Miracle-dz/UniFAR-FTUs huggingface dataset:
KRAS mutation analysis in genomic DNA isolated from formalin-fixed paraffin-embedded ovarian tissue: evaluation of a strip-based reverse-hybridisation assay

Aims To evaluate a reverse-hybridisation assay (strip assay) designed for the sensitive detection of 10 mutations in codons 12 and 13 of the KRAS gene. The strip assay relies on mutant-enriched PCR followed by reverse-hybridisation of biotinylated amplification products to oligonucleotide probes immobilised as an array of parallel lines on nitrocellulose test strips. Methods The strip assay was used to analyse genomic DNA isolated from 120 formalin-fixed paraffin-embedded (FFPE) ovarian tissue samples. The samples were analysed in parallel using a biochip-based protocol (biochip assay) covering the same mutation spectrum, and results were compared with respect to sensitivity, specificity and operational input. Results The strip assay identified 19 (16%) of 120 FFPE samples to carry a KRAS mutation; results were in agreement with those obtained by biochip hybridisation. Both assays had an analytical sensitivity of 1% when performed on FFPE-extracted DNA with approximately the same operational input needed for post-PCR processing. In contrast to the biochip assay, strip assay hybridisation may be automated to a large extent. Conclusions The strip assay is an accurate and sensitive tool for the low to medium throughput detection of KRAS mutation in genomic DNA isolated from FFPE tissue.
Area classification for explosive atmospheres: Comparison between European and North American approaches

The object of this paper is to review various methods of determining the extent of hazardous areas in industrial facilities where explosive gas or vapor atmospheres may be present. Three different approaches are analyzed and compared. The first one is recommended in North American Standards, such as APl500 [1], APl505 [2] and NFPA 497 [3]. The second is one of the proposals for the second edition of the International Standard IEC 60079-10-1 [4] (adopted as European standard EN 60079-10-1). The third approach had been previously worked out with the authors' contribution and had been adopted by the Italian Guide CEI 31-35 since 2001 [5]. The last two approaches are analytical, meanwhile the first one is prescriptive. In the second part of the paper both analytical approaches are applied to the releases which are analyzed in NFPA 497 [3] as practical examples. Resulting hazardous area extents are compared and the differences among the three methods are discussed.
Fluorescent Molecular Peroxidation Products: A Prognostic Biomarker of Early Neurologic Deterioration After Thrombolysis

Background and Purpose— Fluorescent molecular peroxidation products (FMPPs) are considered potential markers of molecular oxidative damage and may provoke increased permeability and disruption of the blood–brain barrier. This study aimed to determine the value of FMPPs as a biomarker to predict neurological worsening related to early hemorrhagic transformation. Methods— Baseline FMPP levels were measured in 186 consecutive acute ischemic stroke patients before tissue plasminogen activator treatment was administered. A serial FMPP profile (baseline before tissue plasminogen activator treatment, and 1, 2, 12, and 24 hours from treatment) was determined in a subset of 100 patients. Computed tomographic scans were performed at admission and repeated at 24 to 48 hours or after neurological worsening occurred. Symptomatic intracranial hemorrhage was defined as blood at any site in the brain associated with neurological deterioration. Results— Patients who worsened had higher median FMPP levels compared with those who did not (59.68 [48.63–85.73] versus 44.87 [36.37–58.90] Uf/mL; P=0.035) at baseline. After logistic regression multivariate analysis, FMPP >48.2 Uf/mL together with age, hypertension, and systolic blood pressure remained baseline predictors of worsening at 48 hours. Moreover, baseline FMPP determination helped to distinguish between patients who worsened and those who did not (Integrated Discrimination Improvement index, 5.7%; P=0.0004). Finally, within patients who had worsened at 48 hours, those with symptomatic intracranial hemorrhage had higher FMPP levels (P=0.038). Conclusions— FMPPs might be a valuable biomarker of poor early neurological outcome and be related to the appearance of symptomatic intracranial hemorrhage in tissue plasminogen activator–treated patients, one of the most feared neurological complications after thrombolytic treatment of acute ischemic stroke.
Opinions about oral cancer prevention and early detection among dentists practising along the Texas-Mexico border.

