Miracle-dz/UniFAR-FTUs huggingface dataset:
Posttreatment Antifungal Resistance among Colonizing Candida Isolates in Candidemia Patients: Results from a Systematic Multicenter Study

ABSTRACT The prevalence of intrinsic and acquired resistance among colonizing Candida isolates from patients after candidemia was investigated systematically in a 1-year nationwide study. Patients were treated at the discretion of the treating physician. Oral swabs were obtained after treatment. Species distributions and MIC data were investigated for blood and posttreatment oral isolates from patients exposed to either azoles or echinocandins for <7 or ≥7 days. Species identification was confirmed using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and internal transcribed spacer (ITS) sequencing, susceptibility was examined by EUCAST EDef 7.2 methodology, echinocandin resistance was examined by FKS sequencing, and genetic relatedness was examined by multilocus sequence typing (MLST). One hundred ninety-three episodes provided 205 blood and 220 oral isolates. MLST analysis demonstrated a genetic relationship for 90% of all paired blood and oral isolates. Patients exposed to azoles for ≥7 days (n = 93) had a significantly larger proportion of species intrinsically less susceptible to azoles (particularly Candida glabrata) among oral isolates than among initial blood isolates (36.6% versus 12.9%; P < 0.001). A similar shift toward species less susceptible to echinocandins among 85 patients exposed to echinocandins for ≥7 days was not observed (4.8% of oral isolates versus 3.2% of blood isolates; P > 0.5). Acquired resistance in Candida albicans was rare (<5%). However, acquired resistance to fluconazole (29.4%; P < 0.05) and anidulafungin (21.6%; P < 0.05) was common in C. glabrata isolates from patients exposed to either azoles or echinocandins. Our findings suggest that the colonizing mucosal microbiota may be an unrecognized reservoir of resistant Candida species, especially C. glabrata, following treatment for candidemia. The resistance rates were high, raising concern in general for patients exposed to antifungal drugs.
Endoscopic palliation in patients with incurable malignant colorectal obstruction by means of self-expanding metal stent: analysis of results and predictors of outcomes in a large multicenter series.

OBJECTIVES To evaluate the short- and long-term efficacy of self-expanding metal stents (SEMSs) in patients with colorectal obstruction and incurable cancer and the related factors that affect outcomes. DESIGN Retrospective analysis of SEMS placement for incurable colorectal obstruction in a 3-year period. SETTING Five tertiary care endoscopic centers. PATIENTS AND INTERVENTION Consecutive patients (N = 201) undergoing stenting for incurable malignant obstruction. MAIN OUTCOME MEASUREMENTS Clinical and technical success of stenting, complications rate, and factors affecting outcomes. RESULTS Technical success was achieved in 184 of 201 patients (91.5%) and clinical success occurred in 165 of 184 patients (89.7%; 82.1% of 201 patients). Technical and clinical failures were more frequent in extrinsic and long colorectal stenoses. Overall, 165 patients had normal bowel movements during follow-up (mean [SD], 115.5 [100.3] days; range, 1-500 days), 15 developed complications, 127 had a functioning SEMS at the time of death, and 23 were alive at completion of the study. Twenty-four (11.9%) major complications occurred: 11 migrations, 12 perforations, and 1 reobstruction. Migration of SEMSs was associated with stent diameter less than 25 mm. Bevacizumab therapy increased the risk of perforation by 19.6-fold. Karnofsky performance status of 50 or less was associated with shorter survival and a 3.7-fold higher risk of death within 6 months after the stent was placed. CONCLUSIONS The use of SEMSs is safe and effective for palliation of incurable malignant colonic obstruction; approximately 75% of patients with SEMSs are able to avoid colostomy.
Asymptotical Computations for a Model of Flow in Concrete

We discuss an initial value problem for an implicit second order ordinary differential equation which arises in models of flow in concrete. Depending on the initial condition, the solution features a sharp interface with derivatives which become numerically unbounded. By using an integrator based on finite difference methods and equipped with adaptive step size selection, it is possible to compute the solution on highly irregular meshes. In this way it is possible to verify and predict asymptotical theory near the interface with remarkable accuracy.
Changes in the Physico-chemical and Microbial Quality during the Production of Pastırma Cured with Different Levels of Sodium Nitrite

