Miracle-dz/UniFAR-FTUs huggingface dataset:
Radiation-Induced Changes of microRNA Expression Profiles in Radiosensitive and Radioresistant Leukemia Cell Lines with Different Levels of Chromosome Abnormalities

In our study, we estimate an effect from chromosome aberrations and genome mutations on changes in microRNA expression profiles in cancer cell lines demonstrating different radiosensitivity. Here, cell viability and microRNA spectrum have been estimated 1, 4, and 24 h after irradiation. MiSeq high-throughput sequencing system (Illumina, San Diego, CA, USA) is employed to perform microRNA spectrum estimation. In the K562 cell line, the number of expressed microRNAs in chromosomes demonstrates a more pronounced variation. An analysis of microRNA effects on signaling pathway activity demonstrates differences in post-transcriptional regulation of the expression of genes included into 40 signaling pathways. In the K562 cell line, microRNA dynamics analyzed for their dependence on chromosome localization show a wider scattering of microRNA expression values for a pair of chromosomes compared to the HL-60 cell line. An analysis of microRNAs expression in the K562 and HL-60 cell lines after irradiation has shown that chromosome abnormalities can affect microRNA expression changes. A study of radiation-induced changes of microRNA expression profiles in the K562 and HL-60 cell lines has revealed a dependence of microRNA expression changes on the number of chromosome aberrations and genome mutations.
Reconfigurable, Defect-Free, Ultrahigh-Q Photonic Crystal Microcavities for Sensing

We propose a new approach for creating reconfigurable high-Q cavities in defect-free photonic crystal slabs (PCSs). The approach relies on selective air-hole infiltration in otherwise defect-free PCSs. We show that using this method we can design ultrahigh-Q microcavities, with Q˜106. Numerical calculations indicate a large number of high-Q modes with high sensitivity, which are ideal for simultaneous, multi-parameter refractive index-based sensing.
On the mechanism of elasto-inertial turbulence.

Elasto-inertial turbulence (EIT) is a new state of turbulence found in inertial flows with polymer additives. The dynamics of turbulence generated and controlled by such additives is investigated from the perspective of the coupling between polymer dynamics and flow structures. Direct numerical simulations of channel flow with Reynolds numbers ranging from 1000 to 6000 (based on the bulk and the channel height) are used to study the formation and dynamics of elastic instabilities and their effects on the flow. The flow topology of EIT is found to differ significantly from Newtonian wall-turbulence. Structures identified by positive (rotational flow topology) and negative (extensional/compressional flow topology) second invariant Qa isosurfaces of the velocity gradient are cylindrical and aligned in the spanwise direction. Polymers are significantly stretched in sheet-like regions that extend in the streamwise direction with a small upward tilt. The Qa cylindrical structures emerge from the sheets of high polymer extension, in a mechanism of energy transfer from the fluctuations of the polymer stress work to the turbulent kinetic energy. At subcritical Reynolds numbers, EIT is observed at modest Weissenberg number (Wi, ratio polymer relaxation time to viscous time scale). For supercritical Reynolds numbers, flows approach EIT at large Wi. EIT provides new insights on the nature of the asymptotic state of polymer drag reduction (maximum drag reduction), and explains the phenomenon of early turbulence, or onset of turbulence at lower Reynolds numbers than for Newtonian flows observed in some polymeric flows.
Prestimulus Oscillatory Activity in the Alpha Band Predicts Visual Discrimination Ability

Although the resting and baseline states of the human electroencephalogram and magnetoencephalogram (MEG) are dominated by oscillations in the alpha band (∼10 Hz), the functional role of these oscillations remains unclear. In this study we used MEG to investigate how spontaneous oscillations in humans presented before visual stimuli modulate visual perception. Subjects had to report if there was a subtle difference in gray levels between two superimposed presented discs. We then compared the prestimulus brain activity for correctly (hits) versus incorrectly (misses) identified stimuli. We found that visual discrimination ability decreased with an increase in prestimulus alpha power. Given that reaction times did not vary systematically with prestimulus alpha power changes in vigilance are not likely to explain the change in discrimination ability. Source reconstruction using spatial filters allowed us to identify the brain areas accounting for this effect. The dominant sources modulating visual perception were localized around the parieto-occipital sulcus. We suggest that the parieto-occipital alpha power reflects functional inhibition imposed by higher level areas, which serves to modulate the gain of the visual stream.
Pitting corrosion of older underground cast iron pipes

