Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of a novel procedure for rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) using the LightMix® modular carbapenemase kits

Objectives Evaluation of the LightMix® modular carbapenemase kits for the rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) and the application of these kits to the direct detection of colonized patients and bacteraemias. Methods The modular multiplex PCR kits targeting blaKPC, blaNDM, blaVIM, blaIMP and blaOXA-48-like carbapenem resistance genes were evaluated in terms of sensitivity and specificity for carbapenemase resistance in a set of 118 labelled clinical isolates. Among these, 96 were CPE genotypically characterized by PCR and sequencing. The limits of detection were calculated for the different carbapenem resistance genes in terms of cfu/mL. In addition, the kits were used to evaluate colonization of patients by CPE by comparing this assay with the Xpert® Carba-R Kit on 127 rectal, perirectal and pharyngeal samples. Blood cultures from bacteraemias (4) and spiked blood cultures (23) with genotypically characterized isolates were also evaluated. Results The overall sensitivity and specificity of the multiplex PCR assay was 99% and 100%, respectively. The limit of detection for blaKPC, blaVIM, blaIMP and blaOXA-48-like is 60 cfu/mL and for blaNDM 500 cfu/mL. The colonization and bacteraemia studies revealed a 100% agreement between the results obtained by this assay and the ones obtained by GeneXpert®. Conclusions The LightMix® modular carbapenemase kits are highly reliable and utilizable assays for both colonized and septic patients, and can help in the improvement of infection control. Their modular design facilitates cost-effective detection of CPE in hospital settings.
Constrained Concept Factorization for Image Representation

Matrix factorization based techniques, such as nonnegative matrix factorization and concept factorization, have attracted great attention in dimensionality reduction and data clustering. Previous studies show that both of them yield impressive results on image processing and document clustering. However, both of them are essentially unsupervised methods and cannot incorporate label information. In this paper, we propose a novel semi-supervised matrix decomposition method for extracting the image concepts that are consistent with the known label information. With this constraint, we call the new approach constrained concept factorization. By requiring that the data points sharing the same label have the same coordinate in the new representation space, this approach has more discriminating power. The experimental results on several corpora show good performance of our novel algorithm in terms of clustering accuracy and mutual information.
2001 Consensus Guidelines for the Management of Women with Cervical Intraepithelial Neoplasia

Objective. To provide consensus guidelines for the management of women with histologically confirmed cervical intraepithelial neoplasia (CIN), which can act as a precursor to invasive cervical cancer and represents one of the most common significant gynecologic diseases of women of reproductive age. Participants. An independent panel of 121 experts in various aspects of the diagnosis and management of cervical cancer precursors, including representatives from 29 participating professional organizations, federal agencies, national and international health organizations, and others invited by the American Society for Colposcopy and Cervical Pathology (ASCCP). Consensus Process. Guidelines for the management of women with CIN were developed through a multistep process. Working groups, who performed formal literature reviews and obtained input from the professional community at large by way of an interactive Internet-based bulletin board, developed draft management guidelines. At the ASCCP Consensus Conference, September 6–8, 2001, in Bethesda, Maryland, all guidelines were discussed, revised, and adopted by formal vote. Conclusions. Evidence-based guidelines have been developed for the management of women with biopsy-confirmed CIN.
Explorer TCPRand : Randomizing TCP Payload Size for TCP Fairness in Data Center Networks

As many-to-one traffic patterns prevail in data center networks, TCP flows often suffer from severe unfairness in sharing bottleneck bandwidth, which is known as the TCP outcast problem. The cause of the TCP outcast problem is the bursty packet losses by a drop-tail queue that triggers TCP timeouts and leads to decreasing the congestion window. This paper proposes TCPRand, a transport layer solution to TCP outcast. The main idea of TCPRand is the randomization of TCP payload size, which breaks synchronized packet arrivals between flows from different input ports. We investigate how TCPRand reduces consecutive packet drops and demonstrate various benefits of TCPRand with extensive experiments and ns-3 simulation. Our evaluation results show that TCPRand guarantees the superior enhancement of TCP fairness with negligible overheads in all of our test cases.
Models of Software Evolution: Life Cycle and Process

