algorithms, including geNorm, Normfinder, BestKeeper, and ΔCt. In addition, RefFinder was used to rank the overall stability of the candidate genes. Finally, we recommend three optimal reference genes for the normalization of qRT-PCR data in the presence of specific variables, which include ACTB, RPL13, and PPI for different developmental stages; RPS18, ACTB, and RPL13 for sexes; RPL13, PRII3, and RPS18 in different tissue types; and RPL13, RPL27, and ACTB in diverse diets. The present study has identified optimal reference genes that could be used in estimating the expression levels of specific genes under these conditions following the Minimum Information for publication of Quantitative real-time PCR Experiments (MIQE) guidelines, which would facilitate in advancements in functional genomics research on A. gifuensis.
Modeling the Maximum Throughput of Bluetooth Low Energy in an Error-Prone Link

We present an analytical model for the maximum throughput of Bluetooth Low Energy (BLE), considering the presence of uncorrelated bit errors and the impact of a key BLE parameter that defines the time between the start of two consecutive connection events. The derived analysis models the generic application of master-to-slave unidirectional data transmission, which also forms an upper bound for bidirectional data transmission throughput. Simulation results show that our model accurately predicts the maximum BLE throughput for all bit error rates and BLE parameter settings evaluated.
Efficient attack strategy to communication networks with partial degree information

We study the tolerance of complex networks to attacks. Due to the large network scale, it is almost impossible for an attacker to have the complete topology information about the whole network. Thus, an efficient attack strategy based on partial degree information is proposed. Using the generating function method we give the exact solution for the attack strategy. A theoretical scale-free random network and the real Internet data are considered as examples, and the results clearly show the performance degradation due to the lack of topology information. By comparing to previous strategies, the efficiency of our strategy is demonstrated.
Selective block of calcium current by lanthanum in single bullfrog atrial cells

A single suction microelectrode voltage-clamp technique was used to study the actions of lanthanum ions (La3+) on ionic currents in single cells isolated from bullfrog right atrium. La3+, added as LaCl3, blocked the "slow" inward Ca2+ current (ICa) in a dose-dependent fashion; 10(-5) M produced complete inhibition. This effect was best fitted by a dose-response curve that was calculated assuming 1:1 binding of La3+ to a site having a dissociation constant of 7.5 x 10(- 7) M. La3+ block was reversed (to 90% of control ICa) following washout and, in the presence of 10(-5) M La3+, was antagonized by raising the Ca2+ concentration from 2.5 to 7.5 mM (ICa recovered to 56% of the control). However, the latter effect took approximately 1 h to develop. Concentrations of La3+ that reduced ICa by 12-67%, 0.1-1.5 x 10(-6) M, had no measurable effect upon the voltage dependence of steady state ICa inactivation, which suggest that at these concentrations there are no significant surface-charge effects of La3+ on this gating mechanism. Three additional findings indicate that doses of La3+ that blocked ICa failed to produce nonspecific effects: (a) 10(-5) M La3+ had no measurable effect on the time-independent inwardly rectifying current, IK1; (b) the same concentration had no effect on the kinetics, amplitude, or voltage dependence of a time- and voltage-dependent K+ current, IK; and (c) 10(-4) M La3+ did not alter the size of the tetrodotoxin-sensitive inward Na+ current, INa, or the voltage dependence of its steady state inactivation. Higher concentrations (0.5- 1.0 mM) reduced both IK1 and IK, and shifted the steady state activation curve for IK toward more positive potentials, presumably by reducing the external surface potential. Our results suggest that at a concentration of less than or equal to 10(-5) M, La3+ inhibits ICa selectively by direct blockade of Ca channels rather than by altering the external surface potential. At higher concentrations, La3+ exhibits nonspecific effects, including neutralization of negative external surface charge and inhibition of other time- and voltage-dependent ionic currents.
A Sample-oriented catalogue of BL Lacertae objects

We present a catalogue of 233 BL Lacertae objects compiled through an extensive bibliographic search updated to mid-1995. A large fraction of the sources listed in the catalogue belongs to well-defined samples and can be used for statistical purposes. A smaller fraction consists of miscellaneous (but confirmed) BL Lacs and of objects classified as BL Lac candidates. We discuss the selection criteria of the different samples, report the discovery of two previously unnoticed BL Lacs in the Palomar-Green survey, and comment on the possible association of some of the still unidentified high galactic latitude gamma-ray (EGRET) sources with BL Lacs. Some statistical properties of the catalogue are also briefly discussed.
Neuroscience and Feminist Theory: A New Directions Essay

As a neuroscientist and feminist studies scholar, I am excited by the wide range of scholarship coming together under what may loosely be referred to as “feminist neuroscience. ” Feminists trained in the humanities, social sciences, biology, and neurosciences have accumulated a critical mass of expertise that actively interrogates and contributes to research in the neurosciences. Many of these scholars are also interested in using data and evidence in the neurosciences to broaden our political scopes. However, even while these varied approaches to the field appear to be thriving, I believe that a common challenge lies at the heart of this work. The question of how we think about difference in the neurosciences is crucial but has thus far been insufficiently interrogated in this quickly developing field. In this New Directions essay, I suggest that if we see the development of feminist neuroscience as a chance to go beyond critiques of empirical methods or existing gendered paradigms and as an opportunity to in fact develop new feminist analyses of the brain, neurons, hormones, and synaptic functions, we need to make a more explicit and concerted effort to think about questions of difference. Thinking about difference, and particularly the status of matter, materiality, and sexual difference in the brain, may in turn allow us to see current neuroscience research on sex and gender differences in a new light and encourage new lines of inquiry for feminist neuroscience.
Predictive Performance Comparison Analysis of Relational & NoSQL Graph Databases

