Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal Strain Persistence of Candida albicans Isolates from Chronic Mucocutaneous Candidiasis Patients

Chronic mucocutaneous candidiasis (CMC) is a primary immunodeficiency disorder characterised by susceptibility to chronic Candida and fungal dermatophyte infections of the skin, nails and mucous membranes. Molecular epidemiology studies of CMC infection are limited in number and scope and it is not clear whether single or multiple strains inducing CMC persist stably or are exchanged and replaced. We subjected 42 C. albicans individual single colony isolates from 6 unrelated CMC patients to multilocus sequence typing (MLST). Multiple colonies were typed from swabs taken from multiple body sites across multiple time points over a 17-month period. Among isolates from each individual patient, our data show clonal and persistent diploid sequence types (DSTs) that were stable over time, identical between multiple infection sites and exhibit azole resistant phenotypes. No shared origin or common source of infection was identified among isolates from these patients. Additionally, we performed C. albicans MLST SNP genotype frequency analysis to identify signatures of past loss of heterozygosity (LOH) events among persistent and azole resistant isolates retrieved from patients with autoimmune disorders including CMC.
FePt nanoparticles as a potential X-ray activated chemotherapy agent for HeLa cells

Nanomaterials have an advantage in “personalized” therapy, which is the ultimate goal of tumor treatment. In order to investigate the potential ability of FePt nanoparticles (NPs) in the diagnosis and chemoradiotherapy treatment of malignant tumors, superparamagnetic, monodispersed FePt (~3 nm) alloy NPs were synthesized, using cysteamine as a capping agent. The NPs were characterized by means of X-ray diffraction; transmission electron microscopy, Physical Property Measurement System, and Fourier transform infrared spectroscopy. The cytotoxicity of FePt NPs on Vero cells was assessed using an MTT assay, and tumor cell proliferation inhibited by individual FePt NPs and FePt NPs combined with X-ray beams were also collected using MTT assays; HeLa human cancer cell lines were used as in vitro models. Further confirmation of the combined effect of FePt NPs and X-rays was verified using HeLa cells, after which, the cellular uptake of FePt NPs was captured by transmission electron microscopy. The results indicated that the growth of HeLa cells was significantly inhibited by FePt NPs in a concentration-dependent manner, and the growth was significantly more inhibited by FePt NPs combined with a series of X-ray beam doses; the individual NPs did not display any remarkable cytotoxicity on Vero cells at a concentration <250 μg/mL. Meanwhile, the FePt NPs showed negative/positive contrast enhancement for MRI/CT molecule imaging at the end of the study. Therefore, the combined results implied that FePt NPs might potentially serve as a promising nanoprobe for the integration of tumor diagnosis and chemoradiotherapy.
Generalized PDE Framework for Image Super Resolution

In this paper, we present a generalized partial differential equation (PDE) method with a generalized regularization term for super-resolution. The generalized regularization term based on fractional order derivatives which can be seem as a generalization of the total variation (TV) regularization term and two order regularization term, which it is possible to obtain better super resolution results in terms of both the similarity of the images and smoothness of the high resolution image. Experiments show the proposed method improves the objective quality as well as the subjective visual quality of the high-resolution images.
EXCEPTION HANDLING AND SOFTWARE-FAULT TOLERANCE

A general model allowing a unified understanding of programmed exception handling (forward recovery) and default exception handling (backward recovery) in systems structured as hierarchies of data abstractions is presented. The cause-effect relationship between software design faults and failure occurrences is explored and the adequacy of backward recovery in providing effective software-fault tolerance is discussed.
Combing Multilevel Green's Function Interpolation Method with Volume Loop Bases for Inductance Extraction Problems

In this paper,a fast integral equation method is developed for extracting the inductances in RF ICs,RF MEMs,IC packages,and deep submicron ICs etc. This method combines a recently developed Multilevel Green's Function Interpolation Method (MLGFIM) (1,2) with the volume integral equation discretized using Volume Loop (VL) basis functions. In it,instead of using the filaments model to simulate the currents flowing in the inductors,we use the conventional SWG basis functions for this kind of basis functions is flexible for problems with complex geometries. The shortest path finding algorithm is also used to find the source loop basis functions. The inductance extractions from the straight line,the spiral inductors,the bump,and the parallel buses in this paper demonstrate the validity and efficiency of this hybrid method.
A User-oriented Multi-service Access Control System