OBJECTIVES The purpose of this study was to assess dentists' opinions about oral cancer (OC) prevention and early detection. METHODS Data were collected by a self-administered mail questionnaire sent to all 398 registered dentists practising along the Texas-Mexico border. RESULTS The effective response rate to the survey was 40%. While 90% of respondents agreed that oral cancer examinations (OCE) should be provided annually for patients 40 years of age and older, only 59% of respondents believed their OC knowledge was current. While 99% agreed that dentists were qualified to perform OCE, only 54 and 68% respectively, agreed that dental hygienists and physicians were similarly qualified. Dentists who rated their undergraduate OC training favorably (OR = 2.68, 1.23-5.81, P = 0.011), had attended their last oral cancer continuing education (OCCE) course within the past 5 years (OR = 2.46, 1.25-4.86, P = 0.009), and those who performed OCE on all patients 40 years and older (OR = 2.64, 1.32-5.26, P = 0.005), were more likely to agree their OC knowledge was current. CONCLUSIONS Respondents expressed diverse opinions about OC prevention and early detection. Positive opinion on currency of OC knowledge was associated with performance of OCE. Results indicate a need for OCCE targeting the study population as well as increased emphasis on OC curriculum in dental schools.
Natural variation in stochastic photoreceptor specification and color preference in Drosophila

Each individual perceives the world in a unique way, but little is known about the genetic basis of variation in sensory perception. Here we investigated natural variation in the development and function of the color vision system of Drosophila. In the fly eye, the random mosaic of color-detecting R7 photoreceptor subtypes is determined by stochastic expression of the transcription factor Spineless (Ss). Individual R7s randomly choose between SsON or SsOFF fates at a ratio of 65:35, resulting in unique patterns but consistent proportions of cell types across genetically identical retinas. In a genome wide association study, we identified a naturally occurring insertion in a regulatory DNA element in the ss gene that lowers the ratio of SsON to SsOFF cells. This change in photoreceptor fates shifts the innate color preference of flies from green to blue. The genetic variant increases the binding affinity for Klumpfuss (Klu), a zinc finger transcriptional repressor that regulates ss expression. Klu is expressed at intermediate levels to determine the normal ratio of SsON to SsOFF cells. Thus, binding site affinity and transcription factor levels are finely tuned to regulate stochastic on/off gene expression, setting the ratio of alternative cell fates and ultimately determining color preference.
DESIGN OF LATERALLY UNSUPPORTED COLUMNS. THE STRENGTH AND BEHAVIOR OF LATERALLY UNSUPPORTED COLUMNS.

Abstract : The report is a study of the behavior of laterally unsupported as-rolled steel beam-columns under constant axial load and monotonically increasing strong-axis end moments. The first part presents the theoretical solutions for the occurrence of inelastic lateral-torsional buckling of beam-columns with restraints provided at the ends to resist weak-axis bending and warping of the section. The solutions are based on either the tangent modulus concept or the reduced modulus concept of unloading of the yielded portions. The different degrees of restraints are studied and their beneficial effects are compared with the solutions for pinned-end beam-columns, free to warp and bend about the weak-axis. The theoretical solutions are then compared with the available test results and the CRC interaction formula. In the second part, the same method is extended to solve the buckling problems in continuous beam-columns with warping and weak-axis bending restraints at the joints. Sample numerical results are obtained for three-span continuous beam-columns. They are used to check the accuracy of the method currently recommended by the AISI and the AISC for predicting the buckling strength of an assembly of beams and beam-columns. (Author)
Human Primary Epithelial Cells Acquire an Epithelial-Mesenchymal-Transition Phenotype during Long-Term Infection by the Oral Opportunistic Pathogen, Porphyromonas gingivalis

