Miracle-dz/UniFAR-FTUs huggingface dataset:
Avoiding False Positive Antigen Detection by Flow Cytometry on Blood Cell Derived Microparticles: The Importance of an Appropriate Negative Control

Background Microparticles (MPs), also called microvesicles (MVs) are plasma membrane-derived fragments with sizes ranging from 0.1 to 1μm. Characterization of these MPs is often performed by flow cytometry but there is no consensus on the appropriate negative control to use that can lead to false positive results. Materials and Methods We analyzed MPs from platelets, B-cells, T-cells, NK-cells, monocytes, and chronic lymphocytic leukemia (CLL) B-cells. Cells were purified by positive magnetic-separation and cultured for 48h. Cells and MPs were characterized using the following monoclonal antibodies (CD19,20 for B-cells, CD3,8,5,27 for T-cells, CD16,56 for NK-cells, CD14,11c for monocytes, CD41,61 for platelets). Isolated MPs were stained with annexin-V-FITC and gated between 300nm and 900nm. The latex bead technique was then performed for easy detection of MPs. Samples were analyzed by Transmission (TEM) and Scanning Electron microscopy (SEM). Results Annexin-V positive events within a gate of 300-900nm were detected and defined as MPs. Our results confirmed that the characteristic antigens CD41/CD61 were found on platelet-derived-MPs validating our technique. However, for MPs derived from other cell types, we were unable to detect any antigen, although they were clearly expressed on the MP-producing cells in the contrary of several data published in the literature. Using the latex bead technique, we confirmed detection of CD41,61. However, the apparent expression of other antigens (already deemed positive in several studies) was determined to be false positive, indicated by negative controls (same labeling was used on MPs from different origins). Conclusion We observed that mother cell antigens were not always detected on corresponding MPs by direct flow cytometry or latex bead cytometry. Our data highlighted that false positive results could be generated due to antibody aspecificity and that phenotypic characterization of MPs is a difficult field requiring the use of several negative controls.
What is the CIM lacking?

The IEC 61970/61968 Common Information Model is undoubtedly one of the core standards of the future smart grid as pointed out by different organizations and recent standardization roadmaps. Its acceptance in the energy sector and the active standardization work is very high and make it one of the most established standards worldwide in the energy domain. But not all requirements are met by the CIM to be the standard of choice in any possible situation. This work tries to specify some of the main gaps identified in different research projects like in the German e-energy projects and in day-to-day business with electric utility companies and the surrounding industry. There is also the attempt to recommend some known approaches to these gaps and to advise general solutions to encounter problems while using the Common Information Model.
The Contribution of Geography to Black/White Differences in the Use of Low Neonatal Mortality Hospitals in New York City

Background:Racial differences in the use of high-quality hospital care contribute to racial disparities in mortality for very low birth weight (VLBW) neonates. Objectives:We explored the role that geographic distribution of hospitals plays in the racial disparity in the use of top-tier hospitals by mothers of VLBW neonates in New York City. Research Design:Retrospective analysis of Vital Statistics and administrative databases. Subjects:VLBW deliveries in New York City from 1996 to 2001 to non-Hispanic Black (n = 4947) and non-Hispanic White (n = 1615) mothers. Results:Black mothers were less likely to deliver in a top-tier hospitals (White = 44%, Black = 28%; P < 0.001) and top-tier hospitals were less likely to be located in Black mothers' neighborhoods (White = 40%, Black = 33%; P < 0.001). Distance, however, did not contribute to the disparity in use of top-tier hospitals. Non-Hispanic Black mothers lived marginally closer to a top-tier hospital than non-Hispanic White mothers (0.65 miles closer; P < 0.001), and mothers of both the races often bypassed their neighborhood hospital (Black = 62% bypassed, White = 71%; P < 0.001). Inattention to recommended prenatal behaviors was associated with using a closer hospital, suggesting that geographic proximity was most important to mothers of vulnerable neonates. Purported measures of hospital quality such as Neonatal Intensive Care Unit level and volume were more strongly associated with use of hospital for White mothers than for Black mothers. Conclusions:The influence of geography on the use of top-tier hospitals for mothers of VLBW neonates is complex. Other personal and hospital characteristics, not just distance or geography, also influenced hospital use in New York City.
Combining an Expert-Based Medical Entity Recognizer to a Machine-Learning System: Methods and a Case Study

