Miracle-dz/UniFAR-FTUs huggingface dataset:
Principles and Applications of LC-MS/MS for the Quantitative Bioanalysis of Analytes in Various Biological Samples

Standard technology for analyte detection in clinical chemistry fields rely on indirect characteristics of an analyte, e.g. its absorption capability of light, chemical reactivity or physicochemical interaction with macro-molecules as like antigen-antibody interaction. Otherwise, analytes are detected directly from molecular characteristics as molecular mass and molecular disintegration patterns in mass spectrometric method. Thus, mass spectrometric technology are very attractive for the quantification of biomarkers or chemicals in the context of diagnostic procedures since those techniques can be provide higher quality of analysis of much higher specificity compared to standard technologies such as photometry or ligand-binding tests. Even if gas chromatography-mass spectrometry (GC-MS) is first introduced mass spectrometric methods to laboratory medicine about 40 years ago and provide highly specific and sensitive quantification of thermo-stable molecules below a molecular weight of about 500, application of GC-MS method remained restricted to few specialized institution in laboratory medicine such as mainly toxicology laboratories, medical centres, and reference laboratories. The handling and maintenance of GC-MS instruments is very demanding and time-consuming; sample preparation is very laborious and includes procedures of sample extraction and analyte derivatisations and long run time with a typical sample throughput of less than 50 samples per day. Over the past decade with introduction of atmospheric pressure ionization (API) techniques, liquid chromatography-mass spectrometry (LC-MS) has undergone tremendous technological improvement allowing for its applications to endogenous components such as proteins, peptides, carbohydrates, DNA, and drugs or metabolites. Furthermore, powerful new technologies of ion-analyses (tandem MS, timeof-flight MS, ion-trap MS) substantially increased the capabilities of MS analyzers with respect to specificity and to the extent of data read out. These developments suggest a more widespread use of MS techniques superior to other analytical methods in routine laboratory medicine. The aims of this chapter is to comprehensively characterize the basic principles of mass spectrometric detection, recent development of MS, bottleneck of LC-MS method associate
Exploiting Fitness Apps for Sustainable Mobility - Challenges Deploying the GoEco! App

The large interest in analyzing one’s own fitness led to the development of more and more powerful smartphone applications. Most are capable of tracking a user’s position and mode of locomotion, data that do not only reflect personal health, but also mobility choices. A large field of research is concerned with mobility analysis and planning for a variety of reasons, including sustainable transport. Collecting data on mobility behavior using fitness tracker apps is a tempting choice, because they include many of the desired functions, most people own a smartphone and installing a fitness tracker is quick and convenient. However, as their original focus is on measuring fitness behavior, there are a number of difficulties in their usage for mobility tracking. In this paper we denote the various challenges we faced when deploying GoEco! Tracker (an app using the Moves fitness tracker to collect mobility measurements), and provide an analysis on how to best overcome them. Finally, we summarize findings after one month of large scale testing with a few hundred users within the GoEco! living lab performed in Switzerland.
Automatic EMI filter design for power electronic converters oriented to high power density

In this paper, a complete computer aided procedure based on the power density concept and aimed at the automatic design of EMI filters for power electronic converters is presented. It is rule-based, and it uses suitable databases built-up by considering information on passive components available from commercial datasheets. The power density constraint is taken into consideration by imposing the minimization of the filter volume and/or weight; nevertheless, the system in which the automatically designed filter is included satisfies the electromagnetic compatibility standards limits. Experimental validations of the proposed procedure are presented for two real case studies, for which the performance and the size of the best filter design are compared with those related to a conventionally designed one.
Intersubject variability and induced gamma in the visual cortex: DCM with empirical Bayes and neural fields

This article describes the first application of a generic (empirical) Bayesian analysis of between‐subject effects in the dynamic causal modeling (DCM) of electrophysiological (MEG) data. It shows that (i) non‐invasive (MEG) data can be used to characterize subject‐specific differences in cortical microcircuitry and (ii) presents a validation of DCM with neural fields that exploits intersubject variability in gamma oscillations. We find that intersubject variability in visually induced gamma responses reflects changes in the excitation‐inhibition balance in a canonical cortical circuit. Crucially, this variability can be explained by subject‐specific differences in intrinsic connections to and from inhibitory interneurons that form a pyramidal‐interneuron gamma network. Our approach uses Bayesian model reduction to evaluate the evidence for (large sets of) nested models—and optimize the corresponding connectivity estimates at the within and between‐subject level. We also consider Bayesian cross‐validation to obtain predictive estimates for gamma‐response phenotypes, using a leave‐one‐out procedure. Hum Brain Mapp 37:4597–4614, 2016. © The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
Thermal-aware kernel mapping for three-dimensional multi-mode channel decoding

