Miracle-dz/UniFAR-FTUs huggingface dataset:
HPLC method for measuring the circulating levels of 25-hydroxy vitamin D: Validation and comparison with ID LC/MS/MS and immunoassay

Twenty five-hydroxy-vitamin D (25OHD) levels are accepted as an indicator for vitamin D status and their measurement is still a challenge. The aim of the present study was to develop a robust and easy to use HPLC-method for simultaneous analysis of 25OHD 2 and 25OHD 3 in human plasma and to assess its analytical performance, Protein precipitation followed by liquid-liquid extraction with n-hexane was used for separation from the matrix substances. A HPLC-system with UV detector (Thermo Scientific Spectra System, USA) was used. HPLC-UV analysis was performed on a Synergy hydro-RP column 4,6x250 mm, 4.0 µm particle size with mobile phase consisting of methanol/acetonitrile/water (70/25/5) under isocratic elution at a flow rate of 1.2 mL/min and UV-detection at 265 nm. Our HPLC-method was compared with a validated ID-LC-MS/MS method and with a commercial immunochemical method. Linear regression was used for data analysis. Linearity of the HPLC-assay was between 5-160 ng/ml for each analyte (r 2 =0.99) with lower limit of detection 4 nmol/L, and limit of quantification 10 nmol/L. Intra-assay precision was determined by extracting and quantifying 10 replicates of 4 QC levels (RSD ≤ 9%). Inter-assay precision was determined over 21 consecutive days analyzing 10 replicates of all QC samples (RSD<10%). All results were within 14.2% deviation of the 25OHD LC-MS/MS method mean. Method comparison demonstrated good agreement between HPLC and LC-MS/MS (r=0.85) and disparity with the commercial immunoassay (r=0.48). This assay demonstrates excellent linearity, acceptable accuracy and precision, a good agreement with a validated ID-LC-MS/MS method. The simple sample preparation and ease of determination make it useful for the routine clinical laboratory.
Coincidences of climate extremes and anomalous vegetation responses: comparing tree ring patterns to simulated productivity

Climate extremes can trigger exceptional re- sponses in terrestrial ecosystems, for instance by altering growth or mortality rates. Such effects are often manifested in reductions in net primary productivity (NPP). Investi- gating a Europe-wide network of annual radial tree growth records confirms this pattern: we find that 28 % of tree ring width (TRW) indices are below two standard deviations in years in which extremely low precipitation, high tem- peratures or the combination of both noticeably affect tree growth. Based on these findings, we investigate possibilities for detecting climate-driven patterns in long-term TRW data to evaluate state-of-the-art dynamic vegetation models such as the Lund-Potsdam-Jena dynamic global vegetation model for managed land (LPJmL). The major problem in this con- text is that LPJmL simulates NPP but not explicitly the ra- dial tree growth, and we need to develop a generic method to allow for a comparison between simulated and observed response patterns. We propose an analysis scheme that quan- tifies the coincidence rate of climate extremes with some bi- otic responses (here TRW or simulated NPP). We find a rel- ative reduction of 34 % in simulated NPP during precipita- tion, temperature and combined extremes. This reduction is comparable to the TRW response patterns, but the model re- sponds much more sensitively to drought stress. We identify 10 extreme years during the 20th century during which both model and measurements indicate high coincidence rates across Europe. However, we detect substantial regional dif- ferences in simulated and observed responses to climatic ex- treme events. One explanation for this discrepancy could be the tendency of tree ring data to originate from climatically stressed sites. The difference between model and observed data is amplified by the fact that dynamic vegetation mod- els are designed to simulate mean ecosystem responses on landscape or regional scales. We find that both simulation re- sults and measurements display carry-over effects from cli- mate anomalies during the previous year. We conclude that radial tree growth chronologies provide a suitable basis for generic model benchmarks. The broad application of coinci- dence analysis in generic model benchmarks along with an increased availability of representative long-term measure- ments and improved process-based models will refine pro- jections of the long-term carbon balance in terrestrial ecosys- tems.
Acid Resistance in Mycobacterium tuberculosis