Major water supply distribution networks in many cities consist of buried cast iron pipes. Often the pipes are internally cement-lined. For these the most severe external pitting corrosion is important because this may cause leakage and eventual structural failure. Herein representative data is reported for 10 pipes, ranging in age from 34 to 129 years and from 200 to 600 mm diameter that are part of a larger data set. The pipes examined were selected by the water utilities from several critical locations. Pit depths over 1-2 m lengths of pipes were measured and examined and soil properties measured. The morphologies of pitting around the pipes were found to be very different, with often much greater pit depths and larger pit areas at the base of the pipes. There were also considerable differences along the length of individual parts of pipes. When plotted on a Gumbel plot for the maximum pit depths, the deepest pits showed a different Gumbel trend compared with the majority of pit depth maxima. Theoretically, this indicates that different pitting mechanisms are involved. This possibility is explored by reference to earlier work on the long-term pitting corrosion of steels in sea water. Comments are made also about empirical fitting with other extreme value distributions, as sometimes suggested.
Non‐alcoholic fatty liver disease (NAFLD) prevalence and its metabolic associations in patients with type 1 diabetes and type 2 diabetes

We investigated non‐alcoholic fatty liver disease (NAFLD) prevalence and its metabolic associations in patients with type 1 diabetes (T1D), and in insulin‐naïve and insulin‐treated patients with type 2 diabetes (T2D). Baseline data from patients who had liver fat content (LFC) evaluated by magnetic resonance imaging in four phase 3 studies of basal insulin peglispro (BIL) were analysed. Associations of NAFLD with clinical characteristics, glycaemic control and diabetes therapy were evaluated. The prevalence of NAFLD (defined as LFC ≥ 6%) was low in T1D (8.8%) but high in T2D, with greater prevalence in insulin‐naïve (75.6%) vs insulin‐treated (61.7%) T2D patients. LFC (mean ± SD) was higher in T2D patients (insulin‐naïve, 13.0% ± 8.4%; insulin‐treated, 10.2% ± 7.8%) than in T1D patients (3.2% ± 3.2%). In T2D, NAFLD was associated with several markers of insulin resistance. In all three populations, there was an absence of association of HbA1c with LFC, but insulin doses were higher in patients with NAFLD.
Layer Decomposition: An Effective Structure-Based Approach for Scientific Workflow Similarity

Scientific workflows have become a valuable tool for large-scale data processing and analysis. This has led to the creation of specialized online repositories to facilitate workflow sharing and reuse. Over time, these repositories have grown to sizes that call for advanced methods to support workflow discovery, in particular for effective similarity search. Here, we present a novel and intuitive workflow similarity measure that is based on layer decomposition. Layer decomposition accounts for the directed dataflow underlying scientific workflows, a property which has not been adequately considered in previous methods. We comparatively evaluate our algorithm using a gold standard for 24 query workflows from a repository of almost 1500 scientific workflows, and show that it a) delivers the best results for similarity search, b) has a much lower runtime than other, often highly complex competitors in structure-aware workflow comparison, and c) can be stacked easily with even faster, structure-agnostic approaches to further reduce runtime while retaining result quality.
Stroke Thrombolysis: Save a Minute, Save a Day