In this work, three thermal-aware kernel mappings are proposed for a three-dimensional multi-mode channel decoding architecture. The proposed kernel mappings can reduce the peak temperature and support different thermal and latency constraints. In our experiments, we show the peak temperature can be reduced from 16.2°C~33.8°C. Besides, we also demonstrate that different mapping is chosen under different thermal and latency constraints.
Overcoming blockages to Collective Innovation in Digital Infrastructures: the Case of Mobile Payment

Decentralized digital technologies increasingly enable multiple organizations to co-create digital infrastructures. However, collective innovation processes often come to a stand-still because of conflicting interests and business models. While existing research suggests various factors that block collective innovation processes, there is still little understanding of how organizations can overcome these blockages. In this paper, we identify patterns that explain how organizations overcome blockages of collective innovation processes for digital infrastructures. We follow a processual approach and develop a conceptual framework based on collective action theory. We evaluate the framework through a longitudinal case study on mobile payment infrastructure development. We find various reconfiguration processes that organizations use to overcome blockages of collective innovation. Theoretically, this paper contributes to the emerging body of research in the Information Infrastructure literature, which utilizes the collective action perspective and related models and frameworks to understand and explain underlying complexities in the digital infrastructures.
Non-culture based diagnostics for intravascular catheter related bloodstream infections

ABSTRACT Introduction: intravascular catheter related bloodstream infection (IVC-BSI) is a leading cause of nosocomial infections and associated with significant morbidity and mortality. Early detection and adequate treatment of causative pathogens is critical for a favourable outcome. However, it takes significant time to receive microbiological results due to the current reference diagnostic method’s reliance on microbial growth. Areas covered: This review discusses culture and non-culture based techniques for the diagnosis of non IVC-BSI and IVC-BSI, including molecular methods and biomarkers. Different diagnostic strategies are evaluated and the potential of new generation of diagnostic assays highlighted. Expert commentary: The development of additional diagnostic methods has potential to beneficially supplement conventional culture diagnosis, and molecular techniques have particular potential to fulfil this need. They would also contribute significant new knowledge on the bacterial species present on catheters that are generally missed by diagnosis using traditionally culture-dependent methods. Advances in molecular strategies, together with new biomarkers, might lead to the development of faster, more sensitive and cheaper technologies and instruments. This review aims to provide a platform for the further development of IVCBSI diagnostic techniques.
The Story of ChronoShare, or How NDN Brought Distributed Secure File Sharing Back

Information sharing among a group of friends or colleagues in real life is usually a distributed process: we tell each other interesting or important news without any mandatory assistance or approval from a third party. Surprisingly, this is not what happens when sharing files among a group of friends over the Internet. While the goal of file sharing is to disseminate files among multiple parties, due to the constraints imposed by IP's point-to-point communication model, most of today's file sharing applications, such as Drop box, Google Drive, etc., resort to a centralized design paradigm: a user first uploads files to the server (cloud), and the server (cloud) re-distributes these files to other users, resulting in unnecessary tussles and inefficient data distribution paths. To bring the truly distributed file sharing back into the cyberspace, this paper presents Chrono Share, a distributed file sharing application built on top of the Named Data Networking (NDN) architecture. By walking through Chrono Share design details, we show how file sharing, as well as many other similar applications, can be effectively implemented over NDN in a truly distributed and secure manner.
Efficient phagocytosis and laccase activity affect the outcome of HIV-associated cryptococcosis.