Responses to acid have been studied extensively in enteric pathogens, such as Escherichia coli, Vibrio cholerae, and Helicobacter pylori that encounter the extremely low pH (pH 2 to 3) of the stomach during ingestion. In contrast, much less is known about how obligate or facultative intracellular bacterial pathogens like Mycobacterium tuberculosis respond, resist, and persist in the moderately acid environment of the phagosome or phagolysosome. The pH of the macrophage compartment, in which M. tuberculosis resides, ranges from pH 6.2 to 4.5, depending on the activation state of the macrophage (55, 81, 99). Phagosomal acidity may provide a critical cue for adaptation of M. tuberculosis to the host niche. At the same time, to ensure survival for what can be decades, the bacterium must prevent excessive entry of protons into its cytosol and expel them when their concentrations threaten the pH homeostasis that most organisms maintain. Here we review current understanding of the ability of M. tuberculosis to adapt to phagosomal levels of acid. It has been challenging to dissect the role of phagosome acidification in the pathogenesis of tuberculosis, because it is accompanied by and synergizes with other host defenses. Similarly, M. tuberculosis acid resistance mechanisms appear to be cross-protective against other forms of stress, making it difficult to directly relate a defect in acid resistance to impaired virulence. Notwithstanding, the phenomenon is central to the pathogenesis of tuberculosis and thus might offer points of vulnerability that could be exploited by new chemotherapeutics.
Certifying for CMM Level 2 and IS09001 with XP@Scrum

This experience report describes the followed road of getting certified for both CMM Level 2 and ISO9001:2000 on a time scale of 2 years by using agile methodologies. We discuss why we selected the combination of extreme programming (XP) and Scrum as the base for our software development process and which "ceremony" we had to add in order to satisfy the requirements ofCMML2 and ISO9001. Also our major challenges at the moment are described, and the way we try to solve them. Furthermore we want to share a number of issues and experiences.
Understanding cholesterol: high is bad but too low may also be risky -- is low cholesterol associated with cancer?

UNLABELLED Cholesterol (CH) is a vital component of cell membranes and of their function. It is entirely justified to warn against haphazard aggressive CH lowering, especially now, when more effective CH-modifying medications are entering the market. Enormous success in lowering the human toll of atherosclerosis and cardiovascular disease (CVD) by treating abnormally elevated lipids may be off set by the therapeutic risk. There are warning reports that low cholesterol is associated with malignity. There is a pressing need to evaluate all reports related to the risk of low CH body stores. New cholesterol management guidelines presented by American professional cardiology societies in November 2013 have reinforced the need to critically evaluate the management with statins and with other CH lowering medications (Tab. 1, Fig. 3, Ref. 58). KEYWORDS total cholesterol (CH), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), cardiovascular disease (CVD), hydroxy-methylglutaryl coenzyme A reductase (HMGCR), randomized control trial (RCT), cancer, statin, low cholesterol risk, lipid treatment guideline.
Predictive value of multiple drag-swab sampling for the detection of Salmonella from occupied or vacant poultry houses.

The results of four independent complete drag-swab samplings of a 31-farm broiler-production complex are described. Samplings of vacant poultry farms (i.e., between flocks) and occupied farms (i.e., containing chickens) were completed in four 3-day intervals beginning in July 1992 and ending in May 1993. During the first two sampling periods, two drag-swab assemblies were dragged through each individual house and pooled into one sample to evaluate overall incidence of Salmonella detection among vacant and occupied houses. During the second two sampling periods, four drag-swab assemblies were dragged through houses to evaluate frequency of Salmonella detection on individual assemblies within each house. Over the four sampling periods, mean isolation frequencies were 42.2% for vacant poultry farms and 76.2% for occupied poultry farms. When four assemblies were dragged in vacant houses and cultured separately, the probability of detecting salmonellae contamination increased with increasing numbers of assemblies, indicating that multiple drag-swab assemblies should be used for sampling either vacant or occupied broiler houses for the presence of Salmonella. On vacant farms, 89.5% of the total isolations occurred in only one house of two-house farms; the remaining 10.5% of farms were positive in both houses. Salmonella isolation from occupied farms occurred in 54.2% of the samplings in only one house, whereas 45.8% of occupied farms were positive in both houses. These data show a higher frequency of Salmonella isolation on multiple swabs in occupied poultry houses, possibly indicating a quantitatively greater presence of Salmonella in these houses.
Recruitment strategies of methamphetamine-using men who have sex with men into an online survey

