Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement of Soluble Biomarkers by Flow Cytometry

Microparticle based flow cytometric assays for determination of the level of soluble biomarkers are widely used in several research applications and in some diagnostic setups. The major advantages of these multiplex systems are that they can measure a large number of analytes (up to 500) at the same time reducing assay time, costs and sample volume. Most of these assays are based on antigen-antibody interactions and work as traditional immunoassays, but nucleic acid alterations – by using special hybridization probes –, enzyme- substrate or receptor-ligand interactions can be also studied with them. The applied beads are nowadays provided by the manufacturers, but cheaper biological microbeads can be prepared by any user. One part of the systems can be used on any research or clinical cytometers, but some companies provide dedicated analyzers for their multiplex bead arrays. Due to the high standardization of the bead production and the preparation of the assay components the analytical properties of these assays are quite reliable with a wide range of available applications. Cytokines, intracellular fusion proteins, activated/phosphorylated components of different signaling pathways, transcription factors and nuclear receptors can be identified and quantitated. The assays may serve the diagnostics of autoimmune disorders, different viral and bacterial infections, as well as genetic alterations such as single nucleotide polymorphisms, small deletions/insertions or even nucleotide triplet expansions can be also identified. The most important principles, technical details and applications of these systems are discussed in this short review.
Combining Thesauri-Based Methods for Biomedical Retrieval

This paper describes our participation in the TREC 2005 Genomics track. We took part in the ad hoc retrieval task and aimed at integrat- ing thesauri in the retrieval model. We developed three thesauri-based methods, two of which made use of the existing MeSH thesaurus. One method uses blind relevance feedback on MeSH terms, the second uses an index of the MeSH thesaurus for query expansion. The third method makes use of a dynamically generated lookup list, by which acronyms and synonyms could be inferred. We show that, despite the relatively minor improve- ments in retrieval performance of individually ap- plied methods, a combination works best and is able to deliver significant improvements over the baseline.
Validation of the Octamouse for Simultaneous 18F-Fallypride Small-Animal PET Recordings from 8 Mice

Data collection in preclinical small-animal PET studies has been hindered by the small number of recordings typically obtained for a single radiosynthesis. Therefore, we tested procedures for obtaining 8 simultaneous small-animal PET recordings from the brains of 8 mice using an acrylic anesthesia distributor (the Octamouse), with the dopamine D2/3 ligand 18F-fallypride serving as a test substance for brain receptor imaging. Methods: The effect of scatter correction on the small-animal PET recordings was first evaluated in phantom studies in which sources of different radioactivity concentration were placed within the chambers of the Octamouse. Next, potential effects of mass on the 18F-fallypride binding potential (BPND) in the striatum were tested in groups of mice receiving 18F-fallypride at 2 different specific activities (140 and 50 GBq/μmol), with and without scatter correction. Finally, the relationship between BPND and injected dose of 18F-fallypride (3.5–17 MBq/mouse) was tested. Results: Scatter correction improved the contrast between sources and air space within the Octamouse phantom. The magnitude of 18F-fallypride BPND in mouse striatum was invariant across the tested range of specific activities, and scatter correction increased BPND by a mean of 6%; covariances of the inter- and intraoperator variability of BPND were 10%. There was a positive correlation between radiochemical dose and BPND with (R2 = 0.53) and without (R2 = 0.63) scatter correction, which was driven by increasing area under the percentage injected dose curve in the striatum. Conclusion: The quantitation of emission sources placed within the Octamouse is linear over a wide range of source activities. In the striatum of living mice, the magnitude of 18F-fallypride BPND was highly reproducible between operators and was constant over a 3-fold range of specific activities, indicating a lack of significant occupancy. Scatter correction improved quantitation but did not entirely correct for the dependence of BPND on injected dose, which was deemed to arise because of effects propagating from detector dead time when the total radiochemical dose in the field of view exceeded 50 MBq. Given this consideration, we were still able to quantify 18F-fallypride BPND in 16 mice from a single radiosynthesis, an economy that should be generalizable to brain studies of diverse radioligands.
A Mobile App to Stabilize Daily Functional Activity of Breast Cancer Patients in Collaboration With the Physician: A Randomized Controlled Clinical Trial