Pastırma, a dry-cured meat product, is produced from the whole muscle and/or muscles obtained from certain parts of beef and water buffalo carcasses. The purpose of this study was to determine the effects of different levels of sodium nitrite on changes in the physicochemical and microbial quality during the production of pastırma. The changes in residual nitrite, salt, pH, moisture, thiobarbutiric acid reactive substances (TBARS), colour (L*, a*, b*), total aerobic mesophilic bacteria (TAMB), lactic acid bacteria (LAB), Micrococcus/Staphylococcus (M/S), mould-yeast (M-Y), and Enterobacteriaceae counts of pastırma with 0, 50, 100 and 150 ppm sodium nitrite were determined during the production. The nitrite levels and the production stages had significant effects (p<0.01) on residual nitrite, TBARS, pH, salt, and colour values. The TBARS values of the pastırma with nitrite were significantly lower (p<0.05) than the control. The final TAMB, LAB, M/S, and M-Y counts of pastırma with 150 ppm nitrite were significantly (p<0.05) lower than the control. Also, the a* (relative redness) values of control pastırma were significantly lower (p<0.05) than the pastırma with nitrite. The production stages had a significant effect (p<0.01) on the moisture.
Fuzzy modelling: a rule based approach

System modelling is an important subject in engineering both from a research point of view and from a practical perspective models have an important role in several intelligent systems and, as it is observed from the research developed in the last years, fuzzy logic is relevant to this topic. This is mainly due to the expressiveness of fuzzy logic that permits the treatment of some kinds of uncertainty largely present in real systems. Also, the if-then rule mechanism is easy to manipulate and, in a certain extent, domain independent. A modelling procedure must produce good models in an effective way. This is the main concern of this paper.
Activation Volume and Energy for Dislocation Nucleation in Multi-Principal Element Alloys

Incipient plasticity in multi-principal element alloys, CoCrNi, CoCrFeMnNi, and Al0.1CoCrFeNi was evaluated by nano-indentation and compared with pure Ni. The tests were performed at a loading rate of 70 μN/s in the temperature range of 298 K to 473 K. The activation energy and activation volume were determined using a statistical approach of analyzing the “pop-in” load marking incipient plasticity. The CoCrFeMnNi and Al0.1CoCrFeNi multi-principal element alloys showed two times higher activation volume and energy compared to CoCrNi and pure Ni, suggesting complex cooperative motion of atoms for deformation in the five component systems. The small calculated values of activation energy and activation volume indicate heterogeneous dislocation nucleation at point defects like vacancy and hot-spot.
The effects of brushing on human enamel surface roughness after NaF gel and theobromine gel exposure

This study aimed to determine the effects of brushing on human enamel surface roughness after different exposure times of 200 mg/L theobromine gel (8, 16, and 32 minutes) and 2% NaF gel (16 minutes). Twenty-four human upper premolars were used and divided into four groups. Group 1 was exposed to 2% NaF gel for 16 minutes. In contrast, groups 2, 3, and 4 were exposed to 200 mg/L theobromine gel for 8 minutes, 16 minutes, and 32 minutes, and each group was then brushed for 9 minutes and 20 seconds. After the treatment, samples were tested using a surface roughness tester (Mitutoyo SJ 301, Japan). The Wilcoxon test showed significant changes (p < 0.05) in roughness values after exposure to the theobromine gel or NaF gel and after brushing for 9 minutes and 20 seconds. It can be concluded that exposure to 200 mg/L theobromine gel or 2% NaF gel can soften the enamel surface and then increase roughness after brushing.
Universal low-rank matrix recovery from Pauli measurements

We study the problem of reconstructing an unknown matrix M of rank r and dimension d using O(rd poly log d) Pauli measurements. This has applications in quantum state tomography, and is a non-commutative analogue of a well-known problem in compressed sensing: recovering a sparse vector from a few of its Fourier coefficients. We show that almost all sets of O(rd log^6 d) Pauli measurements satisfy the rank-r restricted isometry property (RIP). This implies that M can be recovered from a fixed ("universal") set of Pauli measurements, using nuclear-norm minimization (e.g., the matrix Lasso), with nearly-optimal bounds on the error. A similar result holds for any class of measurements that use an orthonormal operator basis whose elements have small operator norm. Our proof uses Dudley's inequality for Gaussian processes, together with bounds on covering numbers obtained via entropy duality.
Metastability in high-entropy alloys: A review