Abstract Recruiting hidden populations into online research remains challenging. In this manuscript, we report lessons learned from our efforts to recruit methamphetamine-using men who have sex with men. Between July and October 2012, we implemented a four-phase recruitment strategy to enroll a total of 343 methamphetamine-using MSM into an online survey about recent substance use, sexual behavior, and various psychosocial measures. The four phases were implemented sequentially. During phase one, we placed advertisements on mobile applications, and during phase two, we placed advertisements on traditional websites formatted for browsers. During phase three, we used e-mail to initiate snowball recruitment, and during phase four, we used social media for snowball recruitment. Advertisements on mobile devices and websites formatted for browsers proved to be expensive options and resulted in few eligible participants. Our attempts to initiate a snowball through e-mail also proved unsuccessful. The majority (n = 320) of observations in our final dataset came from our use of social media. However, participant fraud was a concern, requiring us to implement a strong participant verification protocol. For maximum recruitment and cost-effectiveness, researchers should use social media for recruitment provided they employ strong participant verification protocols.
Expression of the leukotriene D4 receptor CysLT1, COX-2, and other cell survival factors in colorectal adenocarcinomas.

BACKGROUND & AIMS The effects of leukotriene (LT) D(4) on intestinal epithelial cells govern events that are involved in cell survival and colon cancer, notably increased expression of cyclooxygenase (COX)-2 and enhanced production of prostaglandin E(2). We investigated possible correlations between distribution of the recently described LTD(4) receptor CysLT(1)R and factors previously shown to be up-regulated by LTD(4) as well as clinicopathologic traits. METHODS Immunohistochemistry and in situ hybridization were performed on tissue arrays, which were made using colorectal cancer samples from 84 patients. RESULTS CysLT(1)R was significantly correlated to COX-2, 5-lipoxygenase, and Bcl-x(L). Male subjects more often exhibited high levels of this receptor relative to female subjects, and Dukes' B patients with elevated CysLT(1)R expression showed markedly poorer survival than those with low-level expression. Furthermore, this was paralleled by an increased viability of CysLT(1)R-overexpressing cells in a colon cancer cell line. CONCLUSIONS Our results further implicate the involvement of LTs in colorectal carcinoma. Based on our present and earlier findings, we propose that LT/CysLT(1)R signaling facilitates survival of colon cancer cells, which may affect disease outcome. Like COX-2, LTs are accessible targets for pharmacologic treatment.
Are Reductions in Population Sodium Intake Achievable?

The vast majority of Americans consume too much sodium, primarily from packaged and restaurant foods. The evidence linking sodium intake with direct health outcomes indicates a positive relationship between higher levels of sodium intake and cardiovascular disease risk, consistent with the relationship between sodium intake and blood pressure. Despite communication and educational efforts focused on lowering sodium intake over the last three decades data suggest average US sodium intake has remained remarkably elevated, leading some to argue that current sodium guidelines are unattainable. The IOM in 2010 recommended gradual reductions in the sodium content of packaged and restaurant foods as a primary strategy to reduce US sodium intake, and research since that time suggests gradual, downward shifts in mean population sodium intake are achievable and can move the population toward current sodium intake guidelines. The current paper reviews recent evidence indicating: (1) significant reductions in mean population sodium intake can be achieved with gradual sodium reduction in the food supply, (2) gradual sodium reduction in certain cases can be achieved without a noticeable change in taste or consumption of specific products, and (3) lowering mean population sodium intake can move us toward meeting the current individual guidelines for sodium intake.
Perceptions of Canadian Provosts on the Institutional Role of Academic Libraries

This study examines perceptions of provosts from Canadian research-intensive universities regarding their institution’s academic libraries. Interviews conducted with nine provosts explored how they perceive academic libraries in terms of alignment with institutional mission, how they envision the future of their libraries, and what they interpret as indicators of success. The results suggest that provosts perceive libraries making significant contributions to research and student learning, particularly through the provision of access to information and the evolving role of library as place respectively. Other areas of library expertise, such as scholarly communication, appear somewhat less familiar to provosts, suggesting the need for library leaders to promote new roles within the institutional context.
Análisis de foros colaborativos en línea en un curso de formación en TIC para docentes y profesionales de Enfermería

