Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of restriction endonuclease fingerprinting of chromosomal DNA and plasmid profile analysis for characterization of multiresistant coagulase-negative staphylococci in bacteremic neonates

A procedure was developed for restriction endonuclease fingerprinting (REF) of the chromosomal DNA of coagulase-negative staphylococci. A total of 48 isolates comprising 29 Staphylococcus epidermidis and 19 Staphylococcus haemolyticus isolates from blood and mucocutaneous sites of 15 premature neonates were characterized by REF, plasmid profile (PP) analysis, antimicrobial susceptibility testing, biotyping, and slime production. On the basis of REF analysis of chromosomal DNA, the 48 coagulase-negative staphylococcal isolates were subdivided into 10 subgroups, whereas PP analysis subdivided the strains into 20 distinct subgroups. REF analysis of total DNA (i.e., chromosome plus plasmid) resulted in the same 20 subgroups as were subdivided by PP analysis. The high discriminatory power of PP analysis was associated with the variability of plasmid content in coagulase-negative staphylococcal strains isolated during the outbreak. REF patterns were found to be stable both in vitro and in vivo. Isolates carried from 2 to 10 plasmids that ranged in molecular size from 0.9 to 39.5 megadaltons. Plasmids were disseminated among the coagulase-negative staphylococci, regardless of the genetic relatedness of their chromosomal DNAs. Hence, a lack of correlation existed between the grouping of isolates by REF analysis of chromosomal DNA and the grouping by PP analysis. There were one and two distinct chromosomal patterns among 4 of 4 blood cultures and 15 of 15 mucocutaneous cultures of S. haemolyticus, respectively. In contrast, a higher proportion of distinct chromosomal patterns was found for S. epidermidis in blood cultures (7 of 11 cultures) compared with those identified for isolates in mucocutaneous cultures (6 of 18 cultures). In summary, REF analysis of chromosomal DNA, rather than total DNA, is a useful marker for epidemiological investigations of coagulase-negative staphylococci. PP analysis can also be used to provide additional epidemiological information regarding the most recent genetic events.
RNA interference therapy for the Spinocerebellar ataxias

25 Introduction 26 Results 27 Silencing ataxin-7 expression 27 miS4 improves motor phenotypes 29 Reduction of ataxin-7 in the pcs does not induce toxicity 30 miS4 has a therapeutic impact on the SCA7 cerebellum 30 Discussion 32 Materials and methods 35
Ripples on spikes show increased phase‐amplitude coupling in mesial temporal lobe epilepsy seizure‐onset zones

Ripples (80–150 Hz) recorded from clinical macroelectrodes have been shown to be an accurate biomarker of epileptogenic brain tissue. We investigated coupling between epileptiform spike phase and ripple amplitude to better understand the mechanisms that generate this type of pathologic ripple (pRipple) event.
Clinicoeconomics and Outcomes Research Dovepress Medical Resource Utilization and Costs Associated with Autosomal Dominant Polycystic Kidney Disease in the Usa: a Retrospective Matched Cohort Analysis of Private Insurer Data

Background: Autosomal dominant polycystic kidney disease (ADPKD) results in kidney cyst development and enlargement, resulting in chronic kidney disease (CKD) leading to renal failure. This study sought to determine if ADPKD patients in the early stages of CKD contribute to a sizable economic burden for the US health care system. Methods: This was a retrospective, matched cohort study, reviewing medical resource utilization (MRU) and costs for adults in a US private-payer claims database with a diagnosis code of ADPKD (ICD-9-CM 753.13). ADPKD patients were matched by age grouping (0–17, 18–34, 35–44, 45–54, 55–64, and 65+ years) and sex to controls to understand the burden of ADPKD. Descriptive statistics on 6-month MRU and costs were assessed by CKD stages, dialysis use, or previous renal transplant. Results: The analysis included ADPKD patients in CKD stages 1–5 (n=316 to n=860), dialy-sis (n=586), and post-transplant (n=615). Mean ages did not differ across CKD stages (range 43–56 years). Men were the majority in the later stages but the minority in the early stages. The proportion of patients with at least one hospitalization increased with CKD stage, (12% to .40% CKD stage 2 to stage 5, dialysis or post-transplant). The majority had at least one hospital outpatient visit and at least one pharmacy claim. Total 6-month per-patient costs were greater among ADPKD patients than in age-matched and sex-matched healthy non-ADPKD controls (P,0.001 for all comparisons). Conclusion: ADPKD patients with normal kidney function are associated with a significant economic burden to the health care system relative to the general population. Any treatments that delay progression to later stages of CKD may provide potential health care cost offsets.
Central pharmacokinetics of levodopa: Lessons from imaging studies