Abstract : This module presents an introduction to models of software system evolution and their role in structuring software development. It includes a review of traditional software life cycle models as well as software process models that have been recently proposed. It identifies three kinds of alternative models of software evolution that focus attention to either the products, production processes, or production settings as the major source of influence. It examines how different software engineering tools and techniques can support life cycle or process approaches. It also identifies techniques for evaluating the practical utility of a given model of software evolution for development projects in different kinds of organizational settings.
LA MAITRISE DES SITUATIONS DYNAMIQUES

La maitrise des situations est un terme rarement utilise en psychologie ergonomique. La litterature l'evoque toujours indirectement, et toujours negativement, en parlant de defaillance et d'erreur. Cet article propose une clarification et une revision plus positive du concept, fondees sur une serie de resultats recents obtenus en situations dynamiques a risques reels (situations de travail). L'article souligne l'importance de quatre notions cles dans la maitrise de la situation : la notion de competition entre deux types de supervisions, celle du processus physique et celle de la cognition, la notion de « suffisance » dans l'activite intellectuelle, l'avantage d'une adaptation dynamique du controle, et l'importance de la metacognition. La maitrise de la situation impose, pour une efficacite globale en situation critique, un frein dynamique sur l'utilisation des capacites cognitives mise en jeu afin de ne pas se perdre dans des optimums locaux au detriment d'un etat satisfaisant global (au point que ce frein peut apparaitre comme un biais). Les bases d'une theorie cognitive de maitrise des risques, dite de securite ecologique, sont proposees.
Comparative Study Of The D -values of Salmonella spp. and Enterococcus faecium in Wheat Flour

Low-moisture foods contaminated with Salmonella spp. have been implicated in several foodborne illness outbreaks in the United States. The food industry has to incorporate preventive control in their process and validate thermal processes to assure food safety. The thermal destruction of Enterococcus faecium ATTC 8459 and Salmonella spp. was determined at 3 water activity levels (0.11, 0.18 and 0.33) at 80ºC, 85ºC and 90ºC. Aerobic plates counts petrifilms were used as non-selective medium for both bacteria, Enterobacteriaceae petrifilms were used as selective medium for Salmonella spp. , and peptone water modified with sodium azide as a selective medium for Enterococcus faecium. Significant differences were observed for both organisms between the two media with higher D-values on the non-selective medium (p <0.05). Lower D-values were observed for both organisms at higher water activities (p <0.05). The D-values of Salmonella spp. min at 80ºC, 85ºC and 90ºC, respectively at water activity of 0.33. The z-values were determined at each water activity, and there were no significant differences between the three (3) water activities (p≥0.05). Salmonella spp. and Enterococcus faecium had approximately the same z-values. The z-values of Salmonella spp. ranged from 16.53 to 18. 50ºC, while the z-values of Enterococcus faecium ranged from 18.80 to 21. 61ºC. These results suggest that Enterococcus faecium ATTC 8459 can be used as a surrogate for Salmonella spp. in wheat flour at the three levels of water activity used in the study. ACKNOWLEDGMENTS First of all, I want to think God for all the blessings, intelligence and guidance I have received throughout all my life. I would also like to thank my mother Rose Necida Dodier for all the sacrifices she has made for my education. I must thank my brother Evens Daudier for his encouragement during this journey of my Masters program. I would like to express my deepest gratitude to my advisors, Dr. Harshavardhan Thippareddi and Dr. Jeyamkondan Subbiah, for their excellent guidance, caring, patience, and providing me with an excellent atmosphere for doing research. I would like to thank Dr. Kent M. Eskridge for his help with the statistic analysis of my data. Special thanks goes to Dr. John Rupnow, who was willing to participate in my defense committee. A.1. D-values of Salmonella spp. and Enterococcus faecium on the selective media . 63 A.1. D-values of Salmonella spp. and Enterococcus faecium on the selective media…. 63 A.2. z-values of Salmonella spp. and Enterococcus faecium on the non-selective …
Kriegeskorte — Transformations of Lamarckism Tutorial on Pattern Classification in Cell Recording

