Miracle-dz/UniFAR-FTUs huggingface dataset:
Unusual resistance patterns in macrolide-resistant Streptococcus pyogenes harbouring erm(A).

BACKGROUND We identified erm(A)-harbouring Streptococcus pyogenes that expressed three variant phenotypes: (1) low-level resistance to erythromycin (MICs 1-4 mg/L) but high azithromycin MICs in absolute terms (16-64 mg/L; n=6); (2) same as (1) but with a high clindamycin MIC (256 mg/L; n=1); and (3) high-level constitutive MLS (cMLS) resistance (n=1). Here we analysed the genetic basis of these novel phenotypes. METHODS The presence of erm(A) and the absence of macrolide/lincosamide resistance genes erm(B), mef and cfr were confirmed by PCR. erm(A), 23S rRNA, L4 and L22 genes were sequenced. Mutant erm(A) genes were cloned and electrotransformed into the macrolide-susceptible Escherichia coli AG100A. Clonality was determined by emm typing and PFGE. Effects of the identified mutations on free energy changes (DeltaG) and putative configurations of the leader sequence were studied in silico. RESULTS Point mutations (G98A, A137C, C140T and G205A) were observed in the erm(A) regulatory region of all eight erm(A)-harbouring S. pyogenes. Five and two isolates belonged to emm77 and emm89 clones, respectively, and one isolate was an emm1. E. coli transformed with mutant erm(A) harbouring G98A, A137C or C140T mutations (phenotypes 1 and 2) did not express high-level azithromycin or clindamycin resistance. However, cMLS resistance was clearly observed in transformants with erm(A) harbouring both A137C and G205A mutations (phenotype 3). In silico analysis showed that DeltaG was minor except for the G205A mutation. Secondary structure predictions further showed that the A137C and G205A mutations together abolished the hairpin sequestering the ribosome-binding and initiation sites of the erm(A) gene, explaining the cMLS phenotype 3. CONCLUSIONS We report point mutations in the erm(A) regulatory region leading to constitutive methylase expression and the presence of additional, as yet unidentified mechanisms mediating high-level azithromycin and clindamycin resistance in erm(A)-harbouring S. pyogenes.
Putting contacts into context: mobility modeling beyond inter-contact times

Realistic mobility models are crucial for the simulation of Delay Tolerant and Opportunistic Networks. The long standing benchmark of reproducing realistic pairwise statistics (e.g., contact and inter-contact time distributions) is today mastered by state-of-the-art models. However, mobility models should also reflect the macroscopic community structure of who meets whom. While some existing models reproduce realistic community structure - reflecting groups of nodes who work or live together - they fail in correctly capturing what happens between such communities: they are often connected by few bridging links between nodes who socialize outside of the context and location of their home communities. In a first step, we analyze the bridging behavior in mobility traces and show how it differs to that of mobility models. By analyzing the context and location of contacts, we then show that it is the social nature of bridges which makes them differ from intra-community links. Based on these insights, we propose a Hypergraph to model time-synchronized meetings of nodes from different communities as a social overlay. Applying this as an extension to two existing mobility models we show that it reproduces correct bridging behavior while keeping other features of the original models intact.
Reliability and Short-Term Intra-Individual Variability of Telomere Length Measurement Using Monochrome Multiplexing Quantitative PCR

Background Studies examining the association between telomere length and cancer risk have often relied on measurement of telomere length from a single blood draw using a real-time PCR technique. We examined the reliability of telomere length measurement using sequential samples collected over a 9-month period. Methods and Findings Relative telomere length in peripheral blood was estimated using a single tube monochrome multiplex quantitative PCR assay in blood DNA samples from 27 non-pregnant adult women (aged 35 to 74 years) collected in 7 visits over a 9-month period. A linear mixed model was used to estimate the components of variance for telomere length measurements attributed to variation among women and variation between time points within women. Mean telomere length measurement at any single visit was not significantly different from the average of 7 visits. Plates had a significant systematic influence on telomere length measurements, although measurements between different plates were highly correlated. After controlling for plate effects, 64% of the remaining variance was estimated to be accounted for by variance due to subject. Variance explained by time of visit within a subject was minor, contributing 5% of the remaining variance. Conclusion Our data demonstrate good short-term reliability of telomere length measurement using blood from a single draw. However, the existence of technical variability, particularly plate effects, reinforces the need for technical replicates and balancing of case and control samples across plates.
SU(2) WZW D-BRANES AND QUANTIZED WORLD-VOLUME U(1) FLUX ON S2