Background The well-being of breast cancer patients and reporting of adverse events require close monitoring. Mobile apps allow continuous recording of disease- and medication-related symptoms in patients undergoing chemotherapy. Objective The aim of the study was to evaluate the effects of a mobile app on patient-reported daily functional activity in a supervised and unsupervised setting. Methods We conducted a randomized controlled study of 139 breast cancer patients undergoing chemotherapy. Patient status was self-measured using Eastern Cooperative Oncology Group scoring and Common Terminology Criteria for Adverse Events. Participants were randomly assigned to a control group, an unsupervised group that used a mobile app to record data, or a supervised group that used the app and reviewed data with a physician. Primary outcome variables were change in daily functional activity and symptoms over three outpatient visits. Results Functional activity scores declined in all groups from the first to second visit. However, from the second to third visit, only the supervised group improved, whereas the others continued to decline. Overall, the supervised group showed no significant difference from the first (median 90.85, IQR 30.67) to third visit (median 84.76, IQR 18.29, P=.72). Both app-using groups reported more distinct adverse events in the app than in the questionnaire (supervised: n=1033 vs n=656; unsupervised: n=852 vs n=823), although the unsupervised group reported more symptoms overall (n=4808) in the app than the supervised group (n=4463). Conclusions The mobile app was associated with stabilized daily functional activity when used under collaborative review. App-using participants could more frequently report adverse events, and those under supervision made fewer and more precise entries than unsupervised participants. Our findings suggest that patient well-being and awareness of chemotherapy adverse effects can be improved by using a mobile app in collaboration with the treating physician. ClinicalTrial ClinicalTrials.gov NCT02004496; https://clinicaltrials.gov/ct2/show/NCT02004496 (Archived by WebCite at http://www.webcitation.org/6k68FZHo2)
Assessing Trait Covariation and Morphological Integration on Phylogenies Using Evolutionary Covariance Matrices

Morphological integration describes the degree to which sets of organismal traits covary with one another. Morphological covariation may be evaluated at various levels of biological organization, but when characterizing such patterns across species at the macroevolutionary level, phylogeny must be taken into account. We outline an analytical procedure based on the evolutionary covariance matrix that allows species-level patterns of morphological integration among structures defined by sets of traits to be evaluated while accounting for the phylogenetic relationships among taxa, providing a flexible and robust complement to related phylogenetic independent contrasts based approaches. Using computer simulations under a Brownian motion model we show that statistical tests based on the approach display appropriate Type I error rates and high statistical power for detecting known levels of integration, and these trends remain consistent for simulations using different numbers of species, and for simulations that differ in the number of trait dimensions. Thus, our procedure provides a useful means of testing hypotheses of morphological integration in a phylogenetic context. We illustrate the utility of this approach by evaluating evolutionary patterns of morphological integration in head shape for a lineage of Plethodon salamanders, and find significant integration between cranial shape and mandible shape. Finally, computer code written in R for implementing the procedure is provided.
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton

Eukaryotic ribosomal stalk protein L12 and its bacterial orthologue L11 play a central role on ribosomal conformational changes during translocation. Deletion of the two genes encoding L12 in Saccharomyces cerevisiae resulted in a very slow-growth phenotype. Gene RPL12B, but not the RPL12A, cloned in centromeric plasmids fully restored control protein level and the growth rate when expressed in a L12-deprived strain. The same strain has been transformed to express Escherichia coli protein EcL11 under the control of yeast RPL12B promoter. The bacterial protein has been found in similar amounts in washed ribosomes from the transformed yeast strain and from control E. coli cells, however, EcL11 was unable to restore the defective acidic protein stalk composition caused by the absence of ScL12 in the yeast ribosome. Protein EcL11 induced a 10% increase in L12-defective cell growth rate, although the in vitro polymerizing capacity of the EcL11-containing ribosomes is restored in a higher proportion, and, moreover, the particles became partially sensitive to the prokaryotic specific antibiotic thiostrepton. Molecular dynamic simulations using modelled complexes support the correct assembly of bacterial L11 into the yeast ribosome and confirm its direct implication of its CTD in the binding of thiostrepton to ribosomes.
Singularities of Pairs

These are the revised notes of my lectures at the 1995 Santa Cruz summer institute. Changes from the Jan.26,1996 version: Major: 7.1--2; Medium: 3.7, 3.11, 5.3. 3, 7.9. 2, 9.8.
Ventricular septal defect with altitude-dependent pulmonary hypertension.

EXPOSURE to high altitudes may result in increased pulmonary-artery pressure,1 2 3 which at least occasionally reverts toward normal with return to sea-level living.4 In the following case a ventricular septal defect with pulmonary hypertension occurred at moderately high altitude (Denver, Colorado), with a return to normal pulmonary-artery pressure at repeat cardiac catheterization in Boston, Massachusetts, four years later. Case Report J.W. (M.G.H. 147–92–84), a 6-year-old boy, was admitted to the Massachusetts General Hospital for cardiac catheterization in December, 1967. At birth in Denver, Colorado, a heart murmur had been noted. An electrocardiogram demonstrated right ventricular hypertrophy. At 2 years of age .
Study of Magnetothermal Properties of Strontium Doped Lanthanum Manganite Nanoparticles for Hyperthermia Applications