Web-based services have become a major commodity. As an increasing number of ISPs make available an even more increasing number of remote services, security becomes a major concern in order to accomplish a fair exchange of commodities in insecure environments. An exchange of services, in order to be fair and secure, usually involves the service provider, the service requestor and a trusted third party on whose impartiality both rely. In order to provide and receive secure web-based services, trust can be accomplished by means of thorough identification and strong authentication of all the participants. The use of electronic credentials is one way of formal identification and authentication and the adoption of a unique worldwideaccepted digital credential stored in a smart card will provide a higher level of security while allowing total mobility with secure transactions over the web. While this adoption does not take place, the widespread use of digital credentials will inevitably lead to each service requestor having to be in possession of many smart cards just for storing the different electronic credentials needed for all the services he uses. We present a new approach for the use of smart cards as a basis for secure management of web-based services leading to the use of only one smart card per user in a perfectly transparent manner, thus contributing for a more generalized use of the technology.
Effects of exercise training in patients with idiopathic pulmonary arterial hypertension

We determined the physiological effects of exercise training on exercise capacity and quadriceps muscle function in patients with idiopathic pulmonary arterial hypertension (iPAH). In total, 19 clinically stable iPAH patients (New York Heart Association II-III) underwent a supervised exercise training programme for the duration of 12 weeks. Maximal capacity, endurance capacity and quadriceps function were assessed at baseline and after 12 weeks. In 12 patients, serial quadriceps muscle biopsies were obtained. 6-min walk distance and peak exercise capacity did not change after training. However, endurance capacity improved significantly after training, demonstrated by a shift of the anaerobic threshold to a higher workload (from 32±5 to 46±6 W; p = 0.003) together with an increase in exercise endurance time (p<0.001). Moreover, exercise training increased quadriceps strength by 13% (p = 0.005) and quadriceps endurance by 34% (p = 0.001). Training enhanced aerobic capacity of the quadriceps, by increasing capillarisation (1.36±0.10 to 1.78±0.13 capillaries per muscle fibre; p<0.001) and oxidative enzyme activity, especially of the type-I (slow) muscle fibres. No changes were found in cross-sectional area and fibre type distribution. Exercise training in iPAH improves exercise endurance and quadriceps muscle function, which is also reflected by structural changes of the quadriceps.
Selection for energy balance in dairy cows.

In high-yielding dairy cows, the peak of daily feed intake usually occurs after the peak of milk output. This disassociation in timing leads to a period in early lactation when cows cannot meet their energy requirements solely from ingested feed energy and they mobilise body energy to meet the deficit. This state is commonly known as negative energy balance (NEB) and is negatively associated with a range of health traits (Collard et al., 2000; Gillund et al., 2001) and fertility (Veerkamp et al., 2000; Wathes et al., 2002; Dechow et al., 2002). It can generally be considered to be undesirable not only for its direct economic cost but also for its potential effect on the health of the cow from a welfare viewpoint (Nielsen et al., 1998). Selection indices may have favoured bulls whose daughters use body lipid in early life at the expense of production, health and fertility in later life. This has created increasing interest in BCS in dairy cows both as an important management tool and also for use in selection indices. A number of countries (including the UK, Netherlands and Ireland) now collect BCS as part of a national type assessment scheme.
Body Fat Percentage Is a Major Determinant of Total Bilirubin Independently of UGT1A1*28 Polymorphism in Young Obese

Objectives Bilirubin has potential antioxidant and anti-inflammatory properties. The UGT1A1*28 polymorphism (TA repeats in the promoter region) is a major determinant of bilirubin levels and recent evidence suggests that raised adiposity may also be a contributing factor. We aimed to study the interaction between UGT1A1 polymorphism, hematological and anthropometric variables with total bilirubin levels in young individuals. Methods 350 obese (mean age of 11.6 years; 52% females) and 79 controls (mean age of 10.5 years; 59% females) were included. Total bilirubin and C-reactive protein (CRP) plasma levels, hemogram, anthropometric data and UGT1A1 polymorphism were determined. In a subgroup of 74 obese and 40 controls body composition was analyzed by dual-energy X-ray absorptiometry. Results The UGT1A1 genotype frequencies were 49.9%, 42.7% and 7.5% for 6/6, 6/7 and 7/7 genotypes, respectively. Patients with 7/7 genotype presented the highest total bilirubin levels, followed by 6/7 and 6/6 genotypes. Compared to controls, obese patients presented higher erythrocyte count, hematocrit, hemoglobin and CRP levels, but no differences in bilirubin or in UGT1A1 genotype distribution. Body fat percentage was inversely correlated with bilirubin in obese patients but not in controls. This inverse association was observed either in 6/7 or 6/6 genotype obese patients. UGT1A1 polymorphism and body fat percentage were the main factors affecting bilirubin levels within obese patients (linear regression analysis). Conclusion In obese children and adolescents, body fat composition and UGT1A1 polymorphism are independent determinants of total bilirubin levels. Obese individuals with 6/6 UGT1A1 genotype and higher body fat mass may benefit from a closer clinical follow-up.
The experience of social and emotional loneliness among older people in Ireland