We discuss possible D-brane configurations on SU(2) group manifolds in the sigma model approach. When we turn the boundary conditions of the space–time fields into the boundary gluing conditions of chiral currents, we find that for all D-branes except the spherical D2-branes, the gluing matrices Rab depend on the fields, so the chiral Kac–Moody symmetry is broken, but conformal symmetry is maintained. Matching the spherical D2-branes derived from the sigma model with those from the boundary state approach we obtain a U(1) field strength that is consistent with flux quantization.
High-Efficiency Applicator Based on Printed Circuit Board in Millimeter-Wave Region

The purpose of this study is to develop a novel in vitro millimeter-wave (MMW) applicator for an exposure apparatus that allows high power efficiency with reasonably good homogeneity over a sufficient exposure area, as well as the capability of temperature control in biological samples. The applicator is made of a printed circuit board and has a large and circular (90-mm diameter) exposure area that is fed with MMWs using post-wall waveguide technology. The applicator is designed for the exposure of cells to MMWs at 60 GHz. The proposed applicator has an absorption efficiency of 54%, where the absorption efficiency is defined as the ratio of the total power absorbed in the culture medium to the input power. Its efficiency is higher than those of other apparatuses operating at 60 GHz reported in the literature. Most of the cells (89%) are located within the ±5-dB region relative to the average specific absorption rate, which shows reasonably good homogeneity compared with previously reported literature data. The applicator enables efficient temperature control for in vitro experiments to explore unknown and possible nonthermal effects of MMW exposures.
Family caregivers’ quality of life: the case of schizophrenia and affective disorders (A mixed method study)

ii Acknowledgments . iv Chapter 1: Introduction . 1 1.1. Background . 1 1.2. Significance of the study . 5 1.3. Purpose of the study . 7 1.4. Caregiving of mental illness in Iran: an overview of the situation . 8 1.5. Iranian culture with respect to family and health.9 1.6. Mental health services in Iran. 15 Chapter 2: Literature review . 17 2.
Interaction between Calpain-1 and HSP90: New Insights into the Regulation of Localization and Activity of the Protease

Here we demonstrate that heat shock protein 90 (HSP90) interacts with calpain-1, but not with calpain-2, and forms a discrete complex in which the protease maintains its catalytic activity, although with a lower affinity for Ca2+. Equilibrium gel distribution experiments show that this complex is composed by an equal number of molecules of each protein partner. Moreover, in resting cells, cytosolic calpain-1 is completely associated with HSP90. Since calpain-1, in association with HSP90, retains its proteolytic activity, and the chaperone is displaced by calpastatin also in the absence of Ca2+, the catalytic cleft of the protease is not involved in this association. Thus, calpain-1 can form two distinct complexes depending on the availability of calpastatin in the cytosol. The occurrence of a complex between HSP90 and calpain-1, in which the protease is still activable, can prevent the complete inhibition of the protease even in the presence of high calpastatin levels. We also demonstrate that in basal cell conditions HSP90 and calpain-1, but not calpain-2, are inserted in the multi-protein N-Methyl-D-Aspartate receptor (NMDAR) complex. The amount of calpain-1 at the NMDAR cluster is not modified in conditions of increased [Ca2+]i, and this resident protease is involved in the processing of NMDAR components. Finally, the amount of calpain-1 associated with NMDAR cluster is independent from Ca2+-mediated translocation. Our findings show that HSP90 plays an important role in maintaining a given and proper amount of calpain-1 at the functional sites.
Making sense of Community Treatment Orders: the service-user experience

Since their introduction in 2008, Community Treatment Orders (CTOs) have become an increasingly common feature of mental health treatment. Although compulsory community treatment is used in many countries, there is a lack of consistent evidence of its clinical effectiveness and a dearth of methodically robust studies. The international use of CTOs remains contentious based on the ethics of coercion and infringement of autonomy. Detailed understanding and interpretation of the experiential impact on service-users is necessary to inform the ongoing use and development of CTOs. Although some of the extant literature acknowledges the effect of historical and contextual influences on the implementation of CTOs, these influences have not been comprehensively evaluated. Existing exploratory studies reveal wide-ranging, often conflicting responses from service-users, describing mainly ambivalent reactions to a CTO. This indicates a need for rich detailed data and analysis of the service-users’ experience of CTOs. This study aimed to investigate how service-users make sense of their CTO experience. Ten active CTO service-users were purposefully recruited from an Assertive Outreach Team caseload in the north of England. Each participant undertook one or two semi-structured interviews facilitated with photo-journals and diaries. A total of 18 interviews were completed and the data subject to Interpretative Phenomenological Analysis. Themes were generated and organised into three clusters: Pained and Powerless; Alignment and Reconnection; and Consolation and Compensation. Some participants felt powerless to challenge the ‘sentence’ imposed as therapeutic intent. Many participants described feeling disadvantaged, different and labelled, but were also committed to recovery and reintegration into the community. Some participants perceived that small interactions could combine to leave them feeling more secure, less anxious and, paradoxically, more in control. The study proposes a theoretical framework that may unlock the therapeutic potential of CTOs, improving lived experience without compromising their social significance or effectiveness.
Comparative genomics and evolution of proteins involved in RNA metabolism.