BACKGROUND Cryptococcal meningitis (CM) is a leading cause of HIV-associated mortality globally. High fungal burden in cerebrospinal fluid (CSF) at diagnosis and poor fungal clearance during treatment are recognized adverse prognostic markers; however, the underlying pathogenic factors that drive these clinical manifestations are incompletely understood. We profiled a large set of clinical isolates for established cryptococcal virulence traits to evaluate the contribution of C. neoformans phenotypic diversity to clinical presentation and outcome in human cryptococcosis. METHODS Sixty-five C. neoformans isolates from clinical trial patients with matched clinical data were assayed in vitro to determine murine macrophage uptake, intracellular proliferation rate (IPR), capsule induction, and laccase activity. Analysis of the correlation between prognostic clinical and host immune parameters and fungal phenotypes was performed using Spearman's r, while the fungal-dependent impact on long-term survival was determined by Cox regression analysis. RESULTS High levels of fungal uptake by macrophages in vitro, but not the IPR, were associated with CSF fungal burden (r = 0.38, P = 0.002) and long-term patient survival (hazard ratio [HR] 2.6, 95% CI 1.2-5.5, P = 0.012). High-uptake strains were hypocapsular (r = -0.28, P = 0.05) and exhibited enhanced laccase activity (r = 0.36, P = 0.003). Fungal isolates with greater laccase activity exhibited heightened survival ex vivo in purified CSF (r = 0.49, P < 0.0001) and resistance to clearance following patient antifungal treatment (r = 0.39, P = 0.003). CONCLUSION These findings underscore the contribution of cryptococcal-phagocyte interactions and laccase-dependent melanin pathways to human clinical presentation and outcome. Furthermore, characterization of fungal-specific pathways that drive clinical manifestation provide potential targets for the development of therapeutics and the management of CM. FUNDING This work was made possible by funding from the Wellcome Trust (WT088148MF), the Medical Research Council (MR/J008176/1), the NIHR Surgical Reconstruction and Microbiology Research Centre and the Lister Institute for Preventive Medicine (to R.C. May), and a Wellcome Trust Intermediate fellowship (089966, to T. Bicanic). The C. neoformans isolates were collected within clinical trials funded by the British Infection Society (fellowship to T. Bicanic), the Wellcome Trust (research training fellowships WT069991, to A.E. Brouwer and WT081794, to J.N. Jarvis), and the Medical Research Council, United Kingdom (76201). The funding sources had no role in the design or conduct of this study, nor in preparation of the manuscript.
QR code localization using deep neural networks

Usage of computer-readable visual codes became common in our everyday life at industrial environments and private use. The reading process of visual codes consists of two steps, localization and data decoding. This paper introduces a new method for QR code localization using conventional and deep rectifier neural networks. The structure of the neural networks, regularization, and training parameters, like input vector properties, amount of overlapping at samples, and effect of different block sizes are evaluated and discussed. Results are compared to localization algorithms of the literature.
Synaptic and extrasynaptic traces of long-term memory: the ID molecule theory

Abstract It is generally assumed at the time of this writing that memories are stored in the form of synaptic weights. However, it is now also clear that the synapses are not permanent; in fact, synaptic patterns undergo significant change in a matter of hours. This means that to implement the long survival of distant memories (for several decades in humans), the brain must possess a molecular backup mechanism in some form, complete with provisions for the storage and retrieval of information. It is found below that the memory-supporting molecules need not contain a detailed description of mental entities, as had been envisioned in the ‘memory molecule papers’ from 50 years ago, they only need to contain unique identifiers of various entities, and that this can be achieved using relatively small molecules, using a random code (‘ID molecules’). In this paper, the logistics of information flow are followed through the steps of storage and retrieval, and the conclusion reached is that the ID molecules, by carrying a sufficient amount of information (entropy), can effectively control the recreation of complex multineuronal patterns. In illustrations, it is described how ID molecules can be made to revive a selected cell assembly by waking up its synapses and how they cause a selected cell assembly to ignite by sending slow inward currents into its cells. The arrangement involves producing multiple copies of the ID molecules and distributing them at strategic locations at selected sets of synapses, then reaching them through small noncoding RNA molecules. This requires the quick creation of entropy-rich messengers and matching receptors, and it suggests that these are created from each other by small-scale transcription and reverse transcription.
Inducible ablation of mouse Langerhans cells diminishes but fails to abrogate contact hypersensitivity

Langerhans cells (LC) form a unique subset of dendritic cells (DC) in the epidermis but so far their in vivo functions in skin immunity and tolerance could not be determined, in particular in relation to dermal DC (dDC). Here, we exploit a novel diphtheria toxin (DT) receptor (DTR)/DT-based system to achieve inducible ablation of LC without affecting the skin environment. Within 24 h after intra-peritoneal injection of DT into Langerin-DTR mice LC are completely depleted from the epidermis and only begin to return 4 wk later. LC deletion occurs by apoptosis in the absence of inflammation and, in particular, the dDC compartment is not affected. In LC-depleted mice contact hypersensitivity (CHS) responses are significantly decreased, although ear swelling still occurs indicating that dDC can mediate CHS when necessary. Our results establish Langerin-DTR mice as a unique tool to study LC function in the steady state and to explore their relative importance compared with dDC in orchestrating skin immunity and tolerance.
A Review of Vehicle to Vehicle Communication Protocols for VANETs in the Urban Environment