In this chapter, we outline a procedure to decode information from multivariate neural data. We assume that neural recordings have been made from a number of trials in which different conditions were present, and our procedure produces an estimate of how accurately we can predict the labels of these conditions in a new set of data. We call this estimate of future prediction the “decoding/readout accuracy,” and based on this measure we can make inferences about what information is present in the population of neurons and on how this information is coded. The steps we cover to obtain a measure of decoding accuracy include: (1) designing an experiment, (2) formatting the neural data, (3) selecting a classifier to use, (4) applying cross-validation to random splits of the data, (5) evaluating decoding performance through different measures, and (6) testing the integrity of the decoding procedure and significance of the results. We also discuss additional topics, including how to examine questions about neural coding and how to evaluate whether the population is representing stimuli in an invariant/abstract way. Chapter 18 (Singer and Kreiman) discusses statistical classifiers in further detail. The ideas discussed here are applied in several chapters in this book including chapter 2 (Nirenberg), chapter 3 (Poort, Pooresmaeili, and Roelfsema), chapter 7 (Pasupathy and Brincat), chapter 10 (Hung and DiCarlo), chapter 21 (Panzeri and Ince), and chapter 22 (Berens, Logothetis, and Tolias). Chapter 20 discusses related concepts within the domain of functional imaging.
Comparing three statistical techniques for Space-time clusters with county-level fertility data from Costa Rica

Population projections at a small area level are sensitive to random departures in temporal trends of population change components. In order to have robust trends for the county level projections in Costa Rica, the team in charge of forecasting decided to determine county clusters based on the past trends. In this paper, we compare three descriptive techniques used to build space-time clusters for the Crude Birth Rate CBR: Functional Data Analysis (FDA), the scan statistic, and Geographically Weighted Regression GWR. GWR was the technique that yielded clusters related to the diffusion paradigm for fertility decline. However, the scan statistic provided a more parsimonious set of clusters that are more tractable for population projections.
Impaired glucose metabolism in subjects with the Williams-Beuren syndrome: A five-year follow-up cohort study

Objective The Williams-Beuren syndrome (WS) is associated with impaired glucose metabolism (IGM) early in adulthood. However, the pathophysiology of IGM remains poorly defined, due to the lack of longitudinal studies investigating the contribution of β-cell dysfunction and impaired insulin sensitivity. This study aimed at assessing incidence of IGM and the underlying mechanisms in WS adults. Methods This observational, longitudinal (5-year), cohort study enrolled thirty-one consecutive WS subjects attending a tertiary referral center. An oral glucose tolerance test (OGTT) was performed yearly and used to classify patients as normal or IGM, including impaired fasting glucose (IFG) and/or impaired glucose tolerance (IGT) and diabetes mellitus (DM), and to calculate surrogate measures of insulin secretion and/or sensitivity. Results IGM patients were 18 (58.1%, three DM) at baseline and 19 (61.3%, five DM) at end-of-follow-up. However, 13 individuals changed category of glucose homeostasis in both directions during follow-up (8 progressors, 5 regressors) and 18 did not (8 non-progressors, 10 non-regressors). New cases of IGM and DM were 11.1 and 2.53 per 100 persons-year, respectively, and were treated non-pharmacologically. In the whole cohort and, to a higher extent, in progressors, indices of early-phase insulin secretion and insulin sensitivity decreased significantly from baseline to end-of-follow-up, with concurrent reduction of the oral disposition index and insulin secretion-sensitivity index-2 (ISSI-2), compensating insulin secretion for the level of insulin resistance. No baseline measure independently predicted progression, which correlated with change from baseline in ISSI-2. Compared with patients with normal glucose homeostasis, IGT subjects had impaired insulin sensitivity, whereas insulin secretion was reduced only in those with IFG+IGT or DM. Conclusions IGM incidence is high in young adults with WS, suggesting the need of early screening and timed intervention. As in classical type 2 diabetes, impaired insulin sensitivity and β-cell dysfunction contribute, in this sequence, to progression to IGM and DM.
Model-free wind farm control based on random search