RNA metabolism, broadly defined as the compendium of all processes that involve RNA, including transcription, processing and modification of transcripts, translation, RNA degradation and its regulation, is the central and most evolutionarily conserved part of cell physiology. A comprehensive, genome-wide census of all enzymatic and non-enzymatic protein domains involved in RNA metabolism was conducted by using sequence profile analysis and structural comparisons. Proteins related to RNA metabolism comprise from 3 to 11% of the complete protein repertoire in bacteria, archaea and eukaryotes, with the greatest fraction seen in parasitic bacteria with small genomes. Approximately one-half of protein domains involved in RNA metabolism are present in most, if not all, species from all three primary kingdoms and are traceable to the last universal common ancestor (LUCA). The principal features of LUCA's RNA metabolism system were reconstructed by parsimony-based evolutionary analysis of all relevant groups of orthologous proteins. This reconstruction shows that LUCA possessed not only the basal translation system, but also the principal forms of RNA modification, such as methylation, pseudouridylation and thiouridylation, as well as simple mechanisms for polyadenylation and RNA degradation. Some of these ancient domains form paralogous groups whose evolution can be traced back in time beyond LUCA, towards low-specificity proteins, which probably functioned as cofactors for ribozymes within the RNA world framework. The main lineage-specific innovations of RNA metabolism systems were identified. The most notable phase of innovation in RNA metabolism coincides with the advent of eukaryotes and was brought about by the merge of the archaeal and bacterial systems via mitochondrial endosymbiosis, but also involved emergence of several new, eukaryote-specific RNA-binding domains. Subsequent, vast expansions of these domains mark the origin of alternative splicing in animals and probably in plants. In addition to the reconstruction of the evolutionary history of RNA metabolism, this analysis produced numerous functional predictions, e.g. of previously undetected enzymes of RNA modification.
Tracing Bifurcation Branches of High-Dimensional Nonlinear Algebraic Equations Using SPICE

It is very important to calculate the multiple solutions of nonlinear equations, because there are many kind of practical problems in nonlinear electronic circuits and the nonlinear equations in many scientific fields. Therefore, there have been already proposed many algo- rithms for calculating multiple and/or all the solutions. One of the powerful methods is a Newton homotopy technique which can find out the multiple and/or all the solutions lying on the homotopy paths in the global space. Unfortunately, it cannot trace all the solutions when the homotopy path has bifurcation points on it, because the path happens to have separated branches at the point. In this paper, we propose an efficient algo- rithm to find the bifucation points at which a rank of the Jacobian matrix is reduced more than one. After find- ing the points, we fine the directions of branches, and trace them with the arc-length method. Our algorithm is based on the use of Spice and needs not to derive the Jacobian matrix, so that it can be easily applied to many kinds of nonlinear equations.
Digital Storytelling Makes Reading Fun and Entertaining

This paper reports on an ongoing study, which determines whether digital storytelling is fun and entertaining.Since the digital storytelling has attracted research attention, children's experience with regards to fun and entertaining when interacting with it should be studied, because they are the generation to utilize the technology.Hence, this study is carried out.This paper starts with some discussions on the background.It highlights the history of reading materials and their chronology.Also, some previous studies on fun and entertaining are reviewed.Then the activities involved in this study are described, including the development of digital storytelling that adapts the user -centered design approach. Further, a user test of the digital storytelling is elaborated including the results obtained. Next, the results are discussed in relation with the experience, before the conclusion section follows at the end.It was found that digital storytelling is really entertaining and invoking fun.
Enhancing requirements prioritization based on a hybrid technique

There are several requirements prioritization (RP) techniques in software development systems. RP problem is mainly a type of multi-criteria decision making (MCDM) problems. However, selecting an appropriate RP method in a certain situation must subject to a number of evaluation criteria and performance measures. This includes scalability, uncertainty, time consumption and complexity. In this paper, a hybrid-based RP method is proposed. The proposed method is based on a hybrid combination of both of cumulative voting and decision-weighted matrix techniques. The results of an illustrative multiple goals example ensures clarity, simplicity and efficacy of the proposed method.
Towards a Hybrid Federated Cloud Platform to Efficiently Execute Bioinformatics Workflows