Functional imaging may be particularly helpful for the assessment of levodopa (l‐dopa) response and long‐term complications of therapy in Parkinson's disease. Radiotracer imaging allows the quantitative determination of regional changes in blood flow and glucose metabolism, as well as alterations in brain connectivity and network activation and changes in dopamine receptors, non‐dopaminergic neurotransmitter systems, and to a lesser extent, signaling pathways downstream to dopamine receptors. The focus of the present article, however, is the application of positron emission tomography (PET) to study the central pharmacokinetics of l‐dopa. Radioligands with limited affinity for the dopamine D2 receptor are sensitive to changes in the levels of synaptic dopamine and can accordingly provide helpful insights into the magnitude and time course of dopamine release after l‐dopa. Prolonged fluorodopa PET scans can be used to estimate the rate of dopamine turnover. Studies performed with these techniques have demonstrated increased dopamine turnover and increased but shorter duration release of dopamine after l‐dopa as Parkinson's disease (PD) progresses, increased release of dopamine in patients with l‐dopa–induced dyskinesia, and that aberrant patterns of dopamine release may actually predict the future development of motor fluctuations. Taken together, the studies provide in vivo validation for the hypothesis that pulsatile stimulation of dopamine receptors plays a critical role in the emergence of long‐term motor complications of therapy. Similar approaches can be used to study the non‐motor complications of PD and its treatment. © 2014 International Parkinson and Movement Disorder Society
Designing interaction as a dialogue game : Linking social and conceptual dimensions of the learning process

Designing and supporting learning interactions that are genuinely engaging, meaningful and conceptually stimulating within online learning contexts remains a significant challenge in contemporary education. One currently popular approach which aims to address some key aspects of this problem, and motivational issues in particular, involves articulating interaction as a game. This Chapter, whilst in support of this approach, will argue that we need to carefully consider digital gaming approaches in terms of the degree to which they both fit with our learning landscape and define how they actually support the development of social or conceptual processes that are involved in learning. We will then describe a 'dialogue game' approach to online dialogue and interaction that integrates with existing, or near- future, pedagogical and technological practices, and explicitly links the social and cognitive dimensions of learning. This is realised through articulating game-playing activity in terms of the development of dialogical and reasoning skills that lead to improved conceptual understanding and collaborative knowledge refinement. This Chapter will present: the justification, background and theoretical foundations for this approach; summarise computational and empirical studies that support it; describe a socio-cognitive tool called InterLoc (that mediates, structures and manages educational dialogue games); and, provide an exemplar interaction from user trials of this approach. Finally, some key implications this work holds for designing gaming and related types of educational interaction are then discussed.
Virtually networked housing movement: Hyperlink network structure of housing social movement organizations

Using such theories as resource mobilization and social capital, this article examines how housing social movement organizations (SMOs) in the USA are connected through hyperlink networks. In doing so, this article employed hyperlink network analysis (HNA) through data collected from 26 national housing SMOs. Results indicate that the more bridging ties an organization has, the more central they are to the network. Results also show that the more incoming hyperlinks that a particular organization has, the more central they are to the network. These results suggest that the utilization of bridging social capital by a housing SMO has the potential to increase the ability to mobilize resources by that organization. Furthermore, increasing the number of bridging hyperlinks available on a website can improve the web presence of the SMO furthering the goals of the overall movement.
Molecular biodiversity of arbuscular mycorrhizal fungi in trace metal‐polluted soils