Magnetic nanoparticles of strontium doped lanthanum manganite (LSMO) have been synthesized with Sr concentration x = 0.20 and 0.27 using the citrate gel technique. Magnetic and magnetothermal properties have been investigated with the objective of determining their specific absorption rates (SAR's) and comparing them with those obtained using the linear response theory. Adiabatic magnetothermia measurements were carried out in an RF magnetic field of 800 A/m and 214 kHz. Both magnetic and thermomagnetic behaviors of the LSMO nanoparticles are observed to be governed by the strontium content of the samples. The specific absorption rate has been determined using experimental data and good quantitative agreement has been observed between experimentally determined and theoretically derived values. Zero-field-cooled thermal demagnetization measurements were used to obtain the Curie temperature TC, which was found to be 320 K for x = 0.20 and 350 K for x = 0.27. The suitability of these materials for magnetic hyperthermia and self-controlled hyperthermia applications has been demonstrated.
The comparative analysis of online shopping information platform's security based on customer satisfaction

With the massive expansion of Internet and e-commerce technology, Internet platform is providing a lot of services and advantages for online business, especially for online shopping portal. As a result of the Internet, online shopping has expanded in businesses more effectively and online services are collaborating with customers and other associations. For improving online shopping information platform's security, customer satisfaction is one of the most fundamental factors. This paper constructs the measurement of four-dimensional models that are appropriate for measuring customer satisfaction of online shopping information platform's security. This paper also conducts the factor and multiple regression analysis to verify the measurement model. By using questionnaires survey and analysis from the groups of Hohai University students, this research provides suggestions for the development of large online shopping portal and will help to improve customer satisfaction on the security of the online shopping information platforms.
Bringing playfulness to disabilities

This article presents the design case of a robot companion targeted at children who are prevented from playing normally, due to cognitive, developmental or physical impairments. The robot design presents some distinctive qualities. From an instrumental viewpoint it reflects inclusiveness and social exchange. It enables inclusive play activities that promote confidence and self-esteem. All children blossom as children with different abilities, including "fully able" children, collaboratively achieve success, in games that are fun for all. A specific effort in the design was spent in creating consistency between the form, visual qualities, and the behaviours of the robot, in order to enable play scenarios that were specifically targeted at autistic, mild cognitively-impaired and severely motor-impaired children.
Objective and subjective measurement QoE in SDN networks

The need for more efficient transmission of video stream over the network has become more exigent due to the use of video in several domains(video conference, VOD, etc). The video quality is much affected because of delay, packet loss, etc in the network which degrades the user's perceptions. In this paper, we introduce some of objective metrics (network parameters and encoding video parameters) of video streaming that can affect users' quality of experience (QoE) over SDN networks. Our ultimate goal is to understand how the network parameters and encoding video parameters affect the QoE of video streaming in SDN network and obtain a correspondence between objective QoE and subjective QoE. We conclude that the packet loss is the most factor can affect the quality of video and with VQM strictly lower than 0.52, we can highlight that the video quality is excellent. So to realize this work we use Mininet as simulator of the network SDN and floodlight (SDN controller).
High Throughput Surface Characterisation of a Combinatorial Material Library

A material’s surface underpins many of its potential applications, ranging from biomaterials [1] to semiconductors. [2,3] In-deed, in the field of array technology [4] —where large numbers of materials are printed onto a support substrate—surface phenomena underpin the desired properties/responses that are screened. To date, there have been no methods to assess spatially resolved micropatterned array surfaces. Here we report the first high throughput characterisation of the surface chemistry of a large combinatorial library of microarrayed polymers. Methods were developed to allow for rapid, automated X-ray photoelectron spectroscopy (XPS) [5] and time-of-flight secondary ion mass spectrometry (ToF-SIMS) [6] analysis of the combinatorial polymeric library. An important surface property of a material for a wide range of applications is its wettability. Therefore a new approach for high throughput water contact angle measurements (WCA), [7] using picolitre droplets, was developed and applied for the first time. Using new data capture procedures, we were able to rapidly analyse the surfaces of 576 different polymers with all three techniques within a six day timeframe. Complimentary data analysis techniques are also assessed herein to provide a means of handling the large amounts of data produced. We believe the wealth of information that can be obtained using this approach will facilitate the identification of surface structure/ property relationships from large libraries, accelerating the development of new materials with useful surface properties. High throughput material analysis approaches have been developed to determine both physical properties [8] as well as the bulk chemistries of combinatorial polymers. [9] However, to date, high-throughput acquisition and analysis has not been developed to enable rapid surface analysis of arrayed libraries of combinatorial materials. The surface analysis of these large
Early Origin of Genes Encoding Subunits of Biogenesis of Lysosome‐related Organelles Complex‐1, ‐2 and ‐3