ABSTRACT This paper reports a study of the risk factors for social and emotional loneliness among older people in Ireland. Using the ‘Social and Emotional Scale for Adults’, the social and emotional dimensions of loneliness were measured. Emotional loneliness was conceptualised as having elements of both family loneliness and romantic loneliness. The data were collected through a national telephone survey of loneliness in older people conducted in 2004 that completed interviews with 683 people aged 65 or more years. It was found that levels of social and family loneliness were low, but that romantic loneliness was relatively high. Predictors for social loneliness were identified as greater age, poorer health, living in a rural area, and lack of contact with friends. Living in a rural setting, gender (male), having a lower income, being widowed, no access to transport, infrequent contact with children and relatives and caring for a spouse or relative at home were significant predictors of family loneliness. Romantic loneliness was predicted by marital status, in particular being widowed. Never having married or being divorced or separated were also significant predictors for romantic loneliness. The findings indicate that loneliness for older people is variable, multi-dimensional and experienced differently according to life events, with, for example, the death of a partner being followed by the experience of emotional loneliness, or the loss of friends or declining health leading to social loneliness.
High-Throughput Transposon Mutagenesis of Corynebacterium glutamicum and Construction of a Single-Gene Disruptant Mutant Library

ABSTRACT A simple and high-throughput transposon-mediated mutagenesis system employing two different types of transposons in combination with direct genomic DNA amplification and thermal asymmetric interlaced PCR (TAIL-PCR) was developed. Each of the two minitransposons based on IS31831 (ISL3 family) and Tn5 (IS4 family) was integrated into the Corynebacterium glutamicum R genome. By using BLAST and Perl, transposon insertion locations were automatically identified based on the sequences of TAIL-PCR products of mutant cells. Insertion locations of 18,000 mutants were analyzed, and a comprehensive insertion library covering nearly 80% of the 2,990 open reading frames of C. glutamicum R was generated. Eight thousand of the mutants, exhibiting disruption in 2,330 genes, survived on complex medium under normal laboratory conditions, indicating that the genes were not essential for cell survival. Of the 2,330 genes, 30 exhibited high similarity to essential genes of Escherichia coli or Bacillus subtilis. This approach could be useful in furthering genetic understanding of cellular life and facilitating the functional analysis of microorganisms.
Automated learning of subcellular location patterns in confocal fluorescence images from human protein atlas

Proper subcellular location of proteins is critical to cell function. Hence defining and identifying characteristics of subcellular patterns on a proteome-wide basis has gained more and more attention. Due to the larger and larger data sets that have become possible (e.g. through high-throughput microscopy), researchers have been utilizing automated methods for systematic study of location proteomics, most of which combine fluorescence microscopy techniques with pattern recognition and machine learning algorithms so that we can obtain objective and consistent results. In this dissertation, we describe two methodologies to automatically analyze and recognize protein subcellular location patterns. One is under the framework of Discriminative Models. We develop both supervised (classification) and unsupervised (clustering) learning methods to automatically and accurately recognize patterns and to define the concept of "location neighbors". In the other field of Generative Models, we aim to explore the biophysical characteristics that underlie the appearance of the patterns seen in images. Using this approach, not only can we produce compact representations of subcellular patterns, but we can potentially combine models of patterns of different proteins into a single instance (image). The goal is to build up an intact virtual cell with properly organized cell components. Towards this end, we extend and improve generative models for microtubule distribution and use them to identify differences in microtubule patterns between human cell lines. Further, we model the conditional dependence of vesicles on microtubules and simulate the distribution of vesicular proteins from this graphical model.
A general approach for automating outliers identification in categorical data

Outliers identification algorithms for categorical datasets strongly depend on parameter settings that require prior information about the data, e.g. number of outliers in the data, maximum length of itemsets and/or minimum support for frequent itemsets. These input parameters are classified into two groups; (a) intrinsic parameters which are required by an outliers detection method to produce a score measure to each object and (b) decision parameters which are required for deciding on whether an object is an outlier based on the score. In this paper, a general approach for automating decision parameters of outliers identification in multivariate categorical data is proposed. The added value of the proposed approach is that it can be used by any outliers detection algorithm for categorical data that produces a score measure for each object. We provide a simulation approach for computing critical values for any outliers detection algorithm. These critical values are distribution-free statistical measures. They are also based on data-driven characteristics, hence they can be used for the identification of outliers based on the score measure produced by the algorithm. We illustrate this approach using two outliers detection algorithms. Furthermore, real and synthetic datasets are used to evaluate the performance of the proposed approach.
Dynamic Determinants of the Uncontrolled Manifold during Human Quiet Stance