El objetivo de este trabajo es describir y analizar las interacciones en los foros en línea asociados a actividades colaborativas en un curso de formación en TIC para docentes y profesionales de Enfermería desde la perspectiva del aprendizaje colaborativo mediado. Se diseñó una metodología basada en el estudio de casos. Se estudió la comunicación electrónica en los foros, combinando el análisis de indicadores de participación con el análisis de contenido de los mensajes. La mayoría de los mensajes respondieron a comunicación relacionada con la tarea. En el análisis de contenido los indicadores más presentes fueron la contribución de ideas y los referidos a la situación de tarea. Se observó una relación positiva entre la participación y las tareas colaborativas. Es posible caracterizar esta participación a través de indicadores que identifican elementos asociados a la profundidad de los mensajes desde el punto de vista cognitivo y de interacción entre los participantes.
Design of radiation hardened wide tuning range CMOS oscillators

CMOS integrated circuits are prone to hazards such as Single Event Transients (SETs) caused by radiation strikes in high energy radiation environments. For synthesis of high frequency signals for circuits used in such environments, we propose use of quadrature phase LC oscillators. In addition to providing higher tolerance to SETs, these oscillators are also able to provide wider tuning range, which is otherwise difficult to achieve for high frequencies, particularly with low phase noise LC oscillators. Further improvement in the radiation tolerance is provided by addition of parallel capacitors and series resistors in tail current path. Simulation results shown 64% reduction in worst case phase offsets caused by radiation strikes generating 100 fC charge and about 20% improvement in tuning range for 14 GHz LC oscillators.
Inhibition of CYP3A4 by 6′,7′‐dihydroxybergamottin in human CYP3A4 over‐expressed hepG2 cells

Objectives We previously established HepG2‐GS‐3A4, a cell line from hepatoblastoma with overexpression of human CYP3A4 and glutamine synthetase (GS). We further reported that these cells can be applied for screening inhibitors of CYP3A4 in vitro. The purpose of this study was to determine whether our CYP3A4‐overexpresed cell could be applied to evaluate mechanisms of CYP3A4 inhibition by 6′,7′‐dihydroxybergamottin (DHB), which is one of the major furanocoumarins in grapefruit juice, by using these cells.
The CRIT Study: Anemia and blood transfusion in the critically ill—Current clinical practice in the United States*

ObjectiveTo quantify the incidence of anemia and red blood cell (RBC) transfusion practice in critically ill patients and to examine the relationship of anemia and RBC transfusion to clinical outcomes. DesignProspective, multiple center, observational cohort study of intensive care unit (ICU) patients in the United States. Enrollment period was from August 2000 to April 2001. Patients were enrolled within 48 hrs of ICU admission. Patient follow-up was for 30 days, hospital discharge, or death, whichever occurred first. SettingA total of 284 ICUs (medical, surgical, or medical-surgical) in 213 hospitals participated in the study. PatientsA total of 4,892 patients were enrolled in the study. Measurements and Main ResultsThe mean hemoglobin level at baseline was 11.0 ± 2.4 g/dL. Hemoglobin level decreased throughout the duration of the study. Overall, 44% of patients received one or more RBC units while in the ICU (mean, 4.6 ± 4.9 units). The mean pretransfusion hemoglobin was 8.6 ± 1.7 g/dL. The mean time to first ICU transfusion was 2.3 ± 3.7 days. More RBC transfusions were given in study week 1; however, in subsequent weeks, subjects received one to two RBC units per week while in the ICU. The number of RBC transfusions a patient received during the study was independently associated with longer ICU and hospital lengths of stay and an increase in mortality. Patients who received transfusions also had more total complications and were more likely to experience a complication. Baseline hemoglobin was related to the number of RBC transfusions, but it was not an independent predictor of length of stay or mortality. However, a nadir hemoglobin level of <9 g/dL was a predictor of increased mortality and length of stay. ConclusionsAnemia is common in the critically ill and results in a large number of RBC transfusions. Transfusion practice has changed little during the past decade. The number of RBC units transfused is an independent predictor of worse clinical outcome.
Freins au dépistage de la BPCO par le médecin généraliste : une revue systématique de littérature