Medical entity recognition is currently generally performed by data-driven methods based on supervised machine learning. Expert-based systems, where linguistic and domain expertise are directly provided to the system are often combined with data-driven systems. We present here a case study where an existing expert-based medical entity recognition system, Ogmios, is combined with a data-driven system, Caramba, based on a linear-chain Conditional Random Field (CRF) classifier. Our case study specifically highlights the risk of overfitting incurred by an expert-based system. We observe that it prevents the combination of the 2 systems from obtaining improvements in precision, recall, or F-measure, and analyze the underlying mechanisms through a post-hoc feature-level analysis. Wrapping the expert-based system alone as attributes input to a CRF classifier does boost its F-measure from 0.603 to 0.710, bringing it on par with the data-driven system. The generalization of this method remains to be further investigated.
The importance of locality in the visualization of large datasets

Many scientific phenomena in large high‐resolution datasets such as the U.K. Ocean Circulation and Advanced Modelling (OCCAM) ocean model are better discovered through visualization than by algorithmic analysis: it is often more straightforward to see a feature than it is to characterize it numerically. Using traditional rendering techniques, the size of modern datasets presents a challenge for even high‐end graphical supercomputers, and the cost of such hardware limits its availability for day‐to‐day analysis. We present an architecture that brings visual analysis to the desktop by exploiting consumer‐grade graphics hardware in order to provide initial interactive exploration and Web services to enable finer‐grained analysis and interoperability with traditional visualization tools. Copyright © 2006 John Wiley & Sons, Ltd.
SOME METHODOLOGICAL AND PHILOSOPHICAL REFLECTIONS ON INTERVIEW-BASED FIELDWORK IN INDIA AND ELSEWHERE. TAKING QUALITATIVE RESEARCH SERIOUSLY.

Qualitative research has frequently had a bad press and tends to be regarded as non-rigorous, subjectively biassed and in general ‘unscientific’. This paper is restatement of the merits of this type of research allied to a repudiation of the arguments of its various critics. Thus,it takes issue with the supposed greater ‘objectivity’ attained through quantitative and positivistic research methods. But it is equally critical of the overly narrow understanding of language and text in ‘post-modernism’ and of fashionable worries about ‘disempowered’ informants. Instead, it is argued that seeking to understand, interpret and report honestly the things people say and the things people do in all their ‘messy complexity’ enables deep and rich ‘knowledge claims’to be made. But for the full richness of such claims to emerge, it is argued, they must be mediated reflexively and self-consciously through the purposes (and associated theoretical frameworks) the researcher brings to his/her work. An understanding of the Wittgensteinian approach to language if allied with a Marxian framework for the broader understanding of social processes, can provide powerful analytical tools in the practice of qualitative social and economic research.
Effectiveness of the ThinPrep Imaging System: Clinical experience in a low risk screening population