We assessed the indigenous arbuscular mycorrhizal fungi (AMF) community structure from the roots and associated soil of Plantago major (plantain) plants growing on sites polluted with trace metals (TM) and on unpolluted sites. Uncontaminated and TM‐contaminated sites containing As, Cd, Cu, Pb, Sn and Zn were selected based on a survey of the TM concentration in soils of community gardens in the City of Montréal. Total genomic DNA was extracted directly from these samples. PCR followed by denaturing gradient gel electrophoresis (PCR‐DGGE), augmented by cloning and sequencing, as well as direct sequencing techniques, was all used to investigate AMF community structure. We found a decreased diversity of native AMF (assessed by the number of AMF ribotypes) in soils and plant roots harvested from TM‐polluted soils compared with unpolluted soils. We also found that community structure was modified by TM contamination. Various species of Glomus, Scutellospora aurigloba and S. calospora were the most abundant ribotypes detected in unpolluted soil; ribotypes of G. etunicatum, G. irregulare/G. intraradices and G. viscosum were found in both polluted and unpolluted soils, while ribotypes of G. mosseae and Glomus spp. (B9 and B13) were dominant in TM‐polluted soils. The predominance of G. mosseae in metal‐polluted sites suggests the tolerance of this species to TM stress, as well as its potential use for phytoremediation. These data are relevant for our understanding of how AMF microbial communities respond to natural environments that contain a broad variety of toxic inorganic compounds and will substantially expand our knowledge of AMF ecology and biodiversity.
Creatinine‐ versus cystatine C‐based equations in assessing the renal function of candidates for liver transplantation with cirrhosis

Renal dysfunction is frequent in liver cirrhosis and is a strong prognostic predictor of orthotopic liver transplantation (OLT) outcome. Therefore, an accurate evaluation of the glomerular filtration rate (GFR) is crucial in pre‐OLT patients. However, in these patients plasma creatinine (Pcr) is inaccurate and the place of serum cystatine C (CystC) is still debated. New GFR‐predicting equations, based on standardized assays of Pcr and/or CystC, have been recently recommended in the general population but their performance in cirrhosis patients has been rarely studied. We evaluated the performance of the recently published Chronic Kidney Disease Epidemiology Collaboration equations (CKD‐EPI‐Pcr, CKD‐EPI‐CystC, and CKD‐EPI‐Pcr‐CystC) and the more classical ones (4‐ and 6‐variable MDRD and Hoek formulas) in cirrhosis patients referred for renal evaluation before OLT. Inulin clearance was performed in 202 consecutive patients together with the determination of Pcr and CystC with assays traceable to primary reference materials. The performance of the GFR‐predicting equations was evaluated according to ascites severity (no, moderate, or refractory) and to hepatic and renal dysfunctions (MELD score ≤ or >15 and KDOQI stages, respectively). In the whole population, CystC‐based equations showed a better performance than Pcr‐based ones (lower bias and higher 10% and 30% accuracies). CKD‐EPI‐CystC equation showed the best performance whatever the ascites severity and in presence of a significant renal dysfunction (GFR <60 mL/min/1.73 m2). Conclusion: Pcr‐based GFR predicting equations are not reliable in pre‐OLT patients even when an IDMS‐traceable enzymatic Pcr assay is used. Whenever a CystC‐assay traceable to primary reference materials is performed and when a true measurement of GFR is not possible, CystC‐based equations, especially CKD‐EPI‐CystC, may be recommended to evaluate renal function and for KDOQI staging. (Hepatology 2014;59:1522‐1531)
25‐hydroxyvitamin D3 suppresses hepatitis C virus production