Classical alloy design strategies often aim to benefit from metastability. Examples are numerous: metastable transformation- and twinning-induced plasticity steels, cobalt or titanium based alloys, age hardenable aluminum alloys, and severe plastic deformed nanostructured copper. In each of these cases, superior engineering property combinations are achieved by exploring limits of stability. For the case of high-entropy alloys (HEAs), on the other hand, majority of present research efforts focus on exploring compositions that would yield stable single-phase structures. HEA metastability and its effects on microstructure and property development constitute only a relatively small fraction of ongoing work. To help motivate and guide a corresponding shift in HEA research efforts, here in this paper, we provide an overview of the research activities on metastability in HEAs. To this end, we categorize the past research on the topic into two groups based on their focus, namely, compositional and structural stability, and discuss the most relevant and exciting findings.
Active Learning for Statistical Natural Language Parsing

It is necessary to have a (large) annotated corpus to build a statistical parser. Acquisition of such a corpus is costly and time-consuming. This paper presents a method to reduce this demand using active learning, which selects what samples to annotate, instead of annotating blindly the whole training corpus.Sample selection for annotation is based upon "representativeness" and "usefulness". A model-based distance is proposed to measure the difference of two sentences and their most likely parse trees. Based on this distance, the active learning process analyzes the sample distribution by clustering and calculates the density of each sample to quantify its representativeness. Further more, a sentence is deemed as useful if the existing model is highly uncertain about its parses, where uncertainty is measured by various entropy-based scores.Experiments are carried out in the shallow semantic parser of an air travel dialog system. Our result shows that for about the same parsing accuracy, we only need to annotate a third of the samples as compared to the usual random selection method.
Buruli Ulcer in Cameroon: The Development and Impact of the National Control Programme

Background Cameroon is endemic for Buruli ulcer (BU) and organised institutional BU control began in 2002. The objective was to describe the evolution, achievements and challenges of the national BU control programme (NBUCP) and to make suggestions for scaling up the programme. Methods We analysed collated data on BU from 2001 to 2014 and reviewed activity reports NBUCP in Cameroon. Case-detection rates and key BU control indicators were calculated and plotted on a time scale to determine trends in performance. A linear regression analysis of BU detection rate from 2005–2014 was done. The regression coefficient was tested statistically for the significance in variation of BU detection rate. Principal findings In 14 years of BU control, 3700 cases were notified. The BU detection rate dropped significantly from 3.89 to 1.45 per 100 000 inhabitants. The number of BU endemic health districts rose from two to 64. Five BU diagnostic and treatment centres are functional and two more are planned for 2015. The health system has been strengthened and BU research and education has gained more interest in Cameroon. Conclusion/Significance Although institutional BU control Cameroon only began 30 years after the first cases were reported in 1969, a number of milestones have been attained. These would serve as stepping stones for charting the way forward and improving upon control activities in the country if the major challenge of resource allocation is dealt with.
Long‐term nitrogen dynamics of Coweeta Forested Watersheds in the southeastern United States of America

We analyzed long‐term (23 years) data of inorganic N deposition and loss for an extensive network of mature mixed hardwood covered watersheds in the southern Appalachians of North Carolina to assess trends and dynamics of N in baseline ecosystems. We also assessed watershed N saturation in the context of altered N cycles and stream inorganic N responses associated with management practices (cutting prescriptions, species replacement, and prescribed burning) and with natural disturbances (drought and wet years, insect infestations, hurricane damage, and ozone events) on reference watersheds. Reference watersheds were characterized as highly conservative of inorganic N with deposition < 9.0 kg ha−1 yr−1 and stream water exports below 0.25 kg ha−1 yr−1. However, reference watersheds appeared to be in a transition phase between stage 0 and stage 1 of watershed N saturation as evidenced by significant time trend increases in annual flow‐weighted concentrations of NO3− in stream water and increases in the seasonal amplitude and duration of NO3 concentrations during 1972–1994. These stream water chemistry trends were partially attributed to significant increases in NO3− and NH4+ concentrations in bulk precipitation over the same period and/or reduced biological demand due to forest maturation. Levels and annual patterns of stream NO3− concentrations and intra‐annual seasonal patterns characteristic of latter phases of stages 1 and 2 of watershed N saturation were found for low‐elevation and high‐elevation clear‐cut watersheds, respectively, and were related to the dynamics of microbial transformations of N and vegetation uptake. Evidence for stage 3 of N saturation, where the watershed is a net source of N rather than an N sink, was found for the most distributed watershed at Coweeta (hardwood converted to grass, fertilized, limed, treated with herbicide, and subsequently characterized by successional vegetation). Compared to other intensive management practices, prescribed burning had little effect on stream water NO3− concentrations, and stream NO3− losses associated with natural disturbances are small and short‐lived.
The Effect of Glucagon-Like Peptide 1 Receptor Agonists on Weight Loss in Type 2 Diabetes: A Systematic Review and Mixed Treatment Comparison Meta-Analysis

