Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for shutter‐speed variation in CR bolus‐tracking studies of human pathology

The standard pharmacokinetic model for the analysis of MRI contrast reagent (CR) bolus‐tracking (B‐T) data assumes that the mean intracellular water molecule lifetime (τi) is effectively zero. This assertion is inconsistent with a considerable body of physiological measurements. Furthermore, theory and simulation show the B‐T time‐course shape to be very sensitive to the τi magnitude in the physiological range (hundreds of milliseconds to several seconds). Consequently, this standard model aspect can cause significant underestimations (factors of 2 or 3) of the two parameters usually determined: Ktrans, the vascular wall CR transfer rate constant, and ve, the CR distribution volume (the extracellular, extravascular space fraction). Analyses of animal model data confirmed two predicted behaviors indicative of this standard model inadequacy: (1) a specific temporal pattern for the mismatch between the best‐fitted curve and data; and (2) an inverse dependence of the curve's Ktrans and ve magnitudes on the CR dose. These parameters should be CR dose‐independent. The most parsimonious analysis allowing for realistic τi values is the ‘shutter‐speed’ model. Its application to the experimental animal data essentially eliminated the two standard model signature inadequacies. This paper reports the first survey for the extent of this ‘shutter‐speed effect’ in human data. Retrospective analyses are made of clinical data chosen from a range of pathology (the active multiple sclerosis lesion, the invasive ductal carcinoma breast tumor, and osteosarcoma in the leg) that provides a wide variation, particularly of Ktrans. The signature temporal mismatch of the standard model is observed in all cases, and is essentially eliminated by use of the shutter‐speed model. Pixel‐by‐pixel maps show that parameter values from the shutter‐speed analysis are increased by more than a factor of 3 for some lesion regions. This endows the lesions with very high contrast, and reveals heterogeneities that are often not seen in the standard model maps. Normal muscle regions in the leg allow validation of the shutter‐speed model Ktrans, ve, and τi magnitudes, by comparison with results of previous careful rat leg studies not possible for human subjects. Copyright © 2004 John Wiley & Sons, Ltd.
Elastic constants of tapered laminated woven jute/epoxy and woven aloe/epoxy composites under the influence of porosity

Anisotropic nature of plant fiber and various plant fiber-correlated porosities are the major setbacks in evaluating the elastic constants of plant fiber-reinforced polymer composites theoretically. An attempt is made here to get rid of those setbacks and focuses toward the evaluation of accurate elastic constants of composites. In this work, mechanical characteristics such as tensile, flexure, and shear characteristics of woven jute/epoxy and woven aloe/epoxy composites are determined. The experimentally measured elastic constants of composites are further used to find the elastic anisotropy of the jute and aloe fibers using the proposed model which is a combined model of Halpin–Tsai equations and laminate analogy approach with the inclusion of porosity correction factor. Using the theoretically predicted elastic properties of fiber, the elastic constants of the tapered laminated woven jute/epoxy and woven aloe/epoxy composites are evaluated using the proposed model.
Low Delay Random Linear Coding and Scheduling Over Multiple Interfaces

High-performance real-time applications, expected to be of importance in the upcoming 5G era, such as virtual and augmented reality or tele-presence, have stringent requirements on throughput and per-packet in-order delivery delay. Use of multipath transport is gaining momentum for supporting these applications. However, building an efficient, low latency multipath transfer mechanism remains highly challenging. The primary reason for this is that the delivery delay along each path is typically uncertain and time-varying. When the transmitter ignores the stochastic nature of the path delays, then packets sent along different paths frequently arrive out of order and need to be buffered at the receiver to allow in-order delivery to the application. In this paper, we propose Stochastic Earliest Delivery Path First (S-EDPF), a generalization of EDPF which takes into account uncertainty and time-variation in path delays yet has low-complexity suited to practical implementation. Moreover, we integrate a novel low-delay Forward Error Correction (FEC) scheme into S-EDPF in a principled manner by deriving the optimal schedule for coded packets across multiple paths. Finally, we demonstrate, both analytically and empirically, that S-EDPF is effective at mitigating the delay impact of reordering and loss in multipath transport protocols, offering substantial performance gains over the state of the art.
Ensemble Classifier for Epileptic Seizure Detection for Imperfect EEG Data