Because the current interferon (IFN)‐based treatment for hepatitis C virus (HCV) infection has a therapeutic limitation and side effects, a more efficient therapeutic strategy is desired. Recent studies show that supplementation of vitamin D significantly improves sustained viral response via IFN‐based therapy. However, mechanisms and an active molecular form of vitamin D for its anti‐HCV effects have not been fully clarified. To address these questions, we infected HuH‐7 cells with cell culture‐generated HCV in the presence or absence of vitamin D3 or its metabolites. To our surprise, 25‐hydroxyvitamin D3 [25(OH)D3], but not vitamin D3 or 1,25‐dihydroxyvitamin D3, reduced the extra‐ and intracellular levels of HCV core antigen in a concentration‐dependent manner. Single‐cycle virus production assay with a CD81‐negative cell line reveals that the inhibitory effect of 25(OH)D3 is at the level of infectious virus assembly but not entry or replication. Long‐term 25(OH)D3 treatment generates a HCV mutant with acquired resistance to 25(OH)D3, and this mutation resulting in a N1279Y substitution in the nonstructural region 3 helicase domain is responsible for the resistance. Conclusion: 25(OH)D3 is a novel anti‐HCV agent that targets an infectious viral particle assembly step. This finding provides insight into the improved efficacy of anti‐HCV treatment via the combination of vitamin D3 and IFN. Our results also suggest that 25(OH)D3, not vitamin D3, is a better therapeutic option in patients with hepatic dysfunction and reduced enzymatic activity for generation of 25(OH)D3. (HEPATOLOGY 2012)
An Adaptive Hybrid Model for Monthly Streamflow Forecasting

This paper suggests a new algorithm for generating Takagi-Sugeno fuzzy systems applied for time series prediction. The model proposed comprises two phases. First, the model structure is initialized in a constructive offline fashion, via an expectation maximization algorithm (EM). In the second phase the system is modified dynamically, via adding and pruning operators. At this stage, we propose a recursive learning algorithm, which is based on the EM optimization technique. This online algorithm determines automatically the number of rules necessary at each step. In this way, the model structure and parameters are updated during the adaptive training. The adaptive learning process reduces model complexity and defines automatically its structure providing an efficient model. The proposed approach is applied to build a time series model for monthly streamflow forecasting. The performance of the approach is compared with conventional models used to forecast streamflows. Results show similar errors, however, the suggested model presents a simpler and more parsimonious structure.
Similarity Search on Bregman Divergence: Towards Non-Metric Indexing

In this paper, we examine the problem of indexing over non-metric distance functions. In particular, we focus on a general class of distance functions, namely Bregman Divergence [6], to support nearest neighbor and range queries. Distance functions such as KL-divergence and Itakura-Saito distance, are special cases of Bregman divergence, with wide applications in statistics, speech recognition and time series analysis among others. Unlike in metric spaces, key properties such as triangle inequality and distance symmetry do not hold for such distance functions. A direct adaptation of existing indexing infrastructure developed for metric spaces is thus not possible. We devise a novel solution to handle this class of distance measures by expanding and mapping points in the original space to a new extended space. Subsequently, we show how state-of-the-art tree-based indexing methods, for low to moderate dimensional datasets, and vector approximation file (VA-file) methods, for high dimensional datasets, can be adapted on this extended space to answer such queries efficiently. Improved distance bounding techniques and distribution-based index optimization are also introduced to improve the performance of query answering and index construction respectively, which can be applied on both the R-trees and VA files. Extensive experiments are conducted to validate our approach on a variety of datasets and a range of Bregman divergence functions.
Improving Sexual Risk Communication With Adolescents Using Event History Calendars

This study was conducted to explore the effects of an event history calendar (EHC) approach on adolescent sexual risk communication and sexual activity. Adolescent school-linked health clinic patients (n = 30) who reported sexual activity self-administered the EHC that was used by nurse practitioners (NPs; n = 2) during a clinic visit. Immediately pre- and post-visit, and at 1 and 3 months, adolescents reported sexual risk behaviors and perceptions about EHC communication on questionnaires and by interview. NPs reported their perceptions of EHCs by questionnaire after the visit and poststudy interview. The EHC approach facilitated communication and adolescent awareness of their risk behaviors. Scores increased on Amount of Communication, t(29) = 8.174, p < . 001; Satisfaction with Communication, t(29) = 3.112, p = . 004; Client Involvement in Decision Making, t(29) = 3.901, p = . 001, and Client Satisfaction with Interpersonal Style, t(29) = 3.763, p = . 001. Adolescents reported decreased sexual intercourse at 1 month, p = . 031. School nurses could use the EHC approach to facilitate adolescent communication and tailoring of interventions.
Restoring insulin production for type 1 diabetes