Vehicular Ad-hoc Networks (VANETs) have been gaining significant attention from the research community due to their increasing importance for building an intelligent transportation system. The characteristics of VANETs, such as high mobility, network partitioning, intermittent connectivity and obstacles in city environments, make routing a challenging task. Due to these characteristics of VANETs, the performance of a routing protocol is degraded. The position-based routing is considered to be the most significant approach in VANETs. In this paper, we present a brief review of most significant position based unicast routing protocols designed for vehicle to vehicle communications in the urban environment. We provide them with their working features for exchanging information between vehicular nodes. We describe their pros and cons. This study also provides a comparison of the vehicle to vehicle communication based routing protocols. The comparative study is based on some significant factors such as mobility, traffic density, forwarding techniques and method of junction selection mechanism, and strategy used to handle a local optimum situation. It also provides the simulation based study of existing dynamic junction selection routing protocols and a static junction selection routing protocol. It provides a profound insight into the routing techniques suggested in this area and the most valuable solutions to advance VANETs. More importantly, it can be used as a source of references to other researchers in finding literature that is relevant to routing in VANETs.
Non-equilibrium Green function simulations of graphene, silicene, and germanene nanoribbon field-effect transistors

Ballistic performance of graphene, silicene, and germanene-nanoribbon ﬁeld-e ﬀ ect transistors (FETs) with a gate-length of 10 nm has been numerically investigated. The graphene-nanoribbon FET is found to have the largest ON-current when one compare FETs with a nanoribbon channel having a nearly equal band-gap E g (cid:25) 0 : 5 eV. The graphene device exhibits the largest OFF-current due to the smallest e ﬀ ective-mass enhancing the source-drain direct tunneling.
Enhancing Selectivity in Big Data

Today’s companies collect immense amounts of personal data and enable wide access to it within the company. This exposes the data to external hackers and privacy-transgressing employees. This study shows that, for a wide and important class of workloads, only a fraction of the data is needed to approach state-of-the-art accuracy. We propose selective data systems that are designed to pinpoint the data that is valuable for a company’s current and evolving workloads. These systems limit data exposure by setting aside the data that is not truly valuable.
Motor Activity in Children With Autism: A Review of Current Literature

&NA; Physical therapists have expanded their role and visibility in the treatment of children with autism spectrum disorders (ASD). Limitations in motor activity have not been considered in the assessments of core deficits of this population; however, physical therapists should be prepared to discuss and address these limitations in children with ASD. Purpose: The primary purposes of this review were to summarize current evidence for motor activity limitations in children with ASD and suggest further areas of research in physical therapy and autism while considering how physical therapy may benefit children with autism. Method: A literature search was carried out in 2009 and 2010 by using multiple search engines. Results: Forty-nine articles met inclusion criteria and were included in the review. Conclusion: Findings indicate that limitations in motor activity may be present in individuals with ASD, and further research is needed to identify specific functional limitations.
Practice variation in the Dutch long‐term care and the role of supply‐sensitive care: Is access to the Dutch long‐term care equitable?

Abstract Universal access and generous coverage are important goals of the Dutch long‐term care (LTC) system. It is a legal requirement that everyone eligible for LTC should be able to receive it. Institutional care (IC) made up for 90% of Dutch LTC spending. To investigate whether access to IC is as equitable as the Dutch government aspires, we explored practice variation in entitlements to IC across Dutch regions. We used a unique dataset that included all individual applications for Dutch LTC in January 2010–December 2013 (N = 3,373,358). This dataset enabled an accurate identification of the need for care. We examined the local variation in the probability of being granted long‐term IC and in the intensity of the care granted given that individuals have applied for LTC. We also investigated whether the variation observed was related to differences in the local availability of care facilities. Although our analyses indicated the presence of some practice variation, its magnitude was very small by national and international standards (up to 3%). Only a minor part of the practice variation could be accounted for by local supply differences in care facilities. Overall, we conclude that, unlike many other developed countries, the Dutch system ensured equitable access to long‐term IC.
Inferring Social Functions Available in the Metro Station Area from Passengers' Staying Activities in Smart Card Data

The function of a metro station area is vital for city planners to consider when establishing a context-aware Transit-Oriented Development policy around the station area. However, the functions of metro station areas are hard to infer using the static land use distribution and other traditional survey datasets. In this paper, we propose a method to infer the functions occurring around the metro station catchment areas according to the patterns of staying activities derived from smart card data. We first define the staying activities by the spatial and temporal constraints of the two consecutive alighting and boarding records from the individual travel profile. Then we cluster and label the whole staying activities by considering the features of duration, frequency, and start time. By analyzing the percentage of different types of aggregated activities happening around each metro station, we cluster and explore the functions of the metro station area. Taking Wuhan as a case study, we analyze the results of Wuhan metro systems and discuss the similarities and differences between the functions and the land use distribution around the station area. The results show that although there exist some agreements, there is also a gap between the human activities and the land uses around the station area. These findings could give us deeper insight into how people act around the stations by metro systems, which will ultimately benefit the urban planning and policy development.