Porphyromonas gingivalis is a host-adapted oral pathogen associated with chronic periodontitis that successfully survives and persists in the oral epithelium. Recent studies have positively correlated periodontitis with increased risk and severity of oral squamous cell carcinoma (OSCC). Intriguingly, the presence of P. gingivalis enhances tumorigenic properties independently of periodontitis and has therefore been proposed as a potential etiological agent for OSCC. However, the initial host molecular changes induced by P. gingivalis infection which promote predisposition to cancerous transformation through EMT (epithelial-mesenchymal-transition), has never been studied in human primary cells which more closely mimic the physiological state of cells in vivo. In this study, we examine for the first time in primary oral epithelial cells (OECs) the expression and activation of key EMT mediators during long-term P. gingivalis infection in vitro. We examined the inactive phosphorylated state of glycogen synthase kinase-3 beta (p-GSK3β) over 120 h P. gingivalis infection and found p-GSK3β, an important EMT regulator, significantly increases over the course of infection (p < 0.01). Furthermore, we examined the expression of EMT-associated transcription factors, Slug, Snail, and Zeb1 and found significant increases (p < 0.01) over long-term P. gingivalis infection in protein and mRNA expression. Additionally, the protein expression of mesenchymal intermediate filament, Vimentin, was substantially increased over 120 h of P. gingivalis infection. Analysis of adhesion molecule E-cadherin showed a significant decrease (p < 0.05) in expression and a loss of membrane localization along with β-catenin in OECs. Matrix metalloproteinases (MMPs) 2, 7, and 9 are all markedly increased with long-term P. gingivalis infection. Finally, migration of P. gingivalis infected cells was evaluated using scratch assay in which primary OEC monolayers were wounded and treated with proliferation inhibitor, Mitomycin C. The cellular movement was determined by microscopy. Results displayed P. gingivalis infection promoted cell migration which was slightly enhanced by co-infection with Fusobacterium nucleatum, another oral opportunistic pathogen. Therefore, this study demonstrates human primary OECs acquire initial molecular/cellular changes that are consistent with EMT induction during long-term infection by P. gingivalis and provides a critically novel framework for future mechanistic studies.
Characterization of shrinkage effects in micro-injection moulding (µ-IM)

III ACKNOWLEDGEMENTS . V CONTENTS . VI LIST OF FIGURES . XIV LIST OF TABLES . XIX LIST OF ABBREVIATIONS . XXII LIST OF SYMBOLS . XXIV PUBLICATIONS . XXV CHAPTER 1 . INTRODUCTION TO MICRO-INJECTION MOULDING . 1 1.1 General considerations of micro injection moulding . 1 1.2 Conventional injection moulding steps . 2 1.2. 1 The injection moulding cycle . 3 1.3 The micro-injection moulding machine . 4 1.4 The micro powder injection moulding processing . 6 1.5 The thesis structure. 10
Space—time zero‐inflated count models of Harbor seals

Environmental data are spatial, temporal, and often come with many zeros. In this paper, we included space‐time random effects in zero‐inflated Poisson (ZIP) and ‘hurdle’ models to investigate haulout patterns of harbor seals on glacial ice. The data consisted of counts, for 18 dates on a lattice grid of samples, of harbor seals hauled out on glacial ice in Disenchantment Bay, near Yakutat, Alaska. A hurdle model is similar to a ZIP model except it does not mix zeros from the binary and count processes. Both models can be used for zero‐inflated data, and we compared space‐time ZIP and hurdle models in a Bayesian hierarchical model. Space‐time ZIP and hurdle models were constructed by using spatial conditional autoregressive (CAR) models and temporal first‐order autoregressive (AR(1)) models as random effects in ZIP and hurdle regression models. We created maps of smoothed predictions for harbor seal counts based on ice density, other covariates, and spatio‐temporal random effects. For both models predictions around the edges appeared to be positively biased. The linex loss function is an asymmetric loss function that penalizes overprediction more than underprediction, and we used it to correct for prediction bias to get the best map for space‐time ZIP and hurdle models. Published in 2007 by John Wiley & Sons, Ltd.
Autopoiesis and Knowledge in Self-Sustaining Organizational Systems

Knowledge and the communication of knowledge are critical for self-sustaining organizations comprised of people and the tools and machines that extend peoples’ physical and cognitive capacities. Humberto Maturana and Francisco Varela proposed the concept of autopoiesis (“self” “production”) as a definition of life in the 1970s. Nicklas Luhmann extended this concept to establish a theory of social systems, where intangible human social systems were formed by recursive networks of communications. We show here that Luhmann fundamentally misunderstood Maturana and Varela’s autopoiesis by thinking that the self-observation necessary for self-maintenance formed a paradoxically vicious circle. Luhmann tried to resolve this apparent paradox by placing the communication networks on an imaginary plane orthogonal to the networked people. However, Karl Popper’s evolutionary epistemology and the theory of hierarchically complex systems turns what Luhmann thought was a vicious circle into a virtuous spiral of organizational learning and knowledge. There is no closed circle that needs to be explained via Luhmann’s extraordinarily paradoxical linguistic contortions.
Identification of Two New Synthetic Histone Deacetylase Inhibitors That Modulate Globin Gene Expression in Erythroid Cells from Healthy Donors and Patients with Thalassemia