This paper explores a model-free approach based on the random search (RS) algorithm for maximizing wind farms power production. The RS based approach is utilized to find the optimal control parameter of each turbine in maximizing the wind farm total power production. The Horns Rev wind farm model with turbulence interaction between turbines is used to validate the proposed approach. Simulation results demonstrate that the random search approach produces higher total power production as compared to the existing method.
Applicability of Tableside Flat Panel Detector CT Parenchymal Cerebral Blood Volume Measurement in Neurovascular Interventions: Preliminary Clinical Experience

BACKGROUND AND PURPOSE: CBV is a vital perfusion parameter in estimating the viability of brain parenchyma (eg, in cases of ischemic stroke or after interventional vessel occlusion). Recent technologic advances allow parenchymal CBV imaging tableside in the angiography suite just before, during, or after an interventional procedure. The aim of this work was to analyze our preliminary clinical experience with this new imaging tool in different neurovascular interventions. MATERIALS AND METHODS: FPD-CBV measurement was performed on a biplane FPD angiographic system. Eighteen patients (11 women, 7 men) were examined (age range, 18–86 years; median, 58.7 years). In the 10 patients with stroke, the extent of intracranial hypoperfusion was evaluated. The remaining 8 patients had an intracranial hemorrhage; periprocedural CBV was evaluated during the course of interventional treatment. RESULTS: In the 18 cases studied, 23 CBV measurements were performed. Twenty acquisitions were of sufficient diagnostic quality. The remaining 3 acquisitions failed technically, 1 due to motion artifacts and 2 due to injection technique and/or hardware failure. CONCLUSIONS: FPD-CBV measurement in the angiography suite provides a feasible and helpful tool for peri-interventional neuroimaging. It extends the intraprocedural imaging modalities to the level of tissue perfusion. However, the technique has technical limitations and shows room for improvement in the future.
Investigation on low-temperature characteristics of FBG sensors and the technology to enhance sensitivity

The mode of FBG's temperature-sensing is analyzed to and the low temperature performance of FBG is experimental study. Three package technologies can be used for enhancing the sensitivity of FBG under low temperature; the technologies include capillary steel tube package, metallized package and organic polymer package. The results show that the temperature sensitivity of bare FBG under low temperature is 0.00998 nm /°C, the temperature sensitivity of FBG with capillary steel tube package, metallized package and organic polymer package are 0.0213 nm /°C, 0.0283 nm /°C and 0.1376 nm /°C separately, which are 2.02, 3.30, 10.23 times compared with the bare fiber. The temperature sensitivity of FBG sensor under low temperature could be increased effectively by using package technology.
The significance of antibody to hepatitis C virus in patients with chronic hepatitis B

We assessed the prevalence and clinical significance of antibodies to hepatitis C virus among a cohort of 148 patients with chronic hepatitis B virus infection. Sixteen patients (11%) had anti‐hepatitis C virus detectable by enzyme‐linked immunoassay. The results from eight of these patients were positive by recombinant immunoblot assay. The results of recombinant immunoblot assay testing were not consistent; therefore the analysis of the patients' data was based on anti‐hepatitis C virus enzyme‐linked immunoassay results. Patients with chronic hepatitis B with anti‐hepatitis C virus were more likely to be cirrhotic (44% vs. 21%) and to have decompensated liver disease (24% vs. 6%). Hepatitis B virus replication appeared to be suppressed in patients with both infections as measured by hepatitis B virus—associated DNA polymerase activity (mean = 2,055 vs. 2,555 cpm). Human immunodeficiency virus infection was more common in the anti‐hepatitis C virus positive group (36% vs. 11%). Thus hepatitis C virus appears to suppress hepatitis B virus replication and to cause more severe liver disease in patients with chronic hepatitis B infection. (HEPATOLOGY 1991;14:64–67.)
Chinese Text Chunking Using Divide-Conquer Model