From last three decades, the relational databases are being used in many organizations of various natures such as Education, Health, Business and in many other applications. Traditional databases show tremendous performance and are designed to handle structured data with ACID (Atomicity, Consistency, Isolation, Durability) property to manage data integrity. In the current era, organizations are storing more data i.e. videos, images, blogs, etc. besides structured data for decision making. Similarly, social media and scientific applications are generating large amount of semi-structured data of varied nature. Relational databases cannot process properly and manage such large amount of data efficiently. To overcome this problem, another paradigm NoSQL databases is introduced to manage and process massive amount of unstructured data efficiently. NoSQL databases are divided into four categories and each category is used according to the nature and need of the specific problem. In this paper we will compare Oracle relational database and NoSQL graph database using optimized queries and physical database tuning techniques. The comparison is two folded: in the first iteration we compare various kinds of queries such as simpler query, database tuning of Oracle relational database such as sub databases and perform these queries in our desired environments. Secondly, for this comparison we will perform predictive analysis for the results obtained from our experiments.
No Need to Fear Peer Evaluation: an Alternate Model for Expert and Novice Evaluations in Business Studies

This research was conducted to determine if there were consistent differentials, or patterns in the peer grading that could be utilized to further understand the potential impact on student grades with the use of summative peer evaluations in this presentation style of interactive assessment activity for first year business students. The data was reviewed in aggregate, and then on individual, booth by booth comparison. The evaluation grades from the peer or ‘novice’ evaluators were within the same range as those provided by the faculty or ‘expert’ evaluators. The research also introduced a variant on peer evaluation as the peer evaluators were senior year students three years ahead of their ‘peers’. The available information on peer assessment studies targeting year one students is limited (Nulty, 2011) and this case study provides further evidence of the use of peer evaluation in first year of post-secondary.
Multichannel Cochlear Implants in Partially Ossified Cochleas

Deposition of bone within the fluid spaces of the cochlea is encountered commonly in cochlear implant candidates and previously has been considered a relative contraindication to the use of multichannel intracochlear electrodes. This contraindication has been based on possible mechanical difficulty with electrode insertion as well as uncertainty about the potential benefit of the multichannel device in the patient. Fifteen profoundly deaf patients with partial ossification of the basal turn of the cochlea received implants with long intracochlear electrodes (11, Nucleus; 1, University of California at San Francisco/Storz; and 3, Symbion/Inneraid). In 11 cases, ossification had been predicted preoperatively by computed tomographic scan. Electrodes were completely inserted in 14 patients, and partial insertion was accomplished in one patient. All patients currently are using their devices and nine of 12 postlingually deaf patients have achieved some degree of open-set speech discrimination. This series demonstrates that in experienced hands, insertion of long multichannel electrodes into partially ossified cochleas is possible and that results are similar to those achieved in patients who have nonossified cochleas.
Cartesian path planning for arc welding robots: Evaluation of the descartes algorithm

Many industrial robot applications require fewer task constraints than the robot's degrees of freedom. For welding robots, for example, rotations of the welding torch around its axis do not negatively impact welding quality. Furthermore, the tool center point's Cartesian position and desired orientation as a function of time is often determined by the (manufacturing) process. Nevertheless, programming these robots can be time consuming. Reducing or eliminating this programming cost will allow robots to be used for producing small series. Recently, a promising software package for Cartesian path planning with the name Descartes was released by the ROS-Industrial community. To the authors' knowledge, an in-depth description of this algorithm and an experimental evaluation is lacking in literature. This paper describes the path planning approach used by the Descartes package. Moreover, the software's performance is evaluated for several key robot welding tasks and the encountered limitations are discussed. In addition, we show that the planner's performance can be improved by changing the cost function that the planner's graph search algorithm minimises.
A comprehensive review on wormhole attacks in MANET

As MANETs use wireless medium for communication, these are vulnerable to many security attacks. In this paper a comprehensive review is done on the very recent state of the art research results on wormhole attacks and relevant mitigation measures. 100% of the works reviewed here are published in last five years, out of which 80% are published in last three years. The simulation results in NS2 helps to quantify the comparative performances of the different solutions proposed.
Evolved Sensor Fusion and Dissociation in an Embodied Agent

W. Grey Walter first demonstrated that an autonomous robot could follow an environmental gradient to its source. In this paper, neural networks are evolved that allow a simulated, embodied quadrupedal agent to sense and follow an environmental gradient—in this case, local chemical concentration—to its source. Through a series of ablation experiments performed in silico, it is shown how artificial evolution gradually integrates and dissociates the different sensor modalities available to the agent in order to produce chemotacting behaviour. This work builds on that of Walter by indicating that evolutionary methods automatically generate chemotaxis by modulating simpler behaviours (here, forward locomotion) using a sensor modality (chemosensors) separate from those driving the simpler behaviour. This suggests that evolutionary methods are well suited for automatically generating behaviours more complex than chemotaxis by using it in turn as a base behaviour.