Aims To determine the effects of glucagon-like peptide-1 receptor agonists compared with placebo and other anti-diabetic agents on weight loss in overweight or obese patients with type 2 diabetes mellitus. Methods Electronic searches were conducted for randomised controlled trials that compared a glucagon-like peptide-1 receptor agonist therapy at a clinically relevant dose with a comparator treatment (other type 2 diabetes treatment or placebo) in adults with type 2 diabetes and a mean body mass index ≥ 25kg/m2. Pair-wise meta-analyses and mixed treatment comparisons were conducted to examine the difference in weight change at six months between the glucagon-like peptide-1 receptor agonists and each comparator. Results In the mixed treatment comparison (27 trials), the glucagon-like peptide-1 receptor agonists were the most successful in terms of weight loss; exenatide 2mg/week: -1.62kg (95% CrI: -2.95kg, -0.30kg), exenatide 20μg: -1.37kg (95% CI: -222kg, -0.52kg), liraglutide 1.2mg: -1.01kg (95%CrI: -2.41kg, 0.38kg) and liraglutide 1.8mg: -1.51 kg (95% CI: -2.67kg, -0.37kg) compared with placebo. There were no differences between the GLP-1 receptor agonists in terms of weight loss. Conclusions This review provides evidence that glucagon-like peptide-1 receptor agonist therapies are associated with weight loss in overweight or obese patients with type 2 diabetes with no difference in weight loss seen between the different types of GLP-1 receptor agonists assessed.
Eye structure, activity rhythms, and visually-driven behavior are tuned to visual niche in ants

Insects have evolved physiological adaptations and behavioral strategies that allow them to cope with a broad spectrum of environmental challenges and contribute to their evolutionary success. Visual performance plays a key role in this success. Correlates between life style and eye organization have been reported in various insect species. Yet, if and how visual ecology translates effectively into different visual discrimination and learning capabilities has been less explored. Here we report results from optical and behavioral analyses performed in two sympatric ant species, Formica cunicularia and Camponotus aethiops. We show that the former are diurnal while the latter are cathemeral. Accordingly, F. cunicularia workers present compound eyes with higher resolution, while C. aethiops workers exhibit eyes with lower resolution but higher sensitivity. The discrimination and learning of visual stimuli differs significantly between these species in controlled dual-choice experiments: discrimination learning of small-field visual stimuli is achieved by F. cunicularia but not by C. aethiops, while both species master the discrimination of large-field visual stimuli. Our work thus provides a paradigmatic example about how timing of foraging activities and visual environment match the organization of compound eyes and visually-driven behavior. This correspondence underlines the relevance of an ecological/evolutionary framework for analyses in behavioral neuroscience.
HGF/Met-Signaling Contributes to Immune Regulation by Modulating Tolerogenic and Motogenic Properties of Dendritic Cells