Human postural sway during stance arises from coordinated multi-joint movements. Thus, a sway trajectory represented by a time-varying postural vector in the multiple-joint-angle-space tends to be constrained to a low-dimensional subspace. It has been proposed that the subspace corresponds to a manifold defined by a kinematic constraint, such that the position of the center of mass (CoM) of the whole body is constant in time, referred to as the kinematic uncontrolled manifold (kinematic-UCM). A control strategy related to this hypothesis (CoM-control-strategy) claims that the central nervous system (CNS) aims to keep the posture close to the kinematic-UCM using a continuous feedback controller, leading to sway patterns that mostly occur within the kinematic-UCM, where no corrective control is exerted. An alternative strategy proposed by the authors (intermittent control-strategy) claims that the CNS stabilizes posture by intermittently suspending the active feedback controller, in such a way to allow the CNS to exploit a stable manifold of the saddle-type upright equilibrium in the state-space of the system, referred to as the dynamic-UCM, when the state point is on or near the manifold. Although the mathematical definitions of the kinematic- and dynamic-UCM are completely different, both UCMs play similar roles in the stabilization of multi-joint upright posture. The purpose of this study was to compare the dynamic performance of the two control strategies. In particular, we considered a double-inverted-pendulum-model of postural control, and analyzed the two UCMs defined above. We first showed that the geometric configurations of the two UCMs are almost identical. We then investigated whether the UCM-component of experimental sway could be considered as passive dynamics with no active control, and showed that such UCM-component mainly consists of high frequency oscillations above 1 Hz, corresponding to anti-phase coordination between the ankle and hip. We also showed that this result can be better characterized by an eigenfrequency associated with the dynamic-UCM. In summary, our analysis highlights the close relationship between the two control strategies, namely their ability to simultaneously establish small CoM variations and postural stability, but also make it clear that the intermittent control hypothesis better explains the spectral characteristics of sway.
The Rise and Decline of Public Interest in Global Warming: Toward a Pragmatic Conception of Environmental Problems

Contents: Introduction Public and Media Interest in Global Warming Common Sense and Scientific Interpretations of Environmental Problems The Epistemology of Global Warming Social Problems and the Taken-For-Granted A Phenomenology of Social Problems Proposed Solutions and Counter Claims Global Warming in the Media World Building, Relevance, and Global Warming Confronting Global Warming Democracy and Environmental Problems References.
Avoiding divergence in the constant modulus algorithm

One of the most popular algorithms for blind equalization is the constant modulus algorithm (CMA), due to its simplicity and low computational cost. However, if the step-size is not properly chosen or if the initialization is distant from the optimal solution, CMA can diverge or converge to undesirable local minima. In order to avoid divergence, we propose a dual-mode algorithm, which works as CMA with a time-variant step-size, but rejects non-consistent estimates of the transmitted signal. We present a deterministic analysis of the stability of the new algorithm for scalar filters. In the vector case, the good performance of the new algorithm is confirmed through numerical simulations.
Long-distance procurement planning in global sourcing

This research discusses procurement planning problems engaged in global sourcing. The main difficulty is caused by the geographically long distance between buyer and supplier, which results in long lead times when maritime transport is used. Customer demands of ﬁnished products usually evolve during the shipment, thus extra costs will be produced due to unpredictable overstocks or stockouts. This thesis presents adaptive planning approaches to make adequate long-distance procurement plans in a cost-efficient manner. Firstly, an adaptive procurement planning framework is presented. The framework deploys demand forecasting and optimal planning in a rolling horizon scheme. In each subhorizon, demands are assumed to follow some known distribution patterns, while the distribution parameters will be estimated based on up-to-date demand forecasts and forecast accuracy. Then a portable processing module is presented to transform the sub-horizon planning problem into an equivalent standard lot-sizing problem with stochastic demands.Secondly, optimal or near-optimal procurement planning methods are developed to minimize expected total costs including setup, inventory holding and stockout penalty in subhorizons. Two extreme stockout assumptions are considered: backorder and lost sale (or outsourcing). The proposed methods can serve as benchmarks to evaluate other methods. Numerical tests have validated the high efficiency and effectiveness of both sub-horizon planning methods and the overall adaptive planning approaches.
A Fuzzy-Based CAC Scheme for Wireless Cellular Networks Considering Different Priorities

The mobile cellular systems are expected to support multiple services with guaranteed Quality of Service(QoS). But, the ability of wireless systems to accommodate expected growth of traffic load and broadband services is limited by available radio frequency spectrum. Call Admission Control (CAC) is one of the resource management functions, which regulates network access to ensure QoS provisioning. However, the decision for CAC is very challenging issue due to user mobility, limited radio spectrum, and multimedia traffic characteristics. In our previous work, we proposed a fuzzy-based CAC system by considering the priority of the on-going connections. As priority parameter, we considered only one parameter (service request). In this work, we extend our work by adding different priorities. We call this system FACS-MP. We evaluate by simulations the performance of the proposed system. From the simulations results, we conclude that the FACS-MP can differentiate better different services compared with previous system.