Brain status information is captured by physiological electroencephalogram (EEG) signals, which are extensively used to study different brain activities. This study investigates the use of a new ensemble classifier to detect an epileptic seizure from compressed and noisy EEG signals. This noise-aware signal combination (NSC) ensemble classifier combines four classification models based on their individual performance. The main objective of the proposed classifier is to enhance the classification accuracy in the presence of noisy and incomplete information while preserving a reasonable amount of complexity. The experimental results show the effectiveness of the NSC technique, which yields higher accuracies of 90% for noiseless data compared with 85%, 85.9%, and 89.5% in other experiments. The accuracy for the proposed method is 80% when SNR = 1 dB, 84% when SNR = 5 dB, and 88% when SNR = 10 dB, while the compression ratio (CR) is 85.35% for all of the datasets mentioned.
A General Framework of Persistence Strategies for Biological Systems Helps Explain Domains of Life

The nature and cause of the division of organisms in superkingdoms is not fully understood. Assuming that environment shapes physiology, here we construct a novel theoretical framework that helps identify general patterns of organism persistence. This framework is based on Jacob von Uexküll’s organism-centric view of the environment and James G. Miller’s view of organisms as matter-energy-information processing molecular machines. Three concepts describe an organism’s environmental niche: scope, umwelt, and gap. Scope denotes the entirety of environmental events and conditions to which the organism is exposed during its lifetime. Umwelt encompasses an organism’s perception of these events. The gap is the organism’s blind spot, the scope that is not covered by umwelt. These concepts bring organisms of different complexity to a common ecological denominator. Ecological and physiological data suggest organisms persist using three strategies: flexibility, robustness, and economy. All organisms use umwelt information to flexibly adapt to environmental change. They implement robustness against environmental perturbations within the gap generally through redundancy and reliability of internal constituents. Both flexibility and robustness improve survival. However, they also incur metabolic matter-energy processing costs, which otherwise could have been used for growth and reproduction. Lineages evolve unique tradeoff solutions among strategies in the space of what we call “a persistence triangle. ” Protein domain architecture and other evidence support the preferential use of flexibility and robustness properties. Archaea and Bacteria gravitate toward the triangle’s economy vertex, with Archaea biased toward robustness. Eukarya trade economy for survivability. Protista occupy a saddle manifold separating akaryotes from multicellular organisms. Plants and the more flexible Fungi share an economic stratum, and Metazoa are locked in a positive feedback loop toward flexibility.
Natural radioactivity in building material in the European Union: robustness of the activity concentration index I and comparison with a room model

Using a wide database collected in the last 10 years, the authors have calculated the activity concentration index I for many building materials in the European Union. Suggested by a European technical guidance document, the index I has recently been adopted as a screening tool in the proposal for the new Euratom basic safety standards directive. The paper analyses the possible implications of the choice of different parameters for the computation of index I, i.e. background to be subtracted, dose criteria, etc. With the collected data an independent assessment of gamma doses was also made with an ISS room model, choosing reasonable hypotheses on the use of materials. The results of the two approaches, i.e. index I and a room model, were compared.
The gaf Fimbrial Gene Cluster ofEscherichia coli Expresses a Full-Size and a Truncated Soluble Adhesin Protein