Traditional Chinese text chunking approach is to identify phrases using only one model and same features. It has been shown that the limitations of using only one model are that: the use of the same types of features is not suitable for all phrases, and data sparseness may also result. In this paper, the divide-conquer model is proposed and applied in the identification of Chinese phrases. This model divides the task of chunking into several sub-tasks according to sensitive features of each phrase and identifies different phrases in parallel. Then, a two-stage decreasing conflict strategy is used to synthesize each sub-task's answer. Through testing on Chinese Penn Treebank, F score of Chinese chunking using multi-agent strategy achieves to 95.82%, which is higher than the best result that has been reported.
Selection and Validation of Appropriate Reference Genes for Quantitative Real-Time PCR Analysis of Gene Expression in Lycoris aurea

Lycoris aurea (L' Hér.) Herb, a perennial grass species, produces a unique variety of pharmacologically active Amaryllidaceae alkaloids. However, the key enzymes and their expression pattern involved in the biosynthesis of Amaryllidaceae alkaloids (especially for galanthamine) are far from being fully understood. Quantitative real-time polymerase chain reaction (qRT-PCR), a commonly used method for quantifying gene expression, requires stable reference genes to normalize its data. In this study, to choose the appropriate reference genes under different experimental conditions, 14 genes including YLS8 (mitosis protein YLS8), CYP2 (Cyclophilin 2), CYP 1 (Cyclophilin 1), TIP41 (TIP41-like protein), EXP2 (Expressed protein 2), PTBP1 (Polypyrimidine tract-binding protein 1), EXP1 (Expressed protein 1), PP2A (Serine/threonine-protein phosphatase 2A), β-TUB (β-tubulin), α-TUB (α-tubulin), EF1-α (Elongation factor 1-α), UBC (Ubiquitin-conjugating enzyme), ACT (Actin) and GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) were selected from the transcriptome datasets of L. aurea. And then, expressions of these genes were assessed by qRT-PCR in various tissues and the roots under different treatments. The expression stability of the 14 candidates was analyzed by three commonly used software programs (geNorm, NormFinder, and BestKeeper), and their results were further integrated into a comprehensive ranking based on the geometric mean. The results show the relatively stable genes for each subset as follows: (1) EXP1 and TIP41 for all samples; (2) UBC and EXP1 for NaCl stress; (3) PTBP1 and EXP1 for heat stress, polyethylene glycol (PEG) stress and ABA treatment; (4) UBC and CYP2 for cold stress; (5) PTBP1 and PP2A for sodium nitroprusside (SNP) treatment; (6) CYP1 and TIP41 for methyl jasmonate (MeJA) treatment; and (7) EXP1 and TIP41 for various tissues. The reliability of these results was further enhanced through comparison between part qRT-PCR result and RNA sequencing (RNA-seq) data. In summary, our results identified appropriate reference genes for qRT-PCR in L. aurea, and will facilitate gene expression studies under these conditions.
New results and algorithms for computing storage functions: The lossless/all-pass cases

Storage functions, which are also the Algebraic Riccati Inequality (ARI) solutions, play an important role in many optimal control/estimation problems. Extreme storage functions are solutions to the corresponding Algebraic Riccati Equation (ARE). While storage functions exist under assumption of dissipativity, a key assumption in formulation of the ARE/ARI is certain `regularity conditions' on the feedthrough term in the input/state/output representation of the system. For example, lossless and all-pass systems do not meet such regularity conditions (nonsingularity of D + DT and I - DTD respectively). And hence the ARE does not exist for such systems. Consequently, computation of storage functions for lossless/all-pass systems is not possible by conventional ARE based methods, and therefore, for such systems, different techniques are needed. In this paper we present three new algorithms for computation of storage functions for lossless/all-pass systems and compare them for numerical accuracy and computational efficiency. Each of the proposed methods presented in this paper comes from different viewpoints. One is linked to the notion of Bezoutian of two polynomials, while another is motivated by Foster realization of LC circuits and the third method is linked to the notion of trajectories of minimal dissipation in the behavioral approach. A comparative study among the three methods shows that the method based on the Bezoutian is the best from both perspectives: computational time and numerical accuracy.