Background and Purpose— Stroke thrombolysis is highly time-critical, but data on long-term effects of small reductions in treatment delays have not been available. Our objective was to quantify patient lifetime benefits gained from faster treatment. Methods— Observational prospective data of consecutive stroke patients treated with intravenous thrombolysis in Australian and Finnish centers (1998–2011; n=2258) provided distributions of age, sex, stroke severity, onset-to-treatment times, and 3-month modified Rankin Scale in daily clinical practice. Treatment effects derived from a pooled analysis of thrombolysis trials were used to model the shift in 3-month modified Rankin Scale distributions with reducing treatment delays, from which we derived the expected lifetime and level of long-term disability with faster treatment. Results— Each minute of onset-to-treatment time saved granted on average 1.8 days of extra healthy life (95% prediction interval, 0.9–2.7). Benefit was observed in all groups: each minute provided 0.6 day in old severe (age, 80 years; National Institutes of Health Stroke Scale [NIHSS] score, 20) patients, 0.9 day in old mild (age, 80 years; NIHSS score, 4) patients, 2.7 days in young mild (age, 50 years; NIHSS score, 4) patients, and 3.5 days in young severe (age, 50 years; NIHSS score, 20) patients. Women gained slightly more than men over their longer lifetimes. In the whole cohort, each 15 minute decrease in treatment delay provided an average equivalent of 1 month of additional disability-free life. Conclusions— Realistically achievable small reductions in stroke thrombolysis delays would result in significant and robust average health benefits over patients’ lifetimes. The awareness of concrete importance of speed could promote practice change.
Risk of tuberculosis from exposure to tobacco smoke: a systematic review and meta-analysis.

BACKGROUND There is no consensus whether tobacco smoking increases risk of tuberculosis (TB) infection, disease, or mortality. Whether this is so has substantial implications for tobacco and TB control policies. OBJECTIVE To quantify the relationship between active tobacco smoking and TB infection, pulmonary disease, and mortality using meta-analytic methods. METHODS Eight databases (PubMed, Current Contents, BIOSIS, EMBASE, Web of Science, Centers for Disease Control and Prevention Tobacco Information and Prevention Source [TIPS], Smoking and Health Database [Institute for Science and Health], and National Library of Medicine Gateway) and the Cochrane Tobacco Addiction Group Trials Register were searched for relevant articles published between 1953 and 2005. STUDY SELECTION Included were epidemiologic studies that provided a relative risk (RR) estimate for the association between TB (infection, pulmonary disease, or mortality) and active tobacco smoking stratified by (or adjusted for) at least age and sex and a corresponding 95% confidence interval (CI) (or data for calculation). Excluded were reports of extrapulmonary TB, studies conducted in populations prone to high levels of smoking or high rates of TB, and case-control studies in which controls were not representative of the population that generated the cases, as well as case series, case reports, abstracts, editorials, and literature reviews. DATA EXTRACTION Twenty-four studies were included in the meta-analysis. Extracted data included study design, population and diagnostic details, smoking type, and TB outcomes. DATA SYNTHESIS A random-effects model was used to pool data across studies. Separate analyses were performed for TB infection (6 studies), TB disease (13 studies), and TB mortality (5 studies). For TB infection, the summary RR estimate was 1.73 (95% CI, 1.46-2.04); for TB disease, estimates ranged from 2.33 (95% CI, 1.97-2.75) to 2.66 (95% CI, 2.15-3.28). This suggests an RR of 1.4 to 1.6 for development of disease in an infected population. The TB mortality RRs were mostly below the TB disease RRs, suggesting no additional mortality risk from smoking in those with active TB. CONCLUSIONS The meta-analysis produced evidence that smoking is a risk factor for TB infection and TB disease. However, it is not clear that smoking causes additional mortality risk in persons who already have active TB. Tuberculosis control policies should in the future incorporate tobacco control as a preventive intervention.
Rearranged Genomic RNA Segments Offer a New Approach to the Reverse Genetics of Rotaviruses

ABSTRACT Group A rotaviruses (RV), members of the Reoviridae family, are a major cause of infantile acute gastroenteritis. The RV genome consists of 11 double-stranded RNA segments. In some cases, an RNA segment is replaced by a rearranged RNA segment, which is derived from its standard counterpart by partial sequence duplication. We report here a reverse genetics system for RV based on the preferential packaging of rearranged RNA segments. Using this system, wild-type or in vitro-engineered forms of rearranged segment 7 from a human rotavirus (encoding the NSP3 protein), derived from cloned cDNAs and transcribed in the cytoplasm of COS-7 cells with the help of T7 RNA polymerase, replaced the wild-type segment 7 of a bovine helper virus (strain RF). Recombinant RF viruses (i.e., engineered monoreassortant RF viruses) containing an exogenous rearranged RNA were recovered by propagating the viral progeny in MA-104 cells, with no need for additional selective pressure. Our findings offer the possibility to extend RV reverse genetics to segments encoding nonstructural or structural proteins for which no potent selective tools, such as neutralizing antibodies, are available. In addition, the system described here is the first to enable the introduction of a mutated gene expressing a modified nonstructural protein into an infectious RV. This reverse genetics system offers new perspectives for investigating RV protein functions and developing recombinant live RV vaccines containing specific changes targeted for attenuation.
Diuresis and antidiuresis in kidneys autotransplanted to the neck of dogs.