ABSTRACT The GafD lectin of the G (F17) fimbriae of diarrhea-associatedEscherichia coli was overexpressed and purified from the periplasm of E. coli by affinity chromatography on GlcNAc-agarose. The predicted mature GafD peptide comprises 321 amino acids, but the predominant form of GafD recovered from the periplasm was 19,092 Da in size and corresponded to the 178 N-terminal amino acid residues, as judged by mass spectrometry and amino acid sequencing, and was named ΔGafD. Expression of gafD from the clonedgaf gene cluster in DegP-, Lon-, and OmpT-deficient recombinant strains did not significantly decrease the formation of ΔGafD. The peptide was also detected in the periplasm of the wild-type E. coli strain from which the gafgene cluster originally was cloned. We expressed gafDfragments encoding C-terminally truncated peptides. Peptides GafD1-252, GafD1-224, GafD1-189, and the GafD1-178, isolated from the periplasm by affinity chromatography, had apparent sizes closely similar to that of ΔGafD. Only trace amounts of truncated forms with expected molecular sizes were detected in spheroplasts. In contrast, the shorter GafD1-157 peptide was detected in spheroplasts but not in the periplasm, indicating that it was poorly translocated or was degraded by periplasmic proteases. Pulse-chase assays usinggafD indicated that ΔGafD was processed from GafD and is not a primary translation product. The ΔGafD peptide was soluble by biochemical criteria and exhibited specific binding to GlcNAc-agarose. Inhibition assays with mono- and oligosaccharides gave a similar inhibition pattern in the hemagglutination by the G-fimbria-expressing recombinant E. coli strain and in the binding of [14C]ΔGafD to GlcNAc-agarose. ΔGafD bound specifically to laminin, a previously described tissue target for the G fimbria. Our results show that a soluble, protease-resistant subdomain of GafD exhibits receptor-binding specificity similar to that for intact G fimbriae and that it is formed when gafD is expressed alone or from the gaf gene cluster.
Dynamics of cortical responses to tone pairs in relation to task difficulty: A MEG study

We investigated the effect of task difficulty on the dynamics of auditory cortical responses. Whole‐scalp magnetoencephalographic (MEG) signals were recorded while subjects performed a same/different frequency discrimination task on equiprobable tone pairs applied in blocks of five, which were separated by a 10 s intertrial interval. Task difficulty was manipulated by the interpair frequency difference. The manipulation of task difficulty affected the amplitude of the N100m response to the first tone and the latency of the N100m response to the second tone in each pair. The N100m responses were smaller and peaked significantly later in the difficult than in the easy condition. The later processing field (PF) responses were longer in duration in the difficult condition. In both conditions, the duration of the PF response was negatively correlated with the subject's performance in the task, and was longer in the less successful subjects. The PF response may thus reflect the subjects' effort to resolve the task. The N100m and the PF responses did not differ between the tone pairs along the five‐pair trial as a function of task difficulty, suggesting that changes in response along the five‐pair trial are not easily affected by high‐level manipulations. Hum Brain Mapp 2009. © 2008 Wiley‐Liss, Inc.
Functional Exhaustion Limits CD4+ and CD8+ T-Cell Responses to Congenital Cytomegalovirus Infection.

BACKGROUND Cytomegalovirus (CMV) infection during fetal life causes severe symptoms and is associated with prolonged viral excretion. Previous studies reported low CD4(+) T-cell responses to CMV infection in early life, contrasting with large responses of effector CD8(+) T cells. The mechanisms underlying the defective CD4(+) T-cell responses and the possible dissociation with CD8(+) T-cell responses have not been clarified. METHODS The magnitude and the quality of the fetal CD8(+) and CD4(+) T-cell responses to CMV infection were compared to those of adults with primary or chronic infection. RESULTS In utero CMV infection induced oligoclonal expansions of fetal CD4(+) and CD8(+) T lymphocytes expressing a T-helper type 1 or Tc1 effector phenotype similar to that of adult CMV-specific cells. However, the effector cytokine responses and the polyfunctionality of newborn CD4(+) and CD8(+) T cells were markedly lower than those of adult cells. This reduced functionality was associated with a higher expression of the programmed death 1 inhibitory receptor, and blockade of this receptor increased newborn T-cell responses. CONCLUSIONS Functional exhaustion limits effector CD4(+) and CD8(+) T-lymphocyte responses to CMV during fetal life.
Iron‐mediated regulation of liver hepcidin expression in rats and mice is abolished by alcohol