Current generation of high-throughput DNA sequencing machines [1, 35, 66] can generate large amounts of DNA sequence data. For example, the machine HiSeq 2000 from the company Illumina, a current workhorse of genome centers, is capable of generating 600 Giga base-pairs of sequence in one single run [35]. The Human Microbiome project (https://commonfund.nih.gov/hmp) and the 1000 Genomes project (http://www.1000genomes.org) are two examples of projects that are generating terabyte-scale amounts of DNA sequence.
Wikipedia in the eyes of its beholders: A systematic review of scholarly research on Wikipedia readers and readership

Hundreds of scholarly studies have investigated various aspects of Wikipedia. Although a number of literature reviews have provided overviews of this vast body of research, none has specifically focused on the readers of Wikipedia and issues concerning its readership. In this systematic literature review, we review 99 studies to synthesize current knowledge regarding the readership of Wikipedia and provide an analysis of research methods employed. The scholarly research has found that Wikipedia is popular not only for lighter topics such as entertainment but also for more serious topics such as health and legal information. Scholars, librarians, and students are common users, and Wikipedia provides a unique opportunity for educating students in digital literacy. We conclude with a summary of key findings, implications for researchers, and implications for the Wikipedia community.
Prolonged Sox4 Expression in Oligodendrocytes Interferes with Normal Myelination in the Central Nervous System

ABSTRACT The highly related transcription factors Sox4 and Sox11 are both expressed in oligodendrocyte precursors. Yet whether they have a function in oligodendrocyte development is unknown. By overexpressing Sox4 under the control of 3.1 kb of 5′ flanking sequences of the myelin basic protein gene in transgenic mice, we extended Sox4 expression in the oligodendrocyte lineage from oligodendrocyte precursors to cells undergoing terminal differentiation. As a consequence of transgene expression, mice develop the full spectrum of phenotypic traits associated with a severe hypomyelination during the first postnatal weeks. Myelin gene expression was severely reduced, and myelin dramatically thinned in several central nervous system (CNS) regions. Despite these disturbances in CNS myelination, the number of oligodendrocytic cells remained unaltered. Considering that apoptosis rates were normal and proliferation only slightly increased, oligodendrocytes likely persist in a premyelinating to early myelinating state. This shows that prolonged Sox4 expression in cells of the oligodendrocyte lineage is incompatible with the acquisition of a fully mature phenotype and argues that the presence of Sox4, and possibly Sox11, in oligodendrocyte precursors may normally prevent premature differentiation.
Shortfall allowed: loss aversion and habit formation

In this paper we analyze a model of consumption and investment when preferences are loss averse around a habit level and investment yields an uncertain return. Loss aversion is the most natural way of modeling the presence of a habit as it explicitly models aversion to below-habit consumption. Existing approaches either neglect the possibility of below-habit consumption or model habit formation by dividing consumption through a habit. Confronting the traditional model using ratios with the outcome under loss aversion shows that the loss averse model yields a more natural interpretation thus appears more realistic. Starting with an analytical solution for a piecewise-linear utility function, the results are found to be robust for the more general Kahneman-Tversky formulation of the value function.
Improving the Quality of Evidence Elicited from Children Using CUED Recall

Recent amendments to the law allow video recordings of initial interviews with children to be used as evidence in court. In order that children may benefit fully from this change it is crucial that these interviews are of as high a quality as possible and are conducted in a way that is acceptable to the courts. Recently published recommendations for interviewing advocate the use of general, open-ended questions wherever possible (Home Office, 1992) as this technique tends to result in accurate statements. However, recent research has shown that young children questioned in this way are unlikely to report all the relevant information they have. The present recommendations as they stand may in fact discriminate against the very children they are designed to help. This paper demonstrates that the present recommendations are not optimal for interviewing five to six-year-old children and suggests that the use of non-suggestive visual cues may be a way of increasing the overall quality of children's reports.
Emulation of Faults on Cryptoprocessors

this paper describes a block that can be added to a crypto-processor embedded on a FPGA. This block enables to simulate the coprocessor behaviour when faults are injected. Three fault models are used and an example with AES is given. The aim of such a block is to speed up the test of countermeasures on a FPGA before running the chip in fab.
RESOLV: Readers' Representation of Reading Contexts and Tasks

We introduce RESOLV, a theoretical model to account for readers' construction and management of goals during text comprehension and use. RESOLV focuses on readers' experience of their physical, social, and communicative context prior to actually engaging with texts. RESOLV assumes that readers construct two types of mental models prior to reading: The context model is a representation of the physical and social reading context, whereas the task model is a set of goals and plans that drives readers' decisions and actions in reading. We first present the RESOLV model, and we articulate two core hypotheses. We then present and discuss evidence supporting these hypotheses, from past and more recent research conducted in our labs, as well as in others'. The data support the view that reading decisions and processes are guided by readers' perceptions and attributions regarding the task statement but also more implicit cues from the reading context.