We have identified two new histone deacetylase (HDAC) inhibitors (9 and 24) capable of inducing the expression of γ-globin and/or β-globin promoter-driven reporter genes in a synthetic model of Hb switch. Both compounds also increased, with different mechanisms, the γ/(γ+β) ratio expressed in vitro by normal human erythroblasts. Compound 9 increased the levels of γ-globin mRNA and the γ/(γ+β) ratio (both by 2-fold). Compound 24 increased by 3-fold the level of γ-globin and decreased by 2-fold that of β-globin mRNA, increasing the γ/(γ+β) ratio by 6-fold, and raising (by 50%) the cell HbF content. Both compounds raised the acetylation state of histone H4 in primary cells, an indication that their activity was mediated through HDAC inhibition. Compounds 9 and 24 were also tested as γ/(γ+β) mRNA inducers in erythroblasts obtained from patients with β0 thalassemia. Progenitor cells from patients with β0 thalassemia generated in vitro morphologically normal proerythroblasts that, unlike normal cells, failed to mature in the presence of EPO and expressed low β-globin levels but 10 times higher-than-normal levels of the α hemoglobin-stabilizing protein (AHSP) mRNA. Both compounds ameliorated the impaired in vitro maturation in β0 thalassemic erythroblasts, decreasing AHSP expression to normal levels. In the case of two patients (of five analyzed), the improved erythroblast maturation was associated with detectable increases in the γ/(γ+β) mRNA ratio. The low toxicity exerted by compounds 9 and 24 in all of the assays investigated suggests that these new HDAC inhibitors should be considered for personalized therapy of selected patients with β0 thalassemia.
Inactivation, reactivation and pacing dependence of calcium current in frog cardiocytes: correlation with current density.

1. Ca2+ currents were measured in single cells isolated from frog ventricle using the whole‐cell patch clamp technique and a perfused pipette. K+ currents were blocked with intracellular (120 mM) and extracellular (20 mM) Cs+. 2. A single type of Ca2+ current (ICa) was found in these cells. The current activated at voltages positive to ‐30 mV, exhibited a symmetrical current‐voltage relationship with a peak at 0 mV, and was slowly inactivating with Ba2+ as charge carrier. 3. Large variations in ICa amplitude were observed from cell to cell (ICa at 0 mV = 293.1 +/‐ 283.3 pA; N = 152). These variations were not due simply to differences in cell membrane area, which was estimated by cell membrane capacitance (Cm), because the density of Ca2+ current (dICa = ICa/Cm) also varied significantly from cell to cell (1.3‐28 pA/pF at 0 mV; mean +/‐ S.D. = 4.49 +/‐ 3.96; N = 152). 4. The inactivation curve of ICa was a complex function of membrane potential. 200 ms pre‐pulses to voltages between ‐60 and +20 mV progressively inactivated ICa elicited by a subsequent test pulse with half‐maximal inactivation occurring for pre‐pulses to approximately ‐40 mV. With pre‐pulses positive to +20 mV, ICa elicited by the test pulse became progressively larger. The degree of inactivation induced by a 200 ms depolarization to potentials more positive than +20 mV varied significantly from cell to cell, while no such variations were observed in the negative range of membrane potentials. 5. The time course of reactivation (i.e. removal from inactivation) of ICa at ‐80 mV often exhibited an overshoot. The amplitude of the overshoot varied between 100% (i.e. no overshoot) and approximately 180% in eighty‐one cells. 6. The degree of inactivation at positive potentials (+100 mV) and the amplitude of the overshoot were strongly correlated with the Ca2+ current density. The overshoot was more pronounced, the reactivation was faster, and the inactivation at positive potentials was less in cells with lower ICa density. 7. Increasing the stimulation frequency from 0.125 to 2 Hz induced a positive staircase of ICa in cells with ICa density less than 2 pA/pF and a negative staircase in cells with ICa density greater than 3 pA/pF. 8. Perfusing the patch pipette with 5 mM‐BAPTA instead of EGTA reduced the amplitude of the overshoot and slightly slowed the inactivation kinetics. Replacing extracellular Ca2+ ions by Ba2+ ions completely suppressed the overshoot. (ABSTRACT TRUNCATED AT 400 WORDS)
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