Alcohol reduces and iron increases liver hepcidin synthesis. This study investigates the interaction of alcohol and iron in the regulation of hepcidin messenger RNA (mRNA) expression in animal models. Mice were administered 10% ethanol for 7 days after an iron‐overloaded diet. Rats were administered regular or ethanol‐Lieber De Carli diets for 7 weeks with or without carbonyl iron. Hfe−/− mice were used as a model for genetic iron overload. Hepcidin mRNA expression was determined by real‐time polymerase chain reaction (PCR) and northern blotting. Iron elevated and alcohol decreased liver hepcidin expression in mice and rats. Interestingly, despite iron overload, alcohol was capable of suppressing the up‐regulation of hepcidin mRNA expression in both models. Liver iron and ferritin protein expression was elevated in alcohol‐treated rats, but was not elevated further in rats treated with both iron and alcohol. Duodenal ferroportin protein expression was increased both in alcohol‐treated mice and in mice treated with alcohol and iron. Hfe−/− mice treated with ethanol for 7 days exhibited a further decrease in hepcidin mRNA expression. The iron‐induced increase in DNA‐binding activity of the transcription factor CCAAT/enhancer binding protein alpha (C/EBP alpha) was also suppressed by alcohol. Conclusion: Alcohol abolishes the iron‐induced up‐regulation of both liver hepcidin transcription and the DNA‐binding activity of C/EBP alpha. Of note, hepcidin protects the body from the harmful effects of iron overload. Our findings therefore suggest that alcohol negates the protective effect of hepcidin, which may have implications for the liver injury observed in alcoholic liver disease and genetic hemochromatosis in combination with alcohol. (HEPATOLOGY 2007.)
IL-23R and IL-17A polymorphisms correlate with susceptibility of ankylosing spondylitis in a Southwest Chinese population

The association between the IL-23R and IL-17A polymorphisms and ankylosing spondylitis (AS) in the Southwest Chinese Population is still unclear. The purpose of this study is to detect the association between IL-23R and IL-17A polymorphisms and AS. A case–control study consisting of 486 AS patients and 480 healthy controls was performed. We used the high-resolution melting methods (HRM) to genotype five selected single nucleotide polymorphisms (SNPs), rs6693831, rs7517847, rs1884444, rs10889677 in the IL-23R gene and rs2275913 in the IL-17A gene. Meanwhile, the laboratory indexes were recorded. In this study, patients with genotype CC (p = 8.574E-8) and allele C (p = 3.206E-31) on SNP rs6693831 (IL-23R) showed decreased risk of AS. The genotype TT (p = 4.551E-6) and allele T (p = 0.02) on SNP rs1884444 (IL-23R) showed significant lower risk of AS. Individuals carrying the allele A of rs2275913 showed higher morbidity of AS (p = 0.04). We first detected that rs6693831 and rs1884444 in IL-23R gene and rs2275913 in IL-17A gene have genetic association with AS.
Using low-quality video sequences for fish detection and tracking

This study demonstrates computational methods for the automatic detection and tracking of fish from video sequences. The research in this subject is very important especially in fish farming companies and for nature protection around the world. The process of automated control and counting of individual species of fish has a supportive contribution both in the nature conservation and in the food industry. The difficulties and the specific features of the problem have been studied in order to find a solution for the components of the automated fish tracking system. Typical methods in computer vision applications, such as background subtraction, Kalman filtering and Viola-Jones method were implemented for the motion detection, tracking, and estimation of fish parameters. Both the choice of the appropriate methods and results of the experiments strongly depend on the quality and the type of video sequences. The results we received from the practical experiments demonstrated that not all methods can produce good results for a real data set, whereas on a set of synthetic data they operate satisfactorily. These results suggest that the proposed approaches are adequate in estimating the annual amount of fish migrating through the fish pass.
Effects of Rosuvastatin on Glomerular Capillary Size-Selectivity Function in Rats with Renal Mass Ablation