The Cytyc ThinPrep Imaging System was FDA approved based on a multi‐institutional clinical trial, in which the HSIL+ prevalence rate was 0.7%. This study determines the effectiveness of the Imager in clinical practice at an academic medical center with a historical HSIL+ rate of 0.25%. Cytological interpretations were compared for two 12‐month periods pre‐ and post‐Imager implementation. Data was compiled by cytologic diagnoses, and variations in prevalence rates were analyzed for statistical significance. Interpretations of ASC‐US, ASC‐H, and LSIL were correlated with Digene Hybrid Capture2 High Risk HPV DNA testing; interpretations of ASC‐H, LSIL, and HSIL+ were correlated with subsequent surgical follow‐up. ASC‐US, ASC‐H, and LSIL detection rates increased 34, 48, and 29%, respectively, with the Imager (P < 0.001); whereas the detection of HSIL increased 24% (P < 0.051). Surgical correlation revealed no statistical differences in the positive predictive value (PPV) for ASC‐H and LSIL. However, an increase in the PPV of HSIL was found (P < 0.05). High risk HPV results were lower for ASC‐US (P < 0.001), but statistically equivalent for ASC‐H and LSIL. Results of surgical correlation and HPV testing validated an increase in detection rates of ASC‐H, LSIL, and HSIL, as well as increased PPV of HSIL with the ThinPrep Imaging System. Diagn. Cytopathol. 2008;36:155–160. © 2008 Wiley‐Liss, Inc.
MACROMOLECULAR PHYSIOLOGY OF PLASTIDS

Sequential changes occurring in the etioplasts of the primary leaf of 7-day-old dark-grown barley seedlings upon continuous illumination with 20 lux have been investigated by electron microscopy, in vivo spectrophotometry, and thin-layer chromatography. Following photoconversion of the protochlorophyllide pigment to chlorophyllide and the structural transformation of the crystalline prolamellar bodies, the tubules of the prolamellar bodies are dispersed into the primary lamellar layers. As both chlorophyll a and b accumulate, extensive formation of grana takes place. After 4 hr of greening, protochlorophyllide starts to reaccumulate, and concomitantly both large and small crystalline prolamellar bodies are formed. This protochlorophyllide is rapidly photoconverted upon exposure of the leaves to high light intensity, which also effects a rapid reorganization of the recrystallized prolamellar bodies into primary lamellar layers.
Privacy preserving decentralized power system state estimation with phasor measurement units

This paper presents a privacy preserving approach to decentralized state estimation in multi-area power systems. By formulating state estimation as a model-distributed regularized least-squares (MDRLS) problem, we ensure that the state variables and system matrix of each area are hidden from all other areas in order to protect privacy and sensitive information. We present a scheme that solves the primal MDRLS problem using the alternating direction method of multipliers, and a second method that solves the dual problem using a distributed form of the coordinate descent algorithm. Only information related to current measurements on tie-lines linking neighboring areas is exchanged between those areas. The proposed schemes enable the local state estimator in each area to estimate the voltage magnitude and phase angle of each bus in its own control area from phasor measurement units (PMU) without the need for full local PMU-observability. The novelty of the proposed methods is in that they employ the inherently hierarchical architecture of the wide-area monitoring system to perform decentralized state estimation. Our simulation results show that the estimation error of both methods converges to that of the centralized approach.
A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics.

This is an electronic version of an article published in Systematic Biology [Holder, Mark T. , Jeet Sukumaran, and Paul O. Lewis. A justification for reporting majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology, 57(5):814{821, 2008. ] Systematic Biology is available online at informaworld http://dx.doi. org/10.1080/10635150802422308
Antigen Presentation, Autoantigens, and Immune Regulation in Multiple Sclerosis and Other Autoimmune Diseases

Antigen presentation is in the center of the immune system, both in host defense against pathogens, but also when the system is unbalanced and autoimmune diseases like multiple sclerosis (MS) develop. It is not just by chance that a major histocompatibility complex gene is the major genetic susceptibility locus in MS; a feature that MS shares with other autoimmune diseases. The exact etiology of the disease, however, has not been fully understood yet. T cells are regarded as the major players in the disease, but most probably a complex interplay of altered central and peripheral tolerance mechanisms, T-cell and B-cell functions, characteristics of putative autoantigens, and a possible interference of environmental factors like microorganisms are at work. In this review, new data on all these different aspects of antigen presentation and their role in MS will be discussed, probable autoantigens will be summarized, and comparisons to other autoimmune diseases will be drawn.
Parallel Genetic Algorithm Based on the MPI Environment