The tempo and mode of protein evolution have been central questions in biology. Genomic data have shown a strong influence of the expression level of a protein on its rate of sequence evolution (E-R anticorrelation), which is currently explained by the protein misfolding avoidance hypothesis. Here, we show that this hypothesis does not fully explain the E-R anticorrelation, especially for protein surface residues. We propose that natural selection against protein–protein misinteraction, which wastes functional molecules and is potentially toxic, constrains the evolution of surface residues. Because highly expressed proteins are under stronger pressures to avoid misinteraction, surface residues are expected to show an E-R anticorrelation. Our molecular-level evolutionary simulation and yeast genomic analysis confirm multiple predictions of the hypothesis. These findings show a pluralistic origin of the E-R anticorrelation and reveal the role of protein misinteraction, an inherent property of complex cellular systems, in constraining protein evolution.
A voxel based morphometry study on mild cognitive impairment

Background: Mild cognitive impairment (MCI) is the most widely used concept in classifying cognitive impairment in the elderly who do not fulfil the criteria for dementia. MCI is considered to confer an increased risk of progressing to dementia and most often Alzheimer’s disease (AD). Various approaches such as imaging of the brain have been applied to predict the conversion of MCI to dementia. A number of volumetric magnetic resonance imaging (MRI) studies have detected atrophy of the medial temporal lobe in subjects with MCI, but for the other cerebral regions the results have been inconsistent. Objective: To study the pattern of brain atrophy in MCI. Methods: Thirty two controls and 51 individuals with MCI deriving from population based cohorts were studied by MRI using voxel based morphometry. The threshold of t maps was set at p<0.001. Results: Individuals with MCI had significant unilateral atrophy in the medial temporal lobe on the right side. Less extensive atrophy was found elsewhere—for example, in the temporal lobe, left superior parietal lobule, left anterior cingulate gyrus, and bilaterally in the thalami. Conclusions: The MRI findings in MCI resemble those seen in early AD.
The polarization of afterglow emission reveals γ‐ray bursts jet structure

We numerically compute light and polarization curves of γ -ray burst (GRB) afterglows for various configurations of the jet luminosity structure and for different dynamical evolutions. We especially consider the standard homogeneous ‘top hat’ jet and the ‘universal structured jet’ with power-law wings. We also investigate a possible, more physical variation of the ‘top hat’ model: the ‘Gaussian jet’. The polarization curves for the last two jet types are shown here for the first time together with the computation of X-ray and radio polarized fluxes. We show that the light curves of the total flux from these configurations are very similar to each other, and therefore only very high quality data could allow us to pin down the underlying jet structure. We demonstrate instead that polarization curves are a powerful means to solve the jet structure, since the predicted behaviour of polarization and its position angle at times around the jet break are very different, if not opposite. We conclude that the afterglow polarization measurements provide clear footprints of any outflow energy distribution (unlike the light curves of the total flux) and the joint analysis of the total and polarized flux should reveal the jet structure of GRBs.
On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment

Intrinsically disordered proteins are fascinating the community of protein science since the last decade, at least. There is a well-established line of research that intends to reveal the crucial role played by intrinsically disordered proteins (IDPs) in the development of human diseases. The main argument is that IDPs are differentially more present in groups of disease-related proteins. In this note we compare the frequency of disorder in human proteins, both disease-related and not. The frequency of disorder is comparable in the two sub-groups of proteins. Disorder is widespread in human proteins, but it is not a specific pre-requisite of proteins involved in the development of cancer, cardiovascular diseases, diabetes and neurodegenerative diseases. A tendency of cancer-related proteins to be statistically more disordered than the rest of human proteins is confirmed.