Biogenesis of lysosome‐related organelles complex (BLOC)‐1, ‐2 and ‐3 are three multi‐subunit protein complexes that are deficient in various forms of Hermansky‐Pudlak syndrome, a human disease characterized by abnormal formation of lysosome‐related organelles. Contrasting views have arisen on the evolutionary origin of these protein complexes. One view is that the BLOCs represent a recent evolutionary ‘acquisition’ unique to metazoans. However, the yeast proteins Mon1, Ccz1 and She3 have been reported to display homology to the HPS1 and HPS4 subunits of BLOC‐3 and the BLOS2 subunit of BLOC‐1, respectively. In this work, we have systematically searched for orthologs of BLOC subunits in the annotated genomes of over 160 species of eukaryotes, including metazoans and fungi in the Opisthokonta group as well as highly divergent organisms. We have found orthologs of six of the eight BLOC‐1 subunits, two of the three BLOC‐2 subunits, and the two BLOC‐3 subunits, in some non‐opisthokonts such as Dictyostelium discoideum, suggesting an early evolutionary origin for these complexes. On the other hand, we have obtained no evidence in support of the notion that yeast She3 would be an ortholog of BLOS2, and found that yeast Mon1 and Ccz1, despite displaying restricted homology to portions of HPS1 and HPS4, are unlikely to represent the orthologs of these BLOC‐3 subunits. Potential orthologs of Mon1 and Ccz1 were found in humans and several other eukaryotes.
Reconstructing and predicting the hepatitis C virus epidemic in Greece: increasing trends of cirrhosis and hepatocellular carcinoma despite the decline in incidence of HCV infection

Summary. In this study, a comprehensive methodology for modelling the hepatitis C virus (HCV) epidemic is proposed to predict the future disease burden and assess whether the recent decline in the incidence of HCV may affect the future occurrence of cirrhosis and hepatocellular carcinoma (HCC) cases. Using the prevalence of HCV, the distribution of chronic hepatitis C (CHC) patients within the various transmission groups and their infection‐onset times, it was possible to reconstruct the incident infections per year in the past that progressed to CHC in Greece. The natural history of the disease was simulated in subcohorts of newly infected subjects using transition probabilities derived either empirically between fibrosis stages 0–4 or from literature review. Annual estimates of the incidence and prevalence of CHC by fibrosis stage, HCC and mortality in Greece were obtained up to 2030. HCV incidence peaked in the late 1980s at five new infections/10 000 person‐years. Under the assumption of 20–100% decline in HCV incidence after 1990, the cumulative number of incident cirrhosis and HCC cases from 2002–2030 was projected to be lower by 9.6–48.2% and 5.9–29.5%, respectively, than that estimated under the assumption of no decline. However, the prevalent cirrhotic/HCC cases and HCV‐related deaths are predicted to decline in the next 30 years only under the assumption of complete elimination of new HCV infections after 1990. Despite the progress in the reduction of HCV transmission, primary prevention does not seem adequate to reverse the rise in the incidence of cirrhosis and HCC.
Microfabrication for tissue engineering : rethinking the cells-on-a scaffold approach

A summary of results obtained using the PAM (pressure assisted microsyringe) technique for microfabrication of scaffolds for guided cell assembly is presented and discussed. The results of the experiments have enabled general rules for structural scaling and geometrical relations between cells and microstructural interfaces to be constructed, and led to our current tissue engineering philosophy which is based on providing a complex environment for cells using structural, biochemical and mechanical cues in order to guide the process of tissue development.
Creating “Smart” Surfaces Using Stimuli Responsive Polymers

Surfaces modified with stimuli-responsive polymers (SRPs) dynamically alter their physico-chemical properties in response to changes in their environmental conditions. The triggered control of interfacial properties provided by immobilized SRPs at the solid–water interface has application in the design of biomaterials, regenerable biosensors, and microfluidic bioanalytical devices. In this article, we briefly summarize recent research in this area, followed by two recent examples of research from our laboratory on stimuli-responsive surfaces. First, we present a new assay to quantify the phase transition behavior of SRPs at the solid–water interface. This assay, which is based on the distance-dependent colorimetric properties of gold nanoparticles, provides a technically simple and convenient method to determine the effect of different variables on the lower critical solution temperature (LCST) behavior of SRPs at the solid–water interface. Second, we show that stimuli-responsive surfaces can be created by the immobilization of an elastin-like polypeptide (ELP), a thermally responsive biopolymer, on a glass surface. We exploit the phase transition of the ELP at a surface to reversibly address an ELP fusion protein to a surface. This method, which we term thermodynamically reversible addressing of proteins (TRAP), enables the reversible, spatio-temporal modulation of protein binding at the solid-liquid interface, and will enable the realization of new bioanalytical applications.