Current therapies for the treatment of type 1 diabetes include daily administration of exogenous insulin and, less frequently, whole‐pancreas or islet transplantation. Insulin injections often result in inaccurate insulin doses, exposing the patient to hypo‐ and/or hyperglycemic episodes that lead to long‐term complications. Islet transplantation is also limited by lack of high‐quality islet donors, early graft failure, and chronic post‐transplant immunosuppressive treatment. These barriers could be circumvented by designing a safe and efficient strategy to restore insulin production within the patient’s body. Porcine islets have been considered as a possible alternative source of transplantable insulin‐producing cells to replace human cadaveric islets. More recently, embryonic or induced pluripotent stem cells have also been examined for their ability to differentiate in vitro into pancreatic endocrine cells. Alternatively, it may be feasible to generate new β‐cells by ectopic expression of key transcription factors in endogenous non‐β‐cells. Finally, engineering surrogate β‐cells by in vivo delivery of the insulin gene to specific tissues is also being studied as a possible therapy for type 1 diabetes. In the present review, we discuss these different approaches to restore insulin production.
Fusion of the First Metatarsophalangeal Joint and Second to Fifth Metatarsal Head Resection for Rheumatoid Forefoot Deformity

Abstract The goals of the present study were to evaluate the mid‐term results of first metatarsophalangeal joint fusion combined with second to fifth metatarsal head resection in rheumatoid forefoot deformity and identify the prognostic factors. The inclusion criteria were 2010 American College of Rheumatology and/or European League Against Rheumatism criteria for rheumatoid arthritis; symptomatic forefoot deformity; first metatarsophalangeal joint fusion and second to fifth metatarsal head resection; and a minimum of 4 years of follow‐up data available. The patients were evaluated using the Disease Activity Score 28 for rheumatoid arthritis, Health Assessment Questionnaire for Rheumatoid Arthritis, Foot Function Index, forefoot American Orthopaedic Foot and Ankle Society scale, and weightbearing radiographs. Different pre‐, intra‐, and postoperative variables were investigated to identify the prognostic factors. Sixty‐two patients (89 feet) with a mean age of 60.8°± 9.4 years and 85.5°± 22.4 months of follow‐up data were included. The preoperative American Orthopaedic Foot and Ankle Society scale score was 33.4 ± 16 points and improved significantly (p < .001) after surgery (mean 82.9 ± 11.7 points). The mean Foot Function Index improved significantly (p < .001) from 131.6 ± 37.4 to 77.4 ± 46.3 points at the last follow‐up visit. Only the revision surgery variable was significantly (p = .02) related to poor outcomes. Revision was necessary in 8 feet (9%). This procedure produced satisfactory results. Poor outcomes were significantly related to the necessity for revision surgery for nonunion, malunion, inadequate metatarsal resection, and painful hardware. &NA; Level of Clinical Evidence: 4
Triad of bladder agenesis with solitary kidney and ectopic ureter

The bladder agenesis is an extremely rare congenital genitourinary anomaly; only 60 cases have been reported in the English literature and only 19 of these were noted in viable neonates. [1] Our case represents the 20th live birth with bladder agenesis. The triad of bladder agenesis with solitary kidney and ectopic ureter is seldom compatible with life due to associated anomalies. [23] Successful treatment and the long-term prognosis are usually poor because of the associated abnormalities. In our case, function of left solitary kidney was good and child did not have associated life-threatening disorder. Hence child was successfully managed with continent urinary diversion with good quality of life.
Distributed wavelet transform for irregular sensor network grids

Wavelet-based distributed data processing holds much promise for sensor networks; however, irregular sensor node placement precludes the direct application of standard wavelet techniques. In this paper, we develop a new distributed wavelet transform based on lifting that takes into account irregular sampling and provides a piecewise-planar multiresolution representation of the sensed data. We develop the transform theory; outline how to implement it in a multi-hop, wireless sensor network; and illustrate with several simulations. The new transform performs on par with conventional wavelet methods in a head-to-head comparison on a regular grid of sensor nodes