Background: Evidence is accumulating that statins can reduce proteinuria and disease progression in chronic kidney disease. However, some safety concerns have been recently raised on the use of these agents, mainly due to transient episodes of proteinuria observed in patients receiving high doses of rosuvastatin. Methods: We investigated in rats with renal mass ablation (RMR) whether rosuvastatin (5 or 20 mg/day) worsens proteinuria as compared to untreated RMR animals. Moreover, we also examined whether rosuvastatin-induced changes in proteinuria would be due to the effect of the drug on permselective properties of glomerular capillary barrier, measured by the fractional clearance of graded-size Ficoll molecules and/or by proximal tubular mechanisms, by assessing urinary excretion of β2-microglobulin. Results: RMR rats given rosuvastatin for 28 days showed a progressive increase in proteinuria, with values numerically but not significantly higher than those in RMR animals given the vehicle. In RMR rats, rosuvastatin did not significantly affect the fractional clearance of Ficoll as compared to vehicle-treated RMR animals. A significant correlation was found between urinary protein and β2-microglobulin excretion in rats treated with rosuvastatin (r = 0.936, p < 0.001), but not in those given vehicle. Renal function, glomerular and tubulointerstitial injury were comparable in rosuvastatin-treated and untreated RMR rats at the end of the 28-day follow-up. Conclusion: In rats with RMR, rosuvastatin mildly enhances urinary protein excretion rate. This, however, was not the result of further changes in the size-permselective function of glomerular capillary barrier.
Association between Precipitation Upstream of a Drinking Water Utility and Nurse Advice Calls Relating to Acute Gastrointestinal Illnesses

Background The River Göta Älv is a source of fresh-water for the City of Gothenburg (Sweden). We recently identified a clear association between upstream precipitation and indicator bacteria concentrations in the river water outside the intake to the drinking water utility. This study aimed to determine if variation in the incidence of acute gastrointestinal illnesses is associated with upstream precipitation. Methods We acquired data, covering 1494 days, on the daily number of telephone calls to the nurse advice line from citizens in Gothenburg living in areas with Göta Älv as a fresh-water supply. We separated calls relating to gastrointestinal illnesses from other medical concerns, and analyzed their association with precipitation using a distributed lag non-linear Poisson regression model, adjusting for seasonal patterns and covariates. We used a 0–21-day lag period for precipitation to account for drinking water delivery times and incubation periods of waterborne pathogens. Results The study period contained 25,659 nurse advice calls relating to gastrointestinal illnesses. Heavy rainfall was associated with increased calls the same day and around 5–6 days later. Consecutive days of wet weather were also found to be associated with an increase in the daily number of gastrointestinal concerns. No associations were identified between precipitation and nurse advice calls relating to other medical concerns. Conclusion An increase in nurse advice calls relating to gastrointestinal illnesses around 5–6 days after heavy rainfall is consistent with a hypothesis that the cause could be related to drinking water due to insufficient barriers in the drinking water production, suggesting the need for improved drinking water treatment.
Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4–5 in Splicing

Splicing is an important process for regulation of gene expression in eukaryotes, and it has important functional links to other steps of gene expression. Two examples of these linkages include Ceg1, a component of the mRNA capping enzyme, and the chromatin elongation factors Spt4–5, both of which have recently been shown to play a role in the normal splicing of several genes in the yeast Saccharomyces cerevisiae. Using a genomic approach to characterize the roles of Spt4–5 in splicing, we used splicing-sensitive DNA microarrays to identify specific sets of genes that are mis-spliced in ceg1, spt4, and spt5 mutants. In the context of a complex, nested, experimental design featuring 22 dye-swap array hybridizations, comprising both biological and technical replicates, we applied five appropriate statistical models for assessing differential expression between wild-type and the mutants. To refine selection of differential expression genes, we then used a robust model-synthesizing approach, Differential Expression via Distance Synthesis, to integrate all five models. The resultant list of differentially expressed genes was then further analyzed with regard to select attributes: we found that highly transcribed genes with long introns were most sensitive to spt mutations. QPCR confirmation of differential expression was established for the limited number of genes evaluated. In this paper, we showcase splicing array technology, as well as powerful, yet general, statistical methodology for assessing differential expression, in the context of a real, complex experimental design. Our results suggest that the Spt4–Spt5 complex may help coordinate splicing with transcription under conditions that present kinetic challenges to spliceosome assembly or function.