Current genetic algorithm require both management of huge amounts of data and heavy computation, fulfilling these requirements calls for simple ways to implement parallel computing. In this paper, serial genetic algorithm was designed to parallel GA; this technology appears to be particularly well adapted to this task. Here we introduce two related mechanism: elite reserve strategy and MPI. The first can increase the possible to get the optimal solution of the population, while the message passing interface MPI support is adding to form a new coarse-grain model of distributed parallel genetic algorithm. This new algorithm is tested by the classical and effective Knapsack problem, analysis shows that, the introduction of the parallel strategies can reduce the communication between different machines and the scheduling time of the heterogeneous system, thereby accelerate the traditional genetic algorithm search process, ultimately concluded that the parallel genetic algorithm is very promising and this framework could have a wide range of applications while maintaining good computational efficiency, scalability and ease of maintenance. DOI: http://dx.doi. org/10.11591/telkomnika.v10i7. 1566
Evaluation of Microscopic Observation Drug Susceptibility Assay for Detection of Multidrug-Resistant Mycobacterium tuberculosis

ABSTRACT Early detection of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) is of primary importance for both patient management and infection control. Optimal methods for identifying drug-resistant Mycobacterium tuberculosis in a timely and affordable way in resource-limited settings are not yet available. This study prospectively evaluated a low-technology but rapid drug susceptibility testing method, the microscopic observation drug susceptibility assay (MODS), in the concurrent detection of M. tuberculosis and its susceptibilities to isoniazid and rifampin (two drugs defining multidrug-resistant M. tuberculosis) directly from sputum specimens. Sputum samples were collected from 262 smear-positive TB patients in Addis Ababa, Ethiopia. To undertake MODS, 100 μl of decontaminated samples was inoculated into a 24-well plate containing 1 ml of 7H9 broth with and without appropriate drugs. The assay uses an inverted-light microscope to detect characteristic mycobacterial growth in liquid culture. Of 262 smear-positive patients, MODS detected 254 (96.9%) and culture in Löwenstein-Jensen medium detected 247 (94.3%) (P = 0.016). For the 247 cultures, the sensitivity, specificity, and accuracy of MODS for detecting MDR-TB were 92.0, 99.5, and 98.8%, respectively, using the method of proportion as a reference (concordance, 98.8%; kappa value, 0.932). Results for MODS were obtained in a median time of 9 days. MODS is an optimal alternative method for identifying MDR-TB in a timely and affordable way in resource-limited settings.
Prevalence of Early Posttraumatic Seizures in Children With Moderate to Severe Traumatic Brain Injury Despite Levetiracetam Prophylaxis*

Objectives: To evaluate the prevalence of early seizures after levetiracetam prophylaxis in children with moderate to severe traumatic brain injury. Design: Prospective observational study. Setting: Level 1 pediatric trauma center. Patients: We enrolled 34 patients between the ages of 0–18 years with moderate to severe traumatic brain injury admitted to the PICU at a level 1 trauma center who received levetiracetam for early posttraumatic seizure prophylaxis. Measurements and Main Results: Primary outcome was the prevalence of early posttraumatic seizures that were defined as clinical seizures within 7 days of injury. In 6 of 34 patients (17%), clinical seizures developed despite levetiracetam prophylaxis. An additional two patients had nonconvulsive seizures. This prevalence is similar to that reported in the literature in this patient population who do not receive seizure prophylaxis (20–53%) and is higher than that in patients who receive phenytoin prophylaxis (2–15%). Patients with early posttraumatic seizures were younger (median age, 4 mo) (p < 0.001) and more likely to have suffered from abusive head trauma (p < 0.0004). Conclusions: Early clinical posttraumatic seizures occurred frequently in children with moderate to severe traumatic brain injury despite seizure prophylaxis with levetiracetam. Younger children and those with abusive head trauma were at increased risk of seizures. Further studies are needed to evaluate the efficacy of levetiracetam before it is routinely used for seizure prophylaxis in these children, particularly in young children and those who have suffered from abusive head trauma.
Ensuring application integrity in shared sensing environments