Contexte : La BPCO represente un enjeu de sante public important en raison de sa frequence, de la forte morbi-mortalite dont elle est responsable et de son impact economique considerable. Pourtant, cette pathologie est egalement largement sous diagnostiquee. Objectif : L’objectif de cette etude etait de lister les obstacles au depistage de la BPCO en cabinet de medecine generale. Materiel et Methodes : Dans cette revue systematique de litterature realisee selon le protocole PRISMA les articles eligibles etaient ceux publies entre le 01/01/1996 et le 31/12/2016. Resultats : Le manque de temps et une remuneration insuffisante etaient les contraintes les plus frequemment evoquees dans les etudes retenues. La formation, les competences et les connaissances des praticiens semblaient aussi etre en cause dans le sous diagnostic de la BPCO et etaient souvent evoquees par les MG interroges. Les perceptions et les attitudes des MG vis-a-vis de leurs patients et de la BPCO representaient un autre ensemble de facteurs contribuant au sous diagnostic. D’autre part, cette maladie est meconnue du grand public. Enfin, les symptomes respiratoires ont tendance a etre banalises et sous declares par les patients. Conclusion : Plusieurs pistes apparaissent pour ameliorer la situation de sous diagnostic de cette pathologie : combattre la meconnaissance et le scepticisme des praticiens vis-a-vis du diagnostic de la BPCO, proposer aux medecins davantage de formations sur le reperage de cette pathologie, sensibiliser le grand public et augmenter la remuneration des mini spirometries.
Characterization of a novel RNA regulator of Erwinia carotovora ssp. carotovora that controls production of extracellular enzymes and secondary metabolites

The enterobacterium Erwinia carotovora ssp. carotovora strain 71 (hereafter Ecc71) produces extracellular enzymes such as pectate lyase isozymes (Pels), cellulase (Cel), polygalacturonase (Peh) and protease (Prt). These enzymes degrade plant cell wall components and are largely responsible for the elicitation of soft‐rot diseases in plants and plant products. Ecc71 also produces HarpinEcc, the elicitor of hypersensitive reaction (HR) and the quorum‐sensing signal, N‐(3‐oxohexanoyl)‐L‐homoserine lactone (OHL). OHL controls extracellular enzyme and HarpinEcc production. The levels of these enzymes, as well as the expression of hrpNEcc, the structural gene for HarpinEcc, and ohlI, the gene specifying OHL synthesis, are negatively regulated by RsmA. rsmB, formerly aepH, on the other hand, positively regulates extracellular enzyme production. 6His–RsmA recombinant protein purified from E. coli binds rsmB RNA as indicated by gel mobility shift assays. rsmB comprises 547 bp DNA, which is transcribed from a single start site immediately after a σ70‐like promoter. In Ecc71, two rsmB RNA species are detected: a full‐length 479 base rsmB RNA and a 259 base rsmB′ RNA. rsmB′ DNA hybridizes with the 259 base and the 479 base transcripts. A 3′ RNase protection assay revealed that the 259 base and the 479 base RNA species end at the same position immediately after the putative rho‐independent terminator. The expression of rsmB–lacZ transcriptional fusions established that the rsmB′ RNA is not produced because of the activation of an internal promoter. These data strongly suggest that the 259 base rsmB′ RNA is derived by processing of the primary rsmB RNA. In Ecc71, rsmB′ expression driven by the lac promoter causes overproduction of Pel, Peh, Cel and Prt, and accumulation of pel‐1, peh‐1, hrpNEcc and ohlI transcripts. By contrast, a plasmid with the rsmB′ DNA sequence deleted fails to cause overproduction of the extracellular enzymes in Ecc71. The rsmB′ effect also occurs in Escherichia coli as glycogen accumulation is stimulated in the presence of rsmB′. In vivo and in vitro translation as well as mutational analysis of rsmB′ have established that rsmB′ RNA does not yield a translational product. Therefore, we concluded that the rsmB′ RNA itself functions as the regulator. Indeed, the expression of rsmB′ DNA leads to neutralization of the negative effects of the RNA‐binding protein, RsmA, in Ecc71 and Serratia marcescens strain SM274. We propose a model that explains how RsmA and rsmB control the expression of genes for extracellular enzymes.