1. The water diuretic responses of dog kidneys autotransplanted to the neck have been studied. In the presence of a normal kidney the “neck” kidney for one or two weeks following operation shows a normal diuretic response following an oral water load. Between two and four weeks after transplantation the diuretic response falls to half or less than half of the normal kidney and then remains fairly constant over many months. On removal of the normal kidney the “neck” kidney regains a normal diuretic response to water. 2. From the time of transplantation the “neck” kidney excretes urine of low specific gravity. 3. The “neck” kidney retains a normal response to posterior pituitary antidiuretic hormone. 4. In the “neck” kidney the antidiuretic response to faradic stimulation is unaltered from the normal.
A FPGA Core Generator for Embedded Classification Systems

We describe in this work a Core Generator for Pattern Recognition tasks. This tool is able to generate, according to user requirements, the hardware description of a digital architecture, which implements a Support Vector Machine, one of the current state-of-the-art algorithms for Pattern Recognition. The output of the Core Generator consists of a high-level language hardware core description, suitable to be mapped on a reconfigurable device, like a Field Programmable Gate Array (FPGA). As an example of the use of our tool, we compare different solutions, by targeting several reconfigurable devices, and implement the recognition part of a machine vision system for automotive applications.
Mathematical Identification of Influential Parameters on the Elastic Buckling of Variable Geometry Plate

The problem of elastic stability of plates with square, rectangular, and circular holes as well as slotted holes was discussed. The existence of the hole reduces the deformation energy of the plate and it affects the redistribution of stress flow in comparison to a uniform plate which causes a change of the external operation of compressive forces. The distribution of compressive force is defined as the approximate model of plane state of stress. The significant parameters of elastic stability compared to the uniform plate, including the dominant role of the shape, size, and orientation of the hole were identified. Comparative analysis of the shape of the hole was carried out on the data from the literature, which are based on different approaches and methods. Qualitative and quantitative accordance of the results has been found out and it verifies exposed methodology as applicable in the study of the phenomenon of elastic stability. Sensitivity factor is defined that is proportional to the reciprocal value of the buckling coefficient and it is a measure of sensitivity of plate to the existence of the hole. Mechanism of loss of stability is interpreted through the absorption of the external operation, induced by the shape of the hole.
Flow cytometric detection of hepatitis C virus antigens in infected peripheral blood leukocytes: binding and entry.

AIM We designed two synthetic-core-specific peptides core 1 (C1) and core 2 (C2), and an E1-specific peptide (E1). We produced specific polyclonal antibodies against these peptides and used the antibodies for detection of HCV antigens on surface and within infected peripheral blood leukocytes. METHODS Peripheral blood from a healthy individual who tested negative for HCV RNA was incubated with HCV type 4 infected serum for 1 h and 24 h at 37 degrees C. Cells were stained by direct and indirect immunofluorescence and measured by flow cytometry. RESULTS After 1 h of incubation, antibodies against C1, C2, and E1 detected HCV antigens on the surface of 27%, 26% and 73% of monocytes respectively, while 10%, 5% and 9% of lymphocytes were positive with anti-C1, anti-C2 and anti-E1 respectively. Only 1-3% of granulocytes showed positive staining with anti-C1, anti-C2 and anti E1 antibodies. After 24 h of incubation, we found no surface staining with anti-C1, anti-C2 or anti-E1. Direct immunostaining using anti-C2 could not detect intracellular HCV antigens, after 1 h of incubation with the virus, while after 24 h of incubation, 28% of infected cells showed positive staining. Only plus strand RNA was detectable intracellularly as early as 1 h after incubation, and remained detectable throughout 48 h post-infection. Interestingly, minus RNA strand could not be detected after 1 h, but became strongly detectable intracellularly after 24 h post-infection. CONCLUSION Monocytes and lymphocytes are the preferred target cells for HCV infection in peripheral blood leukocytes. Our specific anti-core and anti-E1 antibodies are valuable reagents for demonstration of HCV cell cycle. Also, HCV is capable of infecting and replicating in peripheral blood mononuclear cells as confirmed by detection of minus strand HCV RNA as well as intracellular staining of core HCV antigen.
Overluminous HNC line emission in Arp 220, NGC 4418 and Mrk 231. Global IR pumping or XDRs?