Smart Environments, such as smart offices, must support multiple applications that are deployed and managed by different parties. Smart Environments are always on and application software must therefore be deployed, configured and reconfigured while the system is running. Re-configurable component models provide the basic mechanisms necessary to achieve run-time reconfiguration. However, in cases with shared component instances, ensuring application integrity during 3rd party reconfiguration leads to high developer effort and disruption. This paper addresses this problem through Composition-Swapping, an extension of re-configurable component models wherein state management delegation and extended component meta-data are used to support component-sharing and ensure application integrity. We demonstrate that Composition-Swapping reduces reconfiguration effort and disruption for four concurrently running applications on a real-world smart office environment.
Update on amniotic membrane transplantation

Cryopreserved amniotic membrane modulates adult wound healing by promoting epithelialization while suppressing stromal inflammation, angiogenesis and scarring. Such clinical efficacies of amniotic membrane transplantation have been reported in several hundred publications for a wide spectrum of ophthalmic indications. The success of the aforementioned therapeutic actions prompts investigators to use amniotic membrane as a surrogate niche to achieve ex vivo expansion of ocular surface epithelial progenitor cells. Further investigation into the molecular mechanism whereby amniotic membrane exerts its actions will undoubtedly reveal additional applications in the burgeoning field of regenerative medicine. This article will focus on recent advances in amniotic membrane transplantation and expand to cover its clinical uses beyond the ocular surface.
Patients' decisional control over care: a cross-national comparison from both the patients' and nurses' points of view.

BACKGROUND Patients' decisional control over care is the ability or power for patients to decide what their involvement will be in healthcare decisions. There is evidence of limited agreement between the perceptions of patients and the perceptions of nurses and/or caregivers with regard to the degree of patient involvement in the planning and performance of their care. AIM To analyse and compare patients' and nurses' perceptions of patients' decisional control over their own care. METHOD A multisite cross-sectional comparative survey design was employed. Data were collected from hospitalised surgical inpatients (n = 1315) and their caregivers (n = 960 nurses) in five European countries. The Individualised Care Scale part B was used for collecting data from both the patients and nurses. Ethical standards were followed throughout the study. RESULTS Significant between-country differences were found between patients and nurses. In all countries, both patients and nurses regarded that decisional control over care had been actualised (ICS-B: M = 3.75-4.47 and 3.48-4.33, respectively), but there were significant differences in their perceptions regarding four of the six items of the decisional control factor of the ICS-B. CONCLUSIONS The results show that there are disparities between patients' and nurses' perceptions of patient involvement in care, probably due to cultural issues that need further exploration. CLINICAL RELEVANCE The disparities between patients' and nurses' perceptions on patients' decisional control over their care should be taken into consideration as a potential cause of patient dissatisfaction with nursing care.
Iron uptake and iron-repressible polypeptides in Yersinia pestis

Pigmented (Pgm+) cells of Yersinia pestis are virulent, are sensitive to pesticin, adsorb exogenous hemin at 26 degrees C (Hms+), produce iron-repressible outer membrane proteins, and grow at 37 degrees C in iron-deficient media. These traits are lost upon spontaneous deletion of a chromosomal 102-kb pgm locus (Pgm-). Here we demonstrate that an Hms+ but pesticin-resistant (Pst(r)) mutant acquired a 5-bp deletion in the pesticin receptor gene (psn) encoding IrpB to IrpD. Growth and assimilation of iron by Pgm- and Hms+ Pst(r) mutants were markedly inhibited by ferrous chelators at 37 degrees C; inhibition by ferric and ferrous chelators was less effective at 26 degrees C. Iron-deficient growth at 26 degrees C induced iron-regulated outer membrane proteins of 34, 28.5, and 22.5 kDa and periplasmic polypeptides of 33.5 and 30 kDa. These findings provide a basis for understanding the psn-driven system of iron uptake, indicate the existence of at least one additional 26 degrees C-dependent iron assimilation system, and define over 30 iron-repressible proteins in Y. pestis.