Hepatocyte growth factor (HGF)-signaling via Met can induce mitogenic, morphogenic, and motogenic activity in various cell types. Met expression in the immune system is limited to cells with antigen-presenting capacities, including dendritic cells (DCs). Thus, it appears highly conceivable that Met-signaling impacts on adaptive immune responses. However, the mechanisms by which HGF imparts its effects on immunological responses are not yet fully understood. DCs possess unique functionalities that are critically involved in controlling both tolerance and immunity. HGF conveys immunoregulatory functions, which strongly correlate with that of DCs orchestrating the apt immune response in inflammation. Therefore, this review focuses on the current knowledge of Met-signaling in DCs with specific emphasis on the morphogenic and motogenic activities. HGF has been identified to play a role in peripheral immune tolerance by directing DC differentiation towards a tolerogenic phenotype. In skin immunity, Met-signaling was shown to drive mobilization of DCs by regulating matrix metalloproteinase activities. This is strikingly reminiscent of the role of Met for regulating a cell fate program during embryonic development, wound healing, and in tumor invasion known as epithelial-mesenchymal transition (EMT). Thus, the concept emerges that an EMT program is executed by Met-signaling in DCs, which will be also discussed.
Introduction of alvimopan into an enhanced recovery protocol for colectomy offers benefit in open but not laparoscopic colectomy.

INTRODUCTION Alvimopan coupled with an enhanced recovery protocol (ERP) has been shown to reduce length of stay (LOS) after open colectomy, but its role after laparoscopy remains unknown. This study evaluated alvimopan with an established ERP for laparoscopic (LAP), hand-assisted laparoscopic (HAL), and open colectomy. MATERIALS AND METHODS Consecutive patients who underwent elective colectomy by any technique were retrospectively identified. Patients were excluded if they developed a major intra-abdominal complication, medical complication, or had a complex preoperative evaluation. Patients were stratified into 4 groups based on the surgical approach (open/HAL vs. LAP) and the use of alvimopan. All patients were managed by using an ERP. The incidence of postoperative ileus (POI) and LOS were compared between alvimopan and control groups for each surgical approach. RESULTS There were 282 patients. Demographics were similar across the 4 groups. The mean number of alvimopan doses administered was 6.7±2.6. For patients in the open/HAL group (n=149), the incidence of primary ileus was 9.5% (7/74) and 16% (12/75) for alvimopan and control patients, respectively (P=.231). A significant decrease in LOS was noted with alvimopan (5.6±2.5 vs. 6.8±3.3 days, P=.009). For patients after LAP (n=133), there was no significance difference in POI with or without alvimopan (3.9% [3/76] vs. 3.5% [2/57], P=1.00). There was no difference in LOS (3.9±1 vs. 3.7±1.4 days, P=.305). CONCLUSION The addition of alvimopan to an established ERP will lead to improvement in clinical outcomes in patients after open/HAL colectomy. The benefit of alvimopan after LAP remains negligible.
Minimizing GCV/GML Scores with Multiple Smoothing Parameters via the Newton Method

The (modified) Newton method is adapted to optimize generalized cross validation (GCV) and generalized maximum likelihood (GML) scores with multiple smoothing parameters. The main concerns in solving the optimization problem are the speed and the reliability of the algorithm, as well as the invariance of the algorithm under transformations under which the problem itself is invariant. The proposed algorithm is believed to be highly efficient for the problem, though it is still rather expensive for large data sets, since its operational counts are $(2/3)kn^3 + O(n^2 )$, with k the number of smoothing parameters and n the number of observations. Sensible procedures for computing good starting values are also proposed, which should help in keeping the execution load to the minimum possible. The algorithm is implemented in Rkpack [RKPACK and its applications: Fitting smoothing spline models, Tech. Report 857, Department of Statistics, University of Wisconsin, Madison, WI, 1989] and illustrated by examples of fitting additive and interaction spline models. It is noted that the algorithm can also be applied to the maximum likelihood (ML) and the restricted maximum likelihood (REML) estimation of the variance component models.
SHARP ERROR BOUNDS FOR THE TRAPEZOIDAL RULE AND SIMPSON'S RULE

We give error bounds for the trapezoidal rule and Simpson's rule for "rough" con- tinuous functions—for instance, functions which are Holder continuous, of bounded variation, or which are absolutely continuous and whose derivative is in L p . These differ considerably from the classical results, which require the functions to have continuous higher derivatives. Further, we show that our results are sharp, and in many cases precisely characterize the functions for which equality holds. One consequence of these results is that for rough functions, the error esti- mates for the trapezoidal rule are better (that is, have smaller constants) than those for Simpson's rule.