Context. In recent studies of 3 mm J = 1 - 0 HNC emission from galaxies it is found that the emission is often bright which is unexpected in warm, star forming clouds. We propose that the main cause for the luminous HNC line emission is the extreme radiative and kinematical environment in starburst and active nuclei. Aims. To determine the underlying excitational and chemical causes behind the luminous HNC emission in active galaxies and to establish how HNC emission may serve to identify important properties of the nuclear source. Methods. We present mm and submm JCMT, IRAM 30 m and CSO observations of the J = 3 - 2 line of HNC and its isomer HCN in three luminous galaxies and J = 4 - 3 HNC observations of one galaxy. The observations are discussed in terms of physical conditions and excitation as well as in the context of X-ray influenced chemistry. Results. The ultraluminous mergers Arp 220 and Mrk 231 and the luminous IR galaxy NGC 4418 show the HNC J 3 - 2 emission being brighter than the HCN 3 - 2 emission by factors of 1.5 to 2. We furthermore report the detection of HNC J = 4 - 3 in Mrk 231. Overluminous HNC emission is unexpected in warm molecular gas in ultraluminous galaxies since I( HNC) greater than or similar to I( HCN) is usually taken as a signature of cold (10 - 20 K) dark clouds. Since the molecular gas of the studied galaxies is warm (T(k) greater than or similar to 40 K), we present two alternative explanations to the overluminous HNC: a) HNC excitation is affected by pumping of the rotational levels through the mid-infrared continuum and b) XDRs (X-ray Dominated Regions) influence the abundances of HNC. HNC may become pumped at 21.5 mu m brightness temperatures of T(B) greater than or similar to 50 K, suggesting that HNC-pumping could be common in warm, ultraluminous galaxies with compact IR- nuclei. This means that the HNC emission is no longer dominated by collisions and its luminosity may not be used to deduce information on gas density. On the other hand, all three galaxies are either suspected of having buried AGN - or the presence of AGN is clear (Mrk 231) - indicating that X-rays may affect the ISM chemistry. Conclusions. We conclude that both the pumping and XDR alternatives imply molecular cloud ensembles distinctly different from those of typical starforming regions in the Galaxy, or the ISM of less extreme starburst galaxies. The HNC molecule shows the potential of becoming an additional important tracer of extreme nuclear environments.
Can Anyone Be 'the' One? Evidence on Mate Selection from Speed Dating

Marriage data show a strong degree of positive assortative mating along a variety of attributes. But since marriage is an equilibrium outcome, it is unclear whether positive sorting is the result of preferences rather than opportunities. We assess the relative importance of preferences and opportunities in dating behaviour, using unique data from a large commercial speed dating agency. While the speed dating design gives us a direct observation of individual preferences, the random allocation of participants across events generates an exogenous source of variation in opportunities and allows us to identify the role of opportunities separately from that of preferences. We find that both women and men equally value physical attributes, such as age and weight, and that there is positive sorting along age, height, and education. The role of individual preferences, however, is outplayed by that of opportunities. Along some attributes (such as occupation, height and smoking) opportunities explain almost all the estimated variation in demand. Along other attributes (such as age), the role of preferences is more substantial, but never dominant. Despite this, preferences have a part when we observe a match, i.e., when two individuals propose to one another.